0s autopkgtest [16:32:33]: starting date and time: 2024-03-23 16:32:33+0000 0s autopkgtest [16:32:33]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:32:33]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.h05_zobc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:readline,src:asymptote --apt-upgrade cpptraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=readline/8.2-4 asymptote/2.87+ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-18.secgroup --name adt-noble-ppc64el-cpptraj-20240323-163233-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 103s autopkgtest [16:34:16]: testbed dpkg architecture: ppc64el 103s autopkgtest [16:34:16]: testbed apt version: 2.7.12 103s autopkgtest [16:34:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 106s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 106s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 106s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 106s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 106s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 106s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 106s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 106s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 106s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 106s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 106s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 109s Fetched 9623 kB in 3s (3299 kB/s) 109s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Calculating upgrade... 112s The following packages will be upgraded: 112s cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales 112s python3-markupsafe readline-common 112s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 8999 kB of archives. 112s After this operation, 63.5 kB disk space will be freed. 112s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 113s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 113s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 113s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el readline-common all 8.2-4 [56.4 kB] 113s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 113s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB] 113s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.2-0ubuntu1 [597 kB] 113s Preconfiguring packages ... 114s Fetched 8999 kB in 1s (8911 kB/s) 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 114s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 114s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 114s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 115s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 115s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 115s Setting up libc-bin (2.39-0ubuntu6) ... 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 115s Preparing to unpack .../0-libbsd0_0.12.1-1_ppc64el.deb ... 115s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 115s Preparing to unpack .../1-locales_2.39-0ubuntu6_all.deb ... 115s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 115s Preparing to unpack .../2-readline-common_8.2-4_all.deb ... 115s Unpacking readline-common (8.2-4) over (8.2-3) ... 115s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 115s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 115s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_ppc64el.deb ... 115s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 115s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 115s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 115s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 115s Setting up cloud-init (24.1.2-0ubuntu1) ... 117s Setting up locales (2.39-0ubuntu6) ... 117s Generating locales (this might take a while)... 118s en_US.UTF-8... done 118s Generation complete. 118s Setting up python3-markupsafe (2.1.5-1build1) ... 119s Setting up libbsd0:ppc64el (0.12.1-1) ... 119s Setting up readline-common (8.2-4) ... 119s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 119s Processing triggers for man-db (2.12.0-3) ... 120s Processing triggers for install-info (7.1-3) ... 120s Processing triggers for libc-bin (2.39-0ubuntu6) ... 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s sh: Attempting to set up Debian/Ubuntu apt sources automatically 121s Reading package lists...sh: Distribution appears to be Ubuntu 122s 122s Building dependency tree... 122s Reading state information... 122s eatmydata is already the newest version (131-1). 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s dbus is already the newest version (1.14.10-4ubuntu1). 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s rng-tools-debian is already the newest version (2.4). 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s The following packages will be REMOVED: 123s cloud-init* python3-configobj* python3-debconf* 123s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 123s After this operation, 3256 kB disk space will be freed. 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70156 files and directories currently installed.) 123s Removing cloud-init (24.1.2-0ubuntu1) ... 124s Removing python3-configobj (5.0.8-3) ... 124s Removing python3-debconf (1.5.86) ... 124s Processing triggers for man-db (2.12.0-3) ... 124s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69767 files and directories currently installed.) 124s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 125s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 125s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 125s invoke-rc.d: policy-rc.d denied execution of try-restart. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s linux-generic is already the newest version (6.8.0-11.11+1). 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 125s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 128s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Calculating upgrade... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s autopkgtest [16:34:42]: rebooting testbed after setup commands that affected boot 287s autopkgtest [16:37:18]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 290s autopkgtest [16:37:23]: @@@@@@@@@@@@@@@@@@@@ apt-source cpptraj 299s Get:1 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (dsc) [2160 B] 299s Get:2 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (tar) [28.4 MB] 299s Get:3 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (diff) [6064 B] 299s gpgv: Signature made Tue Jun 27 18:04:29 2023 UTC 299s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 299s gpgv: Can't check signature: No public key 299s dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-3build1.dsc: no acceptable signature found 302s autopkgtest [16:37:35]: testing package cpptraj version 5.1.0+dfsg-3build1 303s autopkgtest [16:37:36]: build not needed 336s autopkgtest [16:38:09]: test command1: preparing testbed 342s Reading package lists... 342s Building dependency tree... 342s Reading state information... 342s Starting pkgProblemResolver with broken count: 0 342s Starting 2 pkgProblemResolver with broken count: 0 342s Done 342s The following additional packages will be installed: 342s cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 libgfortran5 libgomp1 342s libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 libopenmm8.0 libsz2 342s netcdf-bin 342s Suggested packages: 342s libfftw3-bin libfftw3-dev 342s The following NEW packages will be installed: 342s autopkgtest-satdep cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 342s libgfortran5 libgomp1 libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 342s libopenmm8.0 libsz2 netcdf-bin 342s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 342s Need to get 9571 kB/9571 kB of archives. 342s After this operation, 30.6 MB of additional disk space will be used. 342s Get:1 /tmp/autopkgtest.Ktrf5m/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 342s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 343s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 343s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 343s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libarpack2 ppc64el 3.9.1-1 [106 kB] 343s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 343s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libfftw3-double3 ppc64el 3.3.10-1ubuntu1 [440 kB] 344s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 344s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 344s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB] 344s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB] 344s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libnetcdf19 ppc64el 1:4.9.2-3ubuntu1 [597 kB] 344s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el libopenmm8.0 ppc64el 8.0.0+dfsg-6ubuntu1 [893 kB] 344s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el cpptraj ppc64el 5.1.0+dfsg-3build1 [2050 kB] 345s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el netcdf-bin ppc64el 1:4.9.2-3ubuntu1 [239 kB] 345s Fetched 9571 kB in 3s (3741 kB/s) 345s Selecting previously unselected package libblas3:ppc64el. 345s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69712 files and directories currently installed.) 345s Preparing to unpack .../00-libblas3_3.12.0-3_ppc64el.deb ... 345s Unpacking libblas3:ppc64el (3.12.0-3) ... 345s Selecting previously unselected package libgfortran5:ppc64el. 345s Preparing to unpack .../01-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 345s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 345s Selecting previously unselected package liblapack3:ppc64el. 345s Preparing to unpack .../02-liblapack3_3.12.0-3_ppc64el.deb ... 345s Unpacking liblapack3:ppc64el (3.12.0-3) ... 345s Selecting previously unselected package libarpack2:ppc64el. 345s Preparing to unpack .../03-libarpack2_3.9.1-1_ppc64el.deb ... 345s Unpacking libarpack2:ppc64el (3.9.1-1) ... 345s Selecting previously unselected package libgomp1:ppc64el. 345s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 345s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 345s Selecting previously unselected package libfftw3-double3:ppc64el. 345s Preparing to unpack .../05-libfftw3-double3_3.3.10-1ubuntu1_ppc64el.deb ... 345s Unpacking libfftw3-double3:ppc64el (3.3.10-1ubuntu1) ... 345s Selecting previously unselected package libaec0:ppc64el. 345s Preparing to unpack .../06-libaec0_1.1.2-1_ppc64el.deb ... 345s Unpacking libaec0:ppc64el (1.1.2-1) ... 345s Selecting previously unselected package libsz2:ppc64el. 345s Preparing to unpack .../07-libsz2_1.1.2-1_ppc64el.deb ... 345s Unpacking libsz2:ppc64el (1.1.2-1) ... 345s Selecting previously unselected package libhdf5-103-1:ppc64el. 345s Preparing to unpack .../08-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 345s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 345s Selecting previously unselected package libhdf5-hl-100:ppc64el. 345s Preparing to unpack .../09-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ... 345s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 345s Selecting previously unselected package libnetcdf19:ppc64el. 345s Preparing to unpack .../10-libnetcdf19_1%3a4.9.2-3ubuntu1_ppc64el.deb ... 345s Unpacking libnetcdf19:ppc64el (1:4.9.2-3ubuntu1) ... 345s Selecting previously unselected package libopenmm8.0. 345s Preparing to unpack .../11-libopenmm8.0_8.0.0+dfsg-6ubuntu1_ppc64el.deb ... 345s Unpacking libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ... 345s Selecting previously unselected package cpptraj. 345s Preparing to unpack .../12-cpptraj_5.1.0+dfsg-3build1_ppc64el.deb ... 345s Unpacking cpptraj (5.1.0+dfsg-3build1) ... 345s Selecting previously unselected package netcdf-bin. 345s Preparing to unpack .../13-netcdf-bin_1%3a4.9.2-3ubuntu1_ppc64el.deb ... 345s Unpacking netcdf-bin (1:4.9.2-3ubuntu1) ... 345s Selecting previously unselected package autopkgtest-satdep. 345s Preparing to unpack .../14-1-autopkgtest-satdep.deb ... 345s Unpacking autopkgtest-satdep (0) ... 345s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 345s Setting up libaec0:ppc64el (1.1.2-1) ... 345s Setting up libblas3:ppc64el (3.12.0-3) ... 345s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 345s Setting up libfftw3-double3:ppc64el (3.3.10-1ubuntu1) ... 345s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 345s Setting up libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ... 345s Setting up libsz2:ppc64el (1.1.2-1) ... 345s Setting up liblapack3:ppc64el (3.12.0-3) ... 345s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 345s Setting up libarpack2:ppc64el (3.9.1-1) ... 345s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 345s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 345s Setting up libnetcdf19:ppc64el (1:4.9.2-3ubuntu1) ... 345s Setting up cpptraj (5.1.0+dfsg-3build1) ... 345s Setting up netcdf-bin (1:4.9.2-3ubuntu1) ... 345s Setting up autopkgtest-satdep (0) ... 345s Processing triggers for man-db (2.12.0-3) ... 346s Processing triggers for libc-bin (2.39-0ubuntu6) ... 348s (Reading database ... 69803 files and directories currently installed.) 348s Removing autopkgtest-satdep (0) ... 349s autopkgtest [16:38:22]: test command1: mkdir bin && ln -s /usr/bin/cpptraj bin && make -C test test.complete summary 349s autopkgtest [16:38:22]: test command1: [----------------------- 349s make: Entering directory '/tmp/autopkgtest.Ktrf5m/build.o7U/src/test' 349s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 23 16:38 ../bin/cpptraj -> /usr/bin/cpptraj 349s make[1]: Entering directory '/tmp/autopkgtest.Ktrf5m/build.o7U/src/test' 349s ******************************************************************************** 349s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_General 349s 349s CPPTRAJ: General tests 350s 350s All 15 comparisons passed. 350s 350s ******************************************************************************** 350s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Parallel 350s 350s CPPTRAJ: Parallel tests. 350s 350s CPPTRAJ: Parallel test with trajectory offset 350s 350s All 7 comparisons passed. 350s 350s ******************************************************************************** 350s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Strip 350s 350s CPPTRAJ: One frame strip command test 350s 350s CPPTRAJ: Unstrip (Lig/Rec/Complex) command test 350s 350s CPPTRAJ: Multi frame strip command test. 350s 350s CPPTRAJ: Strip topology with PDB info 350s 350s All 11 comparisons passed. 350s 350s ******************************************************************************** 350s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_BrokenTraj 350s 350s CPPTRAJ: Broken Traj: Running good trajectory. 350s 350s CPPTRAJ: Broken Traj: Running broken trajectory. 350s 350s CPPTRAJ: Compressed broken trajectory test 350s 350s All 2 comparisons passed. 350s 350s ******************************************************************************** 350s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_TrajinOffset 350s 350s CPPTRAJ: Normal trajectory read with offsets. 350s 350s CPPTRAJ: Gzipped trajectory read with offsets 350s 350s CPPTRAJ: Bzip2ed trajectory read with offsets 350s 350s CPPTRAJ: Start argument offset 350s 350s All 4 comparisons passed. 350s 350s ******************************************************************************** 350s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_RemdTraj 350s 350s CPPTRAJ: CRD Replica Trajectory Run with offset 350s 350s CPPTRAJ: CRD Replica Trajectory Run 350s 350s CPPTRAJ: NetCDF Replica Trajectory Run test 350s 350s CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj 350s 350s CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj 350s 350s CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj 351s 351s CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj 351s 351s CPPTRAJ: CRD Replica Trajectory Run with remdout 351s 351s All 8 comparisons passed. 351s 351s ******************************************************************************** 351s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_trajout_framerange 351s 351s CPPTRAJ: Trajout Frame Range [Amber Restart] 351s 351s CPPTRAJ: Trajout Frame Range [Amber Coordinates] 351s 351s All 6 comparisons passed. 351s 351s ******************************************************************************** 351s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_PerResRMSD 351s 351s CPPTRAJ: Per-Residue RMSD Test. 351s 351s CPPTRAJ: Per-Residue RMSD Test with averaging 351s 351s CPPTRAJ: Per-Residue RMSD Test with residue centering. 351s 351s All 3 comparisons passed. 351s 351s ******************************************************************************** 351s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_DSSP 351s 351s CPPTRAJ: Secstruct (DSSP) command test. 351s 351s CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. 351s 351s CPPTRAJ: Secstruct (DSSP) command with changing number of residues. 351s 351s CPPTRAJ: Secstruct (DSSP): SS assign output test 351s 351s CPPTRAJ: FtuFabI Assignment test 351s 351s All 10 comparisons passed. 351s 351s ******************************************************************************** 351s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Center 351s 351s CPPTRAJ: Center command test. 351s 351s CPPTRAJ: Center origin command test. 351s 351s CPPTRAJ: Center origin mass command test. 351s 351s CPPTRAJ: Center reference command test. 351s 351s CPPTRAJ: Center point test. 351s 351s All 5 comparisons passed. 351s 351s ******************************************************************************** 351s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Hbond 351s 351s CPPTRAJ: Solute Hbond test 351s 351s CPPTRAJ: Solute Hbond test with disk caching 351s 351s CPPTRAJ: Solute-solvent hbond test 351s 351s CPPTRAJ: Hbond, no intramolecular hydrogen bonds test 351s 351s CPPTRAJ: Hbond, specified solute masks 351s 351s CPPTRAJ: Hbond, no angle cutoff test 351s 351s CPPTRAJ: Hbond, Bridge nointramol test 351s 351s CPPTRAJ: Hbond with imaging 351s 351s CPPTRAJ: Hbond, orthogonal imaging 351s 351s All 23 comparisons passed. 351s 351s ******************************************************************************** 351s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_NCrestart 351s 351s CPPTRAJ: NetCDF Restart Test - TXT->NetCDF 351s 351s CPPTRAJ: NetCDF Restart Test - NetCDF->TXT 351s 351s CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF 351s 351s CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt 351s 351s All 2 comparisons passed. 351s 351s ******************************************************************************** 351s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Image 351s 351s CPPTRAJ: Orthorhombic imaged distance test. 351s 351s CPPTRAJ: Non-orthorhombic imaged distance test. 351s 351s CPPTRAJ: Orthorhombic coordinate imaging test 351s 351s CPPTRAJ: Nonorthorhombic coordinate imaging test 351s 351s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar 351s 351s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM 351s 351s All 6 comparisons passed. 351s 351s ******************************************************************************** 351s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Surf 351s 351s CPPTRAJ: Surface calculation test 352s 352s CPPTRAJ: Partial Surface calculation test 352s 352s CPPTRAJ: LCPO test with GAFF atom types 352s 352s All 3 comparisons passed. 352s 352s ******************************************************************************** 352s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Radgyr 352s 352s CPPTRAJ: Radius of gyration command test 352s 352s All 2 comparisons passed. 352s 352s ******************************************************************************** 352s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Mask 352s 352s CPPTRAJ: Mask single frame test 352s 352s CPPTRAJ: Mask longer command test. 352s 352s All 5 comparisons passed. 352s 352s ******************************************************************************** 352s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Jcoupling 352s 352s CPPTRAJ: J-Coupling single frame test 352s J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. 352s Skipped test: J-Coupling extended test 352s 352s All 1 comparisons passed. 352s 1 comparisons skipped. 352s 352s ******************************************************************************** 352s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Diffusion 352s 352s CPPTRAJ: Diffusion test, no imaging. 352s 352s CPPTRAJ: Diffusion test, old syntax. 352s 352s CPPTRAJ: Diffusion test, new syntax. 352s 352s CPPTRAJ: Diffusion test, nonorthogonal box 352s 352s CPPTRAJ: STFC Diffusion Test 352s 352s CPPTRAJ: STFC Diffusion Test with individual distances 352s 352s CPPTRAJ: STFC Diffusion Test with COM 352s 352s CPPTRAJ: STFC Diffusion Test with second mask 352s 352s All 16 comparisons passed. 352s 352s ******************************************************************************** 352s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Outtraj 352s 352s CPPTRAJ: RMSD Test with outtraj. 352s 352s CPPTRAJ: Outtraj Test with maxmin. 352s 352s All 4 comparisons passed. 352s 352s ******************************************************************************** 352s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Charmm 352s 352s CPPTRAJ: CHARMM PSF/DCD test 352s 352s CPPTRAJ: CHARMM DCD Write, step 1. 352s 352s CPPTRAJ: CHARMM DCD Write, step 2. 352s 352s CPPTRAJ: CHAMBER topology read/strip test. 352s 352s CPPTRAJ: Read CHARMM restart 353s 353s CPPTRAJ: CHARMM PSF write 353s 353s CPPTRAJ: CHARMM COORdinates test 353s 353s All 6 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CharmmParams 353s 353s CPPTRAJ: Test updating topology with Charmm parameters (single residue) 353s 353s All 2 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Rotdif 353s 353s CPPTRAJ: Rotational diffusion calculation test 353s 353s All 4 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_NetcdfTraj 353s 353s CPPTRAJ: Convert mdcrd -> NetCDF 353s 353s CPPTRAJ: Convert NetCDF -> mdcrd 353s 353s All 1 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Runavg 353s 353s CPPTRAJ: Coordinate Running Average test. 353s 353s CPPTRAJ: Coordinate Running Average Traj Write 353s 353s All 2 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_RMSD 353s 353s CPPTRAJ: Basic RMSD tests 353s 353s CPPTRAJ: RMS coordinate rotation/rotation matrices test 353s 353s CPPTRAJ: RMS fit with no coordinates modification test. 353s 353s CPPTRAJ: RMS fit to previous test 353s 353s CPPTRAJ: RMS: imaging after unit cell rotation 353s 353s All 12 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_2DRMS 353s 353s CPPTRAJ: 2D RMSD Test. 353s 353s CPPTRAJ: 2D RMSD Test, mass-weighted. 353s 353s CPPTRAJ: 2D RMSD Test with reference trajectory 353s 353s CPPTRAJ: 2D DME Test. 353s 353s CPPTRAJ: 2D RMSD with reference mask test. 353s 353s CPPTRAJ: 2D RMSD test, no fitting. 353s 353s All 6 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Mol2 353s 353s CPPTRAJ: Mol2 Parm/Traj Read/Write Test. 353s 353s CPPTRAJ: PDB => Mol2 353s 353s CPPTRAJ: Amber Top/Rst => Mol2 353s Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. 353s Skipped test: Amber Top/Rst => Mol2, SYBYL atom types 353s 353s All 4 comparisons passed. 353s 1 comparisons skipped. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_NAstruct 353s 353s CPPTRAJ: NAstruct command test. 353s 353s CPPTRAJ: NAstruct command test, single strand 353s 353s All 11 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_NAstruct_8OG 353s 353s CPPTRAJ: NA test (8OG) 353s 353s All 3 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Average 353s 353s CPPTRAJ: Average Test. 353s 353s All 2 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Pucker 353s 353s CPPTRAJ: Pucker command test 353s 353s CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test 353s 353s CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. 353s 353s All 3 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AtomMap 353s 353s CPPTRAJ: AtomMap Test 353s 353s CPPTRAJ: AtomMap with 'rmsfit' 353s 353s CPPTRAJ: Atom map charmm->amber atom order 353s 353s CPPTRAJ: Atom map charmm->amber atom order, by residue 353s 353s All 9 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Datafile 353s 353s CPPTRAJ: Data file output precision test 353s 353s CPPTRAJ: Standard -> Grace Data 353s 353s CPPTRAJ: Grace -> Standard Data 353s 353s CPPTRAJ: X column format/precision test. 353s 353s CPPTRAJ: Data file group by name test 353s 353s CPPTRAJ: Data file group by aspect test 353s 353s All 6 comparisons passed. 353s 353s ******************************************************************************** 353s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Radial 353s 353s CPPTRAJ: Radial test, non-orthogonal imaging 354s 354s CPPTRAJ: Radial test, orthogonal and no imaging 354s 354s All 9 comparisons passed. 354s 354s ******************************************************************************** 354s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Hist 354s 354s CPPTRAJ: 1D/2D Histogram Analysis test 354s 354s CPPTRAJ: 3D histogram test. 354s 354s All 7 comparisons passed. 354s 354s ******************************************************************************** 354s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Closest 354s 354s CPPTRAJ: Closest command test using first solvent atom. 354s 354s CPPTRAJ: Closest command test using all solvent atoms. 354s 354s CPPTRAJ: Closest command test, using mask center 354s 354s CPPTRAJ: Closest command test, using mask center and solvent mask 354s 354s CPPTRAJ: Closest command test, solvent mask, water oxygen only 354s 354s All 8 comparisons passed. 354s 354s ******************************************************************************** 354s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_DRMSD 354s 354s CPPTRAJ: Distance RMSD test 354s 354s All 1 comparisons passed. 354s 354s ******************************************************************************** 354s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster 354s 354s CPPTRAJ: Cluster command test, in-memory pairwise distances. 354s 354s CPPTRAJ: Cluster command test, read pairwise distances. 354s 354s CPPTRAJ: Cluster command test, read NetCDF pairwise distances. 354s 354s CPPTRAJ: Cluster command test, write ASCII pairwise distances. 354s 354s CPPTRAJ: Cluster command test, read ASCII pairwise distances. 354s 354s All 9 comparisons passed. 354s 354s ******************************************************************************** 354s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_Sieve 354s 354s CPPTRAJ: Cluster, nosieve 355s 355s CPPTRAJ: Cluster, sieve5 355s 355s CPPTRAJ: Cluster, nosieve savepairdist 355s 355s CPPTRAJ: Cluster, nosieve loadpairdist 355s 355s CPPTRAJ: Cluster, sieve5 savepairdist 355s 355s CPPTRAJ: Cluster, sieve5 loadpairdist 355s 355s CPPTRAJ: Cluster, nosieve pairwisecache none 355s 355s CPPTRAJ: Cluster, sieve5 pairwisecache none 355s 355s CPPTRAJ: Cluster, random 355s 355s All 28 comparisons passed. 355s 355s ******************************************************************************** 355s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_RandomSieve 355s 355s CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). 355s 355s CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). 355s 355s All 4 comparisons passed. 355s 355s ******************************************************************************** 355s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_DataSet 355s 355s CPPTRAJ: Clustering, One DataSet 355s 355s CPPTRAJ: Clustering, Two DataSets 355s 355s CPPTRAJ: Clustering, dihedral DataSet 355s 355s CPPTRAJ: Clustering, two dihedral DataSets 355s 355s CPPTRAJ: Clustering, dihedral DataSet, K-means 355s 355s CPPTRAJ: Clustering, two dihedral DataSets, K-means 355s 355s All 8 comparisons passed. 355s 355s ******************************************************************************** 355s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_DBSCAN 355s 355s CPPTRAJ: DBSCAN test 355s 355s CPPTRAJ: DBSCAN automatic parameter determination test. 355s 355s CPPTRAJ: DBSCAN kdist map test 355s 355s CPPTRAJ: DBSCAN with sieve 355s 355s All 4 comparisons passed. 355s 355s ******************************************************************************** 355s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_Kmeans 355s 355s CPPTRAJ: Cpptraj Kmeans 355s 355s CPPTRAJ: Cpptraj Kmeans random 355s 355s All 6 comparisons passed. 355s 355s ******************************************************************************** 355s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_SymmRMSD 355s 355s CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) 355s 355s All 5 comparisons passed. 355s 355s ******************************************************************************** 355s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_TrajWrites 355s 355s CPPTRAJ: Cluster command test, coordinate writes. 356s 356s CPPTRAJ: Cluster command test, coordinate writes using info file. 356s 356s All 8 comparisons passed. 356s 356s ******************************************************************************** 356s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_Dpeaks 356s 356s CPPTRAJ: Density peaks clustering test 356s 356s All 3 comparisons passed. 356s 356s ******************************************************************************** 356s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cluster_Nreps 356s 356s CPPTRAJ: Clustering with specified # reps 356s 356s All 2 comparisons passed. 356s 356s ******************************************************************************** 356s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_IRED 356s 356s CPPTRAJ: IRED vector/matrix test 356s 356s 356s ******************************************************************************** 356s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_RandomizeIons 356s 356s CPPTRAJ: randomizeions test (original algorithm) 356s 356s CPPTRAJ: Randomize (around, overlap) 356s 356s CPPTRAJ: Randomize (around) 357s 357s CPPTRAJ: Randomize (overlap) 357s 357s CPPTRAJ: Randomize (no restrictions) 357s 357s All 5 comparisons passed. 357s 357s ******************************************************************************** 357s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Molsurf 357s 357s CPPTRAJ: Molsurf test 357s 357s All 1 comparisons passed. 357s 357s ******************************************************************************** 357s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Corr 357s 357s CPPTRAJ: Correlation test 357s 357s All 2 comparisons passed. 357s 357s ******************************************************************************** 357s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CheckStructure 357s 357s CPPTRAJ: Structure Check 357s 357s CPPTRAJ: Structure Check with Around and Skip 357s 357s CPPTRAJ: Structure Check with PBC 357s 357s CPPTRAJ: Structure Check with Around 358s 358s All 8 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_RmsAvgCorr 358s 358s CPPTRAJ: RmsAvgCorr Reference 358s 358s CPPTRAJ: RmsAvgCorr First 358s 358s All 3 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Contacts 358s 358s CPPTRAJ: Contacts test. 358s 358s All 3 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Principal 358s 358s CPPTRAJ: Principal Test 358s 358s All 3 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_ClusterDihedral 358s 358s CPPTRAJ: clusterdihedral test 358s 358s All 4 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Vector 358s 358s CPPTRAJ: Basic vector tests 358s 358s CPPTRAJ: Test vector center with magnitude 358s 358s CPPTRAJ: Momentum/velocity vector test. 358s 358s CPPTRAJ: Force vector test. 358s 358s All 14 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Matrix 358s 358s CPPTRAJ: Matrix Tests 358s 358s CPPTRAJ: Generate matrix with trajectory start/stop/offset 358s 358s CPPTRAJ: Generate matrix with action stop/start/offset 358s 358s All 15 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AtomicFluct 358s 358s CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. 358s 358s CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. 358s 358s CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. 358s 358s CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. 358s 358s CPPTRAJ: Atomicfluct test with ADP output 358s 358s CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. 358s 358s All 13 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Grid 358s 358s CPPTRAJ: Dipole test 358s 358s CPPTRAJ: Grid test 358s 358s CPPTRAJ: OpenDX Grid read test 358s 358s CPPTRAJ: Grid with specified center test. 358s 358s CPPTRAJ: Grid with box center offset test. 358s 358s CPPTRAJ: Grid with mask center offset test. 358s 358s CPPTRAJ: Non-orthogonal grid test. 358s 358s CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test 358s 358s CPPTRAJ: Grid generation from 'bounds' test. 358s 358s All 13 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Unwrap 358s 358s CPPTRAJ: Unwrap non-orthogonal test 358s 358s CPPTRAJ: Unwrap orthogonal test 358s 358s All 2 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Project 358s 358s CPPTRAJ: Projection 358s 358s All 1 comparisons passed. 358s 358s ******************************************************************************** 358s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Analyze_Modes 358s 358s CPPTRAJ: Modes analysis, RMS fluctuations 358s 358s CPPTRAJ: Modes analysis, displacements 359s 359s CPPTRAJ: Modes analysis, dipole correlation 359s 359s CPPTRAJ: Modes analysis, pseudo trajectory creation test 359s 359s CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test 359s 359s All 6 comparisons passed. 359s 359s ******************************************************************************** 359s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Watershell 359s 359s CPPTRAJ: Watershell Test, non-orthorhombic imaging. 360s 360s CPPTRAJ: Watershell Test, orthorhombic imaging. 360s 360s CPPTRAJ: Watershell Test, no imaging. 360s 360s All 3 comparisons passed. 360s 360s ******************************************************************************** 360s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AnalysisRunAvg 360s 360s CPPTRAJ: Analysis Running Average 360s 360s All 2 comparisons passed. 360s 360s ******************************************************************************** 360s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Volmap 360s 360s CPPTRAJ: VMD VolMap Algorithm test 360s VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. 360s Skipped test: VMD VolMap Algorithm longer tests 360s 360s All 2 comparisons passed. 360s 1 comparisons skipped. 360s 360s ******************************************************************************** 360s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_SPAM 360s 360s CPPTRAJ: SPAM Test 360s 360s CPPTRAJ: SPAM Pure Solvent Test 362s 362s 1 out of 5 comparisons failed. 362s 362s ******************************************************************************** 362s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_LIE 362s 362s CPPTRAJ: LIE test 362s 362s All 1 comparisons passed. 362s 362s ******************************************************************************** 362s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Density 362s 362s CPPTRAJ: Density along axis tests 362s 362s CPPTRAJ: Multi-frame density along axis test 362s 362s CPPTRAJ: Total system density test 362s 362s All 7 comparisons passed. 362s 362s ******************************************************************************** 362s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_LipidOrder 362s 362s CPPTRAJ: Lipid Order Parameter Test. 362s 362s All 6 comparisons passed. 362s 362s ******************************************************************************** 362s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_LipidSCD 362s 362s CPPTRAJ: Basic lipid order parameter test 362s 362s CPPTRAJ: New Lipid Order Parameter Test, DOPC. 362s 362s All 4 comparisons passed. 362s 362s ******************************************************************************** 362s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_PairDist 362s 362s CPPTRAJ: PairDist Test. 362s 362s CPPTRAJ: Pairdist test, orthogonal imaging. 363s 363s CPPTRAJ: Pairdist test, nonorthogonal imaging. 363s 363s CPPTRAJ: Pairdist test, 2 masks. 363s 363s All 4 comparisons passed. 363s 363s ******************************************************************************** 363s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_ReadData 363s 363s CPPTRAJ: Read vector data test (no origins, origins) 363s 363s CPPTRAJ: Read vector data set (origins, no origins) 363s 363s CPPTRAJ: Read Amber output test 363s 363s CPPTRAJ: Read CHARMM output test 363s 363s CPPTRAJ: 3D data read/write test 363s 363s CPPTRAJ: Standard 3D data write test 363s 363s CPPTRAJ: Standard 3D data read test 363s 363s CPPTRAJ: Standard 3D data read/append test 363s 363s CPPTRAJ: Standard 3D data, sparse 363s 363s CPPTRAJ: Nonorthogonal grid standard write/read tests. 363s 363s CPPTRAJ: Read specific columns test. 363s 363s CPPTRAJ: Write non-square matrix 363s 363s CPPTRAJ: Read non-square matrix 363s 363s CPPTRAJ: Read square matrix 363s 363s All 15 comparisons passed. 363s 363s ******************************************************************************** 363s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_GIST 363s 363s CPPTRAJ: GIST water-water interaction test 365s 365s CPPTRAJ: GIST test, orthogonal cell 367s 367s CPPTRAJ: GIST test, nonorthogonal cell 370s 370s All 11 comparisons passed. 370s 370s ******************************************************************************** 370s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_GIST_Order 370s 370s CPPTRAJ: TIP3P water cluster test 370s 370s CPPTRAJ: TIP4P water cluster test 370s 370s CPPTRAJ: TIP5P water cluster test 370s 370s All 4 comparisons passed. 370s 370s ******************************************************************************** 370s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_systemVF 370s 370s CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test 371s 371s All 1 comparisons passed. 371s 371s ******************************************************************************** 371s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AtomicCorr 371s 371s CPPTRAJ: Atomic Correlation test 371s 371s All 1 comparisons passed. 371s 371s ******************************************************************************** 371s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AutoCorr 371s 371s CPPTRAJ: AutoCorr test. 371s 371s All 1 comparisons passed. 371s 371s ******************************************************************************** 371s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Box 371s 371s CPPTRAJ: Box Test (Add box info) 371s 371s CPPTRAJ: Box test (remove box info) 371s 371s CPPTRAJ: Box test (Modify box length) 371s 371s CPPTRAJ: Box test (auto orthogonal box, no radii) 371s 371s CPPTRAJ: Box test (auto orthogonal box, VDW radii) 371s 371s All 7 comparisons passed. 371s 371s ******************************************************************************** 371s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AtomTypeSelect 371s 371s CPPTRAJ: Selection by atom type test. 371s 371s All 1 comparisons passed. 371s 371s ******************************************************************************** 371s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AvgRef 371s 371s CPPTRAJ: RMSD Test with averaged reference coordinates. 371s 371s All 1 comparisons passed. 371s 371s ******************************************************************************** 371s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Crank_Stat 371s 371s CPPTRAJ: Crankshaft test 371s 371s All 3 comparisons passed. 371s 371s ******************************************************************************** 371s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CreateCrd 371s 371s CPPTRAJ: COORDS data set creation and CRDFLUCT test. 371s 371s CPPTRAJ: COORDS data set creation with velocities test 371s 371s CPPTRAJ: TRAJ data set creation and CRDFLUCT test. 371s 371s CPPTRAJ: TRAJ data set creation with velocities test. 371s 371s CPPTRAJ: COORDS data set append test 371s 371s CPPTRAJ: COORDS test storing frame metadata 372s 372s CPPTRAJ: TRAJ test storing frame metadata 372s 372s All 8 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AutoImage 372s 372s CPPTRAJ: AutoImage test (split DNA duplex) 372s 372s CPPTRAJ: AutoImage test, use anchor mask 372s 372s All 2 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_LoadCrd 372s 372s CPPTRAJ: LoadCrd test. 372s 372s CPPTRAJ: LoadTraj test. 372s 372s CPPTRAJ: LoadTraj from trajin test. 372s 372s CPPTRAJ: LoadCrd append from multiple files test 372s 372s All 4 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_MultiVector 372s 372s CPPTRAJ: Multivector test 372s 372s All 1 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Lifetime 372s 372s CPPTRAJ: Lifetime test. 372s 372s CPPTRAJ: Lifetime test with data set caching. 372s 372s CPPTRAJ: Lifetime average and cumulative average test. 372s 372s All 12 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_FFT 372s 372s CPPTRAJ: FFT test. 372s 372s All 5 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Timecorr 372s 372s CPPTRAJ: Timecorr test. 372s 372s All 7 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CrossCorr 372s 372s CPPTRAJ: CrossCorr test 372s 372s All 1 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_SymmRmsd 372s 372s CPPTRAJ: SymmRmsd 372s 372s CPPTRAJ: ASP symmetry-corrected RMSD test 372s 372s CPPTRAJ: GLU symmetry-corrected RMSD test 372s 372s CPPTRAJ: TYR symmetry-corrected RMSD test 372s 372s CPPTRAJ: Longer symmetry-corrected RMSD test. 372s 372s All 8 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Multidihedral 372s 372s CPPTRAJ: Multidihedral test 372s 372s CPPTRAJ: Multidihedral Nucleotide CHI test 372s 372s CPPTRAJ: Multidihedral protein dihedrals test 372s 372s CPPTRAJ: Multidihedral cyclic molecule test 372s 372s All 6 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Ensemble_MREMD 372s 372s CPPTRAJ: M-REMD sort test. 372s 372s CPPTRAJ: M-REMD actions test. 372s 372s CPPTRAJ: M-REMD ensemble outtraj test. 372s 372s CPPTRAJ: M-REMD no sort, running average test 372s 372s CPPTRAJ: M-REMD, generate RMS data 372s 372s CPPTRAJ: M-REMD, meltcurve analysis 372s 372s All 17 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_MakeStructure 372s 372s CPPTRAJ: Basic makestructure test 372s 372s CPPTRAJ: Makestructure test with reference. 372s 372s All 5 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Rotate 372s 372s CPPTRAJ: Rotation (and inverse) of coords from matrices 372s 372s CPPTRAJ: Rotate with defined axis 372s 372s All 3 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Integrate 372s 372s CPPTRAJ: Integration test. 372s 372s All 2 comparisons passed. 372s 372s ******************************************************************************** 372s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_NativeContacts 372s 372s CPPTRAJ: NativeContacts test. 373s 373s CPPTRAJ: NativeContacts test, save non-native contacts, residue time series 373s 373s CPPTRAJ: NativeContacts test, orthorhombic imaging. 373s 373s All 17 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CheckChiral 373s 373s CPPTRAJ: Check chirality test 373s 373s All 1 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Energy 373s 373s CPPTRAJ: Simple energy tests 373s 373s CPPTRAJ: Test kinetic energy calculation 373s 373s CPPTRAJ: Test total energy calculation 373s 373s CPPTRAJ: Test partial energy calculation 373s 373s All 6 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_LESsplit 373s 373s CPPTRAJ: LES split/average test 373s 373s All 2 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_PermuteDihedrals 373s 373s CPPTRAJ: PermuteDihedrals interval -120, phi psi 373s 373s CPPTRAJ: PermuteDihedrals, random rotations 373s 373s All 4 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CCP4 373s 373s CPPTRAJ: CCP4 read/write and DX conversion test. 373s 373s All 2 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_DihCovar 373s 373s CPPTRAJ: Dihedral Covariance Matrix Test 373s 373s All 3 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CurveFit 373s 373s CPPTRAJ: Curve fitting test. 373s 373s CPPTRAJ: Curve fitting multi-exponential tests. 373s 373s CPPTRAJ: Curve fitting, custom output range. 373s 373s All 6 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Multicurve 373s 373s CPPTRAJ: Multicurve test 373s 373s All 1 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_DataSetAverage 373s 373s CPPTRAJ: Data set averaging and averaging over all sets test. 373s 373s All 2 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_VectorMath 373s 373s CPPTRAJ: Vector dot/cross product test 373s 373s All 2 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Esander 373s SANDER energy tests (long) requires SANDER API from AmberTools. 373s Cpptraj was compiled without SANDER API from AmberTools support. 373s SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. 373s SKIP: SANDER energy tests (long) 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Esander_Short 373s Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. 373s Cpptraj was compiled without SANDER API from AmberTools support. 373s SKIP: Energy via sander API short tests (GB/PME) 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Temperature 373s 373s CPPTRAJ: Temperature test. 373s 373s CPPTRAJ: Temperature with SHAKE on hydrogens. 373s 373s CPPTRAJ: Temperature with SHAKE on all atoms. 373s 373s CPPTRAJ: Temperature calc with extra points. 373s 373s All 5 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Spline 373s 373s CPPTRAJ: Spline test 373s 373s All 1 comparisons passed. 373s 373s ******************************************************************************** 373s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_KDE 373s 373s CPPTRAJ: KDE test. 374s 374s CPPTRAJ: KDE with Kullback-Leibler divergence test 374s 374s All 4 comparisons passed. 374s 374s ******************************************************************************** 374s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Wavelet 374s 374s CPPTRAJ: Wavelet analysis test 374s 374s CPPTRAJ: Wavelet WAFEX test 374s 374s All 3 comparisons passed. 374s 374s ******************************************************************************** 374s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CIF 374s 374s CPPTRAJ: CIF read test 374s 374s CPPTRAJ: Generate offset traj from PDB 374s 374s CPPTRAJ: Generate offset traj from CIF 374s 374s All 2 comparisons passed. 374s 374s ******************************************************************************** 374s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_PDB 374s 374s CPPTRAJ: PDB format read/write test 374s 374s CPPTRAJ: PQR file write with various radii 374s 374s CPPTRAJ: PDB filter alternate atom location IDs test 374s 374s CPPTRAJ: Adding PDB info to topology 374s 374s All 10 comparisons passed. 374s 374s ******************************************************************************** 374s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Align 374s 374s CPPTRAJ: Align Tests. 374s 374s CPPTRAJ: Align, unit cell rotation/imaging test. 374s 374s All 4 comparisons passed. 374s 374s ******************************************************************************** 374s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_VelocityAutoCorr 374s 374s CPPTRAJ: Velocity autocorrelation test 374s 374s All 3 comparisons passed. 374s 374s ******************************************************************************** 374s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_VelFrc 374s 374s CPPTRAJ: Test combining coordinates, velocities, and forces. 374s 374s CPPTRAJ: Test using velocities as coordinates. 374s 374s CPPTRAJ: Test writing velocities (MDVEL) 374s 374s CPPTRAJ: Test using forces as coordinates. 374s 374s CPPTRAJ: Test writing forces (MDFRC) 374s 374s CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. 374s 374s CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. 375s 375s All 5 comparisons passed. 375s 375s ******************************************************************************** 375s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_RotateDihedral 375s 375s CPPTRAJ: Rotate dihedral to target value. 375s 375s CPPTRAJ: Rotate dihedral by increment 375s 375s CPPTRAJ: Rotate dihedral in TRAJ data set 375s 375s All 3 comparisons passed. 375s 375s ******************************************************************************** 375s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_DataSetCmd 375s 375s CPPTRAJ: Data Set commands test 375s 375s All 10 comparisons passed. 375s 375s ******************************************************************************** 375s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Remap 375s 375s CPPTRAJ: Remap Test 375s 375s All 1 comparisons passed. 375s 375s ******************************************************************************** 375s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CompareTop 375s 375s CPPTRAJ: Compare topology test 375s 375s All 1 comparisons passed. 375s 375s ******************************************************************************** 375s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Filter 375s 375s CPPTRAJ: Basic filter test 375s 375s CPPTRAJ: Data filter test. 375s 375s CPPTRAJ: Filter matrix test. 375s 375s All 5 comparisons passed. 375s 375s ******************************************************************************** 375s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CombineCrd 375s 375s CPPTRAJ: Combine COORDS test. 375s 375s CPPTRAJ: Combine COORDS test with box info. 375s 375s CPPTRAJ: Split coords and recombine test. 375s 375s All 5 comparisons passed. 375s 375s ******************************************************************************** 375s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_TopInfo 375s 375s CPPTRAJ: Topology info print test. 376s 376s CPPTRAJ: Topology info with reference coords test 376s 376s All 12 comparisons passed. 376s 376s ******************************************************************************** 376s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_GromacsTrr 376s 376s CPPTRAJ: TRR force/velocity read -> NetCDF write test 376s 376s CPPTRAJ: TRR force/velocity read -> TRR write test 376s 376s CPPTRAJ: CRD => TRR 376s 376s CPPTRAJ: TRR => CRD 376s 376s CPPTRAJ: CRD(1-5) => TRR 376s 376s CPPTRAJ: CRD(6-10) => TRR 376s 376s CPPTRAJ: TRR (appended) => CRD 376s 376s CPPTRAJ: GMX: CRD with offset 376s 376s CPPTRAJ: GMX: TRR with offset 376s 376s All 5 comparisons passed. 376s 376s ******************************************************************************** 376s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_GromacsXtc 376s 376s CPPTRAJ: XTC read test 376s 376s CPPTRAJ: CRD => XTC 376s 376s CPPTRAJ: XTC => CRD 376s 376s CPPTRAJ: CRD(1-5) => XTC 376s 376s CPPTRAJ: CRD(6-10) => XTC 376s 376s CPPTRAJ: XTC (appended) => CRD 376s 376s CPPTRAJ: GMX: CRD with offset 376s 376s CPPTRAJ: GMX: XTC with offset 376s 376s All 4 comparisons passed. 376s 376s ******************************************************************************** 376s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_GromacsTNG 376s 376s CPPTRAJ: TNG read test 377s 377s CPPTRAJ: TNG read test (with offset) 377s 377s All 6 comparisons passed. 377s 377s ******************************************************************************** 377s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Ewald 377s 377s CPPTRAJ: Direct sum test 377s 377s CPPTRAJ: Ewald test (NaCl crystal) 377s 377s CPPTRAJ: Ewald test (trunc. oct) 377s 377s CPPTRAJ: Ewald test (partial system, trunc. oct) 377s Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 377s Skipped test: Ewald test (trunc. oct), 10 frames 377s Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. 377s Skipped test: Ewald test (ortho), 10 frames 377s 377s All 4 comparisons passed. 377s 2 comparisons skipped. 377s 377s ******************************************************************************** 377s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_LibPME 377s 377s CPPTRAJ: Particle mesh Ewald test (NaCl crystal) 377s 377s CPPTRAJ: Particle mesh Ewald test (trunc. oct) 378s 378s CPPTRAJ: Particle mesh Ewald test (ortho) 378s 378s CPPTRAJ: Particle mesh Ewald test (ortho, with mask) 378s 378s CPPTRAJ: PME test (partial system, trunc. oct) 378s PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 378s Skipped test: PME test (trunc. oct), 10 frames 378s 378s All 5 comparisons passed. 378s 1 comparisons skipped. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_LJ_PME 378s 378s CPPTRAJ: LJ PME test. 378s 378s CPPTRAJ: LJ PME kappa sweep test, 0.25 378s 378s CPPTRAJ: LJ PME kappa sweep test, 0.35 378s 378s CPPTRAJ: LJ PME kappa sweep test, 0.45 378s 378s CPPTRAJ: LJ PME kappa sweep test, 0.5 378s 378s CPPTRAJ: LJ with switch function test 378s 378s All 5 comparisons passed. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_TI 378s 378s CPPTRAJ: TI analysis test. 378s 378s All 5 comparisons passed. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_FixImagedBonds 378s 378s CPPTRAJ: Fix imaged bonds test (Ortho.) 378s 378s CPPTRAJ: Fix imaged bonds test (Non-ortho.) 378s 378s All 2 comparisons passed. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Distance 378s 378s CPPTRAJ: Distance tests 378s 378s CPPTRAJ: Orthogonal imaged distance 378s 378s CPPTRAJ: Non-orthogonal imaged distance 378s 378s All 3 comparisons passed. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Volume 378s 378s CPPTRAJ: Volume tests 378s 378s All 1 comparisons passed. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_SetVelocity 378s 378s CPPTRAJ: Set Velocity test 378s 378s CPPTRAJ: Scale velocity test 378s 378s 1 out of 3 comparisons failed. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Remlog 378s 378s CPPTRAJ: Replica log read/analyze test. 378s 378s All 7 comparisons passed. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_AreaPerMol 378s 378s CPPTRAJ: Area per molecule test 378s 378s All 6 comparisons passed. 378s 378s ******************************************************************************** 378s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_DistBasedMask 378s 378s CPPTRAJ: Distance-based atom mask tests (atom, residue) 378s 378s CPPTRAJ: Distance-based atom mask tests (molecule) 379s 379s All 6 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Calc 379s 379s CPPTRAJ: Calc test 379s 379s CPPTRAJ: Calc test with data sets 379s 379s CPPTRAJ: Test math functions 379s 379s All 4 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CalcState 379s 379s CPPTRAJ: Calcstate test 379s 379s All 4 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Change 379s 379s CPPTRAJ: Change atom and residue name tests 379s 379s CPPTRAJ: Change chain ID test 379s 379s CPPTRAJ: Change chain ID of COORDS set test 379s 379s All 3 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CreateReservoir 379s 379s CPPTRAJ: Create RREMD NetCDF reservoir test 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_FixAtomOrder 379s 379s CPPTRAJ: Out of order molecules test 379s 379s All 2 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_LowestCurve 379s 379s CPPTRAJ: LowestCurve test 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_MinImage 379s 379s CPPTRAJ: Minimum Image test. 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Regress 379s 379s CPPTRAJ: Linear regression test. 379s 379s All 3 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Rst 379s 379s CPPTRAJ: Generate restraints (rst) test 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Pairwise 379s 379s CPPTRAJ: Pairwise tests 379s 379s CPPTRAJ: Pairwise test, partial system 379s 379s All 10 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_ParmBox 379s 379s CPPTRAJ: Parmbox test 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Solvent 379s 379s CPPTRAJ: Test solvent command with closest 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Translate 379s 379s CPPTRAJ: Translate test 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_ReplicateCell 379s 379s CPPTRAJ: Replicate cell test 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_ScaleDihedralK 379s 379s CPPTRAJ: Scale dihedral force constant test 379s 379s CPPTRAJ: Scale dihedral force constant with 'useall' 379s 379s All 2 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_PhiPsi 379s 379s CPPTRAJ: Phipsi test 379s 379s All 1 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Control 379s 379s CPPTRAJ: Loop tests 379s 379s CPPTRAJ: Test set command 379s 379s CPPTRAJ: Test reading comma-separated list of strings 379s 379s CPPTRAJ: Test nested loops and variables in loops 379s 379s CPPTRAJ: Test loop over data set blocks 379s 379s CPPTRAJ: Test for filename wildcards and oversets 379s 379s All 13 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_InfraredSpec 379s 379s CPPTRAJ: Infrared spectrum calculation test 379s 379s All 2 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Cphstats 379s 379s CPPTRAJ: Explicit pH REMD ensemble data read / sort 379s 379s CPPTRAJ: Constant pH stats test 379s 379s CPPTRAJ: Sorted implicit constant pH stats test 379s 379s CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats 379s 379s CPPTRAJ: Unsorted pH read/write test 379s 379s All 16 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CmdLine 379s 379s CPPTRAJ: Command line trajectory args test, part 1 379s 379s CPPTRAJ: Command line test trajectory args test, part 2 379s 379s CPPTRAJ: Command line wildcard test, part 1 379s 379s CPPTRAJ: Command line wildcard test, part 2 379s 379s All 2 comparisons passed. 379s 379s ******************************************************************************** 379s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_XYZformat 379s 379s CPPTRAJ: XYZ format write 380s 380s CPPTRAJ: Atom XYZ format read, test 1 380s 380s CPPTRAJ: Atom XYZ format read, test 2 380s 380s CPPTRAJ: Atom XYZ format read, test 3 380s 380s CPPTRAJ: Atom XYZ format read, test 4 380s 380s CPPTRAJ: Atom XYZ format read, test 5 380s 380s CPPTRAJ: Atom XYZ format read, test 6 380s 380s All 6 comparisons passed. 380s 380s ******************************************************************************** 380s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Hausdorff 380s 380s CPPTRAJ: Simple Hausdorff distance test. 380s 380s CPPTRAJ: Hausdorff distance of 2D rms output test. 380s 380s CPPTRAJ: Hausdorff distance of 2D rms output test. 380s 380s All 3 comparisons passed. 380s 380s ******************************************************************************** 380s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_CatCrd 380s 380s CPPTRAJ: Concatenate COORDS data set test 380s 380s All 1 comparisons passed. 380s 380s ******************************************************************************** 380s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_XtalSymm 380s 380s CPPTRAJ: XtalSymm Reference 380s 380s CPPTRAJ: XtalSymm Reimaging by Atom 381s 381s CPPTRAJ: XtalSymm Reimaging by Molecule 382s 382s All 3 comparisons passed. 382s 382s ******************************************************************************** 382s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Time 382s 382s CPPTRAJ: Add time to restart test 382s 382s CPPTRAJ: Remove time from restart test 382s 382s CPPTRAJ: Add time to trajectory test 382s 382s CPPTRAJ: Modify time info test. 382s 382s All 4 comparisons passed. 382s 382s ******************************************************************************** 382s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_SplitCoords 382s 382s CPPTRAJ: SplitCoords test 382s 382s All 1 comparisons passed. 382s 382s ******************************************************************************** 382s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_DihedralRMS 382s 382s CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) 382s 382s CPPTRAJ: Dihedral RMSD test (to previous) 382s 382s CPPTRAJ: Dihedral RMS fluctuation test. 382s 382s All 5 comparisons passed. 382s 382s ******************************************************************************** 382s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Slope 382s 382s CPPTRAJ: Finite difference test. 382s 382s All 1 comparisons passed. 382s 382s ******************************************************************************** 382s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Diagmatrix 382s 382s CPPTRAJ: MW covariance matrix thermo analysis test 382s 382s All 1 comparisons passed. 382s 382s ******************************************************************************** 382s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Emin 382s 382s CPPTRAJ: Basic energy minimization test. 382s 382s CPPTRAJ: Energy minimization with angle term test. 382s 382s CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. 382s 382s CPPTRAJ: Energy minimization with nonbond term test. 382s 382s CPPTRAJ: OpenMM basic energy minimization tests (bonds) 382s 382s CPPTRAJ: OpenMM basic energy minimization tests (angles) 382s 382s CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) 382s 382s CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) 382s 382s CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) 383s 383s All 9 comparisons passed. 383s 383s ******************************************************************************** 383s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_EvalPlateau 383s 383s CPPTRAJ: Evalulate plateau test 383s 383s All 2 comparisons passed. 383s 383s ******************************************************************************** 383s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Graft 383s 383s CPPTRAJ: Graft test 383s 383s All 1 comparisons passed. 383s 383s ******************************************************************************** 383s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Flatten 383s 383s CPPTRAJ: Flatten test. 383s 383s All 1 comparisons passed. 383s 383s ******************************************************************************** 383s TEST: /tmp/autopkgtest.Ktrf5m/build.o7U/src/test/Test_Random 383s 383s CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs 384s 384s CPPTRAJ: PCG32 RNG test. 384s 384s CPPTRAJ: Test Stdlib RNG 384s 384s CPPTRAJ: Test Mersenne Twister RNG 384s 384s All 4 comparisons passed. 384s 384s make[1]: Leaving directory '/tmp/autopkgtest.Ktrf5m/build.o7U/src/test' 384s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 23 16:38 ../bin/cpptraj -> /usr/bin/cpptraj 384s ===================== TEST SUMMARY ====================== 384s 851 out of 859 comparisons OK (2 failed, 0 warnings, 6 skipped). 384s 480 out of 480 program executions completed. 384s 168 out of 173 tests completed with no issues. 384s 2 tests skipped. 384s ========================================================= 384s make: Leaving directory '/tmp/autopkgtest.Ktrf5m/build.o7U/src/test' 384s make: *** [Makefile:662: summary] Error 2 384s autopkgtest [16:38:57]: test command1: -----------------------] 384s command1 FAIL non-zero exit status 2 384s autopkgtest [16:38:57]: test command1: - - - - - - - - - - results - - - - - - - - - - 385s autopkgtest [16:38:58]: test command1: - - - - - - - - - - stderr - - - - - - - - - - 385s make: *** [Makefile:662: summary] Error 2 385s autopkgtest [16:38:58]: @@@@@@@@@@@@@@@@@@@@ summary 385s command1 FAIL non-zero exit status 2 400s Creating nova instance adt-noble-ppc64el-cpptraj-20240323-163233-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...