0s autopkgtest [06:58:53]: starting date and time: 2024-03-18 06:58:53+0000 0s autopkgtest [06:58:53]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [06:58:53]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vigalc4b/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:netcdf,src:curl,src:gnutls28,src:hdf5,src:libpsl,src:nettle,src:openssl,src:orthanc-python --apt-upgrade cpptraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=netcdf/1:4.9.2-5ubuntu3 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 hdf5/1.10.10+repack-3.1ubuntu3 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-20.secgroup --name adt-noble-ppc64el-cpptraj-20240318-065852-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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://ftpmaster.internal/ubuntu/ 145s autopkgtest [07:01:18]: testbed dpkg architecture: ppc64el 145s autopkgtest [07:01:18]: testbed apt version: 2.7.12 145s autopkgtest [07:01:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 146s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 146s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 146s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 146s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [484 kB] 146s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3725 kB] 147s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [643 kB] 147s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 147s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 147s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 147s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3972 kB] 147s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 147s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [48.0 kB] 147s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 150s Fetched 9060 kB in 2s (4198 kB/s) 150s Reading package lists... 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Calculating upgrade... 153s The following packages will be REMOVED: 153s libssl3 153s The following NEW packages will be installed: 153s libssl3t64 153s The following packages have been kept back: 153s curl 153s The following packages will be upgraded: 153s openssl 153s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 153s Need to get 3195 kB of archives. 153s After this operation, 6144 B of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu1 [1028 kB] 154s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu1 [2168 kB] 154s Fetched 3195 kB in 1s (3562 kB/s) 154s (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 ... 70095 files and directories currently installed.) 154s Preparing to unpack .../openssl_3.0.13-0ubuntu1_ppc64el.deb ... 154s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 154s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 154s wget depends on libssl3 (>= 3.0.0). 154s tnftp depends on libssl3 (>= 3.0.0). 154s tcpdump depends on libssl3 (>= 3.0.0). 154s systemd-resolved depends on libssl3 (>= 3.0.0). 154s systemd depends on libssl3 (>= 3.0.0). 154s sudo depends on libssl3 (>= 3.0.0). 154s rsync depends on libssl3 (>= 3.0.0). 154s python3-cryptography depends on libssl3 (>= 3.0.0). 154s openssh-server depends on libssl3 (>= 3.0.10). 154s openssh-client depends on libssl3 (>= 3.0.10). 154s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 154s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 154s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 154s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 154s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 154s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 154s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 154s libnvme1 depends on libssl3 (>= 3.0.0). 154s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 154s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 154s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 154s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 154s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 154s kmod depends on libssl3 (>= 3.0.0). 154s dhcpcd-base depends on libssl3 (>= 3.0.0). 154s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 154s 154s (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 ... 70095 files and directories currently installed.) 154s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 154s Selecting previously unselected package libssl3t64:ppc64el. 154s (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 ... 70084 files and directories currently installed.) 154s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_ppc64el.deb ... 154s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 154s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 154s Setting up openssl (3.0.13-0ubuntu1) ... 154s Processing triggers for man-db (2.12.0-3) ... 155s Processing triggers for libc-bin (2.39-0ubuntu2) ... 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 156s sh: Attempting to set up Debian/Ubuntu apt sources automatically 156s sh: Distribution appears to be Ubuntu 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s eatmydata is already the newest version (131-1). 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s dbus is already the newest version (1.14.10-4ubuntu1). 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s rng-tools-debian is already the newest version (2.4). 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s The following packages will be REMOVED: 158s cloud-init* python3-configobj* python3-debconf* 158s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 158s After this operation, 3252 kB disk space will be freed. 159s (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 ... 70097 files and directories currently installed.) 159s Removing cloud-init (24.1.1-0ubuntu1) ... 159s Removing python3-configobj (5.0.8-3) ... 159s Removing python3-debconf (1.5.86) ... 159s Processing triggers for man-db (2.12.0-3) ... 159s (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 ... 69708 files and directories currently installed.) 159s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 160s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 160s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 160s invoke-rc.d: policy-rc.d denied execution of try-restart. 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s linux-generic is already the newest version (6.8.0-11.11+1). 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 161s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 161s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 163s Reading package lists... 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 164s Calculating upgrade... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s autopkgtest [07:01:37]: rebooting testbed after setup commands that affected boot 207s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 214s autopkgtest [07:02:27]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 216s autopkgtest [07:02:29]: @@@@@@@@@@@@@@@@@@@@ apt-source cpptraj 220s Get:1 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (dsc) [2160 B] 220s Get:2 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (tar) [28.4 MB] 220s Get:3 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (diff) [6064 B] 220s gpgv: Signature made Tue Jun 27 18:04:29 2023 UTC 220s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 220s gpgv: Can't check signature: No public key 220s dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-3build1.dsc: no acceptable signature found 223s autopkgtest [07:02:36]: testing package cpptraj version 5.1.0+dfsg-3build1 224s autopkgtest [07:02:37]: build not needed 231s autopkgtest [07:02:44]: test command1: preparing testbed 233s Reading package lists... 234s Building dependency tree... 234s Reading state information... 234s Starting pkgProblemResolver with broken count: 0 234s Starting 2 pkgProblemResolver with broken count: 0 234s Done 234s The following additional packages will be installed: 234s cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 libgfortran5 libgomp1 234s libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 libopenmm8.0 libsz2 234s netcdf-bin 234s Suggested packages: 234s libfftw3-bin libfftw3-dev 234s The following NEW packages will be installed: 234s autopkgtest-satdep cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 234s libgfortran5 libgomp1 libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 234s libopenmm8.0 libsz2 netcdf-bin 234s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 234s Need to get 9571 kB/9571 kB of archives. 234s After this operation, 30.6 MB of additional disk space will be used. 234s Get:1 /tmp/autopkgtest.Ifomds/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 234s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 235s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 235s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 235s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libarpack2 ppc64el 3.9.1-1 [106 kB] 235s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 235s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libfftw3-double3 ppc64el 3.3.10-1ubuntu1 [440 kB] 235s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 235s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 235s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB] 236s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB] 236s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libnetcdf19 ppc64el 1:4.9.2-3ubuntu1 [597 kB] 236s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el libopenmm8.0 ppc64el 8.0.0+dfsg-6ubuntu1 [893 kB] 236s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el cpptraj ppc64el 5.1.0+dfsg-3build1 [2050 kB] 236s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el netcdf-bin ppc64el 1:4.9.2-3ubuntu1 [239 kB] 236s Fetched 9571 kB in 2s (4519 kB/s) 236s Selecting previously unselected package libblas3:ppc64el. 236s (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 ... 69653 files and directories currently installed.) 236s Preparing to unpack .../00-libblas3_3.12.0-3_ppc64el.deb ... 236s Unpacking libblas3:ppc64el (3.12.0-3) ... 236s Selecting previously unselected package libgfortran5:ppc64el. 236s Preparing to unpack .../01-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 236s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 237s Selecting previously unselected package liblapack3:ppc64el. 237s Preparing to unpack .../02-liblapack3_3.12.0-3_ppc64el.deb ... 237s Unpacking liblapack3:ppc64el (3.12.0-3) ... 237s Selecting previously unselected package libarpack2:ppc64el. 237s Preparing to unpack .../03-libarpack2_3.9.1-1_ppc64el.deb ... 237s Unpacking libarpack2:ppc64el (3.9.1-1) ... 237s Selecting previously unselected package libgomp1:ppc64el. 237s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 237s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 237s Selecting previously unselected package libfftw3-double3:ppc64el. 237s Preparing to unpack .../05-libfftw3-double3_3.3.10-1ubuntu1_ppc64el.deb ... 237s Unpacking libfftw3-double3:ppc64el (3.3.10-1ubuntu1) ... 237s Selecting previously unselected package libaec0:ppc64el. 237s Preparing to unpack .../06-libaec0_1.1.2-1_ppc64el.deb ... 237s Unpacking libaec0:ppc64el (1.1.2-1) ... 237s Selecting previously unselected package libsz2:ppc64el. 237s Preparing to unpack .../07-libsz2_1.1.2-1_ppc64el.deb ... 237s Unpacking libsz2:ppc64el (1.1.2-1) ... 237s Selecting previously unselected package libhdf5-103-1:ppc64el. 237s Preparing to unpack .../08-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 237s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 237s Selecting previously unselected package libhdf5-hl-100:ppc64el. 237s Preparing to unpack .../09-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ... 237s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 237s Selecting previously unselected package libnetcdf19:ppc64el. 237s Preparing to unpack .../10-libnetcdf19_1%3a4.9.2-3ubuntu1_ppc64el.deb ... 237s Unpacking libnetcdf19:ppc64el (1:4.9.2-3ubuntu1) ... 237s Selecting previously unselected package libopenmm8.0. 237s Preparing to unpack .../11-libopenmm8.0_8.0.0+dfsg-6ubuntu1_ppc64el.deb ... 237s Unpacking libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ... 237s Selecting previously unselected package cpptraj. 237s Preparing to unpack .../12-cpptraj_5.1.0+dfsg-3build1_ppc64el.deb ... 237s Unpacking cpptraj (5.1.0+dfsg-3build1) ... 237s Selecting previously unselected package netcdf-bin. 237s Preparing to unpack .../13-netcdf-bin_1%3a4.9.2-3ubuntu1_ppc64el.deb ... 237s Unpacking netcdf-bin (1:4.9.2-3ubuntu1) ... 237s Selecting previously unselected package autopkgtest-satdep. 237s Preparing to unpack .../14-1-autopkgtest-satdep.deb ... 237s Unpacking autopkgtest-satdep (0) ... 237s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 237s Setting up libaec0:ppc64el (1.1.2-1) ... 237s Setting up libblas3:ppc64el (3.12.0-3) ... 237s 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 237s Setting up libfftw3-double3:ppc64el (3.3.10-1ubuntu1) ... 237s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 237s Setting up libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ... 237s Setting up libsz2:ppc64el (1.1.2-1) ... 237s Setting up liblapack3:ppc64el (3.12.0-3) ... 237s 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 237s Setting up libarpack2:ppc64el (3.9.1-1) ... 237s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 237s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 237s Setting up libnetcdf19:ppc64el (1:4.9.2-3ubuntu1) ... 237s Setting up cpptraj (5.1.0+dfsg-3build1) ... 237s Setting up netcdf-bin (1:4.9.2-3ubuntu1) ... 237s Setting up autopkgtest-satdep (0) ... 237s Processing triggers for man-db (2.12.0-3) ... 237s Processing triggers for libc-bin (2.39-0ubuntu2) ... 239s (Reading database ... 69744 files and directories currently installed.) 239s Removing autopkgtest-satdep (0) ... 240s autopkgtest [07:02:53]: test command1: mkdir bin && ln -s /usr/bin/cpptraj bin && make -C test test.complete summary 240s autopkgtest [07:02:53]: test command1: [----------------------- 240s make: Entering directory '/tmp/autopkgtest.Ifomds/build.piX/src/test' 240s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 18 07:02 ../bin/cpptraj -> /usr/bin/cpptraj 240s make[1]: Entering directory '/tmp/autopkgtest.Ifomds/build.piX/src/test' 240s ******************************************************************************** 240s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_General 240s 240s CPPTRAJ: General tests 241s 241s All 15 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Parallel 241s 241s CPPTRAJ: Parallel tests. 241s 241s CPPTRAJ: Parallel test with trajectory offset 241s 241s All 7 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Strip 241s 241s CPPTRAJ: One frame strip command test 241s 241s CPPTRAJ: Unstrip (Lig/Rec/Complex) command test 241s 241s CPPTRAJ: Multi frame strip command test. 241s 241s CPPTRAJ: Strip topology with PDB info 241s 241s All 11 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_BrokenTraj 241s 241s CPPTRAJ: Broken Traj: Running good trajectory. 241s 241s CPPTRAJ: Broken Traj: Running broken trajectory. 241s 241s CPPTRAJ: Compressed broken trajectory test 241s 241s All 2 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_TrajinOffset 241s 241s CPPTRAJ: Normal trajectory read with offsets. 241s 241s CPPTRAJ: Gzipped trajectory read with offsets 241s 241s CPPTRAJ: Bzip2ed trajectory read with offsets 241s 241s CPPTRAJ: Start argument offset 241s 241s All 4 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_RemdTraj 241s 241s CPPTRAJ: CRD Replica Trajectory Run with offset 241s 241s CPPTRAJ: CRD Replica Trajectory Run 241s 241s CPPTRAJ: NetCDF Replica Trajectory Run test 241s 241s CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj 241s 241s CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj 241s 241s CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj 241s 241s CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj 241s 241s CPPTRAJ: CRD Replica Trajectory Run with remdout 241s 241s All 8 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_trajout_framerange 241s 241s CPPTRAJ: Trajout Frame Range [Amber Restart] 241s 241s CPPTRAJ: Trajout Frame Range [Amber Coordinates] 241s 241s All 6 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_PerResRMSD 241s 241s CPPTRAJ: Per-Residue RMSD Test. 241s 241s CPPTRAJ: Per-Residue RMSD Test with averaging 241s 241s CPPTRAJ: Per-Residue RMSD Test with residue centering. 241s 241s All 3 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_DSSP 241s 241s CPPTRAJ: Secstruct (DSSP) command test. 241s 241s CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. 241s 241s CPPTRAJ: Secstruct (DSSP) command with changing number of residues. 241s 241s CPPTRAJ: Secstruct (DSSP): SS assign output test 241s 241s CPPTRAJ: FtuFabI Assignment test 241s 241s All 10 comparisons passed. 241s 241s ******************************************************************************** 241s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Center 241s 241s CPPTRAJ: Center command test. 241s 241s CPPTRAJ: Center origin command test. 242s 242s CPPTRAJ: Center origin mass command test. 242s 242s CPPTRAJ: Center reference command test. 242s 242s CPPTRAJ: Center point test. 242s 242s All 5 comparisons passed. 242s 242s ******************************************************************************** 242s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Hbond 242s 242s CPPTRAJ: Solute Hbond test 242s 242s CPPTRAJ: Solute Hbond test with disk caching 242s 242s CPPTRAJ: Solute-solvent hbond test 242s 242s CPPTRAJ: Hbond, no intramolecular hydrogen bonds test 242s 242s CPPTRAJ: Hbond, specified solute masks 242s 242s CPPTRAJ: Hbond, no angle cutoff test 242s 242s CPPTRAJ: Hbond, Bridge nointramol test 242s 242s CPPTRAJ: Hbond with imaging 242s 242s CPPTRAJ: Hbond, orthogonal imaging 242s 242s All 23 comparisons passed. 242s 242s ******************************************************************************** 242s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_NCrestart 242s 242s CPPTRAJ: NetCDF Restart Test - TXT->NetCDF 242s 242s CPPTRAJ: NetCDF Restart Test - NetCDF->TXT 242s 242s CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF 242s 242s CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt 242s 242s All 2 comparisons passed. 242s 242s ******************************************************************************** 242s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Image 242s 242s CPPTRAJ: Orthorhombic imaged distance test. 242s 242s CPPTRAJ: Non-orthorhombic imaged distance test. 242s 242s CPPTRAJ: Orthorhombic coordinate imaging test 242s 242s CPPTRAJ: Nonorthorhombic coordinate imaging test 242s 242s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar 242s 242s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM 242s 242s All 6 comparisons passed. 242s 242s ******************************************************************************** 242s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Surf 242s 242s CPPTRAJ: Surface calculation test 243s 243s CPPTRAJ: Partial Surface calculation test 243s 243s CPPTRAJ: LCPO test with GAFF atom types 243s 243s All 3 comparisons passed. 243s 243s ******************************************************************************** 243s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Radgyr 243s 243s CPPTRAJ: Radius of gyration command test 243s 243s All 2 comparisons passed. 243s 243s ******************************************************************************** 243s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Mask 243s 243s CPPTRAJ: Mask single frame test 243s 243s CPPTRAJ: Mask longer command test. 243s 243s All 5 comparisons passed. 243s 243s ******************************************************************************** 243s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Jcoupling 243s 243s CPPTRAJ: J-Coupling single frame test 243s J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. 243s Skipped test: J-Coupling extended test 243s 243s All 1 comparisons passed. 243s 1 comparisons skipped. 243s 243s ******************************************************************************** 243s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Diffusion 243s 243s CPPTRAJ: Diffusion test, no imaging. 243s 243s CPPTRAJ: Diffusion test, old syntax. 243s 243s CPPTRAJ: Diffusion test, new syntax. 243s 243s CPPTRAJ: Diffusion test, nonorthogonal box 243s 243s CPPTRAJ: STFC Diffusion Test 243s 243s CPPTRAJ: STFC Diffusion Test with individual distances 243s 243s CPPTRAJ: STFC Diffusion Test with COM 243s 243s CPPTRAJ: STFC Diffusion Test with second mask 243s 243s All 16 comparisons passed. 243s 243s ******************************************************************************** 243s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Outtraj 243s 243s CPPTRAJ: RMSD Test with outtraj. 243s 243s CPPTRAJ: Outtraj Test with maxmin. 243s 243s All 4 comparisons passed. 243s 243s ******************************************************************************** 243s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Charmm 243s 243s CPPTRAJ: CHARMM PSF/DCD test 243s 243s CPPTRAJ: CHARMM DCD Write, step 1. 243s 243s CPPTRAJ: CHARMM DCD Write, step 2. 243s 243s CPPTRAJ: CHAMBER topology read/strip test. 243s 243s CPPTRAJ: Read CHARMM restart 243s 243s CPPTRAJ: CHARMM PSF write 243s 243s CPPTRAJ: CHARMM COORdinates test 243s 243s All 6 comparisons passed. 243s 243s ******************************************************************************** 243s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CharmmParams 243s 243s CPPTRAJ: Test updating topology with Charmm parameters (single residue) 243s 243s All 2 comparisons passed. 243s 243s ******************************************************************************** 243s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Rotdif 243s 243s CPPTRAJ: Rotational diffusion calculation test 244s 244s All 4 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_NetcdfTraj 244s 244s CPPTRAJ: Convert mdcrd -> NetCDF 244s 244s CPPTRAJ: Convert NetCDF -> mdcrd 244s 244s All 1 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Runavg 244s 244s CPPTRAJ: Coordinate Running Average test. 244s 244s CPPTRAJ: Coordinate Running Average Traj Write 244s 244s All 2 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_RMSD 244s 244s CPPTRAJ: Basic RMSD tests 244s 244s CPPTRAJ: RMS coordinate rotation/rotation matrices test 244s 244s CPPTRAJ: RMS fit with no coordinates modification test. 244s 244s CPPTRAJ: RMS fit to previous test 244s 244s CPPTRAJ: RMS: imaging after unit cell rotation 244s 244s All 12 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_2DRMS 244s 244s CPPTRAJ: 2D RMSD Test. 244s 244s CPPTRAJ: 2D RMSD Test, mass-weighted. 244s 244s CPPTRAJ: 2D RMSD Test with reference trajectory 244s 244s CPPTRAJ: 2D DME Test. 244s 244s CPPTRAJ: 2D RMSD with reference mask test. 244s 244s CPPTRAJ: 2D RMSD test, no fitting. 244s 244s All 6 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Mol2 244s 244s CPPTRAJ: Mol2 Parm/Traj Read/Write Test. 244s 244s CPPTRAJ: PDB => Mol2 244s 244s CPPTRAJ: Amber Top/Rst => Mol2 244s Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. 244s Skipped test: Amber Top/Rst => Mol2, SYBYL atom types 244s 244s All 4 comparisons passed. 244s 1 comparisons skipped. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_NAstruct 244s 244s CPPTRAJ: NAstruct command test. 244s 244s CPPTRAJ: NAstruct command test, single strand 244s 244s All 11 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_NAstruct_8OG 244s 244s CPPTRAJ: NA test (8OG) 244s 244s All 3 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Average 244s 244s CPPTRAJ: Average Test. 244s 244s All 2 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Pucker 244s 244s CPPTRAJ: Pucker command test 244s 244s CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test 244s 244s CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. 244s 244s All 3 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AtomMap 244s 244s CPPTRAJ: AtomMap Test 244s 244s CPPTRAJ: AtomMap with 'rmsfit' 244s 244s CPPTRAJ: Atom map charmm->amber atom order 244s 244s CPPTRAJ: Atom map charmm->amber atom order, by residue 244s 244s All 9 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Datafile 244s 244s CPPTRAJ: Data file output precision test 244s 244s CPPTRAJ: Standard -> Grace Data 244s 244s CPPTRAJ: Grace -> Standard Data 244s 244s CPPTRAJ: X column format/precision test. 244s 244s CPPTRAJ: Data file group by name test 244s 244s CPPTRAJ: Data file group by aspect test 244s 244s All 6 comparisons passed. 244s 244s ******************************************************************************** 244s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Radial 244s 244s CPPTRAJ: Radial test, non-orthogonal imaging 245s 245s CPPTRAJ: Radial test, orthogonal and no imaging 245s 245s All 9 comparisons passed. 245s 245s ******************************************************************************** 245s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Hist 245s 245s CPPTRAJ: 1D/2D Histogram Analysis test 245s 245s CPPTRAJ: 3D histogram test. 245s 245s All 7 comparisons passed. 245s 245s ******************************************************************************** 245s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Closest 245s 245s CPPTRAJ: Closest command test using first solvent atom. 245s 245s CPPTRAJ: Closest command test using all solvent atoms. 245s 245s CPPTRAJ: Closest command test, using mask center 245s 245s CPPTRAJ: Closest command test, using mask center and solvent mask 245s 245s CPPTRAJ: Closest command test, solvent mask, water oxygen only 245s 245s All 8 comparisons passed. 245s 245s ******************************************************************************** 245s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_DRMSD 245s 245s CPPTRAJ: Distance RMSD test 245s 245s All 1 comparisons passed. 245s 245s ******************************************************************************** 245s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster 245s 245s CPPTRAJ: Cluster command test, in-memory pairwise distances. 245s 245s CPPTRAJ: Cluster command test, read pairwise distances. 245s 245s CPPTRAJ: Cluster command test, read NetCDF pairwise distances. 245s 245s CPPTRAJ: Cluster command test, write ASCII pairwise distances. 245s 245s CPPTRAJ: Cluster command test, read ASCII pairwise distances. 245s 245s All 9 comparisons passed. 245s 245s ******************************************************************************** 245s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_Sieve 245s 245s CPPTRAJ: Cluster, nosieve 245s 245s CPPTRAJ: Cluster, sieve5 245s 245s CPPTRAJ: Cluster, nosieve savepairdist 245s 245s CPPTRAJ: Cluster, nosieve loadpairdist 245s 245s CPPTRAJ: Cluster, sieve5 savepairdist 246s 246s CPPTRAJ: Cluster, sieve5 loadpairdist 246s 246s CPPTRAJ: Cluster, nosieve pairwisecache none 246s 246s CPPTRAJ: Cluster, sieve5 pairwisecache none 246s 246s CPPTRAJ: Cluster, random 246s 246s All 28 comparisons passed. 246s 246s ******************************************************************************** 246s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_RandomSieve 246s 246s CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). 246s 246s CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). 246s 246s All 4 comparisons passed. 246s 246s ******************************************************************************** 246s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_DataSet 246s 246s CPPTRAJ: Clustering, One DataSet 246s 246s CPPTRAJ: Clustering, Two DataSets 246s 246s CPPTRAJ: Clustering, dihedral DataSet 246s 246s CPPTRAJ: Clustering, two dihedral DataSets 246s 246s CPPTRAJ: Clustering, dihedral DataSet, K-means 246s 246s CPPTRAJ: Clustering, two dihedral DataSets, K-means 246s 246s All 8 comparisons passed. 246s 246s ******************************************************************************** 246s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_DBSCAN 246s 246s CPPTRAJ: DBSCAN test 246s 246s CPPTRAJ: DBSCAN automatic parameter determination test. 246s 246s CPPTRAJ: DBSCAN kdist map test 246s 246s CPPTRAJ: DBSCAN with sieve 246s 246s All 4 comparisons passed. 246s 246s ******************************************************************************** 246s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_Kmeans 246s 246s CPPTRAJ: Cpptraj Kmeans 246s 246s CPPTRAJ: Cpptraj Kmeans random 246s 246s All 6 comparisons passed. 246s 246s ******************************************************************************** 246s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_SymmRMSD 246s 246s CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) 246s 246s All 5 comparisons passed. 246s 246s ******************************************************************************** 246s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_TrajWrites 246s 246s CPPTRAJ: Cluster command test, coordinate writes. 246s 246s CPPTRAJ: Cluster command test, coordinate writes using info file. 246s 246s All 8 comparisons passed. 246s 246s ******************************************************************************** 246s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_Dpeaks 246s 246s CPPTRAJ: Density peaks clustering test 246s 246s All 3 comparisons passed. 246s 246s ******************************************************************************** 246s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cluster_Nreps 246s 246s CPPTRAJ: Clustering with specified # reps 246s 246s All 2 comparisons passed. 246s 247s ******************************************************************************** 247s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_IRED 247s 247s CPPTRAJ: IRED vector/matrix test 247s 247s 247s ******************************************************************************** 247s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_RandomizeIons 247s 247s CPPTRAJ: randomizeions test (original algorithm) 247s 247s CPPTRAJ: Randomize (around, overlap) 247s 247s CPPTRAJ: Randomize (around) 247s 247s CPPTRAJ: Randomize (overlap) 248s 248s CPPTRAJ: Randomize (no restrictions) 248s 248s All 5 comparisons passed. 248s 248s ******************************************************************************** 248s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Molsurf 248s 248s CPPTRAJ: Molsurf test 248s 248s All 1 comparisons passed. 248s 248s ******************************************************************************** 248s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Corr 248s 248s CPPTRAJ: Correlation test 248s 248s All 2 comparisons passed. 248s 248s ******************************************************************************** 248s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CheckStructure 248s 248s CPPTRAJ: Structure Check 248s 248s CPPTRAJ: Structure Check with Around and Skip 248s 248s CPPTRAJ: Structure Check with PBC 248s 248s CPPTRAJ: Structure Check with Around 248s 248s All 8 comparisons passed. 248s 248s ******************************************************************************** 248s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_RmsAvgCorr 248s 248s CPPTRAJ: RmsAvgCorr Reference 248s 248s CPPTRAJ: RmsAvgCorr First 248s 248s All 3 comparisons passed. 248s 248s ******************************************************************************** 248s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Contacts 248s 248s CPPTRAJ: Contacts test. 248s 248s All 3 comparisons passed. 248s 248s ******************************************************************************** 248s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Principal 248s 248s CPPTRAJ: Principal Test 249s 249s All 3 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_ClusterDihedral 249s 249s CPPTRAJ: clusterdihedral test 249s 249s All 4 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Vector 249s 249s CPPTRAJ: Basic vector tests 249s 249s CPPTRAJ: Test vector center with magnitude 249s 249s CPPTRAJ: Momentum/velocity vector test. 249s 249s CPPTRAJ: Force vector test. 249s 249s All 14 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Matrix 249s 249s CPPTRAJ: Matrix Tests 249s 249s CPPTRAJ: Generate matrix with trajectory start/stop/offset 249s 249s CPPTRAJ: Generate matrix with action stop/start/offset 249s 249s All 15 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AtomicFluct 249s 249s CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. 249s 249s CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. 249s 249s CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. 249s 249s CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. 249s 249s CPPTRAJ: Atomicfluct test with ADP output 249s 249s CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. 249s 249s All 13 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Grid 249s 249s CPPTRAJ: Dipole test 249s 249s CPPTRAJ: Grid test 249s 249s CPPTRAJ: OpenDX Grid read test 249s 249s CPPTRAJ: Grid with specified center test. 249s 249s CPPTRAJ: Grid with box center offset test. 249s 249s CPPTRAJ: Grid with mask center offset test. 249s 249s CPPTRAJ: Non-orthogonal grid test. 249s 249s CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test 249s 249s CPPTRAJ: Grid generation from 'bounds' test. 249s 249s All 13 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Unwrap 249s 249s CPPTRAJ: Unwrap non-orthogonal test 249s 249s CPPTRAJ: Unwrap orthogonal test 249s 249s All 2 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Project 249s 249s CPPTRAJ: Projection 249s 249s All 1 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Analyze_Modes 249s 249s CPPTRAJ: Modes analysis, RMS fluctuations 249s 249s CPPTRAJ: Modes analysis, displacements 249s 249s CPPTRAJ: Modes analysis, dipole correlation 249s 249s CPPTRAJ: Modes analysis, pseudo trajectory creation test 249s 249s CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test 249s 249s All 6 comparisons passed. 249s 249s ******************************************************************************** 249s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Watershell 249s 249s CPPTRAJ: Watershell Test, non-orthorhombic imaging. 250s 250s CPPTRAJ: Watershell Test, orthorhombic imaging. 250s 250s CPPTRAJ: Watershell Test, no imaging. 250s 250s All 3 comparisons passed. 250s 250s ******************************************************************************** 250s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AnalysisRunAvg 250s 250s CPPTRAJ: Analysis Running Average 250s 250s All 2 comparisons passed. 250s 251s ******************************************************************************** 251s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Volmap 251s 251s CPPTRAJ: VMD VolMap Algorithm test 251s VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. 251s Skipped test: VMD VolMap Algorithm longer tests 251s 251s All 2 comparisons passed. 251s 1 comparisons skipped. 251s 251s ******************************************************************************** 251s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_SPAM 251s 251s CPPTRAJ: SPAM Test 251s 251s CPPTRAJ: SPAM Pure Solvent Test 252s 252s 1 out of 5 comparisons failed. 252s 252s ******************************************************************************** 252s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_LIE 252s 252s CPPTRAJ: LIE test 253s 253s All 1 comparisons passed. 253s 253s ******************************************************************************** 253s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Density 253s 253s CPPTRAJ: Density along axis tests 253s 253s CPPTRAJ: Multi-frame density along axis test 253s 253s CPPTRAJ: Total system density test 253s 253s All 7 comparisons passed. 253s 253s ******************************************************************************** 253s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_LipidOrder 253s 253s CPPTRAJ: Lipid Order Parameter Test. 253s 253s All 6 comparisons passed. 253s 253s ******************************************************************************** 253s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_LipidSCD 253s 253s CPPTRAJ: Basic lipid order parameter test 253s 253s CPPTRAJ: New Lipid Order Parameter Test, DOPC. 253s 253s All 4 comparisons passed. 253s 253s ******************************************************************************** 253s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_PairDist 253s 253s CPPTRAJ: PairDist Test. 253s 253s CPPTRAJ: Pairdist test, orthogonal imaging. 253s 253s CPPTRAJ: Pairdist test, nonorthogonal imaging. 254s 254s CPPTRAJ: Pairdist test, 2 masks. 254s 254s All 4 comparisons passed. 254s 254s ******************************************************************************** 254s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_ReadData 254s 254s CPPTRAJ: Read vector data test (no origins, origins) 254s 254s CPPTRAJ: Read vector data set (origins, no origins) 254s 254s CPPTRAJ: Read Amber output test 254s 254s CPPTRAJ: Read CHARMM output test 254s 254s CPPTRAJ: 3D data read/write test 254s 254s CPPTRAJ: Standard 3D data write test 254s 254s CPPTRAJ: Standard 3D data read test 254s 254s CPPTRAJ: Standard 3D data read/append test 254s 254s CPPTRAJ: Standard 3D data, sparse 254s 254s CPPTRAJ: Nonorthogonal grid standard write/read tests. 254s 254s CPPTRAJ: Read specific columns test. 254s 254s CPPTRAJ: Write non-square matrix 254s 254s CPPTRAJ: Read non-square matrix 254s 254s CPPTRAJ: Read square matrix 254s 254s All 15 comparisons passed. 254s 254s ******************************************************************************** 254s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_GIST 254s 254s CPPTRAJ: GIST water-water interaction test 255s 255s CPPTRAJ: GIST test, orthogonal cell 257s 257s CPPTRAJ: GIST test, nonorthogonal cell 261s 261s All 11 comparisons passed. 261s 261s ******************************************************************************** 261s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_GIST_Order 261s 261s CPPTRAJ: TIP3P water cluster test 261s 261s CPPTRAJ: TIP4P water cluster test 261s 261s CPPTRAJ: TIP5P water cluster test 261s 261s All 4 comparisons passed. 261s 261s ******************************************************************************** 261s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_systemVF 261s 261s CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test 262s 262s All 1 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AtomicCorr 262s 262s CPPTRAJ: Atomic Correlation test 262s 262s All 1 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AutoCorr 262s 262s CPPTRAJ: AutoCorr test. 262s 262s All 1 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Box 262s 262s CPPTRAJ: Box Test (Add box info) 262s 262s CPPTRAJ: Box test (remove box info) 262s 262s CPPTRAJ: Box test (Modify box length) 262s 262s CPPTRAJ: Box test (auto orthogonal box, no radii) 262s 262s CPPTRAJ: Box test (auto orthogonal box, VDW radii) 262s 262s All 7 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AtomTypeSelect 262s 262s CPPTRAJ: Selection by atom type test. 262s 262s All 1 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AvgRef 262s 262s CPPTRAJ: RMSD Test with averaged reference coordinates. 262s 262s All 1 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Crank_Stat 262s 262s CPPTRAJ: Crankshaft test 262s 262s All 3 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CreateCrd 262s 262s CPPTRAJ: COORDS data set creation and CRDFLUCT test. 262s 262s CPPTRAJ: COORDS data set creation with velocities test 262s 262s CPPTRAJ: TRAJ data set creation and CRDFLUCT test. 262s 262s CPPTRAJ: TRAJ data set creation with velocities test. 262s 262s CPPTRAJ: COORDS data set append test 262s 262s CPPTRAJ: COORDS test storing frame metadata 262s 262s CPPTRAJ: TRAJ test storing frame metadata 262s 262s All 8 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AutoImage 262s 262s CPPTRAJ: AutoImage test (split DNA duplex) 262s 262s CPPTRAJ: AutoImage test, use anchor mask 262s 262s All 2 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_LoadCrd 262s 262s CPPTRAJ: LoadCrd test. 262s 262s CPPTRAJ: LoadTraj test. 262s 262s CPPTRAJ: LoadTraj from trajin test. 262s 262s CPPTRAJ: LoadCrd append from multiple files test 262s 262s All 4 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_MultiVector 262s 262s CPPTRAJ: Multivector test 262s 262s All 1 comparisons passed. 262s 262s ******************************************************************************** 262s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Lifetime 262s 262s CPPTRAJ: Lifetime test. 262s 262s CPPTRAJ: Lifetime test with data set caching. 263s 263s CPPTRAJ: Lifetime average and cumulative average test. 263s 263s All 12 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_FFT 263s 263s CPPTRAJ: FFT test. 263s 263s All 5 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Timecorr 263s 263s CPPTRAJ: Timecorr test. 263s 263s All 7 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CrossCorr 263s 263s CPPTRAJ: CrossCorr test 263s 263s All 1 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_SymmRmsd 263s 263s CPPTRAJ: SymmRmsd 263s 263s CPPTRAJ: ASP symmetry-corrected RMSD test 263s 263s CPPTRAJ: GLU symmetry-corrected RMSD test 263s 263s CPPTRAJ: TYR symmetry-corrected RMSD test 263s 263s CPPTRAJ: Longer symmetry-corrected RMSD test. 263s 263s All 8 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Multidihedral 263s 263s CPPTRAJ: Multidihedral test 263s 263s CPPTRAJ: Multidihedral Nucleotide CHI test 263s 263s CPPTRAJ: Multidihedral protein dihedrals test 263s 263s CPPTRAJ: Multidihedral cyclic molecule test 263s 263s All 6 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Ensemble_MREMD 263s 263s CPPTRAJ: M-REMD sort test. 263s 263s CPPTRAJ: M-REMD actions test. 263s 263s CPPTRAJ: M-REMD ensemble outtraj test. 263s 263s CPPTRAJ: M-REMD no sort, running average test 263s 263s CPPTRAJ: M-REMD, generate RMS data 263s 263s CPPTRAJ: M-REMD, meltcurve analysis 263s 263s All 17 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_MakeStructure 263s 263s CPPTRAJ: Basic makestructure test 263s 263s CPPTRAJ: Makestructure test with reference. 263s 263s All 5 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Rotate 263s 263s CPPTRAJ: Rotation (and inverse) of coords from matrices 263s 263s CPPTRAJ: Rotate with defined axis 263s 263s All 3 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Integrate 263s 263s CPPTRAJ: Integration test. 263s 263s All 2 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_NativeContacts 263s 263s CPPTRAJ: NativeContacts test. 263s 263s CPPTRAJ: NativeContacts test, save non-native contacts, residue time series 263s 263s CPPTRAJ: NativeContacts test, orthorhombic imaging. 263s 263s All 17 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CheckChiral 263s 263s CPPTRAJ: Check chirality test 263s 263s All 1 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Energy 263s 263s CPPTRAJ: Simple energy tests 263s 263s CPPTRAJ: Test kinetic energy calculation 263s 263s CPPTRAJ: Test total energy calculation 263s 263s CPPTRAJ: Test partial energy calculation 263s 263s All 6 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_LESsplit 263s 263s CPPTRAJ: LES split/average test 263s 263s All 2 comparisons passed. 263s 263s ******************************************************************************** 263s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_PermuteDihedrals 263s 263s CPPTRAJ: PermuteDihedrals interval -120, phi psi 264s 264s CPPTRAJ: PermuteDihedrals, random rotations 264s 264s All 4 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CCP4 264s 264s CPPTRAJ: CCP4 read/write and DX conversion test. 264s 264s All 2 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_DihCovar 264s 264s CPPTRAJ: Dihedral Covariance Matrix Test 264s 264s All 3 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CurveFit 264s 264s CPPTRAJ: Curve fitting test. 264s 264s CPPTRAJ: Curve fitting multi-exponential tests. 264s 264s CPPTRAJ: Curve fitting, custom output range. 264s 264s All 6 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Multicurve 264s 264s CPPTRAJ: Multicurve test 264s 264s All 1 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_DataSetAverage 264s 264s CPPTRAJ: Data set averaging and averaging over all sets test. 264s 264s All 2 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_VectorMath 264s 264s CPPTRAJ: Vector dot/cross product test 264s 264s All 2 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Esander 264s SANDER energy tests (long) requires SANDER API from AmberTools. 264s Cpptraj was compiled without SANDER API from AmberTools support. 264s SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. 264s SKIP: SANDER energy tests (long) 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Esander_Short 264s Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. 264s Cpptraj was compiled without SANDER API from AmberTools support. 264s SKIP: Energy via sander API short tests (GB/PME) 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Temperature 264s 264s CPPTRAJ: Temperature test. 264s 264s CPPTRAJ: Temperature with SHAKE on hydrogens. 264s 264s CPPTRAJ: Temperature with SHAKE on all atoms. 264s 264s CPPTRAJ: Temperature calc with extra points. 264s 264s All 5 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Spline 264s 264s CPPTRAJ: Spline test 264s 264s All 1 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_KDE 264s 264s CPPTRAJ: KDE test. 264s 264s CPPTRAJ: KDE with Kullback-Leibler divergence test 264s 264s All 4 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Wavelet 264s 264s CPPTRAJ: Wavelet analysis test 264s 264s CPPTRAJ: Wavelet WAFEX test 264s 264s All 3 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CIF 264s 264s CPPTRAJ: CIF read test 264s 264s CPPTRAJ: Generate offset traj from PDB 264s 264s CPPTRAJ: Generate offset traj from CIF 264s 264s All 2 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_PDB 264s 264s CPPTRAJ: PDB format read/write test 264s 264s CPPTRAJ: PQR file write with various radii 264s 264s CPPTRAJ: PDB filter alternate atom location IDs test 264s 264s CPPTRAJ: Adding PDB info to topology 264s 264s All 10 comparisons passed. 264s 264s ******************************************************************************** 264s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Align 264s 264s CPPTRAJ: Align Tests. 264s 264s CPPTRAJ: Align, unit cell rotation/imaging test. 265s 265s All 4 comparisons passed. 265s 265s ******************************************************************************** 265s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_VelocityAutoCorr 265s 265s CPPTRAJ: Velocity autocorrelation test 265s 265s All 3 comparisons passed. 265s 265s ******************************************************************************** 265s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_VelFrc 265s 265s CPPTRAJ: Test combining coordinates, velocities, and forces. 265s 265s CPPTRAJ: Test using velocities as coordinates. 265s 265s CPPTRAJ: Test writing velocities (MDVEL) 265s 265s CPPTRAJ: Test using forces as coordinates. 265s 265s CPPTRAJ: Test writing forces (MDFRC) 265s 265s CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. 265s 265s CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. 265s 265s All 5 comparisons passed. 265s 265s ******************************************************************************** 265s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_RotateDihedral 265s 265s CPPTRAJ: Rotate dihedral to target value. 265s 265s CPPTRAJ: Rotate dihedral by increment 265s 265s CPPTRAJ: Rotate dihedral in TRAJ data set 265s 265s All 3 comparisons passed. 265s 265s ******************************************************************************** 265s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_DataSetCmd 265s 265s CPPTRAJ: Data Set commands test 265s 265s All 10 comparisons passed. 265s 265s ******************************************************************************** 265s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Remap 265s 265s CPPTRAJ: Remap Test 265s 265s All 1 comparisons passed. 265s 265s ******************************************************************************** 265s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CompareTop 265s 265s CPPTRAJ: Compare topology test 265s 265s All 1 comparisons passed. 265s 265s ******************************************************************************** 265s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Filter 265s 265s CPPTRAJ: Basic filter test 265s 265s CPPTRAJ: Data filter test. 265s 265s CPPTRAJ: Filter matrix test. 265s 265s All 5 comparisons passed. 265s 265s ******************************************************************************** 265s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CombineCrd 265s 265s CPPTRAJ: Combine COORDS test. 265s 265s CPPTRAJ: Combine COORDS test with box info. 265s 265s CPPTRAJ: Split coords and recombine test. 266s 266s All 5 comparisons passed. 266s 266s ******************************************************************************** 266s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_TopInfo 266s 266s CPPTRAJ: Topology info print test. 266s 266s CPPTRAJ: Topology info with reference coords test 266s 266s All 12 comparisons passed. 266s 266s ******************************************************************************** 266s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_GromacsTrr 266s 266s CPPTRAJ: TRR force/velocity read -> NetCDF write test 266s 266s CPPTRAJ: TRR force/velocity read -> TRR write test 266s 266s CPPTRAJ: CRD => TRR 266s 266s CPPTRAJ: TRR => CRD 266s 266s CPPTRAJ: CRD(1-5) => TRR 266s 266s CPPTRAJ: CRD(6-10) => TRR 266s 266s CPPTRAJ: TRR (appended) => CRD 266s 266s CPPTRAJ: GMX: CRD with offset 266s 266s CPPTRAJ: GMX: TRR with offset 266s 266s All 5 comparisons passed. 266s 266s ******************************************************************************** 266s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_GromacsXtc 266s 266s CPPTRAJ: XTC read test 266s 266s CPPTRAJ: CRD => XTC 266s 266s CPPTRAJ: XTC => CRD 267s 267s CPPTRAJ: CRD(1-5) => XTC 267s 267s CPPTRAJ: CRD(6-10) => XTC 267s 267s CPPTRAJ: XTC (appended) => CRD 267s 267s CPPTRAJ: GMX: CRD with offset 267s 267s CPPTRAJ: GMX: XTC with offset 267s 267s All 4 comparisons passed. 267s 267s ******************************************************************************** 267s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_GromacsTNG 267s 267s CPPTRAJ: TNG read test 267s 267s CPPTRAJ: TNG read test (with offset) 267s 267s All 6 comparisons passed. 267s 267s ******************************************************************************** 267s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Ewald 267s 267s CPPTRAJ: Direct sum test 267s 267s CPPTRAJ: Ewald test (NaCl crystal) 267s 267s CPPTRAJ: Ewald test (trunc. oct) 268s 268s CPPTRAJ: Ewald test (partial system, trunc. oct) 268s Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 268s Skipped test: Ewald test (trunc. oct), 10 frames 268s Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. 268s Skipped test: Ewald test (ortho), 10 frames 268s 268s All 4 comparisons passed. 268s 2 comparisons skipped. 268s 268s ******************************************************************************** 268s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_LibPME 268s 268s CPPTRAJ: Particle mesh Ewald test (NaCl crystal) 268s 268s CPPTRAJ: Particle mesh Ewald test (trunc. oct) 268s 268s CPPTRAJ: Particle mesh Ewald test (ortho) 268s 268s CPPTRAJ: Particle mesh Ewald test (ortho, with mask) 268s 268s CPPTRAJ: PME test (partial system, trunc. oct) 268s PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 268s Skipped test: PME test (trunc. oct), 10 frames 268s 268s All 5 comparisons passed. 268s 1 comparisons skipped. 268s 268s ******************************************************************************** 268s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_LJ_PME 268s 268s CPPTRAJ: LJ PME test. 268s 268s CPPTRAJ: LJ PME kappa sweep test, 0.25 268s 268s CPPTRAJ: LJ PME kappa sweep test, 0.35 268s 268s CPPTRAJ: LJ PME kappa sweep test, 0.45 268s 268s CPPTRAJ: LJ PME kappa sweep test, 0.5 268s 268s CPPTRAJ: LJ with switch function test 268s 268s All 5 comparisons passed. 268s 268s ******************************************************************************** 268s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_TI 268s 268s CPPTRAJ: TI analysis test. 268s 268s All 5 comparisons passed. 268s 268s ******************************************************************************** 268s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_FixImagedBonds 268s 268s CPPTRAJ: Fix imaged bonds test (Ortho.) 268s 268s CPPTRAJ: Fix imaged bonds test (Non-ortho.) 268s 268s All 2 comparisons passed. 268s 268s ******************************************************************************** 268s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Distance 268s 268s CPPTRAJ: Distance tests 268s 268s CPPTRAJ: Orthogonal imaged distance 268s 268s CPPTRAJ: Non-orthogonal imaged distance 269s 269s All 3 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Volume 269s 269s CPPTRAJ: Volume tests 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_SetVelocity 269s 269s CPPTRAJ: Set Velocity test 269s 269s CPPTRAJ: Scale velocity test 269s 269s 1 out of 3 comparisons failed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Remlog 269s 269s CPPTRAJ: Replica log read/analyze test. 269s 269s All 7 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_AreaPerMol 269s 269s CPPTRAJ: Area per molecule test 269s 269s All 6 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_DistBasedMask 269s 269s CPPTRAJ: Distance-based atom mask tests (atom, residue) 269s 269s CPPTRAJ: Distance-based atom mask tests (molecule) 269s 269s All 6 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Calc 269s 269s CPPTRAJ: Calc test 269s 269s CPPTRAJ: Calc test with data sets 269s 269s CPPTRAJ: Test math functions 269s 269s All 4 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CalcState 269s 269s CPPTRAJ: Calcstate test 269s 269s All 4 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Change 269s 269s CPPTRAJ: Change atom and residue name tests 269s 269s CPPTRAJ: Change chain ID test 269s 269s CPPTRAJ: Change chain ID of COORDS set test 269s 269s All 3 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CreateReservoir 269s 269s CPPTRAJ: Create RREMD NetCDF reservoir test 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_FixAtomOrder 269s 269s CPPTRAJ: Out of order molecules test 269s 269s All 2 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_LowestCurve 269s 269s CPPTRAJ: LowestCurve test 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_MinImage 269s 269s CPPTRAJ: Minimum Image test. 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Regress 269s 269s CPPTRAJ: Linear regression test. 269s 269s All 3 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Rst 269s 269s CPPTRAJ: Generate restraints (rst) test 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Pairwise 269s 269s CPPTRAJ: Pairwise tests 269s 269s CPPTRAJ: Pairwise test, partial system 269s 269s All 10 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_ParmBox 269s 269s CPPTRAJ: Parmbox test 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Solvent 269s 269s CPPTRAJ: Test solvent command with closest 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Translate 269s 269s CPPTRAJ: Translate test 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_ReplicateCell 269s 269s CPPTRAJ: Replicate cell test 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_ScaleDihedralK 269s 269s CPPTRAJ: Scale dihedral force constant test 269s 269s CPPTRAJ: Scale dihedral force constant with 'useall' 269s 269s All 2 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_PhiPsi 269s 269s CPPTRAJ: Phipsi test 269s 269s All 1 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Control 269s 269s CPPTRAJ: Loop tests 269s 269s CPPTRAJ: Test set command 269s 269s CPPTRAJ: Test reading comma-separated list of strings 269s 269s CPPTRAJ: Test nested loops and variables in loops 269s 269s CPPTRAJ: Test loop over data set blocks 269s 269s CPPTRAJ: Test for filename wildcards and oversets 269s 269s All 13 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_InfraredSpec 269s 269s CPPTRAJ: Infrared spectrum calculation test 269s 269s All 2 comparisons passed. 269s 269s ******************************************************************************** 269s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Cphstats 269s 269s CPPTRAJ: Explicit pH REMD ensemble data read / sort 270s 270s CPPTRAJ: Constant pH stats test 270s 270s CPPTRAJ: Sorted implicit constant pH stats test 270s 270s CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats 270s 270s CPPTRAJ: Unsorted pH read/write test 270s 270s All 16 comparisons passed. 270s 270s ******************************************************************************** 270s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CmdLine 270s 270s CPPTRAJ: Command line trajectory args test, part 1 270s 270s CPPTRAJ: Command line test trajectory args test, part 2 270s 270s CPPTRAJ: Command line wildcard test, part 1 270s 270s CPPTRAJ: Command line wildcard test, part 2 270s 270s All 2 comparisons passed. 270s 270s ******************************************************************************** 270s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_XYZformat 270s 270s CPPTRAJ: XYZ format write 270s 270s CPPTRAJ: Atom XYZ format read, test 1 270s 270s CPPTRAJ: Atom XYZ format read, test 2 270s 270s CPPTRAJ: Atom XYZ format read, test 3 270s 270s CPPTRAJ: Atom XYZ format read, test 4 270s 270s CPPTRAJ: Atom XYZ format read, test 5 270s 270s CPPTRAJ: Atom XYZ format read, test 6 270s 270s All 6 comparisons passed. 270s 270s ******************************************************************************** 270s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Hausdorff 270s 270s CPPTRAJ: Simple Hausdorff distance test. 270s 270s CPPTRAJ: Hausdorff distance of 2D rms output test. 270s 270s CPPTRAJ: Hausdorff distance of 2D rms output test. 270s 270s All 3 comparisons passed. 270s 270s ******************************************************************************** 270s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_CatCrd 270s 270s CPPTRAJ: Concatenate COORDS data set test 270s 270s All 1 comparisons passed. 270s 270s ******************************************************************************** 270s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_XtalSymm 270s 270s CPPTRAJ: XtalSymm Reference 270s 270s CPPTRAJ: XtalSymm Reimaging by Atom 271s 271s CPPTRAJ: XtalSymm Reimaging by Molecule 272s 272s All 3 comparisons passed. 272s 272s ******************************************************************************** 272s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Time 272s 272s CPPTRAJ: Add time to restart test 272s 272s CPPTRAJ: Remove time from restart test 272s 272s CPPTRAJ: Add time to trajectory test 272s 272s CPPTRAJ: Modify time info test. 272s 272s All 4 comparisons passed. 272s 272s ******************************************************************************** 272s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_SplitCoords 272s 272s CPPTRAJ: SplitCoords test 272s 272s All 1 comparisons passed. 272s 272s ******************************************************************************** 272s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_DihedralRMS 272s 272s CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) 272s 272s CPPTRAJ: Dihedral RMSD test (to previous) 272s 272s CPPTRAJ: Dihedral RMS fluctuation test. 272s 272s All 5 comparisons passed. 272s 272s ******************************************************************************** 272s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Slope 272s 272s CPPTRAJ: Finite difference test. 272s 272s All 1 comparisons passed. 272s 272s ******************************************************************************** 272s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Diagmatrix 272s 272s CPPTRAJ: MW covariance matrix thermo analysis test 272s 272s All 1 comparisons passed. 272s 272s ******************************************************************************** 272s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Emin 272s 272s CPPTRAJ: Basic energy minimization test. 272s 272s CPPTRAJ: Energy minimization with angle term test. 272s 272s CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. 272s 272s CPPTRAJ: Energy minimization with nonbond term test. 272s 272s CPPTRAJ: OpenMM basic energy minimization tests (bonds) 272s 272s CPPTRAJ: OpenMM basic energy minimization tests (angles) 272s 272s CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) 272s 272s CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) 273s 273s CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) 274s 274s All 9 comparisons passed. 274s 274s ******************************************************************************** 274s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_EvalPlateau 274s 274s CPPTRAJ: Evalulate plateau test 274s 274s All 2 comparisons passed. 274s 274s ******************************************************************************** 274s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Graft 274s 274s CPPTRAJ: Graft test 274s 274s All 1 comparisons passed. 274s 274s ******************************************************************************** 274s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Flatten 274s 274s CPPTRAJ: Flatten test. 274s 274s All 1 comparisons passed. 274s 274s ******************************************************************************** 274s TEST: /tmp/autopkgtest.Ifomds/build.piX/src/test/Test_Random 274s 274s CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs 274s 274s CPPTRAJ: PCG32 RNG test. 274s 274s CPPTRAJ: Test Stdlib RNG 274s 274s CPPTRAJ: Test Mersenne Twister RNG 274s 274s All 4 comparisons passed. 274s 274s make[1]: Leaving directory '/tmp/autopkgtest.Ifomds/build.piX/src/test' 274s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 18 07:02 ../bin/cpptraj -> /usr/bin/cpptraj 274s ===================== TEST SUMMARY ====================== 274s 851 out of 859 comparisons OK (2 failed, 0 warnings, 6 skipped). 274s 480 out of 480 program executions completed. 274s 168 out of 173 tests completed with no issues. 274s 2 tests skipped. 274s ========================================================= 274s make: Leaving directory '/tmp/autopkgtest.Ifomds/build.piX/src/test' 274s make: *** [Makefile:662: summary] Error 2 274s autopkgtest [07:03:27]: test command1: -----------------------] 275s command1 FAIL non-zero exit status 2 275s autopkgtest [07:03:28]: test command1: - - - - - - - - - - results - - - - - - - - - - 275s autopkgtest [07:03:28]: test command1: - - - - - - - - - - stderr - - - - - - - - - - 275s make: *** [Makefile:662: summary] Error 2 275s autopkgtest [07:03:28]: @@@@@@@@@@@@@@@@@@@@ summary 275s command1 FAIL non-zero exit status 2 286s Creating nova instance adt-noble-ppc64el-cpptraj-20240318-065852-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240318.img (UUID 290ce4c5-ca44-4691-9a55-79589f8700e4)...