0s autopkgtest [13:04:56]: starting date and time: 2024-03-16 13:04:56+0000 0s autopkgtest [13:04:56]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [13:04:56]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gqkf2fin/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@bos03-arm64-9.secgroup --name adt-noble-arm64-cpptraj-20240316-130456-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-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/ 111s autopkgtest [13:06:47]: testbed dpkg architecture: arm64 111s autopkgtest [13:06:47]: testbed apt version: 2.7.12 111s autopkgtest [13:06:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 111s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 113s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 113s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 113s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [473 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3650 kB] 113s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 113s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 113s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 113s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 113s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3974 kB] 113s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 113s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.8 kB] 113s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 114s Fetched 9020 kB in 2s (5641 kB/s) 114s Reading package lists... 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade... 118s The following packages will be REMOVED: 118s libssl3 118s The following NEW packages will be installed: 118s libssl3t64 118s The following packages have been kept back: 118s curl 118s The following packages will be upgraded: 118s openssl ubuntu-minimal ubuntu-standard 118s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 118s Need to get 2775 kB of archives. 118s After this operation, 72.7 kB of additional disk space will be used. 118s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 118s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 118s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 118s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 119s Fetched 2775 kB in 1s (4147 kB/s) 119s (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 ... 74758 files and directories currently installed.) 119s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 119s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 119s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 119s wget depends on libssl3 (>= 3.0.0). 119s u-boot-tools depends on libssl3 (>= 3.0.0). 119s tnftp depends on libssl3 (>= 3.0.0). 119s tcpdump depends on libssl3 (>= 3.0.0). 119s systemd-resolved depends on libssl3 (>= 3.0.0). 119s systemd depends on libssl3 (>= 3.0.0). 119s sudo depends on libssl3 (>= 3.0.0). 119s sbsigntool depends on libssl3 (>= 3.0.0). 119s rsync depends on libssl3 (>= 3.0.0). 119s python3-cryptography depends on libssl3 (>= 3.0.0). 119s openssh-server depends on libssl3 (>= 3.0.10). 119s openssh-client depends on libssl3 (>= 3.0.10). 119s mtd-utils depends on libssl3 (>= 3.0.0). 119s mokutil depends on libssl3 (>= 3.0.0). 119s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 119s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 119s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 119s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 119s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 119s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 119s libnvme1 depends on libssl3 (>= 3.0.0). 119s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 119s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 119s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 119s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 119s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 119s kmod depends on libssl3 (>= 3.0.0). 119s dhcpcd-base depends on libssl3 (>= 3.0.0). 119s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 119s 119s (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 ... 74758 files and directories currently installed.) 119s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 119s Selecting previously unselected package libssl3t64:arm64. 119s (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 ... 74747 files and directories currently installed.) 119s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 119s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 119s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 119s Unpacking ubuntu-minimal (1.536) over (1.535) ... 119s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 119s Unpacking ubuntu-standard (1.536) over (1.535) ... 119s Setting up ubuntu-minimal (1.536) ... 119s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 119s Setting up ubuntu-standard (1.536) ... 119s Setting up openssl (3.0.13-0ubuntu1) ... 119s Processing triggers for man-db (2.12.0-3) ... 120s Processing triggers for libc-bin (2.39-0ubuntu2) ... 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 122s sh: Attempting to set up Debian/Ubuntu apt sources automatically 122s sh: Distribution appears to be Ubuntu 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s eatmydata is already the newest version (131-1). 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s dbus is already the newest version (1.14.10-4ubuntu1). 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s rng-tools-debian is already the newest version (2.4). 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s The following packages will be REMOVED: 127s cloud-init* python3-configobj* python3-debconf* 127s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 127s After this operation, 3252 kB disk space will be freed. 127s (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 ... 74760 files and directories currently installed.) 127s Removing cloud-init (24.1.1-0ubuntu1) ... 128s Removing python3-configobj (5.0.8-3) ... 128s Removing python3-debconf (1.5.86) ... 128s Processing triggers for man-db (2.12.0-3) ... 128s (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 ... 74371 files and directories currently installed.) 128s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 129s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 129s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 129s invoke-rc.d: policy-rc.d denied execution of try-restart. 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s linux-generic is already the newest version (6.8.0-11.11+1). 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 130s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 130s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 132s Reading package lists... 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s Calculating upgrade... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s autopkgtest [13:07:11]: rebooting testbed after setup commands that affected boot 416s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 423s autopkgtest [13:11:59]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 426s autopkgtest [13:12:02]: @@@@@@@@@@@@@@@@@@@@ apt-source cpptraj 430s Get:1 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (dsc) [2160 B] 430s Get:2 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (tar) [28.4 MB] 430s Get:3 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (diff) [6064 B] 430s gpgv: Signature made Tue Jun 27 18:04:29 2023 UTC 430s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 430s gpgv: Can't check signature: No public key 430s dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-3build1.dsc: no acceptable signature found 433s autopkgtest [13:12:09]: testing package cpptraj version 5.1.0+dfsg-3build1 433s autopkgtest [13:12:09]: build not needed 438s autopkgtest [13:12:14]: test command1: preparing testbed 441s Reading package lists... 442s Building dependency tree... 442s Reading state information... 442s Starting pkgProblemResolver with broken count: 0 442s Starting 2 pkgProblemResolver with broken count: 0 442s Done 442s The following additional packages will be installed: 442s cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 libgfortran5 libgomp1 442s libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 libopenmm8.0 libsz2 442s netcdf-bin 442s Suggested packages: 442s libfftw3-bin libfftw3-dev 442s The following NEW packages will be installed: 442s autopkgtest-satdep cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 442s libgfortran5 libgomp1 libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 442s libopenmm8.0 libsz2 netcdf-bin 442s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 442s Need to get 7974 kB/7974 kB of archives. 442s After this operation, 23.7 MB of additional disk space will be used. 442s Get:1 /tmp/autopkgtest.ZrStjE/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 442s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 442s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 442s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 443s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libarpack2 arm64 3.9.1-1 [90.2 kB] 443s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 443s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu1 [380 kB] 443s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 443s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 443s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 443s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 443s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libnetcdf19 arm64 1:4.9.2-3ubuntu1 [470 kB] 443s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmm8.0 arm64 8.0.0+dfsg-6ubuntu1 [948 kB] 443s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 cpptraj arm64 5.1.0+dfsg-3build1 [1641 kB] 443s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 netcdf-bin arm64 1:4.9.2-3ubuntu1 [200 kB] 443s Fetched 7974 kB in 1s (7722 kB/s) 443s Selecting previously unselected package libblas3:arm64. 444s (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 ... 74316 files and directories currently installed.) 444s Preparing to unpack .../00-libblas3_3.12.0-3_arm64.deb ... 444s Unpacking libblas3:arm64 (3.12.0-3) ... 444s Selecting previously unselected package libgfortran5:arm64. 444s Preparing to unpack .../01-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 444s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 444s Selecting previously unselected package liblapack3:arm64. 444s Preparing to unpack .../02-liblapack3_3.12.0-3_arm64.deb ... 444s Unpacking liblapack3:arm64 (3.12.0-3) ... 444s Selecting previously unselected package libarpack2:arm64. 444s Preparing to unpack .../03-libarpack2_3.9.1-1_arm64.deb ... 444s Unpacking libarpack2:arm64 (3.9.1-1) ... 444s Selecting previously unselected package libgomp1:arm64. 444s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 444s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 444s Selecting previously unselected package libfftw3-double3:arm64. 444s Preparing to unpack .../05-libfftw3-double3_3.3.10-1ubuntu1_arm64.deb ... 444s Unpacking libfftw3-double3:arm64 (3.3.10-1ubuntu1) ... 444s Selecting previously unselected package libaec0:arm64. 444s Preparing to unpack .../06-libaec0_1.1.2-1_arm64.deb ... 444s Unpacking libaec0:arm64 (1.1.2-1) ... 444s Selecting previously unselected package libsz2:arm64. 444s Preparing to unpack .../07-libsz2_1.1.2-1_arm64.deb ... 444s Unpacking libsz2:arm64 (1.1.2-1) ... 444s Selecting previously unselected package libhdf5-103-1:arm64. 444s Preparing to unpack .../08-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 444s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 444s Selecting previously unselected package libhdf5-hl-100:arm64. 444s Preparing to unpack .../09-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 444s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 444s Selecting previously unselected package libnetcdf19:arm64. 444s Preparing to unpack .../10-libnetcdf19_1%3a4.9.2-3ubuntu1_arm64.deb ... 444s Unpacking libnetcdf19:arm64 (1:4.9.2-3ubuntu1) ... 444s Selecting previously unselected package libopenmm8.0. 444s Preparing to unpack .../11-libopenmm8.0_8.0.0+dfsg-6ubuntu1_arm64.deb ... 444s Unpacking libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ... 444s Selecting previously unselected package cpptraj. 444s Preparing to unpack .../12-cpptraj_5.1.0+dfsg-3build1_arm64.deb ... 444s Unpacking cpptraj (5.1.0+dfsg-3build1) ... 444s Selecting previously unselected package netcdf-bin. 444s Preparing to unpack .../13-netcdf-bin_1%3a4.9.2-3ubuntu1_arm64.deb ... 444s Unpacking netcdf-bin (1:4.9.2-3ubuntu1) ... 444s Selecting previously unselected package autopkgtest-satdep. 444s Preparing to unpack .../14-1-autopkgtest-satdep.deb ... 444s Unpacking autopkgtest-satdep (0) ... 444s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 444s Setting up libaec0:arm64 (1.1.2-1) ... 444s Setting up libblas3:arm64 (3.12.0-3) ... 444s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 444s Setting up libfftw3-double3:arm64 (3.3.10-1ubuntu1) ... 444s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 444s Setting up libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ... 444s Setting up libsz2:arm64 (1.1.2-1) ... 444s Setting up liblapack3:arm64 (3.12.0-3) ... 444s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 444s Setting up libarpack2:arm64 (3.9.1-1) ... 444s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 444s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 445s Setting up libnetcdf19:arm64 (1:4.9.2-3ubuntu1) ... 445s Setting up cpptraj (5.1.0+dfsg-3build1) ... 445s Setting up netcdf-bin (1:4.9.2-3ubuntu1) ... 445s Setting up autopkgtest-satdep (0) ... 445s Processing triggers for man-db (2.12.0-3) ... 445s Processing triggers for libc-bin (2.39-0ubuntu2) ... 449s (Reading database ... 74407 files and directories currently installed.) 449s Removing autopkgtest-satdep (0) ... 450s autopkgtest [13:12:26]: test command1: mkdir bin && ln -s /usr/bin/cpptraj bin && make -C test test.complete summary 450s autopkgtest [13:12:26]: test command1: [----------------------- 450s make: Entering directory '/tmp/autopkgtest.ZrStjE/build.wNU/src/test' 450s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 16 13:12 ../bin/cpptraj -> /usr/bin/cpptraj 450s make[1]: Entering directory '/tmp/autopkgtest.ZrStjE/build.wNU/src/test' 450s ******************************************************************************** 450s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_General 450s 450s CPPTRAJ: General tests 451s 451s All 15 comparisons passed. 451s 451s ******************************************************************************** 451s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Parallel 451s 451s CPPTRAJ: Parallel tests. 451s 451s CPPTRAJ: Parallel test with trajectory offset 451s 451s All 7 comparisons passed. 451s 451s ******************************************************************************** 451s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Strip 451s 451s CPPTRAJ: One frame strip command test 451s 451s CPPTRAJ: Unstrip (Lig/Rec/Complex) command test 451s 451s CPPTRAJ: Multi frame strip command test. 451s 451s CPPTRAJ: Strip topology with PDB info 451s 451s All 11 comparisons passed. 451s 451s ******************************************************************************** 451s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_BrokenTraj 451s 451s CPPTRAJ: Broken Traj: Running good trajectory. 451s 451s CPPTRAJ: Broken Traj: Running broken trajectory. 451s 451s CPPTRAJ: Compressed broken trajectory test 451s 451s All 2 comparisons passed. 451s 451s ******************************************************************************** 451s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_TrajinOffset 451s 451s CPPTRAJ: Normal trajectory read with offsets. 451s 451s CPPTRAJ: Gzipped trajectory read with offsets 451s 451s CPPTRAJ: Bzip2ed trajectory read with offsets 451s 451s CPPTRAJ: Start argument offset 451s 451s All 4 comparisons passed. 451s 451s ******************************************************************************** 451s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_RemdTraj 451s 451s CPPTRAJ: CRD Replica Trajectory Run with offset 451s 451s CPPTRAJ: CRD Replica Trajectory Run 451s 451s CPPTRAJ: NetCDF Replica Trajectory Run test 451s 451s CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj 451s 451s CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj 451s 451s CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj 451s 451s CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj 451s 451s CPPTRAJ: CRD Replica Trajectory Run with remdout 452s 452s All 8 comparisons passed. 452s 452s ******************************************************************************** 452s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_trajout_framerange 452s 452s CPPTRAJ: Trajout Frame Range [Amber Restart] 452s 452s CPPTRAJ: Trajout Frame Range [Amber Coordinates] 452s 452s All 6 comparisons passed. 452s 452s ******************************************************************************** 452s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_PerResRMSD 452s 452s CPPTRAJ: Per-Residue RMSD Test. 452s 452s CPPTRAJ: Per-Residue RMSD Test with averaging 452s 452s CPPTRAJ: Per-Residue RMSD Test with residue centering. 452s 452s All 3 comparisons passed. 452s 452s ******************************************************************************** 452s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_DSSP 452s 452s CPPTRAJ: Secstruct (DSSP) command test. 452s 452s CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. 452s 452s CPPTRAJ: Secstruct (DSSP) command with changing number of residues. 452s 452s CPPTRAJ: Secstruct (DSSP): SS assign output test 452s 452s CPPTRAJ: FtuFabI Assignment test 452s 452s All 10 comparisons passed. 452s 452s ******************************************************************************** 452s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Center 452s 452s CPPTRAJ: Center command test. 452s 452s CPPTRAJ: Center origin command test. 452s 452s CPPTRAJ: Center origin mass command test. 452s 452s CPPTRAJ: Center reference command test. 452s 452s CPPTRAJ: Center point test. 452s 452s All 5 comparisons passed. 452s 452s ******************************************************************************** 452s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Hbond 452s 452s CPPTRAJ: Solute Hbond test 452s 452s CPPTRAJ: Solute Hbond test with disk caching 452s 452s CPPTRAJ: Solute-solvent hbond test 452s 452s CPPTRAJ: Hbond, no intramolecular hydrogen bonds test 452s 452s CPPTRAJ: Hbond, specified solute masks 452s 452s CPPTRAJ: Hbond, no angle cutoff test 452s 452s CPPTRAJ: Hbond, Bridge nointramol test 453s 453s CPPTRAJ: Hbond with imaging 453s 453s CPPTRAJ: Hbond, orthogonal imaging 453s 453s All 23 comparisons passed. 453s 453s ******************************************************************************** 453s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_NCrestart 453s 453s CPPTRAJ: NetCDF Restart Test - TXT->NetCDF 453s 453s CPPTRAJ: NetCDF Restart Test - NetCDF->TXT 453s 453s CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF 453s 453s CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt 453s 453s All 2 comparisons passed. 453s 453s ******************************************************************************** 453s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Image 453s 453s CPPTRAJ: Orthorhombic imaged distance test. 453s 453s CPPTRAJ: Non-orthorhombic imaged distance test. 453s 453s CPPTRAJ: Orthorhombic coordinate imaging test 453s 453s CPPTRAJ: Nonorthorhombic coordinate imaging test 453s 453s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar 453s 453s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM 453s 453s All 6 comparisons passed. 453s 453s ******************************************************************************** 453s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Surf 453s 453s CPPTRAJ: Surface calculation test 453s 453s CPPTRAJ: Partial Surface calculation test 453s 453s CPPTRAJ: LCPO test with GAFF atom types 454s 454s All 3 comparisons passed. 454s 454s ******************************************************************************** 454s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Radgyr 454s 454s CPPTRAJ: Radius of gyration command test 454s 454s All 2 comparisons passed. 454s 454s ******************************************************************************** 454s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Mask 454s 454s CPPTRAJ: Mask single frame test 454s 454s CPPTRAJ: Mask longer command test. 454s 454s All 5 comparisons passed. 454s 454s ******************************************************************************** 454s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Jcoupling 454s 454s CPPTRAJ: J-Coupling single frame test 454s J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. 454s Skipped test: J-Coupling extended test 454s 454s All 1 comparisons passed. 454s 1 comparisons skipped. 454s 454s ******************************************************************************** 454s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Diffusion 454s 454s CPPTRAJ: Diffusion test, no imaging. 454s 454s CPPTRAJ: Diffusion test, old syntax. 454s 454s CPPTRAJ: Diffusion test, new syntax. 454s 454s CPPTRAJ: Diffusion test, nonorthogonal box 454s 454s CPPTRAJ: STFC Diffusion Test 454s 454s CPPTRAJ: STFC Diffusion Test with individual distances 454s 454s CPPTRAJ: STFC Diffusion Test with COM 454s 454s CPPTRAJ: STFC Diffusion Test with second mask 454s 454s All 16 comparisons passed. 454s 454s ******************************************************************************** 454s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Outtraj 454s 454s CPPTRAJ: RMSD Test with outtraj. 454s 454s CPPTRAJ: Outtraj Test with maxmin. 454s 454s All 4 comparisons passed. 454s 454s ******************************************************************************** 454s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Charmm 454s 454s CPPTRAJ: CHARMM PSF/DCD test 454s 454s CPPTRAJ: CHARMM DCD Write, step 1. 454s 454s CPPTRAJ: CHARMM DCD Write, step 2. 454s 454s CPPTRAJ: CHAMBER topology read/strip test. 454s 454s CPPTRAJ: Read CHARMM restart 454s 454s CPPTRAJ: CHARMM PSF write 454s 454s CPPTRAJ: CHARMM COORdinates test 454s 454s All 6 comparisons passed. 454s 454s ******************************************************************************** 454s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CharmmParams 454s 454s CPPTRAJ: Test updating topology with Charmm parameters (single residue) 454s 454s All 2 comparisons passed. 454s 454s ******************************************************************************** 454s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Rotdif 454s 454s CPPTRAJ: Rotational diffusion calculation test 455s 455s All 4 comparisons passed. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_NetcdfTraj 455s 455s CPPTRAJ: Convert mdcrd -> NetCDF 455s 455s CPPTRAJ: Convert NetCDF -> mdcrd 455s 455s All 1 comparisons passed. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Runavg 455s 455s CPPTRAJ: Coordinate Running Average test. 455s 455s CPPTRAJ: Coordinate Running Average Traj Write 455s 455s All 2 comparisons passed. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_RMSD 455s 455s CPPTRAJ: Basic RMSD tests 455s 455s CPPTRAJ: RMS coordinate rotation/rotation matrices test 455s 455s CPPTRAJ: RMS fit with no coordinates modification test. 455s 455s CPPTRAJ: RMS fit to previous test 455s 455s CPPTRAJ: RMS: imaging after unit cell rotation 455s 455s All 12 comparisons passed. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_2DRMS 455s 455s CPPTRAJ: 2D RMSD Test. 455s 455s CPPTRAJ: 2D RMSD Test, mass-weighted. 455s 455s CPPTRAJ: 2D RMSD Test with reference trajectory 455s 455s CPPTRAJ: 2D DME Test. 455s 455s CPPTRAJ: 2D RMSD with reference mask test. 455s 455s CPPTRAJ: 2D RMSD test, no fitting. 455s 455s All 6 comparisons passed. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Mol2 455s 455s CPPTRAJ: Mol2 Parm/Traj Read/Write Test. 455s 455s CPPTRAJ: PDB => Mol2 455s 455s CPPTRAJ: Amber Top/Rst => Mol2 455s Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. 455s Skipped test: Amber Top/Rst => Mol2, SYBYL atom types 455s 455s All 4 comparisons passed. 455s 1 comparisons skipped. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_NAstruct 455s 455s CPPTRAJ: NAstruct command test. 455s 455s CPPTRAJ: NAstruct command test, single strand 455s 455s All 11 comparisons passed. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_NAstruct_8OG 455s 455s CPPTRAJ: NA test (8OG) 455s 455s All 3 comparisons passed. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Average 455s 455s CPPTRAJ: Average Test. 455s 455s All 2 comparisons passed. 455s 455s ******************************************************************************** 455s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Pucker 455s 455s CPPTRAJ: Pucker command test 456s 456s CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test 456s 456s CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. 456s 456s All 3 comparisons passed. 456s 456s ******************************************************************************** 456s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AtomMap 456s 456s CPPTRAJ: AtomMap Test 456s 456s CPPTRAJ: AtomMap with 'rmsfit' 456s 456s CPPTRAJ: Atom map charmm->amber atom order 456s 456s CPPTRAJ: Atom map charmm->amber atom order, by residue 456s 456s All 9 comparisons passed. 456s 456s ******************************************************************************** 456s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Datafile 456s 456s CPPTRAJ: Data file output precision test 456s 456s CPPTRAJ: Standard -> Grace Data 456s 456s CPPTRAJ: Grace -> Standard Data 456s 456s CPPTRAJ: X column format/precision test. 456s 456s CPPTRAJ: Data file group by name test 456s 456s CPPTRAJ: Data file group by aspect test 456s 456s All 6 comparisons passed. 456s 456s ******************************************************************************** 456s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Radial 456s 456s CPPTRAJ: Radial test, non-orthogonal imaging 456s 456s CPPTRAJ: Radial test, orthogonal and no imaging 456s 456s All 9 comparisons passed. 456s 456s ******************************************************************************** 456s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Hist 456s 456s CPPTRAJ: 1D/2D Histogram Analysis test 456s 456s CPPTRAJ: 3D histogram test. 456s 456s All 7 comparisons passed. 456s 456s ******************************************************************************** 456s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Closest 456s 456s CPPTRAJ: Closest command test using first solvent atom. 456s 456s CPPTRAJ: Closest command test using all solvent atoms. 457s 457s CPPTRAJ: Closest command test, using mask center 457s 457s CPPTRAJ: Closest command test, using mask center and solvent mask 457s 457s CPPTRAJ: Closest command test, solvent mask, water oxygen only 457s 457s All 8 comparisons passed. 457s 457s ******************************************************************************** 457s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_DRMSD 457s 457s CPPTRAJ: Distance RMSD test 457s 457s All 1 comparisons passed. 457s 457s ******************************************************************************** 457s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster 457s 457s CPPTRAJ: Cluster command test, in-memory pairwise distances. 457s 457s CPPTRAJ: Cluster command test, read pairwise distances. 457s 457s CPPTRAJ: Cluster command test, read NetCDF pairwise distances. 457s 457s CPPTRAJ: Cluster command test, write ASCII pairwise distances. 457s 457s CPPTRAJ: Cluster command test, read ASCII pairwise distances. 457s 457s All 9 comparisons passed. 457s 457s ******************************************************************************** 457s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_Sieve 457s 457s CPPTRAJ: Cluster, nosieve 457s 457s CPPTRAJ: Cluster, sieve5 457s 457s CPPTRAJ: Cluster, nosieve savepairdist 458s 458s CPPTRAJ: Cluster, nosieve loadpairdist 458s 458s CPPTRAJ: Cluster, sieve5 savepairdist 458s 458s CPPTRAJ: Cluster, sieve5 loadpairdist 458s 458s CPPTRAJ: Cluster, nosieve pairwisecache none 458s 458s CPPTRAJ: Cluster, sieve5 pairwisecache none 458s 458s CPPTRAJ: Cluster, random 458s 458s All 28 comparisons passed. 458s 458s ******************************************************************************** 458s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_RandomSieve 458s 458s CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). 458s 458s CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). 458s 458s All 4 comparisons passed. 458s 458s ******************************************************************************** 458s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_DataSet 458s 458s CPPTRAJ: Clustering, One DataSet 458s 458s CPPTRAJ: Clustering, Two DataSets 458s 458s CPPTRAJ: Clustering, dihedral DataSet 458s 458s CPPTRAJ: Clustering, two dihedral DataSets 458s 458s CPPTRAJ: Clustering, dihedral DataSet, K-means 458s 458s CPPTRAJ: Clustering, two dihedral DataSets, K-means 458s 458s All 8 comparisons passed. 458s 458s ******************************************************************************** 458s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_DBSCAN 458s 458s CPPTRAJ: DBSCAN test 458s 458s CPPTRAJ: DBSCAN automatic parameter determination test. 458s 458s CPPTRAJ: DBSCAN kdist map test 459s 459s CPPTRAJ: DBSCAN with sieve 459s 459s All 4 comparisons passed. 459s 459s ******************************************************************************** 459s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_Kmeans 459s 459s CPPTRAJ: Cpptraj Kmeans 459s 459s CPPTRAJ: Cpptraj Kmeans random 459s 459s All 6 comparisons passed. 459s 459s ******************************************************************************** 459s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_SymmRMSD 459s 459s CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) 459s 459s All 5 comparisons passed. 459s 459s ******************************************************************************** 459s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_TrajWrites 459s 459s CPPTRAJ: Cluster command test, coordinate writes. 459s 459s CPPTRAJ: Cluster command test, coordinate writes using info file. 459s 459s All 8 comparisons passed. 459s 459s ******************************************************************************** 459s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_Dpeaks 459s 459s CPPTRAJ: Density peaks clustering test 459s 459s All 3 comparisons passed. 459s 459s ******************************************************************************** 459s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cluster_Nreps 459s 459s CPPTRAJ: Clustering with specified # reps 459s 459s All 2 comparisons passed. 459s 459s ******************************************************************************** 459s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_IRED 459s 459s CPPTRAJ: IRED vector/matrix test 460s 460s 460s ******************************************************************************** 460s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_RandomizeIons 460s 460s CPPTRAJ: randomizeions test (original algorithm) 460s 460s CPPTRAJ: Randomize (around, overlap) 460s 460s CPPTRAJ: Randomize (around) 461s 461s CPPTRAJ: Randomize (overlap) 461s 461s CPPTRAJ: Randomize (no restrictions) 461s 461s All 5 comparisons passed. 461s 461s ******************************************************************************** 461s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Molsurf 461s 461s CPPTRAJ: Molsurf test 461s 461s All 1 comparisons passed. 461s 461s ******************************************************************************** 461s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Corr 461s 461s CPPTRAJ: Correlation test 461s 461s All 2 comparisons passed. 461s 461s ******************************************************************************** 461s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CheckStructure 461s 461s CPPTRAJ: Structure Check 461s 461s CPPTRAJ: Structure Check with Around and Skip 462s 462s CPPTRAJ: Structure Check with PBC 462s 462s CPPTRAJ: Structure Check with Around 462s 462s All 8 comparisons passed. 462s 462s ******************************************************************************** 462s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_RmsAvgCorr 462s 462s CPPTRAJ: RmsAvgCorr Reference 462s 462s CPPTRAJ: RmsAvgCorr First 462s 462s All 3 comparisons passed. 462s 462s ******************************************************************************** 462s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Contacts 462s 462s CPPTRAJ: Contacts test. 462s 462s All 3 comparisons passed. 462s 462s ******************************************************************************** 462s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Principal 462s 462s CPPTRAJ: Principal Test 462s 462s All 3 comparisons passed. 462s 462s ******************************************************************************** 462s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_ClusterDihedral 462s 462s CPPTRAJ: clusterdihedral test 462s 462s All 4 comparisons passed. 462s 462s ******************************************************************************** 462s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Vector 462s 462s CPPTRAJ: Basic vector tests 462s 462s CPPTRAJ: Test vector center with magnitude 462s 462s CPPTRAJ: Momentum/velocity vector test. 462s 462s CPPTRAJ: Force vector test. 462s 462s All 14 comparisons passed. 462s 462s ******************************************************************************** 462s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Matrix 462s 462s CPPTRAJ: Matrix Tests 462s 462s CPPTRAJ: Generate matrix with trajectory start/stop/offset 462s 462s CPPTRAJ: Generate matrix with action stop/start/offset 462s 462s All 15 comparisons passed. 462s 462s ******************************************************************************** 462s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AtomicFluct 462s 462s CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. 462s 462s CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. 462s 462s CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. 462s 462s CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. 462s 462s CPPTRAJ: Atomicfluct test with ADP output 462s 463s CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. 463s 463s All 13 comparisons passed. 463s 463s ******************************************************************************** 463s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Grid 463s 463s CPPTRAJ: Dipole test 463s 463s CPPTRAJ: Grid test 463s 463s CPPTRAJ: OpenDX Grid read test 463s 463s CPPTRAJ: Grid with specified center test. 463s 463s CPPTRAJ: Grid with box center offset test. 463s 463s CPPTRAJ: Grid with mask center offset test. 463s 463s CPPTRAJ: Non-orthogonal grid test. 463s 463s CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test 463s 463s CPPTRAJ: Grid generation from 'bounds' test. 463s 463s All 13 comparisons passed. 463s 463s ******************************************************************************** 463s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Unwrap 463s 463s CPPTRAJ: Unwrap non-orthogonal test 463s 463s CPPTRAJ: Unwrap orthogonal test 463s 463s All 2 comparisons passed. 463s 463s ******************************************************************************** 463s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Project 463s 463s CPPTRAJ: Projection 463s 463s All 1 comparisons passed. 463s 463s ******************************************************************************** 463s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Analyze_Modes 463s 463s CPPTRAJ: Modes analysis, RMS fluctuations 463s 463s CPPTRAJ: Modes analysis, displacements 463s 463s CPPTRAJ: Modes analysis, dipole correlation 463s 463s CPPTRAJ: Modes analysis, pseudo trajectory creation test 463s 463s CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test 463s 463s All 6 comparisons passed. 463s 463s ******************************************************************************** 463s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Watershell 463s 463s CPPTRAJ: Watershell Test, non-orthorhombic imaging. 464s 464s CPPTRAJ: Watershell Test, orthorhombic imaging. 464s 464s CPPTRAJ: Watershell Test, no imaging. 464s 464s All 3 comparisons passed. 464s 464s ******************************************************************************** 464s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AnalysisRunAvg 464s 464s CPPTRAJ: Analysis Running Average 464s 464s All 2 comparisons passed. 464s 464s ******************************************************************************** 464s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Volmap 464s 464s CPPTRAJ: VMD VolMap Algorithm test 464s VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. 464s Skipped test: VMD VolMap Algorithm longer tests 464s 464s All 2 comparisons passed. 464s 1 comparisons skipped. 464s 464s ******************************************************************************** 464s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_SPAM 464s 464s CPPTRAJ: SPAM Test 484s *** buffer overflow detected ***: terminated 492s ../MasterTest.sh: line 495: 3083 Aborted (core dumped) $cpptraj_cmd >> $CPPTRAJ_OUTPUT 492s Error: cpptraj exited with status 134 492s 492s CPPTRAJ: SPAM Pure Solvent Test 494s 494s 1 out of 2 executions exited with an error. 494s 2 out of 5 comparisons failed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_LIE 494s 494s CPPTRAJ: LIE test 494s 494s All 1 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Density 494s 494s CPPTRAJ: Density along axis tests 494s 494s CPPTRAJ: Multi-frame density along axis test 494s 494s CPPTRAJ: Total system density test 494s 494s All 7 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_LipidOrder 494s 494s CPPTRAJ: Lipid Order Parameter Test. 494s 494s All 6 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_LipidSCD 494s 494s CPPTRAJ: Basic lipid order parameter test 494s 494s CPPTRAJ: New Lipid Order Parameter Test, DOPC. 494s 494s All 4 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_PairDist 494s 494s CPPTRAJ: PairDist Test. 494s 494s CPPTRAJ: Pairdist test, orthogonal imaging. 495s 495s CPPTRAJ: Pairdist test, nonorthogonal imaging. 495s 495s CPPTRAJ: Pairdist test, 2 masks. 495s 495s All 4 comparisons passed. 495s 495s ******************************************************************************** 495s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_ReadData 495s 495s CPPTRAJ: Read vector data test (no origins, origins) 495s 495s CPPTRAJ: Read vector data set (origins, no origins) 495s 495s CPPTRAJ: Read Amber output test 495s 495s CPPTRAJ: Read CHARMM output test 495s 495s CPPTRAJ: 3D data read/write test 495s 495s CPPTRAJ: Standard 3D data write test 495s 495s CPPTRAJ: Standard 3D data read test 495s 495s CPPTRAJ: Standard 3D data read/append test 495s 495s CPPTRAJ: Standard 3D data, sparse 495s 495s CPPTRAJ: Nonorthogonal grid standard write/read tests. 496s 496s CPPTRAJ: Read specific columns test. 496s 496s CPPTRAJ: Write non-square matrix 496s 496s CPPTRAJ: Read non-square matrix 496s 496s CPPTRAJ: Read square matrix 496s 496s All 15 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_GIST 496s 496s CPPTRAJ: GIST water-water interaction test 497s 497s CPPTRAJ: GIST test, orthogonal cell 499s 499s CPPTRAJ: GIST test, nonorthogonal cell 502s 502s All 11 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_GIST_Order 502s 502s CPPTRAJ: TIP3P water cluster test 502s 502s CPPTRAJ: TIP4P water cluster test 502s 502s CPPTRAJ: TIP5P water cluster test 502s 502s All 4 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_systemVF 502s 502s CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test 503s 503s All 1 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AtomicCorr 503s 503s CPPTRAJ: Atomic Correlation test 503s 503s All 1 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AutoCorr 503s 503s CPPTRAJ: AutoCorr test. 503s 503s All 1 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Box 503s 503s CPPTRAJ: Box Test (Add box info) 503s 503s CPPTRAJ: Box test (remove box info) 503s 503s CPPTRAJ: Box test (Modify box length) 503s 503s CPPTRAJ: Box test (auto orthogonal box, no radii) 503s 503s CPPTRAJ: Box test (auto orthogonal box, VDW radii) 503s 503s All 7 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AtomTypeSelect 503s 503s CPPTRAJ: Selection by atom type test. 503s 503s All 1 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AvgRef 503s 503s CPPTRAJ: RMSD Test with averaged reference coordinates. 503s 503s All 1 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Crank_Stat 503s 503s CPPTRAJ: Crankshaft test 503s 503s All 3 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CreateCrd 503s 503s CPPTRAJ: COORDS data set creation and CRDFLUCT test. 503s 503s CPPTRAJ: COORDS data set creation with velocities test 503s 503s CPPTRAJ: TRAJ data set creation and CRDFLUCT test. 503s 503s CPPTRAJ: TRAJ data set creation with velocities test. 503s 503s CPPTRAJ: COORDS data set append test 503s 503s CPPTRAJ: COORDS test storing frame metadata 503s 503s CPPTRAJ: TRAJ test storing frame metadata 503s 503s All 8 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AutoImage 503s 503s CPPTRAJ: AutoImage test (split DNA duplex) 503s 503s CPPTRAJ: AutoImage test, use anchor mask 503s 503s All 2 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_LoadCrd 504s 504s CPPTRAJ: LoadCrd test. 504s 504s CPPTRAJ: LoadTraj test. 504s 504s CPPTRAJ: LoadTraj from trajin test. 504s 504s CPPTRAJ: LoadCrd append from multiple files test 504s 504s All 4 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_MultiVector 504s 504s CPPTRAJ: Multivector test 504s 504s All 1 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Lifetime 504s 504s CPPTRAJ: Lifetime test. 504s 504s CPPTRAJ: Lifetime test with data set caching. 504s 504s CPPTRAJ: Lifetime average and cumulative average test. 504s 504s All 12 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_FFT 504s 504s CPPTRAJ: FFT test. 504s 504s All 5 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Timecorr 504s 504s CPPTRAJ: Timecorr test. 504s 504s All 7 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CrossCorr 504s 504s CPPTRAJ: CrossCorr test 504s 504s All 1 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_SymmRmsd 504s 504s CPPTRAJ: SymmRmsd 504s 504s CPPTRAJ: ASP symmetry-corrected RMSD test 504s 504s CPPTRAJ: GLU symmetry-corrected RMSD test 504s 504s CPPTRAJ: TYR symmetry-corrected RMSD test 504s 504s CPPTRAJ: Longer symmetry-corrected RMSD test. 504s 504s All 8 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Multidihedral 504s 504s CPPTRAJ: Multidihedral test 504s 504s CPPTRAJ: Multidihedral Nucleotide CHI test 504s 504s CPPTRAJ: Multidihedral protein dihedrals test 504s 504s CPPTRAJ: Multidihedral cyclic molecule test 504s 504s All 6 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Ensemble_MREMD 504s 504s CPPTRAJ: M-REMD sort test. 504s 504s CPPTRAJ: M-REMD actions test. 504s 504s CPPTRAJ: M-REMD ensemble outtraj test. 504s 504s CPPTRAJ: M-REMD no sort, running average test 504s 504s CPPTRAJ: M-REMD, generate RMS data 504s 504s CPPTRAJ: M-REMD, meltcurve analysis 504s 504s All 17 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_MakeStructure 504s 504s CPPTRAJ: Basic makestructure test 504s 504s CPPTRAJ: Makestructure test with reference. 504s 504s All 5 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Rotate 504s 504s CPPTRAJ: Rotation (and inverse) of coords from matrices 504s 504s CPPTRAJ: Rotate with defined axis 504s 504s All 3 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Integrate 504s 504s CPPTRAJ: Integration test. 504s 504s All 2 comparisons passed. 504s 504s ******************************************************************************** 504s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_NativeContacts 504s 504s CPPTRAJ: NativeContacts test. 505s 505s CPPTRAJ: NativeContacts test, save non-native contacts, residue time series 505s 505s CPPTRAJ: NativeContacts test, orthorhombic imaging. 505s 505s All 17 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CheckChiral 505s 505s CPPTRAJ: Check chirality test 505s 505s All 1 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Energy 505s 505s CPPTRAJ: Simple energy tests 505s 505s CPPTRAJ: Test kinetic energy calculation 505s 505s CPPTRAJ: Test total energy calculation 505s 505s CPPTRAJ: Test partial energy calculation 505s 505s All 6 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_LESsplit 505s 505s CPPTRAJ: LES split/average test 505s 505s All 2 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_PermuteDihedrals 505s 505s CPPTRAJ: PermuteDihedrals interval -120, phi psi 505s 505s CPPTRAJ: PermuteDihedrals, random rotations 505s 505s All 4 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CCP4 505s 505s CPPTRAJ: CCP4 read/write and DX conversion test. 505s 505s All 2 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_DihCovar 505s 505s CPPTRAJ: Dihedral Covariance Matrix Test 505s 505s All 3 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CurveFit 505s 505s CPPTRAJ: Curve fitting test. 505s 505s CPPTRAJ: Curve fitting multi-exponential tests. 505s 505s CPPTRAJ: Curve fitting, custom output range. 505s 505s All 6 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Multicurve 505s 505s CPPTRAJ: Multicurve test 505s 505s All 1 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_DataSetAverage 505s 505s CPPTRAJ: Data set averaging and averaging over all sets test. 505s 505s All 2 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_VectorMath 505s 505s CPPTRAJ: Vector dot/cross product test 505s 505s All 2 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Esander 505s SANDER energy tests (long) requires SANDER API from AmberTools. 505s Cpptraj was compiled without SANDER API from AmberTools support. 505s SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. 505s SKIP: SANDER energy tests (long) 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Esander_Short 505s Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. 505s Cpptraj was compiled without SANDER API from AmberTools support. 505s SKIP: Energy via sander API short tests (GB/PME) 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Temperature 505s 505s CPPTRAJ: Temperature test. 505s 505s CPPTRAJ: Temperature with SHAKE on hydrogens. 505s 505s CPPTRAJ: Temperature with SHAKE on all atoms. 506s 506s CPPTRAJ: Temperature calc with extra points. 506s 506s All 5 comparisons passed. 506s 506s ******************************************************************************** 506s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Spline 506s 506s CPPTRAJ: Spline test 506s 506s All 1 comparisons passed. 506s 506s ******************************************************************************** 506s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_KDE 506s 506s CPPTRAJ: KDE test. 506s 506s CPPTRAJ: KDE with Kullback-Leibler divergence test 506s 506s All 4 comparisons passed. 506s 506s ******************************************************************************** 506s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Wavelet 506s 506s CPPTRAJ: Wavelet analysis test 506s 506s CPPTRAJ: Wavelet WAFEX test 506s 506s All 3 comparisons passed. 506s 506s ******************************************************************************** 506s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CIF 506s 506s CPPTRAJ: CIF read test 506s 506s CPPTRAJ: Generate offset traj from PDB 506s 506s CPPTRAJ: Generate offset traj from CIF 506s 506s All 2 comparisons passed. 506s 506s ******************************************************************************** 506s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_PDB 506s 506s CPPTRAJ: PDB format read/write test 506s 506s CPPTRAJ: PQR file write with various radii 506s 506s CPPTRAJ: PDB filter alternate atom location IDs test 506s 506s CPPTRAJ: Adding PDB info to topology 506s 506s All 10 comparisons passed. 506s 506s ******************************************************************************** 506s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Align 506s 506s CPPTRAJ: Align Tests. 506s 506s CPPTRAJ: Align, unit cell rotation/imaging test. 507s 507s All 4 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_VelocityAutoCorr 507s 507s CPPTRAJ: Velocity autocorrelation test 507s 507s All 3 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_VelFrc 507s 507s CPPTRAJ: Test combining coordinates, velocities, and forces. 507s 507s CPPTRAJ: Test using velocities as coordinates. 507s 507s CPPTRAJ: Test writing velocities (MDVEL) 507s 507s CPPTRAJ: Test using forces as coordinates. 507s 507s CPPTRAJ: Test writing forces (MDFRC) 507s 507s CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. 507s 507s CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. 507s 507s All 5 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_RotateDihedral 507s 507s CPPTRAJ: Rotate dihedral to target value. 507s 507s CPPTRAJ: Rotate dihedral by increment 507s 507s CPPTRAJ: Rotate dihedral in TRAJ data set 507s 507s All 3 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_DataSetCmd 507s 507s CPPTRAJ: Data Set commands test 507s 507s All 10 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Remap 507s 507s CPPTRAJ: Remap Test 507s 507s All 1 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CompareTop 507s 507s CPPTRAJ: Compare topology test 507s 507s All 1 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Filter 507s 507s CPPTRAJ: Basic filter test 507s 507s CPPTRAJ: Data filter test. 507s 507s CPPTRAJ: Filter matrix test. 507s 507s All 5 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CombineCrd 507s 507s CPPTRAJ: Combine COORDS test. 507s 507s CPPTRAJ: Combine COORDS test with box info. 507s 507s CPPTRAJ: Split coords and recombine test. 508s 508s All 5 comparisons passed. 508s 508s ******************************************************************************** 508s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_TopInfo 508s 508s CPPTRAJ: Topology info print test. 508s 508s CPPTRAJ: Topology info with reference coords test 508s 508s All 12 comparisons passed. 508s 508s ******************************************************************************** 508s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_GromacsTrr 508s 508s CPPTRAJ: TRR force/velocity read -> NetCDF write test 508s 508s CPPTRAJ: TRR force/velocity read -> TRR write test 508s 508s CPPTRAJ: CRD => TRR 508s 508s CPPTRAJ: TRR => CRD 508s 508s CPPTRAJ: CRD(1-5) => TRR 508s 508s CPPTRAJ: CRD(6-10) => TRR 508s 508s CPPTRAJ: TRR (appended) => CRD 508s 508s CPPTRAJ: GMX: CRD with offset 508s 508s CPPTRAJ: GMX: TRR with offset 508s 508s All 5 comparisons passed. 508s 508s ******************************************************************************** 508s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_GromacsXtc 508s 508s CPPTRAJ: XTC read test 509s 509s CPPTRAJ: CRD => XTC 509s 509s CPPTRAJ: XTC => CRD 509s 509s CPPTRAJ: CRD(1-5) => XTC 509s 509s CPPTRAJ: CRD(6-10) => XTC 509s 509s CPPTRAJ: XTC (appended) => CRD 509s 509s CPPTRAJ: GMX: CRD with offset 509s 509s CPPTRAJ: GMX: XTC with offset 509s 509s All 4 comparisons passed. 509s 509s ******************************************************************************** 509s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_GromacsTNG 509s 509s CPPTRAJ: TNG read test 509s 509s CPPTRAJ: TNG read test (with offset) 509s 509s All 6 comparisons passed. 509s 509s ******************************************************************************** 509s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Ewald 509s 509s CPPTRAJ: Direct sum test 510s 510s CPPTRAJ: Ewald test (NaCl crystal) 510s 510s CPPTRAJ: Ewald test (trunc. oct) 510s 510s CPPTRAJ: Ewald test (partial system, trunc. oct) 510s Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 510s Skipped test: Ewald test (trunc. oct), 10 frames 510s Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. 510s Skipped test: Ewald test (ortho), 10 frames 510s 510s All 4 comparisons passed. 510s 2 comparisons skipped. 510s 510s ******************************************************************************** 510s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_LibPME 510s 510s CPPTRAJ: Particle mesh Ewald test (NaCl crystal) 510s 510s CPPTRAJ: Particle mesh Ewald test (trunc. oct) 510s 510s CPPTRAJ: Particle mesh Ewald test (ortho) 510s 510s CPPTRAJ: Particle mesh Ewald test (ortho, with mask) 511s 511s CPPTRAJ: PME test (partial system, trunc. oct) 511s PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 511s Skipped test: PME test (trunc. oct), 10 frames 511s 511s All 5 comparisons passed. 511s 1 comparisons skipped. 511s 511s ******************************************************************************** 511s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_LJ_PME 511s 511s CPPTRAJ: LJ PME test. 511s 511s CPPTRAJ: LJ PME kappa sweep test, 0.25 511s 511s CPPTRAJ: LJ PME kappa sweep test, 0.35 511s 511s CPPTRAJ: LJ PME kappa sweep test, 0.45 511s 511s CPPTRAJ: LJ PME kappa sweep test, 0.5 511s 511s CPPTRAJ: LJ with switch function test 511s 511s All 5 comparisons passed. 511s 511s ******************************************************************************** 511s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_TI 511s 511s CPPTRAJ: TI analysis test. 511s 511s All 5 comparisons passed. 511s 511s ******************************************************************************** 511s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_FixImagedBonds 511s 511s CPPTRAJ: Fix imaged bonds test (Ortho.) 511s 511s CPPTRAJ: Fix imaged bonds test (Non-ortho.) 511s 511s All 2 comparisons passed. 511s 511s ******************************************************************************** 511s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Distance 511s 511s CPPTRAJ: Distance tests 511s 511s CPPTRAJ: Orthogonal imaged distance 511s 511s CPPTRAJ: Non-orthogonal imaged distance 512s 512s All 3 comparisons passed. 512s 512s ******************************************************************************** 512s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Volume 512s 512s CPPTRAJ: Volume tests 512s 512s All 1 comparisons passed. 512s 512s ******************************************************************************** 512s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_SetVelocity 512s 512s CPPTRAJ: Set Velocity test 512s 512s CPPTRAJ: Scale velocity test 512s 512s 1 out of 3 comparisons failed. 512s 512s ******************************************************************************** 512s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Remlog 512s 512s CPPTRAJ: Replica log read/analyze test. 512s 512s All 7 comparisons passed. 512s 512s ******************************************************************************** 512s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_AreaPerMol 512s 512s CPPTRAJ: Area per molecule test 512s 512s All 6 comparisons passed. 512s 512s ******************************************************************************** 512s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_DistBasedMask 512s 512s CPPTRAJ: Distance-based atom mask tests (atom, residue) 512s 512s CPPTRAJ: Distance-based atom mask tests (molecule) 512s 512s All 6 comparisons passed. 512s 512s ******************************************************************************** 512s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Calc 512s 512s CPPTRAJ: Calc test 512s 512s CPPTRAJ: Calc test with data sets 512s 512s CPPTRAJ: Test math functions 512s 512s All 4 comparisons passed. 512s 512s ******************************************************************************** 512s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CalcState 512s 512s CPPTRAJ: Calcstate test 512s 512s All 4 comparisons passed. 512s 512s ******************************************************************************** 512s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Change 512s 512s CPPTRAJ: Change atom and residue name tests 513s 513s CPPTRAJ: Change chain ID test 513s 513s CPPTRAJ: Change chain ID of COORDS set test 513s 513s All 3 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CreateReservoir 513s 513s CPPTRAJ: Create RREMD NetCDF reservoir test 513s 513s All 1 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_FixAtomOrder 513s 513s CPPTRAJ: Out of order molecules test 513s 513s All 2 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_LowestCurve 513s 513s CPPTRAJ: LowestCurve test 513s 513s All 1 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_MinImage 513s 513s CPPTRAJ: Minimum Image test. 513s 513s All 1 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Regress 513s 513s CPPTRAJ: Linear regression test. 513s 513s All 3 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Rst 513s 513s CPPTRAJ: Generate restraints (rst) test 513s 513s All 1 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Pairwise 513s 513s CPPTRAJ: Pairwise tests 513s 513s CPPTRAJ: Pairwise test, partial system 514s 514s All 10 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_ParmBox 514s 514s CPPTRAJ: Parmbox test 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Solvent 514s 514s CPPTRAJ: Test solvent command with closest 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Translate 514s 514s CPPTRAJ: Translate test 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_ReplicateCell 514s 514s CPPTRAJ: Replicate cell test 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_ScaleDihedralK 514s 514s CPPTRAJ: Scale dihedral force constant test 514s 514s CPPTRAJ: Scale dihedral force constant with 'useall' 514s 514s All 2 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_PhiPsi 514s 514s CPPTRAJ: Phipsi test 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Control 514s 514s CPPTRAJ: Loop tests 514s 514s CPPTRAJ: Test set command 514s 514s CPPTRAJ: Test reading comma-separated list of strings 514s 514s CPPTRAJ: Test nested loops and variables in loops 514s 514s CPPTRAJ: Test loop over data set blocks 514s 514s CPPTRAJ: Test for filename wildcards and oversets 515s 515s All 13 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_InfraredSpec 515s 515s CPPTRAJ: Infrared spectrum calculation test 515s 515s All 2 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Cphstats 515s 515s CPPTRAJ: Explicit pH REMD ensemble data read / sort 515s 515s CPPTRAJ: Constant pH stats test 515s 515s CPPTRAJ: Sorted implicit constant pH stats test 515s 515s CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats 515s 515s CPPTRAJ: Unsorted pH read/write test 515s 515s All 16 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CmdLine 515s 515s CPPTRAJ: Command line trajectory args test, part 1 515s 515s CPPTRAJ: Command line test trajectory args test, part 2 515s 515s CPPTRAJ: Command line wildcard test, part 1 515s 515s CPPTRAJ: Command line wildcard test, part 2 515s 515s All 2 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_XYZformat 515s 515s CPPTRAJ: XYZ format write 515s 515s CPPTRAJ: Atom XYZ format read, test 1 515s 515s CPPTRAJ: Atom XYZ format read, test 2 515s 515s CPPTRAJ: Atom XYZ format read, test 3 515s 515s CPPTRAJ: Atom XYZ format read, test 4 515s 515s CPPTRAJ: Atom XYZ format read, test 5 516s 516s CPPTRAJ: Atom XYZ format read, test 6 516s 516s All 6 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Hausdorff 516s 516s CPPTRAJ: Simple Hausdorff distance test. 516s 516s CPPTRAJ: Hausdorff distance of 2D rms output test. 516s 516s CPPTRAJ: Hausdorff distance of 2D rms output test. 516s 516s All 3 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_CatCrd 516s 516s CPPTRAJ: Concatenate COORDS data set test 516s 516s All 1 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_XtalSymm 516s 516s CPPTRAJ: XtalSymm Reference 516s 516s CPPTRAJ: XtalSymm Reimaging by Atom 517s 517s CPPTRAJ: XtalSymm Reimaging by Molecule 518s 518s All 3 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Time 518s 518s CPPTRAJ: Add time to restart test 518s 518s CPPTRAJ: Remove time from restart test 518s 518s CPPTRAJ: Add time to trajectory test 518s 518s CPPTRAJ: Modify time info test. 518s 518s All 4 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_SplitCoords 518s 518s CPPTRAJ: SplitCoords test 518s 518s All 1 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_DihedralRMS 518s 518s CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) 518s 518s CPPTRAJ: Dihedral RMSD test (to previous) 519s 519s CPPTRAJ: Dihedral RMS fluctuation test. 519s 519s All 5 comparisons passed. 519s 519s ******************************************************************************** 519s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Slope 519s 519s CPPTRAJ: Finite difference test. 519s 519s All 1 comparisons passed. 519s 519s ******************************************************************************** 519s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Diagmatrix 519s 519s CPPTRAJ: MW covariance matrix thermo analysis test 519s 519s All 1 comparisons passed. 519s 519s ******************************************************************************** 519s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Emin 519s 519s CPPTRAJ: Basic energy minimization test. 519s 519s CPPTRAJ: Energy minimization with angle term test. 519s 519s CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. 519s 519s CPPTRAJ: Energy minimization with nonbond term test. 519s 519s CPPTRAJ: OpenMM basic energy minimization tests (bonds) 519s 519s CPPTRAJ: OpenMM basic energy minimization tests (angles) 519s 519s CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) 519s 519s CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) 519s 519s CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) 520s 520s All 9 comparisons passed. 520s 520s ******************************************************************************** 520s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_EvalPlateau 520s 520s CPPTRAJ: Evalulate plateau test 520s 520s All 2 comparisons passed. 520s 520s ******************************************************************************** 520s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Graft 520s 520s CPPTRAJ: Graft test 520s 520s All 1 comparisons passed. 520s 520s ******************************************************************************** 520s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Flatten 520s 520s CPPTRAJ: Flatten test. 520s 520s All 1 comparisons passed. 520s 520s ******************************************************************************** 520s TEST: /tmp/autopkgtest.ZrStjE/build.wNU/src/test/Test_Random 520s 520s CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs 520s 520s CPPTRAJ: PCG32 RNG test. 520s 520s CPPTRAJ: Test Stdlib RNG 520s 521s CPPTRAJ: Test Mersenne Twister RNG 521s 521s All 4 comparisons passed. 521s 521s make[1]: Leaving directory '/tmp/autopkgtest.ZrStjE/build.wNU/src/test' 521s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 16 13:12 ../bin/cpptraj -> /usr/bin/cpptraj 521s ===================== TEST SUMMARY ====================== 521s 850 out of 859 comparisons OK (3 failed, 0 warnings, 6 skipped). 521s 479 out of 480 program executions completed. 521s 168 out of 173 tests completed with no issues. 521s 2 tests skipped. 521s ========================================================= 521s make: *** [Makefile:662: summary] Error 4 521s make: Leaving directory '/tmp/autopkgtest.ZrStjE/build.wNU/src/test' 521s autopkgtest [13:13:37]: test command1: -----------------------] 522s command1 FAIL non-zero exit status 2 522s autopkgtest [13:13:38]: test command1: - - - - - - - - - - results - - - - - - - - - - 522s autopkgtest [13:13:38]: test command1: - - - - - - - - - - stderr - - - - - - - - - - 522s *** buffer overflow detected ***: terminated 522s ../MasterTest.sh: line 495: 3083 Aborted (core dumped) $cpptraj_cmd >> $CPPTRAJ_OUTPUT 522s Error: cpptraj exited with status 134 522s make: *** [Makefile:662: summary] Error 4 522s autopkgtest [13:13:38]: @@@@@@@@@@@@@@@@@@@@ summary 522s command1 FAIL non-zero exit status 2 533s Creating nova instance adt-noble-arm64-cpptraj-20240316-130456-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...