0s autopkgtest [20:54:46]: starting date and time: 2024-03-13 20:54:46+0000 0s autopkgtest [20:54:46]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [20:54:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.llg20b9t/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:fftw3,src:openmpi,src:pmix --apt-upgrade cpptraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=fftw3/3.3.10-1ubuntu2 openmpi/4.1.6-5.1ubuntu3 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-15.secgroup --name adt-noble-arm64-cpptraj-20240313-205446-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 105s autopkgtest [20:56:31]: testbed dpkg architecture: arm64 105s autopkgtest [20:56:31]: testbed apt version: 2.7.12 105s autopkgtest [20:56:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB] 106s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 106s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2820 kB] 106s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 106s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB] 106s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 106s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 106s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 106s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3215 kB] 106s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 106s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [41.7 kB] 106s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 108s Fetched 7326 kB in 2s (4783 kB/s) 108s Reading package lists... 109s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 110s Reading package lists... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 116s The following packages will be upgraded: 116s console-setup console-setup-linux keyboard-configuration 116s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 2202 kB of archives. 116s After this operation, 2048 B of additional disk space will be used. 116s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB] 117s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB] 117s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB] 118s Preconfiguring packages ... 118s Fetched 2202 kB in 2s (1440 kB/s) 118s (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 ... 75867 files and directories currently installed.) 118s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 118s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 118s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 118s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 118s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 118s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 118s Setting up keyboard-configuration (1.226ubuntu1) ... 119s Your console font configuration will be updated the next time your system 119s boots. If you want to update it now, run 'setupcon' from a virtual console. 119s update-initramfs: deferring update (trigger activated) 119s Setting up console-setup-linux (1.226ubuntu1) ... 120s Setting up console-setup (1.226ubuntu1) ... 120s update-initramfs: deferring update (trigger activated) 120s Processing triggers for man-db (2.12.0-3) ... 121s Processing triggers for initramfs-tools (0.142ubuntu20) ... 121s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 121s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 129s System running in EFI mode, skipping. 130s WReading package lists...: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 130s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 130s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 130s 130s Building dependency tree... 130s Reading state information... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 131s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 131s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 131s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 131s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 135s Reading package lists... 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 135s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s Calculating upgrade... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s autopkgtest [20:57:03]: rebooting testbed after setup commands that affected boot 285s autopkgtest [20:59:31]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 287s autopkgtest [20:59:33]: @@@@@@@@@@@@@@@@@@@@ apt-source cpptraj 307s Get:1 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (dsc) [2160 B] 307s Get:2 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (tar) [28.4 MB] 307s Get:3 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (diff) [6064 B] 307s gpgv: Signature made Tue Jun 27 18:04:29 2023 UTC 307s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 307s gpgv: Can't check signature: No public key 307s dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-3build1.dsc: no acceptable signature found 309s autopkgtest [20:59:55]: testing package cpptraj version 5.1.0+dfsg-3build1 309s autopkgtest [20:59:55]: build not needed 477s autopkgtest [21:02:43]: test command1: preparing testbed 481s Reading package lists... 482s Building dependency tree... 482s Reading state information... 482s Starting pkgProblemResolver with broken count: 0 482s Starting 2 pkgProblemResolver with broken count: 0 482s Done 483s The following additional packages will be installed: 483s cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 libgfortran5 libgomp1 483s libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 libopenmm8.0 libsz2 483s netcdf-bin 483s Suggested packages: 483s libfftw3-bin libfftw3-dev 483s The following NEW packages will be installed: 483s autopkgtest-satdep cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 483s libgfortran5 libgomp1 libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 483s libopenmm8.0 libsz2 netcdf-bin 483s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 483s Need to get 7978 kB/7978 kB of archives. 483s After this operation, 23.7 MB of additional disk space will be used. 483s Get:1 /tmp/autopkgtest.BhcY5I/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 483s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 483s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 484s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 485s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libarpack2 arm64 3.9.1-1 [90.2 kB] 485s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 485s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu2 [384 kB] 485s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 485s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 485s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 486s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 486s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libnetcdf19 arm64 1:4.9.2-3ubuntu1 [470 kB] 486s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmm8.0 arm64 8.0.0+dfsg-6ubuntu1 [948 kB] 487s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 cpptraj arm64 5.1.0+dfsg-3build1 [1641 kB] 487s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 netcdf-bin arm64 1:4.9.2-3ubuntu1 [200 kB] 488s Fetched 7978 kB in 5s (1632 kB/s) 488s Selecting previously unselected package libblas3:arm64. 488s (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 ... 75867 files and directories currently installed.) 488s Preparing to unpack .../00-libblas3_3.12.0-3_arm64.deb ... 488s Unpacking libblas3:arm64 (3.12.0-3) ... 488s Selecting previously unselected package libgfortran5:arm64. 488s Preparing to unpack .../01-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 488s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 488s Selecting previously unselected package liblapack3:arm64. 488s Preparing to unpack .../02-liblapack3_3.12.0-3_arm64.deb ... 488s Unpacking liblapack3:arm64 (3.12.0-3) ... 488s Selecting previously unselected package libarpack2:arm64. 488s Preparing to unpack .../03-libarpack2_3.9.1-1_arm64.deb ... 488s Unpacking libarpack2:arm64 (3.9.1-1) ... 488s Selecting previously unselected package libgomp1:arm64. 488s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 488s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 488s Selecting previously unselected package libfftw3-double3:arm64. 488s Preparing to unpack .../05-libfftw3-double3_3.3.10-1ubuntu2_arm64.deb ... 488s Unpacking libfftw3-double3:arm64 (3.3.10-1ubuntu2) ... 488s Selecting previously unselected package libaec0:arm64. 488s Preparing to unpack .../06-libaec0_1.1.2-1_arm64.deb ... 488s Unpacking libaec0:arm64 (1.1.2-1) ... 488s Selecting previously unselected package libsz2:arm64. 488s Preparing to unpack .../07-libsz2_1.1.2-1_arm64.deb ... 488s Unpacking libsz2:arm64 (1.1.2-1) ... 488s Selecting previously unselected package libhdf5-103-1:arm64. 488s Preparing to unpack .../08-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 488s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 488s Selecting previously unselected package libhdf5-hl-100:arm64. 488s Preparing to unpack .../09-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 488s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 488s Selecting previously unselected package libnetcdf19:arm64. 488s Preparing to unpack .../10-libnetcdf19_1%3a4.9.2-3ubuntu1_arm64.deb ... 488s Unpacking libnetcdf19:arm64 (1:4.9.2-3ubuntu1) ... 488s Selecting previously unselected package libopenmm8.0. 488s Preparing to unpack .../11-libopenmm8.0_8.0.0+dfsg-6ubuntu1_arm64.deb ... 488s Unpacking libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ... 488s Selecting previously unselected package cpptraj. 488s Preparing to unpack .../12-cpptraj_5.1.0+dfsg-3build1_arm64.deb ... 488s Unpacking cpptraj (5.1.0+dfsg-3build1) ... 488s Selecting previously unselected package netcdf-bin. 488s Preparing to unpack .../13-netcdf-bin_1%3a4.9.2-3ubuntu1_arm64.deb ... 488s Unpacking netcdf-bin (1:4.9.2-3ubuntu1) ... 488s Selecting previously unselected package autopkgtest-satdep. 488s Preparing to unpack .../14-1-autopkgtest-satdep.deb ... 488s Unpacking autopkgtest-satdep (0) ... 488s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 488s Setting up libaec0:arm64 (1.1.2-1) ... 488s Setting up libblas3:arm64 (3.12.0-3) ... 488s 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 488s Setting up libfftw3-double3:arm64 (3.3.10-1ubuntu2) ... 488s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 488s Setting up libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ... 488s Setting up libsz2:arm64 (1.1.2-1) ... 488s Setting up liblapack3:arm64 (3.12.0-3) ... 488s 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 488s Setting up libarpack2:arm64 (3.9.1-1) ... 488s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 488s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 488s Setting up libnetcdf19:arm64 (1:4.9.2-3ubuntu1) ... 488s Setting up cpptraj (5.1.0+dfsg-3build1) ... 488s Setting up netcdf-bin (1:4.9.2-3ubuntu1) ... 488s Setting up autopkgtest-satdep (0) ... 488s Processing triggers for man-db (2.12.0-3) ... 489s Processing triggers for libc-bin (2.39-0ubuntu2) ... 492s (Reading database ... 75958 files and directories currently installed.) 492s Removing autopkgtest-satdep (0) ... 493s autopkgtest [21:02:59]: test command1: mkdir bin && ln -s /usr/bin/cpptraj bin && make -C test test.complete summary 493s autopkgtest [21:02:59]: test command1: [----------------------- 493s make: Entering directory '/tmp/autopkgtest.BhcY5I/build.7Qt/src/test' 493s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 13 21:02 ../bin/cpptraj -> /usr/bin/cpptraj 493s make[1]: Entering directory '/tmp/autopkgtest.BhcY5I/build.7Qt/src/test' 493s ******************************************************************************** 493s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_General 493s 493s CPPTRAJ: General tests 493s 493s All 15 comparisons passed. 493s 493s ******************************************************************************** 493s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Parallel 493s 493s CPPTRAJ: Parallel tests. 493s 493s CPPTRAJ: Parallel test with trajectory offset 493s 493s All 7 comparisons passed. 493s 493s ******************************************************************************** 493s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Strip 493s 493s CPPTRAJ: One frame strip command test 493s 493s CPPTRAJ: Unstrip (Lig/Rec/Complex) command test 493s 493s CPPTRAJ: Multi frame strip command test. 493s 493s CPPTRAJ: Strip topology with PDB info 493s 493s All 11 comparisons passed. 493s 493s ******************************************************************************** 493s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_BrokenTraj 493s 493s CPPTRAJ: Broken Traj: Running good trajectory. 493s 493s CPPTRAJ: Broken Traj: Running broken trajectory. 494s 494s CPPTRAJ: Compressed broken trajectory test 494s 494s All 2 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_TrajinOffset 494s 494s CPPTRAJ: Normal trajectory read with offsets. 494s 494s CPPTRAJ: Gzipped trajectory read with offsets 494s 494s CPPTRAJ: Bzip2ed trajectory read with offsets 494s 494s CPPTRAJ: Start argument offset 494s 494s All 4 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_RemdTraj 494s 494s CPPTRAJ: CRD Replica Trajectory Run with offset 494s 494s CPPTRAJ: CRD Replica Trajectory Run 494s 494s CPPTRAJ: NetCDF Replica Trajectory Run test 494s 494s CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj 494s 494s CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj 494s 494s CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj 494s 494s CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj 494s 494s CPPTRAJ: CRD Replica Trajectory Run with remdout 494s 494s All 8 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_trajout_framerange 494s 494s CPPTRAJ: Trajout Frame Range [Amber Restart] 494s 494s CPPTRAJ: Trajout Frame Range [Amber Coordinates] 494s 494s All 6 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_PerResRMSD 494s 494s CPPTRAJ: Per-Residue RMSD Test. 494s 494s CPPTRAJ: Per-Residue RMSD Test with averaging 494s 494s CPPTRAJ: Per-Residue RMSD Test with residue centering. 494s 494s All 3 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_DSSP 494s 494s CPPTRAJ: Secstruct (DSSP) command test. 494s 494s CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. 494s 494s CPPTRAJ: Secstruct (DSSP) command with changing number of residues. 494s 494s CPPTRAJ: Secstruct (DSSP): SS assign output test 494s 494s CPPTRAJ: FtuFabI Assignment test 494s 494s All 10 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Center 494s 494s CPPTRAJ: Center command test. 494s 494s CPPTRAJ: Center origin command test. 494s 494s CPPTRAJ: Center origin mass command test. 494s 494s CPPTRAJ: Center reference command test. 494s 494s CPPTRAJ: Center point test. 494s 494s All 5 comparisons passed. 494s 494s ******************************************************************************** 494s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Hbond 494s 494s CPPTRAJ: Solute Hbond test 494s 494s CPPTRAJ: Solute Hbond test with disk caching 494s 494s CPPTRAJ: Solute-solvent hbond test 494s 494s CPPTRAJ: Hbond, no intramolecular hydrogen bonds test 494s 494s CPPTRAJ: Hbond, specified solute masks 494s 494s CPPTRAJ: Hbond, no angle cutoff test 494s 494s CPPTRAJ: Hbond, Bridge nointramol test 495s 495s CPPTRAJ: Hbond with imaging 495s 495s CPPTRAJ: Hbond, orthogonal imaging 495s 495s All 23 comparisons passed. 495s 495s ******************************************************************************** 495s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_NCrestart 495s 495s CPPTRAJ: NetCDF Restart Test - TXT->NetCDF 495s 495s CPPTRAJ: NetCDF Restart Test - NetCDF->TXT 495s 495s CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF 495s 495s CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt 495s 495s All 2 comparisons passed. 495s 495s ******************************************************************************** 495s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Image 495s 495s CPPTRAJ: Orthorhombic imaged distance test. 495s 495s CPPTRAJ: Non-orthorhombic imaged distance test. 495s 495s CPPTRAJ: Orthorhombic coordinate imaging test 495s 495s CPPTRAJ: Nonorthorhombic coordinate imaging test 495s 495s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar 495s 495s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM 495s 495s All 6 comparisons passed. 495s 495s ******************************************************************************** 495s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Surf 495s 495s CPPTRAJ: Surface calculation test 495s 495s CPPTRAJ: Partial Surface calculation test 495s 495s CPPTRAJ: LCPO test with GAFF atom types 495s 495s All 3 comparisons passed. 495s 495s ******************************************************************************** 495s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Radgyr 495s 495s CPPTRAJ: Radius of gyration command test 495s 495s All 2 comparisons passed. 495s 495s ******************************************************************************** 495s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Mask 495s 495s CPPTRAJ: Mask single frame test 495s 495s CPPTRAJ: Mask longer command test. 495s 495s All 5 comparisons passed. 495s 495s ******************************************************************************** 495s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Jcoupling 495s 495s CPPTRAJ: J-Coupling single frame test 495s J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. 495s Skipped test: J-Coupling extended test 495s 495s All 1 comparisons passed. 495s 1 comparisons skipped. 495s 495s ******************************************************************************** 495s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Diffusion 495s 495s CPPTRAJ: Diffusion test, no imaging. 495s 495s CPPTRAJ: Diffusion test, old syntax. 495s 495s CPPTRAJ: Diffusion test, new syntax. 496s 496s CPPTRAJ: Diffusion test, nonorthogonal box 496s 496s CPPTRAJ: STFC Diffusion Test 496s 496s CPPTRAJ: STFC Diffusion Test with individual distances 496s 496s CPPTRAJ: STFC Diffusion Test with COM 496s 496s CPPTRAJ: STFC Diffusion Test with second mask 496s 496s All 16 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Outtraj 496s 496s CPPTRAJ: RMSD Test with outtraj. 496s 496s CPPTRAJ: Outtraj Test with maxmin. 496s 496s All 4 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Charmm 496s 496s CPPTRAJ: CHARMM PSF/DCD test 496s 496s CPPTRAJ: CHARMM DCD Write, step 1. 496s 496s CPPTRAJ: CHARMM DCD Write, step 2. 496s 496s CPPTRAJ: CHAMBER topology read/strip test. 496s 496s CPPTRAJ: Read CHARMM restart 496s 496s CPPTRAJ: CHARMM PSF write 496s 496s CPPTRAJ: CHARMM COORdinates test 496s 496s All 6 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CharmmParams 496s 496s CPPTRAJ: Test updating topology with Charmm parameters (single residue) 496s 496s All 2 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Rotdif 496s 496s CPPTRAJ: Rotational diffusion calculation test 496s 496s All 4 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_NetcdfTraj 496s 496s CPPTRAJ: Convert mdcrd -> NetCDF 496s 496s CPPTRAJ: Convert NetCDF -> mdcrd 496s 496s All 1 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Runavg 496s 496s CPPTRAJ: Coordinate Running Average test. 496s 496s CPPTRAJ: Coordinate Running Average Traj Write 496s 496s All 2 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_RMSD 496s 496s CPPTRAJ: Basic RMSD tests 496s 496s CPPTRAJ: RMS coordinate rotation/rotation matrices test 496s 496s CPPTRAJ: RMS fit with no coordinates modification test. 496s 496s CPPTRAJ: RMS fit to previous test 496s 496s CPPTRAJ: RMS: imaging after unit cell rotation 496s 496s All 12 comparisons passed. 496s 496s ******************************************************************************** 496s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_2DRMS 496s 496s CPPTRAJ: 2D RMSD Test. 497s 497s CPPTRAJ: 2D RMSD Test, mass-weighted. 497s 497s CPPTRAJ: 2D RMSD Test with reference trajectory 497s 497s CPPTRAJ: 2D DME Test. 497s 497s CPPTRAJ: 2D RMSD with reference mask test. 497s 497s CPPTRAJ: 2D RMSD test, no fitting. 497s 497s All 6 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Mol2 497s 497s CPPTRAJ: Mol2 Parm/Traj Read/Write Test. 497s 497s CPPTRAJ: PDB => Mol2 497s 497s CPPTRAJ: Amber Top/Rst => Mol2 497s Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. 497s Skipped test: Amber Top/Rst => Mol2, SYBYL atom types 497s 497s All 4 comparisons passed. 497s 1 comparisons skipped. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_NAstruct 497s 497s CPPTRAJ: NAstruct command test. 497s 497s CPPTRAJ: NAstruct command test, single strand 497s 497s All 11 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_NAstruct_8OG 497s 497s CPPTRAJ: NA test (8OG) 497s 497s All 3 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Average 497s 497s CPPTRAJ: Average Test. 497s 497s All 2 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Pucker 497s 497s CPPTRAJ: Pucker command test 497s 497s CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test 497s 497s CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. 497s 497s All 3 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AtomMap 497s 497s CPPTRAJ: AtomMap Test 497s 497s CPPTRAJ: AtomMap with 'rmsfit' 497s 497s CPPTRAJ: Atom map charmm->amber atom order 497s 497s CPPTRAJ: Atom map charmm->amber atom order, by residue 497s 497s All 9 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Datafile 497s 497s CPPTRAJ: Data file output precision test 497s 497s CPPTRAJ: Standard -> Grace Data 497s 497s CPPTRAJ: Grace -> Standard Data 497s 497s CPPTRAJ: X column format/precision test. 497s 497s CPPTRAJ: Data file group by name test 497s 497s CPPTRAJ: Data file group by aspect test 497s 497s All 6 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Radial 497s 497s CPPTRAJ: Radial test, non-orthogonal imaging 497s 497s CPPTRAJ: Radial test, orthogonal and no imaging 497s 497s All 9 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Hist 497s 497s CPPTRAJ: 1D/2D Histogram Analysis test 497s 497s CPPTRAJ: 3D histogram test. 497s 497s All 7 comparisons passed. 497s 497s ******************************************************************************** 497s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Closest 497s 497s CPPTRAJ: Closest command test using first solvent atom. 498s 498s CPPTRAJ: Closest command test using all solvent atoms. 498s 498s CPPTRAJ: Closest command test, using mask center 498s 498s CPPTRAJ: Closest command test, using mask center and solvent mask 498s 498s CPPTRAJ: Closest command test, solvent mask, water oxygen only 498s 498s All 8 comparisons passed. 498s 498s ******************************************************************************** 498s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_DRMSD 498s 498s CPPTRAJ: Distance RMSD test 498s 498s All 1 comparisons passed. 498s 498s ******************************************************************************** 498s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster 498s 498s CPPTRAJ: Cluster command test, in-memory pairwise distances. 498s 498s CPPTRAJ: Cluster command test, read pairwise distances. 498s 498s CPPTRAJ: Cluster command test, read NetCDF pairwise distances. 498s 498s CPPTRAJ: Cluster command test, write ASCII pairwise distances. 498s 498s CPPTRAJ: Cluster command test, read ASCII pairwise distances. 498s 498s All 9 comparisons passed. 498s 498s ******************************************************************************** 498s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_Sieve 498s 498s CPPTRAJ: Cluster, nosieve 498s 498s CPPTRAJ: Cluster, sieve5 498s 498s CPPTRAJ: Cluster, nosieve savepairdist 498s 498s CPPTRAJ: Cluster, nosieve loadpairdist 498s 498s CPPTRAJ: Cluster, sieve5 savepairdist 498s 498s CPPTRAJ: Cluster, sieve5 loadpairdist 498s 498s CPPTRAJ: Cluster, nosieve pairwisecache none 498s 498s CPPTRAJ: Cluster, sieve5 pairwisecache none 499s 499s CPPTRAJ: Cluster, random 499s 499s All 28 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_RandomSieve 499s 499s CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). 499s 499s CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). 499s 499s All 4 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_DataSet 499s 499s CPPTRAJ: Clustering, One DataSet 499s 499s CPPTRAJ: Clustering, Two DataSets 499s 499s CPPTRAJ: Clustering, dihedral DataSet 499s 499s CPPTRAJ: Clustering, two dihedral DataSets 499s 499s CPPTRAJ: Clustering, dihedral DataSet, K-means 499s 499s CPPTRAJ: Clustering, two dihedral DataSets, K-means 499s 499s All 8 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_DBSCAN 499s 499s CPPTRAJ: DBSCAN test 499s 499s CPPTRAJ: DBSCAN automatic parameter determination test. 499s 499s CPPTRAJ: DBSCAN kdist map test 499s 499s CPPTRAJ: DBSCAN with sieve 499s 499s All 4 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_Kmeans 499s 499s CPPTRAJ: Cpptraj Kmeans 499s 499s CPPTRAJ: Cpptraj Kmeans random 499s 499s All 6 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_SymmRMSD 499s 499s CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) 499s 499s All 5 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_TrajWrites 499s 499s CPPTRAJ: Cluster command test, coordinate writes. 499s 499s CPPTRAJ: Cluster command test, coordinate writes using info file. 499s 499s All 8 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_Dpeaks 499s 499s CPPTRAJ: Density peaks clustering test 499s 499s All 3 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cluster_Nreps 499s 499s CPPTRAJ: Clustering with specified # reps 499s 499s All 2 comparisons passed. 499s 499s ******************************************************************************** 499s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_IRED 499s 499s CPPTRAJ: IRED vector/matrix test 500s 500s 500s ******************************************************************************** 500s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_RandomizeIons 500s 500s CPPTRAJ: randomizeions test (original algorithm) 500s 500s CPPTRAJ: Randomize (around, overlap) 500s 500s CPPTRAJ: Randomize (around) 500s 500s CPPTRAJ: Randomize (overlap) 500s 500s CPPTRAJ: Randomize (no restrictions) 500s 500s All 5 comparisons passed. 500s 500s ******************************************************************************** 500s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Molsurf 500s 500s CPPTRAJ: Molsurf test 501s 501s All 1 comparisons passed. 501s 501s ******************************************************************************** 501s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Corr 501s 501s CPPTRAJ: Correlation test 501s 501s All 2 comparisons passed. 501s 501s ******************************************************************************** 501s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CheckStructure 501s 501s CPPTRAJ: Structure Check 501s 501s CPPTRAJ: Structure Check with Around and Skip 501s 501s CPPTRAJ: Structure Check with PBC 501s 501s CPPTRAJ: Structure Check with Around 501s 501s All 8 comparisons passed. 501s 501s ******************************************************************************** 501s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_RmsAvgCorr 501s 501s CPPTRAJ: RmsAvgCorr Reference 501s 501s CPPTRAJ: RmsAvgCorr First 501s 501s All 3 comparisons passed. 501s 501s ******************************************************************************** 501s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Contacts 501s 501s CPPTRAJ: Contacts test. 501s 501s All 3 comparisons passed. 501s 501s ******************************************************************************** 501s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Principal 501s 501s CPPTRAJ: Principal Test 501s 501s All 3 comparisons passed. 501s 501s ******************************************************************************** 501s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_ClusterDihedral 501s 501s CPPTRAJ: clusterdihedral test 501s 501s All 4 comparisons passed. 501s 501s ******************************************************************************** 501s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Vector 501s 501s CPPTRAJ: Basic vector tests 502s 502s CPPTRAJ: Test vector center with magnitude 502s 502s CPPTRAJ: Momentum/velocity vector test. 502s 502s CPPTRAJ: Force vector test. 502s 502s All 14 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Matrix 502s 502s CPPTRAJ: Matrix Tests 502s 502s CPPTRAJ: Generate matrix with trajectory start/stop/offset 502s 502s CPPTRAJ: Generate matrix with action stop/start/offset 502s 502s All 15 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AtomicFluct 502s 502s CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. 502s 502s CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. 502s 502s CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. 502s 502s CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. 502s 502s CPPTRAJ: Atomicfluct test with ADP output 502s 502s CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. 502s 502s All 13 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Grid 502s 502s CPPTRAJ: Dipole test 502s 502s CPPTRAJ: Grid test 502s 502s CPPTRAJ: OpenDX Grid read test 502s 502s CPPTRAJ: Grid with specified center test. 502s 502s CPPTRAJ: Grid with box center offset test. 502s 502s CPPTRAJ: Grid with mask center offset test. 502s 502s CPPTRAJ: Non-orthogonal grid test. 502s 502s CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test 502s 502s CPPTRAJ: Grid generation from 'bounds' test. 502s 502s All 13 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Unwrap 502s 502s CPPTRAJ: Unwrap non-orthogonal test 502s 502s CPPTRAJ: Unwrap orthogonal test 502s 502s All 2 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Project 502s 502s CPPTRAJ: Projection 502s 502s All 1 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Analyze_Modes 502s 502s CPPTRAJ: Modes analysis, RMS fluctuations 502s 502s CPPTRAJ: Modes analysis, displacements 502s 502s CPPTRAJ: Modes analysis, dipole correlation 502s 502s CPPTRAJ: Modes analysis, pseudo trajectory creation test 502s 502s CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test 502s 502s All 6 comparisons passed. 502s 502s ******************************************************************************** 502s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Watershell 502s 502s CPPTRAJ: Watershell Test, non-orthorhombic imaging. 503s 503s CPPTRAJ: Watershell Test, orthorhombic imaging. 503s 503s CPPTRAJ: Watershell Test, no imaging. 503s 503s All 3 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AnalysisRunAvg 503s 503s CPPTRAJ: Analysis Running Average 503s 503s All 2 comparisons passed. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Volmap 503s 503s CPPTRAJ: VMD VolMap Algorithm test 503s VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. 503s Skipped test: VMD VolMap Algorithm longer tests 503s 503s All 2 comparisons passed. 503s 1 comparisons skipped. 503s 503s ******************************************************************************** 503s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_SPAM 503s 503s CPPTRAJ: SPAM Test 504s 504s CPPTRAJ: SPAM Pure Solvent Test 505s 505s 1 out of 5 comparisons failed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_LIE 505s 505s CPPTRAJ: LIE test 505s 505s All 1 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Density 505s 505s CPPTRAJ: Density along axis tests 505s 505s CPPTRAJ: Multi-frame density along axis test 505s 505s CPPTRAJ: Total system density test 505s 505s All 7 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_LipidOrder 505s 505s CPPTRAJ: Lipid Order Parameter Test. 505s 505s All 6 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_LipidSCD 505s 505s CPPTRAJ: Basic lipid order parameter test 505s 505s CPPTRAJ: New Lipid Order Parameter Test, DOPC. 505s 505s All 4 comparisons passed. 505s 505s ******************************************************************************** 505s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_PairDist 505s 505s CPPTRAJ: PairDist Test. 506s 506s CPPTRAJ: Pairdist test, orthogonal imaging. 506s 506s CPPTRAJ: Pairdist test, nonorthogonal imaging. 506s 506s CPPTRAJ: Pairdist test, 2 masks. 506s 506s All 4 comparisons passed. 506s 506s ******************************************************************************** 506s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_ReadData 506s 506s CPPTRAJ: Read vector data test (no origins, origins) 506s 506s CPPTRAJ: Read vector data set (origins, no origins) 506s 506s CPPTRAJ: Read Amber output test 506s 506s CPPTRAJ: Read CHARMM output test 506s 506s CPPTRAJ: 3D data read/write test 506s 506s CPPTRAJ: Standard 3D data write test 506s 506s CPPTRAJ: Standard 3D data read test 506s 506s CPPTRAJ: Standard 3D data read/append test 507s 507s CPPTRAJ: Standard 3D data, sparse 507s 507s CPPTRAJ: Nonorthogonal grid standard write/read tests. 507s 507s CPPTRAJ: Read specific columns test. 507s 507s CPPTRAJ: Write non-square matrix 507s 507s CPPTRAJ: Read non-square matrix 507s 507s CPPTRAJ: Read square matrix 507s 507s All 15 comparisons passed. 507s 507s ******************************************************************************** 507s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_GIST 507s 507s CPPTRAJ: GIST water-water interaction test 508s 508s CPPTRAJ: GIST test, orthogonal cell 510s 510s CPPTRAJ: GIST test, nonorthogonal cell 513s 513s All 11 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_GIST_Order 513s 513s CPPTRAJ: TIP3P water cluster test 513s 513s CPPTRAJ: TIP4P water cluster test 513s 513s CPPTRAJ: TIP5P water cluster test 513s 513s All 4 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_systemVF 513s 513s CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test 513s 513s All 1 comparisons passed. 513s 513s ******************************************************************************** 513s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AtomicCorr 513s 513s CPPTRAJ: Atomic Correlation test 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AutoCorr 514s 514s CPPTRAJ: AutoCorr test. 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Box 514s 514s CPPTRAJ: Box Test (Add box info) 514s 514s CPPTRAJ: Box test (remove box info) 514s 514s CPPTRAJ: Box test (Modify box length) 514s 514s CPPTRAJ: Box test (auto orthogonal box, no radii) 514s 514s CPPTRAJ: Box test (auto orthogonal box, VDW radii) 514s 514s All 7 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AtomTypeSelect 514s 514s CPPTRAJ: Selection by atom type test. 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AvgRef 514s 514s CPPTRAJ: RMSD Test with averaged reference coordinates. 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Crank_Stat 514s 514s CPPTRAJ: Crankshaft test 514s 514s All 3 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CreateCrd 514s 514s CPPTRAJ: COORDS data set creation and CRDFLUCT test. 514s 514s CPPTRAJ: COORDS data set creation with velocities test 514s 514s CPPTRAJ: TRAJ data set creation and CRDFLUCT test. 514s 514s CPPTRAJ: TRAJ data set creation with velocities test. 514s 514s CPPTRAJ: COORDS data set append test 514s 514s CPPTRAJ: COORDS test storing frame metadata 514s 514s CPPTRAJ: TRAJ test storing frame metadata 514s 514s All 8 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AutoImage 514s 514s CPPTRAJ: AutoImage test (split DNA duplex) 514s 514s CPPTRAJ: AutoImage test, use anchor mask 514s 514s All 2 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_LoadCrd 514s 514s CPPTRAJ: LoadCrd test. 514s 514s CPPTRAJ: LoadTraj test. 514s 514s CPPTRAJ: LoadTraj from trajin test. 514s 514s CPPTRAJ: LoadCrd append from multiple files test 514s 514s All 4 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_MultiVector 514s 514s CPPTRAJ: Multivector test 514s 514s All 1 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Lifetime 514s 514s CPPTRAJ: Lifetime test. 514s 514s CPPTRAJ: Lifetime test with data set caching. 514s 514s CPPTRAJ: Lifetime average and cumulative average test. 514s 514s All 12 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_FFT 514s 514s CPPTRAJ: FFT test. 514s 514s All 5 comparisons passed. 514s 514s ******************************************************************************** 514s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Timecorr 514s 514s CPPTRAJ: Timecorr test. 515s 515s All 7 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CrossCorr 515s 515s CPPTRAJ: CrossCorr test 515s 515s All 1 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_SymmRmsd 515s 515s CPPTRAJ: SymmRmsd 515s 515s CPPTRAJ: ASP symmetry-corrected RMSD test 515s 515s CPPTRAJ: GLU symmetry-corrected RMSD test 515s 515s CPPTRAJ: TYR symmetry-corrected RMSD test 515s 515s CPPTRAJ: Longer symmetry-corrected RMSD test. 515s 515s All 8 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Multidihedral 515s 515s CPPTRAJ: Multidihedral test 515s 515s CPPTRAJ: Multidihedral Nucleotide CHI test 515s 515s CPPTRAJ: Multidihedral protein dihedrals test 515s 515s CPPTRAJ: Multidihedral cyclic molecule test 515s 515s All 6 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Ensemble_MREMD 515s 515s CPPTRAJ: M-REMD sort test. 515s 515s CPPTRAJ: M-REMD actions test. 515s 515s CPPTRAJ: M-REMD ensemble outtraj test. 515s 515s CPPTRAJ: M-REMD no sort, running average test 515s 515s CPPTRAJ: M-REMD, generate RMS data 515s 515s CPPTRAJ: M-REMD, meltcurve analysis 515s 515s All 17 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_MakeStructure 515s 515s CPPTRAJ: Basic makestructure test 515s 515s CPPTRAJ: Makestructure test with reference. 515s 515s All 5 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Rotate 515s 515s CPPTRAJ: Rotation (and inverse) of coords from matrices 515s 515s CPPTRAJ: Rotate with defined axis 515s 515s All 3 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Integrate 515s 515s CPPTRAJ: Integration test. 515s 515s All 2 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_NativeContacts 515s 515s CPPTRAJ: NativeContacts test. 515s 515s CPPTRAJ: NativeContacts test, save non-native contacts, residue time series 515s 515s CPPTRAJ: NativeContacts test, orthorhombic imaging. 515s 515s All 17 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CheckChiral 515s 515s CPPTRAJ: Check chirality test 515s 515s All 1 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Energy 515s 515s CPPTRAJ: Simple energy tests 515s 515s CPPTRAJ: Test kinetic energy calculation 515s 515s CPPTRAJ: Test total energy calculation 515s 515s CPPTRAJ: Test partial energy calculation 515s 515s All 6 comparisons passed. 515s 515s ******************************************************************************** 515s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_LESsplit 515s 515s CPPTRAJ: LES split/average test 516s 516s All 2 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_PermuteDihedrals 516s 516s CPPTRAJ: PermuteDihedrals interval -120, phi psi 516s 516s CPPTRAJ: PermuteDihedrals, random rotations 516s 516s All 4 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CCP4 516s 516s CPPTRAJ: CCP4 read/write and DX conversion test. 516s 516s All 2 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_DihCovar 516s 516s CPPTRAJ: Dihedral Covariance Matrix Test 516s 516s All 3 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CurveFit 516s 516s CPPTRAJ: Curve fitting test. 516s 516s CPPTRAJ: Curve fitting multi-exponential tests. 516s 516s CPPTRAJ: Curve fitting, custom output range. 516s 516s All 6 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Multicurve 516s 516s CPPTRAJ: Multicurve test 516s 516s All 1 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_DataSetAverage 516s 516s CPPTRAJ: Data set averaging and averaging over all sets test. 516s 516s All 2 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_VectorMath 516s 516s CPPTRAJ: Vector dot/cross product test 516s 516s All 2 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Esander 516s SANDER energy tests (long) requires SANDER API from AmberTools. 516s Cpptraj was compiled without SANDER API from AmberTools support. 516s SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. 516s SKIP: SANDER energy tests (long) 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Esander_Short 516s Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. 516s Cpptraj was compiled without SANDER API from AmberTools support. 516s SKIP: Energy via sander API short tests (GB/PME) 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Temperature 516s 516s CPPTRAJ: Temperature test. 516s 516s CPPTRAJ: Temperature with SHAKE on hydrogens. 516s 516s CPPTRAJ: Temperature with SHAKE on all atoms. 516s 516s CPPTRAJ: Temperature calc with extra points. 516s 516s All 5 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Spline 516s 516s CPPTRAJ: Spline test 516s 516s All 1 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_KDE 516s 516s CPPTRAJ: KDE test. 516s 516s CPPTRAJ: KDE with Kullback-Leibler divergence test 516s 516s All 4 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Wavelet 516s 516s CPPTRAJ: Wavelet analysis test 516s 516s CPPTRAJ: Wavelet WAFEX test 516s 516s All 3 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CIF 516s 516s CPPTRAJ: CIF read test 516s 516s CPPTRAJ: Generate offset traj from PDB 516s 516s CPPTRAJ: Generate offset traj from CIF 516s 516s All 2 comparisons passed. 516s 516s ******************************************************************************** 516s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_PDB 516s 516s CPPTRAJ: PDB format read/write test 517s 517s CPPTRAJ: PQR file write with various radii 517s 517s CPPTRAJ: PDB filter alternate atom location IDs test 517s 517s CPPTRAJ: Adding PDB info to topology 517s 517s All 10 comparisons passed. 517s 517s ******************************************************************************** 517s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Align 517s 517s CPPTRAJ: Align Tests. 517s 517s CPPTRAJ: Align, unit cell rotation/imaging test. 517s 517s All 4 comparisons passed. 517s 517s ******************************************************************************** 517s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_VelocityAutoCorr 517s 517s CPPTRAJ: Velocity autocorrelation test 517s 517s All 3 comparisons passed. 517s 517s ******************************************************************************** 517s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_VelFrc 517s 517s CPPTRAJ: Test combining coordinates, velocities, and forces. 517s 517s CPPTRAJ: Test using velocities as coordinates. 517s 517s CPPTRAJ: Test writing velocities (MDVEL) 517s 517s CPPTRAJ: Test using forces as coordinates. 517s 517s CPPTRAJ: Test writing forces (MDFRC) 517s 517s CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. 517s 517s CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. 517s 517s All 5 comparisons passed. 517s 517s ******************************************************************************** 517s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_RotateDihedral 517s 517s CPPTRAJ: Rotate dihedral to target value. 517s 517s CPPTRAJ: Rotate dihedral by increment 517s 517s CPPTRAJ: Rotate dihedral in TRAJ data set 517s 517s All 3 comparisons passed. 517s 517s ******************************************************************************** 517s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_DataSetCmd 517s 517s CPPTRAJ: Data Set commands test 518s 518s All 10 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Remap 518s 518s CPPTRAJ: Remap Test 518s 518s All 1 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CompareTop 518s 518s CPPTRAJ: Compare topology test 518s 518s All 1 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Filter 518s 518s CPPTRAJ: Basic filter test 518s 518s CPPTRAJ: Data filter test. 518s 518s CPPTRAJ: Filter matrix test. 518s 518s All 5 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CombineCrd 518s 518s CPPTRAJ: Combine COORDS test. 518s 518s CPPTRAJ: Combine COORDS test with box info. 518s 518s CPPTRAJ: Split coords and recombine test. 518s 518s All 5 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_TopInfo 518s 518s CPPTRAJ: Topology info print test. 518s 518s CPPTRAJ: Topology info with reference coords test 518s 518s All 12 comparisons passed. 518s 518s ******************************************************************************** 518s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_GromacsTrr 518s 518s CPPTRAJ: TRR force/velocity read -> NetCDF write test 518s 518s CPPTRAJ: TRR force/velocity read -> TRR write test 518s 518s CPPTRAJ: CRD => TRR 518s 518s CPPTRAJ: TRR => CRD 519s 519s CPPTRAJ: CRD(1-5) => TRR 519s 519s CPPTRAJ: CRD(6-10) => TRR 519s 519s CPPTRAJ: TRR (appended) => CRD 519s 519s CPPTRAJ: GMX: CRD with offset 519s 519s CPPTRAJ: GMX: TRR with offset 519s 519s All 5 comparisons passed. 519s 519s ******************************************************************************** 519s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_GromacsXtc 519s 519s CPPTRAJ: XTC read test 519s 519s CPPTRAJ: CRD => XTC 519s 519s CPPTRAJ: XTC => CRD 519s 519s CPPTRAJ: CRD(1-5) => XTC 519s 519s CPPTRAJ: CRD(6-10) => XTC 519s 519s CPPTRAJ: XTC (appended) => CRD 519s 519s CPPTRAJ: GMX: CRD with offset 519s 519s CPPTRAJ: GMX: XTC with offset 519s 519s All 4 comparisons passed. 519s 519s ******************************************************************************** 519s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_GromacsTNG 519s 519s CPPTRAJ: TNG read test 519s 519s CPPTRAJ: TNG read test (with offset) 519s 519s All 6 comparisons passed. 519s 519s ******************************************************************************** 519s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Ewald 519s 519s CPPTRAJ: Direct sum test 520s 520s CPPTRAJ: Ewald test (NaCl crystal) 520s 520s CPPTRAJ: Ewald test (trunc. oct) 520s 520s CPPTRAJ: Ewald test (partial system, trunc. oct) 520s Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 520s Skipped test: Ewald test (trunc. oct), 10 frames 520s Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. 520s Skipped test: Ewald test (ortho), 10 frames 520s 520s All 4 comparisons passed. 520s 2 comparisons skipped. 520s 520s ******************************************************************************** 520s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_LibPME 520s 520s CPPTRAJ: Particle mesh Ewald test (NaCl crystal) 520s 520s CPPTRAJ: Particle mesh Ewald test (trunc. oct) 520s 520s CPPTRAJ: Particle mesh Ewald test (ortho) 520s 520s CPPTRAJ: Particle mesh Ewald test (ortho, with mask) 520s 520s CPPTRAJ: PME test (partial system, trunc. oct) 520s PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 520s Skipped test: PME test (trunc. oct), 10 frames 520s 520s All 5 comparisons passed. 520s 1 comparisons skipped. 520s 520s ******************************************************************************** 520s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_LJ_PME 520s 520s CPPTRAJ: LJ PME test. 520s 520s CPPTRAJ: LJ PME kappa sweep test, 0.25 520s 520s CPPTRAJ: LJ PME kappa sweep test, 0.35 521s 521s CPPTRAJ: LJ PME kappa sweep test, 0.45 521s 521s CPPTRAJ: LJ PME kappa sweep test, 0.5 521s 521s CPPTRAJ: LJ with switch function test 521s 521s All 5 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_TI 521s 521s CPPTRAJ: TI analysis test. 521s 521s All 5 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_FixImagedBonds 521s 521s CPPTRAJ: Fix imaged bonds test (Ortho.) 521s 521s CPPTRAJ: Fix imaged bonds test (Non-ortho.) 521s 521s All 2 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Distance 521s 521s CPPTRAJ: Distance tests 521s 521s CPPTRAJ: Orthogonal imaged distance 521s 521s CPPTRAJ: Non-orthogonal imaged distance 521s 521s All 3 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Volume 521s 521s CPPTRAJ: Volume tests 521s 521s All 1 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_SetVelocity 521s 521s CPPTRAJ: Set Velocity test 521s 521s CPPTRAJ: Scale velocity test 521s 521s 1 out of 3 comparisons failed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Remlog 521s 521s CPPTRAJ: Replica log read/analyze test. 521s 521s All 7 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_AreaPerMol 521s 521s CPPTRAJ: Area per molecule test 521s 521s All 6 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_DistBasedMask 521s 521s CPPTRAJ: Distance-based atom mask tests (atom, residue) 521s 521s CPPTRAJ: Distance-based atom mask tests (molecule) 521s 521s All 6 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Calc 521s 521s CPPTRAJ: Calc test 521s 521s CPPTRAJ: Calc test with data sets 521s 521s CPPTRAJ: Test math functions 521s 521s All 4 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CalcState 521s 521s CPPTRAJ: Calcstate test 521s 521s All 4 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Change 521s 521s CPPTRAJ: Change atom and residue name tests 521s 521s CPPTRAJ: Change chain ID test 521s 521s CPPTRAJ: Change chain ID of COORDS set test 521s 521s All 3 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CreateReservoir 521s 521s CPPTRAJ: Create RREMD NetCDF reservoir test 521s 521s All 1 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_FixAtomOrder 521s 521s CPPTRAJ: Out of order molecules test 521s 521s All 2 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_LowestCurve 521s 521s CPPTRAJ: LowestCurve test 521s 521s All 1 comparisons passed. 521s 521s ******************************************************************************** 521s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_MinImage 521s 521s CPPTRAJ: Minimum Image test. 522s 522s All 1 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Regress 522s 522s CPPTRAJ: Linear regression test. 522s 522s All 3 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Rst 522s 522s CPPTRAJ: Generate restraints (rst) test 522s 522s All 1 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Pairwise 522s 522s CPPTRAJ: Pairwise tests 522s 522s CPPTRAJ: Pairwise test, partial system 522s 522s All 10 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_ParmBox 522s 522s CPPTRAJ: Parmbox test 522s 522s All 1 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Solvent 522s 522s CPPTRAJ: Test solvent command with closest 522s 522s All 1 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Translate 522s 522s CPPTRAJ: Translate test 522s 522s All 1 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_ReplicateCell 522s 522s CPPTRAJ: Replicate cell test 522s 522s All 1 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_ScaleDihedralK 522s 522s CPPTRAJ: Scale dihedral force constant test 522s 522s CPPTRAJ: Scale dihedral force constant with 'useall' 522s 522s All 2 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_PhiPsi 522s 522s CPPTRAJ: Phipsi test 522s 522s All 1 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Control 522s 522s CPPTRAJ: Loop tests 522s 522s CPPTRAJ: Test set command 522s 522s CPPTRAJ: Test reading comma-separated list of strings 522s 522s CPPTRAJ: Test nested loops and variables in loops 522s 522s CPPTRAJ: Test loop over data set blocks 522s 522s CPPTRAJ: Test for filename wildcards and oversets 522s 522s All 13 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_InfraredSpec 522s 522s CPPTRAJ: Infrared spectrum calculation test 522s 522s All 2 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Cphstats 522s 522s CPPTRAJ: Explicit pH REMD ensemble data read / sort 522s 522s CPPTRAJ: Constant pH stats test 522s 522s CPPTRAJ: Sorted implicit constant pH stats test 522s 522s CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats 522s 522s CPPTRAJ: Unsorted pH read/write test 522s 522s All 16 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CmdLine 522s 522s CPPTRAJ: Command line trajectory args test, part 1 522s 522s CPPTRAJ: Command line test trajectory args test, part 2 522s 522s CPPTRAJ: Command line wildcard test, part 1 522s 522s CPPTRAJ: Command line wildcard test, part 2 522s 522s All 2 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_XYZformat 522s 522s CPPTRAJ: XYZ format write 522s 522s CPPTRAJ: Atom XYZ format read, test 1 522s 522s CPPTRAJ: Atom XYZ format read, test 2 522s 522s CPPTRAJ: Atom XYZ format read, test 3 522s 522s CPPTRAJ: Atom XYZ format read, test 4 522s 522s CPPTRAJ: Atom XYZ format read, test 5 522s 522s CPPTRAJ: Atom XYZ format read, test 6 522s 522s All 6 comparisons passed. 522s 522s ******************************************************************************** 522s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Hausdorff 522s 522s CPPTRAJ: Simple Hausdorff distance test. 522s 522s CPPTRAJ: Hausdorff distance of 2D rms output test. 522s 522s CPPTRAJ: Hausdorff distance of 2D rms output test. 523s 523s All 3 comparisons passed. 523s 523s ******************************************************************************** 523s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_CatCrd 523s 523s CPPTRAJ: Concatenate COORDS data set test 523s 523s All 1 comparisons passed. 523s 523s ******************************************************************************** 523s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_XtalSymm 523s 523s CPPTRAJ: XtalSymm Reference 523s 523s CPPTRAJ: XtalSymm Reimaging by Atom 524s 524s CPPTRAJ: XtalSymm Reimaging by Molecule 525s 525s All 3 comparisons passed. 525s 525s ******************************************************************************** 525s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Time 525s 525s CPPTRAJ: Add time to restart test 525s 525s CPPTRAJ: Remove time from restart test 525s 525s CPPTRAJ: Add time to trajectory test 525s 525s CPPTRAJ: Modify time info test. 525s 525s All 4 comparisons passed. 525s 525s ******************************************************************************** 525s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_SplitCoords 525s 525s CPPTRAJ: SplitCoords test 525s 525s All 1 comparisons passed. 525s 525s ******************************************************************************** 525s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_DihedralRMS 525s 525s CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) 525s 525s CPPTRAJ: Dihedral RMSD test (to previous) 525s 525s CPPTRAJ: Dihedral RMS fluctuation test. 525s 525s All 5 comparisons passed. 525s 525s ******************************************************************************** 525s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Slope 525s 525s CPPTRAJ: Finite difference test. 525s 525s All 1 comparisons passed. 525s 525s ******************************************************************************** 525s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Diagmatrix 525s 525s CPPTRAJ: MW covariance matrix thermo analysis test 525s 525s All 1 comparisons passed. 525s 525s ******************************************************************************** 525s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Emin 525s 525s CPPTRAJ: Basic energy minimization test. 525s 525s CPPTRAJ: Energy minimization with angle term test. 525s 525s CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. 525s 525s CPPTRAJ: Energy minimization with nonbond term test. 525s 525s CPPTRAJ: OpenMM basic energy minimization tests (bonds) 525s 525s CPPTRAJ: OpenMM basic energy minimization tests (angles) 525s 525s CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) 525s 525s CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) 525s 525s CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) 526s 526s All 9 comparisons passed. 526s 526s ******************************************************************************** 526s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_EvalPlateau 526s 526s CPPTRAJ: Evalulate plateau test 526s 526s All 2 comparisons passed. 526s 526s ******************************************************************************** 526s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Graft 526s 526s CPPTRAJ: Graft test 526s 526s All 1 comparisons passed. 526s 526s ******************************************************************************** 526s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Flatten 526s 526s CPPTRAJ: Flatten test. 526s 526s All 1 comparisons passed. 526s 526s ******************************************************************************** 526s TEST: /tmp/autopkgtest.BhcY5I/build.7Qt/src/test/Test_Random 526s 526s CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs 526s 526s CPPTRAJ: PCG32 RNG test. 526s 526s CPPTRAJ: Test Stdlib RNG 526s 526s CPPTRAJ: Test Mersenne Twister RNG 526s 526s All 4 comparisons passed. 526s 526s make[1]: Leaving directory '/tmp/autopkgtest.BhcY5I/build.7Qt/src/test' 526s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 13 21:02 ../bin/cpptraj -> /usr/bin/cpptraj 526s ===================== TEST SUMMARY ====================== 526s 851 out of 859 comparisons OK (2 failed, 0 warnings, 6 skipped). 526s 480 out of 480 program executions completed. 526s 168 out of 173 tests completed with no issues. 526s 2 tests skipped. 526s ========================================================= 526s make: *** [Makefile:662: summary] Error 2 526s make: Leaving directory '/tmp/autopkgtest.BhcY5I/build.7Qt/src/test' 526s autopkgtest [21:03:32]: test command1: -----------------------] 527s autopkgtest [21:03:33]: test command1: - - - - - - - - - - results - - - - - - - - - - 527s command1 FAIL non-zero exit status 2 527s autopkgtest [21:03:33]: test command1: - - - - - - - - - - stderr - - - - - - - - - - 527s make: *** [Makefile:662: summary] Error 2 528s autopkgtest [21:03:34]: @@@@@@@@@@@@@@@@@@@@ summary 528s command1 FAIL non-zero exit status 2 556s Creating nova instance adt-noble-arm64-cpptraj-20240313-205446-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID a0e860fd-0684-417f-821d-d8092ab02621)...