0s autopkgtest [00:44:47]: starting date and time: 2024-06-08 00:44:47+0000 0s autopkgtest [00:44:47]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [00:44:47]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fniospgw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade gemmi --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 astropy/6.0.1-4' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-14.secgroup --name adt-oracular-ppc64el-gemmi-20240608-004447-juju-7f2275-prod-proposed-migration-environment-3-85d696ed-3482-4ab0-9c2f-af09336d2db9 --image adt/ubuntu-oracular-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 159s autopkgtest [00:47:26]: testbed dpkg architecture: ppc64el 159s autopkgtest [00:47:26]: testbed apt version: 2.9.3 159s autopkgtest [00:47:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 160s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 160s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 160s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2852 B] 160s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 160s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 160s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [53.6 kB] 161s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1860 B] 161s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [289 kB] 161s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [1768 B] 161s Fetched 850 kB in 1s (1119 kB/s) 161s Reading package lists... 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Calculating upgrade... 164s The following packages will be upgraded: 164s debianutils libheif-plugin-aomdec libheif-plugin-aomenc 164s libheif-plugin-libde265 libheif1 libnetplan1 netplan-generator netplan.io 164s python3-netplan 164s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Need to get 731 kB of archives. 164s After this operation, 5120 B of additional disk space will be used. 164s Get:1 http://ftpmaster.internal/ubuntu oracular/main ppc64el debianutils ppc64el 5.18 [90.5 kB] 164s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el netplan-generator ppc64el 1.0-3ubuntu1 [59.3 kB] 164s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-netplan ppc64el 1.0-3ubuntu1 [21.8 kB] 164s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el netplan.io ppc64el 1.0-3ubuntu1 [66.6 kB] 164s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnetplan1 ppc64el 1.0-3ubuntu1 [138 kB] 164s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-aomdec ppc64el 1.17.6-3 [10.2 kB] 164s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-aomenc ppc64el 1.17.6-3 [16.6 kB] 164s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif1 ppc64el 1.17.6-3 [320 kB] 164s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-libde265 ppc64el 1.17.6-3 [8484 B] 164s Fetched 731 kB in 1s (1336 kB/s) 165s (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 ... 72602 files and directories currently installed.) 165s Preparing to unpack .../debianutils_5.18_ppc64el.deb ... 165s Unpacking debianutils (5.18) over (5.17build1) ... 165s Setting up debianutils (5.18) ... 165s (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 ... 72602 files and directories currently installed.) 165s Preparing to unpack .../0-netplan-generator_1.0-3ubuntu1_ppc64el.deb ... 165s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 165s Unpacking netplan-generator (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 165s Preparing to unpack .../1-python3-netplan_1.0-3ubuntu1_ppc64el.deb ... 165s Unpacking python3-netplan (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 165s Preparing to unpack .../2-netplan.io_1.0-3ubuntu1_ppc64el.deb ... 165s Unpacking netplan.io (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 165s Preparing to unpack .../3-libnetplan1_1.0-3ubuntu1_ppc64el.deb ... 165s Unpacking libnetplan1:ppc64el (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 165s Preparing to unpack .../4-libheif-plugin-aomdec_1.17.6-3_ppc64el.deb ... 165s Unpacking libheif-plugin-aomdec:ppc64el (1.17.6-3) over (1.17.6-1ubuntu4) ... 165s Preparing to unpack .../5-libheif-plugin-aomenc_1.17.6-3_ppc64el.deb ... 165s Unpacking libheif-plugin-aomenc:ppc64el (1.17.6-3) over (1.17.6-1ubuntu4) ... 165s Preparing to unpack .../6-libheif1_1.17.6-3_ppc64el.deb ... 165s Unpacking libheif1:ppc64el (1.17.6-3) over (1.17.6-1ubuntu4) ... 165s Preparing to unpack .../7-libheif-plugin-libde265_1.17.6-3_ppc64el.deb ... 165s Unpacking libheif-plugin-libde265:ppc64el (1.17.6-3) over (1.17.6-1ubuntu4) ... 165s Setting up libnetplan1:ppc64el (1.0-3ubuntu1) ... 165s Setting up python3-netplan (1.0-3ubuntu1) ... 165s Setting up netplan-generator (1.0-3ubuntu1) ... 165s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 165s Setting up netplan.io (1.0-3ubuntu1) ... 165s Setting up libheif-plugin-aomdec:ppc64el (1.17.6-3) ... 165s Setting up libheif-plugin-libde265:ppc64el (1.17.6-3) ... 165s Setting up libheif1:ppc64el (1.17.6-3) ... 165s Setting up libheif-plugin-aomenc:ppc64el (1.17.6-3) ... 165s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 165s Processing triggers for man-db (2.12.1-1) ... 166s Processing triggers for dbus (1.14.10-4ubuntu4) ... 166s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 167s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 167s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 167s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 168s Reading package lists... 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 169s Calculating upgrade... 169s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 169s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s autopkgtest [00:47:40]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 173s autopkgtest [00:47:40]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 178s Get:1 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (dsc) [2280 B] 178s Get:2 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (tar) [1290 kB] 178s Get:3 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (diff) [7104 B] 179s gpgv: Signature made Tue May 21 10:42:01 2024 UTC 179s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 179s gpgv: issuer "merkys@debian.org" 179s gpgv: Can't check signature: No public key 179s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-1.dsc: no acceptable signature found 179s autopkgtest [00:47:46]: testing package gemmi version 0.6.5+ds-1 179s autopkgtest [00:47:46]: build not needed 180s autopkgtest [00:47:47]: test command1: preparing testbed 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 181s Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 181s The following additional packages will be installed: 181s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 181s python3-iniconfig python3-numpy python3-packaging python3-pluggy 181s python3-pytest 181s Suggested packages: 181s gcc gfortran python-numpy-doc python3-dev 181s The following NEW packages will be installed: 181s autopkgtest-satdep gemmi gemmi-dev libblas3 libgfortran5 liblapack3 181s python3-gemmi python3-iniconfig python3-numpy python3-packaging 181s python3-pluggy python3-pytest 181s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 181s Need to get 13.6 MB/13.6 MB of archives. 181s After this operation, 55.3 MB of additional disk space will be used. 181s Get:1 /tmp/autopkgtest.fUiJ04/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [736 B] 181s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ppc64el gemmi ppc64el 0.6.5+ds-1 [1332 kB] 183s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ppc64el gemmi-dev ppc64el 0.6.5+ds-1 [1333 kB] 183s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 184s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.1.0-1ubuntu1 [573 kB] 184s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 184s Get:7 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-gemmi ppc64el 0.6.5+ds-1 [2555 kB] 185s Get:8 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 185s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-10 [4408 kB] 185s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-packaging all 24.0-1 [41.1 kB] 185s Get:11 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 185s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-pytest all 8.2.2-1ubuntu1 [250 kB] 186s Fetched 13.6 MB in 4s (3357 kB/s) 186s Selecting previously unselected package gemmi. 186s (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 ... 72602 files and directories currently installed.) 186s Preparing to unpack .../00-gemmi_0.6.5+ds-1_ppc64el.deb ... 186s Unpacking gemmi (0.6.5+ds-1) ... 186s Selecting previously unselected package gemmi-dev. 186s Preparing to unpack .../01-gemmi-dev_0.6.5+ds-1_ppc64el.deb ... 186s Unpacking gemmi-dev (0.6.5+ds-1) ... 186s Selecting previously unselected package libblas3:ppc64el. 186s Preparing to unpack .../02-libblas3_3.12.0-3build1_ppc64el.deb ... 186s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 186s Selecting previously unselected package libgfortran5:ppc64el. 186s Preparing to unpack .../03-libgfortran5_14.1.0-1ubuntu1_ppc64el.deb ... 186s Unpacking libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 186s Selecting previously unselected package liblapack3:ppc64el. 186s Preparing to unpack .../04-liblapack3_3.12.0-3build1_ppc64el.deb ... 186s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 186s Selecting previously unselected package python3-gemmi. 186s Preparing to unpack .../05-python3-gemmi_0.6.5+ds-1_ppc64el.deb ... 186s Unpacking python3-gemmi (0.6.5+ds-1) ... 186s Selecting previously unselected package python3-iniconfig. 186s Preparing to unpack .../06-python3-iniconfig_1.1.1-2_all.deb ... 186s Unpacking python3-iniconfig (1.1.1-2) ... 186s Selecting previously unselected package python3-numpy. 186s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-10_ppc64el.deb ... 186s Unpacking python3-numpy (1:1.26.4+ds-10) ... 186s Selecting previously unselected package python3-packaging. 186s Preparing to unpack .../08-python3-packaging_24.0-1_all.deb ... 186s Unpacking python3-packaging (24.0-1) ... 186s Selecting previously unselected package python3-pluggy. 186s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 186s Unpacking python3-pluggy (1.5.0-1) ... 186s Selecting previously unselected package python3-pytest. 186s Preparing to unpack .../10-python3-pytest_8.2.2-1ubuntu1_all.deb ... 186s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 186s Selecting previously unselected package autopkgtest-satdep. 186s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 186s Unpacking autopkgtest-satdep (0) ... 186s Setting up python3-iniconfig (1.1.1-2) ... 187s Setting up python3-gemmi (0.6.5+ds-1) ... 187s Setting up gemmi-dev (0.6.5+ds-1) ... 187s Setting up libblas3:ppc64el (3.12.0-3build1) ... 187s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 187s Setting up python3-packaging (24.0-1) ... 187s Setting up libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 187s Setting up python3-pluggy (1.5.0-1) ... 187s Setting up gemmi (0.6.5+ds-1) ... 187s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 187s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 187s Setting up python3-pytest (8.2.2-1ubuntu1) ... 188s Setting up python3-numpy (1:1.26.4+ds-10) ... 190s Setting up autopkgtest-satdep (0) ... 190s Processing triggers for man-db (2.12.1-1) ... 191s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 193s (Reading database ... 73817 files and directories currently installed.) 193s Removing autopkgtest-satdep (0) ... 194s autopkgtest [00:48:01]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 194s autopkgtest [00:48:01]: test command1: [----------------------- 195s ........................................................................ [ 38%] 195s .............................s.................s..............ssssss.... [ 76%] 195s ............................................ [100%] 195s =========================== short test summary info ============================ 195s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 195s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 195s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 195s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 195s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 195s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 195s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 195s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 195s 180 passed, 8 skipped, 3 deselected in 1.25s 196s autopkgtest [00:48:03]: test command1: -----------------------] 196s command1 PASS 196s autopkgtest [00:48:03]: test command1: - - - - - - - - - - results - - - - - - - - - - 196s autopkgtest [00:48:03]: @@@@@@@@@@@@@@@@@@@@ summary 196s command1 PASS 207s nova [W] Using flock in scalingstack-bos02-ppc64el 207s Creating nova instance adt-oracular-ppc64el-gemmi-20240608-004447-juju-7f2275-prod-proposed-migration-environment-3-85d696ed-3482-4ab0-9c2f-af09336d2db9 from image adt/ubuntu-oracular-ppc64el-server-20240607.img (UUID 2e7ff4dd-25ad-4882-8618-1243d2d4ac8e)...