0s autopkgtest [18:09:01]: starting date and time: 2024-11-14 18:09:01+0000 0s autopkgtest [18:09:01]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [18:09:01]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ruekpwrf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:boost1.83,src:openmpi --apt-upgrade prime-phylo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=boost1.83/1.83.0-3.2ubuntu3 openmpi/5.0.5-3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-8.secgroup --name adt-plucky-s390x-prime-phylo-20241114-180901-juju-7f2275-prod-proposed-migration-environment-15-8635c54b-6b0d-459f-a310-ed6c1fba6718 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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/ 102s autopkgtest [18:10:43]: testbed dpkg architecture: s390x 102s autopkgtest [18:10:43]: testbed apt version: 2.9.8 102s autopkgtest [18:10:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 103s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [103 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [933 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.0 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 103s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [112 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [662 kB] 103s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [4084 B] 104s Fetched 1909 kB in 1s (2108 kB/s) 104s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s The following packages will be upgraded: 106s libcap-ng0 pastebinit python3-systemd 106s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 77.8 kB of archives. 106s After this operation, 123 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libcap-ng0 s390x 0.8.5-3build1 [15.9 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pastebinit all 1.7.1-1 [14.9 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-systemd s390x 235-1build5 [46.9 kB] 107s Fetched 77.8 kB in 0s (230 kB/s) 107s (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 ... 55511 files and directories currently installed.) 107s Preparing to unpack .../libcap-ng0_0.8.5-3build1_s390x.deb ... 107s Unpacking libcap-ng0:s390x (0.8.5-3build1) over (0.8.5-1) ... 107s Setting up libcap-ng0:s390x (0.8.5-3build1) ... 107s (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 ... 55511 files and directories currently installed.) 107s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 107s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 107s Preparing to unpack .../python3-systemd_235-1build5_s390x.deb ... 107s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 107s Setting up pastebinit (1.7.1-1) ... 107s Setting up python3-systemd (235-1build5) ... 107s Processing triggers for man-db (2.12.1-3) ... 107s Processing triggers for libc-bin (2.40-1ubuntu3) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 108s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 108s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 108s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 109s Reading package lists... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [18:10:54]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 113s autopkgtest [18:10:54]: @@@@@@@@@@@@@@@@@@@@ apt-source prime-phylo 115s Get:1 http://ftpmaster.internal/ubuntu plucky/universe prime-phylo 1.0.11-12 (dsc) [2366 B] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/universe prime-phylo 1.0.11-12 (tar) [751 kB] 115s Get:3 http://ftpmaster.internal/ubuntu plucky/universe prime-phylo 1.0.11-12 (diff) [10.5 kB] 115s gpgv: Signature made Wed Aug 7 15:34:26 2024 UTC 115s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 115s gpgv: issuer "emollier@debian.org" 115s gpgv: Can't check signature: No public key 115s dpkg-source: warning: cannot verify inline signature for ./prime-phylo_1.0.11-12.dsc: no acceptable signature found 115s autopkgtest [18:10:56]: testing package prime-phylo version 1.0.11-12 115s autopkgtest [18:10:56]: build not needed 116s autopkgtest [18:10:57]: test run-unit-test: preparing testbed 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Starting pkgProblemResolver with broken count: 0 118s Starting 2 pkgProblemResolver with broken count: 0 118s Done 118s The following additional packages will be installed: 118s libblas3 libboost-mpi1.83.0 libboost-serialization1.83.0 118s libevent-pthreads-2.1-7t64 libfabric1 libgfortran5 libhwloc-plugins 118s libhwloc15 liblapack3 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64 118s librdmacm1t64 libxnvctrl0 ocl-icd-libopencl1 prime-phylo 118s Suggested packages: 118s opencl-icd njplot treeviewx muscle probalign mafft python3-biopython mrbayes 118s phyml raxml 118s The following NEW packages will be installed: 118s autopkgtest-satdep libblas3 libboost-mpi1.83.0 libboost-serialization1.83.0 118s libevent-pthreads-2.1-7t64 libfabric1 libgfortran5 libhwloc-plugins 118s libhwloc15 liblapack3 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64 118s librdmacm1t64 libxnvctrl0 ocl-icd-libopencl1 prime-phylo 118s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 8980 kB/8981 kB of archives. 118s After this operation, 31.3 MB of additional disk space will be used. 118s Get:1 /tmp/autopkgtest.RPvhew/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 118s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 119s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x libboost-serialization1.83.0 s390x 1.83.0-3.2ubuntu3 [350 kB] 119s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10 [7870 B] 119s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x librdmacm1t64 s390x 52.0-2ubuntu1 [73.8 kB] 119s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libfabric1 s390x 1.17.0-3ubuntu1 [558 kB] 119s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc15 s390x 2.11.2-1 [176 kB] 119s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libmunge2 s390x 0.5.15-4build1 [15.6 kB] 119s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libpciaccess0 s390x 0.17-3build1 [19.0 kB] 119s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 119s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1build1 [41.1 kB] 119s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc-plugins s390x 2.11.2-1 [16.1 kB] 119s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x libpmix2t64 s390x 5.0.3-2 [718 kB] 120s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x libopenmpi3t64 s390x 5.0.5-3 [2102 kB] 120s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x libboost-mpi1.83.0 s390x 1.83.0-3.2ubuntu3 [271 kB] 120s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 120s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 121s Get:18 http://ftpmaster.internal/ubuntu plucky/universe s390x prime-phylo s390x 1.0.11-12 [842 kB] 122s Fetched 8980 kB in 3s (2929 kB/s) 122s Selecting previously unselected package libblas3:s390x. 122s (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 ... 55516 files and directories currently installed.) 122s Preparing to unpack .../00-libblas3_3.12.0-3build2_s390x.deb ... 122s Unpacking libblas3:s390x (3.12.0-3build2) ... 122s Selecting previously unselected package libboost-serialization1.83.0:s390x. 122s Preparing to unpack .../01-libboost-serialization1.83.0_1.83.0-3.2ubuntu3_s390x.deb ... 122s Unpacking libboost-serialization1.83.0:s390x (1.83.0-3.2ubuntu3) ... 122s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 122s Preparing to unpack .../02-libevent-pthreads-2.1-7t64_2.1.12-stable-10_s390x.deb ... 122s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 122s Selecting previously unselected package librdmacm1t64:s390x. 122s Preparing to unpack .../03-librdmacm1t64_52.0-2ubuntu1_s390x.deb ... 122s Unpacking librdmacm1t64:s390x (52.0-2ubuntu1) ... 122s Selecting previously unselected package libfabric1:s390x. 122s Preparing to unpack .../04-libfabric1_1.17.0-3ubuntu1_s390x.deb ... 122s Unpacking libfabric1:s390x (1.17.0-3ubuntu1) ... 122s Selecting previously unselected package libhwloc15:s390x. 122s Preparing to unpack .../05-libhwloc15_2.11.2-1_s390x.deb ... 122s Unpacking libhwloc15:s390x (2.11.2-1) ... 122s Selecting previously unselected package libmunge2:s390x. 122s Preparing to unpack .../06-libmunge2_0.5.15-4build1_s390x.deb ... 122s Unpacking libmunge2:s390x (0.5.15-4build1) ... 122s Selecting previously unselected package libpciaccess0:s390x. 122s Preparing to unpack .../07-libpciaccess0_0.17-3build1_s390x.deb ... 122s Unpacking libpciaccess0:s390x (0.17-3build1) ... 122s Selecting previously unselected package libxnvctrl0:s390x. 122s Preparing to unpack .../08-libxnvctrl0_510.47.03-0ubuntu4_s390x.deb ... 122s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 122s Selecting previously unselected package ocl-icd-libopencl1:s390x. 122s Preparing to unpack .../09-ocl-icd-libopencl1_2.3.2-1build1_s390x.deb ... 122s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 122s Selecting previously unselected package libhwloc-plugins:s390x. 122s Preparing to unpack .../10-libhwloc-plugins_2.11.2-1_s390x.deb ... 122s Unpacking libhwloc-plugins:s390x (2.11.2-1) ... 122s Selecting previously unselected package libpmix2t64:s390x. 122s Preparing to unpack .../11-libpmix2t64_5.0.3-2_s390x.deb ... 122s Unpacking libpmix2t64:s390x (5.0.3-2) ... 122s Selecting previously unselected package libopenmpi3t64:s390x. 122s Preparing to unpack .../12-libopenmpi3t64_5.0.5-3_s390x.deb ... 122s Unpacking libopenmpi3t64:s390x (5.0.5-3) ... 122s Selecting previously unselected package libboost-mpi1.83.0. 122s Preparing to unpack .../13-libboost-mpi1.83.0_1.83.0-3.2ubuntu3_s390x.deb ... 122s Unpacking libboost-mpi1.83.0 (1.83.0-3.2ubuntu3) ... 122s Selecting previously unselected package libgfortran5:s390x. 122s Preparing to unpack .../14-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 122s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 122s Selecting previously unselected package liblapack3:s390x. 122s Preparing to unpack .../15-liblapack3_3.12.0-3build2_s390x.deb ... 122s Unpacking liblapack3:s390x (3.12.0-3build2) ... 122s Selecting previously unselected package prime-phylo. 122s Preparing to unpack .../16-prime-phylo_1.0.11-12_s390x.deb ... 122s Unpacking prime-phylo (1.0.11-12) ... 122s Selecting previously unselected package autopkgtest-satdep. 122s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 122s Unpacking autopkgtest-satdep (0) ... 122s Setting up libpciaccess0:s390x (0.17-3build1) ... 122s Setting up libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 122s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 122s Setting up libboost-serialization1.83.0:s390x (1.83.0-3.2ubuntu3) ... 122s Setting up libblas3:s390x (3.12.0-3build2) ... 122s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 122s Setting up libmunge2:s390x (0.5.15-4build1) ... 122s Setting up libhwloc15:s390x (2.11.2-1) ... 122s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 122s Setting up ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 122s Setting up librdmacm1t64:s390x (52.0-2ubuntu1) ... 122s Setting up libfabric1:s390x (1.17.0-3ubuntu1) ... 122s Setting up liblapack3:s390x (3.12.0-3build2) ... 122s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 122s Setting up libhwloc-plugins:s390x (2.11.2-1) ... 122s Setting up libpmix2t64:s390x (5.0.3-2) ... 122s Setting up libopenmpi3t64:s390x (5.0.5-3) ... 122s Setting up libboost-mpi1.83.0 (1.83.0-3.2ubuntu3) ... 122s Setting up prime-phylo (1.0.11-12) ... 122s Setting up autopkgtest-satdep (0) ... 122s Processing triggers for man-db (2.12.1-3) ... 122s Processing triggers for libc-bin (2.40-1ubuntu3) ... 124s (Reading database ... 55722 files and directories currently installed.) 124s Removing autopkgtest-satdep (0) ... 125s autopkgtest [18:11:06]: test run-unit-test: [----------------------- 125s treesize: error while loading shared libraries: libmpi_cxx.so.40: cannot open shared object file: No such file or directory 125s autopkgtest [18:11:06]: test run-unit-test: -----------------------] 126s autopkgtest [18:11:07]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 126s run-unit-test FAIL non-zero exit status 127 126s autopkgtest [18:11:07]: @@@@@@@@@@@@@@@@@@@@ summary 126s run-unit-test FAIL non-zero exit status 127 131s nova [W] Using flock in prodstack6-s390x 131s flock: timeout while waiting to get lock 131s Creating nova instance adt-plucky-s390x-prime-phylo-20241114-180901-juju-7f2275-prod-proposed-migration-environment-15-8635c54b-6b0d-459f-a310-ed6c1fba6718 from image adt/ubuntu-plucky-s390x-server-20241114.img (UUID 41a907ef-1f3c-4685-a0eb-228b0d61c6b5)...