0s autopkgtest [12:42:07]: starting date: 2024-03-18 0s autopkgtest [12:42:07]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt 0s autopkgtest [12:42:07]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6e7ktmbw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade prime-phylo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 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@bos03-arm64-7.secgroup --name adt-noble-arm64-prime-phylo-20240318-124207-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://ftpmaster.internal/ubuntu/ 121s autopkgtest [12:44:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 122s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 122s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3727 kB] 124s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 124s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 124s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 124s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 124s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 124s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 124s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 124s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4102 kB] 125s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 125s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 125s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 126s Fetched 9245 kB in 3s (2795 kB/s) 126s Reading package lists... 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s Calculating upgrade... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 132s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 132s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 132s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 134s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Calculating upgrade... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s autopkgtest [12:44:23]: testbed dpkg architecture: arm64 138s autopkgtest [12:44:25]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 138s autopkgtest [12:44:25]: @@@@@@@@@@@@@@@@@@@@ apt-source prime-phylo 139s Get:1 http://ftpmaster.internal/ubuntu noble/universe prime-phylo 1.0.11-10build1 (dsc) [2199 B] 139s Get:2 http://ftpmaster.internal/ubuntu noble/universe prime-phylo 1.0.11-10build1 (tar) [751 kB] 139s Get:3 http://ftpmaster.internal/ubuntu noble/universe prime-phylo 1.0.11-10build1 (diff) [8600 B] 140s gpgv: Signature made Tue Dec 19 15:02:45 2023 UTC 140s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 140s gpgv: Can't check signature: No public key 140s dpkg-source: warning: cannot verify inline signature for ./prime-phylo_1.0.11-10build1.dsc: no acceptable signature found 140s autopkgtest [12:44:27]: testing package prime-phylo version 1.0.11-10build1 140s autopkgtest [12:44:27]: build not needed 141s autopkgtest [12:44:28]: test run-unit-test: preparing testbed 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 145s Done 145s Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 148s The following additional packages will be installed: 148s libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libboost-mpi1.83.0 148s libboost-serialization1.83.0 libdrm-amdgpu1 libevent-pthreads-2.1-7 148s libfabric1 libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins 148s libhwloc15 liblapack3 libllvm17 libmunge2 libopenmpi3 libpciaccess0 libpmix2 148s librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 prime-phylo 148s Suggested packages: 148s opencl-icd njplot treeviewx muscle probalign mafft python3-biopython mrbayes 148s phyml raxml 148s The following NEW packages will be installed: 148s libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libboost-mpi1.83.0 148s libboost-serialization1.83.0 libdrm-amdgpu1 libevent-pthreads-2.1-7 148s libfabric1 libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins 148s libhwloc15 liblapack3 libllvm17 libmunge2 libopenmpi3 libpciaccess0 libpmix2 148s librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 prime-phylo 148s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 148s 1 not fully installed or removed. 148s Need to get 54.7 MB of archives. 148s After this operation, 238 MB of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 148s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-serialization1.83.0 arm64 1.83.0-2ubuntu1 [434 kB] 148s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 148s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 148s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 148s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 148s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 148s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 148s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 148s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 148s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 148s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 148s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2 arm64 5.0.1-4 [659 kB] 148s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 151s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 152s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 152s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 152s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 152s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 152s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 152s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 152s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-mpi1.83.0 arm64 1.83.0-2ubuntu1 [353 kB] 152s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 152s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 152s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 prime-phylo arm64 1.0.11-10build1 [769 kB] 153s Fetched 54.7 MB in 6s (9121 kB/s) 153s Selecting previously unselected package libblas3:arm64. 153s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 153s Preparing to unpack .../00-libblas3_3.12.0-3_arm64.deb ... 153s Unpacking libblas3:arm64 (3.12.0-3) ... 153s Selecting previously unselected package libboost-serialization1.83.0:arm64. 153s Preparing to unpack .../01-libboost-serialization1.83.0_1.83.0-2ubuntu1_arm64.deb ... 153s Unpacking libboost-serialization1.83.0:arm64 (1.83.0-2ubuntu1) ... 153s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 153s Preparing to unpack .../02-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 153s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 153s Selecting previously unselected package libatomic1:arm64. 153s Preparing to unpack .../03-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 153s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 153s Selecting previously unselected package librdmacm1t64:arm64. 153s Preparing to unpack .../04-librdmacm1t64_50.0-2_arm64.deb ... 153s Unpacking librdmacm1t64:arm64 (50.0-2) ... 153s Selecting previously unselected package libfabric1:arm64. 153s Preparing to unpack .../05-libfabric1_1.17.0-3_arm64.deb ... 153s Unpacking libfabric1:arm64 (1.17.0-3) ... 153s Selecting previously unselected package libhwloc15:arm64. 153s Preparing to unpack .../06-libhwloc15_2.10.0-1_arm64.deb ... 153s Unpacking libhwloc15:arm64 (2.10.0-1) ... 153s Selecting previously unselected package libmunge2:arm64. 153s Preparing to unpack .../07-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 153s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 153s Selecting previously unselected package libpciaccess0:arm64. 153s Preparing to unpack .../08-libpciaccess0_0.17-3_arm64.deb ... 153s Unpacking libpciaccess0:arm64 (0.17-3) ... 153s Selecting previously unselected package libxnvctrl0:arm64. 153s Preparing to unpack .../09-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 153s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 153s Selecting previously unselected package ocl-icd-libopencl1:arm64. 153s Preparing to unpack .../10-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 153s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 153s Selecting previously unselected package libhwloc-plugins:arm64. 153s Preparing to unpack .../11-libhwloc-plugins_2.10.0-1_arm64.deb ... 153s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 153s Selecting previously unselected package libpmix2:arm64. 153s Preparing to unpack .../12-libpmix2_5.0.1-4_arm64.deb ... 153s Unpacking libpmix2:arm64 (5.0.1-4) ... 153s Selecting previously unselected package libllvm17:arm64. 153s Preparing to unpack .../13-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 153s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 157s Selecting previously unselected package libamd-comgr2:arm64. 157s Preparing to unpack .../14-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 157s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 157s Selecting previously unselected package libdrm-amdgpu1:arm64. 157s Preparing to unpack .../15-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 157s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 157s Selecting previously unselected package libhsakmt1:arm64. 157s Preparing to unpack .../16-libhsakmt1_5.7.0-1_arm64.deb ... 157s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 157s Selecting previously unselected package libhsa-runtime64-1. 157s Preparing to unpack .../17-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 157s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 157s Selecting previously unselected package libamdhip64-5. 157s Preparing to unpack .../18-libamdhip64-5_5.2.3-12_arm64.deb ... 157s Unpacking libamdhip64-5 (5.2.3-12) ... 157s Selecting previously unselected package libucx0:arm64. 157s Preparing to unpack .../19-libucx0_1.16.0+ds-4_arm64.deb ... 157s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 157s Selecting previously unselected package libopenmpi3:arm64. 157s Preparing to unpack .../20-libopenmpi3_4.1.6-5ubuntu1_arm64.deb ... 157s Unpacking libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 157s Selecting previously unselected package libboost-mpi1.83.0. 157s Preparing to unpack .../21-libboost-mpi1.83.0_1.83.0-2ubuntu1_arm64.deb ... 157s Unpacking libboost-mpi1.83.0 (1.83.0-2ubuntu1) ... 157s Selecting previously unselected package libgfortran5:arm64. 157s Preparing to unpack .../22-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 157s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 157s Selecting previously unselected package liblapack3:arm64. 157s Preparing to unpack .../23-liblapack3_3.12.0-3_arm64.deb ... 157s Unpacking liblapack3:arm64 (3.12.0-3) ... 157s Selecting previously unselected package prime-phylo. 157s Preparing to unpack .../24-prime-phylo_1.0.11-10build1_arm64.deb ... 157s Unpacking prime-phylo (1.0.11-10build1) ... 157s Setting up libpciaccess0:arm64 (0.17-3) ... 157s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 157s Setting up libboost-serialization1.83.0:arm64 (1.83.0-2ubuntu1) ... 157s Setting up libblas3:arm64 (3.12.0-3) ... 157s 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 157s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 157s Setting up libhwloc15:arm64 (2.10.0-1) ... 157s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 157s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 157s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 157s Setting up librdmacm1t64:arm64 (50.0-2) ... 157s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 157s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 157s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 157s Setting up libfabric1:arm64 (1.17.0-3) ... 157s Setting up liblapack3:arm64 (3.12.0-3) ... 157s 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 157s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 157s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 157s Setting up libhsakmt1:arm64 (5.7.0-1) ... 157s Setting up libpmix2:arm64 (5.0.1-4) ... 157s Setting up libhsa-runtime64-1 (5.7.1-1) ... 157s Setting up libamdhip64-5 (5.2.3-12) ... 157s Setting up libucx0:arm64 (1.16.0+ds-4) ... 157s Setting up libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 157s Setting up libboost-mpi1.83.0 (1.83.0-2ubuntu1) ... 157s Setting up prime-phylo (1.0.11-10build1) ... 157s Setting up autopkgtest-satdep (0) ... 157s Processing triggers for man-db (2.12.0-3) ... 157s Processing triggers for libc-bin (2.39-0ubuntu2) ... 160s (Reading database ... 75156 files and directories currently installed.) 160s Removing autopkgtest-satdep (0) ... 161s autopkgtest [12:44:48]: test run-unit-test: [----------------------- 161s PASS Test 1 393s L N alpha time 424s -3785.26 0 1 424s 425s PASS Test 2 425s autopkgtest [12:49:12]: test run-unit-test: -----------------------] 426s autopkgtest [12:49:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 426s run-unit-test PASS 426s autopkgtest [12:49:13]: @@@@@@@@@@@@@@@@@@@@ summary 426s run-unit-test PASS 431s Creating nova instance adt-noble-arm64-prime-phylo-20240318-124207-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...