0s autopkgtest [16:41:38]: starting date and time: 2025-03-15 16:41:38+0000 0s autopkgtest [16:41:38]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:41:38]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b9tutlcq/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade phyml --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-20.secgroup --name adt-plucky-s390x-phyml-20250315-164137-juju-7f2275-prod-proposed-migration-environment-2-e81c5af3-f7a7-4c54-8f28-b1f53fc32a7b --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 144s autopkgtest [16:44:02]: testbed dpkg architecture: s390x 144s autopkgtest [16:44:02]: testbed apt version: 2.9.33 145s autopkgtest [16:44:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 145s autopkgtest [16:44:03]: testbed release detected to be: None 146s autopkgtest [16:44:04]: updating testbed package index (apt update) 146s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 147s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 147s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 147s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 147s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 147s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 147s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 147s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 148s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 148s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 148s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 148s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 148s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 148s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 148s Fetched 1073 kB in 2s (643 kB/s) 149s Reading package lists... 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s Calculating upgrade... 150s Calculating upgrade... 150s The following packages were automatically installed and are no longer required: 150s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 150s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 150s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 150s linux-tools-6.11.0-8-generic 150s Use 'sudo apt autoremove' to remove them. 150s The following packages will be upgraded: 150s pinentry-curses python3-jinja2 strace 150s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 652 kB of archives. 150s After this operation, 27.6 kB of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 151s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 151s Fetched 652 kB in 1s (681 kB/s) 151s (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 ... 81428 files and directories currently installed.) 151s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 151s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 151s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 151s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 151s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 151s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 151s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 151s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 151s Setting up strace (6.13+ds-1ubuntu1) ... 151s Processing triggers for man-db (2.13.0-1) ... 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Solving dependencies... 152s The following packages will be REMOVED: 152s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 152s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 152s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 152s linux-tools-6.11.0-8-generic* 152s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 152s After this operation, 167 MB disk space will be freed. 152s (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 ... 81428 files and directories currently installed.) 152s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 152s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 152s Removing libpython3.12t64:s390x (3.12.9-1) ... 152s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 152s Removing libnsl2:s390x (1.3.0-3build3) ... 152s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 153s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 153s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 153s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 154s Processing triggers for libc-bin (2.41-1ubuntu1) ... 154s (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 ... 56328 files and directories currently installed.) 154s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 154s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 154s autopkgtest [16:44:12]: upgrading testbed (apt dist-upgrade and autopurge) 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 154s Starting 2 pkgProblemResolver with broken count: 0 154s Done 154s Entering ResolveByKeep 155s 155s Calculating upgrade... 155s The following packages will be upgraded: 155s libc-bin libc-dev-bin libc6 libc6-dev locales 155s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Need to get 9512 kB of archives. 155s After this operation, 8192 B of additional disk space will be used. 155s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 157s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 161s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 161s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 167s Preconfiguring packages ... 167s Fetched 9512 kB in 12s (819 kB/s) 167s (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 ... 56326 files and directories currently installed.) 167s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 167s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 167s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 167s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 167s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 167s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 167s Setting up libc6:s390x (2.41-1ubuntu2) ... 167s (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 ... 56326 files and directories currently installed.) 167s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 167s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 167s Setting up libc-bin (2.41-1ubuntu2) ... 167s (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 ... 56326 files and directories currently installed.) 167s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 167s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 167s Setting up locales (2.41-1ubuntu2) ... 167s Generating locales (this might take a while)... 168s en_US.UTF-8... done 168s Generation complete. 168s Setting up libc-dev-bin (2.41-1ubuntu2) ... 168s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 168s Processing triggers for man-db (2.13.0-1) ... 169s Processing triggers for systemd (257.3-1ubuntu3) ... 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 170s Starting pkgProblemResolver with broken count: 0 170s Starting 2 pkgProblemResolver with broken count: 0 170s Done 170s Solving dependencies... 170s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 171s autopkgtest [16:44:29]: rebooting testbed after setup commands that affected boot 190s autopkgtest [16:44:48]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 192s autopkgtest [16:44:50]: @@@@@@@@@@@@@@@@@@@@ apt-source phyml 195s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (dsc) [2131 B] 195s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (tar) [1804 kB] 195s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (diff) [27.1 kB] 196s gpgv: Signature made Sat Nov 30 06:14:54 2024 UTC 196s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 196s gpgv: Can't check signature: No public key 196s dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-4build1.dsc: no acceptable signature found 196s autopkgtest [16:44:54]: testing package phyml version 3:3.3.20220408-4build1 196s autopkgtest [16:44:54]: build not needed 197s autopkgtest [16:44:55]: test run-unit-test: preparing testbed 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 198s Starting pkgProblemResolver with broken count: 0 198s Starting 2 pkgProblemResolver with broken count: 0 198s Done 198s The following NEW packages will be installed: 198s libevent-pthreads-2.1-7t64 libfabric1 libhwloc-plugins libhwloc15 libmunge2 198s libopenmpi40 libpciaccess0 libpmix2t64 librdmacm1t64 libxnvctrl0 198s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common phyml 198s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 198s Need to get 5057 kB of archives. 198s After this operation, 17.9 MB of additional disk space will be used. 198s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10 [7870 B] 198s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x librdmacm1t64 s390x 55.0-1ubuntu1 [73.7 kB] 198s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x libfabric1 s390x 1.17.0-3.1 [558 kB] 199s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc15 s390x 2.12.0-1 [176 kB] 199s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libmunge2 s390x 0.5.16-1 [15.2 kB] 199s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libpciaccess0 s390x 0.17-3build1 [19.0 kB] 199s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 199s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1build1 [41.1 kB] 199s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc-plugins s390x 2.12.0-1 [16.1 kB] 199s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x libpmix2t64 s390x 5.0.6-5 [715 kB] 200s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x libopenmpi40 s390x 5.0.7-1 [2196 kB] 202s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x openmpi-common all 5.0.7-1 [97.9 kB] 202s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x openmpi-bin s390x 5.0.7-1 [200 kB] 202s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x mpi-default-bin s390x 1.18 [2510 B] 202s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x phyml s390x 3:3.3.20220408-4build1 [925 kB] 203s Fetched 5057 kB in 5s (962 kB/s) 203s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 204s (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 ... 56326 files and directories currently installed.) 204s Preparing to unpack .../00-libevent-pthreads-2.1-7t64_2.1.12-stable-10_s390x.deb ... 204s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 204s Selecting previously unselected package librdmacm1t64:s390x. 204s Preparing to unpack .../01-librdmacm1t64_55.0-1ubuntu1_s390x.deb ... 204s Unpacking librdmacm1t64:s390x (55.0-1ubuntu1) ... 204s Selecting previously unselected package libfabric1:s390x. 204s Preparing to unpack .../02-libfabric1_1.17.0-3.1_s390x.deb ... 204s Unpacking libfabric1:s390x (1.17.0-3.1) ... 204s Selecting previously unselected package libhwloc15:s390x. 204s Preparing to unpack .../03-libhwloc15_2.12.0-1_s390x.deb ... 204s Unpacking libhwloc15:s390x (2.12.0-1) ... 204s Selecting previously unselected package libmunge2:s390x. 204s Preparing to unpack .../04-libmunge2_0.5.16-1_s390x.deb ... 204s Unpacking libmunge2:s390x (0.5.16-1) ... 204s Selecting previously unselected package libpciaccess0:s390x. 204s Preparing to unpack .../05-libpciaccess0_0.17-3build1_s390x.deb ... 204s Unpacking libpciaccess0:s390x (0.17-3build1) ... 204s Selecting previously unselected package libxnvctrl0:s390x. 204s Preparing to unpack .../06-libxnvctrl0_510.47.03-0ubuntu4_s390x.deb ... 204s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 204s Selecting previously unselected package ocl-icd-libopencl1:s390x. 204s Preparing to unpack .../07-ocl-icd-libopencl1_2.3.2-1build1_s390x.deb ... 204s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 204s Selecting previously unselected package libhwloc-plugins:s390x. 204s Preparing to unpack .../08-libhwloc-plugins_2.12.0-1_s390x.deb ... 204s Unpacking libhwloc-plugins:s390x (2.12.0-1) ... 204s Selecting previously unselected package libpmix2t64:s390x. 204s Preparing to unpack .../09-libpmix2t64_5.0.6-5_s390x.deb ... 204s Unpacking libpmix2t64:s390x (5.0.6-5) ... 204s Selecting previously unselected package libopenmpi40:s390x. 204s Preparing to unpack .../10-libopenmpi40_5.0.7-1_s390x.deb ... 204s Unpacking libopenmpi40:s390x (5.0.7-1) ... 204s Selecting previously unselected package openmpi-common. 204s Preparing to unpack .../11-openmpi-common_5.0.7-1_all.deb ... 204s Unpacking openmpi-common (5.0.7-1) ... 204s Selecting previously unselected package openmpi-bin. 204s Preparing to unpack .../12-openmpi-bin_5.0.7-1_s390x.deb ... 204s Unpacking openmpi-bin (5.0.7-1) ... 204s Selecting previously unselected package mpi-default-bin. 204s Preparing to unpack .../13-mpi-default-bin_1.18_s390x.deb ... 204s Unpacking mpi-default-bin (1.18) ... 204s Selecting previously unselected package phyml. 204s Preparing to unpack .../14-phyml_3%3a3.3.20220408-4build1_s390x.deb ... 204s Unpacking phyml (3:3.3.20220408-4build1) ... 204s Setting up libpciaccess0:s390x (0.17-3build1) ... 204s Setting up libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 204s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 204s Setting up libmunge2:s390x (0.5.16-1) ... 204s Setting up libhwloc15:s390x (2.12.0-1) ... 204s Setting up ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 204s Setting up openmpi-common (5.0.7-1) ... 204s Setting up librdmacm1t64:s390x (55.0-1ubuntu1) ... 204s Setting up libfabric1:s390x (1.17.0-3.1) ... 204s Setting up libhwloc-plugins:s390x (2.12.0-1) ... 204s Setting up libpmix2t64:s390x (5.0.6-5) ... 204s Setting up libopenmpi40:s390x (5.0.7-1) ... 204s Setting up openmpi-bin (5.0.7-1) ... 204s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 204s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 204s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 204s Setting up mpi-default-bin (1.18) ... 204s Setting up phyml (3:3.3.20220408-4build1) ... 204s Processing triggers for man-db (2.13.0-1) ... 204s Processing triggers for libc-bin (2.41-1ubuntu2) ... 205s autopkgtest [16:45:03]: test run-unit-test: [----------------------- 205s DNA interleaved sequence file, default parameters single processor: 205s + export PHYMLCPUS=1 205s + PHYMLCPUS=1 205s + echo 'DNA interleaved sequence file, default parameters single processor:' 205s + /usr/bin/phyml -i nucleic 205s 205s 205s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 205s 205s 205s 205s 205s 205s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 205s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 205s 205s . Sequence filename: nucleic 205s . Data type: dna 205s . Alphabet size: 4 205s . Sequence format: interleaved 205s . Number of data sets: 1 205s . Nb of bootstrapped data sets: 0 205s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 205s . Model name: HKY85 205s . Ts/tv ratio: estimated 205s . Proportion of invariable sites: 0.000000 205s . RAS model: discrete Gamma 205s . Number of subst. rate catgs: 4 205s . Gamma distribution parameter: estimated 205s . 'Middle' of each rate class: mean 205s . Nucleotide equilibrium frequencies: empirical 205s . Optimise tree topology: yes 205s . Starting tree: BioNJ 205s . Add random input tree: no 205s . Optimise branch lengths: yes 205s . Minimum length of an edge: 1e-08 205s . Optimise substitution model parameters: yes 205s . Run ID: none 205s . Random seed: 1742057189 205s . Subtree patterns aliasing: no 205s . Version: 3.3.3:3.3.20220408-4build1 205s . Byte alignment: 1 205s . AVX enabled: no 205s . SSE enabled: no 205s 205s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 205s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 205s 205s 205s 205s . 382 patterns found (out of a total of 886 sites). 205s 205s . 582 sites without polymorphism (65.69%). 205s 205s 205s . Computing pairwise distances... 205s 205s . Building BioNJ tree... 205s 205s . This analysis requires at least 11 MB of memory space. 206s 206s 206s . Score of initial tree: -5680.04 206s 206s . Starting first round of SPRs... 208s 210s 2s | 1 | lnL= -5433.9 | depth= 2/ 40 | improvements= 18 | delta_lnL= 4.1/ 1000.0 211s 4s | 2 | lnL= -5443.2 | depth= 5/ 24 | improvements= 20 | delta_lnL= 6.2/ 1000.0 212s 6s | 3 | lnL= -5454.7 | depth= 2/ 14 | improvements= 19 | delta_lnL= 18.8/ 1000.0 214s 7s | 4 | lnL= -5455.7 | depth= 4/ 8 | improvements= 23 | delta_lnL= 14.5/ 1000.0 214s 8s | 5 | lnL= -5433.4 | depth= 2/ 10 | improvements= 26 | delta_lnL= 6.5/ 1000.0 214s 9s | 6 | lnL= -5429.6 | depth= 1/ 8 | improvements= 14 | delta_lnL= 0.0/ 50.0 + 214s 214s . Second round of optimization... 215s 215s 9s | 7 | lnL= -5439.8 | depth= 5/ 10 | improvements= 11 | delta_lnL= 10.9/ 50.0 216s 10s | 8 | lnL= -5424.2 | depth= 4/ 9 | improvements= 9 | delta_lnL= 8.8/ 50.0 + 216s 10s | 9 | lnL= -5441.0 | depth= 1/ 8 | improvements= 22 | delta_lnL= 0.0/ 50.0 217s 11s | 10 | lnL= -5431.9 | depth= 3/ 6 | improvements= 23 | delta_lnL= 16.5/ 21.7 217s -74s | 11 | lnL= -5446.3 | depth= 2/ 7 | improvements= 14 | delta_lnL= 4.2/ 21.7 217s -74s | 12 | lnL= -5443.2 | depth= 2/ 6 | improvements= 14 | delta_lnL= 12.2/ 21.7 218s -74s | 13 | lnL= -5432.5 | depth= 1/ 6 | improvements= 17 | delta_lnL= 0.0/ 21.7 218s -73s | 14 | lnL= -5440.4 | depth= 2/ 5 | improvements= 10 | delta_lnL= 16.0/ 33.0 218s -73s | 15 | lnL= -5427.9 | depth= 2/ 6 | improvements= 16 | delta_lnL= 10.9/ 33.0 219s -73s | 16 | lnL= -5428.4 | depth= 1/ 6 | improvements= 8 | delta_lnL= 0.0/ 33.0 219s -72s | 17 | lnL= -5433.1 | depth= 1/ 5 | improvements= 16 | delta_lnL= 0.0/ 33.0 219s 219s . Third round of optimization... 220s 222s -71s | 18 | lnL= -5420.5 | depth= 4/ 10 | improvements= 6 | delta_lnL= 5.1/ 100.0 | triple moves= 5 + 224s -69s | 19 | lnL= -5420.4 | depth= 0/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 224s -67s | 20 | lnL= -5420.4 | depth= 0/ 6 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 224s 224s . Final optimisation steps... 225s 225s 225s . Log likelihood of the current tree: -5420.255816126929858000949025154113769531. 225s 226s . Calculating fast branch supports (using 'aBayes'). 226s 226s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 226s 226s . Time used 0h-1m-5s 226s 226s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 226s AA interleaved sequence file, default parameters single processor: 226s + echo 'AA interleaved sequence file, default parameters single processor:' 226s + /usr/bin/phyml -i proteic -d aa 226s 226s 226s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 226s 226s 226s 226s 226s 226s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 226s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 226s 226s . Sequence filename: proteic 226s . Data type: aa 226s . Alphabet size: 20 226s . Sequence format: interleaved 226s . Number of data sets: 1 226s . Nb of bootstrapped data sets: 0 226s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 226s . Model name: LG 226s . Proportion of invariable sites: 0.000000 226s . RAS model: discrete Gamma 226s . Number of subst. rate catgs: 4 226s . Gamma distribution parameter: estimated 226s . 'Middle' of each rate class: mean 226s . Amino-acid equilibrium frequencies: empirical 226s . Optimise tree topology: yes 226s . Starting tree: BioNJ 226s . Add random input tree: no 226s . Optimise branch lengths: yes 226s . Minimum length of an edge: 1e-08 226s . Optimise substitution model parameters: yes 226s . Run ID: none 226s . Random seed: 1742057124 226s . Subtree patterns aliasing: no 226s . Version: 3.3.3:3.3.20220408-4build1 226s . Byte alignment: 1 226s . AVX enabled: no 226s . SSE enabled: no 226s 226s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 226s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 226s 226s 226s 226s . 429 patterns found (out of a total of 547 sites). 226s 226s . 136 sites without polymorphism (24.86%). 226s 226s 226s . Computing pairwise distances... 226s 226s . Building BioNJ tree... 226s 226s . This analysis requires at least 39 MB of memory space. 226s 226s 229s . Score of initial tree: -12569.85 229s 229s . Starting first round of SPRs... 241s 252s 15s | 1 | lnL= -12466.0 | depth= 1/ 40 | improvements= 16 | delta_lnL= 0.0/ 1000.0 264s 26s | 2 | lnL= -12478.0 | depth= 1/ 24 | improvements= 18 | delta_lnL= 0.0/ 1000.0 275s 38s | 3 | lnL= -12492.3 | depth= 2/ 14 | improvements= 19 | delta_lnL= 6.8/ 1000.0 285s 49s | 4 | lnL= -12472.7 | depth= 2/ 8 | improvements= 17 | delta_lnL= 16.1/ 1000.0 287s 59s | 5 | lnL= -12492.7 | depth= 2/ 8 | improvements= 21 | delta_lnL= 11.5/ 1000.0 287s 61s | 6 | lnL= -12462.0 | depth= 1/ 8 | improvements= 13 | delta_lnL= 0.0/ 50.0 287s 287s . Second round of optimization... 290s 293s 64s | 7 | lnL= -12468.6 | depth= 1/ 10 | improvements= 14 | delta_lnL= 0.0/ 50.0 296s 67s | 8 | lnL= -12485.4 | depth= 3/ 8 | improvements= 18 | delta_lnL= 15.9/ 50.0 298s 70s | 9 | lnL= -12476.6 | depth= 3/ 7 | improvements= 23 | delta_lnL= 14.5/ 50.0 304s 72s | 10 | lnL= -12471.1 | depth= 1/ 7 | improvements= 16 | delta_lnL= 0.0/ 31.8 306s 78s | 11 | lnL= -12450.7 | depth= 2/ 5 | improvements= 8 | delta_lnL= 9.0/ 31.8 + 309s 80s | 12 | lnL= -12480.1 | depth= 2/ 6 | improvements= 15 | delta_lnL= 40.2/ 31.8 312s 83s | 13 | lnL= -12472.0 | depth= 1/ 6 | improvements= 10 | delta_lnL= 0.0/ 31.8 315s 86s | 14 | lnL= -12462.2 | depth= 1/ 5 | improvements= 15 | delta_lnL= 0.0/ 80.3 318s 89s | 15 | lnL= -12467.7 | depth= 1/ 5 | improvements= 18 | delta_lnL= 0.0/ 80.3 321s 92s | 16 | lnL= -12461.5 | depth= 1/ 5 | improvements= 20 | delta_lnL= 0.0/ 80.3 323s 95s | 17 | lnL= -12472.6 | depth= 1/ 5 | improvements= 13 | delta_lnL= 0.0/ 80.3 326s 97s | 18 | lnL= -12456.7 | depth= 3/ 5 | improvements= 13 | delta_lnL= 17.5/ 20.0 328s 100s | 19 | lnL= -12463.7 | depth= 3/ 7 | improvements= 17 | delta_lnL= 12.3/ 20.0 328s 102s | 20 | lnL= -12461.3 | depth= 1/ 7 | improvements= 12 | delta_lnL= 0.0/ 20.0 328s 328s . Third round of optimization... 342s 358s 116s | 21 | lnL= -12443.1 | depth= 2/ 10 | improvements= 5 | delta_lnL= 2.1/ 100.0 | triple moves= 5 + 358s 132s | 22 | lnL= -12443.0 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 6 + 358s 358s . Final optimisation steps... 364s 364s 364s . Log likelihood of the current tree: -12443.048567856896625016815960407257080078. 364s 369s . Calculating fast branch supports (using 'aBayes'). 369s 369s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 369s 369s . Time used 0h2m23s 369s 369s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 369s AA sequential sequence file, with customization single processor: 369s + echo 'AA sequential sequence file, with customization single processor:' 369s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 369s 369s 369s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 369s 369s 369s 369s 369s 369s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 369s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 369s 369s . Sequence filename: example.nex 369s . Data type: dna 369s . Alphabet size: 4 369s . Sequence format: interleaved 369s . Number of data sets: 1 369s . Nb of bootstrapped data sets: 0 369s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 369s . Model name: HKY85 369s . Ts/tv ratio: estimated 369s . Proportion of invariable sites: 0.000000 369s . RAS model: discrete Gamma 369s . Number of subst. rate catgs: 4 369s . Gamma distribution parameter: estimated 369s . 'Middle' of each rate class: mean 369s . Nucleotide equilibrium frequencies: empirical 369s . Optimise tree topology: yes 369s . Starting tree: BioNJ 369s . Add random input tree: no 369s . Optimise branch lengths: yes 369s . Minimum length of an edge: 1e-08 369s . Optimise substitution model parameters: yes 369s . Run ID: none 369s . Random seed: 1742057267 369s . Subtree patterns aliasing: no 369s . Version: 3.3.3:3.3.20220408-4build1 369s . Byte alignment: 1 369s . AVX enabled: no 369s . SSE enabled: no 369s 369s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 369s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 369s 369s 369s 369s . 1037 patterns found (out of a total of 2888 sites). 369s 369s . 1378 sites without polymorphism (47.71%). 369s 369s 369s . Computing pairwise distances... 369s 369s . Building BioNJ tree... 369s 369s . This analysis requires at least 3 MB of memory space. 369s 369s 369s . Score of initial tree: -12664.54 369s 369s . Starting first round of SPRs... 369s 369s 0s | 1 | lnL= -12617.8 | depth= 1/ 40 | improvements= 3 | delta_lnL= 0.0/ 1000.0 369s 369s . Second round of optimization... 369s 369s 0s | 2 | lnL= -12572.9 | depth= 1/ 36 | improvements= 5 | delta_lnL= 0.0/ 1000.0 369s 369s . Third round of optimization... 370s 370s 1s | 3 | lnL= -12563.6 | depth= 0/ 20 | improvements= 0 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 370s 370s . Final optimisation steps... 370s 370s 370s . Log likelihood of the current tree: -12563.118859055624852771870791912078857422. 370s 370s . Calculating fast branch supports (using 'aBayes').+ export PHYMLCPUS=2 370s + PHYMLCPUS=2 370s + echo 'DNA interleaved sequence file, default parameters using 2 processors:' 370s 370s 370s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 370s 370s . Time used 0h0m1s 370s 370s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 370s + /usr/bin/phyml -i nucleic 370s DNA interleaved sequence file, default parameters using 2 processors: 370s 370s 370s . Running the analysis on 2 CPUs.. 370s 370s . Command line: /usr/lib/phyml/bin/phyml-mpi -i nucleic 370s 370s 370s 370s 370s 370s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 370s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 370s 370s . Sequence filename: nucleic 370s . Data type: dna 370s . Alphabet size: 4 370s . Sequence format: interleaved 370s . Number of data sets: 1 370s . Nb of bootstrapped data sets: 0 370s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 370s . Model name: HKY85 370s . Ts/tv ratio: estimated 370s . Proportion of invariable sites: 0.000000 370s . RAS model: discrete Gamma 370s . Number of subst. rate catgs: 4 370s . Gamma distribution parameter: estimated 370s . 'Middle' of each rate class: mean 370s . Nucleotide equilibrium frequencies: empirical 370s . Optimise tree topology: yes 370s . Starting tree: BioNJ 370s . Add random input tree: no 370s . Optimise branch lengths: yes 370s . Minimum length of an edge: 1e-08 370s . Optimise substitution model parameters: yes 370s . Run ID: none 370s . Random seed: 1742057268 370s . Subtree patterns aliasing: no 370s . Version: 3.3.3:3.3.20220408-4build1 370s . Byte alignment: 1 370s . AVX enabled: no 370s . SSE enabled: no 370s 370s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 370s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 370s 370s 370s 370s . 382 patterns found (out of a total of 886 sites). 370s 370s . 582 sites without polymorphism (65.69%). 370s 370s 370s . Computing pairwise distances... 370s 370s . Building BioNJ tree... 370s 370s . This analysis requires at least 11 MB of memory space. 370s 370s 371s . Score of initial tree: -5680.04 371s 371s . Starting first round of SPRs... 372s 374s 2s | 1 | lnL= -5426.5 | depth= 2/ 40 | improvements= 20 | delta_lnL= 3.9/ 1000.0 + 374s 4s | 2 | lnL= -5430.6 | depth= 5/ 24 | improvements= 12 | delta_lnL= 8.0/ 1000.0 374s 374s . Second round of optimization... 375s 377s 5s | 3 | lnL= -5432.6 | depth= 3/ 21 | improvements= 14 | delta_lnL= 4.9/ 1000.0 378s 6s | 4 | lnL= -5437.3 | depth= 13/ 16 | improvements= 16 | delta_lnL= 32.1/ 1000.0 378s 8s | 5 | lnL= -5433.0 | depth= 2/ 17 | improvements= 22 | delta_lnL= 50.8/ 1000.0 379s 8s | 6 | lnL= -5423.0 | depth= 1/ 13 | improvements= 11 | delta_lnL= 0.0/ 64.2 + 379s 8s | 7 | lnL= -5436.2 | depth= 2/ 10 | improvements= 11 | delta_lnL= 18.3/ 64.2 379s 9s | 8 | lnL= -5431.6 | depth= 2/ 8 | improvements= 11 | delta_lnL= 1.0/ 64.2 380s 9s | 9 | lnL= -5469.7 | depth= 6/ 6 | improvements= 19 | delta_lnL= 8.3/ 64.2 380s 10s | 10 | lnL= -5445.2 | depth= 7/ 10 | improvements= 21 | delta_lnL= 31.9/ 36.5 381s 10s | 11 | lnL= -5439.6 | depth= 2/ 11 | improvements= 14 | delta_lnL= 2.5/ 36.5 381s 11s | 12 | lnL= -5425.2 | depth= 5/ 8 | improvements= 21 | delta_lnL= 5.8/ 36.5 382s 11s | 13 | lnL= -5428.2 | depth= 2/ 9 | improvements= 13 | delta_lnL= 3.5/ 36.5 382s 11s | 14 | lnL= -5437.2 | depth= 1/ 7 | improvements= 15 | delta_lnL= 0.0/ 63.8 382s 12s | 15 | lnL= -5438.8 | depth= 2/ 5 | improvements= 17 | delta_lnL= 3.8/ 63.8 382s 382s . Third round of optimization... 384s 385s 14s | 16 | lnL= -5421.1 | depth= 4/ 10 | improvements= 13 | delta_lnL= 5.5/ 100.0 | triple moves= 5 + 387s 15s | 17 | lnL= -5420.4 | depth= 1/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 389s 17s | 18 | lnL= -5420.3 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 389s 19s | 19 | lnL= -5420.3 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 389s 389s . Final optimisation steps... 390s 390s 390s . Log likelihood of the current tree: -5420.255724328937503742054104804992675781. 390s 390s . Calculating fast branch supports (using 'aBayes'). 390s 390s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 390s 390s . Time used 0h0m20s 390s 390s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 390s AA interleaved sequence file, default parameters using 2 processors: 390s + echo 'AA interleaved sequence file, default parameters using 2 processors:' 390s + /usr/bin/phyml -i proteic -d aa 390s 390s 390s . Running the analysis on 2 CPUs.. 390s 390s . Command line: /usr/lib/phyml/bin/phyml-mpi -i proteic -d aa 390s 390s 390s 390s 390s 390s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 390s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 391s 391s . Sequence filename: proteic 391s . Data type: aa 391s . Alphabet size: 20 391s . Sequence format: interleaved 391s . Number of data sets: 1 391s . Nb of bootstrapped data sets: 0 391s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 391s . Model name: LG 391s . Proportion of invariable sites: 0.000000 391s . RAS model: discrete Gamma 391s . Number of subst. rate catgs: 4 391s . Gamma distribution parameter: estimated 391s . 'Middle' of each rate class: mean 391s . Amino-acid equilibrium frequencies: empirical 391s . Optimise tree topology: yes 391s . Starting tree: BioNJ 391s . Add random input tree: no 391s . Optimise branch lengths: yes 391s . Minimum length of an edge: 1e-08 391s . Optimise substitution model parameters: yes 391s . Run ID: none 391s . Random seed: 1742057288 391s . Subtree patterns aliasing: no 391s . Version: 3.3.3:3.3.20220408-4build1 391s . Byte alignment: 1 391s . AVX enabled: no 391s . SSE enabled: no 391s 391s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 391s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 391s 391s 391s 391s . 429 patterns found (out of a total of 547 sites). 391s 391s . 136 sites without polymorphism (24.86%). 391s 391s 391s . Computing pairwise distances... 391s 391s . Building BioNJ tree... 391s 391s . This analysis requires at least 39 MB of memory space. 391s 391s 393s . Score of initial tree: -12569.85 393s 393s . Starting first round of SPRs... 404s 416s 13s | 1 | lnL= -12462.3 | depth= 1/ 40 | improvements= 17 | delta_lnL= 0.0/ 1000.0 426s 24s | 2 | lnL= -12475.1 | depth= 3/ 24 | improvements= 16 | delta_lnL= 19.3/ 1000.0 426s 35s | 3 | lnL= -12456.7 | depth= 1/ 14 | improvements= 13 | delta_lnL= 0.0/ 1000.0 426s 426s . Second round of optimization... 437s 447s 46s | 4 | lnL= -12461.1 | depth= 2/ 12 | improvements= 19 | delta_lnL= 4.0/ 1000.0 449s 56s | 5 | lnL= -12472.5 | depth= 3/ 9 | improvements= 13 | delta_lnL= 26.7/ 1000.0 451s 58s | 6 | lnL= -12458.0 | depth= 1/ 7 | improvements= 14 | delta_lnL= 0.0/ 20.0 454s 60s | 7 | lnL= -12477.3 | depth= 3/ 5 | improvements= 14 | delta_lnL= 3.7/ 20.0 456s 63s | 8 | lnL= -12497.3 | depth= 3/ 7 | improvements= 20 | delta_lnL= 40.8/ 20.0 460s 65s | 9 | lnL= -12473.2 | depth= 2/ 7 | improvements= 19 | delta_lnL= 7.1/ 20.0 464s 68s | 10 | lnL= -12477.3 | depth= 3/ 6 | improvements= 17 | delta_lnL= 18.7/ 81.6 467s 73s | 11 | lnL= -12556.3 | depth= 3/ 7 | improvements= 15 | delta_lnL= 132.8/ 81.6 470s 76s | 12 | lnL= -12489.7 | depth= 2/ 7 | improvements= 20 | delta_lnL= 73.2/ 81.6 470s 79s | 13 | lnL= -12457.0 | depth= 3/ 6 | improvements= 20 | delta_lnL= 11.6/ 81.6 470s 470s . Third round of optimization... 484s 499s 93s | 14 | lnL= -12443.5 | depth= 1/ 10 | improvements= 5 | delta_lnL= 0.0/ 265.5 | triple moves= 5 + 499s 108s | 15 | lnL= -12443.1 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 499s 499s . Final optimisation steps... 507s 507s 507s . Log likelihood of the current tree: -12443.049044394161683158017694950103759766. 507s 511s . Calculating fast branch supports (using 'aBayes'). 511s 511s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 511s 511s . Time used 0h2m0s 511s 511s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 511s AA sequential sequence file, with customization using 2 processors: 511s + echo 'AA sequential sequence file, with customization using 2 processors:' 511s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 512s 512s 512s . Running the analysis on 2 CPUs.. 512s 512s . Command line: /usr/lib/phyml/bin/phyml-mpi -i example.nex -d nt -c 4 -a e 512s 512s 512s 512s 512s 512s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 512s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 512s 512s . Sequence filename: example.nex 512s . Data type: dna 512s . Alphabet size: 4 512s . Sequence format: interleaved 512s . Number of data sets: 1 512s . Nb of bootstrapped data sets: 0 512s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 512s . Model name: HKY85 512s . Ts/tv ratio: estimated 512s . Proportion of invariable sites: 0.000000 512s . RAS model: discrete Gamma 512s . Number of subst. rate catgs: 4 512s . Gamma distribution parameter: estimated 512s . 'Middle' of each rate class: mean 512s . Nucleotide equilibrium frequencies: empirical 512s . Optimise tree topology: yes 512s . Starting tree: BioNJ 512s . Add random input tree: no 512s . Optimise branch lengths: yes 512s . Minimum length of an edge: 1e-08 512s . Optimise substitution model parameters: yes 512s . Run ID: none 512s . Random seed: 1742057409 512s . Subtree patterns aliasing: no 512s . Version: 3.3.3:3.3.20220408-4build1 512s . Byte alignment: 1 512s . AVX enabled: no 512s . SSE enabled: no 512s 512s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 512s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 512s 512s 512s 512s . 1037 patterns found (out of a total of 2888 sites). 512s 512s . 1378 sites without polymorphism (47.71%). 512s 512s 512s . Computing pairwise distances... 512s 512s . Building BioNJ tree... 512s 512s . This analysis requires at least 3 MB of memory space. 512s 512s 512s . Score of initial tree: -12664.54 512s 512s . Starting first round of SPRs... 512s 512s 1s | 1 | lnL= -12573.4 | depth= 1/ 40 | improvements= 1 | delta_lnL= 0.0/ 1000.0 512s 512s . Second round of optimization... 512s 512s 1s | 2 | lnL= -12645.8 | depth= 1/ 36 | improvements= 6 | delta_lnL= 0.0/ 1000.0 512s 1s | 3 | lnL= -12590.2 | depth= 1/ 20 | improvements= 3 | delta_lnL= 0.0/ 1000.0 512s 512s . Third round of optimization... 512s 512s 1s | 4 | lnL= -12563.9 | depth= 1/ 16 | improvements= 3 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 512s 1s | 5 | lnL= -12563.5 | depth= 0/ 12 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 512s 512s . Final optimisation steps... 513s 513s 513s . Log likelihood of the current tree: -12563.118859055624852771870791912078857422. 513s 513s . Calculating fast branch supports (using 'aBayes'). 513s 513s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 513s 513s . Time used 0h0m2s 513s 513s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 513s PASS 513s + echo PASS 513s autopkgtest [16:50:11]: test run-unit-test: -----------------------] 514s autopkgtest [16:50:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 514s run-unit-test PASS 515s autopkgtest [16:50:13]: @@@@@@@@@@@@@@@@@@@@ summary 515s run-unit-test PASS 520s nova [W] Using flock in prodstack6-s390x 520s Creating nova instance adt-plucky-s390x-phyml-20250315-164137-juju-7f2275-prod-proposed-migration-environment-2-e81c5af3-f7a7-4c54-8f28-b1f53fc32a7b from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 520s nova [W] Timed out waiting for 94adb626-14a9-4851-84a8-553d1b4a36ac to get deleted.