0s autopkgtest [14:21:17]: starting date and time: 2025-03-15 14:21:17+0000 0s autopkgtest [14:21:17]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:21:17]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.is2vkjg6/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-32.secgroup --name adt-plucky-arm64-phyml-20250315-142117-juju-7f2275-prod-proposed-migration-environment-20-9f357b92-a717-4e26-97ff-8b47c16939e4 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 166s autopkgtest [14:24:03]: testbed dpkg architecture: arm64 166s autopkgtest [14:24:03]: testbed apt version: 2.9.33 167s autopkgtest [14:24:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 167s autopkgtest [14:24:04]: testbed release detected to be: None 168s autopkgtest [14:24:05]: updating testbed package index (apt update) 168s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 168s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 168s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 169s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 169s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 169s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 169s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 169s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 169s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 169s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 169s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 170s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 170s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 170s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 170s Fetched 1094 kB in 2s (607 kB/s) 171s Reading package lists... 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s Calculating upgrade... 173s Calculating upgrade... 174s The following packages will be upgraded: 174s python3-jinja2 strace 174s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 608 kB of archives. 174s After this operation, 11.3 kB of additional disk space will be used. 174s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 175s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 175s Fetched 608 kB in 1s (489 kB/s) 176s (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 ... 117701 files and directories currently installed.) 176s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 176s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 176s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 176s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 176s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 176s Setting up strace (6.13+ds-1ubuntu1) ... 176s Processing triggers for man-db (2.13.0-1) ... 177s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Solving dependencies... 179s The following packages will be REMOVED: 179s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 179s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 179s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 179s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 179s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 179s After this operation, 267 MB disk space will be freed. 179s (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 ... 117701 files and directories currently installed.) 179s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 179s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 179s Removing libpython3.12t64:arm64 (3.12.9-1) ... 179s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 179s Removing libnsl2:arm64 (1.3.0-3build3) ... 179s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 180s Removing libunwind8:arm64 (1.6.2-3.1) ... 180s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 180s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 182s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 182s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 182s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 182s /etc/kernel/postrm.d/initramfs-tools: 182s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 182s /etc/kernel/postrm.d/zz-flash-kernel: 182s flash-kernel: Kernel 6.11.0-8-generic has been removed. 182s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 183s /etc/kernel/postrm.d/zz-update-grub: 183s Sourcing file `/etc/default/grub' 183s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 183s Generating grub configuration file ... 183s Found linux image: /boot/vmlinuz-6.14.0-10-generic 183s Found initrd image: /boot/initrd.img-6.14.0-10-generic 184s Warning: os-prober will not be executed to detect other bootable partitions. 184s Systems on them will not be added to the GRUB boot configuration. 184s Check GRUB_DISABLE_OS_PROBER documentation entry. 184s Adding boot menu entry for UEFI Firmware Settings ... 184s done 184s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 184s Processing triggers for libc-bin (2.41-1ubuntu1) ... 184s (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 ... 81650 files and directories currently installed.) 184s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 184s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 184s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 185s autopkgtest [14:24:22]: upgrading testbed (apt dist-upgrade and autopurge) 185s Reading package lists... 185s Building dependency tree... 185s Reading state information... 186s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 186s Starting 2 pkgProblemResolver with broken count: 0 186s Done 188s Entering ResolveByKeep 188s 189s Calculating upgrade... 190s The following packages will be upgraded: 190s libc-bin libc-dev-bin libc6 libc6-dev locales 190s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Need to get 9530 kB of archives. 190s After this operation, 0 B of additional disk space will be used. 190s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 192s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 195s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 196s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 200s Preconfiguring packages ... 200s Fetched 9530 kB in 10s (981 kB/s) 200s (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 ... 81647 files and directories currently installed.) 200s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc6:arm64 (2.41-1ubuntu2) ... 201s (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 ... 81647 files and directories currently installed.) 201s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc-bin (2.41-1ubuntu2) ... 202s (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 ... 81647 files and directories currently installed.) 202s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 202s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 202s Setting up locales (2.41-1ubuntu2) ... 203s Generating locales (this might take a while)... 205s en_US.UTF-8... done 205s Generation complete. 205s Setting up libc-dev-bin (2.41-1ubuntu2) ... 205s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 205s Processing triggers for man-db (2.13.0-1) ... 206s Processing triggers for systemd (257.3-1ubuntu3) ... 207s Reading package lists... 208s Building dependency tree... 208s Reading state information... 209s Starting pkgProblemResolver with broken count: 0 209s Starting 2 pkgProblemResolver with broken count: 0 209s Done 210s Solving dependencies... 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s autopkgtest [14:24:48]: rebooting testbed after setup commands that affected boot 234s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 241s autopkgtest [14:25:18]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 244s autopkgtest [14:25:21]: @@@@@@@@@@@@@@@@@@@@ apt-source phyml 247s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (dsc) [2131 B] 247s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (tar) [1804 kB] 247s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (diff) [27.1 kB] 248s gpgv: Signature made Sat Nov 30 06:14:54 2024 UTC 248s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 248s gpgv: Can't check signature: No public key 248s dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-4build1.dsc: no acceptable signature found 248s autopkgtest [14:25:25]: testing package phyml version 3:3.3.20220408-4build1 248s autopkgtest [14:25:25]: build not needed 249s autopkgtest [14:25:26]: test run-unit-test: preparing testbed 249s Reading package lists... 250s Building dependency tree... 250s Reading state information... 251s Starting pkgProblemResolver with broken count: 0 251s Starting 2 pkgProblemResolver with broken count: 0 251s Done 253s The following NEW packages will be installed: 253s libamd-comgr2 libamdhip64-5 libevent-pthreads-2.1-7t64 libfabric1 libgomp1 253s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 253s libibumad3 libllvm17t64 libmunge2 libopenmpi40 libpciaccess0 libpmix2t64 253s librdmacm1t64 libucx0 libxnvctrl0 mpi-default-bin ocl-icd-libopencl1 253s openmpi-bin openmpi-common phyml 253s 0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. 253s Need to get 55.7 MB of archives. 253s After this operation, 234 MB of additional disk space will be used. 253s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-21 [24.9 MB] 273s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 285s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 285s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 285s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5 [9704 kB] 294s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 294s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 55.0-1ubuntu1 [71.5 kB] 294s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3.1 [542 kB] 295s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 295s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.12.0-1 [162 kB] 295s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB] 295s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 295s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 295s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 295s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.12.0-1 [15.9 kB] 295s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.6-5 [666 kB] 296s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 55.0-1ubuntu1 [29.8 kB] 296s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 55.0-1ubuntu1 [43.3 kB] 296s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.18.1+ds-2 [1161 kB] 297s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmpi40 arm64 5.0.7-1 [2419 kB] 300s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 openmpi-common all 5.0.7-1 [97.9 kB] 300s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 openmpi-bin arm64 5.0.7-1 [195 kB] 300s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 mpi-default-bin arm64 1.18 [2510 B] 300s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 phyml arm64 3:3.3.20220408-4build1 [983 kB] 301s Fetched 55.7 MB in 48s (1165 kB/s) 302s Selecting previously unselected package libllvm17t64:arm64. 302s (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 ... 81647 files and directories currently installed.) 302s Preparing to unpack .../00-libllvm17t64_1%3a17.0.6-21_arm64.deb ... 302s Unpacking libllvm17t64:arm64 (1:17.0.6-21) ... 303s Selecting previously unselected package libamd-comgr2:arm64. 303s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 303s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 303s Selecting previously unselected package libhsakmt1:arm64. 303s Preparing to unpack .../02-libhsakmt1_5.7.0-1build1_arm64.deb ... 303s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 303s Selecting previously unselected package libhsa-runtime64-1. 304s Preparing to unpack .../03-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 304s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 304s Selecting previously unselected package libamdhip64-5. 304s Preparing to unpack .../04-libamdhip64-5_5.7.1-5_arm64.deb ... 304s Unpacking libamdhip64-5 (5.7.1-5) ... 304s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 304s Preparing to unpack .../05-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 304s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 304s Selecting previously unselected package librdmacm1t64:arm64. 304s Preparing to unpack .../06-librdmacm1t64_55.0-1ubuntu1_arm64.deb ... 304s Unpacking librdmacm1t64:arm64 (55.0-1ubuntu1) ... 304s Selecting previously unselected package libfabric1:arm64. 304s Preparing to unpack .../07-libfabric1_1.17.0-3.1_arm64.deb ... 304s Unpacking libfabric1:arm64 (1.17.0-3.1) ... 304s Selecting previously unselected package libgomp1:arm64. 304s Preparing to unpack .../08-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 304s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 304s Selecting previously unselected package libhwloc15:arm64. 304s Preparing to unpack .../09-libhwloc15_2.12.0-1_arm64.deb ... 304s Unpacking libhwloc15:arm64 (2.12.0-1) ... 304s Selecting previously unselected package libmunge2:arm64. 304s Preparing to unpack .../10-libmunge2_0.5.16-1_arm64.deb ... 304s Unpacking libmunge2:arm64 (0.5.16-1) ... 304s Selecting previously unselected package libpciaccess0:arm64. 304s Preparing to unpack .../11-libpciaccess0_0.17-3build1_arm64.deb ... 304s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 304s Selecting previously unselected package libxnvctrl0:arm64. 304s Preparing to unpack .../12-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 304s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 304s Selecting previously unselected package ocl-icd-libopencl1:arm64. 304s Preparing to unpack .../13-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ... 304s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 304s Selecting previously unselected package libhwloc-plugins:arm64. 304s Preparing to unpack .../14-libhwloc-plugins_2.12.0-1_arm64.deb ... 304s Unpacking libhwloc-plugins:arm64 (2.12.0-1) ... 304s Selecting previously unselected package libpmix2t64:arm64. 304s Preparing to unpack .../15-libpmix2t64_5.0.6-5_arm64.deb ... 304s Unpacking libpmix2t64:arm64 (5.0.6-5) ... 304s Selecting previously unselected package libibumad3:arm64. 304s Preparing to unpack .../16-libibumad3_55.0-1ubuntu1_arm64.deb ... 304s Unpacking libibumad3:arm64 (55.0-1ubuntu1) ... 305s Selecting previously unselected package libibmad5:arm64. 305s Preparing to unpack .../17-libibmad5_55.0-1ubuntu1_arm64.deb ... 305s Unpacking libibmad5:arm64 (55.0-1ubuntu1) ... 305s Selecting previously unselected package libucx0:arm64. 305s Preparing to unpack .../18-libucx0_1.18.1+ds-2_arm64.deb ... 305s Unpacking libucx0:arm64 (1.18.1+ds-2) ... 305s Selecting previously unselected package libopenmpi40:arm64. 305s Preparing to unpack .../19-libopenmpi40_5.0.7-1_arm64.deb ... 305s Unpacking libopenmpi40:arm64 (5.0.7-1) ... 305s Selecting previously unselected package openmpi-common. 305s Preparing to unpack .../20-openmpi-common_5.0.7-1_all.deb ... 305s Unpacking openmpi-common (5.0.7-1) ... 305s Selecting previously unselected package openmpi-bin. 305s Preparing to unpack .../21-openmpi-bin_5.0.7-1_arm64.deb ... 305s Unpacking openmpi-bin (5.0.7-1) ... 305s Selecting previously unselected package mpi-default-bin. 305s Preparing to unpack .../22-mpi-default-bin_1.18_arm64.deb ... 305s Unpacking mpi-default-bin (1.18) ... 305s Selecting previously unselected package phyml. 305s Preparing to unpack .../23-phyml_3%3a3.3.20220408-4build1_arm64.deb ... 305s Unpacking phyml (3:3.3.20220408-4build1) ... 305s Setting up libpciaccess0:arm64 (0.17-3build1) ... 305s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 305s Setting up libibumad3:arm64 (55.0-1ubuntu1) ... 305s Setting up libibmad5:arm64 (55.0-1ubuntu1) ... 305s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 305s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 305s Setting up libmunge2:arm64 (0.5.16-1) ... 305s Setting up libllvm17t64:arm64 (1:17.0.6-21) ... 305s Setting up libhwloc15:arm64 (2.12.0-1) ... 305s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 305s Setting up openmpi-common (5.0.7-1) ... 305s Setting up librdmacm1t64:arm64 (55.0-1ubuntu1) ... 305s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 305s Setting up libhsakmt1:arm64 (5.7.0-1build1) ... 305s Setting up libfabric1:arm64 (1.17.0-3.1) ... 305s Setting up libhwloc-plugins:arm64 (2.12.0-1) ... 305s Setting up libpmix2t64:arm64 (5.0.6-5) ... 305s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 305s Setting up libamdhip64-5 (5.7.1-5) ... 305s Setting up libucx0:arm64 (1.18.1+ds-2) ... 305s Setting up libopenmpi40:arm64 (5.0.7-1) ... 305s Setting up openmpi-bin (5.0.7-1) ... 305s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 305s 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 305s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 305s Setting up mpi-default-bin (1.18) ... 305s Setting up phyml (3:3.3.20220408-4build1) ... 305s Processing triggers for man-db (2.13.0-1) ... 306s Processing triggers for libc-bin (2.41-1ubuntu2) ... 308s autopkgtest [14:26:25]: test run-unit-test: [----------------------- 308s + export PHYMLCPUS=1 308s + PHYMLCPUS=1 308s + echo 'DNA interleaved sequence file, default parameters single processor:' 308s + /usr/bin/phyml -i nucleic 308s DNA interleaved sequence file, default parameters single processor: 308s 308s 308s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 308s 308s 308s 308s 308s 308s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 308s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 308s 308s . Sequence filename: nucleic 308s . Data type: dna 308s . Alphabet size: 4 308s . Sequence format: interleaved 308s . Number of data sets: 1 308s . Nb of bootstrapped data sets: 0 308s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 308s . Model name: HKY85 308s . Ts/tv ratio: estimated 308s . Proportion of invariable sites: 0.000000 308s . RAS model: discrete Gamma 308s . Number of subst. rate catgs: 4 308s . Gamma distribution parameter: estimated 308s . 'Middle' of each rate class: mean 308s . Nucleotide equilibrium frequencies: empirical 308s . Optimise tree topology: yes 308s . Starting tree: BioNJ 308s . Add random input tree: no 308s . Optimise branch lengths: yes 308s . Minimum length of an edge: 1e-08 308s . Optimise substitution model parameters: yes 308s . Run ID: none 308s . Random seed: 1742048785 308s . Subtree patterns aliasing: no 308s . Version: 3.3.3:3.3.20220408-4build1 308s . Byte alignment: 1 308s . AVX enabled: no 308s . SSE enabled: no 308s 308s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 308s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 308s 308s 308s 308s . 382 patterns found (out of a total of 886 sites). 308s 308s . 582 sites without polymorphism (65.69%). 308s 308s 308s . Computing pairwise distances... 308s 308s . Building BioNJ tree... 308s 308s . This analysis requires at least 11 MB of memory space. 308s 308s 308s . Score of initial tree: -5680.04 308s 308s . Starting first round of SPRs... 311s 311s 2s | 1 | lnL= -5445.2 | depth= 1/ 40 | improvements= 9 | delta_lnL= 0.0/ 1000.0 311s 311s . Second round of optimization... 312s 313s 4s | 2 | lnL= -5439.6 | depth= 5/ 36 | improvements= 19 | delta_lnL= 10.8/ 1000.0 314s 5s | 3 | lnL= -5443.8 | depth= 1/ 20 | improvements= 16 | delta_lnL= 0.0/ 1000.0 316s 6s | 4 | lnL= -5435.4 | depth= 2/ 16 | improvements= 16 | delta_lnL= 3.2/ 1000.0 316s 8s | 5 | lnL= -5434.4 | depth= 2/ 12 | improvements= 17 | delta_lnL= 3.6/ 1000.0 317s 8s | 6 | lnL= -5426.2 | depth= 2/ 9 | improvements= 23 | delta_lnL= 16.5/ 21.6 + 317s 9s | 7 | lnL= -5443.3 | depth= 2/ 7 | improvements= 24 | delta_lnL= 12.2/ 21.6 317s 9s | 8 | lnL= -5430.0 | depth= 1/ 6 | improvements= 19 | delta_lnL= 0.0/ 21.6 318s 9s | 9 | lnL= -5436.6 | depth= 2/ 5 | improvements= 16 | delta_lnL= 15.7/ 21.6 319s 10s | 10 | lnL= -5449.6 | depth= 4/ 6 | improvements= 14 | delta_lnL= 5.6/ 33.1 319s 10s | 11 | lnL= -5428.0 | depth= 2/ 8 | improvements= 18 | delta_lnL= 20.7/ 33.1 319s 11s | 12 | lnL= -5428.0 | depth= 2/ 6 | improvements= 16 | delta_lnL= 9.0/ 33.1 320s 11s | 13 | lnL= -5430.7 | depth= 2/ 6 | improvements= 13 | delta_lnL= 3.1/ 33.1 320s 12s | 14 | lnL= -5443.4 | depth= 1/ 6 | improvements= 15 | delta_lnL= 0.0/ 41.5 320s 12s | 15 | lnL= -5435.5 | depth= 2/ 5 | improvements= 15 | delta_lnL= 20.2/ 41.5 320s 320s . Third round of optimization... 322s 324s 14s | 16 | lnL= -5421.3 | depth= 2/ 10 | improvements= 9 | delta_lnL= 4.5/ 100.0 | triple moves= 5 + 326s 16s | 17 | lnL= -5420.5 | depth= 1/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 328s 18s | 18 | lnL= -5420.3 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 328s 20s | 19 | lnL= -5420.3 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 328s 328s . Final optimisation steps... 329s 329s 329s . Log likelihood of the current tree: -5420.255822139890369726344943046569824219. 329s 329s . Calculating fast branch supports (using 'aBayes'). 329s 329s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 329s 329s . Time used 0h0m21s 329s 329s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 329s AA interleaved sequence file, default parameters single processor: 329s + echo 'AA interleaved sequence file, default parameters single processor:' 329s + /usr/bin/phyml -i proteic -d aa 329s 329s 329s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 329s 329s 329s 329s 329s 329s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 329s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 329s 329s . Sequence filename: proteic 329s . Data type: aa 329s . Alphabet size: 20 329s . Sequence format: interleaved 329s . Number of data sets: 1 329s . Nb of bootstrapped data sets: 0 329s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 329s . Model name: LG 329s . Proportion of invariable sites: 0.000000 329s . RAS model: discrete Gamma 329s . Number of subst. rate catgs: 4 329s . Gamma distribution parameter: estimated 329s . 'Middle' of each rate class: mean 329s . Amino-acid equilibrium frequencies: empirical 329s . Optimise tree topology: yes 329s . Starting tree: BioNJ 329s . Add random input tree: no 329s . Optimise branch lengths: yes 329s . Minimum length of an edge: 1e-08 329s . Optimise substitution model parameters: yes 329s . Run ID: none 329s . Random seed: 1742048806 329s . Subtree patterns aliasing: no 329s . Version: 3.3.3:3.3.20220408-4build1 329s . Byte alignment: 1 329s . AVX enabled: no 329s . SSE enabled: no 329s 329s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 329s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 329s 329s 329s 329s . 429 patterns found (out of a total of 547 sites). 329s 329s . 136 sites without polymorphism (24.86%). 329s 329s 330s . Computing pairwise distances... 330s 330s . Building BioNJ tree... 330s 330s . This analysis requires at least 39 MB of memory space. 330s 330s 333s . Score of initial tree: -12569.85 333s 333s . Starting first round of SPRs... 344s 355s 14s | 1 | lnL= -12483.9 | depth= 2/ 40 | improvements= 22 | delta_lnL= 33.9/ 1000.0 355s 25s | 2 | lnL= -12502.3 | depth= 2/ 24 | improvements= 14 | delta_lnL= 12.2/ 1000.0 355s 355s . Second round of optimization... 366s 377s 36s | 3 | lnL= -12470.2 | depth= 1/ 21 | improvements= 15 | delta_lnL= 0.0/ 1000.0 388s 47s | 4 | lnL= -12511.9 | depth= 1/ 16 | improvements= 15 | delta_lnL= 0.0/ 1000.0 391s 58s | 5 | lnL= -12468.6 | depth= 1/ 12 | improvements= 16 | delta_lnL= 0.0/ 1000.0 393s 61s | 6 | lnL= -12478.4 | depth= 4/ 9 | improvements= 15 | delta_lnL= 41.7/ 20.0 395s 63s | 7 | lnL= -12475.6 | depth= 2/ 8 | improvements= 15 | delta_lnL= 16.2/ 20.0 398s 65s | 8 | lnL= -12502.0 | depth= 3/ 6 | improvements= 17 | delta_lnL= 16.1/ 20.0 401s 68s | 9 | lnL= -12503.4 | depth= 3/ 7 | improvements= 18 | delta_lnL= 14.0/ 20.0 408s 71s | 10 | lnL= -12506.6 | depth= 3/ 7 | improvements= 22 | delta_lnL= 49.2/ 83.5 411s 78s | 11 | lnL= -12456.5 | depth= 2/ 7 | improvements= 26 | delta_lnL= 23.6/ 83.5 411s 81s | 12 | lnL= -12475.6 | depth= 2/ 6 | improvements= 21 | delta_lnL= 14.0/ 83.5 411s 411s . Third round of optimization... 422s 432s 91s | 13 | lnL= -12445.4 | depth= 2/ 10 | improvements= 9 | delta_lnL= 3.6/ 100.0 | triple moves= 5 + 448s 102s | 14 | lnL= -12443.4 | depth= 1/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 6 + 448s 117s | 15 | lnL= -12443.1 | depth= 0/ 6 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 448s 448s . Final optimisation steps... 455s 455s 455s . Log likelihood of the current tree: -12443.048991404908520053140819072723388672. 455s 459s . Calculating fast branch supports (using 'aBayes'). 459s 459s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 459s 459s . Time used 0h2m9s 459s 459s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 459s + echo 'AA sequential sequence file, with customization single processor:' 459s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 459s AA sequential sequence file, with customization single processor: 459s 459s 459s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 459s 459s 459s 459s 459s 459s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 459s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 459s 459s . Sequence filename: example.nex 459s . Data type: dna 459s . Alphabet size: 4 459s . Sequence format: interleaved 459s . Number of data sets: 1 459s . Nb of bootstrapped data sets: 0 459s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 459s . Model name: HKY85 459s . Ts/tv ratio: estimated 459s . Proportion of invariable sites: 0.000000 459s . RAS model: discrete Gamma 459s . Number of subst. rate catgs: 4 459s . Gamma distribution parameter: estimated 459s . 'Middle' of each rate class: mean 459s . Nucleotide equilibrium frequencies: empirical 459s . Optimise tree topology: yes 459s . Starting tree: BioNJ 459s . Add random input tree: no 459s . Optimise branch lengths: yes 459s . Minimum length of an edge: 1e-08 459s . Optimise substitution model parameters: yes 459s . Run ID: none 459s . Random seed: 1742048936 459s . Subtree patterns aliasing: no 459s . Version: 3.3.3:3.3.20220408-4build1 459s . Byte alignment: 1 459s . AVX enabled: no 459s . SSE enabled: no 459s 459s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 459s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 459s 459s 459s 459s . 1037 patterns found (out of a total of 2888 sites). 459s 459s . 1378 sites without polymorphism (47.71%). 459s 459s 459s . Computing pairwise distances... 459s 459s . Building BioNJ tree... 459s 459s . This analysis requires at least 3 MB of memory space. 459s 459s 459s . Score of initial tree: -12664.54 459s 459s . Starting first round of SPRs... 460s 460s 0s | 1 | lnL= -12580.8 | depth= 1/ 40 | improvements= 3 | delta_lnL= 0.0/ 1000.0 460s 460s . Second round of optimization... 460s 460s 1s | 2 | lnL= -12592.8 | depth= 1/ 36 | improvements= 3 | delta_lnL= 0.0/ 1000.0 460s 460s . Third round of optimization... 460s 460s 1s | 3 | lnL= -12564.0 | depth= 1/ 20 | improvements= 4 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 460s 1s | 4 | lnL= -12563.5 | depth= 0/ 16 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 460s 460s . Final optimisation steps... 460s 460s 460s . Log likelihood of the current tree: -12563.118859055624852771870791912078857422. 460s 461s . Calculating fast branch supports (using 'aBayes'). 461s 461s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 461s 461s . Time used 0h0m2s 461s 461s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 461s + export PHYMLCPUS=2 461s + PHYMLCPUS=2 461s + echo 'DNA interleaved sequence file, default parameters using 2 processors:' 461s + /usr/bin/phyml -i nucleic 461s DNA interleaved sequence file, default parameters using 2 processors: 461s 461s 461s . Running the analysis on 2 CPUs.. 461s 461s . Command line: /usr/lib/phyml/bin/phyml-mpi -i nucleic 461s 461s 461s 461s 461s 461s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 461s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 461s 461s . Sequence filename: nucleic 461s . Data type: dna 461s . Alphabet size: 4 461s . Sequence format: interleaved 461s . Number of data sets: 1 461s . Nb of bootstrapped data sets: 0 461s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 461s . Model name: HKY85 461s . Ts/tv ratio: estimated 461s . Proportion of invariable sites: 0.000000 461s . RAS model: discrete Gamma 461s . Number of subst. rate catgs: 4 461s . Gamma distribution parameter: estimated 461s . 'Middle' of each rate class: mean 461s . Nucleotide equilibrium frequencies: empirical 461s . Optimise tree topology: yes 461s . Starting tree: BioNJ 461s . Add random input tree: no 461s . Optimise branch lengths: yes 461s . Minimum length of an edge: 1e-08 461s . Optimise substitution model parameters: yes 461s . Run ID: none 461s . Random seed: 1742048938 461s . Subtree patterns aliasing: no 461s . Version: 3.3.3:3.3.20220408-4build1 461s . Byte alignment: 1 461s . AVX enabled: no 461s . SSE enabled: no 461s 461s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 461s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 461s 461s 461s 461s . 382 patterns found (out of a total of 886 sites). 461s 461s . 582 sites without polymorphism (65.69%). 461s 461s 461s . Computing pairwise distances... 461s 461s . Building BioNJ tree... 461s 461s . This analysis requires at least 11 MB of memory space. 461s 461s 461s . Score of initial tree: -5680.04 461s 461s . Starting first round of SPRs... 463s 463s 2s | 1 | lnL= -5424.4 | depth= 8/ 40 | improvements= 9 | delta_lnL= 10.4/ 1000.0 + 463s 463s . Second round of optimization... 465s 466s 4s | 2 | lnL= -5437.1 | depth= 2/ 36 | improvements= 19 | delta_lnL= 9.1/ 1000.0 467s 5s | 3 | lnL= -5438.2 | depth= 2/ 20 | improvements= 25 | delta_lnL= 14.4/ 1000.0 468s 6s | 4 | lnL= -5448.4 | depth= 7/ 16 | improvements= 20 | delta_lnL= 27.2/ 1000.0 469s 7s | 5 | lnL= -5440.2 | depth= 5/ 12 | improvements= 23 | delta_lnL= 21.2/ 1000.0 469s 8s | 6 | lnL= -5429.3 | depth= 1/ 9 | improvements= 5 | delta_lnL= 0.0/ 54.4 469s 469s . Third round of optimization... 470s 472s 9s | 7 | lnL= -5421.5 | depth= 3/ 10 | improvements= 4 | delta_lnL= 5.4/ 100.0 | triple moves= 5 + 474s 11s | 8 | lnL= -5420.8 | depth= 3/ 8 | improvements= 1 | delta_lnL= 5.3/ 100.0 | triple moves= 5 + 476s 13s | 9 | lnL= -5420.7 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 476s 15s | 10 | lnL= -5420.7 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 476s 476s . Final optimisation steps... 477s 477s 477s . Log likelihood of the current tree: -5420.255827210783536429516971111297607422. 477s 477s . Calculating fast branch supports (using 'aBayes'). 477s 477s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 477s 477s . Time used 0h0m16s 477s 477s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 477s AA interleaved sequence file, default parameters using 2 processors: 477s + echo 'AA interleaved sequence file, default parameters using 2 processors:' 477s + /usr/bin/phyml -i proteic -d aa 478s 478s 478s . Running the analysis on 2 CPUs.. 478s 478s . Command line: /usr/lib/phyml/bin/phyml-mpi -i proteic -d aa 478s 478s 478s 478s 478s 478s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 478s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 478s 478s . Sequence filename: proteic 478s . Data type: aa 478s . Alphabet size: 20 478s . Sequence format: interleaved 478s . Number of data sets: 1 478s . Nb of bootstrapped data sets: 0 478s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 478s . Model name: LG 478s . Proportion of invariable sites: 0.000000 478s . RAS model: discrete Gamma 478s . Number of subst. rate catgs: 4 478s . Gamma distribution parameter: estimated 478s . 'Middle' of each rate class: mean 478s . Amino-acid equilibrium frequencies: empirical 478s . Optimise tree topology: yes 478s . Starting tree: BioNJ 478s . Add random input tree: no 478s . Optimise branch lengths: yes 478s . Minimum length of an edge: 1e-08 478s . Optimise substitution model parameters: yes 478s . Run ID: none 478s . Random seed: 1742048955 478s . Subtree patterns aliasing: no 478s . Version: 3.3.3:3.3.20220408-4build1 478s . Byte alignment: 1 478s . AVX enabled: no 478s . SSE enabled: no 478s 478s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 478s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 478s 478s 478s 478s . 429 patterns found (out of a total of 547 sites). 478s 478s . 136 sites without polymorphism (24.86%). 478s 478s 478s . Computing pairwise distances... 478s 478s . Building BioNJ tree... 478s 478s . This analysis requires at least 39 MB of memory space. 478s 478s 480s . Score of initial tree: -12569.85 480s 480s . Starting first round of SPRs... 491s 501s 13s | 1 | lnL= -12516.2 | depth= 4/ 40 | improvements= 26 | delta_lnL= 38.8/ 1000.0 511s 23s | 2 | lnL= -12484.6 | depth= 2/ 24 | improvements= 18 | delta_lnL= 6.4/ 1000.0 511s 33s | 3 | lnL= -12485.9 | depth= 2/ 14 | improvements= 14 | delta_lnL= 20.1/ 1000.0 511s 511s . Second round of optimization... 522s 531s 44s | 4 | lnL= -12451.1 | depth= 1/ 12 | improvements= 20 | delta_lnL= 0.0/ 1000.0 + 534s 53s | 5 | lnL= -12477.8 | depth= 1/ 9 | improvements= 21 | delta_lnL= 0.0/ 1000.0 536s 56s | 6 | lnL= -12507.1 | depth= 2/ 7 | improvements= 20 | delta_lnL= 12.9/ 20.0 538s 58s | 7 | lnL= -12473.8 | depth= 1/ 6 | improvements= 22 | delta_lnL= 0.0/ 20.0 540s 60s | 8 | lnL= -12477.6 | depth= 3/ 5 | improvements= 14 | delta_lnL= 11.2/ 20.0 543s 62s | 9 | lnL= -12452.2 | depth= 2/ 7 | improvements= 16 | delta_lnL= 45.5/ 20.0 548s 65s | 10 | lnL= -12479.1 | depth= 1/ 6 | improvements= 13 | delta_lnL= 0.0/ 25.9 550s 70s | 11 | lnL= -12450.3 | depth= 1/ 5 | improvements= 14 | delta_lnL= 0.0/ 25.9 + 553s 72s | 12 | lnL= -12475.5 | depth= 2/ 5 | improvements= 12 | delta_lnL= 10.6/ 25.9 555s 75s | 13 | lnL= -12476.3 | depth= 2/ 6 | improvements= 20 | delta_lnL= 17.5/ 25.9 558s 77s | 14 | lnL= -12472.7 | depth= 3/ 6 | improvements= 23 | delta_lnL= 20.7/ 21.3 560s 80s | 15 | lnL= -12467.8 | depth= 1/ 7 | improvements= 20 | delta_lnL= 0.0/ 21.3 562s 82s | 16 | lnL= -12457.1 | depth= 2/ 5 | improvements= 13 | delta_lnL= 8.2/ 21.3 565s 84s | 17 | lnL= -12466.5 | depth= 2/ 6 | improvements= 17 | delta_lnL= 14.4/ 21.3 567s 87s | 18 | lnL= -12490.6 | depth= 2/ 6 | improvements= 22 | delta_lnL= 30.7/ 41.5 569s 89s | 19 | lnL= -12482.6 | depth= 2/ 6 | improvements= 13 | delta_lnL= 32.7/ 41.5 575s 91s | 20 | lnL= -12448.9 | depth= 1/ 6 | improvements= 13 | delta_lnL= 0.0/ 41.5 + 578s 97s | 21 | lnL= -12453.5 | depth= 4/ 5 | improvements= 14 | delta_lnL= 40.2/ 41.5 581s 100s | 22 | lnL= -12469.0 | depth= 1/ 8 | improvements= 14 | delta_lnL= 0.0/ 65.5 584s 103s | 23 | lnL= -12483.1 | depth= 2/ 6 | improvements= 19 | delta_lnL= 22.3/ 65.5 586s 105s | 24 | lnL= -12449.3 | depth= 2/ 6 | improvements= 14 | delta_lnL= 27.4/ 65.5 589s 108s | 25 | lnL= -12453.5 | depth= 2/ 6 | improvements= 14 | delta_lnL= 15.7/ 65.5 591s 111s | 26 | lnL= -12470.5 | depth= 2/ 6 | improvements= 14 | delta_lnL= 12.8/ 54.7 594s 113s | 27 | lnL= -12466.4 | depth= 1/ 6 | improvements= 13 | delta_lnL= 0.0/ 54.7 597s 116s | 28 | lnL= -12480.8 | depth= 3/ 5 | improvements= 14 | delta_lnL= 59.6/ 54.7 597s 119s | 29 | lnL= -12467.7 | depth= 3/ 7 | improvements= 22 | delta_lnL= 101.6/ 54.7 597s 597s . Third round of optimization... 607s 620s 129s | 30 | lnL= -12444.6 | depth= 3/ 10 | improvements= 8 | delta_lnL= 14.7/ 119.1 | triple moves= 5 + 634s 142s | 31 | lnL= -12443.1 | depth= 1/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 634s 156s | 32 | lnL= -12443.0 | depth= 0/ 6 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 634s 634s . Final optimisation steps... 641s 641s 641s . Log likelihood of the current tree: -12443.048577921514151967130601406097412109. 641s 645s . Calculating fast branch supports (using 'aBayes'). 645s 645s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 645s 645s . Time used 0h2m47s 645s 645s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 645s + echo 'AA sequential sequence file, with customization using 2 processors:' 645s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 645s AA sequential sequence file, with customization using 2 processors: 645s 645s 645s . Running the analysis on 2 CPUs.. 645s 645s . Command line: /usr/lib/phyml/bin/phyml-mpi -i example.nex -d nt -c 4 -a e 645s 645s 645s 645s 645s 645s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 645s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 645s 645s . Sequence filename: example.nex 645s . Data type: dna 645s . Alphabet size: 4 645s . Sequence format: interleaved 645s . Number of data sets: 1 645s . Nb of bootstrapped data sets: 0 645s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 645s . Model name: HKY85 645s . Ts/tv ratio: estimated 645s . Proportion of invariable sites: 0.000000 645s . RAS model: discrete Gamma 645s . Number of subst. rate catgs: 4 645s . Gamma distribution parameter: estimated 645s . 'Middle' of each rate class: mean 645s . Nucleotide equilibrium frequencies: empirical 645s . Optimise tree topology: yes 645s . Starting tree: BioNJ 645s . Add random input tree: no 645s . Optimise branch lengths: yes 645s . Minimum length of an edge: 1e-08 645s . Optimise substitution model parameters: yes 645s . Run ID: none 645s . Random seed: 1742049122 645s . Subtree patterns aliasing: no 645s . Version: 3.3.3:3.3.20220408-4build1 645s . Byte alignment: 1 645s . AVX enabled: no 645s . SSE enabled: no 645s 645s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 645s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 645s 645s 645s 645s . 1037 patterns found (out of a total of 2888 sites). 645s 645s . 1378 sites without polymorphism (47.71%). 645s 645s 645s . Computing pairwise distances... 645s 645s . Building BioNJ tree... 645s 645s . This analysis requires at least 3 MB of memory space. 645s 645s 645s . Score of initial tree: -12664.54 645s 645s . Starting first round of SPRs... 645s 645s 0s | 1 | lnL= -12584.2 | depth= 1/ 40 | improvements= 2 | delta_lnL= 0.0/ 1000.0 645s 645s . Second round of optimization... 645s 645s 0s | 2 | lnL= -12571.5 | depth= 1/ 36 | improvements= 5 | delta_lnL= 0.0/ 1000.0 645s 645s . Third round of optimization... 647s 647s + echo PASS 647s 1s | 3 | lnL= -12563.5 | depth= 0/ 20 | improvements= 0 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 647s 647s . Final optimisation steps... 647s 647s 647s . Log likelihood of the current tree: -12563.118859055624852771870791912078857422. 647s 647s . Calculating fast branch supports (using 'aBayes'). 647s 647s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 647s 647s . Time used 0h0m1s 647s 647s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 647s PASS 647s autopkgtest [14:32:04]: test run-unit-test: -----------------------] 648s run-unit-test PASS 648s autopkgtest [14:32:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 648s autopkgtest [14:32:05]: @@@@@@@@@@@@@@@@@@@@ summary 648s run-unit-test PASS 665s nova [W] Using flock in prodstack6-arm64 665s flock: timeout while waiting to get lock 665s Creating nova instance adt-plucky-arm64-phyml-20250315-142117-juju-7f2275-prod-proposed-migration-environment-20-9f357b92-a717-4e26-97ff-8b47c16939e4 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 665s nova [W] Timed out waiting for 3bccfb9f-cd4c-402f-9e0f-c0da201b0275 to get deleted.