0s autopkgtest [02:50:58]: starting date and time: 2024-03-26 02:50:58+0000 0s autopkgtest [02:50:58]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [02:50:58]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._du_4wbc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade examl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-45.secgroup --name adt-noble-amd64-examl-20240326-025058-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 70s autopkgtest [02:52:08]: testbed dpkg architecture: amd64 70s autopkgtest [02:52:08]: testbed apt version: 2.7.12 70s autopkgtest [02:52:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 70s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 71s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 71s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 71s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4027 kB] 71s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 71s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [483 kB] 71s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [731 kB] 71s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 71s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [37.9 kB] 71s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 71s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 71s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1260 kB] 71s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4390 kB] 71s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 71s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [28.6 kB] 71s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.8 kB] 71s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 74s Fetched 11.7 MB in 1s (8295 kB/s) 74s Reading package lists... 75s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Calculating upgrade... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded. 77s sh: Attempting to set up Debian/Ubuntu apt sources automatically 77s sh: Distribution appears to be Ubuntu 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s eatmydata is already the newest version (131-1). 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s dbus is already the newest version (1.14.10-4ubuntu1). 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s rng-tools-debian is already the newest version (2.4). 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s The following packages will be REMOVED: 80s cloud-init* python3-configobj* python3-debconf* 81s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 81s After this operation, 3256 kB disk space will be freed. 81s (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 ... 71864 files and directories currently installed.) 81s Removing cloud-init (24.1.2-0ubuntu1) ... 81s Removing python3-configobj (5.0.8-3) ... 81s Removing python3-debconf (1.5.86) ... 81s Processing triggers for man-db (2.12.0-3) ... 82s (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 ... 71475 files and directories currently installed.) 82s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 83s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 83s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 83s invoke-rc.d: policy-rc.d denied execution of try-restart. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s linux-generic is already the newest version (6.8.0-11.11+1). 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 84s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 84s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 86s Reading package lists... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Calculating upgrade... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s autopkgtest [02:52:25]: rebooting testbed after setup commands that affected boot 104s autopkgtest [02:52:42]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 105s autopkgtest [02:52:43]: @@@@@@@@@@@@@@@@@@@@ apt-source examl 105s Get:1 http://ftpmaster.internal/ubuntu noble/universe examl 3.0.22-4 (dsc) [2008 B] 105s Get:2 http://ftpmaster.internal/ubuntu noble/universe examl 3.0.22-4 (tar) [941 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble/universe examl 3.0.22-4 (diff) [27.1 kB] 106s gpgv: Signature made Wed Jan 31 17:37:40 2024 UTC 106s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 106s gpgv: issuer "tillea@rki.de" 106s gpgv: Can't check signature: No public key 106s dpkg-source: warning: cannot verify inline signature for ./examl_3.0.22-4.dsc: no acceptable signature found 106s autopkgtest [02:52:44]: testing package examl version 3.0.22-4 106s autopkgtest [02:52:44]: build not needed 106s autopkgtest [02:52:44]: test run-unit-test: preparing testbed 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Starting pkgProblemResolver with broken count: 0 107s Starting 2 pkgProblemResolver with broken count: 0 107s Done 107s The following additional packages will be installed: 107s clang-16 examl libamd-comgr2 libamdhip64-5 libasan8 libatomic1 libc-dev-bin 107s libc6-dev libclang-common-16-dev libclang-cpp16 libclang1-16 libcrypt-dev 107s libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libgc1 libgcc-13-dev 107s libgomp1 libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-plugins 107s libhwloc15 libitm1 libllvm16 libllvm17 liblsan0 libmunge2 libobjc-13-dev 107s libobjc4 libopenmpi3 libpciaccess0 libpmix2 libpocl2 libpocl2-common 107s libpsm-infinipath1 libpsm2-2 libquadmath0 librdmacm1t64 libstdc++-13-dev 107s libtsan2 libubsan1 libucx0 libxnvctrl0 linux-libc-dev llvm-16-linker-tools 107s ocl-icd-libopencl1 openmpi-bin openmpi-common pocl-opencl-icd rpcsvc-proto 107s Suggested packages: 107s clang-16-doc wasi-libc glibc-doc manpages-dev libhwloc-contrib-plugins 107s libstdc++-13-doc gfortran | fortran-compiler 107s Recommended packages: 107s llvm-16-dev manpages manpages-dev libc-devtools libclang-rt-16-dev 107s The following NEW packages will be installed: 107s autopkgtest-satdep clang-16 examl libamd-comgr2 libamdhip64-5 libasan8 107s libatomic1 libc-dev-bin libc6-dev libclang-common-16-dev libclang-cpp16 107s libclang1-16 libcrypt-dev libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 107s libgc1 libgcc-13-dev libgomp1 libhsa-runtime64-1 libhsakmt1 libhwasan0 107s libhwloc-plugins libhwloc15 libitm1 libllvm16 libllvm17 liblsan0 libmunge2 107s libobjc-13-dev libobjc4 libopenmpi3 libpciaccess0 libpmix2 libpocl2 107s libpocl2-common libpsm-infinipath1 libpsm2-2 libquadmath0 librdmacm1t64 107s libstdc++-13-dev libtsan2 libubsan1 libucx0 libxnvctrl0 linux-libc-dev 107s llvm-16-linker-tools ocl-icd-libopencl1 openmpi-bin openmpi-common 107s pocl-opencl-icd rpcsvc-proto 107s 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 137 MB/137 MB of archives. 107s After this operation, 645 MB of additional disk space will be used. 107s Get:1 /tmp/autopkgtest.yhpmcM/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 107s Get:2 http://ftpmaster.internal/ubuntu noble/universe amd64 libllvm16 amd64 1:16.0.6-19build1 [25.6 MB] 108s Get:3 http://ftpmaster.internal/ubuntu noble/universe amd64 libclang-cpp16 amd64 1:16.0.6-19build1 [12.6 MB] 108s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 108s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 108s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 108s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 108s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 108s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 108s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 108s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 108s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 108s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 108s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB] 108s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 108s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 108s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 108s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB] 108s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 108s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libgc1 amd64 1:8.2.6-1 [90.2 kB] 108s Get:21 http://ftpmaster.internal/ubuntu noble/universe amd64 libobjc4 amd64 14-20240303-1ubuntu1 [46.4 kB] 108s Get:22 http://ftpmaster.internal/ubuntu noble/universe amd64 libobjc-13-dev amd64 13.2.0-17ubuntu2 [194 kB] 108s Get:23 http://ftpmaster.internal/ubuntu noble/universe amd64 libclang-common-16-dev amd64 1:16.0.6-19build1 [631 kB] 108s Get:24 http://ftpmaster.internal/ubuntu noble/universe amd64 llvm-16-linker-tools amd64 1:16.0.6-19build1 [1300 kB] 108s Get:25 http://ftpmaster.internal/ubuntu noble/universe amd64 libclang1-16 amd64 1:16.0.6-19build1 [7250 kB] 108s Get:26 http://ftpmaster.internal/ubuntu noble/universe amd64 clang-16 amd64 1:16.0.6-19build1 [80.8 kB] 108s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-9 [7802 B] 108s Get:28 http://ftpmaster.internal/ubuntu noble/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [178 kB] 108s Get:29 http://ftpmaster.internal/ubuntu noble/universe amd64 libpsm2-2 amd64 11.2.185-2 [196 kB] 108s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 librdmacm1t64 amd64 50.0-2 [70.7 kB] 108s Get:31 http://ftpmaster.internal/ubuntu noble/universe amd64 libfabric1 amd64 1.17.0-3build1 [657 kB] 108s Get:32 http://ftpmaster.internal/ubuntu noble/universe amd64 libhwloc15 amd64 2.10.0-1 [171 kB] 108s Get:33 http://ftpmaster.internal/ubuntu noble/universe amd64 libmunge2 amd64 0.5.15-3ubuntu1 [14.6 kB] 108s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libpciaccess0 amd64 0.17-3 [18.9 kB] 108s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu1 [11.5 kB] 108s Get:36 http://ftpmaster.internal/ubuntu noble/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1 [38.3 kB] 108s Get:37 http://ftpmaster.internal/ubuntu noble/universe amd64 libhwloc-plugins amd64 2.10.0-1 [15.8 kB] 108s Get:38 http://ftpmaster.internal/ubuntu noble/universe amd64 libpmix2 amd64 5.0.1-4 [695 kB] 108s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libllvm17 amd64 1:17.0.6-5build1 [26.2 MB] 108s Get:40 http://ftpmaster.internal/ubuntu noble/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3 [14.4 MB] 108s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [20.4 kB] 108s Get:42 http://ftpmaster.internal/ubuntu noble/universe amd64 libhsakmt1 amd64 5.7.0-1 [63.0 kB] 108s Get:43 http://ftpmaster.internal/ubuntu noble/universe amd64 libhsa-runtime64-1 amd64 5.7.1-1 [491 kB] 108s Get:44 http://ftpmaster.internal/ubuntu noble/universe amd64 libamdhip64-5 amd64 5.2.3-12 [5204 kB] 108s Get:45 http://ftpmaster.internal/ubuntu noble/universe amd64 libucx0 amd64 1.16.0+ds-4 [1139 kB] 108s Get:46 http://ftpmaster.internal/ubuntu noble/universe amd64 libopenmpi3 amd64 4.1.6-5ubuntu1 [3177 kB] 108s Get:47 http://ftpmaster.internal/ubuntu noble/universe amd64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] 108s Get:48 http://ftpmaster.internal/ubuntu noble/universe amd64 openmpi-bin amd64 4.1.6-5ubuntu1 [124 kB] 108s Get:49 http://ftpmaster.internal/ubuntu noble/universe amd64 examl amd64 3.0.22-4 [983 kB] 108s Get:50 http://ftpmaster.internal/ubuntu noble/universe amd64 libpocl2-common all 5.0-2 [82.5 kB] 108s Get:51 http://ftpmaster.internal/ubuntu noble/universe amd64 libpocl2 amd64 5.0-2 [16.2 MB] 108s Get:52 http://ftpmaster.internal/ubuntu noble/universe amd64 pocl-opencl-icd amd64 5.0-2 [7154 B] 109s Fetched 137 MB in 1s (124 MB/s) 109s Selecting previously unselected package libllvm16:amd64. 109s (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 ... 71420 files and directories currently installed.) 109s Preparing to unpack .../00-libllvm16_1%3a16.0.6-19build1_amd64.deb ... 109s Unpacking libllvm16:amd64 (1:16.0.6-19build1) ... 109s Selecting previously unselected package libclang-cpp16. 109s Preparing to unpack .../01-libclang-cpp16_1%3a16.0.6-19build1_amd64.deb ... 109s Unpacking libclang-cpp16 (1:16.0.6-19build1) ... 110s Selecting previously unselected package libgomp1:amd64. 110s Preparing to unpack .../02-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package libitm1:amd64. 110s Preparing to unpack .../03-libitm1_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package libatomic1:amd64. 110s Preparing to unpack .../04-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package libasan8:amd64. 110s Preparing to unpack .../05-libasan8_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package liblsan0:amd64. 110s Preparing to unpack .../06-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package libtsan2:amd64. 110s Preparing to unpack .../07-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package libubsan1:amd64. 110s Preparing to unpack .../08-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package libhwasan0:amd64. 110s Preparing to unpack .../09-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package libquadmath0:amd64. 110s Preparing to unpack .../10-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 110s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 110s Selecting previously unselected package libgcc-13-dev:amd64. 110s Preparing to unpack .../11-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 110s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 110s Selecting previously unselected package libc-dev-bin. 110s Preparing to unpack .../12-libc-dev-bin_2.39-0ubuntu6_amd64.deb ... 110s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 110s Selecting previously unselected package linux-libc-dev:amd64. 110s Preparing to unpack .../13-linux-libc-dev_6.8.0-11.11_amd64.deb ... 110s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 110s Selecting previously unselected package libcrypt-dev:amd64. 110s Preparing to unpack .../14-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 110s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 110s Selecting previously unselected package rpcsvc-proto. 110s Preparing to unpack .../15-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 110s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 110s Selecting previously unselected package libc6-dev:amd64. 110s Preparing to unpack .../16-libc6-dev_2.39-0ubuntu6_amd64.deb ... 110s Unpacking libc6-dev:amd64 (2.39-0ubuntu6) ... 111s Selecting previously unselected package libstdc++-13-dev:amd64. 111s Preparing to unpack .../17-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 111s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 111s Selecting previously unselected package libgc1:amd64. 111s Preparing to unpack .../18-libgc1_1%3a8.2.6-1_amd64.deb ... 111s Unpacking libgc1:amd64 (1:8.2.6-1) ... 111s Selecting previously unselected package libobjc4:amd64. 111s Preparing to unpack .../19-libobjc4_14-20240303-1ubuntu1_amd64.deb ... 111s Unpacking libobjc4:amd64 (14-20240303-1ubuntu1) ... 111s Selecting previously unselected package libobjc-13-dev:amd64. 111s Preparing to unpack .../20-libobjc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 111s Unpacking libobjc-13-dev:amd64 (13.2.0-17ubuntu2) ... 111s Selecting previously unselected package libclang-common-16-dev. 111s Preparing to unpack .../21-libclang-common-16-dev_1%3a16.0.6-19build1_amd64.deb ... 111s Unpacking libclang-common-16-dev (1:16.0.6-19build1) ... 111s Selecting previously unselected package llvm-16-linker-tools. 111s Preparing to unpack .../22-llvm-16-linker-tools_1%3a16.0.6-19build1_amd64.deb ... 111s Unpacking llvm-16-linker-tools (1:16.0.6-19build1) ... 111s Selecting previously unselected package libclang1-16. 111s Preparing to unpack .../23-libclang1-16_1%3a16.0.6-19build1_amd64.deb ... 111s Unpacking libclang1-16 (1:16.0.6-19build1) ... 111s Selecting previously unselected package clang-16. 111s Preparing to unpack .../24-clang-16_1%3a16.0.6-19build1_amd64.deb ... 111s Unpacking clang-16 (1:16.0.6-19build1) ... 111s Selecting previously unselected package libevent-pthreads-2.1-7:amd64. 111s Preparing to unpack .../25-libevent-pthreads-2.1-7_2.1.12-stable-9_amd64.deb ... 111s Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-9) ... 111s Selecting previously unselected package libpsm-infinipath1. 111s Preparing to unpack .../26-libpsm-infinipath1_3.3+20.604758e7-6.3_amd64.deb ... 111s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) ... 111s Selecting previously unselected package libpsm2-2. 111s Preparing to unpack .../27-libpsm2-2_11.2.185-2_amd64.deb ... 111s Unpacking libpsm2-2 (11.2.185-2) ... 111s Selecting previously unselected package librdmacm1t64:amd64. 111s Preparing to unpack .../28-librdmacm1t64_50.0-2_amd64.deb ... 111s Unpacking librdmacm1t64:amd64 (50.0-2) ... 111s Selecting previously unselected package libfabric1:amd64. 111s Preparing to unpack .../29-libfabric1_1.17.0-3build1_amd64.deb ... 111s Unpacking libfabric1:amd64 (1.17.0-3build1) ... 111s Selecting previously unselected package libhwloc15:amd64. 111s Preparing to unpack .../30-libhwloc15_2.10.0-1_amd64.deb ... 111s Unpacking libhwloc15:amd64 (2.10.0-1) ... 111s Selecting previously unselected package libmunge2:amd64. 111s Preparing to unpack .../31-libmunge2_0.5.15-3ubuntu1_amd64.deb ... 111s Unpacking libmunge2:amd64 (0.5.15-3ubuntu1) ... 111s Selecting previously unselected package libpciaccess0:amd64. 111s Preparing to unpack .../32-libpciaccess0_0.17-3_amd64.deb ... 111s Unpacking libpciaccess0:amd64 (0.17-3) ... 112s Selecting previously unselected package libxnvctrl0:amd64. 112s Preparing to unpack .../33-libxnvctrl0_510.47.03-0ubuntu1_amd64.deb ... 112s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... 112s Selecting previously unselected package ocl-icd-libopencl1:amd64. 112s Preparing to unpack .../34-ocl-icd-libopencl1_2.3.2-1_amd64.deb ... 112s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1) ... 112s Selecting previously unselected package libhwloc-plugins:amd64. 112s Preparing to unpack .../35-libhwloc-plugins_2.10.0-1_amd64.deb ... 112s Unpacking libhwloc-plugins:amd64 (2.10.0-1) ... 112s Selecting previously unselected package libpmix2:amd64. 112s Preparing to unpack .../36-libpmix2_5.0.1-4_amd64.deb ... 112s Unpacking libpmix2:amd64 (5.0.1-4) ... 112s Selecting previously unselected package libllvm17:amd64. 112s Preparing to unpack .../37-libllvm17_1%3a17.0.6-5build1_amd64.deb ... 112s Unpacking libllvm17:amd64 (1:17.0.6-5build1) ... 112s Selecting previously unselected package libamd-comgr2:amd64. 112s Preparing to unpack .../38-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_amd64.deb ... 112s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3) ... 113s Selecting previously unselected package libdrm-amdgpu1:amd64. 113s Preparing to unpack .../39-libdrm-amdgpu1_2.4.120-2_amd64.deb ... 113s Unpacking libdrm-amdgpu1:amd64 (2.4.120-2) ... 113s Selecting previously unselected package libhsakmt1:amd64. 113s Preparing to unpack .../40-libhsakmt1_5.7.0-1_amd64.deb ... 113s Unpacking libhsakmt1:amd64 (5.7.0-1) ... 113s Selecting previously unselected package libhsa-runtime64-1. 113s Preparing to unpack .../41-libhsa-runtime64-1_5.7.1-1_amd64.deb ... 113s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 113s Selecting previously unselected package libamdhip64-5. 113s Preparing to unpack .../42-libamdhip64-5_5.2.3-12_amd64.deb ... 113s Unpacking libamdhip64-5 (5.2.3-12) ... 113s Selecting previously unselected package libucx0:amd64. 113s Preparing to unpack .../43-libucx0_1.16.0+ds-4_amd64.deb ... 113s Unpacking libucx0:amd64 (1.16.0+ds-4) ... 113s Selecting previously unselected package libopenmpi3:amd64. 113s Preparing to unpack .../44-libopenmpi3_4.1.6-5ubuntu1_amd64.deb ... 113s Unpacking libopenmpi3:amd64 (4.1.6-5ubuntu1) ... 113s Selecting previously unselected package openmpi-common. 113s Preparing to unpack .../45-openmpi-common_4.1.6-5ubuntu1_all.deb ... 113s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 113s Selecting previously unselected package openmpi-bin. 113s Preparing to unpack .../46-openmpi-bin_4.1.6-5ubuntu1_amd64.deb ... 113s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 113s Selecting previously unselected package examl. 113s Preparing to unpack .../47-examl_3.0.22-4_amd64.deb ... 113s Unpacking examl (3.0.22-4) ... 113s Selecting previously unselected package libpocl2-common. 113s Preparing to unpack .../48-libpocl2-common_5.0-2_all.deb ... 113s Unpacking libpocl2-common (5.0-2) ... 113s Selecting previously unselected package libpocl2:amd64. 113s Preparing to unpack .../49-libpocl2_5.0-2_amd64.deb ... 113s Unpacking libpocl2:amd64 (5.0-2) ... 114s Selecting previously unselected package pocl-opencl-icd:amd64. 114s Preparing to unpack .../50-pocl-opencl-icd_5.0-2_amd64.deb ... 114s Unpacking pocl-opencl-icd:amd64 (5.0-2) ... 114s Selecting previously unselected package autopkgtest-satdep. 114s Preparing to unpack .../51-1-autopkgtest-satdep.deb ... 114s Unpacking autopkgtest-satdep (0) ... 114s Setting up libpciaccess0:amd64 (0.17-3) ... 114s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 114s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... 114s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 114s Setting up libmunge2:amd64 (0.5.15-3ubuntu1) ... 114s Setting up libpocl2-common (5.0-2) ... 114s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libhwloc15:amd64 (2.10.0-1) ... 114s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libgc1:amd64 (1:8.2.6-1) ... 114s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 114s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1) ... 114s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 114s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libpsm2-2 (11.2.185-2) ... 114s Setting up openmpi-common (4.1.6-5ubuntu1) ... 114s Setting up librdmacm1t64:amd64 (50.0-2) ... 114s Setting up libllvm16:amd64 (1:16.0.6-19build1) ... 114s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... 114s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 114s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libc-dev-bin (2.39-0ubuntu6) ... 114s Setting up libllvm17:amd64 (1:17.0.6-5build1) ... 114s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-9) ... 114s Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... 114s Setting up libfabric1:amd64 (1.17.0-3build1) ... 114s Setting up libclang1-16 (1:16.0.6-19build1) ... 114s Setting up libobjc4:amd64 (14-20240303-1ubuntu1) ... 114s Setting up libclang-common-16-dev (1:16.0.6-19build1) ... 114s Setting up libhwloc-plugins:amd64 (2.10.0-1) ... 114s Setting up llvm-16-linker-tools (1:16.0.6-19build1) ... 114s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 114s Setting up libclang-cpp16 (1:16.0.6-19build1) ... 114s Setting up libc6-dev:amd64 (2.39-0ubuntu6) ... 114s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3) ... 114s Setting up libhsakmt1:amd64 (5.7.0-1) ... 114s Setting up libobjc-13-dev:amd64 (13.2.0-17ubuntu2) ... 114s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 114s Setting up libpmix2:amd64 (5.0.1-4) ... 114s Setting up clang-16 (1:16.0.6-19build1) ... 114s Setting up libpocl2:amd64 (5.0-2) ... 114s Setting up libhsa-runtime64-1 (5.7.1-1) ... 114s Setting up libamdhip64-5 (5.2.3-12) ... 114s Setting up pocl-opencl-icd:amd64 (5.0-2) ... 114s Setting up libucx0:amd64 (1.16.0+ds-4) ... 114s Setting up libopenmpi3:amd64 (4.1.6-5ubuntu1) ... 114s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 114s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 114s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 114s Setting up examl (3.0.22-4) ... 114s Setting up autopkgtest-satdep (0) ... 114s Processing triggers for man-db (2.12.0-3) ... 115s Processing triggers for libc-bin (2.39-0ubuntu6) ... 117s (Reading database ... 75074 files and directories currently installed.) 117s Removing autopkgtest-satdep (0) ... 119s autopkgtest [02:52:57]: test run-unit-test: [----------------------- 119s + pkg=examl 119s + export OMPI_MCA_rmaps_base_oversubscribe=1 119s + OMPI_MCA_rmaps_base_oversubscribe=1 119s + export OMPI_ALLOW_RUN_AS_ROOT=1 119s + OMPI_ALLOW_RUN_AS_ROOT=1 119s + export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 119s + OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 119s + '[' /tmp/autopkgtest.yhpmcM/autopkgtest_tmp = '' ']' 119s + cp -a /usr/share/doc/examl/testData /tmp/autopkgtest.yhpmcM/autopkgtest_tmp 119s + cd /tmp/autopkgtest.yhpmcM/autopkgtest_tmp 119s + gunzip -r testData 119s + parse-examl -s testData/49 -m DNA -n 49.unpartitioned 119s gappyness: 0.074048 119s Pattern compression: ON 119s 119s Alignment has 51 completely undetermined sites that will be automatically removed from the binary alignment file 119s 119s 119s 119s Your alignment has 628 unique patterns 119s 119s 119s Under CAT the memory required by ExaML for storing CLVs and tip vectors will be 119s 1015476 bytes 119s 991 kiloBytes 119s 0 MegaBytes 119s 0 GigaBytes 119s 119s 119s Under GAMMA the memory required by ExaML for storing CLVs and tip vectors will be 119s 3969588 bytes 119s 3876 kiloBytes 119s 3 MegaBytes 119s 0 GigaBytes 119s 119s Please note that, these are just the memory requirements for doing likelihood calculations! 119s To be on the safe side, we recommend that you execute ExaML on a system with twice that memory. 119s 119s 119s Binary and compressed alignment file written to file 49.unpartitioned.binary 119s 119s Parsing completed, exiting now ... 119s 119s + parse-examl -s testData/49 -q testData/49.model -m DNA -n 49.partitioned 119s gappyness: 0.074048 119s Pattern compression: ON 119s 119s Alignment has 51 completely undetermined sites that will be automatically removed from the binary alignment file 119s 119s 119s 119s Your alignment has 642 unique patterns 119s 119s 119s Under CAT the memory required by ExaML for storing CLVs and tip vectors will be 119s 1038114 bytes 119s 1013 kiloBytes 119s 0 MegaBytes 119s 0 GigaBytes 119s 119s 119s Under GAMMA the memory required by ExaML for storing CLVs and tip vectors will be 119s 4058082 bytes 119s 3962 kiloBytes 119s 3 MegaBytes 119s 0 GigaBytes 119s 119s Please note that, these are just the memory requirements for doing likelihood calculations! 119s To be on the safe side, we recommend that you execute ExaML on a system with twice that memory. 119s 119s 119s Binary and compressed alignment file written to file 49.partitioned.binary 119s 119s Parsing completed, exiting now ... 119s 119s + examl -t testData/49.tree -m GAMMA -s 49.unpartitioned.binary -n T1 119s Run MPI on 2 of 2 available processors 119s Use /usr/lib/examl/bin/examl-avx2 and 2 processors 120s 120s This is ExaML FINE-GRAIN MPI Process Number: 0 120s 120s This is ExaML FINE-GRAIN MPI Process Number: 1 120s 120s proc offset length part 120s 0 314 314 0 120s 1 0 314 0 120s 120s #proc #part #sites 120s 0 1 314 120s 1 1 314 120s 120s 120s 120s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 120s 120s 120s Alignment has 628 distinct alignment patterns 120s 120s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 120s 120s ExaML rapid hill-climbing mode 120s 120s Using 1 distinct models/data partitions with joint branch length optimization 120s 120s 120s All free model parameters will be estimated by ExaML 120s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 120s 120s Partition: 0 120s Alignment Patterns: 628 120s Name: No Name Provided 120s DataType: DNA 120s Substitution Matrix: GTR 120s 120s 120s 120s 120s ExaML was called as follows: 120s 120s /usr/lib/examl/bin/examl-avx2 -t testData/49.tree -m GAMMA -s 49.unpartitioned.binary -n T1 120s 120s 120s Memory Saving Option: DISABLED 120s 120s Best rearrangement radius: 5 126s 126s Likelihood of best tree: -16221.368990 126s 126s 126s Overall Time for 1 Inference 6.268115 126s 126s Overall accumulated Time (in case of restarts): 6.268115 126s 126s Likelihood : -16221.368990 126s 126s 126s Model parameters written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_modelFile.T1 126s Final tree written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_result.T1 126s Execution Log File written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_log.T1 126s Execution information file written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_info.T1 126s + examl -s 49.unpartitioned.binary -R ExaML_binaryCheckpoint.T1_5 -m GAMMA -n T1_RESTART 126s Run MPI on 2 of 2 available processors 126s Use /usr/lib/examl/bin/examl-avx2 and 2 processors 126s 126s This is ExaML FINE-GRAIN MPI Process Number: 0 126s 126s This is ExaML FINE-GRAIN MPI Process Number: 1 126s 126s proc offset length part 126s 0 314 314 0 126s 1 0 314 0 126s 126s #proc #part #sites 126s 0 1 314 126s 1 1 314 126s 126s 126s 126s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 126s 126s 126s Alignment has 628 distinct alignment patterns 126s 126s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 126s 126s ExaML rapid hill-climbing mode 126s 126s Using 1 distinct models/data partitions with joint branch length optimization 126s 126s 126s All free model parameters will be estimated by ExaML 126s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 126s 126s Partition: 0 126s Alignment Patterns: 628 126s Name: No Name Provided 126s DataType: DNA 126s Substitution Matrix: GTR 126s 126s 126s 126s 126s ExaML was called as follows: 126s 126s /usr/lib/examl/bin/examl-avx2 -s 49.unpartitioned.binary -R ExaML_binaryCheckpoint.T1_5 -m GAMMA -n T1_RESTART 126s 126s 126s Memory Saving Option: DISABLED 126s ExaML Restart with likelihood: -16221.54674043667182559147477149963378906250000000000000 129s 129s Likelihood of best tree: -16221.368990 129s 129s 129s Overall Time for 1 Inference 2.919645 129s 129s Overall accumulated Time (in case of restarts): 6.154754 129s 129s Likelihood : -16221.368990 129s 129s 129s Model parameters written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_modelFile.T1_RESTART 129s Final tree written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_result.T1_RESTART 129s Execution Log File written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_log.T1_RESTART 129s Execution information file written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_info.T1_RESTART 129s + examl -t testData/49.tree -m GAMMA -s 49.partitioned.binary -n T2 129s Run MPI on 2 of 2 available processors 129s Use /usr/lib/examl/bin/examl-avx2 and 2 processors 130s 130s This is ExaML FINE-GRAIN MPI Process Number: 0 130s 130s 130s proc offset length part 130s 0 0 44 3 130s 0 0 151 0 130s 0 0 126 1 130s 1 0 137 2 130s 1 126 184 1 130s 130s #proc #part #sites 130s 0 3 321 130s 1 2 321 130s 130s 130s 130s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 130s 130s 130s Alignment has 642 distinct alignment patterns 130s 130s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 130s 130s ExaML rapid hill-climbing mode 130s 130s Using 4 distinct models/data partitions with joint branch length optimization 130s 130s 130s All free model parameters will be estimated by ExaML 130s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 130s 130s Partition: 0 130s Alignment Patterns: 151 130s Name: gene1 130s DataType: DNA 130s Substitution Matrix: GTR 130s 130s 130s 130s Partition: 1 130s Alignment Patterns: 310 130s Name: gene2 130s DataType: DNA 130s Substitution Matrix: GTR 130s 130s 130s 130s Partition: 2 130s Alignment Patterns: 137 130s Name: gene3 130s DataType: DNA 130s Substitution Matrix: GTR 130s 130s 130s 130s Partition: 3 130s Alignment Patterns: 44 130s Name: gene4 130s DataType: DNA 130s Substitution Matrix: GTR 130s 130s 130s 130s 130s ExaML was called as follows: 130s 130s /usr/lib/examl/bin/examl-avx2 -t testData/49.tree -m GAMMA -s 49.partitioned.binary -n T2 130s 130s 130s Memory Saving Option: DISABLED 130s This is ExaML FINE-GRAIN MPI Process Number: 1 131s 131s Best rearrangement radius: 5 138s 138s Likelihood of best tree: -16194.095475 138s 138s 138s Overall Time for 1 Inference 8.158180 138s 138s Overall accumulated Time (in case of restarts): 8.158180 138s 138s Likelihood : -16194.095475 138s 138s 138s Model parameters written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_modelFile.T2 138s Final tree written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_result.T2 138s Execution Log File written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_log.T2 138s Execution information file written to: /tmp/autopkgtest.yhpmcM/autopkgtest_tmp/ExaML_info.T2 138s + examl -s 49.unpartitioned.binary -t treeSet -f e -m GAMMA -n T3 138s Run MPI on 2 of 2 available processors 138s Use /usr/lib/examl/bin/examl-avx2 and 2 processors 138s 138s This is ExaML FINE-GRAIN MPI Process Number: 0 138s 138s This is ExaML FINE-GRAIN MPI Process Number: 1 138s 138s proc offset length part 138s 0 314 314 0 138s 1 0 314 0 138s 138s #proc #part #sites 138s 0 1 314 138s 1 1 314 138s 138s 138s 138s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 138s 138s 138s Alignment has 628 distinct alignment patterns 138s 138s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 138s 138s ExaML fast tree evaluation mode 138s 138s Using 1 distinct models/data partitions with joint branch length optimization 138s 138s 138s All free model parameters will be estimated by ExaML 138s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 138s 138s Partition: 0 138s Alignment Patterns: 628 138s Name: No Name Provided 138s DataType: DNA 138s Substitution Matrix: GTR 138s 138s 138s 138s 138s ExaML was called as follows: 138s 138s /usr/lib/examl/bin/examl-avx2 -s 49.unpartitioned.binary -t treeSet -f e -m GAMMA -n T3 138s 138s 138s Memory Saving Option: DISABLED 138s The file treeSet you want to open for reading does not exist, exiting ... 138s -------------------------------------------------------------------------- 138s Primary job terminated normally, but 1 process returned 138s a non-zero exit code. Per user-direction, the job has been aborted. 138s -------------------------------------------------------------------------- 140s -------------------------------------------------------------------------- 140s mpirun detected that one or more processes exited with non-zero status, thus causing 140s the job to be terminated. The first process to do so was: 140s 140s Process name: [[29104,1],0] 140s Exit code: 255 140s -------------------------------------------------------------------------- 140s + true 140s + examl -s 49.unpartitioned.binary -t treeSet -f E -m GAMMA -n T4 140s Run MPI on 2 of 2 available processors 140s Use /usr/lib/examl/bin/examl-avx2 and 2 processors 141s 141s This is ExaML FINE-GRAIN MPI Process Number: 0 141s 141s proc offset length part 141s 0 314 314 0 141s 1 0 314 0 141s 141s #proc #part #sites 141s 0 1 314 141s 1 1 314 141s 141s 141s 141s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 141s 141s 141s Alignment has 628 distinct alignment patterns 141s 141s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 141s 141s ExaML slow tree evaluation mode 141s 141s Using 1 distinct models/data partitions with joint branch length optimization 141s 141s 141s All free model parameters will be estimated by ExaML 141s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 141s 141s Partition: 0 141s Alignment Patterns: 628 141s Name: No Name Provided 141s DataType: DNA 141s Substitution Matrix: GTR 141s 141s 141s 141s 141s ExaML was called as follows: 141s 141s /usr/lib/examl/bin/examl-avx2 -s 49.unpartitioned.binary -t treeSet -f E -m GAMMA -n T4 141s 141s 141s 141s This is ExaML FINE-GRAIN MPI Process Number: 1 141s Memory Saving Option: DISABLED 141s The file treeSet you want to open for reading does not exist, exiting ... 141s -------------------------------------------------------------------------- 141s Primary job terminated normally, but 1 process returned 141s a non-zero exit code. Per user-direction, the job has been aborted. 141s -------------------------------------------------------------------------- 142s -------------------------------------------------------------------------- 142s mpirun detected that one or more processes exited with non-zero status, thus causing 142s the job to be terminated. The first process to do so was: 142s 142s Process name: [[29089,1],0] 142s Exit code: 255 142s -------------------------------------------------------------------------- 142s + true 142s + exit 0 142s autopkgtest [02:53:20]: test run-unit-test: -----------------------] 142s run-unit-test PASS 142s autopkgtest [02:53:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 142s autopkgtest [02:53:20]: @@@@@@@@@@@@@@@@@@@@ summary 142s run-unit-test PASS 152s Creating nova instance adt-noble-amd64-examl-20240326-025058-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240325.img (UUID ba43860b-557a-4db2-b3f0-378a99bca08c)...