0s autopkgtest [00:15:50]: starting date: 2024-03-19 0s autopkgtest [00:15:50]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [00:15:50]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y7lok_ub/out --timeout-copy=6000 --setup-commands 'sed -i "s/ports.ubuntu.com/ftpmaster.internal/; s/ubuntu-ports/ubuntu/" /etc/apt/sources.list `ls /etc/apt/sources.list.d/*.list 2>/dev/null || true`; ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade examl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 pmix/5.0.1-4.1' -- lxd -r lxd-armhf-10.44.124.112 lxd-armhf-10.44.124.112:autopkgtest/ubuntu/noble/armhf 59s autopkgtest [00:16:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 63s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 63s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 64s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 64s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3736 kB] 65s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [585 kB] 66s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 66s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 66s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 66s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3609 kB] 67s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 67s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [35.6 kB] 67s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 78s Fetched 8639 kB in 5s (1596 kB/s) 78s Reading package lists... 95s tee: /proc/self/fd/2: Permission denied 129s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 129s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 129s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 129s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease 129s Hit:5 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 129s Hit:6 http://ftpmaster.internal/ubuntu noble-security InRelease 129s Hit:7 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 129s Hit:8 http://ftpmaster.internal/ubuntu noble-proposed InRelease 136s Reading package lists... 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 139s Calculating upgrade... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Reading package lists... 144s Building dependency tree... 144s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [00:18:20]: rebooting testbed after setup commands that affected boot 191s autopkgtest [00:19:01]: testbed running kernel: Linux 5.4.0-170-generic #188-Ubuntu SMP Wed Jan 10 09:51:10 UTC 2024 196s autopkgtest [00:19:06]: testbed dpkg architecture: armhf 212s autopkgtest [00:19:22]: @@@@@@@@@@@@@@@@@@@@ apt-source examl 220s Get:1 http://ftpmaster.internal/ubuntu noble/universe examl 3.0.22-4 (dsc) [2008 B] 220s Get:2 http://ftpmaster.internal/ubuntu noble/universe examl 3.0.22-4 (tar) [941 kB] 220s Get:3 http://ftpmaster.internal/ubuntu noble/universe examl 3.0.22-4 (diff) [27.1 kB] 222s gpgv: Signature made Wed Jan 31 17:37:40 2024 UTC 222s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 222s gpgv: issuer "tillea@rki.de" 222s gpgv: Can't check signature: No public key 222s dpkg-source: warning: cannot verify inline signature for ./examl_3.0.22-4.dsc: no acceptable signature found 223s autopkgtest [00:19:33]: testing package examl version 3.0.22-4 223s autopkgtest [00:19:33]: build not needed 228s autopkgtest [00:19:38]: test run-unit-test: preparing testbed 245s Reading package lists... 246s Building dependency tree... 246s Reading state information... 248s Correcting dependencies...Starting pkgProblemResolver with broken count: 1 249s Starting 2 pkgProblemResolver with broken count: 1 249s Investigating (0) examl:armhf < none -> 3.0.22-4 @un uN Ib > 249s Broken examl:armhf Depends on libopenmpi3:armhf < none | 4.1.6-5ubuntu1 @un uH > (>= 4.1.6) 249s Considering libopenmpi3:armhf 0 as a solution to examl:armhf 0 249s Holding Back examl:armhf rather than change libopenmpi3:armhf 249s Investigating (0) autopkgtest-satdep:armhf < 0 @iU K Nb Ib > 249s Broken autopkgtest-satdep:armhf Depends on examl:armhf < none | 3.0.22-4 @un uH > 249s Considering examl:armhf 0 as a solution to autopkgtest-satdep:armhf -2 249s Removing autopkgtest-satdep:armhf rather than change examl:armhf 249s Done 250s Done 252s Starting pkgProblemResolver with broken count: 0 252s Starting 2 pkgProblemResolver with broken count: 0 253s Done 255s The following additional packages will be installed: 255s clang-16 libasan8 libatomic1 libc-dev-bin libc6-dev libclang-common-16-dev 255s libclang-cpp16 libclang1-16 libcrypt-dev libgc1 libgcc-13-dev libgomp1 255s libllvm16 libnsl-dev libobjc-13-dev libobjc4 libstdc++-13-dev libtirpc-dev 255s libubsan1 linux-libc-dev llvm-16-linker-tools rpcsvc-proto 255s Suggested packages: 255s clang-16-doc wasi-libc glibc-doc manpages-dev libstdc++-13-doc 255s Recommended packages: 255s llvm-16-dev manpages manpages-dev libc-devtools libclang-rt-16-dev 255s The following packages will be REMOVED: 255s autopkgtest-satdep 255s The following NEW packages will be installed: 255s clang-16 libasan8 libatomic1 libc-dev-bin libc6-dev libclang-common-16-dev 255s libclang-cpp16 libclang1-16 libcrypt-dev libgc1 libgcc-13-dev libgomp1 255s libllvm16 libnsl-dev libobjc-13-dev libobjc4 libstdc++-13-dev libtirpc-dev 255s libubsan1 linux-libc-dev llvm-16-linker-tools rpcsvc-proto 256s 0 upgraded, 22 newly installed, 1 to remove and 0 not upgraded. 256s 1 not fully installed or removed. 256s Need to get 55.6 MB of archives. 256s After this operation, 258 MB of additional disk space will be used. 256s Get:1 http://ftpmaster.internal/ubuntu noble/universe armhf libllvm16 armhf 1:16.0.6-19build1 [24.2 MB] 260s Get:2 http://ftpmaster.internal/ubuntu noble/universe armhf libclang-cpp16 armhf 1:16.0.6-19build1 [11.6 MB] 261s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 14-20240303-1ubuntu1 [125 kB] 261s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libatomic1 armhf 14-20240303-1ubuntu1 [7812 B] 261s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libasan8 armhf 14-20240303-1ubuntu1 [2941 kB] 261s Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libubsan1 armhf 14-20240303-1ubuntu1 [1153 kB] 261s Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-13-dev armhf 13.2.0-17ubuntu2 [900 kB] 261s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libc-dev-bin armhf 2.39-0ubuntu2 [19.1 kB] 261s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf linux-libc-dev armhf 6.8.0-11.11 [1553 kB] 261s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt-dev armhf 1:4.4.36-4 [136 kB] 261s Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-dev armhf 1.3.4+ds-1build1 [207 kB] 261s Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libnsl-dev armhf 1.3.0-3 [65.8 kB] 261s Get:13 http://ftpmaster.internal/ubuntu noble/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu6 [63.7 kB] 261s Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libc6-dev armhf 2.39-0ubuntu2 [1352 kB] 261s Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++-13-dev armhf 13.2.0-17ubuntu2 [2402 kB] 261s Get:16 http://ftpmaster.internal/ubuntu noble/main armhf libgc1 armhf 1:8.2.6-1 [80.5 kB] 261s Get:17 http://ftpmaster.internal/ubuntu noble/universe armhf libobjc4 armhf 14-20240303-1ubuntu1 [38.8 kB] 261s Get:18 http://ftpmaster.internal/ubuntu noble/universe armhf libobjc-13-dev armhf 13.2.0-17ubuntu2 [185 kB] 262s Get:19 http://ftpmaster.internal/ubuntu noble/universe armhf libclang-common-16-dev armhf 1:16.0.6-19build1 [631 kB] 262s Get:20 http://ftpmaster.internal/ubuntu noble/universe armhf llvm-16-linker-tools armhf 1:16.0.6-19build1 [1136 kB] 262s Get:21 http://ftpmaster.internal/ubuntu noble/universe armhf libclang1-16 armhf 1:16.0.6-19build1 [6648 kB] 262s Get:22 http://ftpmaster.internal/ubuntu noble/universe armhf clang-16 armhf 1:16.0.6-19build1 [76.6 kB] 264s Fetched 55.6 MB in 6s (8604 kB/s) 265s (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 ... 58620 files and directories currently installed.) 265s Removing autopkgtest-satdep (0) ... 265s Selecting previously unselected package libllvm16:armhf. 265s (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 ... 58620 files and directories currently installed.) 265s Preparing to unpack .../00-libllvm16_1%3a16.0.6-19build1_armhf.deb ... 265s Unpacking libllvm16:armhf (1:16.0.6-19build1) ... 269s Selecting previously unselected package libclang-cpp16. 269s Preparing to unpack .../01-libclang-cpp16_1%3a16.0.6-19build1_armhf.deb ... 269s Unpacking libclang-cpp16 (1:16.0.6-19build1) ... 271s Selecting previously unselected package libgomp1:armhf. 271s Preparing to unpack .../02-libgomp1_14-20240303-1ubuntu1_armhf.deb ... 271s Unpacking libgomp1:armhf (14-20240303-1ubuntu1) ... 271s Selecting previously unselected package libatomic1:armhf. 271s Preparing to unpack .../03-libatomic1_14-20240303-1ubuntu1_armhf.deb ... 271s Unpacking libatomic1:armhf (14-20240303-1ubuntu1) ... 271s Selecting previously unselected package libasan8:armhf. 272s Preparing to unpack .../04-libasan8_14-20240303-1ubuntu1_armhf.deb ... 272s Unpacking libasan8:armhf (14-20240303-1ubuntu1) ... 272s Selecting previously unselected package libubsan1:armhf. 272s Preparing to unpack .../05-libubsan1_14-20240303-1ubuntu1_armhf.deb ... 272s Unpacking libubsan1:armhf (14-20240303-1ubuntu1) ... 272s Selecting previously unselected package libgcc-13-dev:armhf. 272s Preparing to unpack .../06-libgcc-13-dev_13.2.0-17ubuntu2_armhf.deb ... 272s Unpacking libgcc-13-dev:armhf (13.2.0-17ubuntu2) ... 273s Selecting previously unselected package libc-dev-bin. 273s Preparing to unpack .../07-libc-dev-bin_2.39-0ubuntu2_armhf.deb ... 273s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 273s Selecting previously unselected package linux-libc-dev:armhf. 273s Preparing to unpack .../08-linux-libc-dev_6.8.0-11.11_armhf.deb ... 273s Unpacking linux-libc-dev:armhf (6.8.0-11.11) ... 274s Selecting previously unselected package libcrypt-dev:armhf. 274s Preparing to unpack .../09-libcrypt-dev_1%3a4.4.36-4_armhf.deb ... 274s Unpacking libcrypt-dev:armhf (1:4.4.36-4) ... 274s Selecting previously unselected package libtirpc-dev:armhf. 274s Preparing to unpack .../10-libtirpc-dev_1.3.4+ds-1build1_armhf.deb ... 274s Unpacking libtirpc-dev:armhf (1.3.4+ds-1build1) ... 274s Selecting previously unselected package libnsl-dev:armhf. 274s Preparing to unpack .../11-libnsl-dev_1.3.0-3_armhf.deb ... 274s Unpacking libnsl-dev:armhf (1.3.0-3) ... 274s Selecting previously unselected package rpcsvc-proto. 274s Preparing to unpack .../12-rpcsvc-proto_1.4.2-0ubuntu6_armhf.deb ... 274s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 274s Selecting previously unselected package libc6-dev:armhf. 274s Preparing to unpack .../13-libc6-dev_2.39-0ubuntu2_armhf.deb ... 274s Unpacking libc6-dev:armhf (2.39-0ubuntu2) ... 275s Selecting previously unselected package libstdc++-13-dev:armhf. 275s Preparing to unpack .../14-libstdc++-13-dev_13.2.0-17ubuntu2_armhf.deb ... 275s Unpacking libstdc++-13-dev:armhf (13.2.0-17ubuntu2) ... 276s Selecting previously unselected package libgc1:armhf. 276s Preparing to unpack .../15-libgc1_1%3a8.2.6-1_armhf.deb ... 276s Unpacking libgc1:armhf (1:8.2.6-1) ... 276s Selecting previously unselected package libobjc4:armhf. 276s Preparing to unpack .../16-libobjc4_14-20240303-1ubuntu1_armhf.deb ... 276s Unpacking libobjc4:armhf (14-20240303-1ubuntu1) ... 276s Selecting previously unselected package libobjc-13-dev:armhf. 276s Preparing to unpack .../17-libobjc-13-dev_13.2.0-17ubuntu2_armhf.deb ... 276s Unpacking libobjc-13-dev:armhf (13.2.0-17ubuntu2) ... 276s Selecting previously unselected package libclang-common-16-dev. 276s Preparing to unpack .../18-libclang-common-16-dev_1%3a16.0.6-19build1_armhf.deb ... 276s Unpacking libclang-common-16-dev (1:16.0.6-19build1) ... 277s Selecting previously unselected package llvm-16-linker-tools. 277s Preparing to unpack .../19-llvm-16-linker-tools_1%3a16.0.6-19build1_armhf.deb ... 277s Unpacking llvm-16-linker-tools (1:16.0.6-19build1) ... 277s Selecting previously unselected package libclang1-16. 277s Preparing to unpack .../20-libclang1-16_1%3a16.0.6-19build1_armhf.deb ... 277s Unpacking libclang1-16 (1:16.0.6-19build1) ... 278s Selecting previously unselected package clang-16. 278s Preparing to unpack .../21-clang-16_1%3a16.0.6-19build1_armhf.deb ... 278s Unpacking clang-16 (1:16.0.6-19build1) ... 278s Setting up linux-libc-dev:armhf (6.8.0-11.11) ... 278s Setting up libgomp1:armhf (14-20240303-1ubuntu1) ... 278s Setting up libtirpc-dev:armhf (1.3.4+ds-1build1) ... 278s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 278s Setting up libatomic1:armhf (14-20240303-1ubuntu1) ... 278s Setting up libgc1:armhf (1:8.2.6-1) ... 278s Setting up libubsan1:armhf (14-20240303-1ubuntu1) ... 278s Setting up libnsl-dev:armhf (1.3.0-3) ... 278s Setting up libcrypt-dev:armhf (1:4.4.36-4) ... 278s Setting up libasan8:armhf (14-20240303-1ubuntu1) ... 278s Setting up libllvm16:armhf (1:16.0.6-19build1) ... 278s Setting up libc-dev-bin (2.39-0ubuntu2) ... 278s Setting up libclang1-16 (1:16.0.6-19build1) ... 278s Setting up libobjc4:armhf (14-20240303-1ubuntu1) ... 278s Setting up libclang-common-16-dev (1:16.0.6-19build1) ... 278s Setting up llvm-16-linker-tools (1:16.0.6-19build1) ... 278s Setting up libgcc-13-dev:armhf (13.2.0-17ubuntu2) ... 278s Setting up libclang-cpp16 (1:16.0.6-19build1) ... 278s Setting up libc6-dev:armhf (2.39-0ubuntu2) ... 278s Setting up libobjc-13-dev:armhf (13.2.0-17ubuntu2) ... 278s Setting up libstdc++-13-dev:armhf (13.2.0-17ubuntu2) ... 278s Setting up clang-16 (1:16.0.6-19build1) ... 278s Processing triggers for man-db (2.12.0-3) ... 281s Processing triggers for libc-bin (2.39-0ubuntu2) ... 287s autopkgtest: WARNING: package examl is not installed though it should be 290s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from noble-proposed 300s Reading package lists... 301s Building dependency tree... 301s Reading state information... 303s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 304s Starting 2 pkgProblemResolver with broken count: 0 304s Done 305s Done 306s Starting pkgProblemResolver with broken count: 0 306s Starting 2 pkgProblemResolver with broken count: 0 306s Done 309s The following additional packages will be installed: 309s clang-16 examl libclang-common-16-dev libclang-cpp16t64 libclang1-16t64 309s libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libhwloc-plugins 309s libhwloc15 libllvm16t64 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64 309s libpocl2-common libpocl2t64 librdmacm1t64 libxnvctrl0 llvm-16-linker-tools 309s ocl-icd-libopencl1 openmpi-bin openmpi-common pocl-opencl-icd 309s Suggested packages: 309s clang-16-doc wasi-libc gfortran | fortran-compiler 309s Recommended packages: 309s llvm-16-dev libclang-rt-16-dev 309s The following packages will be REMOVED: 309s libclang-cpp16 libclang1-16 libllvm16 309s The following NEW packages will be installed: 309s examl libclang-cpp16t64 libclang1-16t64 libevent-pthreads-2.1-7 libfabric1 309s libhwloc-plugins libhwloc15 libllvm16t64 libmunge2 libopenmpi3t64 309s libpciaccess0 libpmix2t64 libpocl2-common libpocl2t64 librdmacm1t64 309s libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common pocl-opencl-icd 309s The following packages will be upgraded: 309s clang-16 libclang-common-16-dev libevent-core-2.1-7 llvm-16-linker-tools 309s 4 upgraded, 20 newly installed, 3 to remove and 239 not upgraded. 309s 1 not fully installed or removed. 309s Need to get 50.8 MB of archives. 309s After this operation, 19.0 MB of additional disk space will be used. 309s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 309s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-9build1 [7370 B] 309s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librdmacm1t64 armhf 50.0-2build1 [63.0 kB] 309s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libfabric1 armhf 1.17.0-3build1 [419 kB] 310s Get:5 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc15 armhf 2.10.0-1 [145 kB] 310s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmunge2 armhf 0.5.15-4 [17.1 kB] 310s Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libpciaccess0 armhf 0.17-3 [16.3 kB] 310s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libxnvctrl0 armhf 510.47.03-0ubuntu1 [10.4 kB] 310s Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf ocl-icd-libopencl1 armhf 2.3.2-1 [34.4 kB] 310s Get:10 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc-plugins armhf 2.10.0-1 [13.7 kB] 310s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpmix2t64 armhf 5.0.1-4.1 [616 kB] 311s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libopenmpi3t64 armhf 4.1.6-7ubuntu1 [2041 kB] 312s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-common all 4.1.6-7ubuntu1 [170 kB] 312s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-bin armhf 4.1.6-7ubuntu1 [83.2 kB] 312s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf examl armhf 3.0.22-4build1 [830 kB] 312s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpocl2-common all 5.0-2.1build1 [82.6 kB] 312s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf clang-16 armhf 1:16.0.6-23ubuntu1 [76.5 kB] 312s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf llvm-16-linker-tools armhf 1:16.0.6-23ubuntu1 [1136 kB] 312s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libclang-common-16-dev armhf 1:16.0.6-23ubuntu1 [631 kB] 312s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libllvm16t64 armhf 1:16.0.6-23ubuntu1 [24.2 MB] 315s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libclang-cpp16t64 armhf 1:16.0.6-23ubuntu1 [11.6 MB] 315s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libclang1-16t64 armhf 1:16.0.6-23ubuntu1 [6634 kB] 316s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpocl2t64 armhf 5.0-2.1build1 [1833 kB] 316s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf pocl-opencl-icd armhf 5.0-2.1build1 [7180 B] 317s Fetched 50.8 MB in 7s (7569 kB/s) 317s (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 ... 61559 files and directories currently installed.) 318s Preparing to unpack .../00-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 318s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 318s Selecting previously unselected package libevent-pthreads-2.1-7:armhf. 318s Preparing to unpack .../01-libevent-pthreads-2.1-7_2.1.12-stable-9build1_armhf.deb ... 318s Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 318s Selecting previously unselected package librdmacm1t64:armhf. 318s Preparing to unpack .../02-librdmacm1t64_50.0-2build1_armhf.deb ... 318s Unpacking librdmacm1t64:armhf (50.0-2build1) ... 318s Selecting previously unselected package libfabric1:armhf. 318s Preparing to unpack .../03-libfabric1_1.17.0-3build1_armhf.deb ... 318s Unpacking libfabric1:armhf (1.17.0-3build1) ... 318s Selecting previously unselected package libhwloc15:armhf. 318s Preparing to unpack .../04-libhwloc15_2.10.0-1_armhf.deb ... 318s Unpacking libhwloc15:armhf (2.10.0-1) ... 318s Selecting previously unselected package libmunge2:armhf. 318s Preparing to unpack .../05-libmunge2_0.5.15-4_armhf.deb ... 318s Unpacking libmunge2:armhf (0.5.15-4) ... 318s Selecting previously unselected package libpciaccess0:armhf. 318s Preparing to unpack .../06-libpciaccess0_0.17-3_armhf.deb ... 318s Unpacking libpciaccess0:armhf (0.17-3) ... 318s Selecting previously unselected package libxnvctrl0:armhf. 318s Preparing to unpack .../07-libxnvctrl0_510.47.03-0ubuntu1_armhf.deb ... 318s Unpacking libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 319s Selecting previously unselected package ocl-icd-libopencl1:armhf. 319s Preparing to unpack .../08-ocl-icd-libopencl1_2.3.2-1_armhf.deb ... 319s Unpacking ocl-icd-libopencl1:armhf (2.3.2-1) ... 319s Selecting previously unselected package libhwloc-plugins:armhf. 319s Preparing to unpack .../09-libhwloc-plugins_2.10.0-1_armhf.deb ... 319s Unpacking libhwloc-plugins:armhf (2.10.0-1) ... 319s Selecting previously unselected package libpmix2t64:armhf. 319s Preparing to unpack .../10-libpmix2t64_5.0.1-4.1_armhf.deb ... 319s Unpacking libpmix2t64:armhf (5.0.1-4.1) ... 319s Selecting previously unselected package libopenmpi3t64:armhf. 319s Preparing to unpack .../11-libopenmpi3t64_4.1.6-7ubuntu1_armhf.deb ... 319s Unpacking libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 319s Selecting previously unselected package openmpi-common. 320s Preparing to unpack .../12-openmpi-common_4.1.6-7ubuntu1_all.deb ... 320s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 320s Selecting previously unselected package openmpi-bin. 320s Preparing to unpack .../13-openmpi-bin_4.1.6-7ubuntu1_armhf.deb ... 320s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 320s Selecting previously unselected package examl. 320s Preparing to unpack .../14-examl_3.0.22-4build1_armhf.deb ... 320s Unpacking examl (3.0.22-4build1) ... 320s Selecting previously unselected package libpocl2-common. 320s Preparing to unpack .../15-libpocl2-common_5.0-2.1build1_all.deb ... 320s Unpacking libpocl2-common (5.0-2.1build1) ... 320s Preparing to unpack .../16-clang-16_1%3a16.0.6-23ubuntu1_armhf.deb ... 320s Unpacking clang-16 (1:16.0.6-23ubuntu1) over (1:16.0.6-19build1) ... 321s (Reading database ... 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(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 ... 62021 files and directories currently installed.) 323s Preparing to unpack .../libllvm16t64_1%3a16.0.6-23ubuntu1_armhf.deb ... 323s Unpacking libllvm16t64:armhf (1:16.0.6-23ubuntu1) ... 327s Selecting previously unselected package libclang-cpp16t64. 327s Preparing to unpack .../libclang-cpp16t64_1%3a16.0.6-23ubuntu1_armhf.deb ... 327s Unpacking libclang-cpp16t64 (1:16.0.6-23ubuntu1) ... 328s Selecting previously unselected package libclang1-16t64. 328s Preparing to unpack .../libclang1-16t64_1%3a16.0.6-23ubuntu1_armhf.deb ... 328s Unpacking libclang1-16t64 (1:16.0.6-23ubuntu1) ... 329s Selecting previously unselected package libpocl2t64:armhf. 329s Preparing to unpack .../libpocl2t64_5.0-2.1build1_armhf.deb ... 329s Unpacking libpocl2t64:armhf (5.0-2.1build1) ... 329s Selecting previously unselected package pocl-opencl-icd:armhf. 329s Preparing to unpack .../pocl-opencl-icd_5.0-2.1build1_armhf.deb ... 329s Unpacking pocl-opencl-icd:armhf (5.0-2.1build1) ... 329s Setting up libpciaccess0:armhf (0.17-3) ... 329s Setting up libllvm16t64:armhf (1:16.0.6-23ubuntu1) ... 329s Setting up libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 329s Setting up libmunge2:armhf (0.5.15-4) ... 329s Setting up libpocl2-common (5.0-2.1build1) ... 329s Setting up libhwloc15:armhf (2.10.0-1) ... 329s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 329s Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ... 329s Setting up openmpi-common (4.1.6-7ubuntu1) ... 329s Setting up librdmacm1t64:armhf (50.0-2build1) ... 329s Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 329s Setting up libfabric1:armhf (1.17.0-3build1) ... 329s Setting up libclang-common-16-dev (1:16.0.6-23ubuntu1) ... 329s Setting up libclang1-16t64 (1:16.0.6-23ubuntu1) ... 329s Setting up libhwloc-plugins:armhf (2.10.0-1) ... 329s Setting up libclang-cpp16t64 (1:16.0.6-23ubuntu1) ... 329s Setting up llvm-16-linker-tools (1:16.0.6-23ubuntu1) ... 329s Setting up libpmix2t64:armhf (5.0.1-4.1) ... 329s Setting up libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 329s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 329s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 329s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 329s Setting up clang-16 (1:16.0.6-23ubuntu1) ... 329s Setting up examl (3.0.22-4build1) ... 330s Setting up libpocl2t64:armhf (5.0-2.1build1) ... 330s Setting up pocl-opencl-icd:armhf (5.0-2.1build1) ... 330s Setting up autopkgtest-satdep (0) ... 330s Processing triggers for man-db (2.12.0-3) ... 331s Processing triggers for libc-bin (2.39-0ubuntu2) ... 351s (Reading database ... 62060 files and directories currently installed.) 351s Removing autopkgtest-satdep (0) ... 362s autopkgtest [00:21:52]: test run-unit-test: [----------------------- 365s + pkg=examl 365s + export OMPI_MCA_rmaps_base_oversubscribe=1 365s + OMPI_MCA_rmaps_base_oversubscribe=1 365s + export OMPI_ALLOW_RUN_AS_ROOT=1 365s + OMPI_ALLOW_RUN_AS_ROOT=1 365s + export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 365s + OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 365s + '[' /tmp/autopkgtest.auieyN/autopkgtest_tmp = '' ']' 365s + cp -a /usr/share/doc/examl/testData /tmp/autopkgtest.auieyN/autopkgtest_tmp 365s + cd /tmp/autopkgtest.auieyN/autopkgtest_tmp 365s + gunzip -r testData 365s + parse-examl -s testData/49 -m DNA -n 49.unpartitioned 365s gappyness: 0.074048 365s Pattern compression: ON 365s 365s Alignment has 51 completely undetermined sites that will be automatically removed from the binary alignment file 365s 365s 365s 365s Your alignment has 628 unique patterns 365s 365s 365s Under CAT the memory required by ExaML for storing CLVs and tip vectors will be 365s 1015476 bytes 365s 991 kiloBytes 365s 0 MegaBytes 365s 0 GigaBytes 365s 365s 365s Under GAMMA the memory required by ExaML for storing CLVs and tip vectors will be 365s 3969588 bytes 365s 3876 kiloBytes 365s 3 MegaBytes 365s 0 GigaBytes 365s 365s Please note that, these are just the memory requirements for doing likelihood calculations! 365s To be on the safe side, we recommend that you execute ExaML on a system with twice that memory. 365s 365s 365s Binary and compressed alignment file written to file 49.unpartitioned.binary 365s 365s Parsing completed, exiting now ... 365s 365s + parse-examl -s testData/49 -q testData/49.model -m DNA -n 49.partitioned 365s gappyness: 0.074048 365s Pattern compression: ON 365s 365s Alignment has 51 completely undetermined sites that will be automatically removed from the binary alignment file 365s 365s 365s 365s Your alignment has 642 unique patterns 365s 365s 365s Under CAT the memory required by ExaML for storing CLVs and tip vectors will be 365s 1038114 bytes 365s 1013 kiloBytes 365s 0 MegaBytes 365s 0 GigaBytes 365s 365s 365s Under GAMMA the memory required by ExaML for storing CLVs and tip vectors will be 365s 4058082 bytes 365s 3962 kiloBytes 365s 3 MegaBytes 365s 0 GigaBytes 365s 365s Please note that, these are just the memory requirements for doing likelihood calculations! 365s To be on the safe side, we recommend that you execute ExaML on a system with twice that memory. 365s 365s 365s Binary and compressed alignment file written to file 49.partitioned.binary 365s 365s Parsing completed, exiting now ... 365s 365s + examl -t testData/49.tree -m GAMMA -s 49.unpartitioned.binary -n T1 721s 721s This is ExaML FINE-GRAIN MPI Process Number: 0 721s 721s proc offset length part 721s 0 0 628 0 721s 721s #proc #part #sites 721s 0 1 628 721s 721s 721s 721s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 721s 721s 721s Alignment has 628 distinct alignment patterns 721s 721s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 721s 721s ExaML rapid hill-climbing mode 721s 721s Using 1 distinct models/data partitions with joint branch length optimization 721s 721s 721s All free model parameters will be estimated by ExaML 721s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 721s 721s Partition: 0 721s Alignment Patterns: 628 721s Name: No Name Provided 721s DataType: DNA 721s Substitution Matrix: GTR 721s 721s 721s 721s 721s ExaML was called as follows: 721s 721s examl -t testData/49.tree -m GAMMA -s 49.unpartitioned.binary -n T1 721s 721s 721s Memory Saving Option: DISABLED 721s 721s Best rearrangement radius: 5 721s 721s Likelihood of best tree: -16221.368990 721s 721s 721s Overall Time for 1 Inference 353.421577 721s 721s Overall accumulated Time (in case of restarts): 353.421577 721s 721s Likelihood : -16221.368990 721s 721s 721s Model parameters written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_modelFile.T1 721s Final tree written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_result.T1 721s Execution Log File written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_log.T1 721s Execution information file written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_info.T1 721s + examl -s 49.unpartitioned.binary -R ExaML_binaryCheckpoint.T1_5 -m GAMMA -n T1_RESTART 888s 888s This is ExaML FINE-GRAIN MPI Process Number: 0 888s 888s proc offset length part 888s 0 0 628 0 888s 888s #proc #part #sites 888s 0 1 628 888s 888s 888s 888s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 888s 888s 888s Alignment has 628 distinct alignment patterns 888s 888s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 888s 888s ExaML rapid hill-climbing mode 888s 888s Using 1 distinct models/data partitions with joint branch length optimization 888s 888s 888s All free model parameters will be estimated by ExaML 888s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 888s 888s Partition: 0 888s Alignment Patterns: 628 888s Name: No Name Provided 888s DataType: DNA 888s Substitution Matrix: GTR 888s 888s 888s 888s 888s ExaML was called as follows: 888s 888s examl -s 49.unpartitioned.binary -R ExaML_binaryCheckpoint.T1_5 -m GAMMA -n T1_RESTART 888s 888s 888s Memory Saving Option: DISABLED 888s ExaML Restart with likelihood: -16221.54674043387421988882124423980712890625000000000000 888s 888s Likelihood of best tree: -16221.368990 888s 888s 888s Overall Time for 1 Inference 165.173580 888s 888s Overall accumulated Time (in case of restarts): 366.405370 888s 888s Likelihood : -16221.368990 888s 888s 888s Model parameters written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_modelFile.T1_RESTART 888s Final tree written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_result.T1_RESTART 888s Execution Log File written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_log.T1_RESTART 888s Execution information file written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_info.T1_RESTART 888s + examl -t testData/49.tree -m GAMMA -s 49.partitioned.binary -n T2 1346s 1346s This is ExaML FINE-GRAIN MPI Process Number: 0 1346s 1346s proc offset length part 1346s 0 0 44 3 1346s 0 0 137 2 1346s 0 0 151 0 1346s 0 0 310 1 1346s 1346s #proc #part #sites 1346s 0 4 642 1346s 1346s 1346s 1346s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 1346s 1346s 1346s Alignment has 642 distinct alignment patterns 1346s 1346s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 1346s 1346s ExaML rapid hill-climbing mode 1346s 1346s Using 4 distinct models/data partitions with joint branch length optimization 1346s 1346s 1346s All free model parameters will be estimated by ExaML 1346s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 1346s 1346s Partition: 0 1346s Alignment Patterns: 151 1346s Name: gene1 1346s DataType: DNA 1346s Substitution Matrix: GTR 1346s 1346s 1346s 1346s Partition: 1 1346s Alignment Patterns: 310 1346s Name: gene2 1346s DataType: DNA 1346s Substitution Matrix: GTR 1346s 1346s 1346s 1346s Partition: 2 1346s Alignment Patterns: 137 1346s Name: gene3 1346s DataType: DNA 1346s Substitution Matrix: GTR 1346s 1346s 1346s 1346s Partition: 3 1346s Alignment Patterns: 44 1346s Name: gene4 1346s DataType: DNA 1346s Substitution Matrix: GTR 1346s 1346s 1346s 1346s 1346s ExaML was called as follows: 1346s 1346s examl -t testData/49.tree -m GAMMA -s 49.partitioned.binary -n T2 1346s 1346s 1346s Memory Saving Option: DISABLED 1346s 1346s Best rearrangement radius: 5 1346s 1346s Likelihood of best tree: -16194.095475 1346s 1346s 1346s Overall Time for 1 Inference 456.542077 1346s 1346s Overall accumulated Time (in case of restarts): 456.542077 1346s 1346s Likelihood : -16194.095475 1346s 1346s 1346s Model parameters written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_modelFile.T2 1346s Final tree written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_result.T2 1346s Execution Log File written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_log.T2 1346s Execution information file written to: /tmp/autopkgtest.auieyN/autopkgtest_tmp/ExaML_info.T2 1346s + examl -s 49.unpartitioned.binary -t treeSet -f e -m GAMMA -n T3 1348s 1348s This is ExaML FINE-GRAIN MPI Process Number: 0 1348s 1348s proc offset length part 1348s 0 0 628 0 1348s 1348s #proc #part #sites 1348s 0 1 628 1348s 1348s 1348s 1348s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 1348s 1348s 1348s Alignment has 628 distinct alignment patterns 1348s 1348s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 1348s 1348s ExaML fast tree evaluation mode 1348s 1348s Using 1 distinct models/data partitions with joint branch length optimization 1348s 1348s 1348s All free model parameters will be estimated by ExaML 1348s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 1348s 1348s Partition: 0 1348s Alignment Patterns: 628 1348s Name: No Name Provided 1348s DataType: DNA 1348s Substitution Matrix: GTR 1348s 1348s 1348s 1348s 1348s ExaML was called as follows: 1348s 1348s examl -s 49.unpartitioned.binary -t treeSet -f e -m GAMMA -n T3 1348s 1348s 1348s Memory Saving Option: DISABLED 1348s The file treeSet you want to open for reading does not exist, exiting ... 1348s + true 1348s + examl -s 49.unpartitioned.binary -t treeSet -f E -m GAMMA -n T4 1348s 1348s This is ExaML FINE-GRAIN MPI Process Number: 0 1348s 1348s proc offset length part 1348s 0 0 628 0 1348s 1348s #proc #part #sites 1348s 0 1 628 1348s 1348s 1348s 1348s This is ExaML version 3.0.22 released by Alexandros Stamatakis, Andre Aberer, and Alexey Kozlov in April 21 2020. 1348s 1348s 1348s Alignment has 628 distinct alignment patterns 1348s 1348s Proportion of gaps and completely undetermined characters in this alignment: 7.40% 1348s 1348s ExaML slow tree evaluation mode 1348s 1348s Using 1 distinct models/data partitions with joint branch length optimization 1348s 1348s 1348s All free model parameters will be estimated by ExaML 1348s GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter 1348s 1348s Partition: 0 1348s Alignment Patterns: 628 1348s Name: No Name Provided 1348s DataType: DNA 1348s Substitution Matrix: GTR 1348s 1348s 1348s 1348s 1348s ExaML was called as follows: 1348s 1348s examl -s 49.unpartitioned.binary -t treeSet -f E -m GAMMA -n T4 1348s 1348s 1348s Memory Saving Option: DISABLED 1348s The file treeSet you want to open for reading does not exist, exiting ... 1349s + true 1349s + exit 0 1349s autopkgtest [00:38:19]: test run-unit-test: -----------------------] 1354s run-unit-test PASS 1354s autopkgtest [00:38:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1358s autopkgtest [00:38:28]: @@@@@@@@@@@@@@@@@@@@ summary 1358s run-unit-test PASS