Your message dated Mon, 04 Jan 2021 09:34:06 +0000 with message-id <[email protected]> and subject line Bug#978496: fixed in openmpi 4.1.0-4 has caused the Debian Bug report #978496, regarding mca_op_avx.so: undefined symbol: ompi_op_base_module_t_class (ignored) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 978496: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978496 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: libopenmpi3 Version: 4.1.0-2 Severity: normal The new openmpi version seems to have introduced a new missing symbol. It ignores the problem, but that causes problems with runtime then failing to proceed. Not clear to me if this should be considered an error or a warning that needs to be worked around. The issue appears in dolfinx python demos (e.g. the demo_poisson.py demo) stderr gets the message: E subprocess.CalledProcessError: Command '['/usr/bin/python3', 'demo_poisson.py']' died with <Signals.SIGABRT: 6>. /usr/lib/python3.9/subprocess.py:524: CalledProcessError ----------------------------- Captured stderr call ----------------------------- [monte:518022] mca_base_component_repository_open: unable to open mca_op_avx: /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_op_avx.so: undefined symbol: ompi_op_base_module_t_class (ignored) A process has executed an operation involving a call to the fork() system call to create a child process. As a result, the libfabric EFA provider is operating in a condition that could result in memory corruption or other system errors. For the libfabric EFA provider to work safely when fork() is called, you will need to set the following environment variable: RDMAV_FORK_SAFE However, setting this environment variable can result in signficant performance impact to your application due to increased cost of memory registration. You may want to check with your application vendor to see if an application-level alternative (of not using fork) exists. Your job will now abort. If I set environment variable RDMAV_FORK_SAFE as instructed, then the process will run successfully. But is this the best workaround or should some other action be taken? It does seem odd that mca_op_avx.so references an undefined symbol, ompi_op_base_module_t_class. -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.9.0-5-amd64 (SMP w/8 CPU threads) Kernel taint flags: TAINT_WARN Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE=en_AU:en Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages libopenmpi3 depends on: ii libc6 2.31-6 ii libevent-core-2.1-7 2.1.12-stable-1 ii libevent-pthreads-2.1-7 2.1.12-stable-1 ii libfabric1 1.11.0-2 ii libgcc-s1 10.2.1-3 ii libhwloc-plugins 2.4.0+dfsg-2 ii libhwloc15 2.4.0+dfsg-2 ii libibverbs1 32.0-1+b1 ii libnl-3-200 3.4.0-1+b1 ii libpmix2 4.0.0~rc1-2 ii libpsm-infinipath1 3.3+20.604758e7-6+b1 ii libpsm2-2 11.2.185-1 ii libstdc++6 10.2.1-3 ii libucx0 1.9.0~rc1-2 ii zlib1g 1:1.2.11.dfsg-2 libopenmpi3 recommends no packages. libopenmpi3 suggests no packages. -- no debconf information
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--- Begin Message ---Source: openmpi Source-Version: 4.1.0-4 Done: Alastair McKinstry <[email protected]> We believe that the bug you reported is fixed in the latest version of openmpi, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Alastair McKinstry <[email protected]> (supplier of updated openmpi package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 03 Jan 2021 22:22:09 +0000 Source: openmpi Architecture: source Version: 4.1.0-4 Distribution: unstable Urgency: mediuzm Maintainer: Alastair McKinstry <[email protected]> Changed-By: Alastair McKinstry <[email protected]> Closes: 978496 979041 Changes: openmpi (4.1.0-4) unstable; urgency=mediuzm . * Rename some scripts to drop language suffix - aggregate_profile.pl -> aggregate_profile - profile2mat.pl -> profile2man * Drop dependencies on libpmix* as we use the internal version * Fix for missing plugin mca_op_avx.so. Closes: #979041, #978496 * Update shymlink to jquery.js for version number change Checksums-Sha1: 5705232793955620fc5b91037eb0618f258743e2 2649 openmpi_4.1.0-4.dsc b2d9be8097aad5e84cf3e0363e03ad4a376bd2d9 67852 openmpi_4.1.0-4.debian.tar.xz Checksums-Sha256: 34a2ba1f9e6e3cb04afd6d214f692b5bfd253df9ed229801b5e175d0ce289b0c 2649 openmpi_4.1.0-4.dsc a70310291f0da6e436718f993447b1e3457e2467d44eded454f768001e45141a 67852 openmpi_4.1.0-4.debian.tar.xz Files: ae130c80add399b7d64be3630af71a29 2649 net optional openmpi_4.1.0-4.dsc 61108978221b0e607a869167631a5343 67852 net optional openmpi_4.1.0-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEgjg86RZbNHx4cIGiy+a7Tl2a06UFAl/y3gUACgkQy+a7Tl2a 06W8phAAiRAGgmrwJinavg2h4Y1rzEzNiUJKz3xXw7Rhqfy1Pw3JTfsFHo7De4kf 9uhIrFSJTMSjK0PZj2zFCdaLi7rxrDI/jzmYVCGFZmIYniKUB1FqaXICpvuNFIlA JhiHSPOORdr+UGIpF6/fXujy1smsLiwrK5qM6vzqa7GDxYw5YGTRgdgD9E3ruP8V YxSE0GmbpKMdmK8S6dYpCOBk3SZZQgBahJLRHJzWXhjg5tS3FRXAOres9XKARatg ltLOmrtM6u3V1HJ6CewwLXa6xV6UJXEosbh8zICo3mSRi2KNufLhKSea4Q4QKUg4 mA3NfPhP+nz0eJ8+oOAb6ovoLdMag5L2cjHAxNJJ5QVEDI9pj3nKqWcVIdg0Ci3d O7ECeB03HMTygVS8UnDm0oQAMdrtrrSSa+6Tx3NhO2z+IMKhABLdLRyxNi61WQTg KUXPTCKL3eBnFT3p6Q98tGDO/Nc4uFQWRf7aJQefUIVVIYi0AL446i3+kIwChRVx 4iiu2mR9LXKs50sDdOmNkzPOmJ1zJHmi0uaJLdkJUHBk39Ek84iF+JhuTgiSUaJB Uc3qxM6+FRfZiesw2I0wppwXmxJB/tjItbvJTgW4ov2PliUpwiG9x/QI1AQvyfnb /OyzJuOzEpGGAAECU4ydfk5WWCq9CFwigycUSCdqXjGs2COEbfo= =6Hx7 -----END PGP SIGNATURE-----
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