Your message dated Mon, 04 Jan 2021 09:34:06 +0000
with message-id <e1kwmfa-000czn...@fasolo.debian.org>
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
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immediately.)
--
978496: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978496
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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
--- End Message ---
--- Begin Message ---
Source: openmpi
Source-Version: 4.1.0-4
Done: Alastair McKinstry <mckins...@debian.org>
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 978...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Alastair McKinstry <mckins...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----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 <mckins...@debian.org>
Changed-By: Alastair McKinstry <mckins...@debian.org>
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
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Files:
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