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
