Your message dated Sun, 04 Aug 2019 13:25:50 +0000
with message-id <e1hugwe-0000gx...@fasolo.debian.org>
and subject line Bug#933845: fixed in petsc 3.11.3+dfsg1-2
has caused the Debian Bug report #933845,
regarding libpmi-pmix-dev: MPI failure in dolfin tests
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.
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--
933845: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=933845
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: libpmi-pmix-dev
Version: 3.1.4~rc2-1
Severity: serious
Justification: breaks MPI client tests
Hi Alistair and Debian science,
I'm upgrading dolfin/fenics to 2019.1.0 alongside HYPRE 2.16.0, PETSc
3.11.3, pybind11 2.3.0. The tests of the libraries have passed, but
the build is failing badly with an MPI error:
Run C++ regressions tests (serial)
Test project /home/projects/fenics/build/dolfin/obj-x86_64-linux-gnu
...
Start 13: demo_eigenvalue_serial
3/51 Test #13: demo_eigenvalue_serial ....................***Failed 0.02
sec
*** The MPI_Comm_rank() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[grendel:16518] Local abort before MPI_INIT completed completed successfully,
but am not able to aggregate error messages, and not able to guarantee that all
other processes were killed!
The same error is also triggered when running with mpirun, so the
problem is not due to running an MPI-linked program as a serial job.
I tested the build last week before proceeding with the upgrades and
package uploads, all was fine then. The nature and the timing of the
error suggests to me that pmix 3.1.4~rc2-1 (built last Thursday
1/8/2019) might be involved.
It doesn't make sense that pmix should trigger an error like this, but
I've filed this RC bug against pmix to halt migration while we look
into it.
I've raised a discussion thread with FEniCS upstream at
https://fenicsproject.slack.com/archives/C26N589GV/p1564913720002300
Drew
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.19.0-5-amd64 (SMP w/4 CPU cores)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8),
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages libpmi-pmix-dev depends on:
ii libpmi1-pmix 3.1.4~rc2-1
ii libpmi2-pmix 3.1.4~rc2-1
libpmi-pmix-dev recommends no packages.
libpmi-pmix-dev suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: petsc
Source-Version: 3.11.3+dfsg1-2
We believe that the bug you reported is fixed in the latest version of
petsc, 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 933...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <dpars...@debian.org> (supplier of updated petsc 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, 04 Aug 2019 19:56:06 +0800
Source: petsc
Architecture: source
Version: 3.11.3+dfsg1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Closes: 933845
Changes:
petsc (3.11.3+dfsg1-2) unstable; urgency=medium
.
* debian patch HDF5_refactor_6a0bd752.diff applies upstream patch
6a0bd752 to keep HDF5 support from interfering with PETSc clients
that do not use HDF5. Closes: #933845.
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petsc_3.11.3+dfsg1-2.debian.tar.xz
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