Your message dated Sun, 04 Aug 2019 13:25:50 +0000 with message-id <[email protected]> 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. (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.) -- 933845: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=933845 Debian Bug Tracking System Contact [email protected] 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
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--- 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Drew Parsons <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Drew Parsons <[email protected]> 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. Checksums-Sha1: ecc0fca30883755ac9448114230bccc4e46e9dd7 3364 petsc_3.11.3+dfsg1-2.dsc ef75086b2b29a6b9ebd3cdbb1b2f86710bca7ccd 67276 petsc_3.11.3+dfsg1-2.debian.tar.xz Checksums-Sha256: b77d197b12a41b043a0cffd53cf059578d240b0e80c79596f9ae427244837ee3 3364 petsc_3.11.3+dfsg1-2.dsc c644cd9e40b863e1777900f84a0bc5f4d0b27b6b74acb68f3d6d39663e56a317 67276 petsc_3.11.3+dfsg1-2.debian.tar.xz Files: 7f4a92831afb60930e710b249a9d756d 3364 devel optional petsc_3.11.3+dfsg1-2.dsc 95b0bbcc1fe644926a45fe6372b423f0 67276 devel optional petsc_3.11.3+dfsg1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAl1G1iQACgkQVz7x5L1a AfrwmBAAutcd4TzQ7BEB+q9iiXDua4ZWa49DNMsfY0jlgZWjylEn+u7ZzqxqcGXr EH40oVbeOWOoPS7dOEJOgpzzrsX2A0LpM2zb6orAvGK7hZuMWVM2FFIVuFtHeXb/ HBEcv5C6+MuRqr+18yhcj+A1EOA8SpAq2t3gNqk0ka76MDDkG9jDzQf6bfgQ1YvF EzMTKV9XO5e5HDhUS8PQtqN4m5GVicklveu1gNC5m2Lmuy/oWVuQj4NXP8hFKiXx p4N9IKCNHGf62OhssMR7pFHui6SMv/Y0Qsqi1bTiHCnWI5L8zjZTCrNQgJJJJTLQ bIKBULBiDEN82q7nwKgi5DUHxWALWHvWuBtEAnNsitpK+GCIdRLjEp11LJFzJaME nsOzD5PqdQs2JVOgNVSgW5UFO9RgoXjjxLne8m0fmYmah2+HothdTFltThcOopu/ 1501ToZkxbx/3xHpysOZUjdo/AdgWEsvTY0GU5fGZL1E+MYQA0L0PWghxRh2z9lC DFutkh76c4YvzpI/Fn4/vtWT94Gaf6YBSmVNqrnppnRhvzQJ49t7RMFr6Dhtip9W S+vMwoj/80cabAbTq5NSB3AxfaW2hrEGa3VWyEicPAZC2skAJisQCixehpXJEH/G mAKwiyshsV+TruCBmzhl0G7iSe7QdXbwYJ/wPfAfYWJhb5g08LI= =mOgv -----END PGP SIGNATURE-----
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