Your message dated Thu, 03 Jan 2019 10:34:48 +0000
with message-id <[email protected]>
and subject line Bug#918031: fixed in pmix 3.1.0~rc2-2
has caused the Debian Bug report #918031,
regarding openmpi: mpi_init pmix error (gds_dstore.c line 1030)
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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--
918031: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=918031
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: openmpi
Version: 3.1.3-7
Severity: important
Control: affects -1 mpgrafic
Dear Maintainer,
SUMMARY: mpi_init pmix error on GNU/Hurd (gds_dstore.c line 1030)
DESCRIPTION: mpi_init gives a fatal pmix error on GNU/Hurd.
This occurred for a Debian automatic build for mpgrafic-0.3.16-1
on a machine with two processors, and on the Debian porter machine
exodar on a 1-processor machine for a minimal example (provided here).
MINIMAL EXAMPLE:
On exodar:
$ cat openmpi_hurd_bug.f90
program openmpi_hurd_bug
call MPI_INIT(ierr)
call MPI_FINALIZE(ierr)
end program openmpi_hurd_bug
$ mpifort --show
gfortran -I/usr/lib/i386-gnu/openmpi/include -pthread
-I/usr/lib/i386-gnu/openmpi/lib -Wl,--enable-new-dtags
-L/usr/lib/i386-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr
-lmpi_mpifh -lmpi
$ mpifort openmpi_hurd_bug # compiles with no warnings or errors.
$ mpirun -n 1 a.out
[exodar:00753] PMIX ERROR: INIT in file
../../../../../../src/mca/gds/ds12/gds_dstore.c at line 1030
[exodar:00753] PMIX ERROR: ERROR in file
../../../../../../src/mca/gds/ds12/gds_dstore.c at line 2863
[exodar:00753] PMIX ERROR: UNREACHABLE in file
../../../../../../src/mca/ptl/tcp/ptl_tcp_component.c at line 1423
[exodar:00755] PMIX ERROR: UNREACHABLE in file
../../../../../../src/mca/ptl/tcp/ptl_tcp.c at line 790
[exodar:00755] OPAL ERROR: Unreachable in file ext2x_client.c at line 109
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[exodar:00755] 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!
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
C example on exodar:
$ cat openmpi_hurd_bug_C.c
#include <mpi.h>
int main(int argc, char **argv){
MPI_Init(&argc,&argv);
MPI_Finalize();
return 0;
}
$ mpicc --show
gcc -I/usr/lib/i386-gnu/openmpi/include/openmpi
-I/usr/lib/i386-gnu/openmpi/include -pthread -L/usr/lib/i386-gnu/openmpi/lib
-lmpi
$ mpicc openmpi_hurd_bug_C.c # no warnings or errors
$ mpirun -n 1 ./a.out
[exodar:00962] PMIX ERROR: INIT in file
../../../../../../src/mca/gds/ds12/gds_dstore.c at line 1030
[exodar:00962] PMIX ERROR: ERROR in file
../../../../../../src/mca/gds/ds12/gds_dstore.c at line 2863
[exodar:00962] PMIX ERROR: UNREACHABLE in file
../../../../../../src/mca/ptl/tcp/ptl_tcp_component.c at line 1423
[exodar:00964] PMIX ERROR: UNREACHABLE in file
../../../../../../src/mca/ptl/tcp/ptl_tcp.c at line 790
[exodar:00964] OPAL ERROR: Unreachable in file ext2x_client.c at line 109
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[exodar:00964] 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!
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
CONTEXT of minimal example:
This is on an schroot running sid on exodar:
https://db.debian.org/machines.cgi?host=exodar
$ sessionid=$(schroot -b -c sid)
$ dd-schroot-cmd -c ${sessionid} apt-get update
$ dd-schroot-cmd -c ${sessionid} apt-get upgrade
$ dd-schroot-cmd -c $sessionid apt-get install mpifort mpi-default-dev mpi-default-bin gfortran
$ schroot -e -c ${sessionid}
$ uname -a
GNU exodar 0.9 GNU-Mach 1.8+git20181103-486-dbg/Hurd-0.9 i686-AT386 GNU
$ cat /proc/hostinfo
Basic info:
max_cpus = 1 /* max number of cpus possible */
avail_cpus = 1 /* number of cpus now available */
memory_size = 3221151744 /* size of memory in bytes */
cpu_type = 19 /* cpu type */
cpu_subtype = 1 /* cpu subtype */
$ dpkg -l |egrep "openmpi|pmix|gfortran|gcc|mpifort"
ii gcc 4:8.2.0-2 hurd-i386 GNU
C compiler
ii gcc-8 8.2.0-13 hurd-i386 GNU
C compiler
ii gcc-8-base:hurd-i386 8.2.0-13 hurd-i386
GCC, the GNU Compiler Collection (base package)
ii gfortran 4:8.2.0-2 hurd-i386 GNU
Fortran 95 compiler
ii gfortran-8 8.2.0-13 hurd-i386 GNU
Fortran compiler
ii libgcc-8-dev:hurd-i386 8.2.0-13 hurd-i386 GCC
support library (development files)
ii libgcc1:hurd-i386 1:8.2.0-13 hurd-i386 GCC
support library
ii libgfortran-8-dev:hurd-i386 8.2.0-13 hurd-i386
Runtime library for GNU Fortran applications (development files)
ii libgfortran5:hurd-i386 8.2.0-13 hurd-i386
Runtime library for GNU Fortran applications
ii libopenmpi-dev:hurd-i386 3.1.3-7 hurd-i386
high performance message passing library -- header files
ii libopenmpi3:hurd-i386 3.1.3-7 hurd-i386
high performance message passing library -- shared library
ii libpmix2:hurd-i386 3.0.2-2 hurd-i386
Process Management Interface (Exascale) library
ii openmpi-bin 3.1.3-7 hurd-i386
high performance message passing library -- binaries
ii openmpi-common 3.1.3-7 all
high performance message passing library -- common files
REPRODUCIBILITY:
(1) Again on exodar, same context, compiled fortran file:
$ mpirun -n 1 --mca plm_rsh_agent /bin/false ./a.out
gives the same error messages, apart from the exodar prompt ([exodar:00808]...).
(2) This bug was originally detected on an mpgrafic build:
https://buildd.debian.org/status/fetch.php?pkg=mpgrafic&arch=hurd-i386&ver=0.3.16-1&stamp=1546275082&raw=0
678 This looks like a debian openmpi system.
679 [ironforge:13033] PMIX ERROR: INIT in file
../../../../../../src/mca/gds/ds12/gds_dstore.c at line 1030
680 [ironforge:13033] PMIX ERROR: ERROR in file
../../../../../../src/mca/gds/ds12/gds_dstore.c at line 2863
681 [ironforge:13033] PMIX ERROR: UNREACHABLE in file
../../../../../../src/mca/ptl/tcp/ptl_tcp_component.c at line 1423
682 [ironforge:13035] PMIX ERROR: UNREACHABLE in file
../../../../../../src/mca/ptl/tcp/ptl_tcp.c at line 790
683 [ironforge:13035] OPAL ERROR: Unreachable in file ext2x_client.c at line
109
684 *** An error occurred in MPI_Init
685 *** on a NULL communicator
686 *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
687 *** and potentially your MPI job)
688 [ironforge:13035] 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!
Cheers
Boud
--- End Message ---
--- Begin Message ---
Source: pmix
Source-Version: 3.1.0~rc2-2
We believe that the bug you reported is fixed in the latest version of
pmix, 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 pmix 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: Thu, 03 Jan 2019 10:09:06 +0000
Source: pmix
Binary: libpmix-dev libpmi-pmix-dev libpmi1-pmix libpmi2-pmix libpmix2
Architecture: source amd64
Version: 3.1.0~rc2-2
Distribution: unstable
Urgency: medium
Maintainer: Alastair McKinstry <[email protected]>
Changed-By: Alastair McKinstry <[email protected]>
Description:
libpmi-pmix-dev - Development files for the PMI library (OpenMPI )
libpmi1-pmix - OpenMPI implementation of the PMI v1 library
libpmi2-pmix - OpenMPI implementation of the PMI v2 library
libpmix-dev - Development files for the PMI Exascale library
libpmix2 - Process Management Interface (Exascale) library
Closes: 918031
Changes:
pmix (3.1.0~rc2-2) unstable; urgency=medium
.
* Standards-Version: 4.3.0
* Fix for handle setsockopt(SO_RCVTIMEO) not being supported.
Thanks to Samuel Thibault. Closes: #918031
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