Thank you for the replies. Do I understand correctly that since OpenMPI
v1.10 is no longer supported, I am unlikely to see a bug fix for this
without moving to v2.x or v3.x? I am dealing with clusters where the
administrators may be loathe to update packages until it is absolutely
necessary, and want to present them with a complete outlook on the problem.
Thanks,
Nik
2017-11-07 19:00 GMT-07:00 r...@open-mpi.org <r...@open-mpi.org>:
> Glad to hear it has already been fixed :-)
>
> Thanks!
>
> On Nov 7, 2017, at 4:13 PM, Tru Huynh <t...@pasteur.fr> wrote:
>
> Hi,
>
> On Tue, Nov 07, 2017 at 02:05:20PM -0700, Nikolas Antolin wrote:
>
> Hello,
>
> In debugging a test of an application, I recently came across odd behavior
> for simultaneous MPI_Abort calls. Namely, while the MPI_Abort was
> acknowledged by the process output, the mpirun process failed to exit. I
> was able to duplicate this behavior on multiple machines with OpenMPI
> versions 1.10.2, 1.10.5, and 1.10.6 with the following simple program:
>
> #include <mpi.h>
> #include <stdio.h>
> #include <unistd.h>
> #include <stdbool.h>
>
> int main(int argc, char **argv)
> {
> int rank;
>
> MPI_Init(&argc,&argv);
> MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>
> printf("I am process number %d\n", rank);
> MPI_Abort(MPI_COMM_WORLD, 3);
> return 0;
> }
>
> Is this a bug or a feature? Does this behavior exist in OpenMPI versions
> 2.0 and 3.0?
>
> I compiled your test case on CentOS-7 with openmpi 1.10.7/2.1.2 and
> 3.0.0 and the program seems to run fine.
>
> [tru@borma openmpi-test-abort]$ for i in 1.10.7 2.1.2 3.0.0; do
>
>
> module purge
> && module add openmpi/$i && mpicc aa.c -o aa-$i && ldd aa-$i; mpirun -n 2
> ./aa-$i ; done
>
>
> linux-vdso.so.1 => (0x00007ffe115bd000)
> libmpi.so.12 => /c7/shared/openmpi/1.10.7/lib/libmpi.so.12
> (0x00007f40d7b4a000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f40d78f7000)
> libc.so.6 => /lib64/libc.so.6 (0x00007f40d7534000)
> libopen-rte.so.12 => /c7/shared/openmpi/1.10.7/lib/libopen-rte.so.12
> (0x00007f40d72b8000)
> libopen-pal.so.13 => /c7/shared/openmpi/1.10.7/lib/libopen-pal.so.13
> (0x00007f40d6fd9000)
> libnuma.so.1 => /lib64/libnuma.so.1 (0x00007f40d6dcd000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00007f40d6bc9000)
> librt.so.1 => /lib64/librt.so.1 (0x00007f40d69c0000)
> libm.so.6 => /lib64/libm.so.6 (0x00007f40d66be000)
> libutil.so.1 => /lib64/libutil.so.1 (0x00007f40d64bb000)
> /lib64/ld-linux-x86-64.so.2 (0x000055f6d96c4000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f40d62a4000)
> I am process number 1
> I am process number 0
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 3.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> [borma.bis.pasteur.fr:08511 <http://borma.bis.pasteur.fr:8511/>] 1 more
> process has sent help message help-mpi-api.txt / mpi-abort
> [borma.bis.pasteur.fr:08511 <http://borma.bis.pasteur.fr:8511/>] Set MCA
> parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> linux-vdso.so.1 => (0x00007fffaabcd000)
> libmpi.so.20 => /c7/shared/openmpi/2.1.2/lib/libmpi.so.20
> (0x00007f5bcee39000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5bcebe6000)
> libc.so.6 => /lib64/libc.so.6 (0x00007f5bce823000)
> libopen-rte.so.20 => /c7/shared/openmpi/2.1.2/lib/libopen-rte.so.20
> (0x00007f5bce5a0000)
> libopen-pal.so.20 => /c7/shared/openmpi/2.1.2/lib/libopen-pal.so.20
> (0x00007f5bce2a7000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00007f5bce0a3000)
> libnuma.so.1 => /lib64/libnuma.so.1 (0x00007f5bcde97000)
> libudev.so.1 => /lib64/libudev.so.1 (0x00007f5bcde81000)
> librt.so.1 => /lib64/librt.so.1 (0x00007f5bcdc79000)
> libm.so.6 => /lib64/libm.so.6 (0x00007f5bcd977000)
> libutil.so.1 => /lib64/libutil.so.1 (0x00007f5bcd773000)
> /lib64/ld-linux-x86-64.so.2 (0x000055718df01000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f5bcd55d000)
> libcap.so.2 => /lib64/libcap.so.2 (0x00007f5bcd357000)
> libdw.so.1 => /lib64/libdw.so.1 (0x00007f5bcd110000)
> libattr.so.1 => /lib64/libattr.so.1 (0x00007f5bccf0b000)
> libelf.so.1 => /lib64/libelf.so.1 (0x00007f5bcccf2000)
> libz.so.1 => /lib64/libz.so.1 (0x00007f5bccadc000)
> liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f5bcc8b6000)
> libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f5bcc6a5000)
> I am process number 1
> I am process number 0
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 3.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> [borma.bis.pasteur.fr:08534 <http://borma.bis.pasteur.fr:8534/>] 1 more
> process has sent help message help-mpi-api.txt / mpi-abort
> [borma.bis.pasteur.fr:08534 <http://borma.bis.pasteur.fr:8534/>] Set MCA
> parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> linux-vdso.so.1 => (0x00007ffc09585000)
> libmpi.so.40 => /c7/shared/openmpi/3.0.0/lib/libmpi.so.40
> (0x00007fa208ffc000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fa208da9000)
> libc.so.6 => /lib64/libc.so.6 (0x00007fa2089e6000)
> libopen-rte.so.40 => /c7/shared/openmpi/3.0.0/lib/libopen-rte.so.40
> (0x00007fa208734000)
> libopen-pal.so.40 => /c7/shared/openmpi/3.0.0/lib/libopen-pal.so.40
> (0x00007fa208431000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00007fa20822d000)
> libnuma.so.1 => /lib64/libnuma.so.1 (0x00007fa208021000)
> libudev.so.1 => /lib64/libudev.so.1 (0x00007fa20800b000)
> librt.so.1 => /lib64/librt.so.1 (0x00007fa207e03000)
> libm.so.6 => /lib64/libm.so.6 (0x00007fa207b01000)
> libutil.so.1 => /lib64/libutil.so.1 (0x00007fa2078fd000)
> libz.so.1 => /lib64/libz.so.1 (0x00007fa2076e7000)
> /lib64/ld-linux-x86-64.so.2 (0x000055e717175000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fa2074d0000)
> libcap.so.2 => /lib64/libcap.so.2 (0x00007fa2072cb000)
> libdw.so.1 => /lib64/libdw.so.1 (0x00007fa207084000)
> libattr.so.1 => /lib64/libattr.so.1 (0x00007fa206e7e000)
> libelf.so.1 => /lib64/libelf.so.1 (0x00007fa206c66000)
> liblzma.so.5 => /lib64/liblzma.so.5 (0x00007fa206a40000)
> libbz2.so.1 => /lib64/libbz2.so.1 (0x00007fa20682f000)
> I am process number 0
> I am process number 1
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 3.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> [borma.bis.pasteur.fr:08561 <http://borma.bis.pasteur.fr:8561/>] 1 more
> process has sent help message help-mpi-api.txt / mpi-abort
> [borma.bis.pasteur.fr:08561 <http://borma.bis.pasteur.fr:8561/>] Set MCA
> parameter "orte_base_help_aggregate" to 0 to see all help / error messages
>
> When I increased the number of MPI processes from 2 to 6 (the number of
> cores
> of the desktop), only the openmpi-1.10.7 built version hang (killed with
> ctrl-c),
> no errors with the 2.1.2 and 3.0.0 versions.
>
> [tru@borma openmpi-test-abort]$ for i in 1.10.7 2.1.2 3.0.0; do
>
>
> module purge
> && module add openmpi/$i; echo $i; mpirun -n 6 ./aa-$i ; done
>
>
> 1.10.7
> I am process number 0
> I am process number 1
> I am process number 2
> I am process number 3
> I am process number 4
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 3.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> I am process number 5
>
>
>
> ^Cmpirun: abort is already in progress...hit ctrl-c again to forcibly
> terminate
>
> 2.1.2
> I am process number 2
> I am process number 3
> I am process number 4
> I am process number 0
> I am process number 1
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD
> with errorcode 3.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> I am process number 5
> [borma.bis.pasteur.fr:10542] 5 more processes have sent help message
> help-mpi-api.txt / mpi-abort
> [borma.bis.pasteur.fr:10542] Set MCA parameter "orte_base_help_aggregate"
> to 0 to see all help / error messages
> 3.0.0
> I am process number 2
> I am process number 0
> I am process number 3
> I am process number 5
> I am process number 4
> I am process number 1
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 5 in communicator MPI_COMM_WORLD
> with errorcode 3.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> [borma.bis.pasteur.fr:10570] 5 more processes have sent help message
> help-mpi-api.txt / mpi-abort
> [borma.bis.pasteur.fr:10570] Set MCA parameter "orte_base_help_aggregate"
> to 0 to see all help / error messages
>
> -> some race condition on 1.10.7 ?
> Cheers
>
> Tru
>
>
> --
> Dr Tru Huynh | mailto:t...@pasteur.fr <t...@pasteur.fr> | tel/fax +33 1 45
> 68 87 37 <+33%201%2045%2068%2087%2037>/19
> https://research.pasteur.fr/en/team/structural-bioinformatics/
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
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