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Thread: openSUSE 13.1 - mpirun (openmpi) does not run.

  1. #1

    Default openSUSE 13.1 - mpirun (openmpi) does not run.

    Hello,

    I have installed 13.1 and i tried to run parallel procceses with mpirun and i get the following

    mpirun -n 2 ./john --test
    --------------------------------------------------------------------------
    It looks like opal_init failed for some reason; your parallel process is
    likely to abort. There are many reasons that a parallel process can
    fail during opal_init; some of which are due to configuration or
    environment problems. This failure appears to be an internal failure;
    here's some additional information (which may only be relevant to an
    Open MPI developer):

    opal_shmem_base_select failed
    --> Returned value -1 instead of OPAL_SUCCESS
    --------------------------------------------------------------------------
    --------------------------------------------------------------------------
    It looks like orte_init failed for some reason; your parallel process is
    likely to abort. There are many reasons that a parallel process can
    fail during orte_init; some of which are due to configuration or
    environment problems. This failure appears to be an internal failure;
    here's some additional information (which may only be relevant to an
    Open MPI developer):

    opal_init failed
    --> Returned value Error (-1) instead of ORTE_SUCCESS
    ------------------------------------------------------------
    does anyone has the same problem ?

    uname -a
    Linux wakarako 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013 (e6d4a27) i686 i686 i386 GNU/Linux--------------

    zypper se -s -i mpi
    Loading repository data...
    Reading installed packages...

    S | Name | Type | Version | Arch | Repository
    --+--------------------+---------+--------------+--------+-------------------
    i | libboost_mpi1_53_0 | package | 1.53.0-4.1.2 | i586 | openSUSE-13.1-Oss
    i | libboost_mpi1_53_0 | package | 1.53.0-4.1.2 | i586 | openSUSE-13.1-1.10
    i | mpi-selector | package | 1.0.3-9.1.2 | noarch | openSUSE-13.1-Oss
    i | mpi-selector | package | 1.0.3-9.1.2 | noarch | openSUSE-13.1-1.10
    i | openmpi | package | 1.7.2-2.1.3 | i586 | openSUSE-13.1-Oss
    i | openmpi | package | 1.7.2-2.1.3 | i586 | openSUSE-13.1-1.10

    cat /proc/meminfo
    MemTotal: 5031248 kB
    MemFree: 330036 kB
    Buffers: 93580 kB
    Cached: 3250836 kB
    SwapCached: 7252 kB
    Active: 3139252 kB
    Inactive: 1311504 kB
    Active(anon): 2539224 kB
    Inactive(anon): 713196 kB
    Active(file): 600028 kB
    Inactive(file): 598308 kB
    Unevictable: 0 kB
    Mlocked: 0 kB
    HighTotal: 4206596 kB
    HighFree: 209520 kB
    LowTotal: 824652 kB
    LowFree: 120516 kB
    SwapTotal: 2101240 kB
    SwapFree: 2071512 kB
    Dirty: 3084 kB
    Writeback: 0 kB
    AnonPages: 1099252 kB
    Mapped: 242608 kB
    Shmem: 2146080 kB
    Slab: 93676 kB
    SReclaimable: 69788 kB
    SUnreclaim: 23888 kB
    KernelStack: 3240 kB
    PageTables: 17364 kB
    NFS_Unstable: 0 kB
    Bounce: 0 kB
    WritebackTmp: 0 kB
    CommitLimit: 4616864 kB
    Committed_AS: 7386268 kB
    VmallocTotal: 122880 kB
    VmallocUsed: 58332 kB
    VmallocChunk: 56820 kB
    HardwareCorrupted: 0 kB
    AnonHugePages: 202752 kB
    HugePages_Total: 0
    HugePages_Free: 0
    HugePages_Rsvd: 0
    HugePages_Surp: 0
    Hugepagesize: 2048 kB
    DirectMap4k: 122872 kB
    DirectMap2M: 780288 kB

    cat /proc/cpuinfo
    processor : 0
    vendor_id : GenuineIntel
    cpu family : 6
    model : 15
    model name : Intel(R) Pentium(R) Dual CPU E2160 @ 1.80GHz
    stepping : 13
    microcode : 0xa1
    cpu MHz : 1200.000
    cache size : 1024 KB
    physical id : 0
    siblings : 2
    core id : 0
    cpu cores : 2
    apicid : 0
    initial apicid : 0
    fdiv_bug : no
    f00f_bug : no
    coma_bug : no
    fpu : yes
    fpu_exception : yes
    cpuid level : 10
    wp : yes
    flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc arch_perfmon pebs bts aperfmperf pni dtes64 monitor ds_cpl est tm2 ssse3 cx16 xtpr pdcm lahf_lm dtherm
    bogomips : 3590.82
    clflush size : 64
    cache_alignment : 64
    address sizes : 36 bits physical, 48 bits virtual
    power management:

    processor : 1
    vendor_id : GenuineIntel
    cpu family : 6
    model : 15
    model name : Intel(R) Pentium(R) Dual CPU E2160 @ 1.80GHz
    stepping : 13
    microcode : 0xa1
    cpu MHz : 1200.000
    cache size : 1024 KB
    physical id : 0
    siblings : 2
    core id : 1
    cpu cores : 2
    apicid : 1
    initial apicid : 1
    fdiv_bug : no
    f00f_bug : no
    coma_bug : no
    fpu : yes
    fpu_exception : yes
    cpuid level : 10
    wp : yes
    flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc arch_perfmon pebs bts aperfmperf pni dtes64 monitor ds_cpl est tm2 ssse3 cx16 xtpr pdcm lahf_lm dtherm
    bogomips : 3590.82
    clflush size : 64
    cache_alignment : 64
    address sizes : 36 bits physical, 48 bits virtual

  2. #2

    Default Re: openSUSE 13.1 - mpirun (openmpi) does not run.

    I am considering raising a bug but i am not sure if this is an open suse bug or openMPI 1.7.2 one ?
    Could somebody with 13.1 installation check if mpirun ( openMPI 1.7.2 ) works ? I think a simple command like

    mpirun -np 2 ls

    is enough to verify.

    thanks.

    P.S. I am thinking as an alternative is to compile the source code of openMPI (1.6.5 version) at my own ....

  3. #3

    Default Re: openSUSE 13.1 - mpirun (openmpi) does not run.

    Well i found a solution to the above problem and i am witing it here just for anobody who will affected by the same bug.

    I uninstalled mpi-selector

    zypper rm mpi-selector
    Loading repository data...
    Reading installed packages...
    Resolving package dependencies...

    The following packages are going to be REMOVED:
    boost-devel libboost_graph1_53_0 libboost_mpi1_53_0 mpi-selector openmpi

    5 packages to remove.
    After the operation, 97.2 MiB will be freed.
    Continue? [y/n/? shows all options] (y):
    (1/5) Removing boost-devel-1.53.0-4.1.2 ...............................................................................................................................................[done]
    (2/5) Removing libboost_graph1_53_0-1.53.0-4.1.2 ......................................................................................................................................[done]
    (3/5) Removing libboost_mpi1_53_0-1.53.0-4.1.2 ........................................................................................................................................[done]
    (4/5) Removing openmpi-1.7.2-2.1.3 ....................................................................................................................................................[done]
    Additional rpm output:
    defaultpenmpi-1.7.2
    level:system


    (5/5) Removing mpi-selector-1.0.3-9.1.2 ...............................................................................................................................................[done]

    Then i downloaded openmpi-1.6-3.1.2.i586.rpm and openmpi-devel-1.6-3.1.2.i586.rpm from 12.3 repos,
    installed them

    zypper in ./openmpi-1.6-3.1.2.i586.rpm openmpi-devel-1.6-3.1.2.i586.rpm
    Loading repository data...
    Reading installed packages...
    Resolving package dependencies...

    The following NEW packages are going to be installed:
    mpi-selector openmpi openmpi-devel

    3 new packages to install.
    Overall download size: 5.5 MiB. After the operation, additional 17.4 MiB will be used.
    Continue? [y/n/? shows all options] (y):
    Retrieving package mpi-selector-1.0.3-9.1.2.noarch (1/3), 24.4 KiB ( 48.8 KiB unpacked)
    Retrieving: mpi-selector-1.0.3-9.1.2.noarch.rpm .......................................................................................................................................[done]
    Retrieving package openmpi-devel-1.6-3.1.2.i586 (2/3), 3.7 MiB ( 8.7 MiB unpacked)
    Retrieving package openmpi-1.6-3.1.2.i586 (3/3), 1.8 MiB ( 8.7 MiB unpacked)
    (1/3) Installing: mpi-selector-1.0.3-9.1.2 ............................................................................................................................................[done]
    Retrieving package openmpi-devel-1.6-3.1.2.i586 (1/3), 3.7 MiB ( 8.7 MiB unpacked)
    (2/3) Installing: openmpi-devel-1.6-3.1.2 .............................................................................................................................................[done]
    Retrieving package openmpi-1.6-3.1.2.i586 (2/3), 1.8 MiB ( 8.7 MiB unpacked)
    (3/3) Installing: openmpi-1.6-3.1.2 ...................................................................................................................................................[done]

    After that i got the following error

    mpirun -n 2 ls
    --------------------------------------------------------------------------
    Open RTE was unable to open the hostfile:
    /usr/lib/mpi/gcc/openmpi/etc/openmpi-default-hostfile
    Check to make sure the path and filename are correct.
    --------------------------------------------------------------------------
    [wakarako:10091] [[11317,0],0] ORTE_ERROR_LOG: Not found in file base/ras_base_allocate.c at line 200
    [wakarako:10091] [[11317,0],0] ORTE_ERROR_LOG: Not found in file base/plm_base_launch_support.c at line 99
    [wakarako:10091] [[11317,0],0] ORTE_ERROR_LOG: Not found in file plm_rsh_module.c at line 1167

    The problem is that openMPI is looking for file openmpi-default-hostfile not in /etc where is located in my system but in /usr/lib/mpi/gcc/openmpi/etc
    so i went in /usr/lib/mpi/gcc/openmpi made etc directory and then i changed to that etc and i made a symbolink link for file openmpi-default-hostfile in /etc

    cd /usr/lib/mpi/gcc/openmpi
    mkdir etc
    cd etc
    ln -s /etc/openmpi-default-hostfile

    and YEeeeesssss ....

    mpirun -n 2 ./john --test
    Benchmarking: Traditional DES [128/128 BS SSE2]... (2xMPI) DONE
    Many salts: 4294M c/s real, 4294M c/s virtual
    Only one salt: 4294M c/s real, 4294M c/s virtual

    Benchmarking: BSDI DES (x725) [128/128 BS SSE2]... (2xMPI) DONE
    Many salts: 4294M c/s real, 4294M c/s virtual
    Only one salt: 4294M c/s real, 4294M c/s virtual

    .
    .
    .

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