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Subject: Re: [OMPI users] About openmpi-mpirun
From: Min Zhu (min.zhu_at_[hidden])
Date: 2009-12-17 09:40:32


Hi, Jeff,

Thanks. For bsub -e ERR -o OUT -n 16 openmpi-mpirun /bin/sh -c "ulimit
-s unlimited; ./wrf.exe", I tried and wrf.exe doesn't executed.

Here is the content of openmpi-mpirun file, so maybe something needs to
be changed?

----------------------------------------------
#!/bin/sh
#
# Copyright (c) 2007 Platform Computing
#
# This script is a wrapper for openmpi mpirun
# it generates the machine file based on the hosts
# given to it by Lava.
#

usage() {
        cat <<USEEOF
USAGE: $0
        This command is a wrapper for mpirun (openmpi). It can
        only be run within Lava using bsub e.g.
                bsub -n # "$0 -np # {my mpi command and args}"

        The wrapper will automatically generate the
        machinefile used by mpirun.

        NOTE: The list of hosts cannot exceed 4KBytes.
USEEOF
}

if [ x"${LSB_JOBFILENAME}" = x -o x"${LSB_HOSTS}" = x ]; then
    usage
    exit -1
fi

MYARGS=$*
WORKDIR=`dirname ${LSB_JOBFILENAME}`
MACHFILE=${WORKDIR}/mpi_machines
ARGLIST=${WORKDIR}/mpi_args

# Check if mpirun is in the PATH
T=`which mpirun`
if [ $? -ne 0 ]; then
    echo "Error: mpirun is not in your PATH."
    exit -2
fi

echo "${MYARGS}" > ${ARGLIST}
T=`grep -- -machinefile ${ARGLIST} |wc -l`
if [ $T -gt 0 ]; then
    echo "Error: Do not provide the machinefile for mpirun."
    echo " It is generated automatically for you."
    exit -3
fi

# Make the open-mpi machine file
echo "${LSB_HOSTS}" > ${MACHFILE}.lst
tr '\/ ' '\r\n' < ${MACHFILE}.lst > ${MACHFILE}

MPIRUN=`which --skip-alias mpirun`
${MPIRUN} -x LD_LIBRARY_PATH -machinefile ${MACHFILE} ${MYARGS}

exit $?

----------------------------------------------

Cheers,

Min Zhu

-----Original Message-----
From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On
Behalf Of Jeff Squyres
Sent: 17 December 2009 14:29
To: Open MPI Users
Subject: Re: [OMPI users] About openmpi-mpirun

On Dec 17, 2009, at 9:15 AM, Min Zhu wrote:

> Thanks for your reply. Yes, your mpirun command works for me. But I
need to use bsub job scheduler. I wonder why
> bsub -e ERR -o OUT -n 16 openmpi-mpirun "/bin/sh -c ulimit -s
unlimited; ./wrf.exe" doesn't work.

Try with different quoting...? I don't know the details of the
openmpi-mpirun script, but perhaps it's trying to exec the whole quoted
string as a single executable (which doesn't exist). Perhaps:

bsub -e ERR -o OUT -n 16 openmpi-mpirun /bin/sh -c "ulimit -s unlimited;
./wrf.exe"

That's a (somewhat educated) guess...

-- 
Jeff Squyres
jsquyres_at_[hidden]
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