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Subject: Re: [OMPI users] About openmpi-mpirun
From: Min Zhu (min.zhu_at_[hidden])
Date: 2009-12-17 10:41:49


Hi, Jeroen,

Thanks for your reply. I tried the command bsub -e ERR -o OUT -n 16 "openmpi-mpirun /bin/sh -c 'ulimit -s unlimited; ./wrf.exe ' " and wrf.exe not executed.

Cheers,

Min Zhu

-----Original Message-----
From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Jeroen Kleijer
Sent: 17 December 2009 15:34
To: Open MPI Users
Subject: Re: [OMPI users] About openmpi-mpirun

It's just that the "'s on the command line get parsed by LSF / bash
(or whatever shell you use)

If you wish to use it without the script you can give this a try:
bsub -e ERR -o OUT -n 16 "openmpi-mpirun /bin/sh -c 'ulimit -s
unlimited; ./wrf.exe ' "

This causes to pass the whole string "openmpi-mpirun ...." to be
passed as a single string / command to LSF.
The second line between the single quotes is then passed as a single
argument to /bin/sh which is run by openmpi-mpirun.

Kind regards,

Jeroen Kleijer

On Thu, Dec 17, 2009 at 4:03 PM, Min Zhu <min.zhu_at_[hidden]> wrote:
> Hi, Jeff,
>
> Your script method works for me. Thank you very much,
>
> Cheers,
>
> Min Zhu
>
>
> -----Original Message-----
> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On
> Behalf Of Jeff Squyres
> Sent: 17 December 2009 14:56
> To: Open MPI Users
> Subject: Re: [OMPI users] About openmpi-mpirun
>
> This might be something you need to talk to Platform about...?
>
> Another option would be to openmpi-mpirun a script that is just a few
> lines long:
>
> #!/bin/sh
> ulimit -s unlimited
> ./wrf.exe
>
>
>
> On Dec 17, 2009, at 9:40 AM, Min Zhu wrote:
>
>> 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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>
>
> --
>
> Jeff Squyres
> jsquyres_at_[hidden]
>
>
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