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Subject: Re: [OMPI users] About openmpi-mpirun
From: Min Zhu (min.zhu_at_[hidden])
Date: 2009-12-17 10:03:07


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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CONFIDENTIALITY NOTICE: This e-mail, including any attachments, contains information that may be confidential, and is protected by copyright. It is directed to the intended recipient(s) only.  If you have received this e-mail in error please e-mail the sender by replying to this message, and then delete the e-mail. Unauthorised disclosure, publication, copying or use of this e-mail is prohibited.  Any communication of a personal nature in this e-mail is not made by or on behalf of any RES group company. E-mails sent or received may be monitored to ensure compliance with the law, regulation and/or our policies.