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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] 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....@res-ltd.com> wrote: > Hi, Jeff, > > Your script method works for me. Thank you very much, > > Cheers, > > Min Zhu > > > -----Original Message----- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] 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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] > 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 >> jsquy...@cisco.com >> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> 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. 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