Hi Min Did you get any type of error message in the ERR or OUT files? I don't have mpirun installed in the environment at the moment but giving the following:
bsub -q interq -I "ssh <hostname> /bin/sh -c 'ulimit -s unlimited ; /bin/hostname ' " seems to work for me, so I'm kind of curious what the error message is you're seeing. Kind regards, Jeroen Kleijer On Thu, Dec 17, 2009 at 4:41 PM, Min Zhu <min....@res-ltd.com> wrote: > 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. 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. >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >> >> >> -- >> >> 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. 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. >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> > > _______________________________________________ > 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. 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. > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
