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Subject: Re: [OMPI users] About openmpi-mpirun
From: Min Zhu (min.zhu_at_[hidden])
Date: 2009-12-17 11:32:25


Hi,

This time the OUT file is
--------------------------------
Sender: LSF System <lavaadmin_at_compute-01>
Subject: Job 667: <openmpi-mpirun "/bin/sh -c 'ulimit -s unlimited ; ./wrf.exe ' " > Exited

Job <openmpi-mpirun "/bin/sh -c 'ulimit -s unlimited ; ./wrf.exe ' " > was submitted from host <seamus> by user <mzh>.
Job was executed on host(s) <8*compute-01>, in queue <normal>, as user <mzh>.
                            <8*compute-12>
</home/mzh> was used as the home directory.
</home/mzh/wrf-intel/test/em_real> was used as the working directory.
Started at Thu Dec 17 18:27:58 2009
Results reported at Thu Dec 17 18:28:04 2009

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
openmpi-mpirun "/bin/sh -c 'ulimit -s unlimited ; ./wrf.exe ' "
------------------------------------------------------------

Exited with exit code 2.

Resource usage summary:

    CPU time : 0.07 sec.

The output (if any) follows:

PS:

Read file <ERR> for stderr output of this job.
-------------------------------------

ERR file is,
--------------------------------
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
-s: -c: line 0: unexpected EOF while looking for matching `''
-s: -c: line 1: syntax error: unexpected end of file
------------------------------

Cheers,

Min Zhu

-----Original Message-----
From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Jeroen Kleijer
Sent: 17 December 2009 16:24
To: Open MPI Users
Subject: Re: [OMPI users] About openmpi-mpirun

Hi Min,

Seems like the command ulimit was executed 16 times but after that
(the "; ./wrf.exe") was ignored.
Could you give the following a try:

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

Somewhere, quoting goes wrong and I'm trying to figure out where....

Kind regards,

Jeroen Kleijer

On Thu, Dec 17, 2009 at 5:09 PM, Min Zhu <min.zhu_at_[hidden]> wrote:
> Hi, Jeroen,
>
> Here is the OUT file, ERR file is empty.
>
> --------------------------------------------------------------------------------------
> Sender: LSF System <lavaadmin_at_compute-10>
> Subject: Job 662: <openmpi-mpirun /bin/sh -c 'ulimit -s unlimited; ./wrf.exe ' > Done
>
> Job <openmpi-mpirun /bin/sh -c 'ulimit -s unlimited; ./wrf.exe ' > was submitted from host <seamus> by user <mzh>.
> Job was executed on host(s) <8*compute-10>, in queue <normal>, as user <mzh>.
>                            <8*compute-11>
> </home/mzh> was used as the home directory.
> </home/mzh/wrf-intel/test/run1> was used as the working directory.
> Started at Thu Dec 17 17:37:09 2009
> Results reported at Thu Dec 17 17:37:15 2009
>
> Your job looked like:
>
> ------------------------------------------------------------
> # LSBATCH: User input
> openmpi-mpirun /bin/sh -c 'ulimit -s unlimited; ./wrf.exe '
> ------------------------------------------------------------
>
> Successfully completed.
>
> Resource usage summary:
>
>    CPU time   :      0.05 sec.
>
> The output (if any) follows:
>
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
> unlimited
>
>
> PS:
>
> Read file <ERR> for stderr output of this job.
>
> --------------------------------------------------
>
> Thanks,
>
> Min Zhu
>
>
> -----Original Message-----
> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Jeroen Kleijer
> Sent: 17 December 2009 16:05
> To: Open MPI Users
> Subject: Re: [OMPI users] About openmpi-mpirun
>
> 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.zhu_at_[hidden]> 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-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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