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Subject: Re: [OMPI users] Global Communicator
From: Ralph Castain (rhc_at_[hidden])
Date: 2009-02-06 10:55:56


Hi Ted

 From what I can tell, you are not using Open MPI, but mpich's mpirun.
You might want to ask for help on their mailing list.

Ralph

On Feb 6, 2009, at 8:49 AM, Ted Yu wrote:

> Thanx for the reply.
>
> I guess I should go back a step: I had used the openmpi version on
> my system which is simply:
> "mpirun -machinefile $PBS_NODEFILE -np $NPROCS ${CODE} >/ul/tedhyu/
> fuelcell/HOH/test/HH.out"
>
> This did not work because I was just getting a blank output.
>
> I tried this older version because at least i was getting an output.
> "/opt/mpich-1.2.5.10-ch_p4-gcc/bin/mpirun -machinefile $PBS_NODEFILE
> -np
> $NPROCS ${CODE} >/ul/tedhyu/fuelcell/HOH/test/HH.out"
> I think this older version is failing me for whatever reason. Do
> you have any clue? I read somewhere that new versions of mpirun
> adds extra commandline arguments to the end of the line. Therefore
> the newer version of mpirun may be not be giving an output because
> it sees all extra commandline arguments after my output file >/ul/
> tedhyu/fuelcell/HOH/test/HH.out
>
> This is where I'm reading that there are extra commandline arguments
> for a version of mpirun:
> https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2008-February/029333.html
>
> Again, I'm new at this, and I'm just guessing. Any ideas of where
> to turn would be helpful!
>
> Ted
>
> --- On Thu, 2/5/09, doriankrause <doriankrause_at_[hidden]> wrote:
> From: doriankrause <doriankrause_at_[hidden]>
> Subject: Re: [OMPI users] Global Communicator
> To: tedhyu_at_[hidden], "Open MPI Users" <users_at_[hidden]>
> Date: Thursday, February 5, 2009, 11:14 PM
>
> Ted Yu wrote:
> > I'm trying to run a job based on openmpi. For some reason, the
> program and the global communicator are not in sync and it reads
> that there is
> only one processors, whereas, there should be 2 or more. Any advice
> on where to
> look? Here is my PBS script. Thanx!
> >
> > PBS SCRIPT:
> > #!/bin/sh
> > ### Set the job name
> > #PBS -N HH
> > ### Declare myprogram non-rerunable
> > #PBS -r n
> > ### Combine standard error and standard out to one file.
> > #PBS -j oe
> > ### Have PBS mail you results
> > #PBS -m ae
> > #PBS -M tedhyu_at_[hidden]
> > ### Set the queue name, given to you when you get a reservation.
> > #PBS -q workq
> > ### Specify the number of cpus for your job. This example will
> run on 32
> cpus
> >
> ### using 8 nodes with 4 processes per node.
> > #PBS -l nodes=1:ppn=2,walltime=70:00:00
> > # Switch to the working directory; by default PBS launches
> processes from
> your home directory.
> > # Jobs should only be run from /home, /project, or /work; PBS
> returns
> results via NFS.
> > PBS_O_WORKDIR=/temp1/tedhyu/HH
> > export
> CODE=/project/source/seqquest/seqquest_source_v261j/
> hive_CentOS4.5_parallel/build_261j/quest_ompi.x
> >
> > echo Working directory is $PBS_O_WORKDIR
> > mkdir -p $PBS_O_WORKDIR
> > cd $PBS_O_WORKDIR
> > rm -rf *
> > cp /ul/tedhyu/fuelcell/HOH/test/HH.in ./lcao.in
> > cp /ul/tedhyu/atom_pbe/* .
> > echo Running on host `hostname`
> > echo Time is `date`
> > echo Directory is `pwd`
> > echo This jobs runs on the following processors:
> > echo `cat $PBS_NODEFILE`
> > Number=`wc -l $PBS_NODEFILE | awk '{print $1}'`
> >
> > export Number
> > echo
> ${Number}
> > # Define number of processors
> > NPROCS=`wc -l < $PBS_NODEFILE`
> > # And the number or hosts
> > NHOSTS=`cat $PBS_NODEFILE|uniq|wc -l`
> > echo This job has allocated $NPROCS cpus
> > echo NHOSTS
> > #mpirun -machinefile $PBS_NODEFILE ${CODE}
> >/ul/tedhyu/fuelcell/HOH/test/HH.out
> > #mpiexec -np 2 ${CODE} >/ul/tedhyu/fuelcell/HOH/test/HH.out
> > /opt/mpich-1.2.5.10-ch_p4-gcc/bin/mpirun -machinefile
> $PBS_NODEFILE -np
> $NPROCS ${CODE} >/ul/tedhyu/fuelcell/HOH/test/HH.out
> > cd ..
> > rm -rf HH
> >
> >
> >
>
> Please note, that you are mixing Open MPI (API/Library) with MPICH
> (mpirun). This is a mistake I like to make, too. If you use
> the ompi mpiexec program, it probably works.
>
> Dorian
>
> >
> >
> >
> >
> ------------------------------------------------------------------------
> >
> >
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> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
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