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 <doriankra...@web.de> wrote:
From: doriankrause <doriankra...@web.de>
Subject: Re: [OMPI users] Global Communicator
To: ted...@wag.caltech.edu, "Open MPI Users" <us...@open-mpi.org>
List-Post: users@lists.open-mpi.org
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 ted...@wag.caltech.edu
> ### 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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>
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