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Subject: Re: [OMPI users] Global Communicator
From: doriankrause (doriankrause_at_[hidden])
Date: 2009-02-06 02:14:46


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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