[GE users] OpenMPI job on stay on one node

sgexav xaviercouvelard at gmail.com
Mon Sep 7 12:05:31 BST 2009


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reuti a écrit :
> Hi,
>
> Am 07.09.2009 um 12:04 schrieb sgexav:
>
>   
>> Hi,
>> I am running a parallel code with openmpi.
>> the code needs 12 proc and nodes have 8.
>>
>> With the classicam mpirun -np 12 ........; it works prefectly
>>
>> But with SGE the 12 process stay on one node.
>>
>> qsub script.sh
>> Here is may submission script,
>>  #!/bin/sh
>> #
>> # job name
>> #$ -N ROMS_TEST
>> #
>> # Use current working directory
>> #$ -cwd
>> #
>> # Join stdout and stderr
>> #$ -j y
>>
>> # define queue
>> #$ -q all.q
>>
>> #$ -pe mpi 12
>>
>> # Run job through bash shell
>> #$ -S /bin/bash
>> #
>> echo "Got $NSLOTS processors."
>> echo "Machines:"
>> cat $TMPDIR/machines
>>
>> export PATH=/opt/openmpi-1.3.3/bin/:$PATH
>> export
>> LD_LIBRARY_PATH=/opt/openmpi-1.3.3/lib:/opt/intel/Compiler/11.1/046/ 
>> lib/intel64:$LD_LIBRARY_PATH
>> #export OMPI_MCA_pls_rsh_agent=rsh
>>
>> mpirun -np $NSLOTS  -hostfile $TMPDIR/machines ./roms roms.in
>>     
>
> a) you compiled Open MPI with SGE support?
>
> b) what does your PE look like - you followed the Howto for SGE on  
> the Open MPI site (http://www.open-mpi.org/faq/?category=running#run- 
> n1ge-or-sge)?
>
>   
and if use pe orte 12 which seems to be the good one

i get
Got 12 processors.
Machines:
cat: /tmp/38.1.all.q/machines: No such file or directory
--------------------------------------------------------------------------
Open RTE was unable to open the hostfile:
    /tmp/38.1.all.q/machines
Check to make sure the path and filename are correct.
.....
Xav
> -- Reuti
>
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