[GE users] Submitting parallel environment (MPI) jobs using DRMAA

atlruds atle at numericalrocks.com
Fri Mar 20 14:17:56 GMT 2009


I am using the following command to submit jobs to our SGE queue:
 qsub -A internal -pe orte 32 /net/software/cluster/absperm.sh

How do I specify the "-A internal" and "-pe orte 32" using DRMAA? What 
if I want user input the number of cpu's?

Should I put them in a job category? How do I do that? What if, say, a 
Condor queue is to be used instead? I would also need "-b no" somewhere 
to be able to submit a script and not an executable?

Can I have multiple DRMAA sessions open at the same time? Say I want to 
create a DrmaaSession wrapper object that initializes drmaa in the 
constructor and exits drmaa in the destructor. Would it be possible to 
have multiple of these objects at the same time, or would the second 
init fail?

- Atle

Contents of absperm.sh:

#$ -V
#$ -cwd

export LD_LIBRARY_PATH=/opt/openmpi/lib:${LD_LIBRARY_PATH}
export PATH=/opt/openmpi/bin:${PATH}

echo 'Job launched:'

mpirun -d -np $NSLOTS /net/software/cluster/LB3d_mpi

echo 'Job finished:'


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