Hi, I'm a member of the group that develops OMA.

I think the problem here is that the environment variable (NR_PROCESSES) is being set locally, however qsub doesn't copy the environment variables set on the submission node to the worker nodes by default.

The -V option would copy all environment variables, so that your command listed above would become

export NR_PROCESSES=100
qsub -V -b y -j y -t 1-40 -cwd /usr/local/OMA/bin/OMA

There is also the short-hand (using -v), of

qsub -v NR_PROCESSES=100 -b y -j y -t 1-40 -cwd /usr/local/OMA/bin/OMA

if you only need to set NR_PROCESSES.

The command qstat -j <JOB_ID> lists the environment variables to copy to the worker nodes, so that you can verify it's set.

Best wishes, Alex

Hi,

I think this problem is related to the way you submit the job and the specific configurations of the SGE system. I suggest you try to launch the job with a submission script, e.g.

cat > ./start-oma.sh << EOF
#!/bin/bash
#$ -S /bin/bash
# Request ten minutes of wallclock time
#$ -l h_rt=0:10:0
# Request 2 gigabyte of RAM.
#$ -l h_vmem=2G,tmem=2G
# Set up the job array, e.g. 3 tasks
#$ -t 1-3
# Set the name of the job
#$ -N oma
#$ -cwd

# Run the application.
export NR_PROCESSES=3
/usr/local/OMA/bin/OMA
EOF

The resulting submission script can then be used for submitting to the cluster

qsub start-oma.sh

At least this setup seems to work for me. Your above submission also results in an error for me, so I think chances are high this will work.