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[modeller_usage] Multicore Jobs on QB3 Cluster Nodes



How would I go about passing arguments to sge_qsub_job to get slave node jobs to use multiple cores on the QB3 cluster?

I am familiar with using a SGE script to start parallel jobs on QB3 nodes using qsub. What I would like to do is use Modeller to start multiple jobs on nodes using multiple cores.

For instance in a qsub script I might pass the following arguments

#$ -pe smp 4
#$ -R yes

Which uses 4 cores after using the queue to reserve that slave node.

I am currently using the following Modeller directive to submit multiple jobs to the cluster

j = sge_qsub_job(maxslave=jobparas.maxslave,options =jobparas.optionline,modeller_path=jobparas.modeller_path)

where

jobparas = jobparameters(maxslave=5, arch='opt64', queue='long.q', name='htpg', modeller_path="/diva1/home/modeller/SVN/bin/ modpy.sh \ /diva1/home/modeller/SVN/bin/ modslave.py")

My question, is how do I pass the arguments "-pe smp 4" and "-R yes" for instance? Looking at the Modeller documentation, its not clear how those parameters could be passed as arguments to sge_qsub_job in this instance.

Perhaps there is a better way to issue the parallelization options to Modeller?

Thanks

Albion