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