[modeller_usage] Multicore Jobs on QB3 Cluster Nodes
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Subject: [modeller_usage] Multicore Jobs on QB3 Cluster Nodes
From: Albion Baucom <>
Date: Mon, 8 Dec 2008 14:16:03 -0800
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
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?