[modeller_usage] Multicore Jobs on QB3 Cluster Nodes

[Albion Baucom <baucom@msg.ucsf.edu>]

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