On Sep 14, 2011, at 11:30 AM, Chorny, Ilya wrote:


Any thoughts on how to do this? Can I add an xml tag that gets parsed and set’s 
“ –PE mpi $NSLOTS” in the job template. Can you point me to where the xml get’s 



I'm not that familiar with SGE, but this would be pretty trivial with TORQUE 
assuming a fixed number of MPI processes for the tool. No modifications to the 
job template would be necessary:  tool specific job runner specifies number of 
nodes/ppn or procs; mpiexec (built with TM support) launches appropriate number 
of processes on all nodes assigned to job by TORQUE.

From: Glen Beane [mailto:glen.be...@jax.org]
Sent: Tuesday, September 13, 2011 5:00 PM
To: Chorny, Ilya; 
Subject: RE: [galaxy-dev] Passing the number of mpi processors to SGE from xml 

I think with the current state of Galaxy this would need to be fixed.  You 
would need to hard code the number of processors in the xml wrapper and in the 
corresponding job runner for that tool

[galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Chorny, Ilya 
Sent: Tuesday, September 13, 2011 7:58 PM
To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] Passing the number of mpi processors to SGE from xml file
Any thoughts on how to pass the number of processor I want to use from my xml 
wrapper to the job template. I am trying to wrap pBWA and use mpi.



Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>

Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
(207) 288-6153

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