On Sep 14, 2011, at 11:30 AM, Chorny, Ilya wrote:
Nate,
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 parsed?
Thanks,
Ilya
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.Beane@jax.org]
Sent: Tuesday, September 13, 2011 5:00 PM
To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Passing the number of mpi processors to SGE from xml file
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
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.
Thanks,
Ilya
Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582