Just one little fix on line 261:
261                 if ( len(l) > 1 and l[0] == job_wrapper.tool.id ):

Otherwise it pathetically crashes when non-multithreaded jobs are
submitted. Sorry about that.

Regards,
L-A

Le mardi 19 avril 2011 à 14:33 +0200, Louise-Amélie Schmitt a écrit :

Hello everyone,

I'm using TORQUE with Galaxy, and we noticed that if a tool is
multithreaded, the number of needed cores is not communicated to pbs,
leading to job crashes if the required resources are not available when
the job is submitted.

Therefore I modified a little the code as follows in
lib/galaxy/jobs/runners/pbs.py

256         # define PBS job options
257         attrs.append( dict( name = pbs.ATTR_N, value = str( "%s_%s_%
s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) )
258         mt_file = open('tool-data/multithreading.csv', 'r')
259         for l in mt_file:
260                 l = string.split(l)
261                 if ( l[0] == job_wrapper.tool.id ):
262                         attrs.append( dict( name = pbs.ATTR_l,
resource = 'nodes', value = '1:ppn='+str(l[1]) ) )
263                         attrs.append( dict( name = pbs.ATTR_l,
resource = 'mem', value = str(l[2]) ) )
264                         break
265         mt_file.close()
266         job_attrs = pbs.new_attropl( len( attrs ) +
len( pbs_options ) )

(sorry it didn't come out very well due to line breaking)

The csv file contains a list of the multithreaded tools, each line
containing:
<tool id>\t<number of threads>\t<memory needed>\n

And it works fine, the jobs wait for their turn properly, but
information is duplicated. Perhaps there would be a way to include
something similar in galaxy's original code (if it is not already the
case, I may not be up-to-date) without duplicating data.

I hope that helps :)

Best regards,
L-A

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Hi,

When Galaxy is configured to use the DRMAA job runner is there a way for a tool to tell DRMAA the number of cores it would like to request? The equivalent of bsub -n X in LSF where X is min number of cores to have available on node.

best,
leandro

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