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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