If anyone could take me off this mailing list, that would be great. thanks, Blake Dixon ----- Original Message ----- From: Louise-Amélie Schmitt <louise-amelie.schmitt@embl.de> Date: Tuesday, April 19, 2011 7:39 am Subject: [galaxy-user] suggestion for multithreading To: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
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 whenthe 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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