On further digging, we found that the script is failing in the following part of $GALAXY_HOME/lib/galaxy/jobs/runners/pbs.py:
# submit galaxy_job_id = job_wrapper.job_id log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) ) log.debug("(%s) command is: %s" % ( galaxy_job_id, command_line ) ) job_id = pbs.pbs_submit(c, job_attrs, job_file, pbs_queue_name, None) pbs.pbs_disconnect(c)
# check to see if it submitted if not job_id: errno, text = pbs.error() log.debug( "(%s) pbs_submit failed, PBS error %d: %s" % (galaxy_job_id, errno, text) ) job_wrapper.fail( "Unable to run this job due to a cluster error" ) return
Could this be a problem related to the pbs_python egg (v. pbs_python-4.1.0) being used by Galaxy or a Torque-specific issue? Just to reiterate, we are on a development snapshot of Torque which is hard to replace as many other people using it.
Also, could you please advise which Torque & pbs_python version combinations have you successfully tested against?
PS: pbs_python has a new version 4.3 out (https://subtrac.sara.nl/oss/pbs_python/wiki/TorqueInstallation), why is this not in the PSU egg repository yet? Would that make a difference?
-----Original Message----- From: Sonali Amonkar Sent: Tuesday, February 15, 2011 4:10 PM To: 'Nate Coraor' Cc: Galaxy Dev Subject: RE: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster
We went through the mom_logs. We could see the jobs which were completed successfully in Galaxy. However, the job/ tool run which failed were not seen. These failed jobs were never submitted to PBS queue to be logged in the mom_logs. On another note, is the error, "pbs_submit failed, PBS error 15031: Protocol (ASN.1) error" related to the pbs_python version in Galaxy and the Torque version? Also find attached a workaround we had adapted to get the Galaxy working on a PBS Torque version. Could this problem be related to one of those workarounds? Is there any specific PBS Torque version on which Galaxy has been tested?
Thank you for your time Nate, Warm Regards, Sonali Amonkar
-----Original Message----- From: Nate Coraor [mailto:firstname.lastname@example.org] Sent: Saturday, February 12, 2011 2:10 AM To: Sonali Amonkar Cc: Galaxy Dev Subject: Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster
Nate Coraor wrote:
Sonali Amonkar wrote:
I am currently facing another issue. When I run my Workflow, I am seeing the following error on the server log. This error is not consistent, and occurs in an erratic manner.
galaxy.jobs INFO 2011-02-03 05:17:03,522 job 151 dispatched galaxy.jobs.runners.pbs DEBUG 2011-02-03 05:17:09,755 (150/69156.<primaryserver>) PBS job has left queue galaxy.jobs.runners.pbs DEBUG 2011-02-03 05:17:09,879 (151) submitting file galaxy-dist/database/pbs/151.sh galaxy.jobs.runners.pbs DEBUG 2011-02-03 05:17:09,880 (151) command is: java -cp galaxy-dist/tools/my_tools/jars/PreRef1.jar RefFilterModule galaxy-dist/database/files/000/dataset_192.dat galaxy-dist/database/files/000/dataset_194.dat galaxy-dist/database/files/000/dataset_195.dat galaxy.jobs.runners.pbs DEBUG 2011-02-03 05:17:09,880 (151) pbs_submit failed, PBS error 15031: Protocol (ASN.1) error galaxy.jobs DEBUG 2011-02-03 05:17:13,363 job 150 ended galaxy.jobs ERROR 2011-02-03 05:17:15,816 Unable to cleanup job 152
I am pretty sure this problem is somehow specific to the TORQUE setup, and I see you also posted this to the torquedev list, but unfortunately received no response.
I am not sure what is up here, but you may want to try adjusting the 'tcp_timeout' server setting. (qmgr -c 'set server tcp_timeout = X')
Also, you may want to see if PBS is making an attempt to queue this job on a particular node, and if so, check the mom_logs for that node.
Any help/pointer would be appreciated for this issue. Thank you very much for your time Nate.
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