Nate, thanks for the tip. I'm adding some debugging info around that
block now to inspect what is going on.
One thing I just remembered (been awhile since I debugged Galaxy tools)
- does Galaxy still treat ANY stderr output as an indication of job
failure? There are two warnings in the stderr for the job:
WARNING:galaxy.datatypes.registry:Error loading datatype with extension
'blastxml': 'module' object has no attribute 'BlastXml'
WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype
'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no
attribute 'BlastXml'
--
Branden Timm
bt...@energy.wisc.edu
On 5/8/2013 10:17 AM, Nate Coraor wrote:
On May 8, 2013, at 10:08 AM, Branden Timm wrote:
Hi All,
I've been working to configure a new Galaxy instance to run jobs under
Condor. Things are 99% working at this point, but what seems to be happening
is after the Condor job finishes Galaxy tries to clean up a cluster file that
isn't there, namely the .ec (exit code) file. Relevant log info:
galaxy.jobs DEBUG 2013-05-07 15:02:49,364 (1985) Working directory for job is:
/home/GLBRCORG/galaxy/database/job_working_directory/001/1985
galaxy.jobs.handler DEBUG 2013-05-07 15:02:49,387 (1985) Dispatching to condor
runner
galaxy.jobs DEBUG 2013-05-07 15:02:49,720 (1985) Persisting job destination
(destination id: condor)
galaxy.jobs.handler INFO 2013-05-07 15:02:49,761 (1985) Job dispatched
galaxy.jobs.runners.condor DEBUG 2013-05-07 15:02:56,368 (1985) submitting file
/home/GLBRCORG/galaxy/database/condor/galaxy_1985.sh
galaxy.jobs.runners.condor DEBUG 2013-05-07 15:02:56,369 (1985) command is:
python /home/GLBRCORG/galaxy/galaxy-central/tools/fastq/fastq_to_fasta.py
'/home/GLBRCORG/galaxy/database/files/000/dataset_3.dat'
'/home/GLBRCORG/galaxy/database/files/002/dataset_2842.dat' ''; cd
/home/GLBRCORG/galaxy/galaxy-central;
/home/GLBRCORG/galaxy/galaxy-central/set_metadata.sh
/home/GLBRCORG/galaxy/database/files
/home/GLBRCORG/galaxy/database/job_working_directory/001/1985 .
/home/GLBRCORG/galaxy/galaxy-central/universe_wsgi.ini
/home/GLBRCORG/galaxy/database/tmp/tmpGe1JZJ
/home/GLBRCORG/galaxy/database/job_working_directory/001/1985/galaxy.json
/home/GLBRCORG/galaxy/database/job_working_directory/001/1985/metadata_in_HistoryDatasetAssociation_3161_are5Bg,/home/GLBRCORG/galaxy/database/job_working_directory/001/1985/metadata_kwds_HistoryDatasetAssociation_3161_p73Yus,/home/GLBRCORG/galaxy/database/job_working_directory/001/1985/metadata_out_HistoryDatasetAssociation_3161_tLqep6,/home/G!
LBRCORG/galaxy/database/job_working_directory/001/1985/metadata_results_HistoryDatasetAssociation_3161_3QSW5X,,/home/GLBRCORG/galaxy/database/job_working_directory/001/1985/metadata_override_HistoryDatasetAssociation_3161_JUFvmk
galaxy.jobs.runners.condor INFO 2013-05-07 15:02:58,960 (1985) queued as 15
galaxy.jobs DEBUG 2013-05-07 15:02:59,110 (1985) Persisting job destination
(destination id: condor)
galaxy.jobs.runners.condor DEBUG 2013-05-07 15:02:59,536 (1985/15) job is now
running
galaxy.jobs.runners.condor DEBUG 2013-05-07 15:07:16,966 (1985/15) job is now
running
galaxy.jobs.runners.condor DEBUG 2013-05-07 15:07:17,279 (1985/15) job has
completed
galaxy.jobs.runners DEBUG 2013-05-07 15:07:17,417 (1985/15) Unable to cleanup
/home/GLBRCORG/galaxy/database/condor/galaxy_1985.ec: [Errno 2] No such file or
directory: '/home/GLBRCORG/galaxy/database/condor/galaxy_1985.ec'
galaxy.jobs DEBUG 2013-05-07 15:07:17,560 setting dataset state to ERROR
galaxy.jobs DEBUG 2013-05-07 15:07:17,961 job 1985 ended
galaxy.datatypes.metadata DEBUG 2013-05-07 15:07:17,961 Cleaning up external
metadata files
Hi Branden,
The ec file is optional, and the message that it's unable to be cleaned up is a
red herring in this case. The state is being set to ERROR, i suspect because
the check of its outputs on line 894 of lib/galaxy/jobs/__init__.py is failing:
894 if ( self.check_tool_output( stdout, stderr, tool_exit_code,
job )):
You might need to add some debugging to see where exactly this error
determination is coming from.
--nate
I've done a watch on the condor job directory, and as far as I can tell
galaxy_1985.ec never gets created. From a cursory look at
lib/galaxy/jobs/runners/__init__.py and condor.py, it looks like the cleanup is
happening in the AsynchronousJobState::cleanup method, which iterates on the
cleanup_file_attributes list. I naively tried to override
cleanup_file_attributes in CondorJobState to disinclude 'exit_code_file', to no
avail.
I'm hoping somebody can spot where the hiccup is here. Another question that
is on my mind is should a failure to cleanup cluster files set the dataset
state to ERROR? An inspection of the output file from my job leads me to
believe it finished just fine, and indicating failure to the user because
Galaxy couldn't cleanup a 1b error code file seems a little extreme to me.
Thanks!
--
Branden Timm
bt...@energy.wisc.edu
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