On May 8, 2013, at 12:21 PM, Branden Timm wrote:

> 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?

Yes, unless the tool defines that error codes should be used instead.  Most 
tools do not.

> 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'

This is likely the problem, and should be fixable by updating your 
datatypes_conf.xml from the sample in your release.

--nate

> 
> --
> 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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> 
> 
> 
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