perhaps a 15sec sleep should also be added, since the scheduler is
overwhelmed

{{{
except ( drmaa.DrmCommunicationException ), e:
  # Catch drmaa communication exception, log a warning message and
  # continue to monitor jobs.
  log.warning("(%s/%s) Couldn't communicate with the cluster scheduler to
check job status." %( galaxy_job_id, job_id ))
  # give scheduler time to catch up
  time.sleep( 15 )
  # keep old job state
  new_watched.append( drm_job_state )
  continue
}}}


On Wed, Jan 18, 2012 at 1:07 PM, Edward Kirton <eskir...@lbl.gov> wrote:

> excellent, thanks for the correction!
>
>
> On Wed, Jan 18, 2012 at 8:59 AM, Shantanu Pavgi <pa...@uab.edu> wrote:
>
>>
>>  Ed,
>>
>>  I think you may want to add job with DrmCommunicationException error
>> back into the watched_jobs list.
>> {{{
>>  except ( drmaa.DrmCommunicationException ), e:
>>   # Catch drmaa communication exception, log a warning message and
>>   # continue to monitor jobs.
>>   log.warning("(%s/%s) Couldn't communicate with the cluster scheduler to
>> check job status." %( galaxy_job_id, job_id ))
>>   # keep old job state
>>   new_watched.append( drm_job_state )
>>   continue
>> }}}
>>
>>  Here is a patch and related discussion on it:
>> https://bitbucket.org/galaxy/galaxy-central/pull-request/23/catch-drmcommunication-exception
>>
>>
>>  --
>> Shantanu
>>
>>
>>  On Jan 13, 2012, at 2:11 PM, Edward Kirton wrote:
>>
>>  i had seen the job process die with this error:
>>
>>      if state != old_state:
>> UnboundLocalError: local variable 'state' referenced before assignment
>>
>>  since the DRM timeout is an intermittent error, i'm not absolutely
>> positive i have nailed it (a bit more time will tell -- i'm keeping an eye
>> on it with debug log messages), but it seems so.  i intended to share this
>> as a patched clone when i became sure but when i read your email i just
>> sent what i had immediately.  let us know if that seems to solve the
>> problem for you, so we'll have some confirmation.
>>
>>  glad to help,
>> ed
>>
>>  p.s. i have another patch for "output not returned from cluster" errors
>> that i'm also still validating, due to NFS race since we don't have inode
>> metadata caching turned off as the galaxy developers suggest.
>>
>> On Fri, Jan 13, 2012 at 8:06 AM, Ann Black <annbl...@eng.uiowa.edu>wrote:
>>
>>>  Thanks so much! I have applied the fix to our env.
>>>
>>>  In looking over the logic, there was an existing exception block that
>>> would have caught the communication exception generically – but the job
>>> moved (in this scenario erroneously) the job into a failure workflow.  I
>>> would like to understand what ended up hanging galaxy – so it must be
>>> related to a valid job being moved into failure state ? Did you follow it
>>> down the rabbit hole by any chance to see what caused the hang in your env
>>> ?
>>>
>>>  Thanks again,
>>>
>>>  Ann
>>>
>>>   From: Edward Kirton <eskir...@lbl.gov>
>>> Date: Thu, 12 Jan 2012 13:00:27 -0800
>>> To: Ann Black <annbl...@eng.uiowa.edu>
>>> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>>> Subject: Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException
>>>
>>>  sometimes the scheduler can't keep up with all the work in it's 15sec
>>> cycle, so it doesn't respond to some messages.  here's a fix i've been
>>> trying that seems to work.
>>>
>>>  in lib/galaxy/jobs/runners/drmaa.py:
>>>
>>>      def check_watched_items( self ):
>>>         """
>>>         Called by the monitor thread to look at each watched job and deal
>>>         with state changes.
>>>         """
>>>         new_watched = []
>>>         for drm_job_state in self.watched:
>>>             job_id = drm_job_state.job_id
>>>             galaxy_job_id = drm_job_state.job_wrapper.job_id
>>>             old_state = drm_job_state.old_state
>>>             try:
>>>                 state = self.ds.jobStatus( job_id )
>>>             # InternalException was reported to be necessary on some
>>> DRMs, but
>>>             # this could cause failures to be detected as completion!
>>>  Please
>>>             # report if you experience problems with this.
>>>             except ( drmaa.InvalidJobException, drmaa.InternalException
>>> ), e:
>>>                 # we should only get here if an orphaned job was put
>>> into the queue at app star
>>> tup
>>>                 log.debug("(%s/%s) job left DRM queue with following
>>> message: %s" % ( galaxy_jo
>>> b_id, job_id, e ) )
>>>                 self.work_queue.put( ( 'finish', drm_job_state ) )
>>>                 continue
>>>             # BEGIN DRM TIMEOUT: Don't fail on scheduler communication
>>> error (probably just too busy)
>>>             except ( drmaa.DrmCommunicationException ), e:
>>>                 log.warning("(%s/%s) DRM Communication Exception" % (
>>> galaxy_job_id, job_id
>>>  ))
>>>                 continue
>>>             # END DRM TIMEOUT
>>>
>>> On Wed, Jan 11, 2012 at 9:18 AM, Ann Black <annbl...@eng.uiowa.edu>wrote:
>>>
>>>>  Good Morning galaxy group!
>>>>
>>>>  I was hoping that someone might have some ideas on a problem we have
>>>> experienced a handful of times running galaxy on our local cluster.
>>>>
>>>>  Occasionally we experience some communication timeouts between out
>>>> cluster head node and a compute node which will self heal. However, this in
>>>> turn will hang galaxy.  Below you will see output from our galaxy log file.
>>>>  When the ERROR happens (which is not often) it consistently seems to hang
>>>> galaxy.  We have to kill it off and restart it. We are running galaxy as a
>>>> single PID at this time (we are still just testing it out, etc) and it is
>>>> running on our head node (which we plan to move off of in the future).
>>>>
>>>>  galaxy.jobs.runners.drmaa DEBUG 2012-01-10 19:19:58,800 (1654/698075)
>>>> state change: job is running
>>>> galaxy.jobs.runners.drmaa ERROR 2012-01-10 20:57:47,021 (1654/698075)
>>>> Unable to check job status
>>>> Traceback (most recent call last):
>>>>   File "/data/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 236,
>>>> in check_watched_items
>>>>     state = self.ds.jobStatus( job_id )
>>>>   File
>>>> "/data/galaxy-dist/eggs/drmaa-0.4b3-py2.7.egg/drmaa/__init__.py", line 522,
>>>> in jobStatus
>>>>     _h.c(_w.drmaa_job_ps, jobName, _ct.byref(status))
>>>>   File "/data/galaxy-dist/eggs/drmaa-0.4b3-py2.7.egg/drmaa/helpers.py",
>>>> line 213, in c
>>>>     return f(*(args + (error_buffer, sizeof(error_buffer))))
>>>>   File "/data/galaxy-dist/eggs/drmaa-0.4b3-py2.7.egg/drmaa/errors.py",
>>>> line 90, in error_check
>>>>     raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
>>>> DrmCommunicationException: code 2: failed receiving gdi request
>>>> response for mid=24442 (got syncron message receive timeout error).
>>>> galaxy.jobs.runners.drmaa WARNING 2012-01-10 20:58:05,090
>>>> (1654/698075) job will now be errored
>>>> galaxy.jobs.runners.drmaa DEBUG 2012-01-10 20:59:06,396 (1654/698075)
>>>> User killed running job, but error encountered removing from DRM queue:
>>>> code 2: failed receiving gdi request response for mid=24444 (got syncron
>>>> message receive timeout error).
>>>> galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:06,896 Cleaning up
>>>> external metadata files
>>>> galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:06,947 Failed to
>>>> cleanup MetadataTempFile temp files from
>>>> database/tmp/metadata_out_HistoryDatasetAssociation_2913_ZUTgBy: No JSON
>>>> object could be decoded: line 1 column 0 (char 0)
>>>> galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:09,640 Cleaning up
>>>> external metadata files
>>>> galaxy.jobs INFO 2012-01-10 20:59:09,697 job 1656 unable to run: one
>>>> or more inputs in error state
>>>> galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:10,121 Cleaning up
>>>> external metadata files
>>>> galaxy.jobs INFO 2012-01-10 20:59:10,159 job 1655 unable to run: one
>>>> or more inputs in error state
>>>> galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:12,076 Cleaning up
>>>> external metadata files
>>>> galaxy.jobs INFO 2012-01-10 20:59:12,126 job 1657 unable to run: one
>>>> or more inputs in error state
>>>> galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:13,601 Cleaning up
>>>> external metadata files
>>>> galaxy.jobs INFO 2012-01-10 20:59:13,650 job 1658 unable to run: one
>>>> or more inputs in error state
>>>>
>>>>
>>>>  Has anyone else experienced this or have some ideas on how we can
>>>> further debug to figure out why galaxy hangs?
>>>>
>>>>  Thanks much!
>>>>
>>>>  Ann Black-Ziegelbein
>>>>
>>>> ___________________________________________________________
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>>>>
>>>>  http://lists.bx.psu.edu/
>>>>
>>>
>>>
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>>
>>
>
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