9 p.m.
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 <annblack(a)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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