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Include the regular (Galaxy) job_id with all the PBS debug messages,

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should help with searching the logs and associating PBS messages with
a specific job.  Also, the PBS job name is now the regular job_id,
so you'll see it in qstat and PBS error mail.
This commit is contained in:
Nate Coraor
2007-10-10 17:55:21 +00:00
parent cd1b9436fe
commit 01181fa546
1 changed files with 15 additions and 11 deletions
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lib/galaxy/jobs/runners/pbs.py
+15 -11
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@@ -123,7 +123,7 @@ class PBSJobRunner( object ):
if stagein != '':
stagein += ','
stagein += "%s@%s:%s" % (output_fname, self.app.config.pbs_dataset_server, output_fname)
job_attrs = pbs.new_attropl(4)
job_attrs = pbs.new_attropl(5)
job_attrs[0].name = pbs.ATTR_o
job_attrs[0].value = pbs_ofile
job_attrs[1].name = pbs.ATTR_e
@@ -132,6 +132,8 @@ class PBSJobRunner( object ):
job_attrs[2].value = stagein
job_attrs[3].name = pbs.ATTR_stageout
job_attrs[3].value = stageout
job_attrs[4].name = pbs.ATTR_N
job_attrs[4].value = "%s" % job_wrapper.job_id
exec_dir = self.app.config.pbs_instance_path
# FIXME: pbs_instance_path is broken until we munge PATH and PYTHONPATH here
else:
@@ -154,15 +156,16 @@ class PBSJobRunner( object ):
# FIXME: More information here?
stderr = stdout = ''
galaxy_job_id = job_wrapper.job_id
log.debug("submitting file %s" % job_file )
log.debug("command is: %s" % command_line)
job_id = pbs.pbs_submit(conn, job_attrs, job_file, None, None)
log.debug("queued: %s" % job_id)
log.debug("queued %s: %s" % (galaxy_job_id, job_id) )
pbs.pbs_disconnect(conn)
if not job_id:
stdout = ''
stderr = "Job was not queued, PBS error %d: %s" % pbs.error()
stderr = "Job (%s) was not queued, PBS error %d: %s" % (galaxy_job_id, pbs.error() )
log.debug(stderr)
# Get initial job state
@@ -179,15 +182,15 @@ class PBSJobRunner( object ):
try:
if (jobs[0].attribs[0].name == "job_state"):
old_state = jobs[0].attribs[0].value
log.debug("(%s) initial state is %s" % (job_id, old_state) )
log.debug("(%s/%s) initial state is %s" % (galaxy_job_id, job_id, old_state) )
except:
log.info("(%s) unable to retrieve initial state" % job_id)
log.info("(%s/%s) unable to retrieve initial state" % (galaxy_job_id, job_id) )
# ran immediately
if old_state == "R":
job_wrapper.change_state( "running" )
running = True
log.debug("(%s) job is now running" % job_id)
log.debug("(%s/%s) job is now running" % (galaxy_job_id, job_id) )
# queued
else:
@@ -236,33 +239,34 @@ class PBSJobRunner( object ):
new_watched = []
for pbs_job_state in self.watched:
job_id = pbs_job_state.job_id
galaxy_job_id = pbs_job_state.job_wrapper.job_id
old_state = pbs_job_state.old_state
running = pbs_job_state.running
conn = pbs.pbs_connect( self.pbs_server )
if conn <= 0:
log.debug("(%s) connection to PBS server for state check failed" % job_id)
log.debug("(%s/%s) connection to PBS server for state check failed" % (galaxy_job_id, job_id) )
stat_attrl = pbs.new_attrl(1)
stat_attrl[0].name = 'job_state'
jobs = pbs.pbs_statjob(conn, pbs_job_state.job_id, stat_attrl, 'NULL')
pbs.pbs_disconnect(conn)
if len( jobs ) < 1:
log.debug("(%s) job has left queue" % job_id)
log.debug("(%s/%s) job has left queue" % (galaxy_job_id, job_id) )
self.finish_job( pbs_job_state )
else:
try:
if (jobs[0].attribs[0].name == "job_state"):
state = jobs[0].attribs[0].value
if state != old_state:
log.debug("(%s) job state changed from %s to %s" % ( job_id, old_state, state ) )
log.debug("(%s/%s) job state changed from %s to %s" % ( galaxy_job_id, job_id, old_state, state ) )
if state == "R" and not running:
running = True
pbs_job_state.job_wrapper.change_state( "running" )
log.debug("(%s) job is now running" % job_id)
log.debug("(%s/%s) job is now running" % (galaxy_job_id, job_id) )
old_state = state
pbs_job_state.old_state = old_state
pbs_job_state.running = running
except:
log.exception("(%s) unable to check state" % job_id)
log.exception("(%s/%s) unable to check state" % (galaxy_job_id, job_id) )
new_watched.append( pbs_job_state )
# Replace the watch list with the updated version
self.watched = new_watched