details: http://www.bx.psu.edu/hg/galaxy/rev/b1619e50417f changeset: 3804:b1619e50417f user: Nate Coraor nate@bx.psu.edu date: Fri May 21 16:53:29 2010 -0400 description: Backed out changeset 48432330228e. pbs_python 2.9.8 is causing the job runner to segfault.
diffstat:
eggs.ini | 2 +- lib/galaxy/jobs/runners/pbs.py | 133 ++++++++++++++-------------------------- 2 files changed, 49 insertions(+), 86 deletions(-)
diffs (200 lines):
diff -r 48432330228e -r b1619e50417f eggs.ini --- a/eggs.ini Fri May 14 10:37:36 2010 -0400 +++ b/eggs.ini Fri May 21 16:53:29 2010 -0400 @@ -17,7 +17,7 @@ DRMAA_python = 0.2 MySQL_python = 1.2.3c1 numpy = 1.3.0 -pbs_python = 2.9.8 +pbs_python = 2.9.4 psycopg2 = 2.0.13 pycrypto = 2.0.1 pysam = 0.1.1 diff -r 48432330228e -r b1619e50417f lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Fri May 14 10:37:36 2010 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Fri May 21 16:53:29 2010 -0400 @@ -50,19 +50,6 @@ %s """
-# From pbs' job.h -JOB_EXIT_STATUS = { - 0: "job exec successful", - -1: "job exec failed, before files, no retry", - -2: "job exec failed, after files, no retry", - -3: "job execution failed, do retry", - -4: "job aborted on MOM initialization", - -5: "job aborted on MOM init, chkpt, no migrate", - -6: "job aborted on MOM init, chkpt, ok migrate", - -7: "job restart failed", - -8: "exec() of user command failed", -} - class PBSJobState( object ): def __init__( self ): """ @@ -78,7 +65,6 @@ self.efile = None self.runner_url = None self.check_count = 0 - self.stop_job = False
class PBSJobRunner( object ): """ @@ -207,9 +193,8 @@ pbs_options = self.determine_pbs_options( runner_url ) c = pbs.pbs_connect( pbs_server_name ) if c <= 0: - errno, text = pbs.error() job_wrapper.fail( "Unable to queue job for execution. Resubmitting the job may succeed." ) - log.error( "Connection to PBS server for submit failed: %s: %s" % ( errno, text ) ) + log.error( "Connection to PBS server for submit failed" ) return
# define job attributes @@ -351,78 +336,58 @@ log.debug( "(%s/%s) Skipping state check because PBS server connection failed" % ( galaxy_job_id, job_id ) ) new_watched.append( pbs_job_state ) continue - try: + if statuses.has_key( job_id ): status = statuses[job_id] - except KeyError: + if status.job_state != old_state: + log.debug("(%s/%s) job state changed from %s to %s" % ( galaxy_job_id, job_id, old_state, status.job_state ) ) + if status.job_state == "R" and not pbs_job_state.running: + pbs_job_state.running = True + pbs_job_state.job_wrapper.change_state( model.Job.states.RUNNING ) + if status.job_state == "R" and ( pbs_job_state.check_count % 20 ) == 0: + # Every 20th time the job status is checked, do limit checks (if configured) + if self.app.config.output_size_limit > 0: + # Check the size of the job outputs + fail = False + for outfile, size in pbs_job_state.job_wrapper.check_output_sizes(): + if size > self.app.config.output_size_limit: + pbs_job_state.fail_message = 'Job output grew too large (greater than %s), please try different job parameters or' \ + % nice_size( self.app.config.output_size_limit ) + log.warning( '(%s/%s) Dequeueing job due to output %s growing larger than %s limit' \ + % ( galaxy_job_id, job_id, os.path.basename( outfile ), nice_size( self.app.config.output_size_limit ) ) ) + self.work_queue.put( ( 'fail', pbs_job_state ) ) + fail = True + break + if fail: + continue + if self.job_walltime is not None: + # Check the job's execution time + if status.get( 'resources_used', False ): + # resources_used may not be in the status for new jobs + h, m, s = [ int( i ) for i in status.resources_used.walltime.split( ':' ) ] + time_executing = timedelta( 0, s, 0, 0, m, h ) + if time_executing > self.job_walltime: + pbs_job_state.fail_message = 'Job ran longer than maximum allowed execution time (%s), please try different job parameters or' \ + % self.app.config.job_walltime + log.warning( '(%s/%s) Dequeueing job since walltime has been reached' \ + % ( galaxy_job_id, job_id ) ) + self.work_queue.put( ( 'fail', pbs_job_state ) ) + continue + pbs_job_state.old_state = status.job_state + new_watched.append( pbs_job_state ) + else: try: - # Recheck to make sure it wasn't a communication problem + # recheck to make sure it wasn't a communication problem self.check_single_job( pbs_server_name, job_id ) - log.warning( "(%s/%s) PBS job was not in state check list, but was found with individual state check" % ( galaxy_job_id, job_id ) ) + log.warning( "(%s/%s) job was not in state check list, but was found with individual state check" % ( galaxy_job_id, job_id ) ) new_watched.append( pbs_job_state ) except: errno, text = pbs.error() - if errno == 15001: - # 15001 == job not in queue - log.debug("(%s/%s) PBS job has left queue" % (galaxy_job_id, job_id) ) + if errno != 15001: + log.info("(%s/%s) state check resulted in error (%d): %s" % (galaxy_job_id, job_id, errno, text) ) + new_watched.append( pbs_job_state ) + else: + log.debug("(%s/%s) job has left queue" % (galaxy_job_id, job_id) ) self.work_queue.put( ( 'finish', pbs_job_state ) ) - else: - # Unhandled error, continue to monitor - log.info("(%s/%s) PBS state check resulted in error (%d): %s" % (galaxy_job_id, job_id, errno, text) ) - new_watched.append( pbs_job_state ) - continue - if status.job_state != old_state: - log.debug("(%s/%s) PBS job state changed from %s to %s" % ( galaxy_job_id, job_id, old_state, status.job_state ) ) - if status.job_state == "R" and not pbs_job_state.running: - pbs_job_state.running = True - pbs_job_state.job_wrapper.change_state( model.Job.states.RUNNING ) - if status.job_state == "R" and ( pbs_job_state.check_count % 20 ) == 0: - # Every 20th time the job status is checked, do limit checks (if configured) - if self.app.config.output_size_limit > 0: - # Check the size of the job outputs - fail = False - for outfile, size in pbs_job_state.job_wrapper.check_output_sizes(): - if size > self.app.config.output_size_limit: - pbs_job_state.fail_message = 'Job output grew too large (greater than %s), please try different job parameters or' \ - % nice_size( self.app.config.output_size_limit ) - log.warning( '(%s/%s) Dequeueing job due to output %s growing larger than %s limit' \ - % ( galaxy_job_id, job_id, os.path.basename( outfile ), nice_size( self.app.config.output_size_limit ) ) ) - pbs_job_state.stop_job = True - self.work_queue.put( ( 'fail', pbs_job_state ) ) - fail = True - break - if fail: - continue - if self.job_walltime is not None: - # Check the job's execution time - if status.get( 'resources_used', False ): - # resources_used may not be in the status for new jobs - h, m, s = [ int( i ) for i in status.resources_used.walltime.split( ':' ) ] - time_executing = timedelta( 0, s, 0, 0, m, h ) - if time_executing > self.job_walltime: - pbs_job_state.fail_message = 'Job ran longer than maximum allowed execution time (%s), please try different job parameters or' \ - % self.app.config.job_walltime - log.warning( '(%s/%s) Dequeueing job since walltime has been reached' \ - % ( galaxy_job_id, job_id ) ) - pbs_job_state.stop_job = True - self.work_queue.put( ( 'fail', pbs_job_state ) ) - continue - elif status.job_state == "C": - # "keep_completed" is enabled in PBS, so try to check exit status - try: - assert int( status.exit_status ) == 0 - log.debug("(%s/%s) PBS job has completed successfully" % ( galaxy_job_id, job_id ) ) - except AssertionError: - pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error. Please retry or' - log.error( '(%s/%s) PBS job failed: %s' % ( galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ), 'Unknown error: %s' % status.exit_status ) ) ) - self.work_queue.put( ( 'fail', pbs_job_state ) ) - continue - except AttributeError: - # No exit_status, can't verify proper completion so we just have to assume success. - log.debug("(%s/%s) PBS job has completed" % ( galaxy_job_id, job_id ) ) - self.work_queue.put( ( 'finish', pbs_job_state ) ) - continue - pbs_job_state.old_state = status.job_state - new_watched.append( pbs_job_state ) # Replace the watch list with the updated version self.watched = new_watched
@@ -446,10 +411,9 @@ log.debug("connection to PBS server %s for state check failed" % pbs_server_name ) failures.append( pbs_server_name ) continue - stat_attrl = pbs.new_attrl(3) + stat_attrl = pbs.new_attrl(2) stat_attrl[0].name = pbs.ATTR_state stat_attrl[1].name = pbs.ATTR_used - stat_attrl[2].name = pbs.ATTR_exitstat jobs = pbs.pbs_statjob( c, None, stat_attrl, None ) pbs.pbs_disconnect( c ) statuses.update( self.convert_statjob_to_bunches( jobs ) ) @@ -516,8 +480,7 @@ """ Seperated out so we can use the worker threads for it. """ - if pbs_job_state.stop_job: - self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) ) + self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) ) pbs_job_state.job_wrapper.fail( pbs_job_state.fail_message ) self.cleanup( ( pbs_job_state.ofile, pbs_job_state.efile, pbs_job_state.job_file ) )