# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor nate@bx.psu.edu # Date 1279556993 14400 # Node ID 28e629ad59490af90a28bc45073a7cfc10ed646c # Parent 0f5eb93a7d61478565d63563bddcbffc6b6a59d9 Upgrade pbs_python to 4.1.0 and use PBS exit_status (if keep_completed is set) so we can detect PBS failures. This is a reapplication of 3786:48432330228e, which was backed out in a subsequent revision due to crashes experienced in pbs_python 2.9.8.

--- a/eggs.ini +++ b/eggs.ini @@ -17,7 +17,7 @@ Cheetah = 2.2.2 DRMAA_python = 0.2 MySQL_python = 1.2.3c1 numpy = 1.3.0 -pbs_python = 2.9.4 +pbs_python = 4.1.0 psycopg2 = 2.0.13 pycrypto = 2.0.1 pysam = 0.1.1

--- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -50,6 +50,19 @@ cd %s %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 ): """ @@ -65,6 +78,7 @@ class PBSJobState( object ): self.efile = None self.runner_url = None self.check_count = 0 + self.stop_job = False

class PBSJobRunner( object ): """ @@ -193,8 +207,9 @@ class PBSJobRunner( object ): 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" ) + log.error( "Connection to PBS server for submit failed: %s: %s" % ( errno, text ) ) return

# define job attributes @@ -336,58 +351,78 @@ class PBSJobRunner( object ): log.debug( "(%s/%s) Skipping state check because PBS server connection failed" % ( galaxy_job_id, job_id ) ) new_watched.append( pbs_job_state ) continue - if statuses.has_key( job_id ): + try: status = statuses[job_id] - 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: + except KeyError: 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) job was not in state check list, but was found with individual state check" % ( galaxy_job_id, 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 ) ) new_watched.append( pbs_job_state ) except: errno, text = pbs.error() - if errno != 15001: - log.info("(%s/%s) state check resulted in error (%d): %s" % (galaxy_job_id, job_id, errno, text) ) + if errno == 15001: + # 15001 == job not in queue + log.debug("(%s/%s) PBS 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 ) - else: - log.debug("(%s/%s) job has left queue" % (galaxy_job_id, job_id) ) - self.work_queue.put( ( 'finish', 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

@@ -411,9 +446,10 @@ class PBSJobRunner( object ): 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(2) + stat_attrl = pbs.new_attrl(3) 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 ) ) @@ -480,7 +516,8 @@ class PBSJobRunner( object ): """ Seperated out so we can use the worker threads for it. """ - self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) ) + 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 ) ) 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 ) )

--- a/scripts/scramble/scripts/pbs_python.py +++ b/scripts/scramble/scripts/pbs_python.py @@ -29,8 +29,8 @@ if not os.path.exists( 'setup.py.orig' ) i = open( 'setup.py.orig', 'r' ) o = open( 'setup.py', 'w' ) for line in i.readlines(): - if line == " version = '2.9.0',\n": - line = " version = '2.9.4',\n" + if line == " version = '4.0.0',\n": + line = " version = '4.1.0',\n" print >>o, line, i.close() o.close()