[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/430ea49ff3c2/ changeset: 430ea49ff3c2 user: natefoo date: 2012-11-16 21:36:31 summary: Jobs now have their runner name set prior to actually being submitted to the runner, meaning that runners' recover() methods must handle the case where the job was never actually submitted. affected #: 4 files diff -r 7f7171c52b1d922fb6471c8ce373fa3e50901206 -r 430ea49ff3c2ab00af9e5d602216ac37c489156e lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -359,12 +359,16 @@ def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" + job_id = job.get_job_runner_external_id() + if job_id is None: + self.put( job_wrapper ) + return runner_job_state = RunnerJobState() runner_job_state.ofile = "%s.gjout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) runner_job_state.efile = "%s.gjerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) runner_job_state.ecfile = "%s.gjec" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) runner_job_state.job_file = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) - runner_job_state.external_job_id = str( job.job_runner_external_id ) + runner_job_state.external_job_id = str( job_id ) job_wrapper.command_line = job.command_line runner_job_state.job_wrapper = job_wrapper runner_job_state.runner_url = job.job_runner_name diff -r 7f7171c52b1d922fb6471c8ce373fa3e50901206 -r 430ea49ff3c2ab00af9e5d602216ac37c489156e lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -368,11 +368,15 @@ def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" # TODO Check if we need any changes here + job_id = job.get_job_runner_external_id() + if job_id is None: + self.put( job_wrapper ) + return drm_job_state = CondorJobState() drm_job_state.ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job.id) drm_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id) drm_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.id) - drm_job_state.job_id = str( job.job_runner_external_id ) + drm_job_state.job_id = str( job_id ) drm_job_state.runner_url = job_wrapper.get_job_runner() job_wrapper.command_line = job.command_line drm_job_state.job_wrapper = job_wrapper diff -r 7f7171c52b1d922fb6471c8ce373fa3e50901206 -r 430ea49ff3c2ab00af9e5d602216ac37c489156e lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -411,12 +411,16 @@ def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" + job_id = job.get_job_runner_external_id() + if job_id is None: + self.put( job_wrapper ) + return drm_job_state = DRMAAJobState() drm_job_state.ofile = "%s.drmout" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.efile = "%s.drmerr" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.ecfile = "%s.drmec" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.job_file = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job.get_id()) - drm_job_state.job_id = str( job.get_job_runner_external_id() ) + drm_job_state.job_id = str( job_id ) drm_job_state.runner_url = job_wrapper.get_job_runner_url() job_wrapper.command_line = job.get_command_line() drm_job_state.job_wrapper = job_wrapper diff -r 7f7171c52b1d922fb6471c8ce373fa3e50901206 -r 430ea49ff3c2ab00af9e5d602216ac37c489156e lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -640,12 +640,16 @@ def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" + job_id = job.get_job_runner_external_id() + if job_id is None: + self.put( job_wrapper ) + return pbs_job_state = PBSJobState() pbs_job_state.ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.ecfile = "%s/%s.ec" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job.id) - pbs_job_state.job_id = str( job.get_job_runner_external_id() ) + pbs_job_state.job_id = str( job_id ) pbs_job_state.runner_url = job_wrapper.get_job_runner_url() job_wrapper.command_line = job.command_line pbs_job_state.job_wrapper = job_wrapper https://bitbucket.org/galaxy/galaxy-central/changeset/8bd9f729fb6a/ changeset: 8bd9f729fb6a user: natefoo date: 2012-11-16 21:36:56 summary: Remove the long-deprecated SGE runner. Use the DRMAA runner. affected #: 1 file diff -r 430ea49ff3c2ab00af9e5d602216ac37c489156e -r 8bd9f729fb6a92077b9652690b11877f203902ec lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py +++ /dev/null @@ -1,392 +0,0 @@ -import os, logging, threading, time -from Queue import Queue, Empty - -from galaxy import model -from galaxy.jobs.runners import BaseJobRunner - -from paste.deploy.converters import asbool - -import pkg_resources - -egg_message = """ - -The 'sge' runner depends on 'DRMAA_python' which is not installed. Galaxy's -"scramble" system should make this installation simple, please follow the -instructions found at: - - http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster - -Additional errors may follow: -%s -""" - - -try: - pkg_resources.require( "DRMAA_python" ) - import DRMAA -except Exception, e: - raise Exception( egg_message % str( e ) ) - - -log = logging.getLogger( __name__ ) - -__all__ = [ 'SGEJobRunner' ] - -DRMAA_state = { - DRMAA.Session.UNDETERMINED: 'process status cannot be determined', - DRMAA.Session.QUEUED_ACTIVE: 'job is queued and waiting to be scheduled', - DRMAA.Session.SYSTEM_ON_HOLD: 'job is queued and in system hold', - DRMAA.Session.USER_ON_HOLD: 'job is queued and in user hold', - DRMAA.Session.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold', - DRMAA.Session.RUNNING: 'job is running', - DRMAA.Session.SYSTEM_SUSPENDED: 'job is system suspended', - DRMAA.Session.USER_SUSPENDED: 'job is user suspended', - DRMAA.Session.DONE: 'job finished normally', - DRMAA.Session.FAILED: 'job finished, but failed', -} - -sge_template = """#!/bin/sh -#$ -S /bin/sh -GALAXY_LIB="%s" -if [ "$GALAXY_LIB" != "None" ]; then - if [ -n "$PYTHONPATH" ]; then - PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" - else - PYTHONPATH="$GALAXY_LIB" - fi - export PYTHONPATH -fi -cd %s -%s -""" - -class SGEJobState( object ): - def __init__( self ): - """ - Encapsulates state related to a job that is being run via SGE and - that we need to monitor. - """ - self.job_wrapper = None - self.job_id = None - self.old_state = None - self.running = False - self.job_file = None - self.ofile = None - self.efile = None - self.runner_url = None - -class SGEJobRunner( BaseJobRunner ): - """ - Job runner backed by a finite pool of worker threads. FIFO scheduling - """ - STOP_SIGNAL = object() - def __init__( self, app ): - """Initialize this job runner and start the monitor thread""" - self.app = app - self.sa_session = app.model.context - # 'watched' and 'queue' are both used to keep track of jobs to watch. - # 'queue' is used to add new watched jobs, and can be called from - # any thread (usually by the 'queue_job' method). 'watched' must only - # be modified by the monitor thread, which will move items from 'queue' - # to 'watched' and then manage the watched jobs. - self.watched = [] - self.monitor_queue = Queue() - self.default_cell = self.determine_sge_cell( self.app.config.default_cluster_job_runner ) - self.ds = DRMAA.Session() - self.ds.init( self.default_cell ) - self.monitor_thread = threading.Thread( target=self.monitor ) - self.monitor_thread.start() - self.work_queue = Queue() - self.work_threads = [] - nworkers = app.config.cluster_job_queue_workers - for i in range( nworkers ): - worker = threading.Thread( target=self.run_next ) - worker.start() - self.work_threads.append( worker ) - log.debug( "%d workers ready" % nworkers ) - - def determine_sge_cell( self, url ): - """Determine what SGE cell we are using""" - url_split = url.split("/") - if url_split[0] == 'sge:': - return url_split[2] - # this could happen if sge is started, but is not the default runner - else: - return '' - - def determine_sge_queue( self, url ): - """Determine what SGE queue we are submitting to""" - try: - return url.split('/')[3] or None - except: - return None - - def determine_sge_project( self, url ): - """Determine what SGE project we are submitting to""" - try: - return url.split('/')[4] or None - except: - return None - - def determine_sge_tool_parameters( self, url ): - """Determine what are the tool's specific paramters""" - try: - return url.split('/')[5] or None - except: - return None - - def run_next( self ): - """ - Run the next item in the queue (a job waiting to run or finish ) - """ - while 1: - ( op, obj ) = self.work_queue.get() - if op is self.STOP_SIGNAL: - return - try: - if op == 'queue': - self.queue_job( obj ) - elif op == 'finish': - self.finish_job( obj ) - elif op == 'fail': - self.fail_job( obj ) - except: - log.exception( "Uncaught exception %sing job" % op ) - - def queue_job( self, job_wrapper ): - """Create SGE script for a job and submit it to the SGE queue""" - - try: - job_wrapper.prepare() - command_line = self.build_command_line( job_wrapper, include_metadata = True ) - except: - job_wrapper.fail( "failure preparing job", exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) - return - - runner_url = job_wrapper.get_job_runner_url() - - # This is silly, why would we queue a job with no command line? - if not command_line: - job_wrapper.finish( '', '' ) - return - - # Check for deletion before we change state - if job_wrapper.get_state() == model.Job.states.DELETED: - log.debug( "Job %s deleted by user before it entered the SGE queue" % job_wrapper.job_id ) - job_wrapper.cleanup() - return - - # Change to queued state immediately - job_wrapper.change_state( model.Job.states.QUEUED ) - - if self.determine_sge_cell( runner_url ) != self.default_cell: - # TODO: support multiple cells - log.warning( "(%s) Using multiple SGE cells is not supported. This job will be submitted to the default cell." % job_wrapper.job_id ) - sge_queue_name = self.determine_sge_queue( runner_url ) - sge_project_name = self.determine_sge_project( runner_url ) - sge_extra_params = self.determine_sge_tool_parameters ( runner_url ) - - # define job attributes - ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id) - efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id) - jt = self.ds.createJobTemplate() - jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.job_id) - jt.outputPath = ":%s" % ofile - jt.errorPath = ":%s" % efile - nativeSpec = [] - if sge_queue_name is not None: - nativeSpec.append( "-q '%s'" % sge_queue_name ) - if sge_project_name is not None: - nativeSpec.append( "-P '%s'" % sge_project_name) - if sge_extra_params is not None: - nativeSpec.append( sge_extra_params ) - if len(nativeSpec)>0: - jt.nativeSpecification = ' '.join(nativeSpec) - - script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) - - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0750 ) - - # job was deleted while we were preparing it - if job_wrapper.get_state() == model.Job.states.DELETED: - log.debug( "Job %s deleted by user before it entered the SGE queue" % job_wrapper.job_id ) - self.cleanup( ( ofile, efile, jt.remoteCommand ) ) - job_wrapper.cleanup() - return - - galaxy_job_id = job_wrapper.job_id - log.debug("(%s) submitting file %s" % ( galaxy_job_id, jt.remoteCommand ) ) - log.debug("(%s) command is: %s" % ( galaxy_job_id, command_line ) ) - # runJob will raise if there's a submit problem - job_id = self.ds.runJob(jt) - if sge_queue_name is None: - log.debug("(%s) queued in default queue as %s" % (galaxy_job_id, job_id) ) - else: - log.debug("(%s) queued in %s queue as %s" % (galaxy_job_id, sge_queue_name, job_id) ) - - # store runner information for tracking if Galaxy restarts - job_wrapper.set_runner( runner_url, job_id ) - - # Store SGE related state information for job - sge_job_state = SGEJobState() - sge_job_state.job_wrapper = job_wrapper - sge_job_state.job_id = job_id - sge_job_state.ofile = ofile - sge_job_state.efile = efile - sge_job_state.job_file = jt.remoteCommand - sge_job_state.old_state = 'new' - sge_job_state.running = False - sge_job_state.runner_url = runner_url - - # delete the job template - self.ds.deleteJobTemplate( jt ) - - # Add to our 'queue' of jobs to monitor - self.monitor_queue.put( sge_job_state ) - - def monitor( self ): - """ - Watches jobs currently in the PBS queue and deals with state changes - (queued to running) and job completion - """ - while 1: - # Take any new watched jobs and put them on the monitor list - try: - while 1: - sge_job_state = self.monitor_queue.get_nowait() - if sge_job_state is self.STOP_SIGNAL: - # TODO: This is where any cleanup would occur - self.ds.exit() - return - self.watched.append( sge_job_state ) - except Empty: - pass - # Iterate over the list of watched jobs and check state - self.check_watched_items() - # Sleep a bit before the next state check - time.sleep( 1 ) - - def check_watched_items( self ): - """ - Called by the monitor thread to look at each watched job and deal - with state changes. - """ - new_watched = [] - for sge_job_state in self.watched: - job_id = sge_job_state.job_id - galaxy_job_id = sge_job_state.job_wrapper.job_id - old_state = sge_job_state.old_state - try: - state = self.ds.getJobProgramStatus( job_id ) - except DRMAA.InvalidJobError: - # we should only get here if an orphaned job was put into the queue at app startup - log.debug("(%s/%s) job left SGE queue" % ( galaxy_job_id, job_id ) ) - self.work_queue.put( ( 'finish', sge_job_state ) ) - continue - except Exception, e: - # so we don't kill the monitor thread - log.exception("(%s/%s) Unable to check job status" % ( galaxy_job_id, job_id ) ) - log.warning("(%s/%s) job will now be errored" % ( galaxy_job_id, job_id ) ) - sge_job_state.fail_message = "Cluster could not complete job" - self.work_queue.put( ( 'fail', sge_job_state ) ) - continue - if state != old_state: - log.debug("(%s/%s) state change: %s" % ( galaxy_job_id, job_id, DRMAA_state[state] ) ) - if state == DRMAA.Session.RUNNING and not sge_job_state.running: - sge_job_state.running = True - sge_job_state.job_wrapper.change_state( model.Job.states.RUNNING ) - if state in ( DRMAA.Session.DONE, DRMAA.Session.FAILED ): - self.work_queue.put( ( 'finish', sge_job_state ) ) - continue - sge_job_state.old_state = state - new_watched.append( sge_job_state ) - # Replace the watch list with the updated version - self.watched = new_watched - - def finish_job( self, sge_job_state ): - """ - Get the output/error for a finished job, pass to `job_wrapper.finish` - and cleanup all the SGE temporary files. - """ - ofile = sge_job_state.ofile - efile = sge_job_state.efile - job_file = sge_job_state.job_file - # collect the output - try: - ofh = file(ofile, "r") - efh = file(efile, "r") - stdout = ofh.read( 32768 ) - stderr = efh.read( 32768 ) - except: - stdout = '' - stderr = 'Job output not returned from cluster' - log.debug(stderr) - - try: - sge_job_state.job_wrapper.finish( stdout, stderr ) - except: - log.exception("Job wrapper finish method failed") - - # clean up the sge files - self.cleanup( ( ofile, efile, job_file ) ) - - def fail_job( self, sge_job_state ): - """ - Seperated out so we can use the worker threads for it. - """ - self.stop_job( self.sa_session.query( self.app.model.Job ).get( sge_job_state.job_wrapper.job_id ) ) - sge_job_state.job_wrapper.fail( sge_job_state.fail_message ) - self.cleanup( ( sge_job_state.ofile, sge_job_state.efile, sge_job_state.job_file ) ) - - def cleanup( self, files ): - if not asbool( self.app.config.get( 'debug', False ) ): - for file in files: - if os.access( file, os.R_OK ): - os.unlink( file ) - - def put( self, job_wrapper ): - """Add a job to the queue (by job identifier)""" - # Change to queued state before handing to worker thread so the runner won't pick it up again - job_wrapper.change_state( model.Job.states.QUEUED ) - self.work_queue.put( ( 'queue', job_wrapper ) ) - - def shutdown( self ): - """Attempts to gracefully shut down the monitor thread""" - log.info( "sending stop signal to worker threads" ) - self.monitor_queue.put( self.STOP_SIGNAL ) - for i in range( len( self.work_threads ) ): - self.work_queue.put( ( self.STOP_SIGNAL, None ) ) - log.info( "sge job runner stopped" ) - - def stop_job( self, job ): - """Attempts to delete a job from the SGE queue""" - try: - self.ds.control( job.get_job_runner_external_id(), DRMAA.Session.TERMINATE ) - log.debug( "(%s/%s) Removed from SGE queue at user's request" % ( job.get_id(), job.get_job_runner_external_id() ) ) - except DRMAA.InvalidJobError: - log.debug( "(%s/%s) User killed running job, but it was already dead" % ( job.get_id(), job.get_job_runner_external_id() ) ) - - def recover( self, job, job_wrapper ): - """Recovers jobs stuck in the queued/running state when Galaxy started""" - sge_job_state = SGEJobState() - sge_job_state.ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job.get_id()) - sge_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.get_id()) - sge_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.get_id()) - sge_job_state.job_id = str( job.get_job_runner_external_id() ) - sge_job_state.runner_url = job_wrapper.get_job_runner_url() - job_wrapper.command_line = job.get_command_line() - sge_job_state.job_wrapper = job_wrapper - if job.get_state() == model.Job.states.RUNNING: - log.debug( "(%s/%s) is still in running state, adding to the SGE queue" % ( job.get_id(), job.get_job_runner_external_id() ) ) - sge_job_state.old_state = DRMAA.Session.RUNNING - sge_job_state.running = True - self.monitor_queue.put( sge_job_state ) - elif job.get_state() == model.Job.states.QUEUED: - log.debug( "(%s/%s) is still in SGE queued state, adding to the SGE queue" % ( job.get_id(), job.get_job_runner_external_id() ) ) - sge_job_state.old_state = DRMAA.Session.QUEUED_ACTIVE - sge_job_state.running = False - self.monitor_queue.put( sge_job_state ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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