1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/32ea53484cec/ changeset: 32ea53484cec user: james_taylor date: 2012-12-21 22:43:30 summary: Fix shutdown on python >= 2.6.2 by calling setDaemon when creating threads (these are still cleanly shutdown by atexit). Also add descriptive names to most job worker threads affected #: 7 files

diff -r c54ebfe2c0086b6e690e98a958e2d41ecf722bec -r 32ea53484cec638021a38c0c252d5dc1d4bf5da4 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -61,7 +61,8 @@ # Helper for interruptable sleep self.sleeper = Sleeper() self.running = True - self.monitor_thread = threading.Thread( target=self.__monitor ) + self.monitor_thread = threading.Thread( name="JobHandlerQueue.monitor_thread", target=self.__monitor ) + self.monitor_thread.setDaemon( True )

def start( self ): """ @@ -353,7 +354,8 @@ # Helper for interruptable sleep self.sleeper = Sleeper() self.running = True - self.monitor_thread = threading.Thread( target=self.monitor ) + self.monitor_thread = threading.Thread( name="JobHandlerStopQueue.monitor_thread", target=self.monitor ) + self.monitor_thread.setDaemon( True ) self.monitor_thread.start() log.info( "job handler stop queue started" )

diff -r c54ebfe2c0086b6e690e98a958e2d41ecf722bec -r 32ea53484cec638021a38c0c252d5dc1d4bf5da4 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -68,7 +68,8 @@ # Helper for interruptable sleep self.sleeper = Sleeper() self.running = True - self.monitor_thread = threading.Thread( target=self.__monitor ) + self.monitor_thread = threading.Thread( name="JobManagerQueue.monitor_thread", target=self.__monitor ) + self.monitor_thread.setDaemon( True ) # Recover jobs at startup self.__check_jobs_at_startup() # Start the queue @@ -219,7 +220,8 @@ # Helper for interruptable sleep self.sleeper = Sleeper() self.running = True - self.monitor_thread = threading.Thread( target=self.monitor ) + self.monitor_thread = threading.Thread( name="JobManagerStopQueue.monitor_thread", target=self.monitor ) + self.monitor_thread.setDaemon( True ) self.monitor_thread.start() log.info( "job manager stop queue started" )

diff -r c54ebfe2c0086b6e690e98a958e2d41ecf722bec -r 32ea53484cec638021a38c0c252d5dc1d4bf5da4 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -105,13 +105,14 @@ self.monitor_queue = Queue() self.ds = drmaa.Session() self.ds.initialize() - self.monitor_thread = threading.Thread( target=self.monitor ) + self.monitor_thread = threading.Thread( name="DRMAAJobRunner.monitor_thread", target=self.monitor ) + self.monitor_thread.setDaemon( True ) 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 = threading.Thread( name=( "DRMAAJobRunner.work_threads-%d" % i ), target=self.run_next ) worker.start() self.work_threads.append( worker ) log.debug( "%d workers ready" % nworkers )

diff -r c54ebfe2c0086b6e690e98a958e2d41ecf722bec -r 32ea53484cec638021a38c0c252d5dc1d4bf5da4 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -37,7 +37,8 @@ nworkers = app.config.local_job_queue_workers log.info( "starting workers" ) for i in range( nworkers ): - worker = threading.Thread( target=self.run_next ) + worker = threading.Thread( name=( "LocalJobRunner.threads-%d" % i ), target=self.run_next ) + worker.setDaemon( True ) worker.start() self.threads.append( worker ) log.debug( "%d workers ready", nworkers )

diff -r c54ebfe2c0086b6e690e98a958e2d41ecf722bec -r 32ea53484cec638021a38c0c252d5dc1d4bf5da4 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -229,7 +229,8 @@ nworkers = app.config.local_job_queue_workers log.info( "starting workers" ) for i in range( nworkers ): - worker = threading.Thread( target=self.run_next ) + worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) + worker.setDaemon( True ) worker.start() self.threads.append( worker ) log.debug( "%d workers ready", nworkers )

diff -r c54ebfe2c0086b6e690e98a958e2d41ecf722bec -r 32ea53484cec638021a38c0c252d5dc1d4bf5da4 lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -29,7 +29,8 @@ nworkers = app.config.local_task_queue_workers log.info( "Starting tasked-job runners" ) for i in range( nworkers ): - worker = threading.Thread( target=self.run_next ) + worker = threading.Thread( name=( "TaskedJobRunner-%d" % i ), target=self.run_next ) + worker.setDaemon( True ) worker.start() self.threads.append( worker ) log.debug( "%d workers ready", nworkers )

diff -r c54ebfe2c0086b6e690e98a958e2d41ecf722bec -r 32ea53484cec638021a38c0c252d5dc1d4bf5da4 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -38,6 +38,8 @@ import traceback, sys traceback.print_exc() sys.exit( 1 ) + # Call app's shutdown method when the interpeter exits, this cleanly stops + # the various Galaxy application daemon threads atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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