[galaxy-dev] error after pulling latest updates
Hi All, Just did an update to HEAD, and upon restarting the daemons received the following messages: galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083 in condor runner Traceback (most recent call last): File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/app.py, line 164, in __init__ self.job_manager = manager.JobManager( self ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/manager.py, line 36, in __init__ self.job_handler.start() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 34, in start self.job_queue.start() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 77, in start self.__check_jobs_at_startup() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 125, in __check_jobs_at_startup self.dispatcher.recover( job, job_wrapper ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 620, in recover self.job_runners[runner_name].recover( job, job_wrapper ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/runners/condor.py, line 243, in recover cjs.user_log = os.path.join( self.app.config.cluster_files_directory, '%s.condor.log' % galaxy_id_tag ) NameError: global name 'galaxy_id_tag' is not defined Removing PID file main.pid -- Branden Timm bt...@energy.wisc.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error after pulling latest updates
I was able to work around this error by hacking the condor job runner, there were two obvious errors. First, in recover(), galaxy_id_tag was not being set (hence the NameError). Second, the same method was invoking self.__old_job_state with one argument when it clearly expects two. The latter I just commented out. 243d242 galaxy_id_tag = job_wrapper.get_id_tag() 246c245 #self.__old_state_paths( cjs ) --- self.__old_state_paths( cjs ) Obviously this is a hacky workaround, but I'd like to hear if anybody knows the cause of these errors and whether a patch should be submitted. -- Branden Timm bt...@energy.wisc.edu On 6/5/2013 10:58 AM, Branden Timm wrote: Hi All, Just did an update to HEAD, and upon restarting the daemons received the following messages: galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083 in condor runner Traceback (most recent call last): File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/app.py, line 164, in __init__ self.job_manager = manager.JobManager( self ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/manager.py, line 36, in __init__ self.job_handler.start() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 34, in start self.job_queue.start() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 77, in start self.__check_jobs_at_startup() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 125, in __check_jobs_at_startup self.dispatcher.recover( job, job_wrapper ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 620, in recover self.job_runners[runner_name].recover( job, job_wrapper ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/runners/condor.py, line 243, in recover cjs.user_log = os.path.join( self.app.config.cluster_files_directory, '%s.condor.log' % galaxy_id_tag ) NameError: global name 'galaxy_id_tag' is not defined Removing PID file main.pid -- Branden Timm bt...@energy.wisc.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error after pulling latest updates
On Jun 5, 2013, at 2:11 PM, Branden Timm wrote: I was able to work around this error by hacking the condor job runner, there were two obvious errors. First, in recover(), galaxy_id_tag was not being set (hence the NameError). Second, the same method was invoking self.__old_job_state with one argument when it clearly expects two. The latter I just commented out. 243d242 galaxy_id_tag = job_wrapper.get_id_tag() 246c245 #self.__old_state_paths( cjs ) --- self.__old_state_paths( cjs ) Obviously this is a hacky workaround, but I'd like to hear if anybody knows the cause of these errors and whether a patch should be submitted. Hi Branden, I refactored all of the job runners but wasn't able to fully test all of the changes to the Condor runner, which is how this bug popped up. I've committed the fix to the stable branch in galaxy-central. Thanks for the fix and sorry for the inconvenience. --nate -- Branden Timm bt...@energy.wisc.edu On 6/5/2013 10:58 AM, Branden Timm wrote: Hi All, Just did an update to HEAD, and upon restarting the daemons received the following messages: galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083 in condor runner Traceback (most recent call last): File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/app.py, line 164, in __init__ self.job_manager = manager.JobManager( self ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/manager.py, line 36, in __init__ self.job_handler.start() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 34, in start self.job_queue.start() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 77, in start self.__check_jobs_at_startup() File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 125, in __check_jobs_at_startup self.dispatcher.recover( job, job_wrapper ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 620, in recover self.job_runners[runner_name].recover( job, job_wrapper ) File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/runners/condor.py, line 243, in recover cjs.user_log = os.path.join( self.app.config.cluster_files_directory, '%s.condor.log' % galaxy_id_tag ) NameError: global name 'galaxy_id_tag' is not defined Removing PID file main.pid -- Branden Timm bt...@energy.wisc.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
