Hi,
I am trying to get DRMAA runner working for my local galaxy cluster. However, I am having hard time configuring it my system.
So far,
I have installed Torque 2.5.12 and it seems to work as expected.
I installed drmaa_1.0.17 and here is DRMAA_LIBRARY_PATH galaxy_env)galaxy@GalaxyTest01[/home/galaxy/galaxy-dist]$ echo $DRMAA_LIBRARY_PATH /usr/local/lib/libdrmaa.so
My job.conf.xml <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/> </plugins> <handlers default="handlers"> <handler id="main" tags="handlers"/> </handlers> <destinations default="sge_default"> <destination id="sge_default" runner="drmaa"/> </destinations> </job_conf>
This is the error I am getting when I start galaxy.
galaxy.jobs INFO 2014-04-21 15:37:30,730 Handler 'main' will load all configured runner plugins Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 130, in __init__ self.job_manager = manager.JobManager( self ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in __init__ self.job_handler = handler.JobHandler( app ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 30, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 568, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 489, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 81, in __init__ self.ds.initialize() File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", line 274, in initialize _w.init(contactString) File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/wrappers.py", line 59, in init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) DrmCommunicationException: code 2: (null) Removing PID file paster.pid
I am not sure what is the issue here or how to go about resolving it. I will really appreciate it if someone can tell me how to debug it?
Best regards
Hak