DRMAA configuring issue

21 Apr 2014

      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

Hakeem Almabrazi

Hakeem Almabrazi

John Chilton

tags

participants (2)