Thank you Olivier! The qsub -sync y and the MAX_DYN_EC settings lead me to path of resolution of the error. My galaxy server can now submit jobs to the SGE cluster now. Much appreciated. -Tin On Tue, May 28, 2013 at 5:53 AM, Olivier Inizan < olivier.inizan@versailles.inra.fr> wrote:

Hello tin,

For the error: "DrmCommunicationException: code 2: range_list containes no element" have you checked that you can submit jobs in -sync mode ?

See: http://stackoverflow.com/**questions/4883056/sge-qsub-** fails-to-submit-jobs-in-sync-**mode<http://stackoverflow.com/questions/4883056/sge-qsub-fails-to-submit-jobs-in-sync-mode>

We faced with this error recently and setting MAX_DYN_EC=1000 for SGE fix the problem.

Let me know,

Olivier

Olivier Inizan Unité de Recherches en Génomique-Info (UR INRA 1164), INRA, Centre de recherche de Versailles, bat.18 RD10, route de Saint Cyr 78026 Versailles Cedex, FRANCE

Olivier.Inizan@versailles.**inra.fr <Olivier.Inizan@versailles.inra.fr>

Tél: +33 1 30 83 38 25 Fax: +33 1 30 83 38 99 http://urgi.versailles.inra.fr [urgi.versailles.inra.fr] Twitter: @OlivierInizan

On Thu, 23 May 2013, tin h wrote:

Hello galaxy-dev gurus,

...

I was trying to upgrade my galaxy server... I removed the old galaxy-dist and ran hg clone https://bitbucket.org/galaxy/**galaxy-dist/<https://bitbucket.org/galaxy/galaxy-dist/>

restored universe_wsgi.ini file and various tool-data config, and tried to restart galaxy.

After some twiddling, I see the error message at the end of this email. The strangest thing I see is this /usr/prog/galaxy/galaxy-dist/**eggs/drmaa-0.4b3-py2.6.egg/** drmaa/wrappers.py on my current system, drmaa-0.4b3-py2.6.egg is a file and not a directory...

is the latest code that I just downloaded corrupted or something?

Much thanks in advance for your help in this matter. -Tin

PS. Relevant entry in universe_wsgi.ini on cluster config: start_job_runners = drmaa default_cluster_job_runner = drmaa:///

galaxy.tools.genome_index DEBUG 2013-05-24 08:42:49,150 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2013-05-24 08:42:49,153 Starting job handler galaxy.jobs.runners DEBUG 2013-05-24 08:42:49,155 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2013-05-24 08:42:49,156 Loaded job runner 'galaxy.jobs.runners.local:**LocalJobRunner' as 'local' Traceback (most recent call last): File "/usr/prog/galaxy/galaxy-dist/**lib/galaxy/webapps/galaxy/**buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/prog/galaxy/galaxy-dist/**lib/galaxy/app.py", line 159, in __init__ self.job_manager = manager.JobManager( self ) File "/usr/prog/galaxy/galaxy-dist/**lib/galaxy/jobs/manager.py", line 31, in __init__ self.job_handler = handler.JobHandler( app ) File "/usr/prog/galaxy/galaxy-dist/**lib/galaxy/jobs/handler.py", line 29, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/usr/prog/galaxy/galaxy-dist/**lib/galaxy/jobs/handler.py", line 543, in __init__ self.job_runners = self.app.job_config.get_job_**runner_plugins() File "/usr/prog/galaxy/galaxy-dist/**lib/galaxy/jobs/__init__.py", line 486, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) File "/usr/prog/galaxy/galaxy-dist/**lib/galaxy/jobs/runners/drmaa.**py", line 75, in __init__ self.ds.initialize() File "/usr/prog/galaxy/galaxy-dist/**eggs/drmaa-0.4b3-py2.6.egg/**drmaa/__init__.py", line 274, in initialize _w.init(contactString) File "/usr/prog/galaxy/galaxy-dist/**eggs/drmaa-0.4b3-py2.6.egg/**drmaa/wrappers.py", line 59, in init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File "/usr/prog/galaxy/galaxy-dist/**eggs/drmaa-0.4b3-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: range_list containes no elements