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.ini...@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.ini...@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 >> >> >> >>
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