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
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
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/
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