Solved!!!!!
The problem was I have configured the job_conf.xml two plugins entry with DRMAA. I have deleted the entry:
<plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
And now works!
Thanks
El 25/09/2014, a las 08:12, Pardo Diaz, Alfonso <alfonso.pardo@ciemat.esmailto:alfonso.pardo@ciemat.es> escribió:
Hi,
I have configured a new galaxy-project site with SLURM (version 14). I have one server with a Galaxy-Project instance, one node with SLURM server and two SLURM worker nodes. I have compile SLURM-DRMAA from source codes. When I run “drmaa-run /bin/hostname” it’s work. But, when I try to run the server I got the next error:
Traceback (most recent call last): File "/home/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy-dist/lib/galaxy/app.py", line 141, in __init__ self.job_manager = manager.JobManager( self ) File "/home/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/home/galaxy-dist/lib/galaxy/jobs/handler.py", line 32, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/home/galaxy-dist/lib/galaxy/jobs/handler.py", line 704, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/home/galaxy-dist/lib/galaxy/jobs/__init__.py", line 621, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) File "/home/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 81, in __init__ self.ds.initialize() File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/session.py", line 257, in initialize py_drmaa_init(contactString) File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/wrappers.py", line 73, in py_drmaa_init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) AlreadyActiveSessionException: code 11: DRMAA session already exist. [root@galaxy-project galaxy-dist]#
This is my “job_conf.xml”:
<job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner"> <param id="drmaa_library_path">/usr/local/lib/libdrmaa.so</param> </plugin> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="drmaa_slurm"> <destination id="local" runner="local"/> <destination id="multicore_local" runner="local"> <param id="local_slots">4</param> <param id="embed_metadata_in_job">True</param> <job_metrics /> </destination> <destination id="docker_local" runner="local"> <param id="docker_enabled">true</param> </destination> <destination id="drmaa_slurm" runner="drmaa"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="direct_slurm" runner="slurm"> <param id="nativeSpecification">--time=00:01:00</param> </destination> </destinations> <resources default="default"> <group id="default"></group> <group id="memoryonly">memory</group> <group id="all">processors,memory,time,project</group> </resources> <tools> <tool id="foo" handler="trackster_handler"> <param id="source">trackster</param> </tool> <tool id="bar" destination="dynamic"/> <tool id="longbar" destination="dynamic" resources="all" /> <tool id="baz" handler="special_handlers" destination="bigmem"/> </tools> <limits> <limit type="registered_user_concurrent_jobs">2</limit> <limit type="anonymous_user_concurrent_jobs">1</limit> <limit type="destination_user_concurrent_jobs" id="local">1</limit> <limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit> <limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit> <limit type="destination_total_concurrent_jobs" id="local">16</limit> <limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit> <limit type="walltime">24:00:00</limit> <limit type="output_size">10GB</limit> </limits> </job_conf>
Can you help me? I am newbie with “Galaxy Project” administration.
THANKS IN ADVANCE!!!!
Alfonso Pardo Diaz System Administrator / Researcher c/ Sola nº 1; 10200 Trujillo, ESPAÑA Tel: +34 927 65 93 17 Fax: +34 927 32 32 37
[CETA-Ciemat logo]http://www.ceta-ciemat.es/
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