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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