Dear all,
we have setup a Galaxy instance on a virtual machine, and we want to be
able to submit jobs to our HPC system (SLURM).
Currently, we do not understand how to define that jobs will be sent to
the HPC cluster.
We have set :
export $DRMAA_LIBRARY_PATH=/var/lib/libdrmaa.so
This is our config/job_conf.xml :
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way
it is configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" />
</plugins>
<handlers default="handlers">
<handler id="handler0" tags="handlers" />
<handler id="main" />
</handlers>
<destinations default="slurm">
<destination id="slurm" runner="drmaa">
<param id="nativeSpecification">-P all_5hrs</param>
</destination>
</destinations>
</job_conf>
And the output of "sh run.sh" :
galaxy.jobs.manager DEBUG 2017-02-07 15:50:39,962 Starting job handler
galaxy.jobs INFO 2017-02-07 15:50:39,962 Handler 'main' will load all
configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2017-02-07 15:50:39,971
Loaded 'failure' state handler from module
galaxy.jobs.runners.state_handlers.resubmit
pulsar.managers.util.drmaa DEBUG 2017-02-07 15:50:39,975 Initializing
DRMAA session from thread MainThread
Traceback (most recent call last):
File
"/home/mass/GAL/APP/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line
55, in paste_app_factory
app = galaxy.app.UniverseApplication( global_conf=global_conf,
**kwargs )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/app.py", line 170, in __init__
self.job_manager = manager.JobManager( self )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/manager.py", line 23,
in __init__
self.job_handler = handler.JobHandler( app )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/handler.py", line 32,
in __init__
self.dispatcher = DefaultJobDispatcher( app )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/handler.py", line 723,
in __init__
self.job_runners = self.app.job_config.get_job_runner_plugins(
self.app.config.server_name )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/__init__.py", line
687, in get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ],
**runner.get( 'kwds', {} ) )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/runners/drmaa.py",
line 88, in __init__
self.ds = DrmaaSessionFactory().get()
File
"/usr/local/lib/python2.7/dist-packages/pulsar/managers/util/drmaa/__init__.py",
line 31, in get
return DrmaaSession(session_constructor, **kwds)
File
"/usr/local/lib/python2.7/dist-packages/pulsar/managers/util/drmaa/__init__.py",
line 49, in __init__
DrmaaSession.session.initialize()
File "/usr/local/lib/python2.7/dist-packages/drmaa/session.py", line
257, in initialize
py_drmaa_init(contactString)
File "/usr/local/lib/python2.7/dist-packages/drmaa/wrappers.py", line
73, in py_drmaa_init
return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
File "/usr/local/lib/python2.7/dist-packages/drmaa/errors.py", line
151, in error_check
raise _ERRORS[code - 1](error_string)
InternalException: code 1: cell directory
"/usr/lib/gridengine-drmaa/default" doesn't exist
Could anyone point us in the right direction?
This would be greatly appreciated.
Best regards
Leonor
--
Leonor Palmeira | PhD
Associate Scientist
Department of Human Genetics
CHU de Liège | Domaine Universitaire du Sart-Tilman
4000 Liège | BELGIQUE
Tél: +32-4-366.91.41
Fax: +32-4-366.72.61
e-mail: lpalme...@chu.ulg.ac.be
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