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