Dear all,

we are struggling with the Galaxy documentation to understand how our VM
(with our Galaxy instance running perfectly in local) should be
configured in order to be able to submit jobs to our SLURM Cluster.

We have a shared filesystem named /home/mass/GAL between the Cluster and
the VM. Galaxy is installed in /home/mass/GAL/APP/ and 'drmaa' is
installed on the SLURM Cluster.

The following variables need to be specified but we are struggling to
find out which paths we should give them. We have currently set them
like this and this clearly does not work :

$DRMAA_LIBRARY_PATH=/var/lib/libdrmaa.so
$SGE_ROOT=/usr/lib/gridengine-drmaa (very wild guess)

We would greatly appreciate some help
Thank you in advance
Leo

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: lpalmeira@chu.ulg.ac.be

On 02/07/2017 03:58 PM, Leonor Palmeira wrote:
> 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
>

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