Hello Leonor,

One thing that you should avoid is setting things related to SGE (Sun Grid
Engine)
if you’re trying to interface with Slurm.
The error message`

"/usr/lib/gridengine-drmaa/default"

Points to a problem with SGE … I don’t understand where that is coming into
play if you’re trying to submit jobs to SLURM.

A good bet is to set the path to the drmaa library like so:

...
<plugin id="slurm" type="runner"
load="galaxy.jobs.runners.slurm:SlurmJobRunner">
    <param id="drmaa_library_path">/var/lib/libdrmaa.so</param>
</plugin>
...

If you’re still having trouble let us know.

Best,
Marius
​

On 13 February 2017 at 15:25, Leonor Palmeira <lpalme...@chu.ulg.ac.be>
wrote:

> 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: lpalme...@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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