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/

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). -->
        <plugin id="drmaa" type="runner"
load="" />
    <handlers default="handlers">
        <handler id="handler0" tags="handlers" />
        <handler id="main" />
    <destinations default="slurm">
        <destination id="slurm" runner="drmaa">
                <param id="nativeSpecification">-P all_5hrs</param>

And the output of "sh" : DEBUG 2017-02-07 15:50:39,962 Starting job handler INFO 2017-02-07 15:50:39,962 Handler 'main' will load all
configured runner plugins DEBUG 2017-02-07 15:50:39,971
Loaded 'failure' state handler from module

pulsar.managers.util.drmaa DEBUG 2017-02-07 15:50:39,975 Initializing
DRMAA session from thread MainThread

Traceback (most recent call last):

"/home/mass/GAL/APP/galaxy/lib/galaxy/webapps/galaxy/", line
55, in paste_app_factory

    app = global_conf=global_conf,
**kwargs )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/", line 170, in __init__

    self.job_manager = manager.JobManager( self )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/", line 23,
in __init__

    self.job_handler = handler.JobHandler( app )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/", line 32,
in __init__

    self.dispatcher = DefaultJobDispatcher( app )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/", line 723,
in __init__

    self.job_runners = )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/", line
687, in get_job_runner_plugins

    rval[id] = runner_class(, runner[ 'workers' ],
**runner.get( 'kwds', {} ) )

  File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/runners/",
line 88, in __init__

    self.ds = DrmaaSessionFactory().get()

line 31, in get

    return DrmaaSession(session_constructor, **kwds)

line 49, in __init__


  File "/usr/local/lib/python2.7/dist-packages/drmaa/", line
257, in initialize


  File "/usr/local/lib/python2.7/dist-packages/drmaa/", 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/", 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 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
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at:

Reply via email to