On 20 February 2017 at 15:24, Leonor Palmeira <lpalmeira@chu.ulg.ac.be> wrote:

Hi Marius,

yes, we are using the one from Poznan. Should we give it a try with the
fork?

Best
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: lpalmeira@chu.ulg.ac.be

On 02/20/2017 03:13 PM, Marius van den Beek wrote:
> Hi Leonor,
>
> Are you sure that you are using a drmaa library that is compatible with
> slurm?
> This http://apps.man.poznan.pl/trac/slurm-drmaa should work, IIRC,
> or alternatively you can use Nate Coraor's fork
> here https://github.com/natefoo/slurm-drmaa.
>
> Best,
> Marius
>
> On 20 February 2017 at 15:06, Leonor Palmeira <lpalmeira@chu.ulg.ac.be

> <mailto:lpalmeira@chu.ulg.ac.be>> wrote:
>
> Hi,
>
> we modified our configuration as Marius suggested, but we still get the
> following error. This is an error we had just before, and we were trying
> to fix it by specifying an $SGE_ROOT variable.
>
> I don't know why this error pops up, as we are trying to use SLURM, not
> SGE...
>
> galaxy.jobs.runners.state_handler_factory DEBUG 2017-02-20 14:58:59,768
> Loaded 'failure' state handler from module
> galaxy.jobs.runners.state_handlers.resubmit
> pulsar.managers.util.drmaa DEBUG 2017-02-20 14:58:59,807
> 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: Please set the environment variable SGE_ROOT.
>
> Thanks a lot in advance
> 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 <tel:%2B32-4-366.91.41>
> Fax: +32-4-366.72.61 <tel:%2B32-4-366.72.61>
> e-mail: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be>
>
> On 02/13/2017 03:37 PM, Marius van den Beek wrote:
> > 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 <lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be>

> > <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@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 <tel:%2B32-4-366.91.41>
> <tel:%2B32-4-366.91.41>
> > Fax: +32-4-366.72.61 <tel:%2B32-4-366.72.61>
> <tel:%2B32-4-366.72.61>
> > e-mail: lpalmeira@chu.ulg.ac.be

> <mailto:lpalmeira@chu.ulg.ac.be> <mailto:lpalmeira@chu.ulg.ac.be

> <mailto: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"?>
> > > 
> > > <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 <http://galaxy.jobs> <http://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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