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