On 20 February 2017 at 15:06, Leonor Palmeira <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
Fax: +32-4-366.72.61
e-mail: 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>> 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: 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> 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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