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"?> > <!-- 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 > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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