Hello Leonor,

the log you've sent indicates that you're picking up pulsar from
/usr/local/lib.
That should not happen if you're running galaxy in a virtualenv.

Apart from that you did not mention if you able to submit slurm jobs from
the command line.
That is a prerequisite for launching jobs through galaxy.

Could you post the full startup logs and job_conf.xml file somewhere?

Best,
Marius

On 31 March 2017 at 12:38, Leonor Palmeira <lpalme...@chu.ulg.ac.be> wrote:

> Dear all,
>
> we are struggling with the basics in our Galaxy/SLURM configuration.
>
> - Galaxy is installed on a virtual machine that is physically
> independent from our cluster, but on a shared filesystem that is also
> mounted on the Cluster
>
> - Our Cluster is running SLURM and has 'slurm-drmaa' (Poznan version)
> installed. The shared filesystem is mounted on the same mount point as
> the VM, so their /paths are identical
>
> What do we need so that the Galaxy VM is able to submit jobs to the
> Cluster?
> Currently, running ".run.sh" from the VM as root leads to the $SGE_ROOT
> error I posted in my previous email and that ends like this :
>
>   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.
>
> Any help would be greatly appreciated.
>
> 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: lpalme...@chu.ulg.ac.be
>
> On 02/20/2017 03:57 PM, Marius van den Beek wrote:
> > It doesn't hurt to try this, but I don't think that will solve the
> problem.
> >
> > Just to be sure, the basics are working? You can submit jobs via sbatch?
> > How did you compile/install slurm-drmaa ?
> >
> > Also it looks like drmaa-python is being used from /usr/local/... .
> > Are you running galaxy in a virtualenv?
> > It's strongly recommended to do that.
> > Starting galaxy through run.sh will handle the creation and installation
> > of all necessary dependencies for you.
> > Finally it looks like you're loading pulsar from /usr/local ... this is
> > a bit messy.
> > Please try getting the cluster submission to work using run.sh first.
> >
> >
> > On 20 February 2017 at 15:24, Leonor Palmeira <lpalme...@chu.ulg.ac.be
> > <mailto:lpalme...@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 <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 02/20/2017 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
> >     <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
> >     <https://github.com/natefoo/slurm-drmaa>.
> >     >
> >     > Best,
> >     > Marius
> >     >
> >     > On 20 February 2017 at 15:06, Leonor Palmeira <
> lpalme...@chu.ulg.ac.be <mailto:lpalme...@chu.ulg.ac.be>
> >     > <mailto:lpalme...@chu.ulg.ac.be <mailto: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 <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: lpalme...@chu.ulg.ac.be <mailto:lpalme...@chu.ulg.ac.
> be>
> >     <mailto:lpalme...@chu.ulg.ac.be <mailto: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>
> >     <mailto:lpalme...@chu.ulg.ac.be <mailto:lpalme...@chu.ulg.ac.be>>
> >     >     > <mailto:lpalme...@chu.ulg.ac.be
> >     <mailto:lpalme...@chu.ulg.ac.be> <mailto: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>
> >     <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: lpalme...@chu.ulg.ac.be
> >     <mailto:lpalme...@chu.ulg.ac.be>
> >     >     <mailto:lpalme...@chu.ulg.ac.be
> >     <mailto:lpalme...@chu.ulg.ac.be>> <mailto:lpalme...@chu.ulg.ac.be
> >     <mailto:lpalme...@chu.ulg.ac.be>
> >     >     <mailto: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> <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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