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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