SLURM configuration problem
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 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 -- 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
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 Fax: +32-4-366.72.61 e-mail: 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 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
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> 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 Fax: +32-4-366.72.61 e-mail: 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 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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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. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
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 <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"?> > <!-- 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. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
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 Fax: +32-4-366.72.61 e-mail: lpalmeira@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 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 <lpalmeira@chu.ulg.ac.be <mailto: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 <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 02/13/2017 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> > <mailto: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> <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: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> <mailto: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> <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. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>> > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/> > <http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>> > >
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 <lpalmeira@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 Fax: +32-4-366.72.61 e-mail: lpalmeira@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 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 <lpalmeira@chu.ulg.ac.be <mailto: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 <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 02/13/2017 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> > <mailto: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> <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: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> <mailto: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> <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. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>> > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/> > <http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>> > >
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: lpalmeira@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 <lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@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: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@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 <lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> > <mailto:lpalmeira@chu.ulg.ac.be <mailto: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 <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: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> <mailto:lpalmeira@chu.ulg.ac.be <mailto: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> <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be>> > > <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> <mailto: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> <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: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> > <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be>> <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> > <mailto: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> <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 > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> > <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>> <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> > <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>>> > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/> > <http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>> > > <http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/> > <http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>>> > > > > > >
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 <lpalmeira@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: lpalmeira@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 <lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@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: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@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 < lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> > <mailto:lpalmeira@chu.ulg.ac.be <mailto: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 <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: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac. be> <mailto:lpalmeira@chu.ulg.ac.be <mailto: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> <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be>> > > <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> <mailto: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> <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: lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> > <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be>> <mailto:lpalmeira@chu.ulg.ac.be <mailto:lpalmeira@chu.ulg.ac.be> > <mailto: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> <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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participants (2)
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Leonor Palmeira -
Marius van den Beek