problem with current galaxy to submit job to drmaa/sge

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problem with current galaxy to submit job to drmaa/sge

tin h
Hello galaxy-dev gurus, 

I was trying to upgrade my galaxy server...
I removed the old galaxy-dist and ran 

restored universe_wsgi.ini file and various tool-data config, and tried to restart galaxy.




After some twiddling, I see the error message at the end of this email.
The strangest thing I see is this
             /usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py
on my current system, drmaa-0.4b3-py2.6.egg is a file and not a directory... 

is the latest code that I just downloaded corrupted or something?

Much thanks in advance for your help in this matter.
-Tin


PS.  Relevant entry in universe_wsgi.ini on cluster config:
            start_job_runners = drmaa
            default_cluster_job_runner =  drmaa:///



galaxy.tools.genome_index DEBUG 2013-05-24 08:42:49,150 Loaded genome index tool: __GENOME_INDEX__
galaxy.jobs.manager DEBUG 2013-05-24 08:42:49,153 Starting job handler
galaxy.jobs.runners DEBUG 2013-05-24 08:42:49,155 Starting 4 LocalRunner workers
galaxy.jobs DEBUG 2013-05-24 08:42:49,156 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
Traceback (most recent call last):
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 159, in __init__
    self.job_manager = manager.JobManager( self )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in __init__
    self.job_handler = handler.JobHandler( app )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 29, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 543, in __init__
    self.job_runners = self.app.job_config.get_job_runner_plugins()
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 486, in get_job_runner_plugins
    rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 75, in __init__
    self.ds.initialize()
  File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 274, in initialize
    _w.init(contactString)
  File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py", line 59, in init
    return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
  File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 90, in error_check
    raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
DrmCommunicationException: code 2: range_list containes no elements



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Re: problem with current galaxy to submit job to drmaa/sge

Olivier Inizan
Hello tin,

For the error: "DrmCommunicationException: code 2: range_list containes no
element" have you checked that you can submit jobs in -sync mode ?

See: http://stackoverflow.com/questions/4883056/sge-qsub-fails-to-submit-jobs-in-sync-mode

We faced with this error recently and setting MAX_DYN_EC=1000 for SGE fix
the problem.

Let me know,

Olivier


Olivier Inizan
Unité de Recherches en Génomique-Info (UR INRA 1164),
INRA, Centre de recherche de Versailles, bat.18
RD10, route de Saint Cyr
78026 Versailles Cedex, FRANCE

[hidden email]

Tél: +33 1 30 83 38 25
Fax: +33 1 30 83 38 99
http://urgi.versailles.inra.fr [urgi.versailles.inra.fr]
Twitter: @OlivierInizan


On Thu, 23 May 2013, tin h wrote:

> Hello galaxy-dev gurus, 
>
> I was trying to upgrade my galaxy server...
> I removed the old galaxy-dist and ran 
>      hg clone https://bitbucket.org/galaxy/galaxy-dist/
>
> restored universe_wsgi.ini file and various tool-data config, and tried to restart galaxy.
>
>
>
>
> After some twiddling, I see the error message at the end of this email.
> The strangest thing I see is this
>              /usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py
> on my current system, drmaa-0.4b3-py2.6.egg is a file and not a directory... 
>
> is the latest code that I just downloaded corrupted or something?
>
> Much thanks in advance for your help in this matter.
> -Tin
>
>
> PS.  Relevant entry in universe_wsgi.ini on cluster config:
>             start_job_runners = drmaa
>             default_cluster_job_runner =  drmaa:///
>
>
>
> galaxy.tools.genome_index DEBUG 2013-05-24 08:42:49,150 Loaded genome index tool: __GENOME_INDEX__
> galaxy.jobs.manager DEBUG 2013-05-24 08:42:49,153 Starting job handler
> galaxy.jobs.runners DEBUG 2013-05-24 08:42:49,155 Starting 4 LocalRunner workers
> galaxy.jobs DEBUG 2013-05-24 08:42:49,156 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
> Traceback (most recent call last):
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 159, in __init__
>     self.job_manager = manager.JobManager( self )
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in __init__
>     self.job_handler = handler.JobHandler( app )
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 29, in __init__
>     self.dispatcher = DefaultJobDispatcher( app )
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 543, in __init__
>     self.job_runners = self.app.job_config.get_job_runner_plugins()
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 486, in get_job_runner_plugins
>     rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 75, in __init__
>     self.ds.initialize()
>   File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 274, in initialize
>     _w.init(contactString)
>   File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py", line 59, in init
>     return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
>   File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 90, in error_check
>     raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
> DrmCommunicationException: code 2: range_list containes no elements
>
>
>
>
___________________________________________________________
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:
  http://lists.bx.psu.edu/

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Re: problem with current galaxy to submit job to drmaa/sge

tin h

Thank you Olivier!
The qsub -sync y and the MAX_DYN_EC settings lead me to path of resolution of the error.  
My galaxy server can now submit jobs to the SGE cluster now.

Much appreciated.
-Tin



On Tue, May 28, 2013 at 5:53 AM, Olivier Inizan <[hidden email]> wrote:
Hello tin,

For the error: "DrmCommunicationException: code 2: range_list containes no element" have you checked that you can submit jobs in -sync mode ?

See: http://stackoverflow.com/questions/4883056/sge-qsub-fails-to-submit-jobs-in-sync-mode

We faced with this error recently and setting MAX_DYN_EC=1000 for SGE fix the problem.

Let me know,

Olivier


Olivier Inizan
Unité de Recherches en Génomique-Info (UR INRA 1164),
INRA, Centre de recherche de Versailles, bat.18
RD10, route de Saint Cyr
78026 Versailles Cedex, FRANCE

[hidden email]

Tél: +33 1 30 83 38 25
Fax: +33 1 30 83 38 99
http://urgi.versailles.inra.fr [urgi.versailles.inra.fr]
Twitter: @OlivierInizan



On Thu, 23 May 2013, tin h wrote:

Hello galaxy-dev gurus, 

I was trying to upgrade my galaxy server...
I removed the old galaxy-dist and ran 
     hg clone https://bitbucket.org/galaxy/galaxy-dist/

restored universe_wsgi.ini file and various tool-data config, and tried to restart galaxy.




After some twiddling, I see the error message at the end of this email.
The strangest thing I see is this
             /usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py
on my current system, drmaa-0.4b3-py2.6.egg is a file and not a directory... 

is the latest code that I just downloaded corrupted or something?

Much thanks in advance for your help in this matter.
-Tin


PS.  Relevant entry in universe_wsgi.ini on cluster config:
            start_job_runners = drmaa
            default_cluster_job_runner =  drmaa:///



galaxy.tools.genome_index DEBUG 2013-05-24 08:42:49,150 Loaded genome index tool: __GENOME_INDEX__
galaxy.jobs.manager DEBUG 2013-05-24 08:42:49,153 Starting job handler
galaxy.jobs.runners DEBUG 2013-05-24 08:42:49,155 Starting 4 LocalRunner workers
galaxy.jobs DEBUG 2013-05-24 08:42:49,156 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
Traceback (most recent call last):
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 159, in __init__
    self.job_manager = manager.JobManager( self )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in __init__
    self.job_handler = handler.JobHandler( app )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 29, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 543, in __init__
    self.job_runners = self.app.job_config.get_job_runner_plugins()
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 486, in get_job_runner_plugins
    rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 75, in __init__
    self.ds.initialize()
  File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 274, in initialize
    _w.init(contactString)
  File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py", line 59, in init
    return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
  File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 90, in error_check
    raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
DrmCommunicationException: code 2: range_list containes no elements





___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/