Re: [galaxy-dev] DRMAA configuring issue

2014-04-25 Thread John Chilton 
I feel like someone should respond to this but I must admin I don't
have a lot of ideas.

I assume you are able to use qsub to submit jobs from the Galaxy
server? This is worth verifying that before anything else. If that
doesn't work - the system configuration needs to be modified.

I think there are a couple different implementations of DRMAA for PBS:

http://apps.man.poznan.pl/trac/pbs-drmaa (I think this is recommend one).
http://sourceforge.net/projects/pbspro-drmaa/

It might be worth trying to compile the latest and great of one or
both and target both.

Galaxy also has a PBS runner that many people use for communicating
with Torque. I think the DRMAA runner should work - but this is a
fallback option as well just to get going.

-John
___
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/

Re: [galaxy-dev] DRMAA configuring issue

2014-04-22 Thread Hakeem Almabrazi 
Does anyone have any tips about this, please :)?

Regards

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi
Sent: Monday, April 21, 2014 3:49 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] DRMAA configuring issue

Hi,

I am trying to get DRMAA runner working for my local galaxy cluster.  However, 
I am having hard time configuring it my system.


So far,

I have installed Torque 2.5.12 and it seems to work as expected.

I installed drmaa_1.0.17 and here is DRMAA_LIBRARY_PATH
galaxy_env)galaxy@GalaxyTest01[/home/galaxy/galaxy-dist]$ echo 
$DRMAA_LIBRARY_PATH
/usr/local/lib/libdrmaa.so

My job.conf.xml



   
 
   
   

   
   
  
   


This is the error I am getting when I start galaxy.

galaxy.jobs INFO 2014-04-21 15:37:30,730 Handler 'main' will load all 
configured runner plugins
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 
39, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 130, in __init__
self.job_manager = manager.JobManager( self )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in 
__init__
self.job_handler = handler.JobHandler( app )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 30, in 
__init__
self.dispatcher = DefaultJobDispatcher( app )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 568, in 
__init__
self.job_runners = self.app.job_config.get_job_runner_plugins( 
self.app.config.server_name )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 489, in 
get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 
'kwds', {} ) )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 81, in 
__init__
self.ds.initialize()
  File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", 
line 274, in initialize
_w.init(contactString)
  File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/wrappers.py", 
line 59, in init
return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
  File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-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: (null)
Removing PID file paster.pid

I am not sure what is the issue here or how to go about resolving it.  I will 
really appreciate it if someone can tell me how to debug it?

Best regards

Hak

___
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/

[galaxy-dev] DRMAA configuring issue

2014-04-21 Thread Hakeem Almabrazi 
Hi,

I am trying to get DRMAA runner working for my local galaxy cluster.  However, 
I am having hard time configuring it my system.


So far,

I have installed Torque 2.5.12 and it seems to work as expected.

I installed drmaa_1.0.17 and here is DRMAA_LIBRARY_PATH
galaxy_env)galaxy@GalaxyTest01[/home/galaxy/galaxy-dist]$ echo 
$DRMAA_LIBRARY_PATH
/usr/local/lib/libdrmaa.so

My job.conf.xml



   
 
   
   

   
   
  
   


This is the error I am getting when I start galaxy.

galaxy.jobs INFO 2014-04-21 15:37:30,730 Handler 'main' will load all 
configured runner plugins
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 
39, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 130, in __init__
self.job_manager = manager.JobManager( self )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in 
__init__
self.job_handler = handler.JobHandler( app )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 30, in 
__init__
self.dispatcher = DefaultJobDispatcher( app )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 568, in 
__init__
self.job_runners = self.app.job_config.get_job_runner_plugins( 
self.app.config.server_name )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 489, in 
get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 
'kwds', {} ) )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 81, in 
__init__
self.ds.initialize()
  File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", 
line 274, in initialize
_w.init(contactString)
  File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/wrappers.py", 
line 59, in init
return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
  File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-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: (null)
Removing PID file paster.pid

I am not sure what is the issue here or how to go about resolving it.  I will 
really appreciate it if someone can tell me how to debug it?

Best regards

Hak

___
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/