Question: Problem with SGE_ROOT, SGE / drmaa with Galaxy (updated)
0
gravatar for danielfortin86
21 months ago by
United States
danielfortin86100 wrote:

Hi,

I'm trying to get my local Galaxy to submit jobs to an SGE cluster. However, I'm having problems with the configuration. I'm trying to use DRMAA but am getting an error that my SGE_ROOT isn't set, but I have set it. I've included the relevant lines from my paster.log, job_conf.xml and my $DRMAA_LIBRARY_PATH, $SGE_ROOT. Any suggestions would be greatly appreciated!

 

echo $DRMAA_LIBRARY_PATH
/usr/local/lib

echo $SGE_ROOT

/cm/shared/apps/sge/2011.11p1

 

paster.log:

galaxy.jobs.runners.state_handler_factory DEBUG 2016-02-24 11:21:04,767 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
Traceback (most recent call last):
  File "/opt/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 64, in paste_app_factory
    app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
  File "/opt/galaxy/lib/galaxy/app.py", line 142, in __init__
    self.job_manager = manager.JobManager( self )
  File "/opt/galaxy/lib/galaxy/jobs/manager.py", line 23, in __init__
    self.job_handler = handler.JobHandler( app )
  File "/opt/galaxy/lib/galaxy/jobs/handler.py", line 32, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
  File "/opt/galaxy/lib/galaxy/jobs/handler.py", line 722, in __init__
    self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name )
  File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 668, in get_job_runner_plugins
    rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
  File "/opt/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 83, in __init__
    self.ds.initialize()
  File "/opt/galaxy/eggs/drmaa-0.7.6-py2.6.egg/drmaa/session.py", line 257, in initialize
    py_drmaa_init(contactString)
  File "/opt/galaxy/eggs/drmaa-0.7.6-py2.6.egg/drmaa/wrappers.py", line 73, in py_drmaa_init
    return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
  File "/opt/galaxy/eggs/drmaa-0.7.6-py2.6.egg/drmaa/errors.py", line 151, in error_check
    raise _ERRORS[code - 1](error_string)
InternalException: code 1: Please set the environment variable SGE_ROOT.
Removing PID file paster.pid

 

job_conf.xml:

<?xml version="1.0"?>
<job_conf>
    <plugins workers="4">
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
        <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
    </plugins>
    <handlers>  <handler id="main"/>   </handlers>
    <destinations default="SGE">
        <destination id="local" runner="local"/>
        <destination id="SGE" runner="drmaa">
                <param id="nativeSpecification">-q all.q</param>
        </destination>
    </destinations>

 

sge_root sge cluster drmaa • 887 views
ADD COMMENTlink modified 21 months ago • written 21 months ago by danielfortin86100
1
gravatar for danielfortin86
21 months ago by
United States
danielfortin86100 wrote:

I solved the issue, it turns out that since I'm starting Galaxy as a system service I need to add SGE_ROOT to the /etc/init.d/galaxy.fedora-init file

ADD COMMENTlink written 21 months ago by danielfortin86100
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