[galaxy-dev] DRMAA Slurm error

25 Sep 2014

      Hi,

I have configured a new galaxy-project site with SLURM (version 14). I have one server with a Galaxy-Project instance, one node with SLURM server and two SLURM worker nodes. I have compile SLURM-DRMAA from source codes. When I run “drmaa-run /bin/hostname” it’s work. But, when I try to run the server I got the next error:

Traceback (most recent call last):
  File "/home/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/home/galaxy-dist/lib/galaxy/app.py", line 141, in __init__
    self.job_manager = manager.JobManager( self )
  File "/home/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__
    self.job_handler = handler.JobHandler( app )
  File "/home/galaxy-dist/lib/galaxy/jobs/handler.py", line 32, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
  File "/home/galaxy-dist/lib/galaxy/jobs/handler.py", line 704, in __init__
    self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name )
  File "/home/galaxy-dist/lib/galaxy/jobs/__init__.py", line 621, in get_job_runner_plugins
    rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
  File "/home/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 81, in __init__
    self.ds.initialize()
  File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/session.py", line 257, in initialize
    py_drmaa_init(contactString)
  File "/home/galaxy-dist/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 "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/errors.py", line 151, in error_check
    raise _ERRORS[code - 1](error_string)
AlreadyActiveSessionException: code 11: DRMAA session already exist.
[root@galaxy-project galaxy-dist]#

This is my “job_conf.xml”:

<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"/>
        <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" />
        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
            <param id="drmaa_library_path">/usr/local/lib/libdrmaa.so</param>
        </plugin>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="drmaa_slurm">
        <destination id="local" runner="local"/>
        <destination id="multicore_local" runner="local">
          <param id="local_slots">4</param>
          <param id="embed_metadata_in_job">True</param>
          <job_metrics />
        </destination>
        <destination id="docker_local" runner="local">
          <param id="docker_enabled">true</param>
        </destination>
        <destination id="drmaa_slurm" runner="drmaa">
            <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
            <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
            <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
        </destination>
        <destination id="direct_slurm" runner="slurm">
            <param id="nativeSpecification">--time=00:01:00</param>
        </destination>
    </destinations>
    <resources default="default">
      <group id="default"></group>
      <group id="memoryonly">memory</group>
      <group id="all">processors,memory,time,project</group>
    </resources>
    <tools>
        <tool id="foo" handler="trackster_handler">
            <param id="source">trackster</param>
        </tool>
        <tool id="bar" destination="dynamic"/>
        <tool id="longbar" destination="dynamic" resources="all" />
        <tool id="baz" handler="special_handlers" destination="bigmem"/>
    </tools>
    <limits>
        <limit type="registered_user_concurrent_jobs">2</limit>
        <limit type="anonymous_user_concurrent_jobs">1</limit>
        <limit type="destination_user_concurrent_jobs" id="local">1</limit>
        <limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit>
        <limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit>
        <limit type="destination_total_concurrent_jobs" id="local">16</limit>
        <limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit>
        <limit type="walltime">24:00:00</limit>
        <limit type="output_size">10GB</limit>
    </limits>
</job_conf>

Can you help me? I am newbie with “Galaxy Project” administration.

THANKS IN ADVANCE!!!!

Alfonso Pardo Diaz
System Administrator / Researcher
c/ Sola nº 1; 10200 Trujillo, ESPAÑA
Tel: +34 927 65 93 17 Fax: +34 927 32 32 37

[CETA-Ciemat logo]<http://www.ceta-ciemat.es/>

----------------------------
Confidencialidad: 
Este mensaje y sus ficheros adjuntos se dirige exclusivamente a su destinatario y puede contener información privilegiada o confidencial. Si no es vd. el destinatario indicado, queda notificado de que la utilización, divulgación y/o copia sin autorización está prohibida en virtud de la legislación vigente. Si ha recibido este mensaje por error, le rogamos que nos lo comunique inmediatamente respondiendo al mensaje y proceda a su destrucción.

Disclaimer: 
This message and its attached files is intended exclusively for its recipients and may contain confidential information. If you received this e-mail in error you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited and may be unlawful. In this case, please notify us by a reply and delete this email and its contents immediately. 
----------------------------

[galaxy-dev] DRMAA Slurm error

Pardo Diaz, Alfonso