It has been a while, but checking in again for any possible solution or
advice where to look here?


On Tue, Feb 26, 2013 at 10:06 AM, Joshua Orvis <jor...@gmail.com> wrote:

> Thanks for your response.  That seemed to work, to a point.  I redid the
> same FASTQ->FASTA conversion test and could see using command-line
> utilities that the job started on the grid (SGE is behind it.)
>
> About 10 minutes have gone by though since the job stopped running on the
> grid and the interface is still spinning as if it's running.  I checked the
> Galaxy log for that job ID and I see these entries:
>
> galaxy.jobs.runners.drmaa INFO 2013-02-26 10:51:15,670 (103) queued as
> 5224332
> galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:51:16,390 (103/5224332)
> state change: job is queued and active
> galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:51:30,422 (103/5224332)
> state change: job is running
> galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:52:32,623 (103/5224332) is
> still in running state, adding to the DRM queue
> galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:54:31,961 (103/5224332) job
> left DRM queue with following message: code 18: The job specified by the
> 'jobid' does not exist.
>
> The SGE qacct utility for that job shows me that it took 3.5 minutes to
> run and that the return status was 0, so it executed successfully.
>
> It seems that Galaxy is missing the completion event for the job?
>
> Joshua
>
>
>
>
> On Tue, Feb 26, 2013 at 12:17 AM, Ross <ross.laza...@gmail.com> wrote:
>
>> See if adding the default queue name to the job runner path - eg:
>> default_cluster_job_runner = drmaa:///default
>> works any better?
>> Galaxy will default to the local runner if it can't find the nominated
>> drmaa path AFAIK and I don't think 'default' is the default
>> :)
>>
>>
>>
>> On Tue, Feb 26, 2013 at 4:51 PM, Joshua Orvis <jor...@gmail.com> wrote:
>>
>>> I have a working local Galaxy instance and wanted to enable DRMAA
>>> support to utilize our SGE (or LSF) grid.  Following the guide 
>>> here<http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster> I
>>> set what I appeared to need to make this work.  From the DRMAA_LIBRARY_PATH
>>> env variable to all the configuration settings in universe_wsgi.ini,
>>> reconfiguring the server hosting Galaxy as a submit host, etc.  Some
>>> specific config file changes made:
>>>
>>>     new_file_path =
>>> /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/tmp
>>>     start_job_runners = drmaa
>>>     default_cluster_job_runner = drmaa:///
>>>     set_metadata_externally = True
>>>     outputs_to_working_directory = True
>>>
>>> I then killed and restarted the Galaxy instance and tried a simple FASTQ
>>> -> FASTA test execution, but it ran locally.  I couldn't find any sort of
>>> errors or messages related to DRMAA in the server log, and the job ran to
>>> completion.  I commented out the local tool runner overrides.  What can I
>>> do to test my DRMAA configuration and where should I look for errors?
>>>
>>> Thanks -
>>>
>>> Joshua
>>>
>>> ___________________________________________________________
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>>
>>
>>
>
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