On Apr 8, 2013, at 9:24 PM, Jingzhi Zhu wrote:

> Hi Nate,
> 
> That's it! After I made that change, I was able to see jobs are successfully 
> submitted to the SGE queue and then run. So this is great!
> 
> I now run into another issue. 
> 
> galaxy.jobs.runners.drmaa DEBUG 2013-04-08 21:16:56,386 (15/530948) state 
> change: job finished, but failed
> galaxy.jobs.runners ERROR 2013-04-08 21:16:56,526 (15/530948) Job output not 
> returned from cluster: [Errno 2] No such file or directory: 
> '/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.o'
> galaxy.jobs DEBUG 2013-04-08 21:16:56,559 Tool did not define exit code or 
> stdio handling; checking stderr for success
> galaxy.jobs DEBUG 2013-04-08 21:16:56,603 setting dataset state to ERROR
> galaxy.jobs DEBUG 2013-04-08 21:16:56,796 job 15 ended
> 
> Google search shows a lot of similar errors, but it is never clear how to 
> resolve it. When this job is run, qstat -j shows the following
> 
> stderr_path_list:           
> NONE:KI-GALAXY:/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.e
> 
> stdout_path_list:           
> NONE:KI-GALAXY:/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.o
> 
> script_file:                
> /net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.sh
>  
> I can see the galaxy_15.sh exists in the above directory, but the galaxy_15.o 
> and galaxy_15.e do not exist during the job run. Where are those files saved? 
> Do you have any idea how to fix it? Thank you so much!

Hi Jingzhi,

Please use "reply all" to keep replies on the list.

Does that directory exist on the cluster?  A shared filesystem mounted at the 
same path is (currently) required between Galaxy and the cluster.

--nate


> 
> Jingzhi 
> 
> On Apr 8, 2013, at 4:46 PM, Nate Coraor wrote:
> 
>> Hi Jingzhi,
>> 
>> Unfortunately, there's a mistake in the sample config for that runner 
>> plugin, the line to load the plugin should be:
>> 
>>    <plugin id="drmaa" type="runner" 
>> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
>> 
>> The sample config was fixed in a later commit to the stable branch, and 
>> seeing as there was a security release today I would suggest just updating 
>> your Galaxy installation to the latest stable commit anyway:
>> 
>> % hg pull
>> % hg update stable
>> 
>> --nate
>> 
>> On Apr 8, 2013, at 4:14 PM, Jingzhi Zhu wrote:
>> 
>>> I have downloaded the 04_01 release and tried to configure the Sun Grid 
>>> Engine so that the job can run on our cluster. 
>>> 
>>> I have export the DRMAA_LIBRARY_PATH environment variable (export 
>>> DRMAA_LIBRARY_PATH=/home/love-galaxy/bin/libdrmaa.so.1.0). Then copy 
>>> job_conf.xml.sample_advanced to job_conf.xml. I have deleted some lines on 
>>> the plugins section so it looks like this in job_conf.xml
>>> 
>>>    <plugins workers="4">
>>>        <!-- "workers" is the number of threads for the runner's work queue.
>>>             The default from <plugins> is used if not defined for a 
>>> <plugin>.
>>>          -->
>>>        <plugin id="local" type="runner" 
>>> load="galaxy.jobs.runners.local:LocalJobRunner"/>
>>>        <plugin id="drmaa" type="runner" 
>>> load="galaxy.jobs.runners.drmaa:DRMAARunner"/>
>>>     </plugins>
>>> 
>>> The run.sh returns the following error
>>> 
>>> galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,465 Loaded history export 
>>> tool: __EXPORT_HISTORY__
>>> galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,466 Loaded history import 
>>> tool: __IMPORT_HISTORY__
>>> galaxy.tools.genome_index DEBUG 2013-04-08 15:57:12,472 Loaded genome index 
>>> tool: __GENOME_INDEX__
>>> galaxy.jobs.manager DEBUG 2013-04-08 15:57:12,474 Starting job handler
>>> galaxy.jobs.runners DEBUG 2013-04-08 15:57:12,475 Starting 4 LocalRunner 
>>> workers
>>> galaxy.jobs DEBUG 2013-04-08 15:57:12,477 Loaded job runner 
>>> 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
>>> Traceback (most recent call last):
>>>  File 
>>> "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
>>>  line 37, in app_factory
>>>    app = UniverseApplication( global_conf = global_conf, **kwargs )
>>>  File 
>>> "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/app.py", line 
>>> 159, in __init__
>>>    self.job_manager = manager.JobManager( self )
>>>  File 
>>> "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/manager.py",
>>>  line 31, in __init__
>>>    self.job_handler = handler.JobHandler( app )
>>>  File 
>>> "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py",
>>>  line 29, in __init__
>>>    self.dispatcher = DefaultJobDispatcher( app )
>>>  File 
>>> "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py",
>>>  line 543, in __init__
>>>    self.job_runners = self.app.job_config.get_job_runner_plugins()
>>>  File 
>>> "/net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
>>>  line 476, in get_job_runner_plugins
>>>    runner_class = getattr( module, class_name )
>>> AttributeError: 'module' object has no attribute 'DRMAARunner'
>>> 
>>> Can someone point to me what is going on here? If you have configured the 
>>> SGE successfully with the latest 4.1 release, can you show me what the file 
>>> job_conf.xml should look like? There are a lot of tags in this new XML file 
>>> and I found it is hard to  do it right.
>>> 
>>> Thanks!
>>> 
>>> Jingzhi 
>>> 
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>> 
> 


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