Thanks Björn. Luca, what version of pbs-drmaa are you using now?
On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning <bjoern.gruen...@gmail.com>wrote:
> Hi Nate,
>
> I tried to help Luca today, but I failed totally ...
> He is not using <param id="nativeSpecification"> at all. Or put it that
> way if he isn't using it, he gets the same error.
>
> Cheers,
> Bjoern
>
> Am 02.04.2014 20:34, schrieb Nate Coraor:
>
> Hi Luca,
>>
>> Are you passing any params to the runner for inclusion as PBS submit
>> parameters (<param id="nativeSpecification"> in job_conf.xml)?
>>
>> --nate
>>
>>
>> On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo <lucato...@gmail.com> wrote:
>>
>> Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers
>>>
>>> galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
>>> exception calling queue_job
>>> Traceback (most recent call last):
>>> File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>>> line 62, in run_next
>>> method(arg)
>>> File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
>>> line
>>> 151, in queue_job
>>> external_job_id = self.ds.runJob(jt)
>>> File
>>> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py",
>>> line 331, in runJob
>>> _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
>>> File
>>> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py",
>>> line
>>> 213, in c
>>> return f(*(args + (error_buffer, sizeof(error_buffer))))
>>> File
>>> "/opt/ngs/bin/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))
>>> InvalidAttributeValueException: code 14: Illegal attribute or resource
>>> value: Illegal attribute or resource value
>>>
>>>
>>> If I do
>>> qsub -q NGSq
>>> /opt/ngs/bin/galaxy-dist/database/job_working_
>>> directory/000/249/galaxy_249.sh
>>>
>>> however the qsub returns
>>>
>>> 12345.myserver
>>>
>>>
>>> and the corresponding
>>>
>>> qstat | grep -i galaxy
>>> 12345.myserver galaxy_249.sh galaxy 00:00:00 E NGSq
>>>
>>> Is the above error message perhaps related with
>>> a) PBS 12.1
>>> b) drmaa-0.7-py2.6.egg
>>>
>>> I am trying to compile pbs-drmaa-1.0.17 but there are problems ...
>>>
>>> any advice ?
>>>
>>> any alternative ?
>>>
>>> Thanks
>>> luca
>>>
>>>
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>>
>>
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