Dear Nate, and Björn
thankyou for your help. As Björn said, indeed i get always the same error
message regardless if I use the id=nativeSpecification or not.  How can one
figure out the version of pbs-drmaa that the system is using ? It would be
really useful to have a step-by-step tutorial on how to configure this part
of the system. I've spent already several days trying to get it working and
it constantly fails.

Unfortunately I also got serious problem trying to compile the
pbs-drmaa-1.0.17 as mentioned in my posting.

What can I try next ? I was thinking to modify /jobs/runners/drmaa.py
adding more logging ...

Thankyou for your advice !



2014-04-02 20:43 GMT+02:00 Nate Coraor <n...@bx.psu.edu>:

> 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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