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 <nate@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.gruening@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 <lucatoldo@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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