Hi Luca,

We generally have not provided detailed documentation on this portion since it's not really within the scope of Galaxy itself, and documentation would be likely to become out of date as these external libraries (like pbs-drmaa) are updated, and cluster configurations are very site-specific. We are happy to help, though.

It might be useful to add some debugging about the generated jobTemplate in drmaa.py to see what params are being set.

The value you've set as the path to the drmaa library ($DRMAA_LIBRARY_PATH) might provide some insight on the version, or the output of:

    strings $DRMAA_LIBRARY_PATH | grep 1\.0

What are the problems you're experiencing compiling pbs-drmaa 1.0.17?

--nate

On Wed, Apr 2, 2014 at 2:52 PM, Luca Toldo <lucatoldo@gmail.com> wrote:

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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