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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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.comwrote:

...

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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---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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Thankyou Nate for your prompt and detailed support. Unfortunately I am on a different time zone and I do not have access now to the system. Thankyou for the suggestion you provided me to do the debugging. I will carry that out in about 12 hours from now and let you know. Thankyou again Luca p.s. although I do agree that the problems I am facing are not as "challenging" as the other aspects of galaxy, I am convinced that a detailed explanation on the methodology to use for debugging this kind of low level aspects will be extremely appreciated by many :-)

2014-04-02 21:05 GMT+02:00 Nate Coraor nate@bx.psu.edu:

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

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/