Problems submitting using PBS Pro 12.1

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Problems submitting using PBS Pro 12.1

Luca Toldo
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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Re: Problems submitting using PBS Pro 12.1

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Problems submitting using PBS Pro 12.1

Björn Grüning-3
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 <[hidden email]> 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/
>
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in your mail client.  To manage your subscriptions to this
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Re: Problems submitting using PBS Pro 12.1

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 <[hidden email]> 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 <[hidden email]> 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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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/




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in your mail client.  To manage your subscriptions to this
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Re: Problems submitting using PBS Pro 12.1

Luca Toldo
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 <[hidden email]>:
Thanks Björn. Luca, what version of pbs-drmaa are you using now?


On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning <[hidden email]> 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 <a href="tel:02.04.2014%2020" value="+49204201420" target="_blank">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 <[hidden email]> 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/




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in your mail client.  To manage your subscriptions to this
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To search Galaxy mailing lists use the unified search at:
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Re: Problems submitting using PBS Pro 12.1

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 <[hidden email]> 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 <[hidden email]>:

Thanks Björn. Luca, what version of pbs-drmaa are you using now?


On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning <[hidden email]> 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 <a href="tel:02.04.2014%2020" value="+49204201420" target="_blank">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 <[hidden email]> 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/




___________________________________________________________
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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/





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Re: Problems submitting using PBS Pro 12.1

Luca Toldo
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 <[hidden email]>:
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 <[hidden email]> 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 <[hidden email]>:

Thanks Björn. Luca, what version of pbs-drmaa are you using now?


On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning <[hidden email]> 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 <a href="tel:02.04.2014%2020" value="+49204201420" target="_blank">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 <[hidden email]> 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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Re: Problems submitting using PBS Pro 12.1

Nate Coraor (nate@bx.psu.edu)
In reply to this post by Nate Coraor (nate@bx.psu.edu)
Hi Luca,

Could you send your job_conf.xml please? Also, is there any chance that you modified run.sh to set DRMAA_LIBRARY_PATH there (which would override what you set on the command line)?

--nate


On Thu, Apr 3, 2014 at 9:17 AM, Luca Toldo <[hidden email]> wrote:
Dear All,
after having discovered the mess in which I was, and the incomplete PBS client installation, I've done the following:

1) PBS Pro
a) removed the incomplete pbs installation that I had
b) downloaded the latest version from vendor
c) installed  it in //usr/pbs
d) configured
e) tested it --> worked well

2) drma-pbs
a) downloaded version 1.0.17
b) compiled it (./configure --with-pbs=/usr/pbs ) without any problem
c) installed it in /usr/local/lib

3) modified DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
4) sh run.sh --stop
5) sh run.sh --daemon

Unfortunately, however when I launch a new job I always get the error message

galaxy.jobs DEBUG 2014-04-03 15:13:44,306 (261) Working directory for job is: /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261
galaxy.jobs.handler DEBUG 2014-04-03 15:13:44,321 (261) Dispatching to drmaa runner
galaxy.jobs DEBUG 2014-04-03 15:13:44,434 (261) Persisting job destination (destination id: pbs_default)
galaxy.jobs.handler INFO 2014-04-03 15:13:44,474 (261) Job dispatched
galaxy.tools.deps DEBUG 2014-04-03 15:13:44,659 Building dependency shell command for dependency 'clustalw2'
galaxy.tools.deps WARNING 2014-04-03 15:13:44,660 Failed to resolve dependency on 'clustalw2', ignoring
galaxy.jobs.runners.drmaa DEBUG 2014-04-03 15:13:45,050 (261) submitting file /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy_261.sh
galaxy.jobs.runners.drmaa DEBUG 2014-04-03 15:13:45,050 (261) command is: python /opt/ngs/bin/galaxy-dist/tools/rgenetics/rgClustalw.py -i "/data/imgt.fasta" -o "/opt/ngs/bin/galaxy-dist/database/files/000/dataset_340.dat" -s "ALIGNED" -l "/opt/ngs/bin/galaxy-dist/database/files/000/dataset_341.dat" -t "Clustal_run" -d "DNA" -f "CLUSTAL"; return_code=$?; cd /opt/ngs/bin/galaxy-dist; /opt/ngs/bin/galaxy-dist/set_metadata.sh ./database/files /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261 . /opt/ngs/bin/galaxy-dist/universe_wsgi.ini /opt/ngs/bin/galaxy-dist/database/tmp/tmpq4Rmdl /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy.json /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_in_HistoryDatasetAssociation_347_GsBRYB,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_kwds_HistoryDatasetAssociation_347_dFD5t0,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_out_HistoryDatasetAssociation_347_k0zCP6,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_results_HistoryDatasetAssociation_347_4LVIFs,,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_override_HistoryDatasetAssociation_347_jKfp0r /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_in_HistoryDatasetAssociation_348_Fyy0tJ,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_kwds_HistoryDatasetAssociation_348_9vWiO3,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_out_HistoryDatasetAssociation_348_HL3EIj,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_results_HistoryDatasetAssociation_348_s1gqxk,,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_override_HistoryDatasetAssociation_348_hyQkDF; sh -c "exit $return_code"

galaxy.jobs.runners ERROR 2014-04-03 15:13:45,051 (261) 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 150, 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 from the commandline I do 

qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy_261.sh

then 

I get 1695145.servername

... 

What can I do now ?



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