Hi Ming,
   just an idea, "-w n" might be hiding the error reporting. Is your jobs
getting submitted and executed correctly?

For the queuing , you can add "galaxy" at the end, makes it

drmaa://-w n -l mem_free=1G -l mem_token=1G -l h_vmem=1G/galaxy

here galaxy is queue name.



With Regards,
----------------
Ambarish Biswas,
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,
Tel: +64(22)0855647
Fax: +64(0)3 479 7866




On Thu, Jul 28, 2011 at 6:21 AM, Ka Ming Nip <km...@bcgsc.ca> wrote:

> Answering myself here...
>
> I don't see the error anymore after adding "-w n":
>
> [galaxy:tool_runners]
> ...
> mytoolname = drmaa://-w n -l mem_free=1G -l mem_token=1G -l h_vmem=1G/
> ...
>
> Is this what other Galaxy admins do when using drmaa native options for
> their SGE?
>
> Ka Ming
> ________________________________________
> From: galaxy-dev-boun...@lists.bx.psu.edu [
> galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ka Ming Nip [
> km...@bcgsc.ca]
> Sent: July 26, 2011 10:39 AM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] DRMAA options for SGE
>
> Hi,
>
> I am trying to configure the proper memory resource requests for my Galaxy
> tool.
> This is what I have under the tool_runners section of universe_wsgi.ini
>
> [galaxy:tool_runners]
> ...
> mytoolname = drmaa://-l mem_free=1G -l mem_token=1G -l h_vmem=1G/
> ...
>
> When I execute my tool on Galaxy, I get the error below in the shell that I
> ran "sh run.sh":
>
> galaxy.jobs.runners.drmaa ERROR 2011-07-26 09:54:01,930 Uncaught exception
> queueing job
> Traceback (most recent call last):
>  File "/home/kmnip/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py",
> line 112, in run_next
>    self.queue_job( obj )
>  File "/home/kmnip/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py",
> line 177, in queue_job
>    job_id = self.ds.runJob(jt)
>  File
> "/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/__init__.py",
> line 331, in runJob
>  File
> "/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/helpers.py",
> line 213, in c
>  File
> "/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/errors.py",
> line 90, in error_check
> DeniedByDrmException: code 17: error: no suitable queues
>
> All the flags I used work with qsub commands on the SGE cluster I use. The
> tool runs
> when I comment out the line in universe_wsgi.ini.
>
> Thanks,
> Ka Ming
> ___________________________________________________________
> 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/
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/

Reply via email to