Hi,
this is what is working for me, the the "Output not returned from
cluster" error is also disappeared.
default_cluster_job_runner = drmaa://-q galaxy -V/
if this works, then check your other options to test.
With Regards,
----------------
Ambarish Biswas,
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,
Tel: +64(22)0855647
Fax: +64(0)3 479 7866
On Fri, Jul 29, 2011 at 6:32 AM, Ka Ming Nip <km...@bcgsc.ca> wrote:
> Hi Ambarish,
>
> Using what I had in my previous message:
> mytoolname = drmaa://-w n -l mem_free=1G -l mem_token=1G -l h_vmem=1G/
> my jobs do get submitted to the cluster and I see the other options from
> qstat of the jobs
> ie. hard resource_list: mem_free=1G,mem_token=1G,h_vmem=1G
>
> Ka Ming
> ________________________________________
> From: ambarish biswas [ambarishbis...@gmail.com]
> Sent: July 27, 2011 4:18 PM
> To: Ka Ming Nip
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] DRMAA options for SGE
>
> 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<mailto:
> 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<mailto:
> galaxy-dev-boun...@lists.bx.psu.edu> [galaxy-dev-boun...@lists.bx.psu.edu
> <mailto:galaxy-dev-boun...@lists.bx.psu.edu>] On Behalf Of Ka Ming Nip [
> km...@bcgsc.ca<mailto:km...@bcgsc.ca>]
> Sent: July 26, 2011 10:39 AM
> To: galaxy-dev@lists.bx.psu.edu<mailto: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
> ___________________________________________________________
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