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 <kmnip@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 [ambarishbiswas@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 <kmnip@bcgsc.ca<mailto:kmnip@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-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu>] On Behalf Of Ka Ming Nip [kmnip@bcgsc.ca<mailto:kmnip@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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