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 [galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Ka Ming Nip [kmnip@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: