Hi
default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/
works for me on LSF, so your syntax seems to be correct.

Assuming that -l mem=4gb:nodes=1:ppn=6 works teh way you expect when you start the jobs on your cluster from the shell, read on...

Bearing in mind the the value of the option contains ':' , I'd check that it is read correctly by the parser that parses universe_wsgi.ini and it is passed correctly to drmaa. If it's passed to drmaa correctly, but does not produced desired effect, I'd look closely at the drmaa library. This might be a bug. It's possible to use the drmaa library from a C script - this way you can test if drmaa works the way you want. Also, It was rather straightforward to generate a perl swig wrapper for drmaa and write perl test scripts. Swig wrappers can be generated for any scripting language and also java.

Marina

On 20/06/2011 10:53, Geert Vandeweyer wrote:
Hi,

I'm working on an local installation of galaxy using torque with drmaa (the pbs-torque scramble failed). The torque-drmaa works fine so far, except for one issue.

I'd like to specify some tool-dependent requirements from the tool_runners section in universe.wsgi.ini. For now I've been testing it with the setting below to have global native arguments :

default_cluster_job_runner =  drmaa://-l mem=4gb:nodes=1:ppn=6/

This should request 4gb of memory on a single node with 6 threads, but these requests are ignored. They are not listed on 'qstat -R' and more simultaneous jobs than possible are started if the requirements were taken into account. What am I missing here?

Best regards,

Geert Vandeweyer

___________________________________________________________
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/


--
The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ___________________________________________________________
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