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
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