On May 12, 2011, at 3:43 PM, Nate Coraor wrote:
> Shantanu Pavgi wrote:
>> I need some help in configuring galaxy with SGE scheduler using unified
>> method. The galaxy is running on a system distinct from SGE scheduler
>> install. The cluster nodes can access galaxy install, galaxy-tools and
>> dataset files using NFS. I am not sure how drmaa works and how galaxy
>> submits jobs to the cluster/scheduler. Do we need specify some type of
>> connection string or ssh-config to connect with the cluster/scheduler? Does
>> it need any configuration changes on the SGE scheduler side? Any explanation
>> regarding this will be really helpful.
> Hi Shantanu,
> You'll need to locate your drmaa library, it can be found wherever SGE
> is installed. For example, if SGE is installed for 64-bit Linux in
> /galaxy/sge, then the drmaa library should be located at:
> Once you have the path, do the following (adjusting the value for the
> path to libdrmaa.so.1.0 at your site):
> export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
> Then in universe_wsgi.ini, set:
> start_job_runners = drmaa
> default_cluster_job_runner = drmaa:///
> This should be all you need.
Thanks for the explanation Nate. I will try it out.
Also, after integrating with the cluster is there any pre-processing or
post-processing done on the galaxy system locally? I would like to get some
sense on how much RAM and other system resources will be required for the
galaxy system itself. I am assuming it can be fairly thin system for running
web server, database and job submission processes. Is it a correct assumption
or am I missing something here?
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