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:
/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
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?
-- Shantanu.