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.
Just want to confirm SGE configuration again. As mentioned earlier we started with a separate galaxy VM without any SGE installation. The SGE master node is installed on a separate system altogether. As I understand from your reply, we will need to install SGE on the galaxy VM first and configure it as a submit host with the main SGE master node. Is that correct? Are their any alternative approaches? -- Thanks, Shantanu.