Shantanu Pavgi wrote:
> 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?
I'm not an expert in SGE, so perhaps someone else can verify my
response, but AFAIK there is no way to submit to a remote SGE server via
DRMAA without having a local SGE installation to reference. You *might*
be able to get away with just copying libdrmaa.so into the VM and some
parts of the SGE config which define where the qmaster is, but I don't
know what parts you'd need.
I'd suggest asking in the SGE community if you'd like a definite answer
since it's not a Galaxy-specific issue.
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