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. --nate > > -- > Thanks, > Shantanu. > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
