Derrick,

Take a look at the section entitled "Job runner URL" on http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster. But as I understand it, you don't need to do anything since the drmaa library is part of your SGE installation. Just make the node Galaxy runs on an exec host.

Ryan

On Mon, Jan 9, 2012 at 8:45 PM, Derrick LIN klin938@gmail.com wrote:

Hi guys,

I am trying to configure our test galaxy to run on our SGE cluster http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster.

This is my first time to come across to drmaa, so a bit confused.

I installed teh galaxy on a NFS location where can be accessed clsuter-wide. I have configured in universe_wsgi.ini:

start_job_runners = drmaa default_cluster_job_runner = drmaa:///

and export the libdrmaa path: export DRMAA_LIBRARY_PATH=/opt/sge/lib/lx-amd64/libdrmaa.so.1.0

Sound like that's all. But I am not sure how galaxy can actually bind to my cluster? Anywhere I need to specify the qmaster URL etc?

Or simply configure galaxy host to be a submission host of the cluster, the galaxy will fetch all information by itself?

Kind regards, Derrick

---

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Whoops. That's what I mean...a submission host, not an exec host.

On Mon, Jan 9, 2012 at 11:13 PM, Derrick LIN klin938@gmail.com wrote:

Thanks Ryan,

I have been following that guide. I can configure the galaxy host to be an exec host, although it makes more sense to be a submission host.

I hope this can be clarified in the future revise of the documentation.

Cheers, Derrick

On Tue, Jan 10, 2012 at 12:57 PM, Ryan Golhar <ngsbioinformatics@gmail.com

...

wrote:

...

Derrick,

Take a look at the section entitled "Job runner URL" on http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster. But as I understand it, you don't need to do anything since the drmaa library is part of your SGE installation. Just make the node Galaxy runs on an exec host.

Ryan

On Mon, Jan 9, 2012 at 8:45 PM, Derrick LIN klin938@gmail.com wrote:

...

Hi guys,

I am trying to configure our test galaxy to run on our SGE cluster http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster.

This is my first time to come across to drmaa, so a bit confused.

I installed teh galaxy on a NFS location where can be accessed clsuter-wide. I have configured in universe_wsgi.ini:

start_job_runners = drmaa default_cluster_job_runner = drmaa:///

and export the libdrmaa path: export DRMAA_LIBRARY_PATH=/opt/sge/lib/lx-amd64/libdrmaa.so.1.0

Sound like that's all. But I am not sure how galaxy can actually bind to my cluster? Anywhere I need to specify the qmaster URL etc?

Or simply configure galaxy host to be a submission host of the cluster, the galaxy will fetch all information by itself?

Kind regards, Derrick

---

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/