[StarCluster] Starcluster SGE usage

[Blanchette, Marco]

Of course, should have thought about it... Was looking for a more complicated solution.

Thanks Adam
--  Marco Blanchette, Ph.D.
Stowers Institute for Medical Research
1000 East 50th Street
Kansas City MO 64110
www.stowers.org

Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018

From: Adam Kraut <kraut at bioteam.net<mailto:kraut at bioteam.net>>
Date: Wednesday, May 29, 2013 9:33 AM
To: Marco Blanchette <mab at stowers.org<mailto:mab at stowers.org>>
Cc: "starcluster at mit.edu<mailto:starcluster at mit.edu>" <starcluster at mit.edu<mailto:starcluster at mit.edu>>
Subject: Re: [StarCluster] Starcluster SGE usage

Hi Marco,

This is a good case for a simple starcluster plugin. You can execute the custom qconf commands you need to create the parallel environment and add it to the default queue. Use the SGE plugin as a reference.

Hope this helps,
Adam

On Tuesday, May 28, 2013 at 8:12 PM, Blanchette, Marco wrote:

I would like to revive this thread as I am in a similar situation as the
original author, I would like to run jobs in a parallel environment where
the slot allocation would not extend beyond a given node.

Here is what John last wrote following a long exchange:

On 10/18/2012 01:55 PM, John St. John wrote:
Ok just submitted a pull request. I modified the sge template
"sge_pe_template" so that you can modify the allocation type in a
new parallel environment. I modified the SGE plugin so that it
makes by_node as well as ORTE, and by_node uses the $pe_slots
allocation type. I have tested this out with creating a cluster
(haven't tried adding/deleting nodes) and it seems to work. The
changes are pretty minimal to get here so I feel pretty confident
that I didn't add any new bugs.

Best, John

However, I don't see any trace of these modifications in the repos? Was
this abandoned?

Could you suggest a strategy to enable the by_node parallel environment
and have it added to the all.q queue at init time? (I see that I can
initialize it with qconf ­ap by_node then add it manually with qconf -mq
all.q)

Thanks


-- Marco Blanchette, Ph.D.
Stowers Institute for Medical Research
1000 East 50th Street
Kansas City MO 64110
www.stowers.org<http://www.stowers.org>


Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018


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