Re: sge submit host question

Justin Riley

February 24, 2012 4:47 PM

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Hi Chris,

By default all of the nodes in the cluster *should* be admin, submit,
and exec hosts.

With that said I'd love for folks to start customizing the new SGE
plugin on git (will be released with 0.93.2 as well). You can find the
new plugin in "plugins/sge.py".

Each SGE customization should be implemented as an optional keyword
argument to the plugin's __init__ method - other plugin methods should
then read these parameters and perform the customizations in run(),
on_add_node(), etc. I'm happy to help folks get started if interested.

~Justin

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Chris Dagdigian

February 24, 2012 3:58 PM

It is *extremely* common for all SGE nodes in a cluster to be both admin and submit hosts.

The reason for making every node a submit host is that there are cluster workflows that often include jobs running on a node that either do new job submissions directly or else alter things like hold_jid or the parameters of a job array.

For small clusters that are persistant, the CLI command is "qconf -as <hostname>" to add a submit host.

Starcluster uses an SGE autoinstallation template file (I think ...) to automate the process of cluster building. Within this template file there is a parameter where you can list out your Admin and Submit hosts.

I imagine it would be pretty simple to customize or override the default StarCluster autoinstallation file so that all your nodes become submit host.

And if that is too complicated it's pretty trivial to iterate over the hostnames and run the "qconf -as" command ...

My $.02 of course!

-Chris

Chris Dagdigian Principal Consultant, BioTeam Inc.
http://bioteam.net  

My latest BioTeam Blog Post: Metrum moves to the cloud

David Erickson

February 24, 2012 3:38 PM

I ran into this too and found out I had to source
/etc/profile.d/sge.sh. I also am curious if there is a better solution,
presumably this is an interactive vs noninteractive shell issue.

-D
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Robert Yu

February 24, 2012 3:07 PM

Hi,

This is more of a best-practice question.

Let's say I am on machine A. From it, I create a cluster. I can then
ssh into the "master" and launch jobs. Can this also be done from
machine A directly? I know one can do "starcluster sshmaster -u
sgeadmin <clustername> 'some command'" but then I typically run into
environment issues. Is there (simple) a way to make machine A an sge
submit host?