[GE users] Using gridengine to administer the cluster

Michael James Michael.James at csiro.au
Wed Aug 30 01:16:58 BST 2006

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On Tue, 29 Aug 2006 11:50 pm, Daniel Templeton wrote:
> An easier way to submit once to each host would be
> to set up a consumable with a value of 1 for each host. 
> All you'd have to do then is submit n jobs,
> each requesting the consumable, where "n" is the number of hosts.

On Tue, 29 Aug 2006 11:28 pm, Chris Dagdigian wrote:
> I second Joe's recommendation regarding pdsh.
> There are several tools designed to automate
> the execution of commands across clusters   
> (including groups and subgroups of nodes)
> and they all work very well for admin centric tasks.
> Grid Engine may not be the best tool for this particular job.

Thanks to everybody for the excellent responses,
 I must look into  pdsh and pdcp.

But if I start using external commands,
how do I schedule them into gridengine?

ie: On a fairly full local data partition I want to run this:
biofile>  rsync -a --delete /nfs/master/data/ /data/
"biofile"  is the owner of the biological databases.

At present I have to wait for a quiet moment,
 (or make one) and then run the job.
Otherwise I risk SGE sending a blast on nr while it's being updated.

The attraction of setting a consumable and slots
 is that I can schedule the update and it waits
 until it can monopolise each node and do its job undisturbed.
Clever scheduling would even mean I could set a limit
 that only a third of my cluster are allowed
 to take themselves offline for maintenance at any one time.


Michael James                         michael.james at csiro.au
System Administrator                    voice:  02 6246 5040
CSIRO Bioinformatics Facility             fax:  02 6246 5166

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