[GE users] [OT] Running R under SGE and OpenMPI

Ron Chen ron_chen_123 at yahoo.com
Thu Oct 9 14:55:50 BST 2008


--- On Thu, 10/9/08, Davide Cittaro wrote:
> I've used Rmpi with SGE and lam tight integration.
> I've had some issues with batch and interactive jobs:
> - batch jobs: I had to specify in the R script how many
> nodes you  
> should spawn with Rmpi... if you submit your job with a
> slot range you  
> have to play in R to understand how many slots you are
> using.  
> Otherwise you may run qsub with a fixed -pe value but you
> may not have available nodes...

Can you pass in the number of slots to R, or R needs to have the number of slots hard coded somewhere before it even starts?

In the job SGE sets the number of slots the current job has, can you just pass that into R? Or are we talking about different things!?


> - interactive jobs: I'm still working on making R aware
> that lam has  
> been launched... :-( probably OpenMPI is a different
> situation...

LAM-MPI is not in active development. But OpenMPI is actively developed, and supports tight integration with SGE. Can't we treat R/Rmpi as yet another OpenMPI application?

Or is there something special in Rmpi?

 -Ron


> 
> d
> 
> 
> 
> /*
> Davide Cittaro
> 
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
> 
> tel.: +39(02)574303007
> e-mail: davide.cittaro at ifom-ieo-campus.it
> */
> 
> 
> 
> 
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