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

Davide Cittaro davide.cittaro at ifom-ieo-campus.it
Thu Oct 9 15:01:59 BST 2008

On Oct 9, 2008, at 3:55 PM, Ron Chen wrote:
> 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!?

One hack could be playing with R/system communication to get the  
number of slots used by calling qstat or reading SGE variables...
> 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?

I would like to move to OpenMPI but I'm planning to substitute the  
entire little cluster so I won't spend much more time on MPI  
implementation :-)

> Or is there something special in Rmpi?

Mmm, I think it's only  a matter of Rmpi reading the number of  
available slots (he needs it to explicitly invoke a cluster facility)


Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano

tel.: +39(02)574303007
e-mail: davide.cittaro at ifom-ieo-campus.it

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