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

Davide Cittaro davide.cittaro at ifom-ieo-campus.it
Thu Oct 9 14:29:50 BST 2008

Hi Sean,

> I would like to run R in this system and use the Rmpi library.  Has
> anyone successfully done so?  If so, what is the incantation to get an
> interactive R session, start up Rmpi, and then launch slaves?

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


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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