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

Reuti reuti at staff.uni-marburg.de
Thu Oct 9 15:45:48 BST 2008


Am 09.10.2008 um 16:16 schrieb Sean Davis:

> On Thu, Oct 9, 2008 at 9:55 AM, Ron Chen <ron_chen_123 at yahoo.com>  
> wrote:
>> --- 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?
>>
>
> No.  Under ordinary MPI, there is a function mpi.spawn.Rslaves() that
> will spawn the maximum number of slaves possible given the hostfile.
> Under tight integration, I would expect the behavior to be the same
> with the number of slaves and the machines they are on defaulting to
> the SGE-defined hostfile equivalent.
>
>> 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?
>
> There shouldn't be something special about Rmpi except that only the
> master should be running interactively and the slaves are actually
> started from within that interactive session.  So, the simple question
> is, if I do:
>
> qrsh -pe orte 16

Which version of the Open MPI / SGE are you using? - Reuti

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