R help - Oct 2008 - Running R under Sun Grid Engine with OpenMPI tight integration

We have spent some time setting up Sun Grid Engine and OpenMPI on a
group of linux boxes.  I have created a parallel environment and
everything seems to be working.  I have Rmpi 0.5.5-5 installed on all
machines.  I would like to start an interactive R session using, say,
8 processors and then start the Rmpi cluster.  I haven't been able to
find what needs to be done in order to accomplish this task.  Is
anyone using R in such an environment that can point me in the right
direction?

Thanks,
Sean

On 9 October 2008 at 09:18, Sean Davis wrote:
| We have spent some time setting up Sun Grid Engine and OpenMPI on a
| group of linux boxes.  I have created a parallel environment and
| everything seems to be working.  I have Rmpi 0.5.5-5 installed on all
| machines.  I would like to start an interactive R session using, say,
| 8 processors and then start the Rmpi cluster.  I haven't been able to
| find what needs to be done in order to accomplish this task.  Is
| anyone using R in such an environment that can point me in the right
| direction?

You could have a look at the slides from my UseR! 2008 tutorial [1] on
'high-performance computing with R' which covered Open MPI / Rmpi and
includes examples. 

It may just be that you are expecting something that cannot be done.  There
is no 'R session on 8 processors'.  R is still single-threaded, and
neither
Open MPI nor the Sun Grid Engine changes that.  But what you can do is to
start R on a node in your cluster and then use Open MPI to distribute load
across the 8 processors.  There are examples in my slides.

Hope this helps, Dirk

[1] http://dirk.eddelbuettel.com/presentations.html

-- 
Three out of two people have difficulties with fractions.

Did you make any progress in using R in the SGE / OpenMPI environment?
I am asking, because I am struggling with the same problem. Using qsub
does not give me an interactive session which I can use (wherefore I
don't see a way of using RMPISNOW and getMPIcluster()) and the
spawning (makeMPIcluster()) when R is running only yields slave
processes on the node on which the master is running.
I have the feeling, that I am missing something really basic - but what is it...

Rainer

On Thu, Oct 9, 2008 at 3:18 PM, Sean Davis <sdavis2 at mail.nih.gov>
wrote:
> We have spent some time setting up Sun Grid Engine and OpenMPI on a
> group of linux boxes.  I have created a parallel environment and
> everything seems to be working.  I have Rmpi 0.5.5-5 installed on all
> machines.  I would like to start an interactive R session using, say,
> 8 processors and then start the Rmpi cluster.  I haven't been able to
> find what needs to be done in order to accomplish this task.  Is
> anyone using R in such an environment that can point me in the right
> direction?
>
> Thanks,
> Sean
>
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

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