[R] Running R under Sun Grid Engine with OpenMPI tight integration

Dirk Eddelbuettel edd at debian.org
Thu Oct 9 16:02:56 CEST 2008

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.

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