[R] running Rmpi with SGE on a cluster

[Loris Bennett]

David Winsemius <dwinsemius using comcast.net> writes:

>> On Jul 1, 2018, at 6:32 AM, Jeremie Juste <jeremiejuste using gmail.com> wrote:
>> 
>> 
>> Hello,
>> 
>> I would like to know how to use Rmpi on a cluster but usually the
>> workflow of the cluster uses sun grid engine to launch jobs.
>> 
>> I found this reference on the web
>> http://borisv.lk.net/howtos/grid-mpi-r-howto.html.
>> 
>> But I could not even reproduce that example some errors with
>>> n.cores <- mpi.universe.size()
>> 
>
> "Some errors"? I'm not sure how you could be any more vague.
>
>
>> But regardless of this error do you have any resources on running R on a
>> cluster?

In keeping with the vagueness of the posting, I can contribute my
experience that installing Rmpi on a cluster is in general not trivial.
You potentially have to ensure that your are using the correct
combination of compiler and MPI implementation to build the packages and
then ensure that the environment is correspondingly set up for the jobs
you submit to the cluster.

I would maintain that installing Rmpi should normally be done by the
cluster administrator and the he/she should then be able to provide the
users with the information about how to use it.

Cheers,

Loris

-- 
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin         Email loris.bennett using fu-berlin.de