[GE users] Rmpi under SGE

seandavi seandavi at gmail.com
Thu Dec 23 14:01:27 GMT 2010


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On Wed, Dec 22, 2010 at 2:16 PM, arnuschky <arne.brutschy at ulb.ac.be<mailto:arne.brutschy at ulb.ac.be>> wrote:
Hey,

> >        start_proc_args    /opt/gridengine/mpi/startmpi.sh -catch_rsh $pe_hostfile
> >        stop_proc_args     /opt/gridengine/mpi/stopmpi.sh
>
> Aren't you using Open MPI? Then these two entries can be set to NONE.

Yes, I do. I will change these entries then.

> Open MPI on its own is working fine with more than 20 nodes? How is Open MPI called
> by R - just a plain `mpiexec`, or any special arguments?

Yes, I tested with 50 nodes, worked both with $fill_up and $round_robin.

Regarding the mpiexec: I have honestly no idea. I will try to read the
source code - I am not using R and the Rmpi package myself, I am (only)
the admin of the cluster. Maybe someone on this mailing list can answer
this question?


You can ask questions like that on the R-sig-hpc mailing list.  There are probably more "users" on that list and the author of Rmpi subscribes to that list as well.

Sean

Have some happy holidays, if you have some!
Cheers and Thanks for all the replies,
Arne

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