[BioBrew Users] 'R Project' using parallelism

[John-Paul Robinson]

We've had success with the stock R rpms in centos and snow using the
LAM/MPI envirionment.  We use the "loose" lam integration for SGE 
described here:

  http://gridengine.sunsource.net/howto/lam-integration/lam-integration.html

which takes care of starting and stopping the lam daemons on each node 
assigned by SGE.  I assume a similar solution should be possible with PVM.

The one issue we had problems with was staring R when using snow, 
particularly when using packages which invoke snow internally.  Snow takes 
care of start the mpi parallelism for you so you shouldn't invode R via 
mpirun in the SGE job script.  Simply using the lam_loose_rsh environment 
and putting the command "R CMD BATCH script.that.uses.snow" in the job 
file is sufficient.

~jpr

On Thu, 27 Jul 2006, adolfo rafael martinez wrote:

> Now, I just need to automate the startup of the PVM daemons on each
> node, and make certain jobs can use the SGE qsub mechanism.
> 
> If anyone has any tips, they would certainly be appreciated.