[R] Problem installing Rmpi with lam on SGI SLES9

[Hendrik Fuß]

On 25/04/07, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> "Hendrik Fuß" <fuss-h at ulster.ac.uk> writes:
> > I'm trying to use the papply package. However, when I do:
> >
> >> library(papply)
> >> papply(list(1:10, 1:15, 1:20), sum)
> >         1 slaves are spawned successfully. 0 failed.
> > master (rank 0, comm 1) of size 2 is running on: behemoth
> > slave1 (rank 1, comm 1) of size 2 is running on: behemoth
> > [1] "Running serial version of papply\n"
> >
> > Papply only spawns one slave and then decides to run the serial
> > version instead. I'm not sure how to tell it to use all the 64
> > processors available.
>
> Hendrik,
>
> Are you starting the lam daemons before starting R?
>
> % lamboot
>
> You might need to specify a 'hosts' argument to lamboot. The default
> way Rmpi calls lamboot is with no arguments, and this might simply
> create a single lam daemon.

Thanks, that was a pointer in the right direction.

The solution is to edit the file /etc/lam/lam-bhost.def and specify
the number of cpus (see man bhost)

cheers
Hendrik

-- 
Hendrik Fuß
PhD student
Systems Biology Research Group

University of Ulster, School of Biomedical Sciences
Cromore Road, Coleraine, BT52 1SA, Northern Ireland