Re: [R] rpvm/snow packages on a cluster with dual-processor machi nes

From: Ramon Diaz-Uriarte <rdiaz_at_cnio.es>
Date: Thu 17 Aug 2006 - 18:56:05 EST

Dear Paul,

(I forgot to answer over the weekend). With mpi it is essentially the same. When using makeCluster, specify the number of slaves. If you have three machines, and you want each to run two slave processes, just use a 6.

Before that, though, you should tell LAM/MPI how to set up the "lam universe". The simplest way is to specify that in a configuration file for LAM. Put something like this (using appropriate IPs or host names; cpu=xx indicates that you want each physical node to run those many xx slaves; it might, or might not, be related to the actual number of CPUs) in a file called, say, lamb-conf1.def

192.168.2.2 cpu=2
192.168.2.3 cpu=2
192.168.2.4 cpu=2



Now do (as user, NOT root)

lamboot -v lamb-conf1.def

If that works, then start R, and use snow.

A very good explanation on how to use mpi with R appeared in R news a while ago by the author of Rmpi.

HTH, R.

On Monday 14 August 2006 16:17, Liaw, Andy wrote:
> That's what I've tried before, on three dual-Xeon boxes, so I know it
> worked (as documented a that time).
>
> Andy
>
> From: Paul Y. Peng
>
> > Luke Tierney just reminded me that makeCluster() can take a
> > number greater than the number of machines in a cluster. It
> > seems to be a solution to this problem. But I haven't tested it yet.
> >
> > Paul.
> >
> > Ryan Austin wrote:
> > > Hi,
> > >
> > > Adding a node twice gives a duplicate node error.
> > > However, adding the parameter sp=2000 to your pvm hostfile should
> > > enable dual processors.
> > >
> > > Ryan
> > >
> > > Liaw, Andy wrote:
> > >> Caveat: I've only played with this a couple of years ago...
> > >>
> > >> I believe you can just add each host _twice_ (or as many
> >
> > times as the
> >
> > >> number of CPUs at that host) to get both CPUs to work.
> > >>
> > >> Andy
> > >>
> > >> From: Paul Y. Peng
> > >>
> > >>> Hi,
> > >>>
> > >>> does anybody know how to use the dual processors in the
> >
> > machines of
> >
> > >>> a cluster? I am using R with rpvm and snow packages. I
> >
> > usually start
> >
> > >>> pvm daemon and add host machines first, and then run R to
> >
> > start my
> >
> > >>> computing work. But I find that only one processor in
> >
> > each machine
> >
> > >>> is used in this way and the other one always stays idle. Is there
> > >>> any simple way to tell pvm to use the two processors at the same
> > >>> time? In other words, I would like to see two copies of R
> >
> > running on
> >
> > >>> each machine's two processors when using pvm. Any hints/help are
> > >>> greatly appreciated.
> > >>>
> > >>> Paul.
> > >>>
> > >>> ______________________________________________
> > >>> R-help@stat.math.ethz.ch mailing list
> > >>> https://stat.ethz.ch/mailman/listinfo/r-help
> > >>> PLEASE do read the posting guide
> > >>> http://www.R-project.org/posting-guide.html
> > >>> and provide commented, minimal, self-contained, reproducible code.
> > >>
> > >> ______________________________________________
> > >> R-help@stat.math.ethz.ch mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-help
> > >> PLEASE do read the posting guide
> > >> http://www.R-project.org/posting-guide.html
> > >> and provide commented, minimal, self-contained, reproducible code.
> > >
> > > ______________________________________________
> > > R-help@stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> > ______________________________________________
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented, minimal,
> self-contained, reproducible code.

-- 
Ramón Díaz-Uriarte
Bioinformatics 
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)



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Received on Thu Aug 17 19:04:46 2006

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