Re: [R] Snow & rvpm

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Fri 02 Dec 2005 - 06:03:05 EST

In the example at
http://www.stat.uiowa.edu/~luke/R/cluster/cluster.html clusterCall divides the parameter R by the number of nodes -- what you've done is calculate 999 bootstraps on each node, and compared the execution time to 999 bootstraps on one node.

You probably want 'clusterCall' to be smart enough to partition the bootstraps between nodes, and then collate the results. It doesn't do that.

Martin

vittorio <vdemart1@tin.it> writes:

> At office, using the internal LAN at my disposal, I'm having a go at parallel
> computing - to begin with - with pvm, rpvm & snow.
> The two boxes are as follows
>
> Remote machine uffbsd:
> CPU: Intel(R) Pentium(R) 4 CPU 2.00GHz (1994.13-MHz 686-class CPU)
> Origin = "GenuineIntel" Id = 0xf24 Stepping = 4
> real memory = 260046848 (248 MB)
>
> This machine NbBSD:
> CPU: Mobile Intel(R) Pentium(R) 4 - M CPU 2.00GHz (1993.54-MHz 686-class CPU)
> real memory = 536674304 (511 MB)
>
> And starting library snow under R I have the following situation
>
> clusterCall(cl, function() Sys.info()[c("sysname",
> "release","nodename","machine")])
> [[1]]
> sysname release nodename machine
> "FreeBSD" "5.4-RELEASE" "uffbsd.myd" "i386"
>
> [[2]]
> sysname release nodename machine
> "FreeBSD" "6.0-RELEASE" "NbBSD.myd" "i386"
>
> NOW,
> using the example of boot in the end of page
> http://www.stat.uiowa.edu/~luke/R/cluster/cluster.html
>
> I find this amazing result:
>
>> system.time(cl.nuke.boot<-
> clusterCall(cl,boot,nuke.data,nuke.fun,R=999,m=1,fit.pred=new.fit,x.pred=new.data))
> [1] 0.0078125 0.0078125 27.9609375 0.0000000 0.0000000
>> system.time(nuke.boot<-
> boot(nuke.data,nuke.fun,R=999,m=1,fit.pred=new.fit,x.pred=new.data))
> [1] 26.976562 0.109375 28.484375 0.000000 0.000000
>>
> There's not that much gain in time between my cluster and the local
> computation, isn't it.
> Now my question is:
> What could have been gone wrong and what should I verify?
>
> Ciao
> Vittorio
>
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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 Received on Fri Dec 02 06:25:33 2005

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