question about Rpvm, SNOW, etc.

[Liaw, Andy]

Dear R-devel,

Inspired by Michael Li's talk at JSM, I decided to try rpvm and snow on our
two linux boxes.  It only took me a couple of hours of screwing around to
get it working (sooner if I had RTFM).  

Our setup is: 2 dual PIII-866 Xeons, one with 2GB RDRAM, the other with
1.28GB RDRAM.  The first machine is acting as the NIS/NFS server.  both /usr
and /home are exported to the second machine, so both are seeing the same
copy of R.

I managed to get the following, using the same example that Prof. Tierney
used:

> system.time(nuke.boot <-
+             boot(nuke.data, nuke.fun, R=999, m=1,
+                  fit.pred=new.fit, x.pred=new.data))
[1] 29.38  0.52 30.68  0.00  0.00
> system.time(cl.nuke.boot <-
+             clusterCall(cl,boot,nuke.data, nuke.fun, R=500, m=1,
+                         fit.pred=new.fit, x.pred=new.data))
[1]  0.03  0.00 15.44  0.00  0.00

So I'm getting almost twice the performance, which is great.

Now the questions:

1.  Since each of these boxes has two CPUs, how do I spawn more than one
slave process on them?

2.  I was hoping I can see similar gain with randomForest, but that doesn't
seem to be the case:

> system.time(iris.rf <- randomForest(iris[,1:4], iris[,5], ntree=10000))
[1] 8.52 1.00 9.61 0.00 0.00
> system.time(cl.iris.rf <- clusterCall(cl, randomForest, iris[,1:4],
+                                       iris[,5], ntree=5000))
[1]  1.38  0.14 15.50  0.00  0.00

What am I missing here?  Is there anything I can do to see similar gain as
the boot() example?

Thanks very much in advance for any pointers, and big thanks to the
developers of these great stuff!!

Regards,
Andy
Andy I. Liaw, PhD
Biometrics Research          Phone: (732) 594-0820
Merck & Co., Inc.              Fax: (732) 594-1565
P.O. Box 2000, RY84-16            Rahway, NJ 07065
mailto:andy_liaw@merck.com



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