From rossini@u.washington.edu  Mon Aug 19 20:27:26 2002
From: rossini@u.washington.edu (A.J. Rossini)
Date: 19 Aug 2002 12:27:26 -0700
Subject: question about Rpvm, SNOW, etc.
In-Reply-To: <51F9C42DA15CD311BD220008C707D81906FFC5AD@usrymx10.merck.com>
References: <51F9C42DA15CD311BD220008C707D81906FFC5AD@usrymx10.merck.com>
Message-ID: <87bs7y1wf5.fsf@jeeves.blindglobe.net>

>>>>> "andy" == Andy Liaw <Liaw> writes:

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

Which is why we wrote TFM.... :-).  It's the annoying part of
clustering (true for nearly every clustering system currently
available).

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

Create a cluster of more virtual machines.  There isn't necessarily a
1-1 map from virtual machines to real machines (i.e. you can run 3
virtual machines on 1 host, but don't expect ANY gain...).

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

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

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

Monitor the processes with XPVM, as Michael showed.  If you were at
the session, you would've noted Antony's comment on visualization and
how nice it would've been if it was real time -- it was false, xpvm
does real-time monitoring.  

You also might write Michael for the augmentations he's done for
SNOW.  lina@u.washington.edu

best,
-tony

-- 
A.J. Rossini				Rsrch. Asst. Prof. of Biostatistics
U. of Washington Biostatistics		rossini@u.washington.edu	
FHCRC/SCHARP/HIV Vaccine Trials Net	rossini@scharp.org
-------------- http://software.biostat.washington.edu/ ----------------
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question about Rpvm, SNOW, etc.
A.J. Rossini