[BioC] Bioc/R on openMosix HPC cluster

Michael Benjamin msb1129 at bellsouth.net
Wed Dec 10 02:20:35 MET 2003

Inspired by Ramon Diaz-Uriarte, I wanted to see how R/Bioconductor works
on a cluster.  After a few false starts, I successfully linked three lab
computers (my laptop, a P-III 750 and a P-4 1.7) using openMosix.  I
found an easy solution in Cluster Knoppix, which magically turns Win-2k
boxes into cluster nodes.  I used an inherited old 10 megabit hub to
make connections.

I found that processes did migrate during operations like reading in an
expression table, but on the whole, things were slower than my Athlon XP
1800 at home.

Does anybody have any experience of running R/Bioconductor on a cluster
using openMosix?

I'll put a nice install document up on my website forum,
www.cancergenome.net, if anybody's interested.

Michael Benjamin, MD
Emory University
Winship Cancer Institute
Atlanta, GA USA

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