[BioC] High-performance Bioconductor experiments

Michael Benjamin msb1129 at bellsouth.net
Thu Dec 11 04:15:42 MET 2003

Progress update (summarized from my forum for such matters at

Briefly, I created a four-node cluster out of Pentium-III boxes and
Debian Linux/openMosix.  I saw no significant performance boost of
ReadAffy or expresso using the set of 165 .CEL files from Harvard.  None
of the processes migrated, as they say in the world of high-performance
computing.  R.bin runs in one process, and everything it does seems to
stay in that process.  No real opportunity for parallelization here, at
least not on openMosix.

I'd like to analyze these chips in a reasonable amount of time, without
paying Dell $45,000 for 4-Xeon SMP server.

I worry what we'll do with 1,000 .CEL files.  The analytical techniques
work well, but pretty slow even if your amp "goes to 11."

Any thoughts?

Michael Benjamin, MD
Emory University

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