Green Destiny + mpiBLAST = Bioinfomagic

This paper outlines how our highly efficient, power-aware supercomputer called Green Destiny and our open-source parallelization of BLAST called mpiBLAST combine to create a bit of “bioinfomagic.” Green Destiny, featured in The New York Times and winner of a 2003 R&D 100 Award, revolutionized high-performance computing by re-defining performance to focus on issues of efficiency, reliability, and availability. Green Destiny is a 240-processor supercomputer that operates at a peak rate of 240 billion floating-point operations per second (or 240 gigaflops) but fits in six square feet and sips as little as 3.2 kilowatts of power. Consequently, it does not require any special infrastructure to operate, i.e., no cooling, no raised floor, no air filtration, and no humidification control. These attributes resulted in interest from several pharmaceutical and bioinformatics institutions, which likewise did not have special infrastructure to house traditional supercomputing clusters. Subsequent interactions with these pharmaceutical and bioinformatics institutions led to the birth of mpiBLAST, an open-source parallelization of BLAST that achieves super-linear speed-up via a technique called database segmentation. Database segmentation allows each computing node to search a smaller portion of the database (one that fits entirely in memory), thus eliminating disk I/O and vastly improving performance. When used in concert with Green Destiny, we demonstrate that a 300-kB BLAST query that takes nearly one full day to complete on a traditional PC or workstation takes only minutes on Green Destiny.