Exploring the viability of the Cell Broadband Engine for bioinformatics applications

Authors:
Vipin Sachdeva;Michael Kistler;Evan Speight;Tzy-Hwa Kathy Tzeng
Affiliations:
IBM Future Technology Solution Design Center, IBM Systems and Technology Group, Indianapolis, IN, Austin, TX Poughkeepsie, NY, United States;IBM Future Technology Solution Design Center, IBM Systems and Technology Group, Indianapolis, IN, Austin, TX Poughkeepsie, NY, United States;IBM Future Technology Solution Design Center, IBM Systems and Technology Group, Indianapolis, IN, Austin, TX Poughkeepsie, NY, United States;IBM Future Technology Solution Design Center, IBM Systems and Technology Group, Indianapolis, IN, Austin, TX Poughkeepsie, NY, United States
Venue:
Parallel Computing
Year:
2008

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Abstract

This paper evaluates the performance of bioinformatics applications on the Cell Broadband Engine (Cell/B.E.) recently developed at IBM. In particular we focus on three highly popular bioinformatics applications - FASTA, ClustalW, and HMMER. The characteristics of these bioinformatics applications, such as small critical time-consuming code size, regular memory accesses, existing vectorized code and embarrassingly parallel computation, make them uniquely suitable for the Cell/B.E. processing platform. The price and power advantages afforded by the Cell/B.E. processor also make it an attractive alternative to general purpose processors. We report preliminary performance results for these applications, and contrast these results with the state-of-the-art hardware.