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	SCHEDULE: NOV 11-17, 2006 Pairwise Alignments on the Cell Processor Session: Poster Reception Event Type: Poster Time: 5:15pm - 7:15pm Author(s): Vipin Sachdeva, Mike Kistler, Evan Speight Location: Ballroom Corridor Abstract: We are evaluating the performance of bioinformatics applications on the CBE recently developed at IBM. The characteristics of pairwise alignment, critical to bioinformatics applications, makes it uniquely suitable for the Cell processor. We have implemented two different strategies for pairwise alignment on Cell. We analyze the bottlenecks for each strategy, a diagonal approach which uses the vector processing capabilities of the SPE and a row wise approach in which cells are dependant and has expensive branches. Despite the presence of branches, the row-wise approach outperforms a 2.4 Ghz Opteron by almost 5X, the diagonal approach spending a majority of time looking up the alignment matrix. Also, due to the commonality of all-to-all pairwise comparisons in bioinformatics codes, we have implemented a framework for these computations on the Cell with minimum load imbalance and minimal PPU intervention. We evaluate the performance of popular bioinformatics codes Clustalw and HMMER using such a framework, in which the workload is shared among the PPU and the SPUs. Chair/Author Details: Vipin Sachdeva IBM Research Mike Kistler IBM Research Evan Speight IBM Research
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