Accelerating Smith-Waterman Algorithm for Biological Database Search on CUDA-Compatible GPUs

Yuma MUNEKAWA  Fumihiko INO  Kenichi HAGIHARA  

IEICE TRANSACTIONS on Information and Systems   Vol.E93-D   No.6   pp.1479-1488
Publication Date: 2010/06/01
Online ISSN: 1745-1361
DOI: 10.1587/transinf.E93.D.1479
Print ISSN: 0916-8532
Type of Manuscript: Special Section PAPER (Special Section on Info-Plosion)
Category: Parallel and Distributed Architecture
Smith-Waterman algorithm,  sequence alignment,  acceleration,  GPU,  CUDA,  

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This paper presents a fast method capable of accelerating the Smith-Waterman algorithm for biological database search on a cluster of graphics processing units (GPUs). Our method is implemented using compute unified device architecture (CUDA), which is available on the nVIDIA GPU. As compared with previous methods, our method has four major contributions. (1) The method efficiently uses on-chip shared memory to reduce the data amount being transferred between off-chip video memory and processing elements in the GPU. (2) It also reduces the number of data fetches by applying a data reuse technique to query and database sequences. (3) A pipelined method is also implemented to overlap GPU execution with database access. (4) Finally, a master/worker paradigm is employed to accelerate hundreds of database searches on a cluster system. In experiments, the peak performance on a GeForce GTX 280 card reaches 8.32 giga cell updates per second (GCUPS). We also find that our method reduces the amount of data fetches to 1/140, achieving approximately three times higher performance than a previous CUDA-based method. Our 32-node cluster version is approximately 28 times faster than a single GPU version. Furthermore, the effective performance reaches 75.6 giga instructions per second (GIPS) using 32 GeForce 8800 GTX cards.