Accelerating tandem MS protein database searches using OpenCL

Authors:
Rick Weber;David D. Jenkins;Nicholas Lineback;Gregory D. Peterson
Affiliations:
University of Tennessee, Knoxville, TN, USA;University of Tennessee, Knoxville, TN, USA;University of Tennessee, Knoxville, TN, USA;University of Tennessee, Knoxville, TN, USA
Venue:
Proceedings of the 3rd international workshop on Emerging computational methods for the life sciences
Year:
2012

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Abstract

GPUs and multicore processors are now pervasive in com- putational sciences and high-performance computing. Their high arithmetic throughput and memory bandwidth com- bined with their ever increasing programmability make them suitable for a widening variety of applications. We give a high level overview of Specmaster, a peptide search al- gorithm running on multi-core processors and GPUs via OpenCL. We give details and benchmarks highlighting per- formance tradeoffs on three devices: Intel's Sandy Bridge, Nvidia's GTX 480, and AMD's Radeon 7970. We demon- strate a single codebase running on all three architectures and give a description on how to improve performance for specific architectures while still maintaining one code base in future work.