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2001

A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm for Sequence Comparison

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A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm for Sequence Comparison
This paper discusses the issues involved in implementing a dynamic programming algorithm for biological sequence comparison on a generalpurpose parallel computing platform based on a ne-grain event-driven multithreaded program execution model. Fine-grain multithreading permits e cient parallelism exploitation in this application both by taking advantage of asynchronous point-to-point synchronizations and communication with low overheads and by e ectively tolerating latency through the overlapping of computation and communication. We have implemented our scheme on EARTH, a ne-grain event-driven multithreaded execution and architecture model which has been ported to a number of parallel machines with o -the-shelf processors. Our experimental results show that the dynamic programming algorithm can be e ciently implemented on EARTH systems with high performance e.g., speedup of 90 on 120 nodes, good programmability and reasonable cost.
W. S. Martins, Juan del Cuvillo, F. J. Useche, Kev
Added 31 Oct 2010
Updated 31 Oct 2010
Type Conference
Year 2001
Where PSB
Authors W. S. Martins, Juan del Cuvillo, F. J. Useche, Kevin B. Theobald, Guang R. Gao
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