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.

• Type: Conference
• Year: 2001
• Where: PSB
• Authors: W. S. Martins, Juan del Cuvillo, F. J. Useche, Kevin B. Theobald, Guang R. Gao
• Keywords: Dynamic Programming Algorithm, Event-driven Multithreaded Execution, Event-driven Multithreaded Program, PSB 2001, PSB 2007