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Parallel Computation for Extended Edit Distances Using the Shared Memory on GPU

GPU의 공유메모리를 활용한 확장편집거리 병렬계산

  • 김영호 (인하대학교 컴퓨터정보공학과) ;
  • 나중채 (세종대학교 컴퓨터공학과) ;
  • 심정섭 (인하대학교 컴퓨터정보공학과)
  • Received : 2015.02.16
  • Accepted : 2015.05.07
  • Published : 2015.07.31

Abstract

Given two strings X and Y (|X|=m, |Y|=n) over an alphabet ${\Sigma}$, the extended edit distance between X and Y can be computed using dynamic programming in O(mn) time and space. Recently, a parallel algorithm that takes O(m+n) time and O(mn) space using m threads to compute the extended edit distance between X and Y was presented. In this paper, we present an improved parallel algorithm using the shared memory on GPU. The experimental results show that our parallel algorithm runs about 19~25 times faster than the previous parallel algorithm.

Acknowledgement

Grant : 유전체 분석용 슈퍼컴퓨팅 시스템 개발

Supported by : 정보통신기술진흥센터, 한국연구재단

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