Computing Maximum Subsequence in Parallel

The maximum subsequence problem finds the contiguous subsequence of n real numbers with the highest sum. This is an important problem that arises in several contexts in Computational Biology in the analysis of DNA or protein sequences. The maximum subsequence problem of n given scores can be solved sequentially in O(n) time. In this paper we present an efficient BSP/CGM parallel algorithm that requires a constant number of communication rounds. In the proposed algorithm, the input is partitioned equally among the processors and the sequence stored on each processor is reduced to only five numbers. This reduction is crucial as it allows all the resulting values to be concentrated on a single processor which runs an adaptation of the sequential algorithm to obtain the result. The amount of data transmitted is 5p where p is the number of processors, thus independent of the input size n. The good performance of the parallel algorithm is confirmed by experimental results run on a 64-node...

• Type: Conference
• Year: 2003
• Where: WOB
• Authors: Carlos E. R. Alves, Edson Cáceres, Siang W. Song
• Keywords: BSP/CGM Parallel Algorithm, Maximum Subsequence Problem, Parallel Algorithm, WOB 2003, WOB 2008