Paper Info
Title
Parallel Smith-Waterman Comparison on Multicore and Manycore Computing Platforms with BSP++.
Abstract
Biological Sequence Comparison is an important operation in Bioinformatics that is often used to relate organisms. Smith and Waterman proposed an exact algorithm that compares two sequences in quadratic time and space. Due to high computing power and memory requirements, SW is usually executed on High Performance Computing (HPC) platforms such as multicore clusters and CellBEs. Since HPC architectures exhibit very different hardware characteristics, porting an application to them is an error-prone time-consuming task. BSP++ is an implementation of BSP that aims to facilitate parallel programming, reducing the effort to port code. In this paper, we propose and evaluate a parallel BSP++ strategy to execute SW on multiple multicore and manycore platforms. Given the same base code, we generated MPI, OpenMP, MPI/OpenMP, CellBE and MPI/CellBE versions, which were executed on heterogeneous platforms with up to 6,144 cores. The results obtained with real DNA sequences show that the performance of our versions is comparable to the hand-tuned strategies in the literature, evidencing the appropriateness and flexibility of our approach.
Year
DOI
Venue
2013
10.1007/s10766-012-0209-6
International Journal of Parallel Programming
Keywords
Field
DocType
Bioinformatics, Parallel programming, Parallel hybrid architectures
Supercomputer,Exact algorithm,Computer science,Parallel computing,Smith–Waterman algorithm,Porting,Time complexity,Multi-core processor
Journal
Volume
Issue
ISSN
41
1
1573-7640
Citations 
PageRank 
References 
8
0.60
19
Authors
5
Name
Order
Citations
PageRank
Khaled Hamidouche118019.45
Fernando Machado Mendonca2112.00
Joel Falcou39611.30
Alba Cristina Magalhaes Alves De Melo425333.90
Daniel Etiemble530042.43