Parallel Biological Sequence Comparison on Heterogeneous High Performance Computing Platforms with BSP++

• Khaled Hamidouche Universite Paris-Sud
• Fernando M. Mendonca UnB
• Joel Falcou Universite Paris-Sud
• Daniel Etiemble Universite Paris-Sud

Abstract

Biological Sequence Comparison is an important operation in Bioinformatics that is often used to relate organisms. Smith and Waterman proposed an exact algorithm (SW) that compares two sequences in quadratic time and space. Due to high computing and memory requirements, SW is usually executed on HPC platforms such as multicore clusters and CellBEs. Since HPC architectures exhibit very different hardware characteristics, porting an application between them is an error-prone time-consuming task. BSP++ is an implementation of BSP that aims to reduce the effort to write parallel code. In this paper, we propose and evaluate a parallel BSP++ strategy to execute SW in multiple platforms like MPI, OpenMP, MPI/OpenMP, CellBE and MPI/CellBE. The results obtained with real DNA sequences show that the performance of our versions is comparable to the ones in the literature, evidencing the appropriateness and flexibility of our approach.

Keywords: Program processors, Object oriented modeling, Vectors, DNA, Biological information theory, Multicore processing