Parallel Smith-Waterman Comparison on Multicore and Manycore Computing Platforms with BSP

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.