Performance Analysis of Hybrid MPI and OpenMP on Smith-Waterman Algorithm

Abstract

In the rapidly advancing field of bioinformatics, sequence alignment is a pivotal task for elucidating genetic statistics and evolutionary relationships. As the volume and complexity of biological data continue to grow, it becomes imperative to employ effective computational techniques to manage this expansion. The Smith-Waterman algorithm is a key tool for sequence alignment; however, its performance can be constrained by the substantial size of contemporary datasets. To overcome this limitation, this paper explores a hybrid parallelization strategy that integrates message passing interface (MPI) with open multi-processing (OpenMP). This approach aims to significantly enhance the algorithm's efficiency by leveraging the strengths of both parallelization models. By optimizing the scalability and execution speed of the Smith-Waterman algorithm on advanced high-performance computing (HPC) systems, the hybrid technique not only improves performance but also enables more rapid and accurate biological data analysis. © 2025 IEEE.