DNA sequence alignment: An assignment for OpenMP, MPI, and CUDA/OpenCL

TL;DR

This paper presents a comprehensive parallel computing assignment for DNA sequence alignment, illustrating various parallel programming models like OpenMP, MPI, and CUDA/OpenCL, to enhance student understanding of complex concepts.

Contribution

It introduces a multi-model parallel assignment for DNA alignment that addresses key parallel computing concepts and is suitable for educational purposes.

Findings

Implemented as a practical course assignment since 2017/2018.

Addresses key parallel programming challenges like race conditions and reductions.

Supports student learning in advanced parallel computing topics.

Abstract

We present an assignment for a full Parallel Computing course. Since 2017/2018, we have proposed a different problem each academic year to illustrate various methodologies for approaching the same computational problem using different parallel programming models. They are designed to be parallelized using shared-memory programming with OpenMP, distributed-memory programming with MPI, and GPU programming with CUDA or OpenCL. The problem chosen for this year implements a brute-force solution for exact DNA sequence alignment of multiple patterns. The program searches for exact coincidences of multiple nucleotide strings in a long DNA sequence. The sequential implementation is designed to be clear and understandable to students while offering many opportunities for parallelization and optimization. This assignment addresses key concepts many students find difficult to apply in practical scenarios: race conditions, reductions, collective operations, and point-to-point communications. It also covers the problem of parallel generation of pseudo-random sequences and strategies to notify and stop speculative computations when matches are found. This assignment serves as an exercise that reinforces basic knowledge and prepares students for more complex parallel computing concepts and structures. It has been successfully implemented as a practical assignment in a Parallel Computing course in the third year of a Computer Engineering degree program. Supporting materials for this and previous assignments in this series are publicly available.