Evaluating Performance and Portability of a core bioinformatics kernel on multiple vendor GPUs

Abstract

Traditional scientific simulations have for quite some time, dominated the workloads of high-performance computing infrastructures across the world. With recent advancement in data generation capabilities of systems biology equipment, a rise in bioinformatics workloads has been observed. Bioinformatics applications deploy algorithmic motifs that use unique memory access patterns and rely heavily on integer-only computations. These applications place unique requirements on modern programming environments as well as GPU accelerators which are becoming an integral part of next generation of supercomputers. In this paper, we evaluate the performance and code portability of a core bioinformatics kernel that uses dynamic programming method for performing DNA and protein sequence alignments in several bioinformatics software pipelines. Our study evaluates the performance of a GPU accelerated sequence alignment algorithm across multiple vendor GPUs and programming models. We use a highly optimized adaptation of sequence alignment kernel and find the most productive way of porting it across multiple vendor GPUs and then assess its performance portability using Pennycook's method. Methods used in this paper and the insights drawn from those can be extended to a large number of integer-heavy scientific kernels and may aid in future accelerator design and design of programming model requirements.