Assessing Opportunities of SYCL for Biological Sequence Alignment on GPU-based Systems

TL;DR

This paper demonstrates that migrating a CUDA-based biological sequence alignment tool to SYCL using Intel's oneAPI is feasible with minimal effort, enabling cross-platform GPU and CPU deployment without performance loss.

Contribution

It presents the migration process of a CUDA tool to SYCL, showing minimal programmer intervention and consistent performance across multiple hardware architectures.

Findings

Complete migration with minimal hand-coding

No performance degradation across NVIDIA GPUs

Stable performance across different SYCL implementations

Abstract

Bioinformatics and Computational Biology are two fields that have been exploiting GPUs for more than two decades, being CUDA the most used programming language for them. However, as CUDA is an NVIDIA proprietary language, it implies a strong portability restriction to a wide range of heterogeneous architectures, like AMD or Intel GPUs. To face this issue, the Khronos Group has recently proposed the SYCL standard, which is an open, royalty-free, cross-platform abstraction layer, that enables the programming of a heterogeneous system to be written using standard, single-source C++ code. Over the past few years, several implementations of this SYCL standard have emerged, being oneAPI the one from Intel. This paper presents the migration process of the SW\# suite, a biological sequence alignment tool developed in CUDA, to SYCL using Intel's oneAPI ecosystem. The experimental results show that SW\# was completely migrated with a small programmer intervention in terms of hand-coding. In addition, it was possible to port the migrated code between different architectures (considering multiple vendor GPUs and also CPUs), with no noticeable performance degradation on 5 different NVIDIA GPUs. Moreover, performance remained stable when switching to another SYCL implementation. As a consequence, SYCL and its implementations can offer attractive opportunities for the Bioinformatics community, especially considering the vast existence of CUDA-based legacy codes.