Viability Study of SYCL as a Unified Programming Model for Heterogeneous Systems Based on GPUs in Bioinformatics

Abstract

Bioinformatics and Computational Biology are disciplines that have used GPUs for over two decades to accelerate data processing in computational applications, where CUDA has been the most utilized programming language. However, the exclusive use of CUDA presents a portability issue, as it is only compatible with NVIDIA GPUs and not with other heterogeneous architectures, such as AMD or Intel GPUs, or any other type of accelerator. To address this portability challenge, the Khronos Group recently introduced the SYCL standard, a multi-platform programming model that offers a high-level programming interface. This standard facilitates the development of portable applications that can efficiently leverage the capabilities of different hardware devices, such as NVIDIA, Intel, and AMD GPUs, without needing significant modifications to the source code. Therefore, this thesis set out as its general objective to evaluate the feasibility of SYCL as a unified, portable, and efficient heterogeneous programming model for the design and development of computationally demanding applications on heterogeneous GPU-based systems, specifically in the field of bioinformatics.

Initially, a detailed investigation was conducted about heterogeneous programming models, performance metrics, and bioinformatics concepts, in order to establish the theoretical foundations of this thesis. Then, the SW# suite was chosen as the case study, as it represents a clear example of a CUDA-based bioinformatics application for biological sequence alignment. Using the SYCLomatic tool, a complete migration of the CUDA code to SYCL was carried out, which involved modifying the generated code and solving runtime errors. Additionally, the functionality was verified, optimizations were applied, and the resulting SYCL code was standardized to be compatible with other SYCL implementations.

Subsequently, multiple experiments were conducted to evaluate the functionality and performance portability of the software migrated to SYCL. These experiments involved running the application on a wide variety of HPC platforms, including different CPUs and GPUs from various manufacturers. The results obtained demonstrated performance comparable to CUDA in most configurations, confirming the effectiveness of SYCL. Moreover, good performance portability across platforms was observed due to SYCL's ability to run on various hardware combinations. Furthermore, performance remained consistent when switching SYCL implementations. In conclusion, this study demonstrates that SYCL is a viable alternative as a unified, portable, and efficient programming model in the context of heterogeneous computing with GPUs for bioinformatics applications. The findings of this study lay the groundwork for the transition of legacy applications and the development of new solutions leveraging the capabilities of SYCL.