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Assessing opportunities of SYCL for biological sequence alignment on GPU-based systems

Manuel Costanzo, Enzo Rucci, Carlos García-Sanchez, Marcelo Naiouf, Manuel Prieto-Matías
Facultad de Informática, III-LIDI, UNLP – CIC, 1900 La Plata, Buenos Aires, Argentina
The Journal of Supercomputing, 2024

@article{costanzo2024assessing,

   title={Assessing opportunities of SYCL for biological sequence alignment on GPU-based systems},

   author={Costanzo, Manuel and Rucci, Enzo and Garc{‘i}a-Sanchez, Carlos and Naiouf, Marcelo and Prieto-Mat{‘i}as, Manuel},

   journal={The Journal of Supercomputing},

   pages={1–24},

   year={2024},

   publisher={Springer}

}

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Bioinformatics and computational biology are two fields that have been exploiting GPUs for more than two decades, with 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 five 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.
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