27559

Assessing Opportunities of SYCL and Intel oneAPI for Biological Sequence Alignment

Manuel Costanzo, Enzo Rucci, Carlos García Sánchez, Marcelo Naiouf, Manuel Prieto-Matías
III-LIDI, Facultad de Informatica, UNLP – CIC. La Plata (1900), Bs As, Argentina
arXiv:2211.10769 [cs.PL], (19 Nov 2022)

@misc{https://doi.org/10.48550/arxiv.2211.10769,

   doi={10.48550/ARXIV.2211.10769},

   url={https://arxiv.org/abs/2211.10769},

   author={Costanzo, Manuel and Rucci, Enzo and Sánchez, Carlos García and Naiouf, Marcelo and Prieto-Matías, Manuel},

   keywords={Programming Languages (cs.PL), Distributed, Parallel, and Cluster Computing (cs.DC), FOS: Computer and information sciences, FOS: Computer and information sciences},

   title={Assessing Opportunities of SYCL and Intel oneAPI for Biological Sequence Alignment},

   publisher={arXiv},

   year={2022},

   copyright={Creative Commons Attribution Non Commercial Share Alike 4.0 International}

}

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Background and objectives. The computational biology area is growing up over the years. The interest in researching and developing computational tools for the acquisition, storage, organization, analysis, and visualization of biological data generates the need to create new hardware architectures and new software tools that allow processing big data in acceptable times. In this sense, heterogeneous computing takes an important role in providing solutions but at the same time generates new challenges for developers in relation to the impossibility of porting source code between different architectures. Methods. Intel has recently introduced oneAPI, a new unified programming environment that allows code developed in the SYCL-based Data Parallel C++ (DPC++) language to be run on different devices such as CPUs, GPUs, and FPGAs, among others. Due to the large amount of CUDA software in the field of bioinformatics, this paper presents the migration process of the SW# suite, a biological sequence alignment tool developed in CUDA, to DPC++ through the oneAPI compatibility tool dpc (recently renowned as SYCLomatic). Results. SW# has been completely migrated with a small programmer intervention in terms of hand-coding. Moreover, it has been possible to port the migrated code between different architectures (considering different target platforms and vendors), with no noticeable performance degradation. Conclusions. The SYCLomatic tool presented a great performance-portability rate. SYCL and Intel oneAPI can offer attractive opportunities for the Bioinformatics community, especially considering the vast existence of CUDA-based legacy codes.
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