OSWALD: OpenCL Smith–Waterman on Altera's FPGA for Large Protein Databases. (May 2018)

• Record Type: Journal Article
• Authors: Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; De Giusti, Armando E; Naiouf, Marcelo; Prieto-Matias, Manuel
• Other Names: Vega-Rodríguez Miguel A guest-editor.; Rubio-Largo Álvaro guest-editor.
• Is Part Of: International journal of high performance computing applications. Volume 32:Number 3(2018)
• Page Start: 337
• Page End: 350
• Publication Date: 2018-05
• Subjects: Bioinformatics -- Smith–Waterman -- FPGA -- Altera -- OpenCL; High performance computing -- Periodicals; Supercomputers -- Periodicals; 004.1105
• DOI: 10.1177/1094342016654215
• Languages: English
• ISSNs: 1094-3420

Abstract

The well-known Smith–Waterman algorithm is a high-sensitivity method for local sequence alignment. Unfortunately, the Smith–Waterman algorithm has quadratic time complexity, which makes it computationally demanding for large protein databases. In this paper, we present OSWALD, a portable, fully functional and general implementation to accelerate Smith–Waterman database searches in heterogeneous platforms based on Altera's FPGA. OSWALD exploits OpenMP multithreading and SIMD computing through SSE and AVX2 extensions on the host while taking advantage of pipeline and vectorial parallelism by way of OpenCL on the FPGAs. Performance evaluations on two different heterogeneous architectures with real amino acid datasets show that OSWALD is competitive in comparison with other top-performing Smith–Waterman implementations, attaining up to 442 GCUPS peak with the best GCUPS/watts ratio.