High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

Conference paper (2017)

Authors

E.J. Houtgast Bluebee Research & Development Bluebee BV, Computer Engineering - EEMCS
V.M. Sima Bluebee Research & Development Bluebee BV
Z. Al-Ars Computer Engineering - EEMCS
Research Group
Computer Engineering (EEMCS) (TU Delft)
FPGA Smith-Waterman OpenCL Systolic array
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Published Date

2017

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

Department

Quantum & Computer Engineering

Research Group

Computer Engineering

Abstract

The Smith-Waterman algorithm is widely used in bioinformatics and is often used as a benchmark of FPGA performance. Here we present our highly optimized Smith- Waterman implementation on Intel FPGAs using OpenCL.
Our implementation is both faster and more efficient than other current Smith-Waterman implementations, obtaining a theoretical performance of 214 GCUPS. Moreover, due to the streaming, implicit synchronizing nature of our implementation, which streams alignments and places no restrictions on
the number of alignments in flight, it achieves 99.8% of this performance in practice, almost three times as fast as previous implementations. The expressiveness of OpenCL results in a significant reduction in lines of code, and in a significant reduction of development time compared to programming in
regular hardware description languages.