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

Ernst Houtgast; Vlad Sima; Zaid Al-Ars

doi:10.1109/BIBE.2017.000-6

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

Ernst Houtgast, Vlad Sima, Zaid Al-Ars

Computer Engineering

Research output: Chapter in Book/Conference proceedings/Edited volume › Conference contribution › Scientific › peer-review

13 Citations (Scopus)

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.

Original language	English
Title of host publication	2017 IEEE 17th International Conference on BioInformatics and BioEngineering (BIBE)
Place of Publication	Piscataway
Publisher	IEEE
Pages	492-496
Number of pages	5
ISBN (Electronic)	978-1-5386-1324-5
ISBN (Print)	978-1-5386-1325-2
DOIs	https://doi.org/10.1109/BIBE.2017.000-6
Publication status	Published - 2017
Event	BIBE 2017: 17th IEEE International Conference on BioInformatics and BioEngineering - Washington DC, United States Duration: 23 Oct 2017 → 25 Oct 2017 http://bibe2017.com/index.html

Conference

Conference	BIBE 2017
Abbreviated title	BIBE 2017
Country/Territory	United States
City	Washington DC
Period	23/10/17 → 25/10/17
Internet address	http://bibe2017.com/index.html

Keywords

FPGA
OpenCL
Smith-Waterman
systolic array

Access to Document

10.1109/BIBE.2017.000-6

Cite this

@inproceedings{e21d377d0fd54e7fa080cb8d9c0acdf6,

title = "High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL",

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 onthe 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 inregular hardware description languages.",

keywords = "FPGA, OpenCL, Smith-Waterman, systolic array",

author = "Ernst Houtgast and Vlad Sima and Zaid Al-Ars",

year = "2017",

doi = "10.1109/BIBE.2017.000-6",

language = "English",

isbn = "978-1-5386-1325-2",

pages = "492--496",

booktitle = "2017 IEEE 17th International Conference on BioInformatics and BioEngineering (BIBE)",

publisher = "IEEE",

address = "United States",

note = "BIBE 2017 : 17th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2017 ; Conference date: 23-10-2017 Through 25-10-2017",

url = "http://bibe2017.com/index.html",

}

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL. / Houtgast, Ernst; Sima, Vlad; Al-Ars, Zaid.
2017 IEEE 17th International Conference on BioInformatics and BioEngineering (BIBE). Piscataway: IEEE, 2017. p. 492-496.

Research output: Chapter in Book/Conference proceedings/Edited volume › Conference contribution › Scientific › peer-review

TY - GEN

T1 - High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

AU - Houtgast, Ernst

AU - Sima, Vlad

AU - Al-Ars, Zaid

PY - 2017

Y1 - 2017

N2 - 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 onthe 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 inregular hardware description languages.

AB - 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 onthe 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 inregular hardware description languages.

KW - FPGA

KW - OpenCL

KW - Smith-Waterman

KW - systolic array

U2 - 10.1109/BIBE.2017.000-6

DO - 10.1109/BIBE.2017.000-6

M3 - Conference contribution

SN - 978-1-5386-1325-2

SP - 492

EP - 496

BT - 2017 IEEE 17th International Conference on BioInformatics and BioEngineering (BIBE)

PB - IEEE

CY - Piscataway

T2 - BIBE 2017

Y2 - 23 October 2017 through 25 October 2017

ER -

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

Abstract

Conference

Keywords

Access to Document

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Cite this