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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 volumeConference contributionScientificpeer-review

Harvard

Houtgast, E, Sima, V & Al-Ars, Z 2017, High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL. in 2017 IEEE 17th International Conference on BioInformatics and BioEngineering (BIBE). IEEE, Piscataway, pp. 492-496, BIBE 2017, Washington DC, United States, 23/10/17. https://doi.org/10.1109/BIBE.2017.000-6

APA

Houtgast, E., Sima, V., & Al-Ars, Z. (2017). High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL. In 2017 IEEE 17th International Conference on BioInformatics and BioEngineering (BIBE) (pp. 492-496). Piscataway: IEEE. https://doi.org/10.1109/BIBE.2017.000-6

Vancouver

Houtgast E, Sima V, Al-Ars Z. High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL. In 2017 IEEE 17th International Conference on BioInformatics and BioEngineering (BIBE). Piscataway: IEEE. 2017. p. 492-496 https://doi.org/10.1109/BIBE.2017.000-6

Author

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

BibTeX

@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",

}

RIS

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

ER -

ID: 30800136