Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL

Hasitha Muthumala Waidyasooriya; Masanori Hariyama; Kota Kasahara

doi:10.1109/ICIS.2016.7550743

Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara

INF - Computer and Mathematical Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

9 Citations (Scopus)

Abstract

Molecular dynamics (MD) simulations are very important to study physical properties of the atoms and molecules. However, a huge amount of processing time is required to simulate a few nano-seconds of an actual experiment. Although the hardware acceleration using FPGAs provides promising results, huge design time and hardware design skills are required to implement an accelerator successfully. In this paper, we propose an FPGA accelerator designed using C-based OpenCL. We achieved over 4.6 times of speed-up compared to CPU-based processing, by using only 36% of the Stratix V FPGA resources. Maximum of 18.4 times speed-up is possible by using 80% of the FPGA resources.

Original language	English
Title of host publication	2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings
Editors	Kuniaki Uehara, Masahide Nakamura
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9781509008063
DOIs	https://doi.org/10.1109/ICIS.2016.7550743
Publication status	Published - 2016 Aug 23
Event	15th IEEE/ACIS International Conference on Computer and Information Science, ICIS 2016 - Okayama, Japan Duration: 2016 Jun 26 → 2016 Jun 29

Publication series

Name	2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings

Other

Other	15th IEEE/ACIS International Conference on Computer and Information Science, ICIS 2016
Country/Territory	Japan
City	Okayama
Period	16/6/26 → 16/6/29

Keywords

OpenCL for FPGA
hardware acceleration
molecular dynamics simulation
scientific computing

ASJC Scopus subject areas

Computer Science(all)
Energy Engineering and Power Technology
Control and Optimization

Access to Document

10.1109/ICIS.2016.7550743

Cite this

Waidyasooriya, H. M., Hariyama, M., & Kasahara, K. (2016). Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL. In K. Uehara, & M. Nakamura (Eds.), 2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings [7550743] (2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICIS.2016.7550743

Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL. / Waidyasooriya, Hasitha Muthumala ; Hariyama, Masanori; Kasahara, Kota.

2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings. ed. / Kuniaki Uehara; Masahide Nakamura. Institute of Electrical and Electronics Engineers Inc., 2016. 7550743 (2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Waidyasooriya, HM , Hariyama, M & Kasahara, K 2016, Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL. in K Uehara & M Nakamura (eds), 2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings., 7550743, 2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings, Institute of Electrical and Electronics Engineers Inc., 15th IEEE/ACIS International Conference on Computer and Information Science, ICIS 2016, Okayama, Japan, 16/6/26. https://doi.org/10.1109/ICIS.2016.7550743

Waidyasooriya HM , Hariyama M, Kasahara K. Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL. In Uehara K, Nakamura M, editors, 2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings. Institute of Electrical and Electronics Engineers Inc. 2016. 7550743. (2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings). doi: 10.1109/ICIS.2016.7550743

Waidyasooriya, Hasitha Muthumala ; Hariyama, Masanori ; Kasahara, Kota. / Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL. 2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings. editor / Kuniaki Uehara ; Masahide Nakamura. Institute of Electrical and Electronics Engineers Inc., 2016. (2016 IEEE/ACIS 15th International Conference on Computer and Information Science, ICIS 2016 - Proceedings).

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Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL

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