Accelerating Molecular Dynamics with the Lennard-Jones potential for FPGAs

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Standard

Accelerating Molecular Dynamics with the Lennard-Jones potential for FPGAs. / Thegler, Alberte; Johnsen, Carl Johannes; Skovhede, Kenneth; Vinter, Brian.

Proceedings - 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021. IEEE, 2021.

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Harvard

Thegler, A, Johnsen, CJ, Skovhede, K & Vinter, B 2021, Accelerating Molecular Dynamics with the Lennard-Jones potential for FPGAs. in Proceedings - 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021. IEEE, 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021, Virtual, San Diego, United States, 25/04/2021. https://doi.org/10.1109/COPA51043.2021.9541435

APA

Thegler, A., Johnsen, C. J., Skovhede, K., & Vinter, B. (2021). Accelerating Molecular Dynamics with the Lennard-Jones potential for FPGAs. In Proceedings - 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021 IEEE. https://doi.org/10.1109/COPA51043.2021.9541435

Vancouver

Thegler A, Johnsen CJ, Skovhede K, Vinter B. Accelerating Molecular Dynamics with the Lennard-Jones potential for FPGAs. In Proceedings - 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021. IEEE. 2021 https://doi.org/10.1109/COPA51043.2021.9541435

Author

Thegler, Alberte ; Johnsen, Carl Johannes ; Skovhede, Kenneth ; Vinter, Brian. / Accelerating Molecular Dynamics with the Lennard-Jones potential for FPGAs. Proceedings - 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021. IEEE, 2021.

Bibtex

@inproceedings{f8dabe34b2d94b358020dcd28cfc03b2,

title = "Accelerating Molecular Dynamics with the Lennard-Jones potential for FPGAs",

abstract = "The requirements for more advanced, longer, and more precise molecular dynamics simulations are greater than ever. Even though we are better at optimizing and have more computational power than previously, there is also a continuing need to make simulations even faster, more reliable, and cheaper to run. In this paper, we are presenting a method for running a molecular dynamics simulation on an FPGA device by using Synchronous Message Exchange. The molecular dynamics simulation presented in this paper is a basic simulation using the Lennard-Jones potential. It is a work in progress, but the results are promising compared to a Python implementation using matrix calculations. We present a proof of concept of an initial solution and its performance provides results that make us believe that a full molecular dynamics implementation would be feasible and competitive.",

keywords = "FPGA, Lennard-Jones, Molecular Dynamics Simulation, Synchronous Message Exchange",

author = "Alberte Thegler and Johnsen, {Carl Johannes} and Kenneth Skovhede and Brian Vinter",

note = "Publisher Copyright: {\textcopyright} 2021 IEEE.; 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021 ; Conference date: 25-04-2021 Through 28-04-2021",

year = "2021",

doi = "10.1109/COPA51043.2021.9541435",

language = "English",

booktitle = "Proceedings - 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021",

publisher = "IEEE",

}

RIS

TY - GEN

T1 - Accelerating Molecular Dynamics with the Lennard-Jones potential for FPGAs

AU - Thegler, Alberte

AU - Johnsen, Carl Johannes

AU - Skovhede, Kenneth

AU - Vinter, Brian

PY - 2021

Y1 - 2021

N2 - The requirements for more advanced, longer, and more precise molecular dynamics simulations are greater than ever. Even though we are better at optimizing and have more computational power than previously, there is also a continuing need to make simulations even faster, more reliable, and cheaper to run. In this paper, we are presenting a method for running a molecular dynamics simulation on an FPGA device by using Synchronous Message Exchange. The molecular dynamics simulation presented in this paper is a basic simulation using the Lennard-Jones potential. It is a work in progress, but the results are promising compared to a Python implementation using matrix calculations. We present a proof of concept of an initial solution and its performance provides results that make us believe that a full molecular dynamics implementation would be feasible and competitive.

AB - The requirements for more advanced, longer, and more precise molecular dynamics simulations are greater than ever. Even though we are better at optimizing and have more computational power than previously, there is also a continuing need to make simulations even faster, more reliable, and cheaper to run. In this paper, we are presenting a method for running a molecular dynamics simulation on an FPGA device by using Synchronous Message Exchange. The molecular dynamics simulation presented in this paper is a basic simulation using the Lennard-Jones potential. It is a work in progress, but the results are promising compared to a Python implementation using matrix calculations. We present a proof of concept of an initial solution and its performance provides results that make us believe that a full molecular dynamics implementation would be feasible and competitive.

KW - FPGA

KW - Lennard-Jones

KW - Molecular Dynamics Simulation

KW - Synchronous Message Exchange

UR - http://www.scopus.com/inward/record.url?scp=85116552649&partnerID=8YFLogxK

U2 - 10.1109/COPA51043.2021.9541435

DO - 10.1109/COPA51043.2021.9541435

M3 - Article in proceedings

AN - SCOPUS:85116552649

BT - Proceedings - 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021

PB - IEEE

T2 - 2021 Concurrent Processes Architectures and Embedded Systems Conference, COPA 2021

Y2 - 25 April 2021 through 28 April 2021

ER -

ID: 282095449

Department of Computer Science