skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

Abstract

We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.

Authors:
 [1];  [2];  [3]
  1. Department of Elec. and Comp. Eng., Purdue University, West Lafayette, IN 47907 (United States)
  2. Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, MS 50F-1650, Berkeley, CA 94720 (United States)
  3. Department of Computer Science, Purdue University, West Lafayette, IN 47907 (United States)
Publication Date:
OSTI Identifier:
22314897
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Computational Physics; Journal Volume: 272; Other Information: Copyright (c) 2014 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ACCURACY; COMPARATIVE EVALUATIONS; COMPUTERIZED SIMULATION; IMPLEMENTATION; MOLECULAR DYNAMICS METHOD; OPTIMIZATION; P CODES; PERFORMANCE; SILICA; WATER

Citation Formats

Kylasa, S.B., E-mail: skylasa@purdue.edu, Aktulga, H.M., E-mail: hmaktulga@lbl.gov, and Grama, A.Y., E-mail: ayg@cs.purdue.edu. PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs. United States: N. p., 2014. Web. doi:10.1016/J.JCP.2014.04.035.
Kylasa, S.B., E-mail: skylasa@purdue.edu, Aktulga, H.M., E-mail: hmaktulga@lbl.gov, & Grama, A.Y., E-mail: ayg@cs.purdue.edu. PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs. United States. doi:10.1016/J.JCP.2014.04.035.
Kylasa, S.B., E-mail: skylasa@purdue.edu, Aktulga, H.M., E-mail: hmaktulga@lbl.gov, and Grama, A.Y., E-mail: ayg@cs.purdue.edu. Mon . "PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs". United States. doi:10.1016/J.JCP.2014.04.035.
@article{osti_22314897,
title = {PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs},
author = {Kylasa, S.B., E-mail: skylasa@purdue.edu and Aktulga, H.M., E-mail: hmaktulga@lbl.gov and Grama, A.Y., E-mail: ayg@cs.purdue.edu},
abstractNote = {We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.},
doi = {10.1016/J.JCP.2014.04.035},
journal = {Journal of Computational Physics},
number = ,
volume = 272,
place = {United States},
year = {Mon Sep 01 00:00:00 EDT 2014},
month = {Mon Sep 01 00:00:00 EDT 2014}
}