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

Title: Optimizing the performance of reactive molecular dynamics simulations for many-core architectures

Journal Article · · International Journal of High Performance Computing Applications
 [1];  [2];  [2];  [3];  [4];  [2]
  1. Michigan State Univ., East Lansing, MI (United States). Dept. of Computer Science and Engineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division
  2. Argonne National Lab. (ANL), Argonne, IL (United States). Argonne Leadership Computing Facility
  3. Michigan State Univ., East Lansing, MI (United States). Dept. of Computer Science and Engineering
  4. Sandia National Lab. (SNL-CA), Livermore, CA (United States). Multiscale Science Dept.
+ Show Author Affiliations

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this article, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for many-core architectures. As hybrid parallelism allows better leverage of the increasing on-node parallelism, we adopt thread parallelism in the construction of bonded and nonbonded lists and in the computation of complex ReaxFF interactions. To mitigate the I/O overheads due to large volumes of trajectory data produced and to save users the burden of post-processing, we also develop a novel in situ tool for molecular species analysis. We analyze the performance of the resulting ReaxC-OMP package on two different architectures: (i) Mira, an IBM Blue Gene/Q system and (ii) Cori-II, a Cray XC-40 sytem with Knights Landing processors. For Pentaerythritol tetranitrate (PETN) systems of sizes ranging from 32 thousand to 16.6 million particles, we observe speedups in the range of 1.5-4.5x. We observe sustained performance improvements for up to 262,144 cores (1,048,576 processes) of Mira and a weak scaling efficiency of 91.5% in large simulations containing 16.6 million particles. Finally, the in situ molecular species analysis tool incurs only insignificant overheads across various system sizes and runs configurations.

Research Organization:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Argonne Leadership Computing Facility
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1530430
Journal Information:
International Journal of High Performance Computing Applications, Vol. 33, Issue 2; ISSN 1094-3420
Publisher:
SAGECopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 16 works
Citation information provided by
Web of Science

References (36)

General purpose molecular dynamics simulations fully implemented on graphics processing units journal May 2008
Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques journal January 2012
GPU-accelerated molecular visualization on petascale supercomputing platforms conference January 2013
A Flexible Framework for Asynchronous in Situ and in Transit Analytics for Scientific Simulations conference May 2014
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs journal September 2014
Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics journal April 2013
Classical atomistic simulations of surfaces and heterogeneous interfaces with the charge-optimized many body (COMB) potentials journal September 2013
The ReaxFF reactive force-field: development, applications and future directions journal March 2016
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions journal January 2005
GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal February 2008
Charge equilibration for molecular dynamics simulations journal April 1991
Global optimization of parameters in the reactive force field ReaxFF for SiOH journal July 2013
An empirical valence bond approach for comparing reactions in solutions and in enzymes journal September 1980
Macroscale superlubricity enabled by graphene nanoscroll formation journal May 2015
Dynamic topology aware load balancing algorithms for molecular dynamics applications conference January 2009
Fast Parallel Algorithms for Short-Range Molecular Dynamics journal March 1995
A reactive potential for hydrocarbons with intermolecular interactions journal April 2000
Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics journal April 2013
ReaxFF:  A Reactive Force Field for Hydrocarbons journal October 2001
Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system journal December 2013
Parallel Optimization of a Reactive Force Field for Polycondensation of Alkoxysilanes journal September 2014
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin journal March 1988
GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems journal July 1986
Exploring SIMD for Molecular Dynamics, Using Intel® Xeon® Processors and Intel® Xeon Phi Coprocessors
  • Pennycook, Simon J.; Hughes, Chris J.; Smelyanskiy, M.
  • 2013 IEEE International Symposium on Parallel & Distributed Processing (IPDPS), 2013 IEEE 27th International Symposium on Parallel and Distributed Processing https://doi.org/10.1109/IPDPS.2013.44
conference May 2013
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins † journal April 1998
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques journal April 2012
Electronegativity-equalization method for the calculation of atomic charges in molecules journal July 1986
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules journal May 1995
A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations journal January 2008
General Multiobjective Force Field Optimization Framework, with Application to Reactive Force Fields for Silicon Carbide journal March 2014
In-Situ Feature Extraction of Large Scale Combustion Simulations Using Segmented Merge Trees
  • Landge, Aaditya G.; Pascucci, Valerio; Gyulassy, Attila
  • SC14: International Conference for High Performance Computing, Networking, Storage and Analysis https://doi.org/10.1109/SC.2014.88
conference November 2014
Damaris/Viz: A nonintrusive, adaptable and user-friendly in situ visualization framework conference October 2013
Methods of conjugate gradients for solving linear systems journal December 1952
The Curious Case of the Hydrated Proton journal August 2011
A divide-and-conquer/cellular-decomposition framework for million-to-billion atom simulations of chemical reactions journal February 2007
Zonal methods for the parallel execution of range-limited N-body simulations journal January 2007

Cited By (2)

Inertial extended-Lagrangian scheme for solving charge equilibration models journal January 2019
Inertial Extended-Lagrangian Scheme for Solving Charge Equilibration Models text January 2019

Similar Records

Related Subjects

97 MATHEMATICS AND COMPUTING
hybrid MPI/OpenMP parallelism
LAMMPS-ReaxC-OMP
multi-core architectures
reactive molecular dynamics
ReaxFF
many-core architectures