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Title: Optimizing the Performance of Reactive Molecular Dynamics Simulations for Multi-core Architectures

Journal Article ·
OSTI ID:1427253
 [1];  [2];  [3];  [2];  [2]
  1. Michigan State Univ., East Lansing, MI (United States)
  2. Argonne National Lab. (ANL), Argonne, IL (United States)
  3. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
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Hybrid parallelism allows high performance computing applications to better leverage the increasing on-node parallelism of modern supercomputers. In this paper, we present a hybrid parallel implementation of the widely used LAMMPS/ReaxC package, where the construction of bonded and nonbonded lists and evaluation of complex ReaxFF interactions are implemented efficiently using OpenMP parallelism. Additionally, the performance of the QEq charge equilibration scheme is examined and a dual-solver is implemented. We present the performance of the resulting ReaxC-OMP package on a state-of-the-art multi-core architecture Mira, an IBM BlueGene/Q supercomputer. For system sizes ranging from 32 thousand to 16.6 million particles, speedups in the range of 1.5-4.5x are observed using the new ReaxC-OMP software. Sustained performance improvements have been observed for up to 262,144 cores (1,048,576 processes) of Mira with a weak scaling efficiency of 91.5% in larger simulations containing 16.6 million particles.

Research Organization:
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA)
DOE Contract Number:
AC04-94AL85000
OSTI ID:
1427253
Report Number(s):
SAND-2015-10550J; 614977
Country of Publication:
United States
Language:
English

Figures / Tables (12)

Fig. 1(p. 4)figure Fig. 1
Fig. 2(p. 4)figure Fig. 2
Algorithm 1(p. 6)figure Algorithm 1
Fig. 3(p. 8)figure Fig. 3
Fig. 4(p. 9)figure Fig. 4
Algorithm 2(p. 10)figure Algorithm 2
Fig. 5(p. 14)figure Fig. 5
Table 1(p. 16)table Table 1
Table 2(p. 17)table Table 2
Fig. 6(p. 19)figure Fig. 6
Fig. 7(p. 19)figure Fig. 7
Fig. 8(p. 21)figure Fig. 8

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