A Scalable, Linear-Time Dynamic Cutoff Algorithm for Molecular Dynamics

  • Paul Springer
  • Ahmed E. Ismail
  • Paolo Bientinesi
Conference paper

DOI: 10.1007/978-3-319-20119-1_12

Part of the Lecture Notes in Computer Science book series (LNCS, volume 9137)
Cite this paper as:
Springer P., Ismail A.E., Bientinesi P. (2015) A Scalable, Linear-Time Dynamic Cutoff Algorithm for Molecular Dynamics. In: Kunkel J., Ludwig T. (eds) High Performance Computing. ISC High Performance 2015. Lecture Notes in Computer Science, vol 9137. Springer, Cham

Abstract

Recent results on supercomputers show that beyond 65 K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems of arbitrarily large size. The idea consists in adopting a cutoff-based method in which the cutoff is chosen on a particle-by-particle basis, according to the distance from the interface. Computationally, the challenge is shifted from the long-range solvers to the detection of the interfaces and to the computation of the particle-interface distances. For these tasks, we present linear-time algorithms that do not rely on global communication patterns. As a result, the DCM algorithm is suited for large systems of particles and massively parallel computers. To demonstrate its potential, we integrated DCM into the LAMMPS open-source molecular dynamics package, and simulated large liquid/vapor systems on two supercomputers: SuperMuc and JUQUEEN. In all cases, the accuracy of DCM is comparable to the traditional particle-particle particle-mesh (PPPM) algorithm, while the performance is considerably superior for large numbers of particles. For JUQUEEN, we provide timings for simulations running on the full system (458, 752 cores), and show nearly perfect strong and weak scaling.

Keywords

Dynamic cutoff Interface detection Linear-time complexity Scalability Molecular dynamics Fast sweeping method 

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Paul Springer
    • 1
  • Ahmed E. Ismail
    • 1
  • Paolo Bientinesi
    • 1
  1. 1.Aachen Institute for Advanced Study in Computational Engineering ScienceRWTH Aachen UniversityAachenGermany

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