An algorithm for computing short-range forces in molecular dynamics simulations with non-uniform particle densities

Research output: Contribution to journalArticlepeer-review

Authors

Colleges, School and Institutes

External organisations

  • University of Warwick
  • Intel Corporation, United Kingdom
  • University of York

Abstract

We present projection sorting, an algorithmic approach to determining pairwise short-range forces between particles in molecular dynamics simulations. We show it can be more effective than the standard approaches when particle density is non-uniform. We implement tuned versions of the algorithm in the context of a biophysical simulation of chromosome condensation, for the modern Intel Broadwell and Knights Landing architectures, across multiple nodes. We demonstrate up to 5× overall speedup and good scaling to large problem sizes and processor counts.

Bibliographic note

Funding Information: This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK ( FC001003 ), the UK Medical Research Council ( FC001003 ), and the Wellcome Trust, UK ( FC001003 ), and by the Engineering and Physical Sciences Research Council, UK and Intel Corporation, United States (CASE award 1365607 ). This work used the ARCHER UK National Supercomputing Service. Funding Information: This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001003), the UK Medical Research Council (FC001003), and the Wellcome Trust, UK (FC001003), and by the Engineering and Physical Sciences Research Council, UK and Intel Corporation, United States (CASE award 1365607). This work used the ARCHER UK National Supercomputing Service. Publisher Copyright: © 2019 The Author(s)

Details

Original languageEnglish
Pages (from-to)1-11
Number of pages11
JournalJournal of Parallel and Distributed Computing
Volume130
Publication statusPublished - Aug 2019

Keywords

  • Algorithms, ARCHER, Many-core, Molecular dynamics, MPI, Simulation