Accelerating dissipative particle dynamics simulations for soft matter systems

Trung Dac Nguyen*, Steven J. Plimpton

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

Abstract

Dissipative particle dynamics (DPD) is a coarse-grained particle-based simulation method that offers microscopic-scale insights into soft matter systems. We present an efficient implementation of a DPD model for graphical processing units (GPUs). As implemented in the LAMMPS molecular dynamics package, it can run effectively on current-generation supercomputers which often have hybrid nodes containing multi-core CPUs and (one or more) GPUs. Using efficient communication of information between the CPUs and GPUs, DPD interactions can be computed on the GPU while other portions of a full simulation model (boundary conditions, constraints, bonded interactions, diagnostic calculations, etc.) can be performed on the CPU. Our GPU-enhanced runs show a speedup of up to 9.5x versus many-core CPU simulations, and can run scalably across thousands of compute nodes. We briefly discuss how the new GPU implementation was validated against the CPU version for thermodynamics, diffusion, and hydrodynamic behavior. We also highlight large-scale models which the faster DPD implementation has enabled, for studies of monolayer self-assembly and thin-film instabilities.

Original languageEnglish (US)
Pages (from-to)173-180
Number of pages8
JournalComputational Materials Science
Volume100
Issue numberPB
DOIs
StatePublished - Apr 1 2015

Funding

The GPU and CPU DPD models described here are part of the open-source LAMMPS distribution, available for download at http://lammps.sandia.gov . T.D.N. thanks W. M. Brown for helpful discussion regarding the implementation of the GPU package and Arnold N. Tharrington for comments on the random number generators on the GPU. This research used resources of the Leadership Computing Facility at Oak Ridge National Laboratory and was conducted under the auspices of the Office of Advanced Scientific Computing Research, Office of Science, U.S. Department of Energy under Contract No. DE-AC05-00OR22725 with UT-Battelle, LLC .

Keywords

  • Dissipative particle dynamics
  • GPU acceleration
  • High-performance computing
  • Hybrid CPU/GPU
  • Hybrid MPI/GPU
  • LAMMPS

ASJC Scopus subject areas

  • General Computer Science
  • General Chemistry
  • General Materials Science
  • Mechanics of Materials
  • General Physics and Astronomy
  • Computational Mathematics

Fingerprint

Dive into the research topics of 'Accelerating dissipative particle dynamics simulations for soft matter systems'. Together they form a unique fingerprint.

Cite this