Blog
About

  • Record: found
  • Abstract: found
  • Article: found
Is Open Access

Strong scaling of general-purpose molecular dynamics simulations on GPUs

Preprint

Read this article at

Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, J. Comp. Phys. 117, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., J. Comp. Phys. 227, 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3,375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5x.

      Related collections

      Most cited references 1

      • Record: found
      • Abstract: not found
      • Article: not found

      General purpose molecular dynamics simulations fully implemented on graphics processing units

        Bookmark

        Author and article information

        Journal
        10 December 2014
        1412.3387 10.1016/j.cpc.2015.02.028

        http://arxiv.org/licenses/nonexclusive-distrib/1.0/

        Custom metadata
        30 pages, 14 figures
        physics.comp-ph

        Mathematical & Computational physics

        Comments

        Comment on this article