On eliminating synchronous communication in molecular simulations to improve scalability

T. P. Straatsma, Daniel G. Chavarría-Miranda

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern massively concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive. This paper illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put-notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load.

Original languageEnglish
Pages (from-to)2634-2640
Number of pages7
JournalComputer Physics Communications
Volume184
Issue number12
DOIs
StatePublished - Dec 2013
Externally publishedYes

Funding

This work was presented in honor of Professor Ria Broer at the symposium “Quantum Chemistry in the Solid State: Magnetic Coupling and Excited States” organized by the Theoretical Chemistry Department of the University of Groningen, August 31–September 1, 2012. This work has been supported by the Extreme Scale Computing Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory . Computational resources were provided by the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research , and by the Pacific Northwest National Laboratory Institutional Computing Facility . The Pacific Northwest National Laboratory is operated for the US Department of Energy by Battelle.

Keywords

  • Global arrays
  • Molecular dynamics
  • One-sided communication

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