Load balancing of molecular dynamics simulation with NWChem

  • Authors:

  • T. P. Straatsma;J. A. McCammon

  • Affiliations:

  • Molecular Sciences Software Group, Theory, Modeling and Simulation Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washingt ...;Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California

  • Venue:
  • IBM Systems Journal - Deep computing for the life sciences
  • Year:
  • 2001

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Abstract

NWChem is a computational chemistry software suite developed for massively parallel computers in the W. R. Wiley Environmental Molecular Sciences Laboratory at the U.S. Department of Energy's Pacific Northwest National Laboratory. This software integrates a range of modules for computational chemistry applications, including classical molecular dynamics simulations and quantum mechanical calculations. This contribution provides details of the classical molecular dynamics module and focuses on issues related to load balancing on massively parallel computers, in particular the IBM SPTM and the Cray T3ETM as examples of distributed and shared memory massively parallel architectures. The implementation of the molecular dynamics module of NWChem is based on a domain decomposition of the chemical system, taking advantage of the distribution of data to reduce the memory requirements and the locality of intermolecular interactions to reduce the communication requirements. This approach results in a more complex implementation because of the requirement of periodic atomic reassignments and the need for sophisticated load-balancing techniques.