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Load balancing of molecular dynamics simulation with NWChem

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2 Author(s)
Straatsma, T.P. ; Molecular Sciences Software Group, Theory, Modeling and Simulation Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington 99352-0999, USA ; McCammon, J.A.

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 software computational chemistry applications classical molecular dynamics quantum mechanical calculations architecture memory domain decomposition intermolecular interactions periodic atomic reassignmentsoratory. 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 SP™ and the Cray T3E™ 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 chemic al 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.

Note: The Institute of Electrical and Electronics Engineers, Incorporated is distributing this Article with permission of the International Business Machines Corporation (IBM) who is the exclusive owner. The recipient of this Article may not assign, sublicense, lease, rent or otherwise transfer, reproduce, prepare derivative works, publicly display or perform, or distribute the Article.  

Published in:

IBM Systems Journal  (Volume:40 ,  Issue: 2 )