Logo image
Back
Scalable time-parallelization of molecular dynamics simulations in nano mechanics
Conference proceeding   Peer reviewed

Scalable time-parallelization of molecular dynamics simulations in nano mechanics

Yanan Yu, Ashok Srinivasan and Namas Chandra
2006 INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING, PROCEEDINGS, pp.119-126
Proceedings of the International Conference on Parallel Processing
International Conference on Parallel Processing (ICPP'06) (Columbus, OH, USA, 08/14/2006–08/18/2006)
01/01/2006
DOI: https://doi.org/10.1109/ICPP.2006.64
Web of Science ID: WOS:000241495500013

Metrics

42 Record Views
6 Times Cited - Web of Science

Abstract

Molecular Dynamics (MD) is an important atomistic simulation technique, with widespread use in computational chemistry, biology, and materials. An important limitation of MD is that the time step size is small, requiring a large number of iterations to simulate realistic time spans. Conventional parallelization is not very effective for this. We recently introduced a new approach to parallelization, where data from related prior simulations are used to parallelize a new computation along the time domain. In our prior work, the size of the physical system in the current simulation needed to be identical to that of the prior simulations. The significance of this paper lies in demonstrating a strategy that enables this approach to be used even when the physical systems differ in size. Furthermore, this method scaled up to almost 1000 processors with close to ideal speedup in one case, where conventional methods scale to only 2 - 3 processors.

Details

Logo image