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Memory-Efficient Implementation of a Rigid-Body Molecular Dynamics Simulation

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2 Author(s)
Eckhardt, W. ; Dept. of Inf., Tech. Univ. Munchen, Munich, Germany ; Neckel, T.

Molecular dynamics simulations are usually optimized with regard to runtime rather than memory consumption. In this paper, we investigate two distinct implementational aspects of the frequently used Linked-Cell algorithm for rigid-body molecular dynamics simulations: the representation of particle data for the force calculation, and the layout of data structures in memory. We propose a low memory footprint implementation, which comes with no costs in terms of runtime. To prove the approach, it was implemented in the programme Mardyn and evaluated on a standard cluster as well as on a Blue Gene/P for representative scenarios.

Published in:

Parallel and Distributed Computing (ISPDC), 2012 11th International Symposium on

Date of Conference:

25-29 June 2012