Dynamic-domain-decomposition parallel molecular dynamics

• Published in: Computer physics communications Vol. 102; no. 1; pp. 44 - 58
• Main Authors: Srinivasan, S.G., Ashok, I., Jônsson, Hannes, Kalonji, Gretchen, Zahorjan, John
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-05-1997
• Subjects: 02.70.-c; 02.70.Ns; 89.90.+h; 89.90.+n; Domain decomposition; Dynamic load balancing; Molecular dynamics; Parallel computers; Runtime system; 89.90.+n; 02.70.Ns; 02.70.-c; Parallel computers; Dynamic load balancing; Molecular dynamics; Runtime system; 89.90.+h; Domain decomposition
• ISSN: 0010-4655; 1879-2944
• DOI: 10.1016/S0010-4655(97)00016-7

Parallel molecular dynamics with short-range forces can suffer from load-imbalance problems and attendant performance degradation due to density variations in the simulated system. In this paper, we describe an approach to dynamical load balancing, enabled by the Ādhāra runtime system. The domain assigned to each processor is automatically and dynamically resized so as to evenly distribute the molecular dynamics computations across all the processors. The algorithm was tested on an Intel Paragon parallel computer for two and three-dimensional Lennard-Jones systems containing 99 458 and 256000 atoms, respectively, and using up to 256 processors. In these benchmarks, the overhead for carrying out the load-balancing operations was found to be small and the total computation time was reduced by as much as 50%.