Parallel short-range molecular dynamics using the Adhara runtime system
Srinivasan, SG; Ashok, I; Jonsson, H; Kalonji, G; Zahorjan, J
COMPUTER PHYSICS COMMUNICATIONS, 102 (1-3): 28-43 MAY 1997
We describe a parallel program for simulating molecular dynamics subject to short-ranged molecular interactions. The program uses a runtime system, (A) over bar dh (a) over bar ra, for atom definition, partitioning and distribution over the processors as well as dynamical load balancing between processors. A significant speedup is achieved by eliminating the usual test for the minimum image criterion, using conditional statements, that is applied to pairs of atoms during the force calculation. Instead, coordinates of boundary atoms are adjusted for the periodic boundary condition just before communication. The algorithm uses domain decomposition and the link-cell method as well as a neighbor list within cells. Benchmark simulations of systems with 864 and up to 5000000 atoms run on an Intel Paragon computer are described.
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