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Parallel molecular dynamics: communication requirements for massively parallel machines

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3 Author(s)
V. E. Taylor ; Dept. of Electr. Eng. & Comput. Sci., Northwestern Univ., Evanston, IL, USA ; R. L. Stevens ; K. E. Arnold

Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems, from large-scale computations of materials to the design and modeling of drug compounds. In this paper we address two major issues: a good decomposition method that can take advantage of future massively parallel processing systems for modest-sized problems in the range of 50,000 atoms and the communication requirements needed to achieve 30 to 40% efficiency on MPPs. We analyzed a scalable benchmark molecular dynamics program executing on the Intel Touchstone Deleta parallelized with an interaction decomposition method. Using a validated analytical performance model of the code, we determined that for an MPP with a four-dimensional mesh topology and 400 MHz processors the communication startup time must be at most 90 clock cycles and the network bandwidth must be at least 2.3 GB/s. This configuration results in 30 to 40% efficiency of the MPP for a problem with 50,000 atoms executing on 50,000 processors

Published in:

Frontiers of Massively Parallel Computation, 1995. Proceedings. Frontiers '95., Fifth Symposium on the

Date of Conference:

6-9 Feb 1995