Benchmarking GPU acceleration of a parallel molecular dynamics simulation

Authors

Zed Harold E. Fernandez National Institute of Physics, University of the Philippines Diliman
Lloyd Francis L. Co Department of Physical Sciences, Polytechnic University of the Philippines
Francis N. C. Paraan National Institute of Physics, University of the Philippines Diliman

Abstract

The parallel speedup of component subroutines in a molecular dynamics simulation is measured after implementing MPI-based CPU parallelization and GPU acceleration. GPU acceleration was observed to yield an order of magnitude reduction in simulation times (13.9×–23.6× relative to a serial run). Slightly less speedup is achieved by CPU parallelization (7.5×) over nine processors. Performance scaling is diminished by communication operations as the number of processes launched begin to exceed the number of available physical CPU cores.

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Issue

2016: Proceedings of the 34th Samahang Pisika ng Pilipinas Physics Conference

Article ID

SPP-2016-PA-19

Section

Poster Session PA

Published

2016-08-18

How to Cite

[1]

ZHE Fernandez, LFL Co, and FNC Paraan, Benchmarking GPU acceleration of a parallel molecular dynamics simulation, Proceedings of the Samahang Pisika ng Pilipinas 34, SPP-2016-PA-19 (2016). URL: https://proceedings.spp-online.org/article/view/SPP-2016-PA-19.