Benchmarking GPU acceleration of a parallel molecular dynamics simulation

Authors

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

Physics at the front and center: Strengthening core values in physics research
18–21 August 2016, University of the Philippines Visayas, Iloilo City

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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.