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.

Proceedings SPP 2016 Cover

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Published

2016-08-18

Issue

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

Section

Poster Session PA

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How to Cite

[1]
“Benchmarking GPU acceleration of a parallel molecular dynamics simulation”, Proc. SPP, vol. 34, no. 1, p. SPP-2016-PA-19, Aug. 2016, Accessed: Apr. 16, 2026. [Online]. Available: https://proceedings.spp-online.org/article/view/SPP-2016-PA-19