Comparison studies of large-scale conventional molecular dynamics simulation on parallel machines

Yun-Che Wang, Chun Yi Wu, I. Hsin Chung

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Molecular dynamics simulation is an important and powerful tool in studying physical and chemical properties of materials, in particular, at the nanoscales. Conventional molecular dynamics, as oppose to the ab initio molecular dynamics, adopts the Newton's second law to predict particle position in the next time step with the assistance of empirical interatomic potential to calculate the forces between neighboring particles. Large-scale MD systems, consisting millions of atoms, require sophisticated parallelization in computer codes to improve computational efficiency. In this work, the IBM Blue Gene/P, a linux PC cluster and GPU/CUDA are used to test the computation performance of the MD code, LAMMPS, and other codes. Furthermore, strong and weak scaling were tested to determine the parallel efficiency of the codes, and to study effects of system size and number of computing cores. It is found that both strong and weak scaling are achievable in the tested problem sizes. Furthermore, due to reduced CPU clock frequency in the Blue Gene/P machine, its performance is inferior than that of the linux cluster if the number of the computing cores involved is small. Effects of computation algorithms also strongly influence the performance of the codes on the machines. Blue Gene/P is extremely suitable for large-scale problem sizes with many processors involved. When the problem fits in the GPU architecture, the performance of the GPU/CUDA may be comparable with that of Blue Gene/P. In addition to the parallel performance, the accuracy of the physical problem is verified to ensure the MD simulation produce correct results.

Original languageEnglish
Title of host publicationProceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012
Pages959-963
Number of pages5
DOIs
Publication statusPublished - 2012 Dec 7
Event14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012 - Liverpool, United Kingdom
Duration: 2012 Jun 252012 Jun 27

Publication series

NameProceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012

Other

Other14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012
CountryUnited Kingdom
CityLiverpool
Period12-06-2512-06-27

Fingerprint

Molecular dynamics
Genes
Computer simulation
Computational efficiency
Chemical properties
Program processors
Large scale systems
Clocks
Physical properties
Atoms
Graphics processing unit
Linux

All Science Journal Classification (ASJC) codes

  • Software

Cite this

Wang, Y-C., Wu, C. Y., & Chung, I. H. (2012). Comparison studies of large-scale conventional molecular dynamics simulation on parallel machines. In Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012 (pp. 959-963). [6332275] (Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012). https://doi.org/10.1109/HPCC.2012.139
Wang, Yun-Che ; Wu, Chun Yi ; Chung, I. Hsin. / Comparison studies of large-scale conventional molecular dynamics simulation on parallel machines. Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012. 2012. pp. 959-963 (Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012).
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Wang, Y-C, Wu, CY & Chung, IH 2012, Comparison studies of large-scale conventional molecular dynamics simulation on parallel machines. in Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012., 6332275, Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012, pp. 959-963, 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012, Liverpool, United Kingdom, 12-06-25. https://doi.org/10.1109/HPCC.2012.139

Comparison studies of large-scale conventional molecular dynamics simulation on parallel machines. / Wang, Yun-Che; Wu, Chun Yi; Chung, I. Hsin.

Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012. 2012. p. 959-963 6332275 (Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Wang Y-C, Wu CY, Chung IH. Comparison studies of large-scale conventional molecular dynamics simulation on parallel machines. In Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012. 2012. p. 959-963. 6332275. (Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012). https://doi.org/10.1109/HPCC.2012.139