An evaluation of molecular dynamics performance on the hybrid cray XK6 supercomputer

W. Michael Brown; Trung Dac Nguyen; Miguel Fuentes-Cabrera; Jason D. Fowlkes; Philip D. Rack; Mark Berger; Arthur S. Bland

doi:10.1016/j.procs.2012.04.020

An evaluation of molecular dynamics performance on the hybrid cray XK6 supercomputer

W. Michael Brown^*, Trung Dac Nguyen, Miguel Fuentes-Cabrera, Jason D. Fowlkes, Philip D. Rack, Mark Berger, Arthur S. Bland

^*Corresponding author for this work

Chemical and Biological Engineering

Research output: Contribution to journal › Conference article › peer-review

28 Scopus citations

Abstract

For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little modification to existing codes. Engineering and electrical power constraints have disrupted this trend, requiring more drastic changes to both hardware and software solutions. Here, we present details of the Cray XK6 architecture that achieves increased performance with the use of GPU accelerators. We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers. We present benchmark results for solid-state, biological, and mesoscopic systems and discuss some challenges for utilizing hybrid systems. We present some early work in improving application performance on the XK6 and performance results for the simulation of liquid copper nanostructures with the embedded atom method.

Original language	English (US)
Pages (from-to)	186-195
Number of pages	10
Journal	Procedia Computer Science
Volume	9
DOIs	https://doi.org/10.1016/j.procs.2012.04.020
State	Published - 2012
Event	12th Annual International Conference on Computational Science, ICCS 2012 - Omaha, NB, United States Duration: Jun 4 2012 → Jun 6 2012

Funding

This research was conducted in part under the auspices of the Office of Advanced Scientific Computing Research, Office of Science, U.S. Department of Energy under Contract No. DE-AC05-00OR22725 with UT-Battelle, LLC. This research used resources of the Leadership Computing Facility at Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725 with UT-Battelle, LLC. Accordingly, the U.S. Government retains a non-exclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. M.F.C, J.D.F and P.D.R. acknowledge support from the U.S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division for supporting the portions of this work related to the design of molecular dynamics computational experiments. The authors thank Yuxing Peng (University of Chicago) for help with long-range partitions. Additionally, we thank Wayne Joubert and the referees for their critical review of the work.

Keywords

Embedded atom method
GPU
Materials
Molecular dynamics
Supercomputer

ASJC Scopus subject areas

General Computer Science

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10.1016/j.procs.2012.04.020

Cite this

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title = "An evaluation of molecular dynamics performance on the hybrid cray XK6 supercomputer",

abstract = "For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little modification to existing codes. Engineering and electrical power constraints have disrupted this trend, requiring more drastic changes to both hardware and software solutions. Here, we present details of the Cray XK6 architecture that achieves increased performance with the use of GPU accelerators. We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers. We present benchmark results for solid-state, biological, and mesoscopic systems and discuss some challenges for utilizing hybrid systems. We present some early work in improving application performance on the XK6 and performance results for the simulation of liquid copper nanostructures with the embedded atom method.",

keywords = "Embedded atom method, GPU, Materials, Molecular dynamics, Supercomputer",

author = "Brown, {W. Michael} and Nguyen, {Trung Dac} and Miguel Fuentes-Cabrera and Fowlkes, {Jason D.} and Rack, {Philip D.} and Mark Berger and Bland, {Arthur S.}",

note = "Funding Information: This research was conducted in part under the auspices of the Office of Advanced Scientific Computing Research, Office of Science, U.S. Department of Energy under Contract No. DE-AC05-00OR22725 with UT-Battelle, LLC. This research used resources of the Leadership Computing Facility at Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725 with UT-Battelle, LLC. Accordingly, the U.S. Government retains a non-exclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. M.F.C, J.D.F and P.D.R. acknowledge support from the U.S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division for supporting the portions of this work related to the design of molecular dynamics computational experiments. The authors thank Yuxing Peng (University of Chicago) for help with long-range partitions. Additionally, we thank Wayne Joubert and the referees for their critical review of the work.; 12th Annual International Conference on Computational Science, ICCS 2012 ; Conference date: 04-06-2012 Through 06-06-2012",

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AU - Nguyen, Trung Dac

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AU - Fowlkes, Jason D.

AU - Rack, Philip D.

AU - Berger, Mark

AU - Bland, Arthur S.

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AB - For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little modification to existing codes. Engineering and electrical power constraints have disrupted this trend, requiring more drastic changes to both hardware and software solutions. Here, we present details of the Cray XK6 architecture that achieves increased performance with the use of GPU accelerators. We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers. We present benchmark results for solid-state, biological, and mesoscopic systems and discuss some challenges for utilizing hybrid systems. We present some early work in improving application performance on the XK6 and performance results for the simulation of liquid copper nanostructures with the embedded atom method.

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An evaluation of molecular dynamics performance on the hybrid cray XK6 supercomputer

Abstract

Funding

Keywords

ASJC Scopus subject areas

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