The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States

doi:10.1021/ct600260u

Title: The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States

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Abstract

Molecular dynamics calculations composed of many independent simulations are frequently encountered in free energy simulations, as well as many other simulation approaches. In principal, the availability of a large number of independent tasks should make possible the development of highly scalable parallel code that executes these tasks concurrently. This paper discusses the use of processor groups to write simulation codes of this type and describes results a code that evaluates the volume dependence of the Helmholtz free energy for clusters of an immiscible fluid in a solvent. The results show that very high levels of scalability can be achieved using processor groups with corresponding reductions in the time to completion. The main limitation to scaling appears to be load imbalance due to variations in the execution times of the individual tasks.

Authors:: Palmer, Bruce J.; Kathmann, Shawn M.; Krishnan, Manoj Kumar; Tipparaju, Vinod; Nieplocha, Jarek

Publication Date:: Sun Apr 01 00:00:00 EDT 2007

Research Org.:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 908948

Report Number(s):: PNNL-SA-51253
KP1303000; TRN: US200722%%828

DOE Contract Number:: AC05-76RL01830

Resource Type:: Journal Article

Resource Relation:: Journal Name: Journal of Chemical Theory and Computation, 3(2):583-592; Journal Volume: 3; Journal Issue: 2

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; COMPUTER CODES; AVAILABILITY; FREE ENERGY; COMPUTERIZED SIMULATION; MOLECULAR DYNAMICS METHOD

Citation Formats


                    Palmer, Bruce J., Kathmann, Shawn M., Krishnan, Manoj Kumar, Tipparaju, Vinod, and Nieplocha, Jarek. The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States.  United States: N. p., 2007. 
        Web.  doi:10.1021/ct600260u.

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                    Palmer, Bruce J., Kathmann, Shawn M., Krishnan, Manoj Kumar, Tipparaju, Vinod, & Nieplocha, Jarek. The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States.  United States.  doi:10.1021/ct600260u.

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                    Palmer, Bruce J., Kathmann, Shawn M., Krishnan, Manoj Kumar, Tipparaju, Vinod, and Nieplocha, Jarek. Sun .  
        "The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States".  United States.  
        doi:10.1021/ct600260u.

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@article{osti_908948,

  title        = {The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States},

  author       = {Palmer, Bruce J. and Kathmann, Shawn M. and Krishnan, Manoj Kumar and Tipparaju, Vinod and Nieplocha, Jarek},

  abstractNote = {Molecular dynamics calculations composed of many independent simulations are frequently encountered in free energy simulations, as well as many other simulation approaches. In principal, the availability of a large number of independent tasks should make possible the development of highly scalable parallel code that executes these tasks concurrently. This paper discusses the use of processor groups to write simulation codes of this type and describes results a code that evaluates the volume dependence of the Helmholtz free energy for clusters of an immiscible fluid in a solvent. The results show that very high levels of scalability can be achieved using processor groups with corresponding reductions in the time to completion. The main limitation to scaling appears to be load imbalance due to variations in the execution times of the individual tasks.},

  doi          = {10.1021/ct600260u},

  journal      = {Journal of Chemical Theory and Computation, 3(2):583-592},

  number       = 2,

  volume       = 3,

  place        = {United States},

  year         = {Sun Apr 01 00:00:00 EDT 2007},

  month        = {Sun Apr 01 00:00:00 EDT 2007}

}

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DOI: 10.1021/ct600260u

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