Parallel molecular dynamics: Communication requirements for massively parallel machines

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Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems from large-scale computations of materials to the design and modeling of drug compounds. In this paper we address two major issues: a good decomposition method that can take advantage of future massively parallel processing systems for modest-sized problems in the range of 50,000 atoms and the communication requirements needed to achieve 30 to 40% efficiency on MPPs. We analyzed a scalable benchmark molecular dynamics program executing on the Intel Touchstone Deleta parallelized with an interaction decomposition method. Using a validated analytical performance model of the code, ... continued below

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8 p.

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Taylor, V.E.; Stevens, R.L. & Arnold, K.E. June 1, 1995.

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  • Taylor, V.E. Northwestern Univ., Evanston, IL (United States). Dept. of Electrical Engineering and Computer Science
  • Stevens, R.L.
  • Arnold, K.E. Argonne National Lab., IL (United States)

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Description

Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems from large-scale computations of materials to the design and modeling of drug compounds. In this paper we address two major issues: a good decomposition method that can take advantage of future massively parallel processing systems for modest-sized problems in the range of 50,000 atoms and the communication requirements needed to achieve 30 to 40% efficiency on MPPs. We analyzed a scalable benchmark molecular dynamics program executing on the Intel Touchstone Deleta parallelized with an interaction decomposition method. Using a validated analytical performance model of the code, we determined that for an MPP with a four-dimensional mesh topology and 400 MHz processors the communication startup time must be at most 30 clock cycles and the network bandwidth must be at least 2.3 GB/s. This configuration results in 30 to 40% efficiency of the MPP for a problem with 50,000 atoms executing on 50,000 processors.

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8 p.

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OSTI as DE95012948

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  • Frontiers 95: a workshop on future directions of massively parallel processing, McLean, VA (United States), 6-9 Feb 1995

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  • Other: DE95012948
  • Report No.: ANL/MCS/CP--84761
  • Report No.: CONF-9502101--2
  • Grant Number: W-31-109-ENG-38
  • Office of Scientific & Technical Information Report Number: 69403
  • Archival Resource Key: ark:/67531/metadc702023

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  • June 1, 1995

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  • Sept. 12, 2015, 6:31 a.m.

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  • Dec. 15, 2015, 12:17 p.m.

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Taylor, V.E.; Stevens, R.L. & Arnold, K.E. Parallel molecular dynamics: Communication requirements for massively parallel machines, article, June 1, 1995; Illinois. (digital.library.unt.edu/ark:/67531/metadc702023/: accessed November 16, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.