Article

An 8.61 Tflop/s molecular dynamics simulation for NaCl with a special-purpose computer: MDM

Authors:

Takahiro KoishiAuthors Info & Claims

SC '01: Proceedings of the 2001 ACM/IEEE conference on Supercomputing

Page 26

https://doi.org/10.1145/582034.582060

Published: 10 November 2001 Publication History

Abstract

We performed molecular dynamics (MD) simulation of 33 million pairs of NaCl ions with the Ewald summation and obtained a calculation speed of 8.61 Tflop/s. In this calculation we used a special-purpose computer, MDM, which we have developed for the calculations of the Coulomb and van der Waals forces. The MDM enabled us to perform large scale MD simulations without truncating the Coulomb force. It is composed of MDGRAPE-2, WINE-2 and a host computer. MDGRAPE-2 accelerates the calculation for real-space part of the Coulomb and van der Waals forces. WINE-2 accelerates the calculation for wavenumber-space part of the Coulomb force. The host computer performs other calculations. With the completed MDM system we performed an MD simulation similar to what was the basis of our SC2000 submission for a Gordon Bell prize. With this large scale MD simulation, we can dramatically decrease the fluctuation of the temperature less than 0.1 Kelvin.

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Stewart CMüller MLingwall M(2006)Progress towards petascale applications in biologyProceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing10.5555/1765606.1765638(289-303)Online publication date: 29-Aug-2006
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cover image ACM Conferences

SC '01: Proceedings of the 2001 ACM/IEEE conference on Supercomputing

November 2001

756 pages

ISBN:158113293X

DOI:10.1145/582034

Conference Chair:
Charles Slocomb
Los Alamos National Laboratory

Copyright © 2001 ACM.

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Published: 10 November 2001

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SC '01: International Conference for High Performance Computing, Networking, Storage and Analysis

November 10 - 16, 2001

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Cited By

Janežič DBorštnik UPraprotnik M(2009)Parallel Approaches in Molecular Dynamics SimulationsParallel Computing10.1007/978-1-84882-409-6_10(281-305)Online publication date: 2009
https://doi.org/10.1007/978-1-84882-409-6_10
Stewart CMüller MLingwall M(2006)Progress towards petascale applications in biologyProceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing10.5555/1765606.1765638(289-303)Online publication date: 29-Aug-2006
https://dl.acm.org/doi/10.5555/1765606.1765638
Scrofano RPrasanna VHorner-Miller B(2006)Preliminary investigation of advanced electrostatics in molecular dynamics on reconfigurable computersProceedings of the 2006 ACM/IEEE conference on Supercomputing10.1145/1188455.1188550(90-es)Online publication date: 11-Nov-2006
https://dl.acm.org/doi/10.1145/1188455.1188550
Bowers KChow EXu HDror REastwood MGregersen BKlepeis JKolossvary IMoraes MSacerdoti FSalmon JShan YShaw DHorner-Miller B(2006)Scalable algorithms for molecular dynamics simulations on commodity clustersProceedings of the 2006 ACM/IEEE conference on Supercomputing10.1145/1188455.1188544(84-es)Online publication date: 11-Nov-2006
https://dl.acm.org/doi/10.1145/1188455.1188544
Bowers KChow DXu HDror REastwood MGregersen BKlepeis JKolossvary IMoraes MSacerdoti FSalmon JShan YShaw D(2006)Scalable Algorithms for Molecular Dynamics Simulations on Commodity ClustersACM/IEEE SC 2006 Conference (SC'06)10.1109/SC.2006.54(43-43)Online publication date: Nov-2006
https://doi.org/10.1109/SC.2006.54
Scrofano RPrasanna V(2006)Preliminary Investigation of Advanced Electrostatics in Molecular Dynamics on Reconfigurable ComputersACM/IEEE SC 2006 Conference (SC'06)10.1109/SC.2006.49(45-45)Online publication date: Nov-2006
https://doi.org/10.1109/SC.2006.49
Hartenstein R(2006)Morphware and ConfigwareHandbook of Nature-Inspired and Innovative Computing10.1007/0-387-27705-6_11(343-386)Online publication date: 2006
https://doi.org/10.1007/0-387-27705-6_11
Kawai AMakino JEbisuzaki T(2004)Performance Analysis of High‐Accuracy Tree Code Based on the Pseudoparticle Multipole MethodThe Astrophysical Journal Supplement Series10.1086/381391151:1(13-33)Online publication date: Mar-2004
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Sumanth JSwanson DJiang a(2004)Scheduling many-body short range MD simulations on a cluster of workstations and custom VLSI hardwareProceedings of the 11th international conference on High Performance Computing10.1007/978-3-540-30474-6_22(166-175)Online publication date: 19-Dec-2004
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Höfinger S(2004)What Size Cluster Equals a Dedicated ChipRecent Advances in Parallel Virtual Machine and Message Passing Interface10.1007/978-3-540-30218-6_54(397-404)Online publication date: 2004
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