Article

Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations

Authors:

Noriyuki Futatsugi,

Atsushi Suenaga,

Akihiko KonagayaAuthors Info & Claims

SC '03: Proceedings of the 2003 ACM/IEEE conference on Supercomputing

Page 15

https://doi.org/10.1145/1048935.1050166

Published: 15 November 2003 Publication History

Abstract

We are developing the 'Protein Explorer' system, a petaflops special-purpose computer system for molecular dynamics simulations. The Protein Explorer is a PC cluster equipped with special-purpose engines that calculate nonbonded interactions between atoms, which is the most time-consuming part of the simulations. A dedicated LSI 'MDGRAPE-3 chip' performs these force calculations at a speed of 165 gigaflops or higher. The system will have 6,144 MDGRAPE-3 chips to achieve a nominal peak performance of one petaflop. The system will be completed in 2006. In this paper, we describe the project plans and the architecture of the Protein Explorer.

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cover image ACM Conferences

SC '03: Proceedings of the 2003 ACM/IEEE conference on Supercomputing

November 2003

859 pages

ISBN:1581136951

DOI:10.1145/1048935

General Chair:
James R. McGraw

Copyright © 2003 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 15 November 2003

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November 15 - 21, 2003

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Cited By

Bandara SDucimo AWu CHerbordt M(2024)Long-Range MD Electrostatics Force Computation on FPGAsIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2024.343434735:10(1690-1707)Online publication date: Oct-2024
https://doi.org/10.1109/TPDS.2024.3434347
Mo PLi CZhao DZhang YShi MLi JLiu J(2022)Accurate and efficient molecular dynamics based on machine learning and non von Neumann architecturenpj Computational Materials10.1038/s41524-022-00773-z8:1Online publication date: 9-May-2022
https://doi.org/10.1038/s41524-022-00773-z
Jones DAllen JYang YDrew Bennett WGokhale MMoshiri NRosing T(2022)Accelerators for Classical Molecular Dynamics Simulations of BiomoleculesJournal of Chemical Theory and Computation10.1021/acs.jctc.1c0121418:7(4047-4069)Online publication date: 16-Jun-2022
https://doi.org/10.1021/acs.jctc.1c01214
Morimoto GKoyama YZhang HKomatsu TOhno YNishida KOhmura IKoyama HTaiji Mde Supinski BHall MGamblin T(2021)Hardware acceleration of tensor-structured multilevel ewald summation method on MDGRAPE-4A, a special-purpose computer system for molecular dynamics simulationsProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3458817.3476190(1-15)Online publication date: 14-Nov-2021
https://dl.acm.org/doi/10.1145/3458817.3476190
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Shaw DGrossman JBank JBatson BButts JChao JDeneroff MDror REven AFenton CForte AGagliardo JGill GGreskamp BHo CIerardi DIserovich LKuskin JLarson RLayman TLee LLerer ALi CKillebrew DMackenzie KMok SMoraes MMueller RNociolo LPeticolas JQuan TRamot DSalmon JScarpazza DBen Schafer USiddique NSnyder CSpengler JTang PTheobald MToma HTowles BVitale BWang SYoung CDamkroger TDongarra J(2014)Anton 2Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1109/SC.2014.9(41-53)Online publication date: 16-Nov-2014
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Scarpazza DIerardi DLerer AMackenzie KPan ABank JChow EDror RGrossman JKillebrew DMoraes MPredescu CSalmon JShaw D(2013)Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose MachineProceedings of the 2013 IEEE 27th International Symposium on Parallel and Distributed Processing10.1109/IPDPS.2013.93(933-945)Online publication date: 20-May-2013
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