research-article

A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3

Authors:

Eiji Nishibori,

Takahiro Koishi,

Tahir H. Tahirov,

Masashi Miyano,

Ryutaro Himeno,

Toshikazu Ebisuzaki,

Makoto TaijiAuthors Info & Claims

SC '07: Proceedings of the 2007 ACM/IEEE conference on Supercomputing

Article No.: 56, Pages 1 - 10

https://doi.org/10.1145/1362622.1362698

Published: 10 November 2007 Publication History

Abstract

We have achieved a sustained calculation speed of 281 Tflops for the optimization of the 3-D structures of proteins from the X-ray experimental data by the Genetic Algorithm - Direct Space (GA-DS) method. In this calculation we used MDGRAPE-3, special-purpose computer for molecular simulations, with the peak performance of 752 Tflops. In the GA-DS method, a set of selected parameters which define the crystal structures of proteins is optimized by the Genetic Algorithm. As a criterion to estimate the model parameters, we used the reliability factor R¹ which indicates the statistical difference between the calculated and the measured diffraction data. To evaluate this factor it is necessary to reconstruct the diffraction patterns of the model structures every time the model is updated. Therefore, in this method the nonequispaced Discrete Fourier Transformation (DFT) used to calculate the diffraction patterns dominates most of the computation time. To accelerate DFT calculations, we used the special-purpose computer, MDGRAPE-3. A molecule, Carbamoyl-Phosphate Synthetase was investigated. The final reliability factors were much smaller than the typical values obtained in other methods such as the Molecular Replacement (MR) method. Our results successfully demonstrate that high-performance computing with GA-DS method on special-purpose computers is effective for the structure determination of biological molecules and the method has a potential to be widely used in near future.

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Cited By

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
Liu YLi YZhang YZhang X(2014)Memory Efficient Two-Pass 3D FFT Algorithm for Intel® Xeon PhiTM CoprocessorJournal of Computer Science and Technology10.1007/s11390-014-1484-z29:6(989-1002)Online publication date: 17-Nov-2014
https://doi.org/10.1007/s11390-014-1484-z
Cao ZLiu XLi QLiu XWang ZAn X(2014)An Intra-Server Interconnect Fabric for Heterogeneous ComputingJournal of Computer Science and Technology10.1007/s11390-014-1483-029:6(976-988)Online publication date: 17-Nov-2014
https://doi.org/10.1007/s11390-014-1483-0
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A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3
1. Applied computing
  1. Life and medical sciences

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cover image ACM Conferences

SC '07: Proceedings of the 2007 ACM/IEEE conference on Supercomputing

November 2007

723 pages

ISBN:9781595937643

DOI:10.1145/1362622

General Chair:
Becky Verastegui
Oak Ridge National Laboratory

Copyright © 2007 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: 10 November 2007

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SC '07: International Conference for High Performance Computing, Networking, Storage and Analysis

November 10 - 16, 2007

Nevada, Reno

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Cited By

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
Liu YLi YZhang YZhang X(2014)Memory Efficient Two-Pass 3D FFT Algorithm for Intel® Xeon PhiTM CoprocessorJournal of Computer Science and Technology10.1007/s11390-014-1484-z29:6(989-1002)Online publication date: 17-Nov-2014
https://doi.org/10.1007/s11390-014-1484-z
Cao ZLiu XLi QLiu XWang ZAn X(2014)An Intra-Server Interconnect Fabric for Heterogeneous ComputingJournal of Computer Science and Technology10.1007/s11390-014-1483-029:6(976-988)Online publication date: 17-Nov-2014
https://doi.org/10.1007/s11390-014-1483-0
Peng LNakano ATan GVashishta PFan DZhang HKalia RSong FCascaval CTrancoso PPrasanna V(2011)Performance analysis and optimization of molecular dynamics simulation on Godson-T many-core processorProceedings of the 8th ACM International Conference on Computing Frontiers10.1145/2016604.2016643(1-10)Online publication date: 3-May-2011
https://dl.acm.org/doi/10.1145/2016604.2016643
Cao ZTang HLi QLi BChen FWang KAn XSun N(2011)Design of HPC Node with Heterogeneous ProcessorsProceedings of the 2011 IEEE International Conference on Cluster Computing10.1109/CLUSTER.2011.23(130-138)Online publication date: 26-Sep-2011
https://dl.acm.org/doi/10.1109/CLUSTER.2011.23
Ohno YNarumi TTaiji M(2010)Petascale Special-Purpose Computer for Molecular Dynamics SimulationsPetascale Computing10.1201/9781584889106.ch10(183-209)Online publication date: 31-Jan-2010
https://doi.org/10.1201/9781584889106.ch10
Takahashi THamada T(2009)GPU‐accelerated boundary element method for Helmholtz' equation in three dimensionsInternational Journal for Numerical Methods in Engineering10.1002/nme.266180:10(1295-1321)Online publication date: 7-Jul-2009
https://doi.org/10.1002/nme.2661

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