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Volumn 7, Issue 6, 2012, Pages 1312-1328

Parallel processor design and implementation for molecular dynamics simulations on a FPGA-Based supercomputer

Author keywords

Field programmable gate array (FPGA); High performance reconfigurable Computing; Molecular Dynamics

Indexed keywords

COMPUTATIONAL POWER; FPGA CORE; HARDWARE ACCELERATION; HIGH PERFORMANCE RECONFIGURABLE COMPUTING; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MULTIPLE NODES; NONBONDED INTERACTION; PARALLEL COMPUTER; PARALLEL MACHINE; PARALLEL PROCESSOR; PERFORMANCE GAIN; PROCESSOR CORES; PROTEIN SYSTEM; SOFTWARE IMPLEMENTATION; TIMING PERFORMANCE;

EID: 84860999033     PISSN: 1796203X     EISSN: None     Source Type: Journal    
DOI: 10.4304/jcp.7.6.1312-1328     Document Type: Article
Times cited : (11)

References (47)
  • 3
    • 0029979312 scopus 로고    scopus 로고
    • Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study
    • Feb
    • Z. R. Wasserman and C. N. Hodge, "Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study", J. Proteins: Structure, Function, and Bioinformatics, vol. 24, no. 2, pp. 227-237, Feb. 1996.
    • (1996) J. Proteins: Structure, Function, and Bioinformatics , vol.24 , Issue.2 , pp. 227-237
    • Wasserman, Z.R.1    Hodge, C.N.2
  • 4
    • 0030157593 scopus 로고    scopus 로고
    • A structural and energetics analysis of the binding of a series of N-acetylneuraminicacid-based inhibitors to influenza virus sialidase
    • June
    • N. R. Taylor and M. Itzstein, "A structural and energetics analysis of the binding of a series of N-acetylneuraminicacid-based inhibitors to influenza virus sialidase", J. Computer-Aided Molecular Design, vol. 10, no. 3, pp. 233-246, June 1996.
    • (1996) J. Computer-Aided Molecular Design , vol.10 , Issue.3 , pp. 233-246
    • Taylor, N.R.1    Itzstein, M.2
  • 5
    • 0030586030 scopus 로고    scopus 로고
    • The first step in sugar transport: Crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: Sugar phosphotransferase system and a model of the phosphotransfer complex with HPr
    • July
    • D. I. Liao, E. Silverton, Y. J. Seok, B. R. Lee, A. Peterkofsky and D. R. Davies, "The first step in sugar transport: crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: sugar phosphotransferase system and a model of the phosphotransfer complex with HPr.", J. Structure, vol. 4, no. 7, pp. 861-872, July 1996.
    • (1996) J. Structure , vol.4 , Issue.7 , pp. 861-872
    • Liao, D.I.1    Silverton, E.2    Seok, Y.J.3    Lee, B.R.4    Peterkofsky, A.5    Davies, D.R.6
  • 6
    • 0030585428 scopus 로고    scopus 로고
    • Solution structure of the donor site of a transsplicing RNA
    • June
    • N. L. Greenbaum, I. Radhakrishnan, D. J. Patel and D. Hirsh, "Solution structure of the donor site of a transsplicing RNA", J. Structure, vol. 4, no. 6, pp. 725-733, June 1996.
    • (1996) J. Structure , vol.4 , Issue.6 , pp. 725-733
    • Greenbaum, N.L.1    Radhakrishnan, I.2    Patel, D.J.3    Hirsh, D.4
  • 8
    • 84977266737 scopus 로고
    • Evaluation of optical and electrostatic lattice potentials
    • P. P. Ewald, "Evaluation of optical and electrostatic lattice potentials", Ann. Phys Leipzig, vol. 64, pp. 253-287, 1921.
    • (1921) Ann. Phys Leipzig , vol.64 , pp. 253-287
    • Ewald, P.P.1
  • 9
    • 22944467757 scopus 로고
    • Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
    • July
    • L. Verlet, "Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules", Physical Review, vol. 159, no. 1, pp. 98-103, July 1967.
    • (1967) Physical Review , vol.159 , Issue.1 , pp. 98-103
    • Verlet, L.1
  • 10
    • 0000394426 scopus 로고
    • Some Multistep Methods for Use in Molecular Dynamics Calculations
    • Feb
    • D. Beeman, "Some Multistep Methods for Use in Molecular Dynamics Calculations", J. Computational Physics, vol. 20, pp. 130-139, Feb. 1976.
    • (1976) J. Computational Physics , vol.20 , pp. 130-139
    • Beeman, D.1
  • 11
    • 33646650705 scopus 로고
    • Reversible multiple time-scale molecular dynamics
    • March
    • M.E. Tuckerman, G.J. Martyna and B.J. Berne, "Reversible multiple time-scale molecular dynamics", J. Chemical Physics, vol. 97, no. 3, pp. 1990-2001, March 1992.
    • (1992) J. Chemical Physics , vol.97 , Issue.3 , pp. 1990-2001
    • Tuckerman, M.E.1    Martyna, G.J.2    Berne, B.J.3
  • 13
    • 84860996170 scopus 로고    scopus 로고
    • GROMACS-4.0.7, available at, Dec
    • GROMACS-4.0.7, "Download website for GROMACS 4.0.7", available at http://www.gromacs.org, Dec. 2009.
    • (2009) Download Website for GROMACS 4.0.7
  • 15
    • 84861005048 scopus 로고    scopus 로고
    • NAMD-2.7b2, available at, Nov
    • NAMD-2.7b2, "Download website for NAMD 2.7b2", available at http://www.ks.uiuc.edu/Research/namd, Nov. 2009.
    • (2009) Download Website for NAMD 2.7b2
  • 16
    • 84861005047 scopus 로고    scopus 로고
    • LAMMPS, available at, Jan
    • LAMMPS, "Download website for LAMMPS", available at http://lammps.sandia.gov, Jan. 2010.
    • (2010) Download Website for LAMMPS
  • 17
    • 33749169503 scopus 로고    scopus 로고
    • A highly parallelized special-purpose computer for many-body simulations with an arbitrary central force: MD-GRAPE
    • Sep
    • F. Toshiyuki, T. Makoto, M. Junichiro, E. Toshikazu and S. Duiichiro, "A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE", Astrophysical Journal, vol. 468, pp. 51-61, Sep. 1996.
    • (1996) Astrophysical Journal , vol.468 , pp. 51-61
    • Toshiyuki, F.1    Makoto, T.2    Junichiro, M.3    Toshikazu, E.4    Duiichiro, S.5
  • 18
    • 0001489848 scopus 로고    scopus 로고
    • Fast and accurate molecular dynamics sumulation of a protein using a special-purpose computer
    • Sep
    • Y. Komeiji, M. Uebayasi, R. Takata, A. Shimizu, K. Itsukashi and M. Taiji, "Fast and Accurate Molecular Dynamics Sumulation of a Protein Using a Special-Purpose Computer", J. Computational Chemistry, vol. 18, no. 12, pp. 1546-1563, Sep. 1997.
    • (1997) J. Computational Chemistry , vol.18 , Issue.12 , pp. 1546-1563
    • Komeiji, Y.1    Uebayasi, M.2    Takata, R.3    Shimizu, A.4    Itsukashi, K.5    Taiji, M.6
  • 24
    • 43049179828 scopus 로고    scopus 로고
    • Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations
    • May
    • Y. Gu, T. VanCourt and M. C. Herbordt, "Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations", Elsevier Parallel Computing, vol. 34, no. 4, pp. 261-277, May 2008.
    • (2008) Elsevier Parallel Computing , vol.34 , Issue.4 , pp. 261-277
    • Gu, Y.1    vanCourt, T.2    Herbordt, M.C.3
  • 27
    • 84861004361 scopus 로고    scopus 로고
    • LAMMPS, available at, Jan
    • LAMMPS, "LAMMPS manual", available at http://lammps.sandia.gov/doc/Manual.html, Jan. 2010.
    • (2010) LAMMPS Manual
  • 28
    • 0000396658 scopus 로고
    • A Fast Algorithm for Particle Simulations
    • Dec
    • L. Greengard and V. Rokhlin, "A Fast Algorithm for Particle Simulations", J. Computational Physics, vol. 73, no.2, pp. 325-348, Dec. 1987.
    • (1987) J. Computational Physics , vol.73 , Issue.2 , pp. 325-348
    • Greengard, L.1    Rokhlin, V.2
  • 29
    • 5244247401 scopus 로고
    • Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions
    • Sep
    • H. Q. Ding, N. Karasawa and W. A. Goddard, "Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions", J. Chemical Physics, vol. 97, no. 6, pp. 4309-4315, Sep. 1992.
    • (1992) J. Chemical Physics , vol.97 , Issue.6 , pp. 4309-4315
    • Ding, H.Q.1    Karasawa, N.2    Goddard, W.A.3
  • 31
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
    • June
    • T. Darden, D. York and L. Pedersen, "Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems", J. Chemical Physics, vol. 98, no. 12, pp. 10089-10092, June 1993.
    • (1993) J. Chemical Physics , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 32
    • 0002467378 scopus 로고
    • Fast Parallel Algorithms for Short-Range Molecular Dynamics
    • Mar
    • S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics", J. Computational Physics, vol. 117, no. 1, pp. 1-19, Mar. 1995.
    • (1995) J. Computational Physics , vol.117 , Issue.1 , pp. 1-19
    • Plimpton, S.1
  • 34
    • 0030172529 scopus 로고    scopus 로고
    • Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems
    • June
    • E. L. Pollock and J. Glosli, "Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems", Computer Physics Communications, vol. 95, no. 2, pp. 93-110, June 1996.
    • (1996) Computer Physics Communications , vol.95 , Issue.2 , pp. 93-110
    • Pollock, E.L.1    Glosli, J.2
  • 36
    • 84860996172 scopus 로고    scopus 로고
    • FHPCA, Edinburgh, U.K, available at
    • FHPCA, Edinburgh, U.K., "The FHPCA website", available at http://www.fhpca.org, 2010.
    • (2010) The FHPCA Website
  • 37
    • 84861005050 scopus 로고    scopus 로고
    • Alpha Data Ltd., Edinburgh, U.K, available at, May
    • Alpha Data Ltd., Edinburgh, U.K., "ADM-XRC-4FX Datasheet", available at http://www.alphadata.co.uk./admadm-xrc-4fx.html, May 2007.
    • (2007) ADM-XRC-4FX Datasheet
  • 38
    • 84861005051 scopus 로고    scopus 로고
    • Nallatech Ltd., Glasgow, U.K, available at, May
    • Nallatech Ltd., Glasgow, U.K., "H100 Series Datasheet", available at http://www.nallatech.com/meadiLibrary/images/english/5595.pdf, May 2007.
    • (2007) H100 Series Datasheet
  • 40
    • 84861008637 scopus 로고    scopus 로고
    • FHPCA, Edinburgh, U.K, available at, Mar
    • FHPCA, Edinburgh, U.K., "PowerPoint presentation", available at http://www.fhpca.org/download/MRSC07-Mar07.ppt, Mar. 2007.
    • (2007) PowerPoint Presentation
  • 41
    • 84861013600 scopus 로고    scopus 로고
    • Argonne National Lab, Argonne, IL, avail able at
    • Argonne National Lab, Argonne, IL, "MPI manual", avail able at http://www.unix.mcs.anl.gov/mpi/www/www3/MPI_Wtime.html, 2009.
    • (2009) MPI Manual
  • 42
    • 84861005538 scopus 로고    scopus 로고
    • OpenCores website, available at
    • OpenCores website, "Floating Point Adder and Multiplier", available at http://opencores.org/project,fpuvhdl, 2009.
    • (2009) Floating Point Adder and Multiplier
  • 43
  • 44
    • 84861000437 scopus 로고    scopus 로고
    • Xilinx Inc., San Jose, CA, available at, May
    • Xilinx Inc., San Jose, CA, "Virtex-4 datasheets", available at http://www.xilinx.com/products/silicon_solutions/fpgas/virtex/virtex4/index.htm, May 2007.
    • (2007) Virtex-4 Datasheets
  • 45
    • 84986471218 scopus 로고
    • Error evaluation in the design of a specialpurpose processor that calculates nonbonded forces in molecular dynamics simulations
    • Sep
    • T. Amisaki, T. Fujiwara, A. Kusumi, H. Miyagawa and K. Kitamura, "Error evaluation in the design of a specialpurpose processor that calculates nonbonded forces in molecular dynamics simulations", J. Computational Chemistry, vol. 16, no. 9, pp. 1120-1130, Sep. 1995.
    • (1995) J. Computational Chemistry , vol.16 , Issue.9 , pp. 1120-1130
    • Amisaki, T.1    Fujiwara, T.2    Kusumi, A.3    Miyagawa, H.4    Kitamura, K.5
  • 47
    • 33846844133 scopus 로고    scopus 로고
    • A case study in porting a production scientific supercomputing application to a reconfigurable computer
    • April
    • V. Kindratenko, D. Pointer, "A case study in porting a production scientific supercomputing application to a reconfigurable computer", Proc. IEEE Symp. Field-Programmable Custom Computing Machines, pp. 13-22, April 2006.
    • (2006) Proc. IEEE Symp. Field-Programmable Custom Computing Machines , pp. 13-22
    • Kindratenko, V.1    Pointer, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.