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Volumn 31, Issue 1, 2005, Pages 1-17

Dual-level parallelism for ab initio molecular dynamics: Reaching teraflop performance with the CPMD code

Author keywords

Car Parrinello molecular dynamics; MPI; OpenMP; Parallelization

Indexed keywords

ALGORITHMS; CHEMICAL REACTIONS; ELECTRONIC STRUCTURE; MICROPROCESSOR CHIPS; PARALLEL PROCESSING SYSTEMS; PHASE TRANSITIONS; PROBABILITY DENSITY FUNCTION; SUPERCOMPUTERS; VECTORS;

EID: 14644432997     PISSN: 01678191     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.parco.2004.12.004     Document Type: Article
Times cited : (60)

References (26)
  • 1
    • 4243606192 scopus 로고
    • Unified approach for molecular dynamics and density-functional theory
    • R. Car, and M. Parrinello Unified approach for molecular dynamics and density-functional theory Physical Review Letters 55 1985 2471 2474
    • (1985) Physical Review Letters , vol.55 , pp. 2471-2474
    • Car, R.1    Parrinello, M.2
  • 2
    • 0000323669 scopus 로고    scopus 로고
    • Ab-initio molecular dynamics: Theory and implementation
    • Modern Methods and Algorithms of Quantum Chemistry, J. Grotendorst FZ Jülich Germany
    • D. Marx, and J. Hutter Ab-initio molecular dynamics: Theory and implementation Modern Methods and Algorithms of Quantum Chemistry J. Grotendorst NIC Series vol. 1 2000 FZ Jülich Germany see also http://www.fz-juelich. de/nic-series/Volume1
    • (2000) NIC Series , vol.1
    • Marx, D.1    Hutter, J.2
  • 3
    • 0033707721 scopus 로고    scopus 로고
    • New advances in chemistry and materials science with CPMD and parallel computing
    • W. Andreoni, and A. Curioni New advances in chemistry and materials science with CPMD and parallel computing Parallel Computing 26 2000 819 842
    • (2000) Parallel Computing , vol.26 , pp. 819-842
    • Andreoni, W.1    Curioni, A.2
  • 4
    • 0036025449 scopus 로고    scopus 로고
    • Ab initio molecular dynamics with density functional theory
    • J.S. Tse Ab initio molecular dynamics with density functional theory Annual Review of Physical Chemistry 53 2002 249 290
    • (2002) Annual Review of Physical Chemistry , vol.53 , pp. 249-290
    • Tse, J.S.1
  • 5
    • 0039304480 scopus 로고
    • Implementation of the Car-Parrinello algorithm for ab initio total energy calculations on a massively parallel computer
    • K.D. Brommer, B.E. Larson, M. Needels, and J.D. Joannopoulos Implementation of the Car-Parrinello algorithm for ab initio total energy calculations on a massively parallel computer Computers in Physics 7 3 1993 350 362
    • (1993) Computers in Physics , vol.7 , Issue.3 , pp. 350-362
    • Brommer, K.D.1    Larson, B.E.2    Needels, M.3    Joannopoulos, J.D.4
  • 6
    • 0026938185 scopus 로고
    • Large-scale ab initio total energy calculations on parallel computers
    • L.J. Clarke, I. Štich, and M.C. Payne Large-scale ab initio total energy calculations on parallel computers Computer Physics Communications 72 1993 14 28
    • (1993) Computer Physics Communications , vol.72 , pp. 14-28
    • Clarke, L.J.1    Štich, I.2    Payne, M.C.3
  • 7
    • 0028445233 scopus 로고
    • A parallel implementation of the Car-Parrinello method by orbital decomposition
    • J. Wiggs, and H. Jónsson A parallel implementation of the Car-Parrinello method by orbital decomposition Computer Physics Communications 81 1994 1 18; J. Wiggs, and H. Jónsson A hybrid decomposition parallel implementation of the Car-Parrinello method Computer Physics Communications 87 1995 319 340
    • (1994) Computer Physics Communications , vol.81 , pp. 1-18
    • Wiggs, J.1    Jónsson, H.2
  • 8
    • 6044219893 scopus 로고
    • A hybrid decomposition parallel implementation of the Car-Parrinello method
    • J. Wiggs, and H. Jónsson A parallel implementation of the Car-Parrinello method by orbital decomposition Computer Physics Communications 81 1994 1 18; J. Wiggs, and H. Jónsson A hybrid decomposition parallel implementation of the Car-Parrinello method Computer Physics Communications 87 1995 319 340
    • (1995) Computer Physics Communications , vol.87 , pp. 319-340
    • Wiggs, J.1    Jónsson, H.2
  • 9
  • 11
    • 14644425357 scopus 로고    scopus 로고
    • Copyright IBM Corp. 1990-2003, Copyright MPI für Festkörperforschung, Stuttgart
    • CPMD V3.8, Copyright IBM Corp. 1990-2003, Copyright MPI für Festkörperforschung, Stuttgart, 1997-2001. See also http://www.cpmd.org
    • (1997) CPMD V3.8
  • 12
  • 13
    • 18344379950 scopus 로고    scopus 로고
    • Water molecule dipole in the gas and in the liquid phase
    • P.L. Silvestrelli, and M. Parrinello Water molecule dipole in the gas and in the liquid phase Physical Review Letters 82 1999 3308 3311
    • (1999) Physical Review Letters , vol.82 , pp. 3308-3311
    • Silvestrelli, P.L.1    Parrinello, M.2
  • 14
    • 0037338058 scopus 로고    scopus 로고
    • Excited state nuclear forces from the Tamm-Dancoff approximation to time-dependent density functional theory within the plane wave basis set framework
    • J. Hutter Excited state nuclear forces from the Tamm-Dancoff approximation to time-dependent density functional theory within the plane wave basis set framework Journal of Chemical Physics 118 2003 3928 3934
    • (2003) Journal of Chemical Physics , vol.118 , pp. 3928-3934
    • Hutter, J.1
  • 16
    • 0000671855 scopus 로고    scopus 로고
    • Efficient and general algorithms for path integral Car-Parrinello molecular dynamics
    • M.E. Tuckerman, D. Marx, M.L. Klein, and M. Parrinello Efficient and general algorithms for path integral Car-Parrinello molecular dynamics Journal of Chemical Physics 104 1996 5579 5588
    • (1996) Journal of Chemical Physics , vol.104 , pp. 5579-5588
    • Tuckerman, M.E.1    Marx, D.2    Klein, M.L.3    Parrinello, M.4
  • 17
    • 0000928098 scopus 로고    scopus 로고
    • A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
    • M. Eichinger, P. Tavan, J. Hutter, and M. Parrinello A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields Journal of Chemical Physics 110 1999 10452 10467; A. Laio, J. VandeVondele, and U. Rothlisberger A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations Journal of Chemical Physics 116 2002 6941 6947; T. Mordasini, A. Curioni, and W. Andreoni Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of Bam HI restriction endonuclease from combined quantum-classical simulations Journal of Biological Chemistry 287 2003 4381 4384; D. Fischer, A. Curioni, and W. Andreoni Decanethiols on gold: The structure of self-assembled monolayers unravelled with computer simulations Langmuir 19 2003 3567 3571
    • (1999) Journal of Chemical Physics , vol.110 , pp. 10452-10467
    • Eichinger, M.1    Tavan, P.2    Hutter, J.3    Parrinello, M.4
  • 18
    • 0037156101 scopus 로고    scopus 로고
    • A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
    • M. Eichinger, P. Tavan, J. Hutter, and M. Parrinello A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields Journal of Chemical Physics 110 1999 10452 10467; A. Laio, J. VandeVondele, and U. Rothlisberger A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations Journal of Chemical Physics 116 2002 6941 6947; T. Mordasini, A. Curioni, and W. Andreoni Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of Bam HI restriction endonuclease from combined quantum-classical simulations Journal of Biological Chemistry 287 2003 4381 4384; D. Fischer, A. Curioni, and W. Andreoni Decanethiols on gold: The structure of self-assembled monolayers unravelled with computer simulations Langmuir 19 2003 3567 3571
    • (2002) Journal of Chemical Physics , vol.116 , pp. 6941-6947
    • Laio, A.1    Vandevondele, J.2    Rothlisberger, U.3
  • 19
    • 0038136893 scopus 로고    scopus 로고
    • Why do divalent metal ions either promote or inhibit enzymatic reactions? the case of Bam HI restriction endonuclease from combined quantum-classical simulations
    • M. Eichinger, P. Tavan, J. Hutter, and M. Parrinello A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields Journal of Chemical Physics 110 1999 10452 10467; A. Laio, J. VandeVondele, and U. Rothlisberger A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations Journal of Chemical Physics 116 2002 6941 6947; T. Mordasini, A. Curioni, and W. Andreoni Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of Bam HI restriction endonuclease from combined quantum-classical simulations Journal of Biological Chemistry 287 2003 4381 4384; D. Fischer, A. Curioni, and W. Andreoni Decanethiols on gold: The structure of self-assembled monolayers unravelled with computer simulations Langmuir 19 2003 3567 3571
    • (2003) Journal of Biological Chemistry , vol.287 , pp. 4381-4384
    • Mordasini, T.1    Curioni, A.2    Andreoni, W.3
  • 20
    • 0038342171 scopus 로고    scopus 로고
    • Decanethiols on gold: The structure of self-assembled monolayers unravelled with computer simulations
    • M. Eichinger, P. Tavan, J. Hutter, and M. Parrinello A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields Journal of Chemical Physics 110 1999 10452 10467; A. Laio, J. VandeVondele, and U. Rothlisberger A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations Journal of Chemical Physics 116 2002 6941 6947; T. Mordasini, A. Curioni, and W. Andreoni Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of Bam HI restriction endonuclease from combined quantum-classical simulations Journal of Biological Chemistry 287 2003 4381 4384; D. Fischer, A. Curioni, and W. Andreoni Decanethiols on gold: The structure of self-assembled monolayers unravelled with computer simulations Langmuir 19 2003 3567 3571
    • (2003) Langmuir , vol.19 , pp. 3567-3571
    • Fischer, D.1    Curioni, A.2    Andreoni, W.3
  • 21
    • 0000251219 scopus 로고
    • Integrating the Car-Parrinello equations. I. Basic integration techniques
    • M.E. Tuckerman, and M. Parrinello Integrating the Car-Parrinello equations. I. Basic integration techniques Journal of Chemical Physics 101 1994 1302 1315
    • (1994) Journal of Chemical Physics , vol.101 , pp. 1302-1315
    • Tuckerman, M.E.1    Parrinello, M.2
  • 22
    • 0027642189 scopus 로고
    • Rotating a three-dimensional array in an optimal position for vector processing: Case study for a three-dimensional fast Fourier transform
    • S. Goedecker Rotating a three-dimensional array in an optimal position for vector processing: Case study for a three-dimensional fast Fourier transform Computer Physics Communications 76 1993 294 300
    • (1993) Computer Physics Communications , vol.76 , pp. 294-300
    • Goedecker, S.1
  • 24
    • 14644429136 scopus 로고    scopus 로고
    • The HPCx Consortium, namely UoE HPCX Ltd, is led by the University of Edinburgh (www.ed.ac.uk), with the Central Laboratory for the Research Councils (CLRC) (www.clrc.ac.uk) and IBM (www.ibm.com). The project is funded by EPSRC (www.epsrc.ac.uk)
    • http://www.hpcx.ac.uk The HPCx Consortium, namely UoE HPCX Ltd, is led by the University of Edinburgh (www.ed.ac.uk), with the Central Laboratory for the Research Councils (CLRC) (www.clrc.ac.uk) and IBM (www.ibm.com). The project is funded by EPSRC (www.epsrc.ac.uk)
  • 26
    • 14644406307 scopus 로고    scopus 로고
    • HPC computing: Strategy and directions
    • Göttingen, Germany, 4 March
    • P. Williams, HPC computing: Strategy and directions, Presentation at Scicomp7 Meeting, Göttingen, Germany, 4 March 2003
    • (2003) Scicomp7 Meeting
    • Williams, P.1


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