메뉴 건너뛰기




Volumn 182, Issue 5, 2011, Pages 1120-1129

Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision

Author keywords

Dynamics of supercooled liquids; GPU computing; Molecular dynamics simulations

Indexed keywords

ACCELERATED SIMULATIONS; COMPUTING RESOURCE; CRITICAL PARTS; FLOATING POINTS; FLOATING-POINT ARITHMETIC; GLASSY DYNAMICS; GPU COMPUTING; GRAPHICS PROCESSING UNITS; LENNARD JONES FLUID; LENNARD-JONES MIXTURES; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MOMENTUM CONSERVATIONS; PROGRAMMING INTERFACE; SLOW DYNAMICS; SPEED-UP FACTORS; SPEED-UPS; SUPERCOOLED LIQUIDS; SYSTEM SIZE; TIME STABILITY;

EID: 79952004866     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2011.01.009     Document Type: Article
Times cited : (72)

References (36)
  • 1
    • 41249087856 scopus 로고    scopus 로고
    • General purpose molecular dynamics simulations fully implemented on graphics processing units
    • J.A. Anderson, C.D. Lorenz, and A. Travesset General purpose molecular dynamics simulations fully implemented on graphics processing units J. Comp. Phys. 227 10 2008 5342 5359
    • (2008) J. Comp. Phys. , vol.227 , Issue.10 , pp. 5342-5359
    • Anderson, J.A.1    Lorenz, C.D.2    Travesset, A.3
  • 3
    • 52949096873 scopus 로고    scopus 로고
    • Accelerating molecular dynamics simulations using graphics processing units with CUDA
    • W. Liu, B. Schmidt, G. Voss, and W. Müller-Wittig Accelerating molecular dynamics simulations using graphics processing units with CUDA Comput. Phys. Commun. 179 9 2008 634 641
    • (2008) Comput. Phys. Commun. , vol.179 , Issue.9 , pp. 634-641
    • Liu, W.1    Schmidt, B.2    Voss, G.3    Müller-Wittig, W.4
  • 5
    • 33846339776 scopus 로고    scopus 로고
    • GPU accelerated molecular dynamics simulation of thermal conductivities
    • J. Yang, Y. Wang, and Y. Chen GPU accelerated molecular dynamics simulation of thermal conductivities J. Comp. Phys. 221 2 2007 799 804
    • (2007) J. Comp. Phys. , vol.221 , Issue.2 , pp. 799-804
    • Yang, J.1    Wang, Y.2    Chen, Y.3
  • 6
    • 77955764321 scopus 로고    scopus 로고
    • Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units
    • Elsevier
    • D. Xu, M.J. Williamson, and R.C. Walker Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units Annual Reports in Computational Chemistry vol. 6 2010 Elsevier pp. 2-19
    • (2010) Annual Reports in Computational Chemistry , vol.6
    • Xu, D.1    Williamson, M.J.2    Walker, R.C.3
  • 7
    • 76149136021 scopus 로고    scopus 로고
    • Molecular simulation of ab initio protein folding for a millisecond folder NTL9(139)
    • V.A. Voelz, G.R. Bowman, K. Beauchamp, and V.S. Pande Molecular simulation of ab initio protein folding for a millisecond folder NTL9(139) J. Am. Chem. Soc. 132 5 2010 1526 1528 pMID: 20070076
    • (2010) J. Am. Chem. Soc. , vol.132 , Issue.5 , pp. 1526-1528
    • Voelz, V.A.1    Bowman, G.R.2    Beauchamp, K.3    Pande, V.S.4
  • 8
    • 67650099787 scopus 로고    scopus 로고
    • ACEMD: Accelerating biomolecular dynamics in the microsecond time scale
    • M.J. Harvey, G. Giupponi, and G.D. Fabritiis ACEMD: Accelerating biomolecular dynamics in the microsecond time scale J. Chem. Theory Comput. 5 6 2009 1632 1639
    • (2009) J. Chem. Theory Comput. , vol.5 , Issue.6 , pp. 1632-1639
    • Harvey, M.J.1    Giupponi, G.2    Fabritiis, G.D.3
  • 9
    • 67349267818 scopus 로고    scopus 로고
    • GPU accelerated Monte Carlo simulation of the 2D and 3D Ising model
    • T. Preis, P. Virnau, W. Paul, and J.J. Schneider GPU accelerated Monte Carlo simulation of the 2D and 3D Ising model J. Comp. Phys. 228 12 2009 4468 4477
    • (2009) J. Comp. Phys. , vol.228 , Issue.12 , pp. 4468-4477
    • Preis, T.1    Virnau, P.2    Paul, W.3    Schneider, J.J.4
  • 10
    • 77955307017 scopus 로고    scopus 로고
    • Multi-GPU accelerated multi-spin Monte Carlo simulations of the 2D Ising model
    • B. Block, P. Virnau, and T. Preis Multi-GPU accelerated multi-spin Monte Carlo simulations of the 2D Ising model Comput. Phys. Commun. 181 9 2010 1549 1556
    • (2010) Comput. Phys. Commun. , vol.181 , Issue.9 , pp. 1549-1556
    • Block, B.1    Virnau, P.2    Preis, T.3
  • 11
    • 84921925775 scopus 로고    scopus 로고
    • Complex Dynamics of Glass-Forming Liquids: A Mode-Coupling Theory
    • Oxford University Press Oxford
    • W. Götze Complex Dynamics of Glass-Forming Liquids: A Mode-Coupling Theory International Series of Monographs on Physics 2009 Oxford University Press Oxford
    • (2009) International Series of Monographs on Physics
    • Götze, W.1
  • 12
    • 77953092737 scopus 로고    scopus 로고
    • Probing a critical length scale at the glass transition
    • M. Mosayebi, E. Del Gado, P. Ilg, and H.C. Öttinger Probing a critical length scale at the glass transition Phys. Rev. Lett. 104 20 2010 205704
    • (2010) Phys. Rev. Lett. , vol.104 , Issue.20 , pp. 205704
    • Mosayebi, M.1    Del Gado, E.2    Ilg, P.3    Öttinger, H.C.4
  • 13
    • 78349272359 scopus 로고    scopus 로고
    • Dynamic heterogeneity in a glass forming fluid: Susceptibility, structure factor, and correlation length
    • E. Flenner, and G. Szamel Dynamic heterogeneity in a glass forming fluid: susceptibility, structure factor, and correlation length Phys. Rev. Lett. 105 21 2010 217801
    • (2010) Phys. Rev. Lett. , vol.105 , Issue.21 , pp. 217801
    • Flenner, E.1    Szamel, G.2
  • 17
    • 77955723319 scopus 로고    scopus 로고
    • NVIDIA CUDA SDK code samples, 2009, http://developer.download.nvidia.com/ compute/cuda/sdk/website/samples.html.
    • (2009) NVIDIA CUDA SDK Code Samples
  • 18
    • 0001248480 scopus 로고
    • A three-dimensional Hilbert curve
    • H. Sagan A three-dimensional Hilbert curve Int. J. Math. Educ. Sci. Technol. 24 4 1993 541 545
    • (1993) Int. J. Math. Educ. Sci. Technol. , vol.24 , Issue.4 , pp. 541-545
    • Sagan, H.1
  • 20
    • 0000810983 scopus 로고
    • A floating-point technique for extending the available precision
    • T.J. Dekker A floating-point technique for extending the available precision Numer. Math. 18 3 1971 224 242
    • (1971) Numer. Math. , vol.18 , Issue.3 , pp. 224-242
    • Dekker, T.J.1
  • 22
    • 79952003681 scopus 로고    scopus 로고
    • IEEE standard for binary floating-point arithmetic, ANSI/IEEE Std 754-1985
    • IEEE standard for binary floating-point arithmetic, ANSI/IEEE Std 754-1985.
  • 23
    • 33751029285 scopus 로고    scopus 로고
    • Basic building blocks for a triple-double intermediate format
    • INRIA, September
    • C.Q. Lauter, Basic building blocks for a triple-double intermediate format, Tech. Rep. RR-5702, INRIA, September 2005, http://hal.inria.fr/inria- 00070314/en.
    • (2005) Tech. Rep. RR-5702
    • Lauter, C.Q.1
  • 24
    • 34250374503 scopus 로고    scopus 로고
    • Implementation of float-float operators on graphics hardware
    • Nancy, France arXiv:cs/0603115v1[cs.AR]
    • G.D. Graçca, D. Defour, Implementation of float-float operators on graphics hardware, in: 7th Conference on Real Numbers and Computers, Nancy, France, 2006, arXiv:cs/0603115v1 [cs.AR].
    • (2006) 7th Conference on Real Numbers and Computers
    • Graçca, G.D.1
  • 28
    • 0002467378 scopus 로고
    • Fast parallel algorithms for short-range molecular dynamics
    • S.J. Plimpton Fast parallel algorithms for short-range molecular dynamics J. Comp. Phys. 117 1995 1 19 http://lammps.sandia.gov
    • (1995) J. Comp. Phys. , vol.117 , pp. 1-19
    • Plimpton, S.J.1
  • 29
    • 79952003643 scopus 로고    scopus 로고
    • NVIDIA CUDA programming guide version 2.2
    • NVIDIA CUDA programming guide version 2.2.
  • 31
    • 36849103820 scopus 로고
    • Role of repulsive forces in determining the equilibrium structure of simple liquids
    • J.D. Weeks, D. Chandler, and H.C. Andersen Role of repulsive forces in determining the equilibrium structure of simple liquids J. Chem. Phys. 54 12 1971 5237 5247
    • (1971) J. Chem. Phys. , vol.54 , Issue.12 , pp. 5237-5247
    • Weeks, J.D.1    Chandler, D.2    Andersen, H.C.3
  • 33
    • 4243306133 scopus 로고
    • Scaling behavior in the β-relaxation regime of a supercooled Lennard-Jones mixture
    • W. Kob, and H.C. Andersen Scaling behavior in the β-relaxation regime of a supercooled Lennard-Jones mixture Phys. Rev. Lett. 73 10 1994 1376 1379 (Pubitemid 24975870)
    • (1994) Physical Review Letters , vol.73 , Issue.10 , pp. 1376-1379
    • Kob, W.1    Andersen, H.C.2
  • 34
    • 6144288607 scopus 로고
    • Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture. I: The van Hove correlation function
    • W. Kob, and H.C. Andersen Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture. I: The van Hove correlation function Phys. Rev. E 51 5 1995 4626 4641
    • (1995) Phys. Rev. e , vol.51 , Issue.5 , pp. 4626-4641
    • Kob, W.1    Andersen, H.C.2
  • 35
    • 6444235056 scopus 로고
    • Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture. II. Intermediate scattering function and dynamic susceptibility
    • W. Kob, and H.C. Andersen Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture. II. Intermediate scattering function and dynamic susceptibility Phys. Rev. E 52 4 1995 4134 4153
    • (1995) Phys. Rev. e , vol.52 , Issue.4 , pp. 4134-4153
    • Kob, W.1    Andersen, H.C.2
  • 36
    • 79952008335 scopus 로고    scopus 로고
    • Lorentz-like power-law decay of velocity anti-correlations in a supercooled liquid
    • Rome
    • F. Höfling, P.H. Colberg, Lorentz-like power-law decay of velocity anti-correlations in a supercooled liquid, in: Abstracts of the International Workshop on Dynamics in Viscous Liquids, Rome, 2011, http://www.viscous-liquids. de.
    • (2011) Abstracts of the International Workshop on Dynamics in Viscous Liquids
    • Höfling, F.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.