DOI: 10.1016/j.cpc.2011.01.009. Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision

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

10.1016/j.cpc.2011.01.009

Crossref journal-article

Elsevier BV

Computer Physics Communications (78)

Bibliography

Colberg, P. H., & HÃ¶fling, F. (2011). Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision. Computer Physics Communications, 182(5), 1120â1129.

Authors 2

Peter H. Colberg (first)
Felix Höfling (additional)

References 36 Referenced 65

10.1016/j.jcp.2008.01.047 / J. Comp. Phys. / General purpose molecular dynamics simulations fully implemented on graphics processing units by Anderson (2008)
10.1080/08927020701744295 / Mol. Simul. / Harvesting graphics power for MD simulations by van Meel (2008)
10.1016/j.cpc.2008.05.008 / Comput. Phys. Commun. / Accelerating molecular dynamics simulations using graphics processing units with CUDA by Liu (2008)
10.1002/jcc.20829 / J. Comput. Chem. / Accelerating molecular modeling applications with graphics processors by Stone (2007)
10.1016/j.jcp.2006.06.039 / J. Comp. Phys. / GPU accelerated molecular dynamics simulation of thermal conductivities by Yang (2007)
{'key': '10.1016/j.cpc.2011.01.009_br0060', 'article-title': 'Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units', 'volume': 'vol. 6', 'author': 'Xu', 'year': '2010'} / Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units by Xu (2010)
10.1021/ja9090353 / J. Am. Chem. Soc. / Molecular simulation of ab initio protein folding for a millisecond folder NTL9(139) by Voelz (2010)
10.1021/ct9000685 / J. Chem. Theory Comput. / ACEMD: Accelerating biomolecular dynamics in the microsecond time scale by Harvey (2009)
10.1016/j.jcp.2009.03.018 / J. Comp. Phys. / GPU accelerated Monte Carlo simulation of the 2D and 3D Ising model by Preis (2009)
10.1016/j.cpc.2010.05.005 / Comput. Phys. Commun. / Multi-GPU accelerated multi-spin Monte Carlo simulations of the 2D Ising model by Block (2010)
{'key': '10.1016/j.cpc.2011.01.009_br0110', 'article-title': 'Complex Dynamics of Glass-Forming Liquids: A Mode-Coupling Theory', 'author': 'Götze', 'year': '2009'} / Complex Dynamics of Glass-Forming Liquids: A Mode-Coupling Theory by Götze (2009)
10.1103/PhysRevLett.104.205704 / Phys. Rev. Lett. / Probing a critical length scale at the glass transition by Mosayebi (2010)
10.1103/PhysRevLett.105.217801 / Phys. Rev. Lett. / Dynamic heterogeneity in a glass forming fluid: susceptibility, structure factor, and correlation length by Flenner (2010)
{'key': '10.1016/j.cpc.2011.01.009_br0140', 'series-title': 'The Art of Molecular Dynamics Simulation', 'author': 'Rapaport', 'year': '2004'} / The Art of Molecular Dynamics Simulation by Rapaport (2004)
{'key': '10.1016/j.cpc.2011.01.009_br0150', 'series-title': 'The Art of Computer Programming, vol. 3, Sorting and Searching', 'author': 'Knuth', 'year': '1998'} / The Art of Computer Programming, vol. 3, Sorting and Searching by Knuth (1998)
{'key': '10.1016/j.cpc.2011.01.009_br0160', 'first-page': '712', 'article-title': 'Radix sort for vector multiprocessors', 'author': 'Zagha', 'year': '1991'} / Radix sort for vector multiprocessors by Zagha (1991)
NVIDIA CUDA SDK code samples, 2009, http://developer.download.nvidia.com/compute/cuda/sdk/website/samples.html.
10.1080/0020739930240405 / Int. J. Math. Educ. Sci. Technol. / A three-dimensional Hilbert curve by Sagan (1993)
J. Wang, J. Shan, Space-filling curve based point clouds index, in: Proceedings of the 8th International Conference on GeoComputation, University of Michigan, 2005.
10.1007/BF01397083 / Numer. Math. / A floating-point technique for extending the available precision by Dekker (1971)
{'key': '10.1016/j.cpc.2011.01.009_br0210', 'series-title': 'The Art of Computer Programming, vol. 2, Seminumerical Algorithms', 'author': 'Knuth', 'year': '1997'} / The Art of Computer Programming, vol. 2, Seminumerical Algorithms by Knuth (1997)
IEEE standard for binary floating-point arithmetic, ANSI/IEEE Std 754-1985.
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.
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].
D.H. Bailey, Fortran-90 double-single package, 2005, http://crd.lbl.gov/~dhbailey/mpdist.
{'key': '10.1016/j.cpc.2011.01.009_br0260', 'series-title': 'Theory of Simple Liquids', 'author': 'Hansen', 'year': '2006'} / Theory of Simple Liquids by Hansen (2006)
{'key': '10.1016/j.cpc.2011.01.009_br0270', 'series-title': 'Understanding Molecular Simulation', 'author': 'Frenkel', 'year': '2001'} / Understanding Molecular Simulation by Frenkel (2001)
10.1006/jcph.1995.1039 / J. Comp. Phys. / Fast parallel algorithms for short-range molecular dynamics by Plimpton (1995)
NVIDIA CUDA programming guide version 2.2.
P.H. Colberg, F. Höfling, HALMD—highly accelerated large-scale molecular dynamics package, http://research.colberg.org/projects/halmd.
10.1063/1.1674820 / J. Chem. Phys. / Role of repulsive forces in determining the equilibrium structure of simple liquids by Weeks (1971)
10.1063/1.2431176 / J. Chem. Phys. / A common, avoidable source of error in molecular dynamics integrators by Lippert (2007)
10.1103/PhysRevLett.73.1376 / Phys. Rev. Lett. / Scaling behavior in the β-relaxation regime of a supercooled Lennard-Jones mixture by Kob (1994)
10.1103/PhysRevE.51.4626 / Phys. Rev. E / Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture. I: The van Hove correlation function by Kob (1995)
10.1103/PhysRevE.52.4134 / Phys. Rev. E / Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture. II. Intermediate scattering function and dynamic susceptibility by Kob (1995)
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.

Dates

Type	When
Created	14 years, 7 months ago (Jan. 22, 2011, 4:24 a.m.)
Deposited	4 years, 5 months ago (April 3, 2021, 4:12 a.m.)
Indexed	3 months, 3 weeks ago (May 12, 2025, 6:21 p.m.)
Issued	14 years, 4 months ago (May 1, 2011)
Published	14 years, 4 months ago (May 1, 2011)
Published Print	14 years, 4 months ago (May 1, 2011)

Funders 0

None

BibTeX

@article{Colberg_2011, title={Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision}, volume={182}, ISSN={0010-4655}, url={http://dx.doi.org/10.1016/j.cpc.2011.01.009}, DOI={10.1016/j.cpc.2011.01.009}, number={5}, journal={Computer Physics Communications}, publisher={Elsevier BV}, author={Colberg, Peter H. and Höfling, Felix}, year={2011}, month=may, pages={1120–1129} }

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