메뉴 건너뛰기




Volumn , Issue , 2008, Pages 143-150

Overheads in accelerating molecular dynamics simulations with GPUs

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER HARDWARE; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; VAN DER WAALS FORCES;

EID: 58249097973     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/PDCAT.2008.68     Document Type: Conference Paper
Times cited : (6)

References (24)
  • 1
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • M. Karplus and J. A. McCammon, "Molecular dynamics simulations of biomolecules", Nat. Struct. Biol., 9, (2002), pp 646-52.
    • (2002) Nat. Struct. Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 2
  • 3
    • 38349098051 scopus 로고    scopus 로고
    • A High-Speed Special-Purpose Computer for Molecular Dynamics Simulations: MDGRAPE-3
    • Proceedings of NIC Workshop 2006, From Computational Biophysics to Systems Biology, Julich
    • T. Narumi, Y. Ohno, N. Futatsugi, N. Okimoto, A. Suenaga, R. Yanai, and M. Taiji, "A High-Speed Special-Purpose Computer for Molecular Dynamics Simulations: MDGRAPE-3", In Proceedings of NIC Workshop 2006, From Computational Biophysics to Systems Biology, Julich, NIC Series, 34, (2006), pp. 29-35.
    • (2006) NIC Series , vol.34 , pp. 29-35
    • Narumi, T.1    Ohno, Y.2    Futatsugi, N.3    Okimoto, N.4    Suenaga, A.5    Yanai, R.6    Taiji, M.7
  • 5
    • 58249116176 scopus 로고    scopus 로고
    • Jun
    • http://www.playstation.com/ (Jun. 2008)
    • (2008)
  • 6
    • 58249121212 scopus 로고    scopus 로고
    • http://www.nvidia.com/object/cuda learn products.html (Jun. 2008)
    • http://www.nvidia.com/object/cuda learn products.html (Jun. 2008)
  • 7
  • 9
    • 0033593647 scopus 로고    scopus 로고
    • Computational Physics - Astrophysics on the GRAPE Family of Special-Purpose Computers
    • P. Hut, and J. Makino, "Computational Physics - Astrophysics on the GRAPE Family of Special-Purpose Computers", Science, 283, 5401 (1999), pp 501-505.
    • (1999) Science , vol.283 , Issue.5401 , pp. 501-505
    • Hut, P.1    Makino, J.2
  • 10
    • 85140869206 scopus 로고    scopus 로고
    • Accelerating molecular dynamics simulations on PLAYSTATION 3 using 'Virtual-GRAPE' programming model
    • in press
    • T. Narumi, S. Kameoka, M. Taiji, and K. Yasuoka, "Accelerating molecular dynamics simulations on PLAYSTATION 3 using 'Virtual-GRAPE' programming model", SIAM Journal on Scientific Computing, in press.
    • SIAM Journal on Scientific Computing
    • Narumi, T.1    Kameoka, S.2    Taiji, M.3    Yasuoka, K.4
  • 11
    • 47749153637 scopus 로고    scopus 로고
    • The Chamomile Scheme: An optimized algorithm for N-body simulations on programmable graphics processing units
    • astro-ph/073100
    • T. Hamada and T. Iitaka, "The Chamomile Scheme: An optimized algorithm for N-body simulations on programmable graphics processing units", ArXiv Astrophysics e-prints, astro-ph/073100, (2007).
    • (2007) ArXiv Astrophysics e-prints
    • Hamada, T.1    Iitaka, T.2
  • 12
    • 44849094749 scopus 로고    scopus 로고
    • Fast N-body simulation with CUDA
    • edited by H. Nguyen, AddisonWesley
    • L. Nyland, M. Harris, and J. Prins, "Fast N-body simulation with CUDA", GPU Gems 3, edited by H. Nguyen, AddisonWesley, (2007), pp 677-695.
    • (2007) GPU Gems 3 , pp. 677-695
    • Nyland, L.1    Harris, M.2    Prins, J.3
  • 13
    • 58249095581 scopus 로고    scopus 로고
    • Jun
    • http://progrape.jp/cs/ (Jun. 2008)
    • (2008)
  • 16
    • 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", Journal of Computational Physics, 227,10, (2008), pp 5342-5359.
    • (2008) Journal of Computational Physics , vol.227 , Issue.10 , pp. 5342-5359
    • Anderson, J.A.1    Lorenz, C.D.2    Travesset, A.3
  • 17
    • 33751225374 scopus 로고    scopus 로고
    • Performance tuning of JV-body codes on modern microprocessors: I. Direct integration with a hermite scheme on x86.64 architecture
    • K. Nitadori, J. Makino and P. Hut, "Performance tuning of JV-body codes on modern microprocessors: I. Direct integration with a hermite scheme on x86.64 architecture", New Astron., 12,3 (2006), pp. 169-181.
    • (2006) New Astron , vol.12 , Issue.3 , pp. 169-181
    • Nitadori, K.1    Makino, J.2    Hut, P.3
  • 18
    • 58249118340 scopus 로고    scopus 로고
    • Jun
    • http://grape.astron.s.u-tokyo.ac.jp/~nitadori/phantom/ (Jun. 2008)
    • (2008)
  • 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 (1971), pp 224-242.
    • (1971) Numer. Math , vol.18 , pp. 224-242
    • Dekker, T.J.1
  • 21
    • 58249098037 scopus 로고    scopus 로고
    • High-accuracy N-body simulations on GPU
    • Princeton
    • K. Nitadori, "High-accuracy N-body simulations on GPU", Poster in AstroGPU 2007, Princeton, (2007).
    • (2007) Poster in AstroGPU 2007
    • Nitadori, K.1
  • 22
    • 58249106417 scopus 로고    scopus 로고
    • D. A. Case, T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. W. Caldwell, W. S. Ross, P. A. Kollman, Amber 8.0, University of California San Francisco (2004).
    • D. A. Case, T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. W. Caldwell, W. S. Ross, P. A. Kollman, Amber 8.0, University of California San Francisco (2004).
  • 23
    • 58249117249 scopus 로고    scopus 로고
    • Pentium Pro Inside: I. A Treecode at 430 Gigaflops on ASCI Red II. Price/Performance of $50/Mflop on Loki and Hyglac
    • San Jose, CD-ROM
    • M. S. Warren, J. K. Salmon, D. J. Becker, M. P. Goda, T. Sterling, "Pentium Pro Inside: I. A Treecode at 430 Gigaflops on ASCI Red II. Price/Performance of $50/Mflop on Loki and Hyglac", In Proceedings of SC97, San Jose, (1997), CD-ROM.
    • (1997) Proceedings of SC97
    • Warren, M.S.1    Salmon, J.K.2    Becker, D.J.3    Goda, M.P.4    Sterling, T.5
  • 24
    • 33846823909 scopus 로고
    • Particle Mesh Ewald: An N Log(N) Method for Ewald Sums in Large Systems
    • T. Darden, D. York, and L. Pedersen, "Particle Mesh Ewald: An N Log(N) Method for Ewald Sums in Large Systems", J. Chem. Phys., 98(12) (1993), pp. 10089-10092.
    • (1993) J. Chem. Phys , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.