GPGPU supported cooperative acceleration in molecular dynamics

Proceedings of the 2009 13th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2009

Volumn , Issue , 2009, Pages 113-118

  Chen, Gang ^a   Li, Guobo ^a   Pei, Songwen ^a   Wu, Baifeng ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

Brook+; GPGPU; GPU; Molecular dynamics (MD)

Indexed keywords

ATOMIC LEVELS; BROOK+; COMPUTATIONAL APPROACH; COMPUTATIONAL REQUIREMENTS; COMPUTATIONAL TIME; COMPUTING RESOURCE; GENERAL PURPOSE; GPGPU; GPU; GRAPHICS PROCESSING UNIT; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; PERFORMANCE/COST RATIO; PHYSICAL PHENOMENA; PROGRAMMABILITY; PROGRAMMING ENVIRONMENT; SCIENTIFIC APPLICATIONS; SEQUENTIAL IMPLEMENTATION; TIME-SCALES;

DYNAMICS; GROUPWARE; INTERACTIVE COMPUTER SYSTEMS; MOLECULAR DYNAMICS; PARALLEL ALGORITHMS;

PROGRAM PROCESSORS;

EID: 69649106850     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSCWD.2009.4968044     Document Type: Conference Paper

References (24)

1. John D. Owens, David Luebke, Naga Govindaraju, Mark Harris, Jens Krüger, Aaron E. Lefohn, Timothy J. Purcell, A survey of general-purpose computation on graphics hardware, Computer Graphics Forum 34 (March) (2007) 80-113. (Pubitemid 46481097)
2. SENGUPTA S., HARRIS M., ZHANG Y., OWENS J. D.: Scan Primitives for GPU Computing. In Graphics Hardware 2007 (Aug. 2007), ACM, pp. 97-106.
3. Daniel Horn Jeremy Sugerman Kayvon Fatahalian Mike Houston Ian Buck, Tim Foley and Pat Hanrahan. Brook for GPUs: Stream Computing on Graphics Hardware. Computer Science Department, Stanford University, SIGGRAPH, 2004.
4. J. Bolz, I. Farmer, E. Grinspun, and P. Schröder. Sparse matrix solvers on the GPU: conjugate gradients and multigrid. ACM Trans. Graph. (SIGGRAPH), 22(3):917-924, 2003.
5. J. Krüger and R. Westermann. Linear algebra operators for GPU implementation of numerical algorithms. ACM Trans. Graph. (SIGGRAPH), 22(3):908-916, 2003.
6. Moreland, K., Angel, E.: The fft on a GPU. In: Proceedings SIGGRAPH/ Eurographics Workshop on Graphics Hardware, pp. 112-119 (2003)
7. RUDOMY N, T., MILLAN, E., and HERNANDEZ, B. 2005. Fragment shaders for agent animation using finite state machines. Simulation Modelling Practice and Theory 13(8), 741-751. (Pubitemid 41400658)
8. M. Macedonia, The GPU enters computing's mainstream, IEEE Computer 36 (2003) 106-108.
9. D.C. Rapaport, The Art of Molecular Dynamics Simulation, second ed., University Press, Cambridge, 2004.
10. S. J. Plimpton. Computational Limits of Classical Molecular-Dynamics Simulations, Computational Materials Science, 1995.
11. B. A. Hendrickson S. J. Plimpton. Parallel Molecular Dynamics Algorithms for Simulation of Molecular Systems. American Chemical Society, Symposium Series 592, 1995.
12. M.P. Allen, Introduction to molecular dynamics simulation, in: Computational Soft Matter-From Synthetic Polymers to Proteins, NIC Series, vol.23, John von Neumann Institute for Computing, 2004.
13. T. Maximova, C. Keasar, A novel algorithm for nonbonded-list updating in molecular simulations, J. Comp. Biol. 13 (2006) 1041-1048.
14. S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, Journal of Computational Physics 117 (1995) 1-19.
15. J.E. Lennard-Jones, Cohesion, in: Proceedings of Physical Society, 1931, pp. 461-482.
16. AMD Stream Computing SDK User Guide. URL http://ati.amd.com/technology/ streamcomputing/Stream-Computing-User-Guide.pdf
17. B.G. Fitch, et al., Blue matter: Strong scaling of molecular dynamics on blue Gene/L, in: Proc. International Conf. on Computational Science (ICCS 2006), in: LNCS, vol.3992, Springer-Verlag, 2006, pp. 846-854. (Pubitemid 44152593)
18. K.J. Bowers, et al., Scalable Algorithms for molecular dynamics simulations on commodity clusters, in: Proc. ACM/IEEE Conf. on Supercomputing (SC06) Tampa, FL, 2006.
19. M. Taufer, C. An, A. Kerstens, C.L. Brooks III, Predictor@Home: A protein structure prediction supercomputer based on global computing, IEEE Transactions on Parallel and Distributed Systems 17 (8) (2006) 786-796.
20. D.E. Shaw, et al., Anton: A special-purpose machine for molecular dynamics simulation, in: Proceedings of the 34th Annual International Symposium on Computer Architecture, San Diego, California, 2007.
21. S. Toyoda, Development of MD engine: High-speed accelerator with parallel processor design for molecular dynamics simulations, Journal Computational. Chemistry 20 (1999) 185-199. (Pubitemid 129653027)
22. W.G. Liu, B. Schmidt, Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA, Computer Physics Communications Volume179, Issue 9, 1 November 2008, Pages 634-641.
23. J. Yang, Y. Wang, Y.C. Chen, GPU accelerated molecular dynamics simulation of thermal conductivities, Journal of Computational Physics 221 (2) (2007) 799-804. (Pubitemid 351688372)
24. J.A. Anderson, C.D. Lorenz, A. Travesset, General purpose molecular dynamics simulations fully implemented on graphics processing units, Journal of Computational Physics 227 (2008) 5342-5359.