Accelerating Molecular Dynamics Simulations with GPUs

21st ISCA International Conference on Parallel and Distributed Computing and Communication Systems, PDCCS 2008

Volumn , Issue , 2008, Pages 44-49

  Walters, John Paul ^a   Balu, Vidyananth ^a   Chaudhary, Vipin ^a   Kofke, David ^a   Schultz, Andrew ^a  

^a University at Buffalo ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROGRAM PROCESSORS;

DYNAMICS SIMULATION; LENNARD JONES; RUNTIMES;

MOLECULAR DYNAMICS;

EID: 84963626200     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (16)

1. M. P. Allen and D. J. Tildesley. Computer Simulation of Liquids. Oxford University Press, 1989.
2. 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.
3. H.J.C. Berendsen, D. van der Spoel, and R. van Drunen. GROMACS: A Message-Passing Parallel Molecular Dynamics Implementation. Computer Physics Communications, 91:43-56, September 1995.
4. K.J. Bowers, E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, and D.E. Shaw. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. In SC'06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing. ACM, 2006.
5. I. Buck, T. Foley, D. Horn, J. Sugerman, K. Fatahalian, M. Houston, and P. Hanrahan. Brook for GPUs: Stream Computing on Graphics Hardware. In ACM SIGGRAPH, pages 777-786. ACM, 2004.
6. D. Frenkel and B. Smit. Understanding Molecular Simulation: From Algorithms to Applications. Academic Press, 2nd edition, 2002.
7. F. Gygi, R.K. Yates, J. Lorenz, E.W. Draeger, F. Franchetti, C.W. Ueberhuber, B.R. de Supinski, S. Kral, J.A. Gunnels, and J.C. Sexton. Large-Scale First-Principles Molecular Dynamics simulations on the BlueGene/L Platform using the Qbox code. In SC '05: Proceedings of the 2005 ACM/IEEE conference on Supercomputing, page 24, Washington, DC, USA, 2005. IEEE Computer Society.
8. S. Kumar, H. Chao, G. Almasi, and L.V. Kale. Achieving Strong Scaling with NAMD on Blue Gene/L. In Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International, April 2006.
9. W. Liu, B. Schmidt, G. Voss, and W. Muller-Wittig. Molecular Dynamics Simulations on Commodity GPUs with CUDA. In Proceedings of HiPC: The International Conference on High Performance Computing, LNCS, volume 4873. Springer-Verlag, 2007.
10. T. Narumi, Y. Ohno N. Okimoto, A. Suenaga, R. Yanai, and M. Taiji. A High-Speed Special-Purpose Computer for Molecular Dynamics Simulations: MDGRAPE-3. NIC Workshop, 34:29-36, 2006.
11. NVIDIA. Compute Unified Device Architecture (CUDA) Programming Guide, version 1.0 edition.
12. S. Olivier, J. Prins, J. Derby, and K. Vu. Porting the GROMACS Molecular Dynamics Code to the Cell Processor. In IPDPS: The International Parallel and Distributed Processing Symposium. IEEE Computer Society, March 2007.
13. J.C. Phillips, G. Zheng, S. Kumar, and L.V. Kalé. NAMD: Biomolecular Simulation on Thousands of Processors. In Supercomputing'02: Proceedings of the 2002 ACM/IEEE conference on Supercomputing, pages 1-18. IEEE Computer Society Press, 2002.
14. D.E. Shaw, M.M. Deneroff, R.O. Dror, J.S. Kuskin, R.H. Larson, J.K. Salmon, C. Young, B. Batson, K.J. Bowers, J.C. Chao, M.P. Eastwood, J. Gagliardo, J.P. Grossman, C.R. Ho, D.J. Ierardi, I. Kolossváry, J.L. Klepeis, T. Layman, C. McLeavey, M.A. Moraes, R. Mueller, E.C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, and S.C. Wang. Anton, A Special-Purpose Machine for Molecular Dynamics Simulation. In ISCA'07: Proceedings of the 34th Annual International Symposium on Computer Architecture, pages 1-12. ACM, 2007.
15. J.E. Stone, J.C. Phillips, P.L. freddolino, D.J. Hardy, L.G. Trabuco, and K. Schulten. Accelerating Molecular Modeling Applications with Graphics Processors. Journal of Computational Chemistry, 28(16), 2007.
16. S. Tomov, M. McGuigan, R. Bennett, G. Smith, and J. Spiletic. Benchmarking and Implementation of Probability-Based Simulations on Programmable Graphics Cards. Computers and Graphics, 29(1):71-80, 2005.