GPU algorithms for molecular modeling

Scientific Computing with Multicore and Accelerators

Volumn , Issue , 2010, Pages 351-372

  Stone, John E ^a   Hardy, David J ^a   Isralewitz, Barry ^a   Schulten, Klaus ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL CHEMISTRY; COMPUTER GRAPHICS; GRAPHICS PROCESSING UNIT; HARDWARE; MOLECULAR DYNAMICS; MOLECULAR MODELING; PROGRAM PROCESSORS;

COMPUTATIONAL CAPABILITY; COMPUTATIONAL SCIENCE AND ENGINEERINGS; DATA PARALLEL ALGORITHMS; FULLY PROGRAMMABLES; HARDWARE ARCHITECTURE; MOLECULAR DYNAMICS SIMULATIONS; PARALLEL COM- PUTING; SCIENTIFIC APPLICATIONS;

COMPUTER HARDWARE;

EID: 85054441478     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b10376     Document Type: Chapter

References (24)

1. Anton Arkhipov, Jana Hüve, Martin Kahms, Reiner Peters, and Klaus Schulten. Continuous uorescence microphotolysis, and correlation spectroscopy using 4Pi microscopy. Biophys. J., 93: 4006-4017, 2007.
2. David H. Bailey. High-precision oating-point arithmetic in scientific computation. Comput. Sci. Eng., 7(3): 54-61, 2005.
3. David Callahan, John Cocke, and Ken Kennedy. Estimating interlock, and improving balance for pipelined architectures. J. Paral. Distr. Comp., 5(4): 334-358, 1988.
4. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. A smooth particle mesh Ewald method. J. Chem. Phys., 103: 8577-8593, 1995.
5. James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, and Klaus Schulten. Regulation of the protein-conducting channel by a bound ribosome. Structure, 17: 1453-1464, 2009.
6. David J. Hardy, John E. Stone, and Klaus Schulten. Multilevel summation of electrostatic potentials using graphics processing units. J. Paral. Comp., 35: 164-177, 2009.
7. Yun He, and Chris H. Q. Ding. Using accurate arithmetics to improve numerical reproducibility, and stability in parallel applications. In ICS '00: Proceedings of the 14th International Conference on Supercomputing, pages 225-234, New York, NY, USA, 2000. ACM Press.
8. R. W. Hockney, and J. W. Eastwood. Computer Simulation Using Particles. McGraw-Hill, New York, 1981.
9. William Humphrey, Andrew Dalke, and Klaus Schulten. VMD|Visual molecular dynamics. J. Mol. Graphics, 14: 33-38, 1996.
10. Volodymyr V. Kindratenko, Jeremy J. Enos, Guochun Shi, Michael T. Showerman, Galen W. Arnold, John E. Stone, James C. Phillips, and Wen-mei Hwu. GPU clusters for high-performance computing. In Cluster Computing, and Workshops, 2009. CLUSTER '09. IEEE International Conference on, pages 1-8, New Orleans, LA, USA, 2009.
11. Erik Lindholm, John Nickolls, Stuart Oberman, and John Montrym. NVIDIA Tesla: A unified graphics, and computing architecture. IEEE Micro, 28(2): 39-55, 2008.
12. Aaftab Munshi. OpenCL Specification Version 1.0, December 2008. http://www.khronos.org/registry/cl/.
13. John Nickolls, Ian Buck, Michael Garland, and Kevin Skadron. Scalable parallel programming with CUDA. ACM Queue, 6(2): 40-53, 2008.
14. NVIDIA. CUDA Compute Unified Device Architecture Programming Guide. NVIDIA, Santa Clara, CA, USA, 2007.
15. NVIDIA’s next generation CUDA compute architecture: Fermi. White Paper, NVIDIA, 2009. Available online (Version 1.1, 22 pages).
16. John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and James C. Phillips. GPU computing. Proc. IEEE, 96: 879-899, 2008.
17. John D. Owens, David Luebke, Naga Govindaraju, Mark Harris, Jens Kruger, Aaron E. Lefohn, and Timothy J. Purcell. A survey of generalpurpose computation on graphics hardware. Comput. Graph. Forum, 26(1): 80-113, 2007.
18. James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. J. Comp. Chem., 26: 1781-1802, 2005.
19. James C. Phillips, John E. Stone, and Klaus Schulten. Adapting a message-driven parallel application to GPU-accelerated clusters. In SC '08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, Piscataway, NJ, USA, 2008. IEEE Press.
20. Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, and Wen-mei W. Hwu. GPU acceleration of cutoff pair potentials for molecular modeling applications. In CF’08: Proceedings of the 2008 Conference on Computing Frontiers, pages 273-282, New York, NY, USA, 2008. ACM.
21. John E. Stone, David Gohara, and Guochun Shi. OpenCL: A parallel programming standard for heterogeneous computing systems. Computing in Science, and Engineering, 12: 66-73, 2010.
22. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Accelerating molecular modeling applications with graphics processors. J. Comp. Chem., 28: 2618-2640, 2007.
23. John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wenmei W. Hwu, and Klaus Schulten. High performance computation, and interactive display of molecular orbitals on GPUs, and multi-core CPUs. In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pages 9-18, 2009.
24. Leonardo G. Trabuco, Christopher B Harrison, Eduard Schreiner, and Klaus Schulten. Recognition of the regulatory nascent chain TnaC by the ribosome. Structure, 18: 627-637, 2010.