Towards microsecond biological molecular dynamics simulations on hybrid processors

Proceedings of the 2010 International Conference on High Performance Computing and Simulation, HPCS 2010

Volumn , Issue , 2010, Pages 98-107

  Hampton, Scott ^a   Agarwal, Pratul K ^a   Alam, Sadaf R ^b   Crozier, Paul S ^c  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b Centro Svizzero Di Calcolo Scientifico   (Switzerland)

^c SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

Biomolecular simulations; GPUs; Hybrid multi core processors; LAMMPS; MD

Indexed keywords

BIOMOLECULAR SIMULATION; GPUS; LAMMPS; MD; MULTI-CORE PROCESSOR;

BIOCHEMISTRY; HARDWARE; MESSAGE PASSING; MICROPROCESSOR CHIPS; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; OPTIMIZATION;

PROGRAM PROCESSORS;

EID: 77956962231     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/HPCS.2010.5547149     Document Type: Conference Paper

References (19)

1. P. K. Agarwal, "Enzymes: An integrated view of structure, dynamics and function," Microbial Cell Factories, vol. 5, pp. 2, Jan 12 2006.
2. Y. Duan and P. A. Kollman, "Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution," Science, vol. 282, pp. 740-744, Oct 23 1998.
3. J. V. Sumanth, et al., "Performance and cost effectiveness of a cluster of workstations and MD-GRAPE 2 for MD simulations," Second International Symposium on Parallel and Distributed Computing, Proceedings, pp. 244-249, 2003.
4. D. E. Shaw, et al., "Anton, a special-purpose machine for molecular dynamics simulation," Communications of the ACM, vol. 51, pp. 91-97, Jul. 2008.
5. S. R. Alam, et al., "Using FPGA devices to accelerate biomolecular simulations," Computer, vol. 40, pp. 66-73, Mar 2007.
6. E. Cho, et al., "An FPGA design to achieve fast and accurate results for molecular dynamics simulations," Parallel and Distributed Processing and Applications, Proceedings, vol. 4742, pp. 256-267, 2007.
7. J. E. Stone, et al., "Accelerating molecular modeling applications with graphics processors," Journal of Computational Chemistry, vol. 28, pp. 2618-2640, Dec 2007.
8. X. D. Yang, et al., "FPGA-accelerated molecular dynamics simulations: An overview," Reconfigurable Computing: Architectures, Tools and Applications, vol. 4419, pp. 293-301, 2007.
9. J. A. Anderson, et al., "General purpose molecular dynamics simulations fully implemented on graphics processing units," Journal of Computational Physics, vol. 227, pp. 5342-5359, May 1 2008.
10. M. C. Herbordt, et al., "Computing Models for FPGABased Accelerators," Computing in Science & Engineering, vol. 10, pp. 35-45, Nov-Dec 2008.
11. J. D. Owens, et al., "GPU computing," Proceedings of the IEEE, vol. 96, pp. 879-899, May 2008.
12. D. J. Hardy, et al., "Multilevel summation of electrostatic potentials using graphics processing units," Parallel Computing, vol. 35, pp. 164-177, Mar 2009.
13. M. J. Harvey and G. De Fabritiis, "An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware," Journal of Chemical Theory and Computation, vol. 5, pp. 2371-2377, Sep 2009.
14. M. S. Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," Journal of Computational Chemistry, vol. 30, pp. 864-872, Apr 30 2009.
15. J. E. Davis, et al., "Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors," Bioinformatics and Computational Biology, Proceedings, vol. 5462, pp. 176-186, 450, 2009.
16. S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular-Dynamics," Journal of Computational Physics, vol. 117, pp. 1-19, Mar 1 1995.
17. E. Lindholm, et al., "NVIDIA Tesla: A unified graphics and computing architecture," IEEE Micro, vol. 28, pp. 39-55, Mar-Apr 2008.
18. M. F. Crowley, et al., "Adventures in improving the scaling and accuracy of a parallel molecular dynamics program," Journal of Supercomputing, vol. 11, pp. 255-278, 1997.
19. B. Hess, et al., "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation," Journal of Chemical Theory and Computation, vol. 4, pp. 435-447, Mar 2008.