Scalable algorithms for molecular dynamics simulations on commodity clusters

Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC'06

Volumn , Issue , 2006, Pages

  Bowers, Kevin J ^a   Chow, Edmond ^a   Xu, Huafeng ^a   Dror, Ron O ^a   Eastwood, Michael P ^a   Gregersen, Brent A ^a   Klepeis, John L ^a   Kolossvary, Istvan ^a   Moraes, Mark A ^a   Sacerdoti, Federico D ^a   Salmon, John K ^a   Shan, Yibing ^a   Shaw, David E ^a  

^a D E SHAW RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SYSTEMS; COMMODITY CLUSTERS; MOLECULAR DYNAMICS SIMULATIONS; SCALABLE ALGORITHMS;

CODES (SYMBOLS); COMPUTATION THEORY; COMPUTER SIMULATION; MESSAGE PASSING; MOLECULAR DYNAMICS; NUMERICAL METHODS;

ALGORITHMS;

EID: 34548283148     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1188455.1188544     Document Type: Conference Paper

References (48)

1. G. Almasi, C. Archer, J. G. Castanos, et al, Design and Implementation of Message-Passing Services for the Blue Gene/L Supercomputer, IBM J. Res. & Dev., 49(2-3): 393-406, 2005.
2. + Antiporter, submitted, 2006.
3. K. J. Bowers, Speed Optimal Implementation of a Fully Relativistic 3D Particle Push with a Charge Conserving Current Accumulate on Modern Processors, presented at 18th International Conference on the Numerical Simulation of Plasmas, Cape Cod, MA, 2003.
4. K. J. Bowers, R. O. Dror, and D. E. Shaw, Overview of Neutral Territory Methods for the Parallel Evaluation of Pairwise Particle Interactions, J. Phys. Conf. Ser., 16: 300-304, 2005.
5. K. J. Bowers, R. O. Dror, and D. E. Shaw, The Midpoint Method for Parallelization of Particle Simulations, J. Chem. Phys., 124: 184109, 2006.
6. K. J. Bowers, R. O. Dror, and D. E. Shaw, Zonal Methods for the Parallel Execution of Range-Limited JV-Body Problems, in press, J. Comput. Phys., 2006.
7. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, et al., CHARMM: A Program, for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comput. Chem., 4: 187-217, 1983.
8. C. L. Brooks, B. M. Pettit, and M. Karplus, Structural and Energetic Effects of Truncating Long Ranged Interactions in Ionic and Polar Fluids, J. Chem. Phys., 83(11): 5897-5908, 1985.
9. F. Cappello and D. Etiemble, MPI Versus MPI+OpenMP on the IBM SP for the NAS Benchmarks, presented at ACM/IEEE SC2000 Conference, Dallas, TX, 2000.
10. D. A. Case, T. E. Cheatham, III, T. Darden, et al., The Amber Biomolecular Simulation Programs, J. Comput. Chem., 26(16): 1668-1688,2005.
11. E. Chow and D. Hysom, Assessing Performance of Hybrid MPI/OpenMP Programs on SMP Clusters, Lawrence Livermore National Laboratory UCRL-JC-143957, 2001.
12. 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): 10089-10092, 1993.
13. Y. Duan and P. A. Kollman, Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution, Science, 282(5389): 740-744, 1998.
14. M. Eleftheriou, B. G. Fitch, A. Rayshubskiy, et al, Scalable Framework for 3D FFTs on the Blue Gene/L Supercomputer: Implementation and Early Performance Measurements, IBM J. Res. & Dev., 49(2-3): 457-464, 2005.
15. B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, et al., Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L, IBM RC23888, February 22, 2006.
16. B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, et al., Blue Matter: Approaching the Limits of Concurrency for Classical Molecular Dynamics, IBM RC23956, May 12, 2006.
17. B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, et al., Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L, IBM RC23688, August 5, 2005.
18. M. Frigo and S. G. Johnson, The Design and Implementation of FFTW3, Proceedings of the IEEE, 93(2): 216-231, 2005.
19. R. S. Germain, B. Fitch, A. Rayshubskiy, et al, Blue Matter on Blue Gene/L: Massively Parallel Computation for Biomolecular Simulation, presented at 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis (CODES+ISSS '05), New York, NY, 2005.
20. T. A. Halgren, MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-Interaction Energies and Geometries, J. Comput. Chem., 20(7): 730-748, 1999.
21. G. S. Heffelfinger, Parallel Atomistic Simulations, Comput. Phys. Commun., 128(1-2): 219-237, 2000.
22. W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, J. Am. Chem. Soc., 118(45): 11225-11236, 1996.
23. P. A. Kollman, R. W. Dixon, W. D. Cornell, et al, "The Development/Application of a "Minimalist" Organic/ Biomolecular Mechanic Forcefield Using a Combination of Ab Initio Calculations and Experimental Data," in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, W. F. van Gunsteren and P. K. Weiner, Eds. Dordrecht, Netherlands: ESCOM, 1997, 83-96.
24. S. Kumar, G. Almasi, C. Huang, et al., Achieving Strong Scaling with NAMD on Blue Gene/L, presented at IEEE International Parallel & Distributed Processing Symposium, Rhodes Island, Greece, 2006.
25. J. Liu, J. Wu, and D. K. Panda, High Performance RDMABased MPI Implementation over InfiniBand, presented at 17th International Conference on Supercomputing, San Francisco, CA, 2003.
26. J. MacKerell, A. D., D. Bashford, M. Bellott, et al., All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B, 102(18): 3586-3616, 1998.
27. P. Mark and L. Nilsson, Structure and Dynamics of Liquid Water with Different Long-Range Interaction Truncation, and Temperature Control Methods in Molecular Dynamics Simulations, J. Comput. Chem., 23(13): 1211-1219, 2002.
28. Mellanox Technologies, Mellanox IB-Verbs API (VAPI): Mellanox Software Programmer's Interface for InfiniBand Verbs, 2001.
29. T. Narumi, A. Kawai, and T. Koishi, An 8.61 Tflop/s Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM, presented at ACM/IEEE SC2001 Conference, Denver, Colorado, 2001.
30. J. Norberg and L. Nilsson, On the Truncation of Long-Range Electrostatic Interactions in DNA, Biophys. J., 79(3): 1537-1553, 2000.
31. V. S. Pande, I. Baker, J. Chapman, et al., Atomistic Protein Folding Simulations on the Submillisecond Time Scale Using Worldwide Distributed Computing, Biopolymers, 68(1): 91-109, 2003.
32. P. M. Papadopoulos, M. J. Katz, and G. Bruno, NPACI Rocks: Tools and Techniques for Easily Deploying Manageable Linux Clusters, Concurrency Comput. Pract. Ex., 15(7-8): 707-725, 2003.
33. M. Patra, M. Karttunen, T. Hyvönen, et al., Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions, Biophys. J., 84: 3636-3645, 2003.
34. J. C. Phillips, R. Braun, W. Wang, et al., Scalable Molecular Dynamics with NAMD, J. Comput. Chem., 26(16): 1781-1802, 2005.
35. J. C. Phillips, G. Zheng, S. Kumar, et al., NAMD: Biomolecular Simulation on Thousands of Processors, presented at ACM/IEEE SC2002 Conference, Baltimore, 2002.
36. S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular-Dynamics, J. Comput. Phys., 117(1): 1-19, 1995.
37. S. Plimpton and B. Hendrickson, Parallel Molecular-Dynamics Simulations of Organic Materials, Int. J. Mod. Phys. C., 5(2): 295-298, 1994.
38. S. Plimpton and B. Hendrickson, A New Parallel Method for Molecular Dynamics Simulation, of Macromolecular Systems, J. Comput. Chem., 17(3): 326-337, 1996.
39. W. R. P. Scott, P. H. Hünenberger, I. G. Tironi, et al., The GROMOS Biomolecular Simulation Program Package, J. Phys. Chem. A, 103(19): 3596-3607, 1999.
40. M. M. Seibert, A. Patriksson, B. Hess, et al., Reproducible Polypeptide Folding and Structure Prediction Using Molecular Dynamics Simulations, J. MoIl Biol, 354(1): 173-183, 2005.
41. Y. Shan, J. L. Klepeis, M. P. Eastwood, et al., Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation, J. Chem. Phys., 122: 054101, 2005.
42. T. Shanley, InfiniBand Network Architecture. Boston: Addison-Wesley, 2003.
43. D. E. Shaw, A Fast, Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle Interactions, J. Comput. Chem., 26(13): 1318-1328, 2005.
44. M. Snir, A Note on N-Body Computations with Cutoffs, Theor. Comput. Syst., 37: 295-318, 2004.
45. D. van der Spoel, E. Lindahl, B. Hess, et al., GROMACS: Fast, Flexible, and Free, Journal of Computational Chemistry, 26(16): 1701-1718, 2005.
46. M. Taiji, T. Narumi, Y. Ohno, et al., Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations, presented at ACM/IEEE SC2003 Conference, Phoenix, Arizona, 2003.
47. R. Zhou and B. J. Berne, A New Molecular Dynamics Method Combining the Reference System Propagator Algorithm with a Fast Multipole Method for Simulating Proteins and Other Complex Systems, J. Chem. Phys., 103(21): 9444-9459, 1995.
48. R. Zhou, E. Harder, H. Xu, et al, Efficient Multiple Time Step Method for Use with Ewald and Particle Mesh Ewald for Large Biomolecular Systems, J. Chem. Phys., 115(5): 2348-2358, 2001.