Kevin J. Bowers
ABSTRACT
Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current state-of-the-art codes. These include a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time. We have also developed numerical techniques that maintain high accuracy while using single precision computation in order to exploit processor-level vector instructions. These methods are embodied in a newly developed MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters. Our results suggest that Desmond's parallel performance substantially surpasses that of any previously described code. For example, on a standard benchmark, Desmond's performance on a conventional Opteron cluster with 2K processors slightly exceeded the reported performance of IBM's Blue Gene/L machine with 32K processors running its Blue Matter MD code.
- 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. Google Scholar
Digital Library
- I. T. Arkin, H. Xu, K. J. Bowers, et al., Mechanism of a Na+/H+ Antiporter, submitted, 2006.Google Scholar
- 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.Google Scholar
- 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.Google ScholarCross Ref
- K. J. Bowers, R. O. Dror, and D. E. Shaw, The Midpoint Method for Parallelization of Particle Simulations, J. Chem. Phys., 124: 184109, 2006.Google ScholarCross Ref
- K. J. Bowers, R. O. Dror, and D. E. Shaw, Zonal Methods for the Parallel Execution of Range-Limited N-Body Problems, in press, J. Comput. Phys., 2006. Google ScholarDigital Library
- 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.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- 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. Google ScholarDigital Library
- D. A. Case, T. E. Cheatham, III, T. Darden, et al., The Amber Biomolecular Simulation Programs, J. Comput. Chem., 26(16): 1668--1688, 2005.Google Scholar
- E. Chow and D. Hysom, Assessing Performance of Hybrid MPI/OpenMP Programs on SMP Clusters, Lawrence Livermore National Laboratory UCRL-JC-143957, 2001.Google Scholar
- 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.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- 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. Google ScholarDigital Library
- 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.Google Scholar
- 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.Google Scholar
- 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.Google Scholar
- M. Frigo and S. G. Johnson, The Design and Implementation of FFTW3, Proceedings of the IEEE, 93(2): 216--231, 2005.Google ScholarCross Ref
- 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. Google ScholarDigital Library
- 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.Google ScholarCross Ref
- G. S. Heffelfinger, Parallel Atomistic Simulations, Comput. Phys. Commun., 128(1-2): 219--237, 2000.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- 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.Google Scholar
- 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. Google ScholarDigital Library
- J. Liu, J. Wu, and D. K. Panda, High Performance RDMA-Based MPI Implementation over InfiniBand, presented at 17th International Conference on Supercomputing, San Francisco, CA, 2003. Google ScholarDigital Library
- 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.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- Mellanox Technologies, Mellanox IB-Verbs API (VAPI): Mellanox Software Programmer's Interface for InfiniBand Verbs, 2001.Google Scholar
- 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. Google ScholarDigital Library
- J. Norberg and L. Nilsson, On the Truncation of Long-Range Electrostatic Interactions in DNA, Biophys. J., 79(3): 1537--1553, 2000.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- J. C. Phillips, R. Braun, W. Wang, et al., Scalable Molecular Dynamics with NAMD, J. Comput. Chem., 26(16): 1781--1802, 2005.Google ScholarCross Ref
- J. C. Phillips, G. Zheng, S. Kumar, et al., NAMD: Biomolecular Simulation on Thousands of Processors, presented at ACM/IEEE SC2002 Conference, Baltimore, 2002. Google ScholarDigital Library
- S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular-Dynamics, J. Comput. Phys., 117(1): 1--19, 1995. Google ScholarDigital Library
- S. Plimpton and B. Hendrickson, Parallel Molecular-Dynamics Simulations of Organic Materials, Int. J. Mod. Phys. C., 5(2): 295--298, 1994.Google ScholarCross Ref
- S. Plimpton and B. Hendrickson, A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems, J. Comput. Chem., 17(3): 326--337, 1996.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- M. M. Seibert, A. Patriksson, B. Hess, et al., Reproducible Polypeptide Folding and Structure Prediction Using Molecular Dynamics Simulations, J. Mol. Biol., 354(1): 173--183, 2005.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- T. Shanley, InfiniBand Network Architecture. Boston: Addison-Wesley, 2003. Google ScholarDigital Library
- 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.Google ScholarCross Ref
- M. Snir, A Note on N-Body Computations with Cutoffs, Theor. Comput. Syst., 37: 295--318, 2004.Google ScholarCross Ref
- D. van der Spoel, E. Lindahl, B. Hess, et al., GROMACS: Fast, Flexible, and Free, Journal of Computational Chemistry, 26(16): 1701--1718, 2005.Google ScholarCross Ref
- 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. Google ScholarDigital Library
- 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.Google ScholarCross Ref
- 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.Google ScholarCross Ref
Index Terms
- Scalable algorithms for molecular dynamics simulations on commodity clusters
Recommendations
MPPs and clusters for scalable computing
ISPAN '96: Proceedings of the 1996 International Symposium on Parallel Architectures, Algorithms and NetworksThis article assess the state-of-the-art technology in massively parallel processors (MPPs) and clusters of workstations (COWs) for scalable parallel computing. We evaluate the IBM SP2, the Intel Paragon, the Cray T3D/T3E, and the ASCI TeraFLOPS system ...
Massively parallel molecular dynamics simulations of lysozyme unfolding
We have performed molecular dynamics simulations for a total duration of more than 10 µs (with most molecular trajectories being 1 µs in duration) to study, the effect of a single mutation on hen lysozyme protein stability and denaturing, using an IBM ...
Identification of novel PI3Kδ inhibitors by docking, ADMET prediction and molecular dynamics simulations
Graphical abstractThe virtual screening, molecular docking, ADMET prediction and molecular dynamics simulations were performed on Asinex database to find the novel compounds against PI3Kδ, which were demonstrated as the following flow chart:
...Highlights- Phosphoinositide-3-kinase Delta (PI3Kδ) is a well-validated target for anticancer drug design and development.
Abstract BackgroundPhosphoinositide-3-kinase Delta (PI3Kδ) plays a key role in B-cell signal transduction and inhibition of PI3Kδ is confirmed to have clinical benefit in certain types of activation of B-cell malignancies. Virtual ...
Comments