Abstract
Recent evolution of supercomputer architectures toward massively multi-cores nodes equipped with many-core accelerators is leading to make MPI-only applications less effective. To fully tap into the potential of these architectures, hybrid approaches – mixing MPI, threads and CUDA or OpenCL – usually meet performance expectations, but at the price of huge development and optimization efforts.
In this paper, we present a programming framework specialized for molecular dynamics simulations. This framework allows end-users to develop their computation kernels in the form of sequential-looking functions and generates multi-level parallelism combining vectorized and SIMD kernels, multi-threading and communications. We report on preliminary performance results obtained on different architectures with widely used force computation kernels.
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Alder, B.J., Wainwright, T.E.: Phase Transition for a Hard Sphere System. The Journal of Chemical Physics 27(5), 1208–1209 (1957)
Allen, M., Tildesley, D.: Computer Simulation of Liquids. Clarendon Press (1987)
Berendsen, H., van der Spoel, D., van Drunen, R.: GROMACS: A Message-passing Parallel Molecular Dynamics Implementation. Computer Physics Communications 91(1-3), 43–56 (1995)
Contreras, G., Martonosi, M.: Characterizing and Improving the Performance of Intel Threading Building Blocks. In: IEEE International Symposium on Workload Characterization, IISWC 2008, pp. 57–66 (2008)
Coplien, J.O.: Curiously Recurring Template Patterns. C++ Rep. 7(2), 24–27 (1995)
Daw, M.S., Baskes, M.I.: Embedded-atom Method: Derivation and Application to Impurities, Surfaces, and other Defects in Metals. Phys. Rev. B 29, 6443–6453 (1984)
Daw, M.S., Foiles, S.M., Baskes, M.I.: The embedded-atom Method: a Review of Theory and Applications. Materials Science Reports 9(7-8), 251–310 (1993)
Foiles, S.M., Baskes, M.I., Daw, M.S.: Embedded-atom Method Functions for the FCC Metals Cu, Ag, Au, Ni, Pd, Pt, and their Alloys. Phys. Rev. B 33, 7983–7991 (1986)
Germann, T.C., Kadau, K., Swaminarayan, S.: 369 Tflop/s Molecular Dynamics Simulations on the Petaflop Hybrid Supercomputer ‘Roadrunner’. Concurrency and Computation: Practice and Experience 21(17), 2143–2159 (2009)
Greengard, L., Rokhlin, V.: A Fast Algorithm for Particle Simulations. Journal of Computational Physics 73(2), 325–348 (1987)
Hoover, W.G., De Groot, A.J., Hoover, C.G., Stowers, I.F., Kawai, T., Holian, B.L., Boku, T., Ihara, S., Belak, J.: Large-scale Elastic-plastic Indentation Simulations via Nonequilibrium Molecular Dynamics. Phys. Rev. A 42(10), 5844–5853 (1990)
Johnson, R.A.: Alloy Models with the Embedded-atom Method. Phys. Rev. B 39, 12554–12559 (1989)
Jones, J.E.: On the Determination of Molecular Fields. II. From the Equation of State of a Gas. Proceedings of the Royal Society of London. Series A 106(738), 463–477 (1924)
Leimkuhler, B.J., Reich, S., Skeel, R.D.: Integration Methods for Molecular Dynamics. In: Mesirov, J.P., Schulten, K., Sumners, D.W. (eds.) Mathematical Approaches to Biomolecular Structure and Dynamics. The IMA Volumes in Mathematics and its Applications, vol. 82, pp. 161–185. Springer, New York (1996)
Nelson, M.T., Humphrey, W., Gursoy, A., Dalke, A., Kalé, L.V., Skeel, R.D., Schulten, K.: NAMD: a Parallel, Object-oriented Molecular Dynamics Program. International Journal of High Performance Computing Applications 10(4), 251–268 (1996)
Plimpton, S.: Fast Parallel Algorithms for Short-range Molecular Dynamics. Journal of Computational Physics 117(1), 1–19 (1995)
Sandia National Laboratories: LAMMPS User Manual (2014), http://lammps.sandia.gov/doc/Manual.html
Soulard, L.: Molecular Dynamics Study of the Micro-spallation. The European Physical Journal D 50(3) (2008)
Stillinger, F.H., Weber, T.A.: Computer Simulation of Local Order in Condensed Phases of Silicon. Phys. Rev. B 31, 5262–5271 (1985)
Sutton, A.P., Chen, J.: Long-range Finnis-Sinclair Potentials. Philosophical Magazine Letters 61(3), 139–146 (1990)
Tersoff, J.: New Empirical Approach for the Structure and Energy of Covalent Systems. Phys. Rev. B 37, 6991–7000 (1988)
Wolff, D., Rudd, W.G.: Tabulated Potentials in Molecular Dynamics Simulations. Computer Physics Communications 120(1), 20–32 (1999)
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Cieren, E., Colombet, L., Pitoiset, S., Namyst, R. (2014). ExaStamp: A Parallel Framework for Molecular Dynamics on Heterogeneous Clusters. In: Lopes, L., et al. Euro-Par 2014: Parallel Processing Workshops. Euro-Par 2014. Lecture Notes in Computer Science, vol 8806. Springer, Cham. https://doi.org/10.1007/978-3-319-14313-2_11
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DOI: https://doi.org/10.1007/978-3-319-14313-2_11
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