Abstract
Molecular dynamics and many similar time-dependent computing tasks are defined as simple state updates over multiple time steps. In recent years, modern supercomputing clusters have enjoyed fast-growing compute capability and moderate-growing memory bandwidth, but their improvement of network bandwidth/latency is limited. In this paper, we propose a new communication-avoiding algorithmic model based on asynchronous communications which, unlike BSP, records and handles multiple iterative states together. The basic idea is to let computation run in small regular time steps while communications over longer dynamic time steps. Computation keeps checking inaccuracies so that the intervals between communications are small in volatile scenarios but longer when dynamics is smooth. This helps reduce the number of data exchanges via network communication and hence improve the overall performance when communication is the bottleneck. We test MD simulation of condensed covalent materials on the Sunway TaihuLight. For best time-to-solution, the general-purpose supercomputer Sunway TaihuLight performs 11.8 K steps/s for a system with 2.1 million silicon atoms and 5.1 K steps/s for 50.4 million silicon atoms. This time-to-solution performance is close to those of state-of-art hardware solution. A software solution using general-purpose supercomputers makes the technology more accessible to the general scientific users.
Supported by National Key R&D Program of China under Grants No. 2017YFB0202000.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Shaw, D.E., Grossman, J.P., Bank, J.A., et al.: Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2014, New Orleans, LA, USA, 16–21 November, 2014, pp. 41–53 (2014)
Shaw, D.E., Deneroff, M.M., Dror, R.O., et al.: Anton, a special-purpose machine for molecular dynamics simulation. In: 34th International Symposium on Computer Architecture (ISCA 2007), San Diego, California, USA, 9–13 June, 2007, pp. 1–12 (2007)
Höhnerbach, M., Ismail, A.E., Bientinesi, P.: The vectorization of the tersoff multi-body potential: an exercise in performance portability. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2016, Salt Lake City, UT, USA, 13–18 November, 2016, pp. 69–81 (2016)
Abraham, M.J., Murtola, T., Schulz, R., et al.: GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. Softwarex 1–2(C), 19–25 (2015)
Páll, S., Abraham, M.J., Kutzner, C., et al.: Tackling exascale software challenges in molecular dynamics simulations with GROMACS, CoRR, vol. 70, pp. 3–27 (2014)
Phillips, J.C., Sun, Y., Jain, N., et al.: Mapping to irregular torus topologies and other techniques for petascale biomolecular simulation. In: International Conference for High Performance Computing, p. 81 (2014)
Phillips, J.C., et al.: Scalable molecular dynamics with namd. J. Comput. Chem. 26(16), 1781–1802 (2005)
Valiant, L.: A bridging model for parallel computation. Commun. ACM 33(8), 103–111 (1990)
Baffico, L., Bernard, S., Maday, Y., et al.: Parallel-in-time molecular-dynamics simulations. Phys. Rev. E 66(2), 057701 (2002)
Lions, J.-L., et al.: Resolution EDP par unschema en temps parareal. C. R. Acad. Sci. Numer. Anal. 332(7), 661–668 (2001)
Bahi, J.M., Contassot-Vivier, S., Couturier, R.: Evaluation of the asynchronous iterative algorithms in the context of distant heterogeneous clusters. Parallel Comput. 31(5), 439–461 (2005)
Boukai, A.I., Bunimovich, Y., Tahir-Kheli, J., et al.: Silicon nanowires as efficient thermoelectric materials. Nature 451(7175), 168–171 (2008)
Tian, B., Kempa, T.J., Lieber, C.M.: Single nanowire photovoltaics. Chem. Soc. Rev. 38(1), 16–24 (2009)
Yang, N., Zhang, G., Li, B.: Violation of fourier’s law and anomalous heat diffusion in silicon nanowires. Nano Today 5(2), 85–90 (2010)
Schelling, P.K., Phillpot, S.R., Keblinski, P.: Comparison of atomic-level simulation methods for computing thermal conductivity. Phys. Rev. B 65(14), 144306–144317 (2002)
Tersoff, J.: New empirical approach for the structure and energy of covalent systems. Phys. Rev. B 37(14), 6991–7000 (1988)
Tersoff, J.: Empirical interatomic potential for silicon with improved elastic properties. Phys. Rev. B 38(14), 9902–9905 (1988)
He, Y., Savic, I., Donadio, D., Galli, G.: Lattice thermal conductivity of semiconducting bulk materials: atomistic simulations. Phys. Chem. Chem. Phys. 14(47), 16209–16222 (2012)
Cruz, C., Termentzidis, K., Chantrenne, P., Kleber, X.: Molecular dynamics simulation for the prediction of thermal conductivity of bulk silicon and silicon nanowires: influence of interatomic potentials and boundary conditions. J. Appl. Phys 110(3), 34309–34316 (2011)
Park, M., Lee, I., Kim, Y.: Lattice thermal conductivity of crystalline and amorphous silicon with and without isotopic effects from the ballistic to diffusive thermal transport regime. J. Appl. Phys. 116(4), 43514–43522 (2014)
Krzeminski, C., Brulin, Q., Cuny, V., et al.: Molecular dynamics simulation of the recrystallization of amorphous Si layers: comprehensive study of the dependence of the recrystallization velocity on the interatomic potential. J. Appl. Phys. 101(12), 6336-4 (2011)
Lee, B.M., Baik, H.K., Seong, B.S., et al.: Molecular-dynamics analysis of the nucleation and crystallization process of Si. Phys. B Condens. Matter 392(1–2), 266–271 (2007)
Hou, C.F., Xu, J., Wang, P., et al.: Petascale molecular dynamics simulation of crystalline silicon on Tianhe-1A. Int. J. High Perform. C. 184(5), 1364–1371 (2013)
Perez, D., Huang, R., Voter, A.F.: Long-time molecular dynamics simulations on massively parallel platforms: a comparison of parallel replica dynamics and parallel trajectory splicing. J. Mat. Res. 33(7), 813–822 (2018)
Elber, R.: Perspective: computer simulations of long time dynamics. J. Chem. Phys. 144(6), 98–103 (2016)
Fu, H., Liao, J., Yang, J., et al.: The sunway TaihuLight supercomputer: system and applications. Sci. China Inf. Sci. 59(7), 072001 (2016)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this paper
Cite this paper
Wang, B., Chen, Y., Hou, C. (2020). A Communication-Avoiding Algorithm for Molecular Dynamics Simulation. In: Wen, S., Zomaya, A., Yang, L. (eds) Algorithms and Architectures for Parallel Processing. ICA3PP 2019. Lecture Notes in Computer Science(), vol 11944. Springer, Cham. https://doi.org/10.1007/978-3-030-38991-8_6
Download citation
DOI: https://doi.org/10.1007/978-3-030-38991-8_6
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-38990-1
Online ISBN: 978-3-030-38991-8
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)