Abstract
We have implemented the computation of Coulomb interactions in particle systems using the performance portable C++ framework Kokkos. Coulomb interactions are evaluated with an Ewald-sum-based solver, where the interactions are split into long- and short-range contributions. The short-range contributions are calculated using pair-wise contributions of particles while long-range interactions are calculated using Fourier sums. We evaluate the performance portability of the implementation on Intel CPUs, including Intel Xeon Phi, and Nvidia GPUs.
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References
Arnold, A., et al.: Comparison of scalable fast methods for long-range interactions. Phys. Rev. E 88, 063308 (2013)
Beckingsale, D., Hornung, R., Scogland, T., Vargas, A.: Performance portable C++ programming with RAJA. In: Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming, PPoPP 2019, pp. 455–456. ACM, New York (2019). https://doi.org/10.1145/3293883.3302577
Carter Edwards, H., Trott, C.R., Sunderland, D.: Kokkos: enabling manycore performance portability through polymorphic memory access patterns. J. Parallel Distrib. Comput. 74(12), 3202–3216 (2014). https://doi.org/10.1016/j.jpdc.2014.07.003
Deserno, M., Holm, C.: How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. J. Chem. Phys. 109, 7678 (1998)
Ewald, P.P.: Die Berechnung optischer und elektrostatischer Gitterpotentiale. Annalen der Physik 369(3), 253–287 (1921). https://doi.org/10.1002/andp.19213690304
Fincham, D.: Optimisation of the Ewald sum for large systems. Mol. Simul. 13(1), 1–9 (1994). https://doi.org/10.1080/08927029408022180
Frenkel, D., Smit, B.: Understanding Molecular Simulation: From Algorithms to Applications, 2nd edn. Academic Press, San Diego (2001)
Halver, R., Homberg, W., Sutmann, G.: Function portability of molecular dynamics on heterogeneous parallel architectures with OpenCL. J. Supercomput. 74(4), 1522–1533 (2018). https://doi.org/10.1007/s11227-017-2232-2
Intel: Intel® 64 and IA-32 Architectures Optimization Reference Manual, April 2019
JSC: Forschungszentrum Jülich - Jülich Supercomputing Centre (JSC) (2019). https://www.fz-juelich.de/ias/jsc/
Luty, B., Davis, M., Tironi, I., van Gunsteren, W.: A comparison of particle-particle, particle-mesh and Ewald methods for calculating electrostatic interactions in periodic molecular systems. Mol. Simul. 14, 11–20 (1994)
NVIDIA: CUDA C Programming Guide, March 2019. http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html
Pollock, E.L., Glosli, J.: Comments on P\(^3\)M, FMM, and the Ewald method for large periodic Coulombic systems. Comput. Phys. Commun. 95, 93–110 (1996)
Sutmann, G.: Molecular dynamics - vision and reality. In: Grotendorst, J., Blügel, S., John von Neumann-Institut für Computing (eds.) Computational Nanoscience: Do It Yourself! Winter School, 14–22 February 2006, Forschungszentrum Jülich, Germany; Lecture Notes. No. 31 in NIC Series, NIC-Secretariat, Research Centre Jülich, Jülich (2006). oCLC: 181556319
Top500: TOP500 Supercomputer Sites. https://www.top500.org/
Torrellas, J., Lam, H.S., Hennessy, J.L.: False sharing and spatial locality in multiprocessor caches. IEEE Trans. Comput. 43(6), 651–663 (1994). https://doi.org/10.1109/12.286299
Toukmaji, A.Y., Board Jr., J.A.: Ewald summation techniques in perspective: a survey. Comput. Phys. Commun. 95, 73–92 (1996)
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Halver, R., Meinke, J.H., Sutmann, G. (2020). Examining Performance Portability with Kokkos for an Ewald Sum Coulomb Solver. In: Wyrzykowski, R., Deelman, E., Dongarra, J., Karczewski, K. (eds) Parallel Processing and Applied Mathematics. PPAM 2019. Lecture Notes in Computer Science(), vol 12044. Springer, Cham. https://doi.org/10.1007/978-3-030-43222-5_4
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DOI: https://doi.org/10.1007/978-3-030-43222-5_4
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