Large-scale MD simulation of heterogeneous systems with ls1 mardyn - PowerPoint PPT Presentation

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Large-scale MD simulation of heterogeneous systems with ls1 mardyn M. T. Horsch, R. Srivastava, S. J. Werth, C. Niethammer, C. W. Glass, W. Eckhardt, A. Heinecke, N. Tchipev, H.-J. Bungartz, S. Eckelsbach, J. Vrabec and H. Hasse TU Kaiserslautern, Engineering Thermodynamics (LTD) TU München, Scientific Computing in Computer Science (SCCS) High Performance Computing Centre Stuttgart (HLRS) University of Paderborn, Thermodynamics and Energy Technology (ThEt) Frankfurt am Main, 23 rd March 2015 ProcessNet International Workshop MolMod

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Parallelization by volume decomposition Linked-cell data structure suitable for spatial domain decomposition: (non-blocking, overlap- ping MPI send/receive operations) l arge s ystems “ 1 ”: m olecul ar dyn amics http://www.ls1-mardyn.de/ Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 2

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Parallelization by volume decomposition Linked-cell data structure suitable for spatial domain decomposition: (non-blocking, overlap- ping MPI send/receive operations) Methods for heterogeneous or fluctuating particle distributions: Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 3

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Scale separation and long-range correction short range long range For planar interfaces: (explicit) (correction) Long-range correction from the density profile, following Janeček . cutoff radius Full evaluation of all pairwise interactions is too expensive ... ... instead, short-range interactions are evaluated for neighbours . Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 4

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Scale separation and long-range correction short range long range For planar interfaces: (explicit) (correction) Long-range correction from the density profile, following Janeček . cutoff radius Angle-averaging expression for multi-site models, following Lustig . Full evaluation of all pairwise interactions is too expensive ... ... instead, short-range interactions are evaluated for neighbours . Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 5

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Molecular simulation of fluids at interfaces For planar interfaces: Two-centre LJ fluid (2CLJ) Long-range correction from the surface tension / εσ -2 density profile, following Janeček . 1 nm Janeček-Lustig term no angle averaging no correction at all Angle-averaging expression for multi-site models, following Lustig . cutoff radius / σ For arbitrary geometries, e.g. the fast multipole method can be employed. Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 6

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Molecular simulation of fluids at interfaces 2CLJQ models: • 2 LJ centres • Quadrupole Test of predictivity for interfacial properties Model validation and optimization Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 7

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Molecular simulation of fluids at interfaces ● Adsorption (fluid-fluid and fluid-solid) LJTS ● Vapour-liquid surface tension ● Curved vapour-liquid interfaces ● Contact angle and contact line pinning T = 0.8 ε θ pl = 90° Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 8

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse MD simulation of nanofluidics Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 9

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Scale bridging from nano- to microfluidics Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 10

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Scaling of ls1 mardyn on hermit Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 11

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Scaling of ls1 mardyn on hermit homogeneous cavitation CO 2 ( T = 280 K and ρ = 17.2 mol/l), 3CLJQ 25 million molecules on 110 592 cores Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 12

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Optimization of ls1 mardyn for SuperMUC SuperMUC (LRZ Garching): 3 PFLOPS Intel Xeon Sandy Bridge cluster. forces acting on molecules are only stored while the cell is inside the sliding window hyperthreaded sliding window Efficient vectorization: ● Optimization by hand, using advanced vector extensions (AVX). ● Conversion from array of structures (AoS) to structure of arrays (SoA). Discussed in detail by Nikola Tchipev tomorrow. Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 13

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Large-scale MD simulations on SuperMUC Scaling of ls1 mardyn examined on up to 146 016 cores, i.e. the whole SuperMUC, by Wolfgang Eckhardt and Alexander Heinecke in 2013. speedup (relative to 128 cores) homogeneous LJTS liquid with 4.8 billion molecules g n i l a c s g n o r t observed strong scaling s l a e d i number of cores Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 14

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Large-scale MD simulations on SuperMUC Up to N = 4 · 10 12 molecules on SuperMUC speedup weak scaling with 31.5 million molecules per core 2013 number of cores Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 15

Laboratory of Engineering Thermodynamics (LTD) Prof. Dr.-Ing. H. Hasse Release of ls1 mardyn released as Free Software (BSD license) Free registration for ls1 mardyn at http://www.ls1-mardyn.de/ Horsch, Srivastava, Werth, Niethammer, Glass, Eckhardt, Heinecke, Tchipev, Bungartz, Eckelsbach, Vrabec and Hasse 16