Accelerating dissipative particle dynamics simulations for soft matter systems
TD Nguyen and SJ Plimpton, COMPUTATIONAL MATERIALS SCIENCE, 100, 173-180 (2015).
Dissipative particle dynamics (DPD) is a coarse-grained particle-based simulation method that offers microscopic-scale insights into soft matter systems. We present an efficient implementation of a DPD model for graphical processing units (GPUs). As implemented in the LAMMPS molecular dynamics package, it can run effectively on current-generation supercomputers which often have hybrid nodes containing multi-core CPUs and (one or more) GPUs. Using efficient communication of information between the CPUs and GPUs, DPD interactions can be computed on the GPU while other portions of a full simulation model (boundary conditions, constraints, bonded interactions, diagnostic calculations, etc.) can be performed on the CPU. Our GPU-enhanced runs show a speedup of up to 9.5x versus many-core CPU simulations, and can run scalably across thousands of compute nodes. We briefly discuss how the new GPU implementation was validated against the CPU version for thermodynamics, diffusion, and hydrodynamic behavior. We also highlight large-scale models which the faster DPD implementation has enabled, for studies of monolayer self- assembly and thin-film instabilities. (C) 2014 Elsevier B.V. All rights reserved.
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