Supercomputing for Molecular Dynamics Simulations

Handling Multi-Trillion Particles in Nanofluidics

By: Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz

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eText | 30 March 2015

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This work presents modern implementations of relevant molecular dynamics algorithms using ls1 mardyn, a simulation program for engineering applications. The text focuses strictly on HPC-related aspects, covering implementation on HPC architectures, taking Intel Xeon and Intel Xeon Phi clusters as representatives of current platforms. The work describes distributed and shared-memory parallelization on these platforms, including load balancing, with a particular focus on the efficient implementation of the compute kernels. The text also discusses the software-architecture of the resulting code.