Supercomputing for Molecular Dynamics Simulations: Handling Multi-Trillion Particles in Nanofluidics

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 impleme...