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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.

Computer Science. --- System Performance and Evaluation. --- Simulation and Modeling. --- Engineering Fluid Dynamics. --- Special Purpose and Application-Based Systems. --- Computer science. --- Software engineering. --- Computer system performance. --- Computer simulation. --- Hydraulic engineering. --- Informatique --- Génie logiciel --- Simulation par ordinateur --- Technologie hydraulique --- Engineering & Applied Sciences --- Computer Science --- Engineering, Hydraulic --- Computer modeling --- Computer models --- Modeling, Computer --- Models, Computer --- Simulation, Computer --- Computer software engineering --- Informatics --- Special purpose computers. --- Computer system failures. --- Fluid mechanics. --- Electromechanical analogies --- Mathematical models --- Simulation methods --- Model-integrated computing --- Science --- Engineering --- Fluid mechanics --- Hydraulics --- Shore protection --- Special purpose computers --- Computers --- Hydromechanics --- Continuum mechanics --- Computer failures --- Computer malfunctions --- Computer systems --- Failure of computer systems --- System failures (Engineering) --- Fault-tolerant computing --- Failures