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

• Main Authors: Heinecke, Alexander (Author), Eckhardt, Wolfgang (Author), Horsch, Martin (Author), Bungartz, Hans-Joachim (Author)
• Corporate Author: SpringerLink (Online service)
• Format: Electronic eBook
• Language: English
• Published: Cham : Springer International Publishing : Imprint: Springer, 2015.
• Series: SpringerBriefs in Computer Science,
• Subjects: Computer science.; Special purpose computers.; Computer system failures.; Computer simulation.; Fluid mechanics.; Computer Science.; System Performance and Evaluation.; Simulation and Modeling.; Engineering Fluid Dynamics.; Special Purpose and Application-Based Systems.
• Physical Description: X, 76 p. 35 illus., 13 illus. in color. online resource.
• ISBN: 9783319171487
• ISSN: 2191-5768

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.