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Supercomputing for Molecular Dynamics Simulations [electronic resource] : Handling Multi-Trillion Particles in Nanofluidics / by Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz.

By: Heinecke, Alexander [author.].
Contributor(s): Eckhardt, Wolfgang [author.] | Horsch, Martin [author.] | Bungartz, Hans-Joachim [author.] | SpringerLink (Online service).
Material type: materialTypeLabelBookSeries: SpringerBriefs in Computer Science: Publisher: Cham : Springer International Publishing : Imprint: Springer, 2015Description: X, 76 p. 35 illus., 13 illus. in color. online resource.Content type: text Media type: computer Carrier type: online resourceISBN: 9783319171487.Subject(s): 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 SystemsAdditional physical formats: Printed edition:: No titleDDC classification: 004.24 Online resources: Click here to access online
Contents:
Introduction -- Molecular Dynamics Simulation -- Parallelization of MD Algorithms and Load Balancing -- Efficient Implementation of the Force Calculation in MD Simulations -- Experiments -- Conclusion.
In: Springer eBooksSummary: 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.
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Introduction -- Molecular Dynamics Simulation -- Parallelization of MD Algorithms and Load Balancing -- Efficient Implementation of the Force Calculation in MD Simulations -- Experiments -- Conclusion.

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.

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