Heinecke, Alexander.
Supercomputing for Molecular Dynamics Simulations Handling Multi-Trillion Particles in Nanofluidics / [electronic resource] : by Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz. - X, 76 p. 35 illus., 13 illus. in color. online resource. - SpringerBriefs in Computer Science, 2191-5768 . - SpringerBriefs in Computer Science, .
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.
9783319171487
10.1007/978-3-319-17148-7 doi
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.
QA76.9.E94
004.24
Supercomputing for Molecular Dynamics Simulations Handling Multi-Trillion Particles in Nanofluidics / [electronic resource] : by Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz. - X, 76 p. 35 illus., 13 illus. in color. online resource. - SpringerBriefs in Computer Science, 2191-5768 . - SpringerBriefs in Computer Science, .
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.
9783319171487
10.1007/978-3-319-17148-7 doi
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.
QA76.9.E94
004.24