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Erschienen in:
Behavioral Emulation for Scalable Design-Space Exploration of Algorithms and Architectures Kapitel lesen Erstes Kapitel lesen

2016 | OriginalPaper | Buchkapitel

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

verfasst von : John E. Stone, Antti-Pekka Hynninen, James C. Phillips, Klaus Schulten

Erschienen in: High Performance Computing

Verlag: Springer International Publishing

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Abstract

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.

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Vorheriges Kapitel Early Application Performance at the Hartree Centre with the OpenPOWER Architecture
Nächstes Kapitel Exploring Energy Efficiency for GPU-Accelerated POWER Servers
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Metadaten
Titel
Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms
verfasst von
John E. Stone
Antti-Pekka Hynninen
James C. Phillips
Klaus Schulten
Copyright-Jahr
2016
Buch
High Performance Computing

Print ISBN: 978-3-319-46078-9

Electronic ISBN: 978-3-319-46079-6

Copyright-Jahr: 2016

DOI
https://doi.org/10.1007/978-3-319-46079-6_14

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