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2015 | OriginalPaper | Buchkapitel

Asynchronous in Situ Processing with Gromacs: Taking Advantage of GPUs

verfasst von : Monica L. Hernandez, Matthieu Dreher, Carlos J. Barrios, Bruno Raffin

Erschienen in: High Performance Computing

Verlag: Springer International Publishing

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Abstract

Numerical simulations using supercomputers are producing an ever growing amount of data. Efficient production and analysis of these data are the key to future discoveries. The in situ paradigm is emerging as a promising solution to avoid the I/O bottleneck encountered in the file system for both the simulation and the analytics by treating the data as soon as they are produced in memory. Various strategies and implementations have been proposed in the last years to support in situ treatments with a low impact on the simulation performance. Yet, little efforts have been made when it comes to perform in situ analytics with hybrid simulations supporting accelerators like GPUs. In this article, we propose a study of the in situ strategies with Gromacs, a molecular dynamic simulation code supporting multi-GPUs, as our application target. We specifically focus on the computational resources usage of the machine by the simulation and the in situ analytics. We finally extend the usual in situ placement strategies to the case of in situ analytics running on a GPU and study their impact on both Gromacs performance and the resource usage of the machine. We show in particular that running in situ analytics on the GPU can be a more efficient solution than on the CPU especially when the CPU is the bottleneck of the simulation.

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Metadaten
Titel
Asynchronous in Situ Processing with Gromacs: Taking Advantage of GPUs
verfasst von
Monica L. Hernandez
Matthieu Dreher
Carlos J. Barrios
Bruno Raffin
Copyright-Jahr
2015
Buch
High Performance Computing

Print ISBN: 978-3-319-26927-6

Electronic ISBN: 978-3-319-26928-3

Copyright-Jahr: 2015

DOI
https://doi.org/10.1007/978-3-319-26928-3_7

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