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SNAP: Strong scaling high fidelity molecular dynamics simulations on leadership-class computing platforms

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Trott, Christian R.; Hammond, Simon D.; Thompson, Aidan P.

The rapidly improving compute capability of contemporary processors and accelerators is providing the opportunity for significant increases in the accuracy and fidelity of scientific calculations. In this paper we present performance studies of a new molecular dynamics (MD) potential called SNAP. The SNAP potential has shown great promise in accurately reproducing physics and chemistry not described by simpler potentials. We have developed new algorithms to exploit high single-node concurrency provided by three different classes of machine: the Titan GPU-based system operated by Oak Ridge National Laboratory, the combined Sequoia and Vulcan BlueGene/Q machines located at Lawrence Livermore National Laboratory, and the large-scale Intel Sandy Bridge system, Chama, located at Sandia. Our analysis focuses on strong scaling experiments with approximately 246,000 atoms over the range 1-122,880 nodes on Sequoia/Vulcan and 40-18,630 nodes on Titan. We compare these machine in terms of both simulation rate and power efficiency. We find that node performance correlates with power consumption across the range of machines, except for the case of extreme strong scaling, where more powerful compute nodes show greater efficiency. This study is a unique assessment of a challenging, scientifically relevant calculation running on several of the world's leading contemporary production supercomputing platforms. © 2014 Springer International Publishing.

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TYPE Conference YEAR 2014
DOIOSTIScopusDOIOSTIScopus

Reducing the bulk of the bulk synchronous parallel model

Parallel Processing Letters

Barrett, Richard F.; Vaughan, Courtenay T.; Hammond, Simon D.

For over two decades the dominant means for enabling portable performance of computational science and engineering applications on parallel processing architectures has been the bulk-synchronous parallel programming (BSP) model. Code developers, motivated by performance considerations to minimize the number of messages transmitted, have typically pursued a strategy of aggregating message data into fewer, larger messages. Emerging and future high-performance architectures, especially those seen as targeting Exascale capabilities, provide motivation and capabilities for revisiting this approach. In this paper we explore alternative configurations within the context of a large-scale complex multi-physics application and a proxy that represents its behavior, presenting results that demonstrate some important advantages as the number of processors increases in scale.

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TYPE Journal Article YEAR 2013
OSTIDOI

The impact of hybrid-core processors on MPI message rate

ACM International Conference Proceeding Series

Barrett, Brian B.; Brightwell, Ronald B.; Hammond, Simon D.; Hemmert, Karl S.

Power and energy concerns are motivating chip manufacturers to consider future hybrid-core processor designs that combine a small number of traditional cores optimized for single-thread performance with a large number of simpler cores optimized for throughput performance. This trend is likely to impact the way compute resources for network protocol processing functions are allocated and managed. In particular, the performance of MPI match processing is critical to achieving high message throughput. In this paper, we analyze the ability of simple and more complex cores to perform MPI matching operations for various scenarios in order to gain insight into how MPI implementations for future hybrid-core processors should be designed.

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TYPE Conference YEAR 2013
OSTIScopus
Results 226–250 of 266
Results 226–250 of 266