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ExaStamp: A Parallel Framework for Molecular Dynamics on Heterogeneous Clusters

  • Emmanuel Cieren
  • Laurent Colombet
  • Samuel Pitoiset
  • Raymond Namyst
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8806)

Abstract

Recent evolution of supercomputer architectures toward massively multi-cores nodes equipped with many-core accelerators is leading to make MPI-only applications less effective. To fully tap into the potential of these architectures, hybrid approaches – mixing MPI, threads and CUDA or OpenCL – usually meet performance expectations, but at the price of huge development and optimization efforts.

In this paper, we present a programming framework specialized for molecular dynamics simulations. This framework allows end-users to develop their computation kernels in the form of sequential-looking functions and generates multi-level parallelism combining vectorized and SIMD kernels, multi-threading and communications. We report on preliminary performance results obtained on different architectures with widely used force computation kernels.

Keywords

Molecular dynamics MPI threads TBB vectorization OpenCL object-oriented design Lennard-Jones EAM 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Emmanuel Cieren
    • 1
  • Laurent Colombet
    • 1
  • Samuel Pitoiset
    • 2
  • Raymond Namyst
    • 2
  1. 1.CEA, DAM, DIFArpajonFrance
  2. 2.Université de Bordeaux, INRIATalence CedexFrance

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