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From Knights Corner to Landing: A Case Study Based on a Hodgkin-Huxley Neuron Simulator

  • George ChatzikonstantisEmail author
  • Diego Jiménez
  • Esteban Meneses
  • Christos Strydis
  • Harry Sidiropoulos
  • Dimitrios Soudris
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10524)

Abstract

Brain modeling has been presenting significant challenges to the world of high-performance computing (HPC) over the years. The field of computational neuroscience has been developing a demand for physiologically plausible neuron models, that feature increased complexity and thus, require greater computational power. We explore Intel’s newest generation of Xeon Phi computing platforms, named Knights Landing (KNL), as a way to match the need for processing power and as an upgrade over the previous generation of Xeon Phi models, the Knights Corner (KNC). Our neuron simulator of choice features a Hodgkin-Huxley-based (HH) model which has been ported on both generations of Xeon Phi platforms and aggressively draws on both platforms’ computational assets. The application uses the OpenMP interface for efficient parallelization and the Xeon Phi’s vectorization buffers for Single-Instruction Multiple Data (SIMD) processing. In this study we offer insight into the efficiency with which the application utilizes the assets of the two Xeon Phi generations and we evaluate the merits of utilizing the KNL over its predecessor. In our case, an out-of-the-box transition on Knights Landing, offers on average 2.4\(\times \) speed up while consuming 48% less energy than KNC.

Keywords

Intel Xeon Phi Knights landing Computational neuroscience 

Notes

Acknowledgments

This work is partially supported by European Commission project H2020–687628–VINEYARD.

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • George Chatzikonstantis
    • 1
    Email author
  • Diego Jiménez
    • 2
  • Esteban Meneses
    • 2
    • 3
  • Christos Strydis
    • 4
  • Harry Sidiropoulos
    • 1
  • Dimitrios Soudris
    • 1
  1. 1.Microprocessors and Digital Systems LabNational Technical University of AthensAthensGreece
  2. 2.Advanced Computing LaboratoryCosta Rica National High Technology CenterSan JoséCosta Rica
  3. 3.School of ComputingCosta Rica Institute of TechnologyCartagoCosta Rica
  4. 4.Neuroscience DepartmentErasmus Medical Center RotterdamRotterdamNetherlands

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