From knights corner to landing: A case study based on a hodgkin-huxley neuron simulator

George Chatzikonstantis*, Diego Jiménez, Esteban Meneses, Christos Strydis, Harry Sidiropoulos, Dimitrios Soudris

*Corresponding author for this work

Research output: Chapter/Conference proceedingConference proceedingAcademicpeer-review

2 Citations (Scopus)

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 2.4x speed up while consuming 48% less energy than KNC.

Original languageEnglish
Title of host publicationHigh Performance Computing - ISC High Performance 2017 International Workshops, DRBSD, ExaComm, HCPM, HPC-IODC, IWOPH, IXPUG, P^3MA, VHPC, Visualization at Scale, WOPSSS, Revised Selected Papers
EditorsRio Yokota, Julian M. Kunkel, Michela Taufer, John Shalf
PublisherSpringer-Verlag
Pages363-375
Number of pages13
ISBN (Print)9783319676296
DOIs
Publication statusPublished - 2017
Event32nd International Conference on High Performance Computing, ISC High Performance 2017 - Frankfurt, Germany
Duration: 18 Jun 201722 Jun 2017

Publication series

SeriesLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10524 LNCS
ISSN0302-9743

Conference

Conference32nd International Conference on High Performance Computing, ISC High Performance 2017
Country/TerritoryGermany
CityFrankfurt
Period18/06/1722/06/17

Bibliographical note

Publisher Copyright:
© Springer International Publishing AG 2017.

Fingerprint

Dive into the research topics of 'From knights corner to landing: A case study based on a hodgkin-huxley neuron simulator'. Together they form a unique fingerprint.

Cite this