poster

First impressions from detailed brain model simulations on a Xeon/Xeon-Phi node

Authors:

George Chatzikonstantis,

Dimitrios Rodopoulos,

Christos Strydis,

Chris I. De Zeeuw,

Dimitrios SoudrisAuthors Info & Claims

CF '16: Proceedings of the ACM International Conference on Computing Frontiers

Pages 361 - 364

https://doi.org/10.1145/2903150.2903477

Published: 16 May 2016 Publication History

Abstract

The development of physiologically plausible neuron models comes with increased complexity, which poses a challenge for many-core computing. In this work, we have chosen an extension of the demanding Hodgkin-Huxley model for the neurons of the Inferior Olivary Nucleus, an area of vital importance for motor skills. The computing fabric of choice is an Intel Xeon-Xeon Phi system, widely-used in modern computing infrastructure. The target application is parallelized with combinations of MPI and OpenMP. The best configurations are scaled up to human InfOli numbers.

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Cited By

Chatzikonstantis GRodopoulos DStrydis CDe Zeeuw CSoudris D(2017)Optimizing Extended Hodgkin-Huxley Neuron Model Simulations for a Xeon/Xeon Phi NodeIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2017.268638928:9(2581-2594)Online publication date: 1-Sep-2017
https://dl.acm.org/doi/10.1109/TPDS.2017.2686389
Smaragdos GChatzikonstantis GKukreja RSidiropoulos HRodopoulos DSourdis IAl-Ars ZKachris CSoudris DDe Zeeuw CStrydis C(2017)BrainFrame: a node-level heterogeneous accelerator platform for neuron simulationsJournal of Neural Engineering10.1088/1741-2552/aa7fc514:6(066008)Online publication date: 13-Nov-2017
https://doi.org/10.1088/1741-2552/aa7fc5
Chatzikonstantis GJiménez DMeneses EStrydis CSidiropoulos HSoudris D(2017)From Knights Corner to Landing: A Case Study Based on a Hodgkin-Huxley Neuron SimulatorHigh Performance Computing10.1007/978-3-319-67630-2_27(363-375)Online publication date: 20-Oct-2017
https://doi.org/10.1007/978-3-319-67630-2_27

Index Terms

First impressions from detailed brain model simulations on a Xeon/Xeon-Phi node
1. Applied computing
  1. Life and medical sciences
    1. Computational biology
      1. Biological networks

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Information & Contributors

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Published In

cover image ACM Conferences

CF '16: Proceedings of the ACM International Conference on Computing Frontiers

May 2016

487 pages

ISBN:9781450341288

DOI:10.1145/2903150

General Chairs:
Gianluca Palermo
Politecnico di Milano, IT
,
John Feo
Pacific Northwest National Laboratory and Northwest Institute for Advanced Computing
,
Program Chairs:
Antonino Tumeo
Pacific Northwest National Laboratory, USA
,
Hubertus Franke
New York University and IBM Research, USA

Copyright © 2016 Owner/Author.

Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

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ACM: Association for Computing Machinery
Politecnico di Milano: Politecnico di Milano
SIGMICRO: ACM Special Interest Group on Microarchitectural Research and Processing
IBM: IBM

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 16 May 2016

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Sponsor:

Micron Foundation
ACM
Politecnico di Milano
SIGMICRO
IBM

CF'16: Computing Frontiers Conference

May 16 - 19, 2016

Como, Italy

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CF '16 Paper Acceptance Rate 30 of 94 submissions, 32%;

Overall Acceptance Rate 273 of 785 submissions, 35%

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Cited By

Chatzikonstantis GRodopoulos DStrydis CDe Zeeuw CSoudris D(2017)Optimizing Extended Hodgkin-Huxley Neuron Model Simulations for a Xeon/Xeon Phi NodeIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2017.268638928:9(2581-2594)Online publication date: 1-Sep-2017
https://dl.acm.org/doi/10.1109/TPDS.2017.2686389
Smaragdos GChatzikonstantis GKukreja RSidiropoulos HRodopoulos DSourdis IAl-Ars ZKachris CSoudris DDe Zeeuw CStrydis C(2017)BrainFrame: a node-level heterogeneous accelerator platform for neuron simulationsJournal of Neural Engineering10.1088/1741-2552/aa7fc514:6(066008)Online publication date: 13-Nov-2017
https://doi.org/10.1088/1741-2552/aa7fc5
Chatzikonstantis GJiménez DMeneses EStrydis CSidiropoulos HSoudris D(2017)From Knights Corner to Landing: A Case Study Based on a Hodgkin-Huxley Neuron SimulatorHigh Performance Computing10.1007/978-3-319-67630-2_27(363-375)Online publication date: 20-Oct-2017
https://doi.org/10.1007/978-3-319-67630-2_27

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