A Collaborative Simulation-Analysis Workflow for Computational Neuroscience Using HPC

  • Johanna Senk
  • Alper Yegenoglu
  • Olivier Amblet
  • Yury Brukau
  • Andrew Davison
  • David Roland Lester
  • Anna Lührs
  • Pietro Quaglio
  • Vahid Rostami
  • Andrew Rowley
  • Bernd Schuller
  • Alan Barry Stokes
  • Sacha Jennifer van Albada
  • Daniel Zielasko
  • Markus Diesmann
  • Benjamin Weyers
  • Michael Denker
  • Sonja Grün
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10164)

Abstract

Workflows for the acquisition and analysis of data in the natural sciences exhibit a growing degree of complexity and heterogeneity, are increasingly performed in large collaborative efforts, and often require the use of high-performance computing (HPC). Here, we explore the reasons for these new challenges and demands and discuss their impact with a focus on the scientific domain of computational neuroscience. We argue for the need of software platforms integrating HPC systems that allow scientists to construct, comprehend and execute workflows composed of diverse data generation and processing steps using different tools. As a use case we present a concrete implementation of such a complex workflow, covering diverse topics such as HPC-based simulation using the NEST software, access to the SpiNNaker neuromorphic hardware platform, complex data analysis using the Elephant library, and interactive visualization methods for facilitating further analysis. Tools are embedded into a web-based software platform under development by the Human Brain Project, called the Collaboratory. On the basis of this implementation, we discuss the state of the art and future challenges in constructing large, collaborative workflows with access to HPC resources.

Keywords

High-performance computing Workflows Collaboration Reproducibility Provenance tracking Simulation Neuromorphic hardware Comparative data analysis Visualization 

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Johanna Senk
    • 1
  • Alper Yegenoglu
    • 1
  • Olivier Amblet
    • 2
  • Yury Brukau
    • 2
  • Andrew Davison
    • 3
  • David Roland Lester
    • 4
  • Anna Lührs
    • 5
  • Pietro Quaglio
    • 1
  • Vahid Rostami
    • 1
  • Andrew Rowley
    • 4
  • Bernd Schuller
    • 5
  • Alan Barry Stokes
    • 4
  • Sacha Jennifer van Albada
    • 1
  • Daniel Zielasko
    • 6
    • 7
  • Markus Diesmann
    • 1
    • 8
    • 9
  • Benjamin Weyers
    • 6
    • 7
  • Michael Denker
    • 1
  • Sonja Grün
    • 1
    • 10
  1. 1.Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-BRAIN Institute I, Forschungszentrum JülichJülichGermany
  2. 2.Human Brain ProjectÉcole Polytechnique Fédérale de LausanneGenevaSwitzerland
  3. 3.Unité de Neurosciences, Information et Complexité (UNIC)Centre National de la Recherche ScientifiqueGif-sur-YvetteFrance
  4. 4.Department of Computer ScienceUniversity of ManchesterManchesterUK
  5. 5.Jülich Supercomputing Centre (JSC), Forschungszentrum JülichJülichGermany
  6. 6.Visual Computing InstituteRWTH Aachen UniversityAachenGermany
  7. 7.JARA-HPCAachenGermany
  8. 8.Department of Psychiatry, Psychotherapy and Psychosomatics, Medical FacultyRWTH Aachen UniversityAachenGermany
  9. 9.Department of Physics, Faculty 1RWTH Aachen UniversityAachenGermany
  10. 10.Theoretical Systems NeurobiologyRWTH Aachen UniversityAachenGermany

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