High Performance Computing for neuroscience: Hands-on introduction to supercomputing usage, tools and applications

3rd HBP Curriculum Workshop Series - ICT for non-specialists

9-11 July 2019 | Forschungszentrum Jülich, Germany


2nd ict workshop

Neuroscience research has become increasingly interdisciplinary in recent years. New imaging technologies deliver ultra-high resolution images, and new simulator technology enables scientists to simulate larger and more detailed neural networks. Such data can no longer be analysed and such simulations can no longer be run solely on a user’s computer in the office: clusters, supercomputers and good data management strategies have become indispensable. This HBP Education Workshop will set the grounds for the students to get started with high-performance computing (HPC)-based research and thus lays the foundation for them to advance the state of the art in their fields.

The workshop will teach the basics of supercomputing needed for starting to use HPC systems for (neuroscience) research. This includes on the one hand introductory lectures with hands-on sessions about scientific computing in Python and an introduction to the usage of HPC systems and (big) data management. On the other hand, the students will get hands-on training for tools and applications that can both be used on a supercomputer as well as on the user’s local computer, for instance the simulators NEST (for point-neuron models) and Arbor (for morphologically detailed neuron models), and visualisation tools that can handle large imaging or simulation data as generated on a supercomputer. The tools and applications presented are developed in the HBP High Performance Analytics and Computing (HPAC) Platform. The introductory lectures also enable the students to make efficient use of the other HBP Platforms, in particular the Neuroinformatics, the Brain Simulation and the Neurorobotics Platforms that use the HPAC Platform as a back-end.


Application deadline: 3 June 2019






The scientific programme will be available soon.



  • Benjamin Cumming - Getting started with Arbor 
    Swiss National Supercomputing Centre (CSCS), Switzerland
  • Fahad Khalid - Introduction to Python part I & II
    Forschungszentrum Jülich (JUELICH), Germany
  • Wouter Klijn - Scientific computing in Python part I  & II
    Forschungszentrum Jülich (JUELICH), Germany
  • Susanne Kunkel - Getting started with NEST 
    Norwegian University of Life Sciences (NMBU), Norway
  • Alberto Madonna - Introduction to High-Performance Computing 
    Swiss National Supercomputing Centre (CSCS), Switzerland
  • Jan Meinke - Introduction to parallel computing part I & II
    Forschungszentrum Jülich (JUELICH), Germany
  • Abigail Morrison
    - Welcome & introduction by the Scientific Chair 
    - Introduction to the focus exercises 
    Forschungszentrum Jülich (JUELICH), Germany
  • Andreas Müller - Guided tour to the supercomputing facilities at Jülich Supercomputing Centre
    Forschungszentrum Jülich (JUELICH), Germany
  • Lena Oden - HPC data management 
    FernUniversität in Hagen, Germany
  • Benjamin Weyers - Interactive visual data analysis 
    RWTH Aachen University (RWTH), Germany


Abigail Morrison | JUELICH



Lisa-Marie Leichter | MUI
Anna Lührs | JUELICH
Alexander Peyser | JUELICH



The Open Day of the Jülich Research Centre will take place 2 days prior to the workshop (Sunday, 7 July 2019). If you are interested in exploring the campus and if you want to visit several institutions or talk to the Jülich scientists, you can visit the Open Day for free. Find more information about it on the website.