HLRS High Performance Computing Center Stuttgart: GENE/GENE-X user training and tutorial

Prerequisites and content levels

Prerequisites:

Participants are expected to have basic skills in Unix-based operating systems, including navigating terminals and using SSH, as well as some familiarity with text editors such as vi/emacs. Knowledge of compiling code is helpful but not strictly necessary.
Additionally, participants should have a basic understanding of Python, as it is required for both preprocessing and post-processing simulation in- and output.
To participate in the program, individuals preferably have their own account on a cluster or supercomputer where the GENE and/or GENE-X codes can be installed. It is recommended that participants contact the organizers beforehand to confirm that their cluster is suited for this workshop and to clarify any questions they may have. Finally, participants should have a small budget (few kCPUh) allocated on a cluster to perform code verification tests and hands-on submissions of small test jobs.
- For EU residents it is possible to get a workshop account on Leonardo Booster at CINECA through ENCCS and SIDE. Please indicate the necessity in the registration form. A short basic introductory course can be attended online on Monday morning, where working on Leonardo Booster is introduced.

Content levels:

Advanced: 27 hours 45 minutes

Learn more about course curricula and content levels.

Instructors

Learning outcomes

The training is addressed to plasma turbulence specialists and/or PhD/Master students, who want to learn (or improve their knowledge of) corresponding GENE/GENE-X simulations skills.

Agenda

The presentation times listed in the agenda are tentative.
1st day – Monday, 12 January 2026

12:45 - 13:00 Join in
13:00 - 13:10 Welcome
13:10 - 13:55 Introduction to GENE - GENE Family, Physics Models used in GENE
13:55 - 14:40 GENE - Numerical Methods
14:40 - 15:10 Break
15:10 - 15:55 GENE - optimization approaches
15:55 - 16:40 Post-processing GENE generated files
16:40 - 17:00 Q & A and requests for the next day

2nd day – Tuesday, 13 January 2026

09:00 - 10:00 Installing and Running GENE - basic introduction
10:00 - 11:00 Setting up GENE simulations - avoiding pitfalls on CPU/GPU, parameter scans, etc
11:00 - 11:15 Break
11:15 - 12:00 Hands-On Session I: Starting a number of GENE flux-tube simulations
12:00 - 13:30 Lunch
13:30 - 14:30 Hands-On Session II: Flux-tube simulations and analysis
14:30 - 15:00 Break
15:00 - 16:30 Hands-On Session III: Global GENE simulations
16:30 - 17:00 Q & A and closing

3rd day – Wednesday, 14 January 2026

09:00 - 10:30 Introduction to GENE-X for users
10:30 - 11:00 Break
11:00 - 11:45 Installing the code: first steps
11:45 - 13:00 Lunch
13:00 - 14:00 Parameters required for a GENE-X simulation
14:00 - 15:00 Hands on: installation and first steps
15:00 - 15:30 Break
15:30 - 17:00 Hands on: setting up a simulation test case

4rd day – Thursday, 15 January 2026

09:00 - 10:15 Overview of GENE-X postprocessing tools
10:15 - 10:30 Break
10:30 - 11:00 How to install the Torx library
11:00 - 12:00 Hands on: installation of Torx and first steps
12:00 - 13:30 Lunch
13:30 - 15:00 Creating your own postprocessing notebooks with Torx
15:00 - 15:30 Break
15:30 - 16:15 Optimize simulation performance
16:15 - 17:00 Simulation pitfalls

5th day – Friday, 16 January 2026

09:00 - 10:15 GENE-X equilibrium and data preprocessing
10:15 - 10:30 Break
10:30 - 12:00 Hands on: bring your own case to preprocess
12:00 - 13:30 Lunch
13:30 - 14:45 Hands on: setup your own case
14:45 - 15:00 Break
15:00 - 16:40 Reserved for requests / Closing

Handout

A link to the course material (slides and exercises) will be available at course start

Registration information

Register via the button at the top of this page.
This course will be hybrid, i.e. it will take place at the Max Planck Computing & Data Facility (MPCDF) in Garching on-site but it will also be possible to attend online. Participants, online as well as on-site, have to be aware and agree that they might appear in the live video stream taken by a camera in the back of the lecture room or by a webcam on laptops. We strongly recommend to attend this course on-site since on-site attendance is much more effective and efficient in our experience, also this helps to foster collaborations and community-building. Therefore we might give priority to on-site over online participants during registration.

Please be aware that the Zoom session will be recorded. You declare that you are aware of and consent to the recording by registering.

Registration closes on Monday, 5 January 2026.

Fees

Students without Master's degree or equivalent. Participants from EU or EuroCC countries only: 0 EUR
PhD students or employees at a German university or public research institute: 0 EUR
PhD students or employees at a university or public research institute in an EU or EuroCC country other than Germany: 0 EUR.
Other participants, e.g., from industry, other public service providers, or government. Participants from EU or EuroCC countries only: 0 EUR

Our course fee includes coffee breaks (in classroom courses only).

For lists of EU and EuroCC countries have a look at the Horizon Europe and EuroCC website.

Only participants from institutions belonging to these countries can take part in this course.

Contact

Tobias Haas phone 0711 685 87223, training(at)hlrs.de

HLRS Training Collaborations in HPC and AI

HLRS is part of the Gauss Centre for Supercomputing (GCS), together with JSC in Jülich and LRZ in Garching near Munich. SIDE is the German National Competence Centre (NCC) for High-Performance Computing. HLRS is also a member of the Baden-Württemberg initiative bwHPC.
Since 2025, HLRS has been coordinating one of the AI Factories of the EuroHPC JU: HammerHAI.

This is a joint training event of Max Planck Institute of Plasma Physics (IPP), Max Planck Computing and Data Facility (MPCDF) in collaboration with the Plasma-PEPSC CoE and SIDE, ENCCS.

Acknowledgements

Within the scope of the EuroCC2 project this training is offered free of charge. By participating in a training free of charge, companies receive state-aid corresponding to the regular market-prices listed in the service portfolio. Please note state-aid regulations in Germany.

EuroCC 2 and EuroCC4SEE have received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 101101903 and No 101191697. The JU receives support from the European Union’s Digital Europe Programme and Germany, Bulgaria, Austria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, Greece, Hungary, Ireland, Italy, Lithuania, Latvia, Poland, Portugal, Romania, Slovenia, Spain, Sweden, France, Netherlands, Belgium, Luxembourg, Slovakia, Norway, Türkiye, Republic of North Macedonia, Iceland, Montenegro, Serbia, Bosnia and Herzegovina.

Further courses and training team

See the training overview and the Supercomputing Academy pages.
See also information about the HLRS training department and staff.

High-Performance Computing Center Stuttgart

GENE/GENE-X user training and tutorial

Location

Prerequisites and content levels

Prerequisites:

Content levels:

Instructors

Learning outcomes

Agenda

Handout

Registration information

Fees

Contact

HLRS Training Collaborations in HPC and AI

Acknowledgements

Further courses and training team

Related training

All training

Introduction to OpenMP Offloading with AMD GPUs

Scientific Visualization

Hackathon: Porting and Optimization for Hunter

HiDALGO2: From Building to City Energy Simulation

Fortran for Scientific Computing

Hybrid Programming in HPC – MPI+X

Supercomputing Academy: HPC-Cluster - Design, Cost, and Sustainability

Introduction to Computational Fluid Dynamics

CFD with OpenFOAM®

Iterative Linear Solvers and Parallelization