Workshop: How to run GROMACS efficiently on the LUMI supercomputer

Lecture and hands-on material for the workshop How to run GROMACS efficiently on the LUMI supercomputer,  24 – 25 January 2024, online.

The workshop gives practical tips on how to run GROMACS simulations efficiently on LUMI-G, i.e. on AMD GPUs. The participants learn how to assess and tune GROMACS performance.  In addition the course provides an overview on LUMI architecture, GROMACS heterogeneous parallelization, with a special attention to AMD GPU. The event is organized by BioExcel in collaboration with CSC and PDC

Topics

• LUMI architecture - Rasmus Kronberg (CSC)
• Brief Introduction to GROMACS - Alessandra Villa (KTH, Royal Institute of Technology)
• GROMACS parallelization / heterogeneous/GPU algorithms - Szilárd Páll (KTH, Royal Institute of Technology)
• AMD GPU support in GROMACS - Andrey Alekseenko (KTH, Royal Institute of Technology)
• How to run on LUMI - Rasmus Kronberg (CSC)
• Assessing and tuning performance of GROMACS simulations - Szilárd Páll (KTH, Royal Institute of Technology)
• Hands-on on  GPU accelerated simulations, Scaling GROMACS across multiple GPUs, Ensemble parallelization across multiple GPUs (including input files for STMV and aquaporin system, and help-with-solution files) 
• Batch scripts and reference log files for hands-on exercises can be downloaded here