November 2022 to October 2025


Ivo Kabadshow

Building 16.3 / Room R 215

+49 2461/61-8714



Computational time optimized exascale simulations for biomedical applications

High-performance computing (HPC) is now one of the fundamental research methods in many scientific disciplines. High-performance computers have been reaching the exaflop performance class (at least 1018 operations per second) since this year. For applications to efficiently exploit the power of exascale systems, scalability must be improved on very large and heterogeneous systems. A variety of components are required for modern high-performance computing: from processors to data storage and file systems to software and algorithms. All these components also require new technologies and adaptations to specific applications and interfaces.

The objective of the FlexFMM project led by JSC is the realistic simulation of large interacting biomolecules via GROMACS on upcoming exascale hardware. Emphasis is placed on a scalable and flexible Fast Multipole Method (FMM) as an electrostatic solver. Its low communication complexity, dynamic protonation features, and support for non-periodic and highly inhomogeneous particle systems allow for new biomedical developments. Additionally, the project is focused on fully leveraging SiPearl’s upcoming ARM hardware with SVE vector units and HBM memory to future-proof well-established simulation tools and pave the way for exascale.

Molecular simulations are fundamental to our understanding of biological processes and are an important part of medical research. For example, they contribute to the understanding of diseases or help in the development of new drugs. The new energy-efficient simulation methods significantly expand the possibilities of novel exascale systems and the range of applications.