Berk Hess is a project leader in the development of GROMACS, one of the most popular molecular dynamics software packages available today. He is an Associate Professor in the Department of Biophysics at KTH in Stockholm.
Strong and ensemble scaling of biomolecular simulation with GROMACS
Molecular dynamics simulations of biomolecules are an extreme strong scaling challenge, as the system size is fixed, but billions of time steps need to be computed sequentially. This puts strong demands on both hardware and software. On the other hand, the goal is never to compute a single number, but always involves properties of distributions from ensembles. In this talk challenges and scaling approaches in the GROMACS molecular simulation package will be discussed, with a focus on hybrid CPU-GPU acceleration. This work has been done in the context of BioExcel, the EU Centre of Excellence for Computational Biomolecular Research, which focuses on scalability and usability of biomolecular software.