Large-scale benchmarks with molecular-dynamics code gromacs on HPC system Viper

A team of researchers including the MPCDF used the HPC system Viper (CPU) at MPCDF to perform large-scale performance benchmarks with the molecular-dynamics simulation code gromacs.

A team of researchers led by the MPI for Multidisciplinary Natural Sciences (Goettingen), together with the MPI of Biophysics (Frankfurt) and the MPCDF (Garching) have successfully used the HPC system Viper at the MPCDF for performing large-scale benchmarks with the classical molecular dynamics (MD) code GROMACS. Their study entitled "Scaling of the GROMACS molecular dynamics code to 65k CPU cores on an HPC cluster" was recently published in the Journal of Computational Chemistry. The  benchmarks used up to 65,536 cores (in 512 nodes) of the AMD EPYC 9554 Genoa CPUs mounted in Viper (which is 2/3 of the entire machine) to simulate MD systems of various size ranging from a moderate 82,000 atoms making up a biological membrane system up an extremely large MD systems with 204 million atoms which models the so-called hNPC scaffold, which is known as the largest protein assembly in human cells. The authors emphasize that “all of these are MD systems that have actually been or are being used in scientific projects and are not synthetic benchmarks”.

The team concludes that "the combination of powerful CPUs, a fast interconnect, and well-tuned software makes it possible today to simulate extremely large MD systems with up to several hundred million atoms. For the largest system with 204 million atoms, the scaling behavior was shown to be close to ideal, with parallel efficiencies above 0.9 even at the highest parallelization levels (512 nodes with altogether 65,536 cores), while maintaining high energy efficiency. This demonstrates that modern HPC machines now provide the level of performance needed for simulating MD systems of the size of viruses, organelles, and eventually, small cells”.

Original publication: Kutzner, C., Miletić, V., Palacio Rodríguez, K., Rampp, M., Hummer, G., de Groot, B.L. and Grubmüller, H. (2025), Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. J Comput Chem, 46: e70059. https://doi.org/10.1002/jcc.70059