Developer Blog: Creating Faster Molecular Dynamics Simulations with GROMACS 2020

GROMACS—one of the most widely used HPC applications— has received a major upgrade with the release of GROMACS 2020. The new version includes exciting new performance improvements resulting from a long-term collaboration between NVIDIA and the core GROMACS developers.

As a simulation package for biomolecular systems, GROMACS evolves particles using the Newtonian equations of motion. Forces dictate movement: for example, two positively charged ions repel each other. Calculating forces is the most expensive part of the simulation because all pairs of particles can potentially interact, and simulations involve many particles.

In previous GROMACS releases, GPU acceleration was already supported for these force classes (the CUDA Fast Fourier Transform library is used within the PME force calculation). The most recent addition was GPU bonded forces in the 2019 series, developed through a previous collaboration between NVIDIA and the core GROMACS developers.

However, there was still a problem. The force calculations have become so fast on modern GPUs that other parts of the simulation have become very significant in term of computational expense, especially when you want to use multiple GPUs for a single simulation.

This post describes the new performance features available in the 2020 version that address this issue.  For many typical simulations, the whole timestep can now run on the GPU, avoiding CPU and PCIe bottlenecks. Inter-GPU communication operations can now operate directly between GPU memory spaces. The results from this work demonstrate large performance improvements.

Comparison of GROMACS 2019 to GROMACS 2020 using three multi-GPU simulation examples.

Read the full post, Creating Faster Molecular Dynamics Simulations with GROMACS 2020, on the NVIDIA Developer Blog.