Performance improvements#
Improved performance for inhomogeneous systems#
The performance of systems with a lot of empty space is improved by optimizing the pair search grid for the effective atom density.
Flexible hydrogen mass repartitioning using grompp#
Instead of using pdb2gmx, which modifies the topology, a flexible
scheme for hydrogen mass repartitioning is now available in grompp
through the mass-repartition-factor mdp option. This provides
easy access to a performance improvement of close to a factor two.
Small performance regression to achieve more accurate pressure#
To lower the effect on Lennard-Jones pair interaction on the pressure, the Verlet buffer has been increased for most simulations using default mdp settings. This can lead to a few percent performance loss, in particular when using GPUs. The effect will be strongest for systems with no or weak electrostatics, which includes most coarse-grained systems.
HeFFTe multi-GPU FFT plan options are now configurable#
New environment variables GMX_HEFFTE_RESHAPE_ALGORITHM,
GMX_HEFFTE_USE_GPU_AWARE, GMX_HEFFTE_USE_PENCILS, and
GMX_HEFFTE_USE_REORDER permit the HeFFTe plan options to be
configured at run time. The performance obtained can vary with the
quality of implementation of e.g. the GPU-aware MPI library, as well
as the layout and number of the GPUs participating in the 3D-FFT.
Users can now find and use the best settings for their case. See
the HeFFTe documentation for more details.