GROMACS version: 2023.1 and later
GROMACS modification: Yes/No
I want to run FE code on GPU only. In GROMACS tutorials it is recommended to use SD integrator, which is not supported in GROMACS 2023.1 on GPU. Also, from my tests, I see that virtual sites are not supported on GPU, and constraints = all-bonds. I wonder:
- Is there a list of options that are currently compatible with running on GPU only?
- Is there a list of .mdp options recommended for FE simulations (in particular, for a protein-ligand system of 20k atoms is it ok to run FE with v-rescale thermostat and c-rescale barostat and md integrator, or sd integrator would be anyway preferred? Same question for a membrane protein-ligand system of 150k atoms?)
- Is there a plan for implementing virtual sites support on GPU for FE code?
After careful reading of documentation, I found this list. But it does not seem complete to me. integrator=sd in combination with mdrun -update GPU does not work. So I wonder if there is a more complete list of limitations somewhere
Also, after reading this part, it is not 100% clear to me if FE code is actually run CPU only or not. If FE code can only be run on CPU, I wonder if there is maybe some internal (or external) benchmark available on how many CPUs are worth using for systems of different sizes when all/some of the tasks are offloaded on GPUs.
Hi!
The list you linked refers to the limitations of specifically PME on GPU. Unfortunately, we don’t have such a list for GPU update / GPU-resident mode; but the code should be pretty readable. We have plans of implementing SD integrator on GPUs in GROMACS 2025; no plans for VSites that I know of.