[gmx-users] numerical reproducibility on Gromacs 2018.3 GPU
mark.j.abraham at gmail.com
Mon Oct 22 11:33:10 CEST 2018
On Mon, Oct 22, 2018 at 11:11 AM Hubert Santuz <hubert.santuz at gmail.com>
> Hi everyone,
> I'm trying to get numerical identical results on a test system (di-alanine
> in water) with Gromacs 2018.3 version with GPU. I'm doing 100 steps in NVE.
> When I'm using GPU (gmx mdrun -nt 1 -nb gpu), I'm not getting exactly the
> same results when I launch 2 separated times the same system (same mdp,
> same gromacs version). The numerical values start to diverge at step ~1-2.
That is expected, and is by design. See
> When I discard GPU (gmx mdrun -nt 1 -nb cpu), I can get the same exactly
> results when I launch 2 separated times.
That case will work reproducibly, but in others you would want gmx mdrun
> I tried to play with verlet-buffer-tolerance = 0.00000005 or
> vdw-modifier/coulomb-modifier = None.
> I also tried the "-reprod" option in mdrun.
> Is this an expected behavior with GPU? I tried to search for documentation
> about that without success.
> Can I achieve identical numerical results with GPU in the same way as CPU?
No. That code would be slow, for no known value to users. A reproducible
force reduction could help prove the absence of some kinds of bugs, but not
that the code is correct enough (which itself depends on the particular
purpose). Even if it was reproducible, you could rotate the input box by
whatever angle, and now the trajectory will be different. Which one is
> Thanks in advance,
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