[gmx-users] Possible bug: energy changes with the number of nodes for energy minimization

[Justin A. Lemkul]

On 5/29/12 6:22 AM, Stephen Cox wrote:
> Hi,
>
> I'm running a number of energy minimizations on a clathrate supercell and I get
> quite significantly different values for the total energy depending on the
> number of mpi processes / number of threads I use. More specifically, some
> numbers I get are:
>
> #cores      energy
> 1        -2.41936409202696e+04
> 2        -2.43726425776809e+04
> 3        -2.45516442350804e+04
> 4        -2.47003944216983e+04
>
> #threads    energy
> 1        -2.41936409202696e+04
> 2        -2.43726425776792e+04
> 3        -2.45516442350804e+04
> 4        -2.47306458924815e+04
>
>
> I'd expect some numerical noise, but these differences seem to0 large for that.

The difference is only 2%, which by MD standards, is quite good, I'd say ;) 
Consider the discussion here:

http://www.gromacs.org/Documentation/Terminology/Reproducibility

To an extent, the information here may also be relevant:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation

> Before submitting a bug report, I'd like to check:
> a) if someone has seen something similar;

Sure.  Energies can be different due to a whole host of factors (discussed 
above), and MPI only complicates matters.

> b) should I just trust the serial version?

Maybe, but I don't know that there's evidence to say that any of the above tests 
are more or less accurate than the others.  What happens if you run with mdrun 
-reprod on all your tests?

> c) have I simply done something stupid (grompp.mdp appended below);
>

Nope, looks fine.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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