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
--
========================================
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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