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On 30/05/2012 9:42 PM, Stephen Cox wrote:
<blockquote
cite="mid:CANkWg=-012pk50NcOzt_JHyBoS8Kgk-jGjxAhfHSD=G5OJawrw@mail.gmail.com"
type="cite">Hi Justin,<br>
<br>
Thanks for getting back and posting the links.<br>
<br>
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<br>
On 5/29/12 6:22 AM, Stephen Cox wrote:<br>
> Hi,<br>
><br>
> I'm running a number of energy minimizations on a
clathrate supercell and I get<br>
> quite significantly different values for the total energy
depending on the<br>
> number of mpi processes / number of threads I use. More
specifically, some<br>
> numbers I get are:<br>
><br>
> #cores energy<br>
> 1 -2.41936409202696e+04<br>
> 2 -2.43726425776809e+04<br>
> 3 -2.45516442350804e+04<br>
> 4 -2.47003944216983e+04<br>
><br>
> #threads energy<br>
> 1 -2.41936409202696e+04<br>
> 2 -2.43726425776792e+04<br>
> 3 -2.45516442350804e+04<br>
> 4 -2.47306458924815e+04<br>
><br>
><br>
> I'd expect some numerical noise, but these differences
seem to0 large for that.<br>
<br>
The difference is only 2%, which by MD standards, is quite
good, I'd say ;)<br>
Consider the discussion here:<br>
</blockquote>
<div><br>
I agree for MD this wouldn't be too bad, but I'd expect energy
minimization to get very close to the same local minimum from
a given starting configuration. The thing is I want to compute
a binding curve for my clathrate and compare to DFT values for
the binding energy (amongst other things), and the difference
in energy between different number of cores is rather
significant for this purpose.<br>
</div>
</div>
</blockquote>
<br>
Given the usual roughness of the PE surface to which you are
minimizing, some variation in end point is expected.<br>
<br>
<blockquote
cite="mid:CANkWg=-012pk50NcOzt_JHyBoS8Kgk-jGjxAhfHSD=G5OJawrw@mail.gmail.com"
type="cite">
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<br>
Furthermore, if I only calculate the energy for nsteps = 0
(i.e. a single point energy for identical structures) I get
the same trend as above (both mpi/openmp with domain/particle
decomposition). Surely there shouldn't be such a large
difference in energy for a single point calculation? <br>
</div>
</div>
</blockquote>
<br>
nsteps = 0 is not strictly a single-point energy, since the
constraints act before EM step 0. mdrun -s -rerun will give a single
point. This probably won't change your observations. You should also
be sure you're making observations with the latest release (4.5.5).<br>
<br>
If you can continue to observe this trend for more processors
(overallocating?), then you may have evidence of a problem - but a
full system description and an .mdp file will be in order also.<br>
<br>
Mark<br>
<br>
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cite="mid:CANkWg=-012pk50NcOzt_JHyBoS8Kgk-jGjxAhfHSD=G5OJawrw@mail.gmail.com"
type="cite">
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<br>
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<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
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<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Reproducibility"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a><br>
<br>
To an extent, the information here may also be relevant:<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation</a><br>
<br>
> Before submitting a bug report, I'd like to check:<br>
> a) if someone has seen something similar;<br>
<br>
Sure. Energies can be different due to a whole host of
factors (discussed<br>
above), and MPI only complicates matters.<br>
<br>
> b) should I just trust the serial version?<br>
<br>
Maybe, but I don't know that there's evidence to say that any
of the above tests<br>
are more or less accurate than the others. What happens if
you run with mdrun<br>
-reprod on all your tests?<br>
</blockquote>
<div><br>
Running with -reprod produces the same trend as above. If it
was numerical noise, I would have thought that the numbers
would fluctuate around some average value, not follow a
definite trend where the energy decreases with the number of
cores/threads... <br>
<br>
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<br>
> c) have I simply done something stupid (grompp.mdp
appended below);<br>
><br>
<br>
Nope, looks fine.<br>
<br>
-Justin<br>
<br>
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Thanks again for getting back to me.<br>
<br>
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