I dont'know if this is the right way to test that things
converge to the same value...but I have made an energy
minimization on CPU of the two output (parallel and
serial). I have obtained this results:
FROM PARALLEL OUTPUT
Potential Energy = -1.6960029e+04
Maximum force = 1.7282695e+03 on atom 364
Norm of force = 4.6171844e+02
FROM SERIAL OUTPUT
Potential Energy = -1.7814945e+04
Maximum force = 2.1551072e+03 on atom 496
Norm of force = 2.9537823e+02
Thanks,
Giulia
On Wed, 14 Apr 2010 16:58:37 +1000
Mark Abraham <[email protected]> wrote:
On 14/04/2010 4:52 PM, PACIELLO GIULIA wrote:
Ok...so how could I know the energies among atoms?
Since it's not reported, you can't get breakdowns of
energies. That's a limitation from the use of GPU. If you
want this information, perhaps do your simulation on the
GPU and re-rerun selected frames from your trajectory on
a different machine that does not use GPUs.
And how can I test if
my parallel code is running in the correct manner?
MD is chaotic. Tiny differences at an early stage lead
to wildly
different results later. That's inevitable. However
ensemble averages
should converge to the same value.
Do things converge to the same values? There's a chance
that mdrun -reprod will lead to equivalent total energies
after only one step, if that's been implemented that way.
Mark
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