Hello,
I am not sure that this is really a problem. You will tend to have
deviations between the two versions mostly because of reductions when
working in parallel (MPI_(All)_Reduce).
Seeing deviations after 500 steps is therefore not unsurprising,
especially because you use a 2 fs timestep (which is somewhat a limit
here). Try reducing the timestep to 1 fs or even 0.5 fs and you
will/should see that both MD are similar for a longer time (better than
linearly I mean).
Gerald.
On 12/01/2017 06:26 PM, Yinglong Miao wrote:
> Hi All,
>
> As I tried MPI code of the latest AMBER for both the CPU and GPU versions,
> energies output from the MPI code start to deviate from those of serial
> code after hundreds of MD steps. The energies are so different that they
> lead to different temperatures (and probably trajectories) of system:
>
> diff md-1-cpu.out md-1-cpu-mpi.out | grep "NSTEP " | more
> < NSTEP = 583 TIME(PS) = 41.166 TEMP(K) = 306.91 PRESS
> = 0.0
>> NSTEP = 583 TIME(PS) = 41.166 TEMP(K) = 306.90 PRESS
> = 0.0
> ...
> < NSTEP = 900 TIME(PS) = 41.800 TEMP(K) = 302.37 PRESS
> = 0.0
>> NSTEP = 900 TIME(PS) = 41.800 TEMP(K) = 300.97 PRESS
> = 0.0
>
> The system I tested was the very small alanine dipeptide (input files are
> attached). I would expect the deviation may happen sooner for bigger
> systems like proteins. Yes, there could be accumulated rounding errors, but
> how do we evaluate whether our MPI simulations are still accurate, with no
> errors in the code?
>
> A naive question, but I will appreciate any suggestions ...
>
> Yinglong
>
>
>
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
____________________________________________________________________________
Prof. Gerald MONARD
Directeur du mésocentre EXPLOR
Université de Lorraine
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e-mail : Gerald.Monard.univ-lorraine.fr
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Received on Fri Dec 01 2017 - 12:30:03 PST
