Hi Fernando,
It would help to see select excerpts from your output files in order to be
able to understand exactly what you are describing here. Firstly why the
GPU code is deterministic on identical hardware this is not necessarily
true when changing the value of ntpr. The reason for this is that the code
only calculates the energy when it is needed for printing. Normally it
just calculates the gradients. Hence when you change ntpr you change the
amount of work being done and this leads to different rounding differences
that will lead to natural divergence of the MD trajectory. This is
perfectly fine since you should always be running sufficient length runs
to converge the properties you are interested in.
Thus what you are reporting is probably reasonable but it would need a lot
more info to understand fully.
Another note though. You mention CUDA 4.0. Currently AMBER 12 with the
latest patches, including a number of bug fixes for GPU only supports CUDA
4.2. This suggests to me that you are running with unlatched code. I would
suggest running configure to apply the latest patches and then recompiling
from scratch with cuda 4.2.
All the best
Ross
On 11/23/12 3:14 AM, "Fernando Martín García" <fmgarcia.cbm.uam.es> wrote:
> Dear Amber users,
>
> I have a doubt about ntpr option and GPU (and maybe CPU). I usually run
> my simulations with ntpr =1000. But we have been trying with different
> values (1, 500, 1000 and 10000). The system is running on Amber 12, GPU
> c2070, cuda 4.0.
>
> We observed that not difference in energy values between ntpr = 1000
> and 10000, but they change with ntpr = 1 and 500 (between them and with
> the other values). I would like to know if it is caused because the
> frequency in writing the energies what provoke the changes in them
> (proportional to the frequency). I think I read something about that
> while energies are been printed, leap-frog algorithm continues with the
> calculation of the coordinates, what would change dt.
>
> Thanks
>
> Fernando
>--
> ==============================================
> Fernando Martín García
> Molecular Modelling Group - Lab 312.1
> Molecular Biology Center "Severo Ochoa"
> C/ NICOLáS CABRERA, 1.
> UAM University. Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
> Web: http://fertoledo.wordpress.com/
> ==============================================
>
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Received on Fri Nov 23 2012 - 17:30:02 PST
