Hi Massimiliano,
> I was doing some benchmarks on my system using the
> GPU boards I have and the 16 cores CPU of my machine.
>
> After minimising and equilibrating the system, I ran four 1ns
> simulation using:
>
> - 16 cores of my CPU
> - 1 Tesla C2070
> - 2 Teslas C2070
> - 1 GeForce GTX 470
These results are almost certainly NOT converged. When comparing CPU and GPU
results we have typically run around 50 simulations, each of 100ns and even
then the RMSFs are not fully converged. The GPU runs will all be the same
since that code is deterministic. You don't give your input settings so it
is hard to comment more but for example if you are using NTT=3 the random
number generator on the CPU is different from that used on the 3 GPU runs
which would account for the differences in such short runs.
I would suggest repeating the GPU runs with different random number seeds
and the same for the 16 cores of the CPU (try 8 cores and 1 core as well for
comparison). I'm betting you'll see differences between individual runs that
are larger than the differences you see here which will give you an idea of
how unconverged the results are.
> Then, after centering (ptraj center) and re-imaging (ptraj image) and
> aligning (ptraj rms)
> the produced trajectories I have worked out the RMSF and I obtained a
> substantial
> difference between the 16cores CPU trajectory and the GPU ones
> (RMSFs obtained from the 3 different GPU runs are practically the
> same).
Also what version of the code are you using, which patch level in terms of
bugfixes etc.
> Any idea on which is the correct one?
I suspect all of them are correct, and equally incorrect.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Jul 06 2012 - 15:00:02 PDT
