[gmx-users] different results when using different number cpus

Carsten Kutzner ckutzne at gwdg.de
Wed Dec 5 14:10:06 CET 2007

Hi Dechang,

it is normal that results are not binary identical if you compare the
"same" MD system on different numbers of processors. If you use PME then
you will probably get slightly different charge grids for 2 and for 16
processors - since the charge grid has to be divisible by the number of
CPUs in x- and y-direction. Even if you manually set the grid dimensions
to be the same for both cases, your simulations could diverge when using
version 3.x of the FFTW. This version has a build-in timer and chooses
the fastest of several algorithms which could be another even in two
runs on the same number of processors - depending on the timing results.
With different algorithms you get slight differences in the last digit
of the computed numbers (rounding / truncation / order of evaluation)
which will then grow during the simulation and lead to diverging
trajectories. Of course the averaged properties of the simulation are
unaffected by those differences and should be the same if averaged long
You could use FFTW 2.x and manually set the FFT grid size to the same
value for the 2 and 16 CPU case - but I am not shure if this is enough
to get binary identical results.
You could also repeat your simulations several times with (slightly)
different starting conditions (maybe different starting velocities) to
get a better picture of the average behaviour of your system. If in all
16 processor cases you see the proteins diverge and in all 2 processor
cases you see them converge, I would guess something is wrong.

Hope that helps,

Dechang Li wrote:
>  Dear all,
>   I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p).
> I run two similar simulations, one for 2 cpus, while the other for 16 cpus.
> The two simulations have the same .gro, .top, and the same .mdp files. I found
> the results were not the same. In the 2 cpus simulation, the two proteins 
> run closer and closer. But they run apart in the 16 cpus simulation.
>    Is that normal the different results when using different number cpus? The 
> size of my simulation box is 9*7*7.
> Best regards,
> 2007-12-5
> ========================================= 				
> Dechang Li, PhD Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> PR China 
> Tel:   +86-10-62773779(O) 
> Email: li.dc06 at gmail.com
> =========================================     
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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