[gmx-users] Gromacs parellal run:: getting difference in two trajectories

Carsten Kutzner ckutzne at gwdg.de
Thu Sep 11 13:29:43 CEST 2008

vivek sharma wrote:
> Hi There,
> I am running gromacs parellal version on cluster, with different -np 
> options.

which version of gromacs exactly are you using?

> On analyzing the 5 nsec trajectory using ngmx, I am finding difference 
> in the trajectory of two similar runs (only thing varying in two runs in 
> -np i.e 20 and 64 ), where mdp file and input files are same in two cases.
> I am wondering why I am getting this difference in two trajectories ?
> I am looking for the advice whether I did something wrong or what may be 
> the probable reason for this difference.

There are many reasons why a parallel run does not yield binary identical
results to a run with another number of processors, even if you start from
the same tpr file. If you use PME, then the FFTW could pick a slightly
different algorithm (it will select the fastest for that number of processors.
This feature you can turn off by passing --disable-fftw-measure to the
gromacs configure script). But still you can get results that are not
binary identical if you do FFTs on a varying number of CPUs. Also, for
limited accuracy which is inherent to any computer, additions need not
be associative, which can show up in parallel additions.

Generally, if you run in double precision, these effects will be way smaller,
but nevertheless you won't get binary identical results. This will in all
cases lead to trajectories which slowly diverge from each other. However,
in the fist few hundred time steps, you should not see any difference in
the first couple of decimals of the variables (positions, velocities,
energies ...)

> Also, I am not able to run gromacs faster by increasing the -np issue, 

Please provide the exact command line you used.

> Is there any max limit for scaling gromacs on parellal cluster ?

Yes, depending on your MD system and on the cluster you use :)


> With Thanks,
> Vivek
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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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