[gmx-users] Unexplained crashes with Gromacs-4.0

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 16 04:14:28 CEST 2008

Berk Hess wrote:

> If you run in parallel, the dynamic load balancing can affective 
> reprodibility.
> You can turn it off with -dlb no

I have a situation now that, without fail, has crashed with the same issues I've 
described before while using "-dlb auto."  Using "-dlb no" the run does not 
fail.  The .tpr file has now produced that strange error three times, and I have 
run mdrun with the "-debug 1" flag.  Would providing these .log files and .xvg 
files provide any useful information?

I can also provide the .tpr file in a bugzilla, if that would be useful.

Please let me know and I will upload whatever files you might need.


> Another source of non-reproducibility is FFTW (with PME).
> By default FFTW times which of different codes is the fastest and uses that.
> Configuring FFTW with SSE makes all codes faster and the differences 
> smaller,
> so you can configure Gromacs with --disable-fftw-measure to remove
> the run time optimization without performance loss.
> For debugging purposes the new -reprod switch of mdrun will try to turn
> off all optimizations which might affect reproducibilty.
> Berk
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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