[gmx-users] Unexplained crashes with Gromacs-4.0

[Berk Hess]

Hi,

I have no clue what the problem could be.
But now I thought a bit longer, I realized that with domain decomposition
the ci error should never occur, since the domain decomposition
puts the charge groups inside the DD cells, so also inside the ns cells.
This seems to indicate that there is a bug somewhere.

We will need all the information we can get, so please file a bugzilla
and include the details on the machine, compiler,
attach the tpr file, log file and mdrun debug files.

Thanks,

Berk

> Date: Wed, 15 Oct 2008 22:14:28 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0
> 
> 
> 
> 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.
> 
> -Justin
> 
> > 
> > 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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