[gmx-users] Unexplained crashes with Gromacs-4.0

[Till Rudack]

Hi,

I think I had a similar error in GROMACS 3.3.1 (I posted it in June to 
the User List 
http://www.gromacs.org/pipermail/gmx-users/2008-June/034411.html). I 
also got a not reproducable error for the ci variable.

I made some test and found out that for my system the error occures with 
semiisotropic pressure coupling and not with isotropic pressure 
coupling. Another way to avoid the error with semiisotropic pressure 
coupling was to change from double to single precision. By the way 
setting tau_p to 5 fs just shifts the error to a later time step.   May 
be the mistake has something to do with the pressure coupling?

Till


Berk Hess wrote:
>
>
>
>
> ------------------------------------------------------------------------
> > Date: Tue, 14 Oct 2008 07:19:45 -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:
> > > Hi,
> > >
> > > I don't really know what could be the problem here.
> > >
> > > 0..180 is (confusingly) not including the end, so 180 is out of range.
> > >
> > > The only thing I can think of (except for unknown bugs of coarse),
> > > is that I corrected the coupling time of the Parrinello-Rahman 
> barostat
> > > when going from 4.0 RC4 to the official 4.0 release.
> > > I guess all your old simulations were with older Gromacs releases.
> > > So to get the same coupling as before, so would need to multiply 
> tau_t
> > > by 16.6.
> > > I don't know if this would help.
> >
> > I did see this same error under RC2, but noticed that you fixed this 
> bug shortly
> > after I saw it, and that's what I assumed it was. But now I have 
> seen it under
> > the official 4.0 release.
> >
> > >
> > > You did not get pressure coupling warnings before the crash?
> > >
> >
> > There are no messages printed before this error pops up. What's really
> > confusing is that if I simply try the same .tpr file again, it runs 
> without a
> > problem. I know that's not terribly scientific, but it seemed odd to 
> me that my
> > systems running for 40+ ns suddenly had a problem.
> >
> > Is there any diagnostic information I can provide? This problem 
> seems like it
> > would be elusive, since even I can't fully reproduce it.
> >
> > -Justin
>
> If you run in parallel, the dynamic load balancing can affective 
> reprodibility.
> You can turn it off with -dlb no
>
> 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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