[gmx-users] Unexplained crashes with Gromacs-4.0

[Berk Hess]

Hi,

That issue in 3.3.1 is completely unrelated to this issue in 4.0.

Was your problem in 3.3.1 with parrinello-rahman coupling?
If so, that problem is probably solved by a bug fix in the PR pressure coupling
I introduced in the 4.0 release.

Berk


> Date: Thu, 16 Oct 2008 14:06:19 +0200
> From: till at bph.rub.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0
> 
> 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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> >
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