AW: AW: AW: Atoms moving too fast only with CUDA version.

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 28 2012 - 00:21:11 CDT

I only use GPU versions of namd. For all systems, for all states of simulation and I never observed something like that, but I could imagine that you could have used a feature that is maybe currently broken in the GPU version. Have you used something special that you turned off after the equilibration run like restraints?

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von amin_at_imtech.res.in
> Gesendet: Mittwoch, 27. Juni 2012 16:41
> An: Norman Geist
> Cc: broomsday_at_gmail.com; namd-l_at_ks.uiuc.edu
> Betreff: Re: AW: AW: namd-l: Atoms moving too fast only with CUDA
> version.
>
> I completed the equilibration run on CPU and then tried the production
> run using
> NAMD2.9-CUDA and now it works without any error.Also my GPU memory
> tests showed
> no errors. So I believe the robustness of the integrator is the
> key.Thanks for
> the replies
>
> Amin.
>
>
> > Also, as it is the initial step of your simulation, you could try to
> remove
> the
> > restraint stuff and constant pressure and fixed atoms if you have and
> see if
> it's working. I remember someone with the same problem and that was due
> to false
> > defined restraints.
> >
> > Norman Geist.
> >
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: Norman Geist [mailto:norman.geist_at_uni-greifswald.de]
> >> Gesendet: Mittwoch, 27. Juni 2012 10:23
> >> An: 'amin_at_imtech.res.in'
> >> Cc: Namd Mailing List (namd-l_at_ks.uiuc.edu)
> >> Betreff: AW: AW: namd-l: Atoms moving too fast only with CUDA
> version.
> >> > -----Ursprüngliche Nachricht-----
> >> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag
> von amin_at_imtech.res.in
> >> > Gesendet: Mittwoch, 27. Juni 2012 09:10
> >> > An: Norman Geist
> >> > Cc: namd-l_at_ks.uiuc.edu
> >> > Betreff: Re: AW: namd-l: Atoms moving too fast only with CUDA
> >> version.
> >> >
> >> > I have only one GPU. I get the error after all the minimization
> steps are
> completed, just at the first heating step.
> >> Yes, same for me. Minimization doesn't compute velocities, only
> forces and
> energies that get optimized. It's no real atom movement. It just moves
> atoms
> randomly a little amount, compute energies, see if total energy is
> lower than
> before. If it is lower it keeps the new positions, if not it goes back.
> Than it
> starts over. So a error computation during minimization causes only
> that the
> minimizer thinks it has done a bad move, but does not break the
> simulation. A
> too high force computed during molecular dynamic causes unusual
> behavior and to
> strong
> >> velocities that break the simulation. You should try that memtest
> thing. But
> if it is a GPU or PCIE-BUS(on GPU) error, the memory test won't show up
> I think.
> The best would be to try another GPU. Bad that you only have one.
> >> Also, does other molecular systems break the same way on the GPU?
> Maybe try
> some of the test systems from the namd site.
> >> > Thanks.
> >> > Amin.
> >> >
> >> >
> >> > > Hi,
> >> > >
> >> > >
> >> > >
> >> > > I had the same problem when I had a broken GPU. If you have
> >> multiple
> >> > GPUs, try
> >> > > them separately to see if it only crashes when a special GPU
> >> > participates.
> >> > >
> >> > > Also it would be important if you get the error directly at
> start
> >> or
> >> > later.
> >> > >
> >> > >
> >> > >
> >> > > Good luck
> >> > >
> >> > >
> >> > >
> >> > > Norman Geist.
> >> > >
> >> > >
> >> > >
> >> > > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu]
> Im
> >> > Auftrag von
> >> > > Aron Broom
> >> > > Gesendet: Mittwoch, 27. Juni 2012 07:52
> >> > > An: amin_at_imtech.res.in
> >> > > Cc: namd-l_at_ks.uiuc.edu
> >> > > Betreff: Re: namd-l: Atoms moving too fast only with CUDA
> version.
> >> > >
> >> > >
> >> > >
> >> > > I'm not sure you necessarily did anything wrong. I would
> suggest
> >> > that your
> >> > > system even after 50,000 steps still has some kind of problems,
> but
> >> > the CPU
> >> > > integrator is robust enough to muscle through it, whereas the
> CUDA
> >> > one is not.
> >> > >
> >> > > You should consider slowly heating your system from say 100K or
> >> > something of the
> >> > > sort, as I would imagine you have jumped straight to 300K which
> >> > generally works,
> >> > > but requires a decent starting point.
> >> > >
> >> > > Keep in mind that even though the minimizer in NAMD is smarter
> than
> >> > just
> >> > > steepest descent, it will still be easily trapped in local
> minima,
> >> so
> >> > doing more
> >> > > minimization without some kind of dynamics is unlikely to get
> you
> >> > closer to the
> >> > > global minimum and away from whatever problems you have.
> >> > >
> >> > > Did you have a look at the structure also, and which atoms are
> >> > causing the
> >> > > problem?
> >> > >
> >> > > ~Aron
> >> > >
> >> > > On Wed, Jun 27, 2012 at 1:37 AM, <amin_at_imtech.res.in> wrote:
> >> > >
> >> > > Dear all,
> >> > > I am trying to run an equilibration using NAMD 2.9-CUDA on
> >> Linux.
> >> > However,
> >> > > I keep getting "Atoms moving too fast error".I increased the
> >> > minimization
> >> > > upto 50000 steps but it doesn't work. But when I tried to run
> the
> >> > exact
> >> > > same config file using the non-CUDA version it ran without any
> >> error
> >> > even
> >> > > at 10000 minimization steps.And the error is reproducible. Can
> >> > someone
> >> > > please tell me what may have gone wrong.
> >> > >
> >> > > Regards.
> >> > >
> >> > > Amin.
> >> > >
> >> > >
> >> >
> >>
> ______________________________________________________________________
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> >> औद्योगिक
> >> > अनुसंधान परिषद)
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> >> > >
> >> > >
> >> > >
> >> > > --
> >> > > Aron Broom M.Sc
> >> > > PhD Student
> >> > > Department of Chemistry
> >> > > University of Waterloo
> >> > >
> >> > >
> >> >
> >> >
> >> >
> >>
> ______________________________________________________________________
> >> > सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक
> औद्योगिक अनुसंधान परिषद)
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> >> CSIR)
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> कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
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> >
> >
>
>
>
>
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक
> अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202

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