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

From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Jun 27 2012 - 02:12:40 CDT

To follow-up on Norman's suggestion, you might want to google OpenMM and
find on their website the CUDA-memtest binary. It will let you run a test
on your GPU memory to see if anything is faulty. I had a lot of problems
both in NAMD and AMBER with a GTX 580 that I later learned had bad memory.

~Aron

On Wed, Jun 27, 2012 at 3:10 AM, <amin_at_imtech.res.in> wrote:

> I have only one GPU. I get the error after all the minimization steps are
> completed, just at the first heating step.
> 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.
> >
> > ______________________________________________________________________
> > 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
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> >
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> >
> >
>
>
> ______________________________________________________________________
> 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
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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