From: amin_at_imtech.res.in
Date: Wed Jun 27 2012 - 02:10:04 CDT
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
> दूरभाष/EPABX :0172 6665 201-202
>
>
>
>
> --
> 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
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