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

From: amin_at_imtech.res.in
Date: Wed Jun 27 2012 - 09:40:38 CDT

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.
>> > >
>> > >
>> >
>> ______________________________________________________________________
>> > > 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
>
>
>

______________________________________________________________________
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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:43 CST