From: James Starlight (jmsstarlight_at_gmail.com)
Date: Wed Sep 11 2013 - 01:31:05 CDT
Axel, thanks for suggestions!
So as I understood GPU-namd use ONLY single precision math for calculation
and cpu version enable use DP, doesn't it ? Should I define in conf file or
in launch command some flag to activate DP in case when I perform
simulation on CPU or DP always turned on in case of such simulations ?
James
2013/9/10 Axel Kohlmeyer <akohlmey_at_gmail.com>
> On Tue, Sep 10, 2013 at 4:06 PM, James Starlight <jmsstarlight_at_gmail.com>
> wrote:
> > The problem was solved by running minimization without CUDA (on cpu
> only).
> > So as I've told previously cuda-based namd has some problems with the
> > minimization implementation.
>
> no. the problem is not understanding the implications of using the GPU
> accelerated version.
> GPU accelerated force kernels use single precision math and that will
> much more easily overflow an create bogus data then with double
> precision math. now, if you feed NAMD an initial structure with bad
> contacts and then just depend on the minimizer to right this, then you
> must not use the cuda version. you don't expect a race car to have an
> automatic transmission, or do you?
>
> a better solution is to identify the bad contacts and figure out how
> they came to be, and then avoid this entire issue.
> the next time around the situation may be worse and may be resolved
> with full double precision math either.
>
> axel.
>
>
> >
> >
> > James
> >
> >
> > 2013/9/9 James Starlight <jmsstarlight_at_gmail.com>
> >>
> >> Dear NAmd users!
> >>
> >> I've forced with the serious problem of the equilibration large systems
> >> mainly consists of the hydrated lipids.
> >>
> >>
> >> Briefly I've done long minimization after which tried to equilibrate my
> >> system in npt ensemble and obtained crash at the begining of the
> >> equilibration phase with the below listened errors
> >>
> >> colvars: Writing the state file "step6.1_equilibration.
> >> restart.colvars.state".
> >> colvars: Synchronizing (emptying the buffer of) trajectory file
> >> "step6.1_equilibration.colvars.traj".
> >> ERROR: Constraint failure in RATTLE algorithm for atom 14039!
> >>
> >> ERROR: Constraint failure; simulation has become unstable.
> >> ERROR: Constraint failure in RATTLE algorithm for atom 8959!
> >>
> >> ERROR: Constraint failure; simulation has become unstable.
> >> ERROR: Constraint failure in RATTLE algorithm for atom 66!
> >>
> >> ERROR: Constraint failure; simulation has become unstable.
> >> ERROR: Constraint failure in RATTLE algorithm for atom 15321!
> >>
> >> ERROR: Constraint failure; simulation has become unstable.
> >> ERROR: Constraint failure in RATTLE algorithm for atom 13670!
> >>
> >> ERROR: Constraint failure; simulation has become unstable.
> >> ERROR: Constraint failure in RATTLE algorithm for atom 9380!
> >>
> >> Here you can find example of the bilayer which i"Ve tried to simulate in
> >> GPU-based regime
> >> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378378701
> >>
> >> could someone tell me
> >>
> >> 1) What additions should I add to the conf files to increase stability
> of
> >> the simulations in case of gpu-based calculations ?
> >>
> >> 2) How I could performed simulation in the cpu-only regime (turned of
> the
> >> gpu) on the namd 2.7 compiled with the cuda support.
> >>
> >> Thanks for help
> >> James
> >>
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
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