Re: Equilibration of the membrane bilayers with CUDA-support

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 10 2013 - 09:14:55 CDT

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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