Re: PMF calculation using CPU and GPU

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jun 08 2018 - 08:55:15 CDT

First of all, check the doc of the new CUDA NAMD code to make sure you're
up to date. With all due respect to the hard work put in to write it, NAMD
2.9 is nonetheless almost history in that regard.

Changes in precision will affect averaging of thermodynamic quantities, but
the magnitude of these effects depends on what you're averaging over.
Averaging over terms with opposing signs (such as the atomic contributions
to the virial pressure) is notably worse on single- and mixed-precision
than in double-precision (pure CPU run). This is also mentioned at the doc
page you link.

For ABF, and in general every method where total forces are used for the TI
free-energy estimator, you should try to figure out whether the total force
on the collective variable (total CV-force) is a sum of very different
terms. Comparing the variance of the total forces involved vs. the square
of the total CV-force may be a way of doing it. If the two are different
by many orders of magnitude, the accuracy will be lower with GPUs.

Giacomo

On Fri, Jun 8, 2018 at 9:36 AM, Souvik Sinha <souvik.sinha893_at_gmail.com>
wrote:

> Hi,
> I was wondering, for converged PMFs (calculated using ABF-MW simulations),
> will there be any difference in the landscapes calculated with GPUs and
> without GPUs?
>
> In the thread 'http://www.ks.uiuc.edu/Research/namd/2.9/ug/node88.html',
> it is mentioned that the force calculation slightly differs in GPU
> accelerated runs. Does it really mean that convergence I attain using
> CPU-only calculations (along a specific reaction coordinate) will not be
> the same if I repeat it with some GPU resources? I guess it will but not
> sure of the reasons.
>
> Any advice will be helpful. Thanks
> --
> Souvik Sinha
> Research Fellow
> Bioinformatics Centre
> Bose Institute
>
> Contact: 033 25693275
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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