[gmx-developers] Double Precision on GPUs
Michael R Shirts
Michael.Shirts at Colorado.EDU
Wed Jul 31 20:54:56 CEST 2019
Fixed precision would be kind of cool for reproducibility. I doubt I have the time (or the coding ability), but I'm interested to hear discussion in this and advise/brainstorm on the numerical stability and potential integrator issues.
Best,
~~~~~~~~~~~~~~~~
Michael Shirts
Associate Professor
michael.shirts at colorado.edu
http://www.colorado.edu/lab/shirtsgroup/
Phone: (303) 735-7860
Office: JSCBB C123
Department of Chemical and Biological Engineering
University of Colorado Boulder
On 7/31/19, 12:38 PM, "gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Szilárd Páll" <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of pall.szilard at gmail.com> wrote:
Hi,
My gut feeling is that, while it would be slightly more effort, a
mixed precision with 64-bit fixed precision coordinates would be
better for performance (in particular on consumer GPUs). We've also
discussed in the past fixed precision (32 or 64-bit depending on the
use-case) force/energy accumulation/reductions too which would also
allow a mix-precision mode with reproducibility. Even if at first not
tuned for production, it would at least be very useful to have such a
set of GPU kernels for "mdrun -reprod" mode.
I had plans to work on such extensions, but other projects have been
keeping me busy, so I've not had the time. If somebody is interested
in contributing, I can help to at least coordinate, and when I'm a bit
less busy also with the coding.
Cheers,
--
Szilárd
On Wed, Jul 31, 2019 at 7:33 PM David Lister <me at davidlister.ca> wrote:
>
> That sounds really interesting! It makes sense, that it would be the case. How would I go about implementing that to test?
>
> Would this also help with minimization? I find that minimized geometries are also fairly different between single and double precision. It seems as though single precision considers vdw much less than double precision, whereas double precision doesn't. This is most apparent in cases without solvents.
>
> Cheers,
> David
>
> On Wed, Jul 31, 2019 at 10:45 AM Michael R Shirts <Michael.Shirts at colorado.edu> wrote:
>>
>>
>>
>> I think that in many cases the single precision force computation is not what is limiting the accuracy. It is rather the integration and in particular the constraints using single precision.
>>
>>
>>
>> I recall talking over old results with Erik (many years ago) that showed exactly this, and seem to have been found by other people; integration and constraints cannot really be done well in single precision; but if they are in double precision (or even mixed precision, with careful analysis of rounding steps), with the force in single precision, then numerical performance is much, much better.
>>
>>
>>
>> Best,
>>
>> ~~~~~~~~~~~~~~~~
>>
>> Michael Shirts
>>
>> Associate Professor
>>
>> michael.shirts at colorado.edu
>>
>> http://www.colorado.edu/lab/shirtsgroup/
>>
>> Phone: (303) 735-7860
>>
>> Office: JSCBB C123
>>
>> Department of Chemical and Biological Engineering
>>
>> University of Colorado Boulder
>>
>>
>>
>>
>>
>> From: <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on behalf of Berk Hess <hess at kth.se>
>> Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
>> Date: Wednesday, July 31, 2019 at 8:42 AM
>> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
>> Subject: Re: [gmx-developers] Double Precision on GPUs
>>
>>
>>
>> Hi,
>>
>> I think that in many cases the single precision force computation is not what is limiting the accuracy. It is rather the integration and in particular the constraints using single precision. Another solution is to have integration and constraints in double precision and (parts of) the force computation in single precision.
>>
>> Cheers,
>>
>> Berk
>>
>> On 7/31/19 4:35 PM, David Lister wrote:
>>
>> Hello,
>>
>>
>>
>> Sorry this isn't part of the email thread from earlier, I found the thread in the archives and decided to chime in. Not sure how to reply to old threads, but the link is here for consistency. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2019-July/010488.html
>>
>>
>>
>> I am also be very interested in having double precision supported on GPUs. I'm using gromacs for a project that stretches the target use case and have found the single precision just doesn't give good results. The same simulation run in both single and double gives different results, with the double precision simulation giving the results expected by theory. Unfortunately though, double precision is much slower.
>>
>>
>>
>> Having GPU support for double precision would be a really big help for me as well.
>>
>>
>>
>> Cheers,
>>
>> David
>>
>>
>>
>>
>>
>> --
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