Yep. skin_permit should avoid rebuilds if the test passes the more
permissive threshold. And I do actually seem to remember seeing that code,
or something to the effect "don't rebuild pair list if we just created it"
in the comments as I was working on the turbo mode. So whatever that code
is, it is pretty ancient and may affect test cases if we purge it, even
though that is probably a good idea.
Dave
On Tue, Nov 10, 2020 at 3:51 PM Scott Le Grand <varelse2005.gmail.com>
wrote:
> So looking at skin_permit, it looks like I can blow away this junk and
> skin_permit will do the rest?
>
> On Tue, Nov 10, 2020 at 12:16 PM Scott Le Grand <varelse2005.gmail.com>
> wrote:
>
> > ~line 2000 of kNeighborList.cu:
> >
> > extern "C" void kNLSkinTest(gpuContext gpu)
> > {
> > static unsigned counter = 0;
> > static unsigned lastCounter = gpu->sim.skinnb * 14;
> >
> > int counterCut = lastCounter*0.2;
> > unsigned interval = 1;
> > if (counter++ > counterCut && (counter % interval) == 0) {
> >
> > etc...
> >
> > Not only is this uncool, it's done with local static variables which is
> > just horrible...
> >
> > On Tue, Nov 10, 2020 at 12:07 PM David Cerutti <dscerutti.gmail.com>
> > wrote:
> >
> >> I wasn't aware of the code doing anything like NB skin tests only every
> >> other step. The "turbo" mode is enabled by setting skin_permit to a
> value
> >> between 0.5 and 1.0. See here:
> >>
> >> http://ambermd.org/GPUPerformance.php
> >>
> >> Where in the code is the call to the pairlist check being skipped on
> half
> >> the steps?
> >>
> >> Dave
> >>
> >>
> >> On Tue, Nov 10, 2020 at 2:03 PM Scott Le Grand <varelse2005.gmail.com>
> >> wrote:
> >>
> >> > At some point, PMEMD stopped doing NB skin tests every step and it now
> >> does
> >> > them every other step. No matter what your view on the validity of
> doing
> >> > so, doing this under the hood all the time without informing the user
> is
> >> > uncool to the max.
> >> >
> >> > I am turning this off by default. Any objections? Dave, how does one
> >> enable
> >> > your turbo mode? Because this seems cool there, just not on 100% of
> the
> >> > time with no option to turn it off.
> >> >
> >> > Scott
> >> > _______________________________________________
> >> > AMBER-Developers mailing list
> >> > AMBER-Developers.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >> >
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >
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Received on Tue Nov 10 2020 - 13:00:04 PST
