Agreed.
On Tue, Nov 10, 2020 at 3:57 PM Scott Le Grand <varelse2005.gmail.com>
wrote:
> I suspect we could calculate a safe number of steps past a rebuild to skip
> in your turbo mode. But that's for another day. This code needs to go...
>
>
> On Tue, Nov 10, 2020 at 12:56 PM David Cerutti <dscerutti.gmail.com>
> wrote:
>
> > 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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> > > >>
> > > >
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> >
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Received on Tue Nov 10 2020 - 13:00:05 PST
