With a smaller skin value you end up with more non-bond cells and each of
those non-bond cells have memory allocated to them that is in excess of
what they would normally need so you might be getting some sort of weird
trade-off between more smaller cells and fewer larger cells. The other
thing to ask is whether there are any other processes running on the GPU
that might be eating memory.
On Fri, Jun 25, 2021, 06:33 Stephan Schott <schottve.hhu.de> wrote:
> It's 743538 SIRAH particles. The memory reported is 16160 MB, non
> virtualized. Using skinnb = 3 is using 9340 MB right now.
>
> El vie, 25 jun 2021 a las 15:22, Scott Le Grand (<varelse2005.gmail.com>)
> escribió:
>
> > How many atoms? How much memory on the V100? Is it virtualized?
> >
> > On Fri, Jun 25, 2021 at 1:53 AM Stephan Schott <schottve.hhu.de> wrote:
> >
> > > Hi everyone,
> > > I am playing around with a SIRAH system and just stumbled upon this
> > message
> > > consistently whenever I use the default skinnb value of 2, but it runs
> > > without issue when it is increased to 3 for whatever reason. Just for
> > some
> > > info, this is on a Tesla V100, driver 460.32.03, using Amber 21
> compiled
> > > with CUDA 11.0 and gcc 9.3.
> > > My GPU architecture knowledge is very barebones, but it seems like
> there
> > > might be something odd going on, as I would expect more memory usage
> the
> > > more particles are included in skinnb, right? Has this something to do
> > with
> > > the partitioning within the GPU memory? I would be grateful if someone
> > > could tell me if I am just missing something here.
> > > Best regards,
> > >
> > > --
> > > Stephan Schott Verdugo
> > > Biochemist
> > >
> > > Heinrich-Heine-Universitaet Duesseldorf
> > > Institut fuer Pharm. und Med. Chemie
> > > Universitaetsstr. 1
> > > 40225 Duesseldorf
> > > Germany
> > > _______________________________________________
> > > AMBER-Developers mailing list
> > > AMBER-Developers.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
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> >
>
>
> --
> Stephan Schott Verdugo
> Biochemist
>
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Fri Jun 25 2021 - 07:00:03 PDT
