Ok interesting. Could that account for almost twice as much as needed with
skinnb=3 though? I can tell you that when the processes are spawning, they
seem to break at around 4 GBs. Of course, the resolution of nvidia-smi
might just not be enough to resolve a very rapid spike.
The GPUs are allocated solely for this; no other process is reported on
nvidia-smi at least.
El vie, 25 jun 2021 a las 15:35, Scott Le Grand (<varelse2005.gmail.com>)
escribió:
> 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
> > > >
> > > _______________________________________________
> > > AMBER-Developers mailing list
> > > AMBER-Developers.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
> >
> >
> > --
> > 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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> AMBER-Developers.ambermd.org
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>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Fri Jun 25 2021 - 07:00:03 PDT
