Is there somewhere else you can try to run it with a 16 GB GPU? I've seen
some issues with containers not playing nice with AMBER recently, but not
this particular issue.
On Fri, Jun 25, 2021 at 6:42 AM Stephan Schott <schottve.hhu.de> wrote:
> I cannot do that, it is in an HPC 😅. But I have tried in multiple nodes if
> that helps somehow.
>
> El vie, 25 jun 2021 a las 15:41, Scott Le Grand (<varelse2005.gmail.com>)
> escribió:
>
> > You've tried rebooting the system I assume?
> >
> > On Fri, Jun 25, 2021, 06:39 Stephan Schott <schottve.hhu.de> wrote:
> >
> > > 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
> > > > >
> > > > _______________________________________________
> > > > 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
> > >
> > _______________________________________________
> > 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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Received on Fri Jun 25 2021 - 07:00:04 PDT
