[gmx-users] # of threads different than # of cores -> gmx hangs.

[Mark Abraham]

OK, thanks. We would like to fix that so that it does not hang, but we
might need to know some more details. So far, I have failed to replicate
your symptoms using 30 threads across 2 nodes with 32 total cores. However,
my mpirun and/or OpenMP library was setting thread affinities for me. That
may or may not have been the case for you. Can you please open an issue at
redmine.gromacs.org with .tpr, .log, stdout, stderr for both a working and
failing case?

Mark


On Mon, Nov 25, 2013 at 3:25 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> For the record.
>
> gmx-4.6.4 hangs when number of threads is not a multiple of the number of
> nodes.
>
> XAvier.
>
> On Nov 22, 2013, at 7:14 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> >
> > Ok, tks. I'll try then :))
> >
> > XAvier.
> >
> > On Nov 22, 2013, at 4:31 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> >> Hardware detection and management of the results is greatly improved
> since
> >> 4.6.1, so we would expect relevant changes, particularly if -pin off
> makes
> >> it work (very slowly)
> >>
> >> Mark
> >> On Nov 21, 2013 7:37 PM, "XAvier Periole" <x.periole at rug.nl> wrote:
> >>
> >>>
> >>> For the record:
> >>>
> >>> I do not expect this issue to be affected by an update to gmx4.6.4 …
> >>>
> >>> But the problem is fixed by turning the pin option off.
> >>>
> >>> XAvier.
> >>>
> >>> On Nov 21, 2013, at 6:04 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> It's not expected, but instead of trying to figure out what the issues
> >>>> is with 4.6.1, you should really update to the latest version. If the
> >>>> problem persists with 4.6.4, we shall have a closer look.
> >>>>
> >>>> Cheers,
> >>>> --
> >>>> Szilárd
> >>>>
> >>>>
> >>>> On Thu, Nov 21, 2013 at 11:38 AM, XAvier Periole <x.periole at rug.nl>
> >>> wrote:
> >>>>>
> >>>>> Dears,
> >>>>>
> >>>>> When running on multiple nodes I get GMX-461 hanging if the number of
> >>> threads is not a multiple of the number of cores.
> >>>>>
> >>>>> example: with 11 nodes having 24 cores each, defining 253 threads (23
> >>> threads per node) or 264 threads (24 threads per node) would work but
> >>> defining 256 threads would result in mdrun to hang for long time.
> >>>>>
> >>>>> That might be expected and not really an issue but that be nice if
> >>> anyone knows why.
> >>>>>
> >>>>> Thanks,
> >>>>> XAvier.
> >>>>> --
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