[gmx-users] how to increase GMX_OPENMP_MAX_THREADS

[Szilárd Páll]

On Mon, Feb 25, 2019 at 9:15 PM Schulz, Roland <roland.schulz at intel.com>
wrote:

> That's not my experience. In my experience , for single node runs, it is
> usually faster to use 72 OPENMP threads rather than using 72 (t)MPI threads.
>

I believe that will depend on system size, compiler (with gcc/gomp wide
ranks are slower), whether SMT is used (though it's likely that 72 threads
is 2x18C with HT).

With 72 hardware threads I doubt it -ntmpi 1 -ntomp 72 is even the default
unless there is a GPU in the system (which there seems to be one). If there
is a GPU, it is highly unlikely that -ntmpi 1 -ntomp 36 -pinstride 2 won't
be faster. Even if there is no GPU in the system, I struggle to find in my
archive of benchmarks use-cases where >48 threads/rank with no DD is faster
than Dd with 2-4 threads per rank.

So the questions to the OP: what is the use-case (system size, simulation
setup, hardware)?


> Roland
>
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> > Szilárd Páll
> > Sent: Monday, February 25, 2019 7:31 AM
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS
> >
> > What are you trying to do? Using 72 threads per rank in most cases
> (except
> > some extreme and unusual) will not be efficient at all. If you are sure
> that
> > you still want to do that, you can override this at compile time using
> cmake -
> > DGMX_OPENMP_MAX_THREADS=
> >
> >
> >
> > --
> > Szilárd
> >
> >
> > On Thu, Feb 21, 2019 at 5:58 AM Lalehan Ozalp <lalehan.ozalp at gmail.com>
> > wrote:
> >
> > > Hello all,
> > > I'd been running simulation with GROMACS 2018 using 72 open mpi
> > > threads without problem until (I assume) it was updated to 2019
> > > version. When I execute mdrun with option -nt 72 (which is the number
> > > of cores of my
> > > terminal) it says:
> > >
> > > "you are using 72 openmp threads, which is larger than
> > > GMX_OPENMP_MAX_THREADS (64). Decrease the number of OpenMP
> > threads or
> > > rebuild GROMACS with a larger value for GMX_OPENMP_MAX_THREADS."
> > >
> > > In the documentation of GROMACS 2019 release, it's written:  "mdrun
> > > can run with more than GMX_OPENMP_MAX_THREADS threads."
> > >
> > > Could you please help me how to get around this issue?
> > >
> > > Thank you in advance.
> > > Lalehan
> > > --
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