[gmx-developers] Hardware threads vs. OpenMP threads

[Mark Abraham]

Hi,

Node sharing cannot be automagically supported, because there's no
"reliable" source of information except the user. This is nothing new (e.g.
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Pinning_threads_to_physical_cores).
mdrun can't know whether omp_get_num_procs or OMP_NUM_THREADS is more
reliable in the general case (naturally, every job scheduler is different,
and we can't even assume that there is a job scheduler who might do it
right, e.g. the case of users sharing an in-house machine). However, if
only omp_get_num_procs is set, then maybe we can use that rather than
assume that the number of hardware threads is appropriate to use? We'd
still report the difference to the user.

Agree with Berk that a scheduler that only used this mechanism to declare
the number of available physical cores would be flawed, e.g. consider a
pthreads or TBB code.

Mark

On Thu, Jun 4, 2015 at 1:46 PM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 04/06/15 12:51, Berk Hess wrote:
> > PS There is something strange on that machine. If Gromacs detects 16
> > threads, omp_get_num_procs should return 16, not 8.
> Nope.
> The queue system allocates 8 cores out of 16 physical cores to my job.
> GROMACS see both values, reports a conflict, and follows the hardware
> rather than OpenMP settings. I would think it should do the reverse.
>
> >
> > Berk
> >
> > On 2015-06-04 12:49, Berk Hess wrote:
> >> Hi,
> >>
> >> I don't think anything changed in the master branch.
> >>
> >> But we do adhere to the OpenMP environment. The value reported in the
> >> message comes from omp_get_num_procs, which should be a report about
> >> the hardware available. OMP_NUM_THREADS sets the number of OpenMP
> >> threads to use, that is respected.
> >>
> >> Cheers,
> >>
> >> Berk
> >>
> >> On 2015-06-04 11:21, David van der Spoel wrote:
> >>> Hi,
> >>>
> >>> why does GROMACS in the master branch not adhere to the OpenMP
> >>> environment?
> >>>
> >>> Number of hardware threads detected (16) does not match the number
> >>> reported by OpenMP (8).
> >>> Consider setting the launch configuration manually!
> >>> Reading file md.tpr, VERSION 5.1-beta1-dev-20150603-99a1e1f-dirty
> >>> (single precision)
> >>> Changing nstlist from 10 to 40, rlist from 1.1 to 1.1
> >>>
> >>> Using 1 MPI process
> >>> Using 16 OpenMP threads
> >>>
> >>> Cheers,
> >>
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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