[gmx-developers] mpi and thread command line options

Szilárd Páll szilard.pall at cbr.su.se
Wed Jul 11 05:20:27 CEST 2012

On Wed, Jul 11, 2012 at 2:26 AM, Shirts, Michael (mrs5pt)
<mrs5pt at eservices.virginia.edu> wrote:
>> Additionally, do we want to keep "-nt" on the long run? To me it
>> sounds too general especially that the thread-MPI parallelization is
>> not even "proper" multithreading. So I'd rather make it more verbose
>> e.g. "-ntmpi" and have with the same functionality as the deprecated
>> -nt.
> The one thing about current -nt / thread-MPI is that it just works with
> pretty much linear scaling, no matter what the deal with the cluster is or
> the MPI installed. We end up running most of our batch calculations this
> way.  Having something provide full speed out of the box regardless of how
> good the cluster admin that is hard to break is very important to most
> users.  So I wouldn't hide it or obscure it.

Hiding or obscuring the thread-MPI has never been the goal. However,
we need to think forward, and although thread-MPI has been
conveniently called and referred to as "multithreading" or
"threading," this has to change. Not only that already the current
OpenMP implementation is often slightly faster than thread-MPI only
runs, on the way forward we surely will have some sort of
parallelization (most probably a form of multithreading) targeting the
multicore/shared-memory level of computer systems.

Therefore, it is better to start moving now in the direction where we
want to be in a few years and deprecate/re-purpose naming schemes to
avoid major naming clashes. part of this move was the renaming of
GMX_THREADS to GMX_THREAD_MPI and I think in a similar manner -nt
should be renamed to -ntmpi.

> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
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