[gmx-users] Scaling on IBM/SP2 Power3
Anton Feenstra
feenstra at chem.vu.nl
Wed Nov 6 12:26:26 CET 2002
David van der Spoel wrote:
>
> On Wed, 2002-11-06 at 12:01, Anton Feenstra wrote:
> > Hi All,
> >
> >
> > I'm examining the scaling properties on our IBM/SP2 Power3 AIX4.3
> > 16/32 cpus/node machine here. Problem is, at 10 cpu's (all on one
> > node) scaling is down to 50-55% (for a 40000 atoms system). Looking
> > at the scaling benchmarks on the Gromacs page, I'd expect something
> > well above 70-80% at least! Worse, for the 2 cpu job scaling is
> > already only 94% while that should be close(r) to 100%.
> >
> > I am now trying to convince the loadleveler to run a new job with
> > MP_EAGER_LIMIT=65536, which should reduce message sending latency
> > for MPI. I've already set '#@network.mpi = csss,shared,us' and
> > MP_SHARED_MEMORY=yes, which should convince MPI to use shared
> > memory communication.
> >
> > I'd appreciate any comments and/or other suggestions!
> You are omitting the most important information: is this with PME or
> with a cut-off? With cut-off you should be able to reproduce the gmx
> benchmarks, with PME it won't be as nice... Erik (and me) are working on
> this though...
That is one of the reasons I have not (yet) switched to using PME... ;-}
So, I'm using cut-offs which should give me better scaling than I have.
--
Groetjes,
Anton
________ ___________________________________________________________
| | Anton Feenstra |
| . | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |---- | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands |
| |---- | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| ' __ | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
| / \ |-----------------------------------------------------------|
| ( ) | Dept. of Biophysical Chemistry - University of Groningen |
| \__/ | Nijenborgh 4 - 9747 AG Groningen - The Netherlands |
| __ | Tel +31 50 363 4327 - Fax +31 50 363 4800 |
| / \ | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton |
| ( ) |-----------------------------------------------------------|
| \__/ | "It's Bicycle Repair Man !" (Monty Python) |
|________|___________________________________________________________|
More information about the gromacs.org_gmx-users
mailing list