[gmx-users] Parallel message passing

[David van der Spoel]

On Thu, 2005-06-09 at 09:50 -0500, Nathan Moore wrote:
> >
> >> > The PME algorithm uses full all-to-all communication. However in
> >> general
> >> > you want to reduce communication to a minimum (by using clever
> >> > algorithms). What kind of network do you have?
> >>
> >> A very fast one.  Processors are relatively slow (~700MHz ppc32), nodes
> >> are connected on a torus, distributed memory, 256 or 512MB/processor
> >> node
> >> - no virtual memory.  I compile with xlC, to be practically useful
> >> GROMACS
> >> has to scale to >=512 processors...
> > Blue Gene?
> 
> good guess!
> 
> How can I enable load-balancing in a parallel job?  I remember seeing
> discussion of grompp options "-sort" and "-shuffle" in the manual as
> parallel optimizations .  Is a change in performance resulting from this
> noted in the log file?
there's only static load balancing using -shuffle which only works for
simple multicomponent systems. Apart from that you can try your luck
with the grompp -load option.
> 
> regards,
> 
> NT
> 
> 
> 
> 
> 
> 
> 
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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