[gmx-users] Parallel message passing
nmoore at physics.umn.edu
Thu Jun 9 16:50:50 CEST 2005
>> > The PME algorithm uses full all-to-all communication. However in
>> > 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
>> - no virtual memory. I compile with xlC, to be practically useful
>> has to scale to >=512 processors...
> Blue Gene?
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?
> 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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