David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 29 09:04:38 CEST 2007
chris.neale at utoronto.ca wrote:
> I now have a well tested desorting program + methodology. It means that
> I can scale to 100% on 4cpus and I have been using -shuffle -sort for
> all my parallel runs for many months now. Basically it is the same one
> that I posted to the users list a while ago. Is it useful for me to
> develop good comments for g_desort and upload to users contributions so
> that it can go into a future gromacs release or is this all going to be
> useless in gromacs4?
as a matter of fact, yes it wil be. sorting is inherent in domain
decomposition, but Berk has also implemented in on single processors
with significant speedup. Of course the output files are now in the same
order as the input file, so there will not be any need for desorting.
That said, it could still be useful for 3.3 users.
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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://folding.bmc.uu.se
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