[gmx-developers] Parallelized g_rdf

[Christoph Junghans]

He Nikos,

the VOTCA packages comes with a trivial parallelized version of g_rdf,
called multi_g_rdf, it is just a script:
<http://code.google.com/p/votca/source/browse/scripts/multi_g_rdf.in?repo=csg>

We divide the trajectory in blocks over time and calculate the rdf of 
every block in parallel.

e.g. replace
echo "A\nA" | g_rdf -bin 0.05
by
echo "A\nA" | multi_g_rdf -8 -- -bin 0.05
and it will the same job using 8 tasks

See 'multi_g_rdf --help' for more informations

Cheers,

Christoph

Am 09.06.2010 22:53, schrieb Nikos Bentenitis:
> Hello all,
>
> I would like to request for two features to be included in future
> versions of g_rdf.
>
> 1. Would it be possible to parallelize g_rdf? Because I am simulating
> 20 thousand molecules and averaging center-of-mass rdfs for 2.5 ns,
> g_rdf takes approximately 20 hours on a single CPU.
> 2. I am simulating solute A in solvent B, and I need to calculate
> three radial distribution functions: g_AA, g_BB and g_AB. With the
> current implementation of g_rdf, I need to run the program twice: once
> to
> calculate g_AA, and g_AB and once to calculate g_BB. Because I am
> simulating 20 thousand molecules, each run takes about 20 hours on a
> single core, for a total of approximately 40 hours on a single core.
> Would it be possible to have g_rdf produce all three rdfs for each
> run?
>
> Thank you
>
> Nikos Bentenitis
> Department of Chemistry and Biochemistry
> Southwestern University
> Georgetown TX 78626

-- 
Dipl.-Phys. Christoph Junghans
Max Planck Institute for Polymer Research
Theory Group
POBox 3148
D 55021 Mainz, Germany

Phone: +49 6131 379 335
Web: http://www.mpip-mainz.mpg.de/~junghans