XAvier Periole wrote:
Dears,
I am having troubles finding the better balance between the PME CPUs and
the rest.
I played with the rdd, rcon and -npme options but nothing really appears
very
straightforwardly best.
I'd appreciate if some of you could post their experience in that
matter. I mean the
number of pme nodes as compared the total number of CPUs used.
I think this info as been discussed recently on the list but the archive
is not accessible.
It may matter that I have a system containing about 70000 atoms, a
protein in a bilayer.
Some advice that I got from Berk long ago has worked beautifully for me. You
want a 3:1 PP:PME balance for a regular triclinic cell (grompp will report the
relative PME load as 25% if your parameters create such a balance), 2:1 for an
octahedron. My scaling has been great using this information, without having to
alter -rdd, -rcon, etc.
-Justin
Best,
XAvier.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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