AMBER Archive (2007)

Subject: AMBER: PMEMD internals !!

From: Sampath Koppole (sampathkoppole_at_yahoo.com)
Date: Fri Dec 14 2007 - 03:13:49 CST

Dear All,
I am going through the PMEMD code to understand how
scaling is achieved.

I guess I understand that : all atoms are divided
among the processors (using
do_initial_pme_atom_division routine) and each
processor owns a subset of atoms. I want to understand
how the long-range non-bonded and electrostatic
interactions (most expensive, I guess !!) taken into
account during force calculations and how do you
minimize communication between the processors.

Its interesting to see that: If required the atoms are
redistributed using do_atm_redistribution during
pressure calculations (since its molecule based). But
I still don't understand why and when do you have to
redistribute atoms !!

Could anyone please give "highlights" of how PMEMD
achieves reasonably good scaling.

This information is not available anywhere and it
might be a good idea to put it in the Amber mailing
list for a curious users !!

Thanks a lot,
Cheers,
Sampath.

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