I think pmemd outputs the number of allocated integers and floating point
numbers allocated for each simulation, so run a 0-step minimization and look
for those numbers.
Note that each thread, I believe, allocates about the same amount of memory
(a little bit more) than the only thread of a serial pmemd job. It has some
atom-ownership maps in addition to the normal data structures, but that's
~1/3 the size of just the coordinate, velocity, force, and old velocity
arrays (which leaves a relatively small imprint).
HTH,
Jason
On Thu, May 26, 2011 at 5:08 PM, Dmitry Osolodkin <divanych.rambler.ru>wrote:
> Dear AMBER developers,
>
> we are going to perform a MD simulation for an extremely huge system
> (ca. 10 millions atoms, maybe twice more). How to calculate memory
> requirements per processor for such task? We'll probably use pmemd.
>
> Thanks in advance
> Dmitry
>
> --
> Dmitry Osolodkin.
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu May 26 2011 - 21:30:02 PDT
