Dear Jason,
Unfortunately right now we don't have the system available, and only a
rough estimate is needed. Is it possible to extrapolate the memory data
from small systems? If yes, how to do it?
On 05/27/2011 08:01 AM, Jason Swails wrote:
> 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
>>
>
>
>
--
Dmitry Osolodkin
Researcher
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
e-mail: dmitry_o.qsar.chem.msu.ru
Phone: +7-495-9393557
Fax: +7-495-9390290
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Received on Fri May 27 2011 - 04:30:02 PDT
