Dear Bob,
Thank you for detailed responce.
On 05/27/2011 07:05 PM, Robert Duke wrote:
> You are talking about some really big system sizes here; I am guessing you
> would want to start with 128 nodes or more (non gpu code metric here; I
> really don't know about the gpu code - sorry to say).
We will definitely not use GPU code. Our first task is to make a
requirements specification for a supercomputer possible to perform such
simulation, especially RAM per CPU requirements. We'll start with large
number of nodes, but not extremely large -- maybe 1024. Are there any
recommendations about reasonable atom per CPU ratio? Do they depend on
the system size?
All the best,
Dmitry.
>
> Best wishes - Bob Duke
>
> (bottom line - the memory numbers at startup from the master are at best a
> wild and low guess, due to the adaptive nature of the code)
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Thursday, May 26, 2011 9:01 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] RAM requirements
>
> 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.
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 27 2011 - 11:30:02 PDT
