I would suspect the GPU to crap out at 2M atoms or so. Not that it
couldn't be upgraded to handle larger systems but the demand wasn't
there at the time. It *is* the sort of thing worth adding if the PME
section can ever be parallelized to multi-GPU IMO.
On Fri, May 27, 2011 at 11:01 AM, Dmitry Osolodkin <divanych.rambler.ru> wrote:
> 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
>
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Received on Fri May 27 2011 - 11:30:04 PDT
