[gmx-users] gromacs memory usage
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Mar 3 06:14:58 CET 2010
Hi Amit,
I think the presentation gives right what you want: a rough estimate.
Now as Berk pointed out, to allocate more than 2GB of memory, you need
to compile in 64bit. Then, if you want to have a real feel for the
memory usage, there's no other way than trying. But fortunately, the
memory requirements of a (very) long simulation are equal to that of a
very short one, so it doesn't need to cost much time.
Cheers,
Tsjerk
On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey <kgp.amit at gmail.com> wrote:
> Hi Mark,
>
> Yes thats one way to go about it. But it would have been great if i could
> get a rough estimation.
>
> Thank you.
>
> amit
>
>
> On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham <Mark.Abraham at anu.edu.au>
> wrote:
>>
>> On 3/03/2010 12:53 PM, Amit Choubey wrote:
>>>
>>> Hi Mark,
>>>
>>> I quoted the memory usage requirements from a presentation by Berk
>>> Hess, Following is the link to it
>>>
>>>
>>>
>>> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
>>>
>>> l. In that presentation on pg 27,28 Berk does talk about memory
>>> usage but then I am not sure if he referred to any other specific
>>> thing.
>>>
>>> My system only contains SPC water. I want Berendsen T coupling and
>>> Coulomb interaction with Reaction Field.
>>>
>>> I just want a rough estimate of how big of a system of water can be
>>> simulated on our super computers.
>>
>> Try increasingly large systems until it runs out of memory. There's your
>> answer.
>>
>> Mark
>>
>>> On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham <mark.abraham at anu.edu.au
>>> <mailto:mark.abraham at anu.edu.au>> wrote:
>>>
>>> ----- Original Message -----
>>> From: Amit Choubey <kgp.amit at gmail.com <mailto:kgp.amit at gmail.com>>
>>> Date: Saturday, February 27, 2010 10:17
>>> Subject: Re: [gmx-users] gromacs memory usage
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>>
>>>
>>> > Hi Mark,
>>> > We have few nodes with 64 GB memory and many other with 16 GB of
>>> memory. I am attempting a simulation of around 100 M atoms.>
>>>
>>> Well, try some smaller systems and work upwards to see if you have a
>>> limit in practice. 50K atoms can be run in less than 32GB over 64
>>> processors. You didn't say whether your simulation system can run on
>>> 1 processor... if it does, then you can be sure the problem really
>>> is related to parallelism.
>>>
>>> > I did find some document which says one need (50bytes)*NATOMS on
>>> master node, also one needs
>>> > (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute
>>> nodes. Is this true?>
>>>
>>> In general, no. It will vary with the simulation algorithm you're
>>> using. Quoting such without attributing the source or describing the
>>> context is next to useless. You also dropped a parenthesis.
>>>
>>> Mark
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--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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