[gmx-users] gromacs memory usage

[Tsjerk Wassenaar]

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