[gmx-users] gromacs memory usage

[Amit Choubey]

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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