[gmx-users] gromacs memory usage

[Amit Choubey]

Hi Tsjerk,

I tried to do a test run based on the presentation. But there was a memory
related error (I had given a leverage of more than 2 GB).

I did not understand the 64 bit issue, could you let me know wheres the
documentation? I need to look into that.

Thank you,
amit

On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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