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.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
----- Original Message -----
From: Amit Choubey <kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>>
Date: Saturday, February 27, 2010 10:17
Subject: Re: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@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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