[gmx-users] gromacs memory usage

Mark Abraham mark.abraham at anu.edu.au
Sat Feb 27 00:56:52 CET 2010

----- Original Message -----
From: Amit Choubey <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>

> 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.


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