[gmx-users] gromacs memory usage

[Amit Choubey]

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.

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?


Thank you,
amit

On Fri, Feb 26, 2010 at 2:57 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:)

> ----- Original Message -----
> From: Amit Choubey <kgp.amit at gmail.com>
> Date: Friday, February 26, 2010 20:05
> Subject: [gmx-users] gromacs memory usage
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> > Hi,
> > I am having trouble with running gromacs with a large system. I am trying
> to use several processors for the md. The error is a memory allocation error
> and it might be due to low RAM or large no of particles. I want to know the
> detailed memory usage of mdrun ie say for N atoms how much memory does the
> master node need and then also whats the memory requirement for the other
> nodes. By master node i mean the node that does the domain decomposition
> calculation etc during the start of mdrun. A webpage which describes the
> memory requirement at various stages during mdrun will be very helpful.
>
> The master node does not have a significantly larger memory footprint than
> any other, during setup or the run... For example, a 50K-atom system runs
> fine on 64 BlueGene/L processors with a hard limit of 500MB per processor
> for OS+code+data+MPI.
>
> Does your system run on 1 processor, with and without MPI? How much
> (physical) memory do you have for how large a system?
>
> Mark
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