[gmx-users] gromacs memory usage

Mark Abraham mark.abraham at anu.edu.au
Fri Feb 26 23:57:45 CET 2010

----- 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?


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