[gmx-users] g_covar & g_anaeig problems

Mark Abraham mark.abraham at anu.edu.au
Tue Sep 7 03:44:20 CEST 2010

----- Original Message -----
From: Sebastian Breuers <breuerss at uni-koeln.de>
Date: Tuesday, September 7, 2010 0:42
Subject: Re: [gmx-users] g_covar & g_anaeig problems
To: gmx-users at gromacs.org

> Hey everyone,
> searching the list for the answer to a g_covar problem I've 
> found this post of Arne who describes the very same problem that 
> I encounter.
> I'm observing this problem on a linux cluster with 32GB memory 
> on each node. The g_covar_d application was compiled in double 
> precision with an intel compiler and works fine up to a number 
> of atoms of around 15408. In tests I could find out that above 
> this number +/- 48 atoms I receive the following error output:
> Calculating the average structure ...
> Last frame         50 
> time 5000.000
> Constructing covariance matrix (46368x46368) ...
> Reading frame       0 
> time    0.000   Segmentation fault
> Meaning a matrix over around 46224x46224 elements starts to 
> generate this problem.
> Did anyone encounter the same problem or does anyone has a hint 
> to solve this issue?

Get more memory or use fewer atoms :-) The memory needs and run time will scale at least as high as the square of the number of atoms. Probably you can ignore at least your hydrogen atoms...


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