[gmx-users] g_covar & g_anaeig problems
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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