[gmx-users] g_covar & g_anaeig problems

[Sebastian Breuers]

Hey,

taking fewer atoms by ignoring the hydrogens is a good advice. Thanks a 
lot.

I was wondering if a more appropriate error message could be generated 
before the program messes around in the memory. The program acts as if 
it could handle the system size and then crashes with a Segmentation 
fault meaning it does not properly handle its memory.

Nonetheless thanks again for the hydrogen advice. Had'nt really thought 
about it before.

Kind regards

Sebastian


Am 07.09.2010 03:44, schrieb Mark Abraham:
>
>
> ----- 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...
>
> Mark 


-- 
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Sebastian Breuers               Tel: +49-221-470-4108
EMail: breuerss at uni-koeln.de

Universität zu Köln             University of Cologne
Department für Chemie           Department of Chemistry
Organische Chemie               Organic Chemistry

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D-50939 Köln                    D-50939 Cologne, Federal Rep. of Germany
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