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?
Kind regards
Sebastian
Am 25.03.2010 10:05, schrieb arne.wag...@student.uib.no:
Hi everyone,
I've got the following two problems - hopefully someone can help me
fixing them.
1.:
I have a larger system ~20000 atoms where I performed an MD run and
now I want to analyze the entropy. I tried a combination of g_covar
and g_anaeig to get the values.
Input:
g_covar -f XXX_md_eq.xtc -n XXX.ndx -s XXX_md_eq.tpr -v XXX_eivec.trr
-mwa -l XXX_covar.log
If I choose a larger sub-part of the system (approx. > 4000 elements)
I get the following error message after the average structure is
calculated:
Constructing covariance matrix ...
Reading frame 0 time 0.000 Segmentation fault
Is this a result of insufficient memory or is there an error in the
whole procedure?
2.:
In smaller sub-parts I can get the eigenvectors and when I put them
into g_anaeig,
g_anaeig -v XXX.trr -entropy
I get values for the quasi-harmonical-approximation but
an 'inf' oder 'nan' for the Schlitter entropy calculation - even with
additional/maximum input. Why?
Thanks a lot!
Awa
--
_____________________________________________________________________________
Sebastian Breuers Tel: +49-221-470-4108
EMail: breue...@uni-koeln.de
Universität zu Köln University of Cologne
Department für Chemie Department of Chemistry
Organische Chemie Organic Chemistry
Greinstraße 4 Greinstraße 4
D-50939 Köln D-50939 Cologne, Federal Rep. of Germany
_____________________________________________________________________________
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