[gmx-users] dynamic selection memory allocation problem
gigo at ibb.waw.pl
Fri Jun 27 14:34:18 CEST 2014
I noticed, that the dynamic selection method, for example in gmx
distance, easily fails because of the memory allocation problem.
I wanted to call gmx distance from a python script, which builds really
long selections. An illustrating example, built of the same pairs of
atoms connected by 'plus':
gmx distance -s eq03.tpr -f eq03.xtc -oall qweqwe.xvg -xvg none -select
'((resid 14497 and resname SOL and name LP1) or (resname LIG and name
P)) plus ((resid 14497 and resname SOL and name LP1) or (resname LIG and
This one works. However, if you add several '((resid 14497 and resname
SOL and name LP1) or (resname LIG and name P))' blocks more (13 in this
particular case), soon you will see something like:
*** Error in `gmx': realloc(): invalid next size: 0x0000000000fa57e0 ***
The rationale behind using the dynamic selection was simplification of
the script that I've been working on - no need for writing and using an
index file. I want to calculate about 40 different distances, which is
currently far beyond the reach of gmx distance. I'm using
gromacs-5.0-rc1. All limits related to memory allocation (stacksize etc)
were removed. I tried it on a computer with loads of memory (and the
number shown in the error message is rather small).
If you have any suggestions, I would be very grateful.
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