[gmx-users] Error when reading xtc trajectory

David spoel at xray.bmc.uu.se
Tue Aug 16 17:18:11 CEST 2005

On Tue, 2005-08-16 at 16:26 +0200, Christian Burisch wrote:
> Hello everyone,
> in some Gromacs 3.2.1 tools (namely g_dist and trjconv in my case) we 
> encountered the following or very similar errors:
> Reading frame       0 time    0.000   *** glibc detected *** double 
> free or corruption (!prev): 0x081de720 ***
> Abort
> or
> Reading frame       0 time    0.000
> Precision of md.xtc is 0.0001 (nm)
> *** glibc detected *** double free or corruption (out): 0x08255198 ***
> Abort
> In all cases we tried to read xtc trajectories (tried several from 
> independent runs) with xtc_precision=10000 in conjunction with a tpr 
> file (which of course is mandatory for g_dist and could be avoided by 
> alternatively using a gro file for trjconv). In trjconv the error only 
> seems to occur when I use the -fit rot+trans flag.
> Gromacs, fftw and mpich_gm were compiled from scratch under SuSE 9.3 
> with gcc version 3.3.5 20050117 (prerelease) (SUSE Linux) and glibc 2.3.4.
> The error still shows (with the same xtc file though) when I compile 
> Gromacs with no fancy configure options and without fftw/MPI support.
> Thanks in advance for any help or comments

There is always the possibility of a bug somewhere. To test this I would
like to ask you to compile one of the programs with the efence library.
You type first
make trjconv
then you cut and paste the linking line and add -lefence as the last
library. Then run the program again. What we need to know is *which*
pointer is free'd multiple times.
You may also have to compile with CFLAGS=-g
make clean
make CFLAGS=-g LDFLAGS=-lefence trjconv
might work at once.

> Christian
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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