[gmx-users] Error when reading xtc trajectory

[Christian Burisch]

David wrote:

> 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.

Thanks for your help!
Configuring and compiling Gromacs from scratch with CFLAGS=-g and 
LDFLAGS=-lefence set seemed to work best for me. I then used gdb to 
start trjconv, which threw the following output at me:

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1214921024 (LWP 12935)]
0x080836ca in calc_1se (g=0xb6ee7fd8, il=0xbfff9660, ftype=0xb772e588, 
nbond=0xb6eb18ec, natoms=11145) at mshift.c:191
191             nbond[iaa+2] = 2;

The same for g_dist:

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1214921024 (LWP 13082)]
0x080799f6 in calc_1se (g=0xb6fc0fd8, il=0xb787d2c0, ftype=0xb782a588, 
nbond=0xb6fc28ec, natoms=11145) at mshift.c:191
191             nbond[iaa+2] = 2;

I hope that is the info you wanted!

Thanks again

Christian