[gmx-developers] make_ndx 4.0 segfaults with tprs

Carsten Kutzner ckutzne at gwdg.de
Tue Oct 14 13:48:04 CEST 2008


we have a problem with make_ndx of Gromacs 4.0 here. While it works
fine with gro files, it always segfaults when it has to deal with
a tpr file. I have an older version dated 2008-08-11 in which the
problem is not present. I have attached some debugger information.


Reading file g_opt_0.tpr, VERSION 4.0 (single precision)

Reading structure file
Reading file g_opt_0.tpr, VERSION 4.0 (single precision)
*** glibc detected *** /home/ckutzne/gromacs/4.0/src/tools/make_ndx: double free or corruption (!prev): 0x00000000007ffcf0 ***
======= Backtrace: =========

Here is the debugger info:

Program received signal SIGABRT, Aborted.
0x00002b8bba560b45 in raise () from /lib64/libc.so.6
(gdb) up
#1  0x00002b8bba5620e0 in abort () from /lib64/libc.so.6
(gdb) up
#2  0x00002b8bba598fbb in ?? () from /lib64/libc.so.6
(gdb) up
#3  0x00002b8bba59e21d in ?? () from /lib64/libc.so.6
(gdb) up
#4  0x00002b8bba59ff76 in free () from /lib64/libc.so.6
(gdb) up
#5  0x000000000041fc87 in save_free (name=0x599b00 "at->resname", file=0x599ab0 "typedefs.c", line=230, ptr=0x7ffcf0) at smalloc.c:195
(gdb) up
#6  0x000000000043eb23 in done_atom (at=0x7fc148) at typedefs.c:230
(gdb) up
#7  0x000000000043eb5a in done_moltype (molt=0x7fc140) at typedefs.c:238
(gdb) up
#8  0x000000000043ecc0 in done_mtop (mtop=0x7c6050, bDoneSymtab=0) at typedefs.c:272
(gdb) up
#9  0x000000000040c21b in read_stx_conf (infile=0x7c66e0 "g_opt_0.tpr", title=0x7ffff0bfc460 "GUANYLIN (A-FORM) (ENDOGENOUS LIGAND TO THE HEAT STABLE in water", atoms=0x7c64d0, x=0x7d6800, v=0x7e2720, 
ePBC=0x7ffff0bfc454, box=0x7ffff0bfc430) at confio.c:1341
(gdb) up
#10 0x0000000000406a79 in main (argc=1, argv=0x7ffff0bfd5d8) at make_ndx.c:1116

Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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