[gmx-developers] Bug in g_density

[CROUZY Serge 119222]

Dear developpers,

I'm running into a bug with g_density in GROMACS 4.5.5 which was already reported almost two years ago

>On Mon, Nov 22, 2010 at 2:55 PM, Sanku M <msanku65 at yahoo.com> wrote:

>>> 2. when using g_density command , after processing data , gromacs 4.5.3
>>> gives an error :
> *** glibc detected *** double free or corruption (out): 0x00000000006d8ce0
>> ***
>> Aborted
>
>> But, the same g_density with gromacs 4.0.7 and gromacs 3.3.3 works
>> smoothly.
>

The answer from Roland was :

> That seems to be a problem in g_density. Please open a bug on
>bugzilla.gromacs.org with enough detail to reproduce the error.

>Roland

I hope a bug fix has been found

In my particular case g_density sometimes works, sometimes crashes with "core dumped" and sometimes is more
verbose like :

Last frame      10000 time 9000000.000
*** glibc detected *** g_density: double free or corruption (out): 0x0000000002295aa0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7dda6)[0x7f04ce2e8da6]
/lib64/libc.so.6(+0x7f08e)[0x7f04ce2ea08e]
/usr/local/gromacs/lib/libgmxana_mpi.so.6(calc_density+0x510)[0x7f04d0098ef0]
/usr/local/gromacs/lib/libgmxana_mpi.so.6(gmx_density+0x559)[0x7f04d009a2e9]
g_density[0x400569]
/lib64/libc.so.6(__libc_start_main+0xed)[0x7f04ce28c69d]
g_density[0x400599]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fd:00 2500499                            /usr/local/gromacs/bin/g_density
00600000-00601000 rw-p 00000000 fd:00 2500499                            /usr/local/gromacs/bin/g_density
0226a000-02376000 rw-p 00000000 00:00 0                                  [heap]
7f04cd616000-7f04cd62b000 r-xp 00000000 fd:00 5112037                    /lib64/libgcc_s-4.6.3-20120306.so.1
7f04cd62b000-7f04cd82a000 ---p 00015000 fd:00 5112037                    /lib64/libgcc_s-4.6.3-20120306.so.1
7f04cd82a000-7f04cd82b000 rw-p 00014000 fd:00 5112037                    /lib64/libgcc_s-4.6.3-20120306.so.1
7f04cd82b000-7f04cd842000 r-xp 00000000 fd:00 5111914                    /lib64/libpthread-2.14.90.so
7f04cd842000-7f04cda41000 ---p 00017000 fd:00 5111914                    /lib64/libpthread-2.14.90.so
7f04cda41000-7f04cda42000 r--p 00016000 fd:00 5111914                    /lib64/libpthread-2.14.90.so
7f04cda42000-7f04cda43000 rw-p 00017000 fd:00 5111914                    /lib64/libpthread-2.14.90.so
7f04cda43000-7f04cda47000 rw-p 00000000 00:00 0
7f04cda47000-7f04cda4e000 r-xp 00000000 fd:00 5111930                    /lib64/librt-2.14.90.so
Abort

I'm using Fedora 16 on a Linux 64 bit workstation
and
Name        : glibc
Version     : 2.14.90
Release     : 24.fc16.7
Architecture: i686


Thanks for your help
Serge