[gmx-developers] Bug in g_density

[David van der Spoel]

On 2012-07-19 09:43, CROUZY Serge 119222 wrote:
>
> Dear developpers,
>
> I'm running into a bug with g_density in GROMACS 4.5.5 which was already reported almost two years ago
>
If it is reproducible please report it on redmine.gromacs.org with the 
files needed to reproduce it.


>> 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
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se