[gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

[Mark Abraham]

On 8/04/2010 10:22 AM, Camilo Andrés Jimenez Cruz wrote:
> Hi all
>
> I am using gromacs-3.3.99's g_sas_s  in a long trajectory and I get this
> error right away. I assume its memory capacity, is there a way (other
> than cutting the trj in smaller chunks?)

Use a bigger computer? See g_sas -h for some built-in options to do a 
smaller part of the calculation.

Mark

> Select a group: Select a group: *** glibc detected ***
> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s: malloc(): memory corruption:
>   0x000000000a809680 ***
> ======= Backtrace: =========
> /lib64/libc.so.6[0x38b8c71d21]
> /lib64/libc.so.6(__libc_calloc+0xc3)[0x38b8c72bb3]
> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x4257d5]
> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x40419a]
> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x405b1a]
> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x402de3]
> /lib64/libc.so.6(__libc_start_main+0xf4)[0x38b8c1d8b4]
> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x402d19]
> ======= Memory map: ========
> 00400000-00599000 r-xp 00000000 08:05 813706
> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s
> 00799000-007a2000 rwxp 00199000 08:05 813706
> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s
> 007a2000-007ad000 rwxp 007a2000 00:00 0
> 0a7dd000-0a840000 rwxp 0a7dd000 00:00 0
>
> thanks in advance
>
> --
> Camilo Andrés Jiménez Cruz
>