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

[Camilo Andrés Jimenez Cruz]

Thanks, I found the problem, I was using a wrong index file :P My bad,



On Wed, Apr 7, 2010 at 8:32 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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
>>
>>  --
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-- 
Camilo Andrés Jiménez Cruz
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