[gmx-developers] glibc qsort bug crashing mdrun

[Szilárd Páll]

Hi,

The crashes were reproduced with gcc 4.3.3 + 2.9-4ubuntu6.2 and gcc
4.4.1 + glibc 2.5, in both cases x86_64.

However, as Berk said it takes quite a bit of "luck" to get it triggered.

--
Szilárd



On Mon, Jun 21, 2010 at 6:30 PM, Alexey Shvetsov <alexxyum at gmail.com> wrote:
> Hi,
>
> What versions of glibc has this bug?
> I didnt see any crashed with threaded mdrun version with glibc-2.11.x
> on x86_64 (both with gcc-4.4 and gcc-4.5)
>
> 2010/6/21 Berk Hess <hess at cbr.su.se>:
>> Hi,
>>
>> I just discovered that there is a bug in qsort in glibc that makes it
>> non thread safe.
>> So mdrun with the GMX thread library could crash randomly. This occured
>> very seldomly.
>> We have one system that we managed to crash with certain compiler
>> settings in 1% of the runs.
>> This could explain some crashes people have experienced (gcc 4.1 is
>> another danger).
>> I have now replaced qsort by our own qsort in case we use threads.
>>
>> Berk
>>
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>
>
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexxyum at gmail.com
> mailto:alexxy at gentoo.org
> mailto:alexxy at omrb.pnpi.spb.ru
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