[gmx-developers] Re: Memory allocation bug in g_traj (cvs + 3.3.1)

[David van der Spoel]

wolfram at picb.ac.cn wrote:
> Hello Berk,
> 
> I do not really know why the index becomes negative, I did not
> use the -shuffle option. Looks like something goes wrong here,
> maybe while building the topology?
> If you are looking for an example, the error happens e.g. with the system
> in gromacs/tutor/methanol, but I also encountered the bug with another
> small system.
> Throwing a fatal error instead is not the best option I think, as we
> can avoid it by simply checking if isize[i] becomes negative.


can you please submit a bugzilla with example files? That makes it much 
easier to debug, plus we document the bug and its resolution.

> 
> Cheers,
> Wolfram
> 
> 
>> I think I am too tired...
>> The atndx should be there, so ignore my previous mail.
>>
>> I have committed a check in g_traj to the CVS head branch.
>> I would assume your system would now give a fatal_error
>> instead of producing a negative isize[i].
>>
>> Berk.
>>
>>
>>
>>
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se