[ghemical-devel] Fwd: Bug#580828: ghemical: Segmentation fault on running MOPAC energy calculation

[Tommi Hassinen]

Hello Jose,

I completely agree with you ; the exact input file which causes the crash and
information about exactly what operation caused the crash are both needed
in order to reproduce (and later fix) the problem.

with Best Regards,
Tommi

________________________________________
From: Jose R. Valverde [jrvalverde at cnb.csic.es]
Sent: Tuesday, May 11, 2010 10:12 AM
To: Tommi Hassinen
Cc: Daniel Leidert; ghemical-devel at bioinformatics.org
Subject: Re: [ghemical-devel] Fwd: Bug#580828: ghemical: Segmentation fault on running MOPAC energy calculation

On Mon, 10 May 2010 15:14:51 +0300
Tommi Hassinen <tommi.hassinen at uef.fi> wrote:
> On running ghemical from a terminal segfault occurs after the molecular coordinates are read in during a MOPAC energy calculation.

While I'm not a maintainer, I'd like to suggest that some extra
specificity might be beneficial. While reading the sentence it
is not clear if the problem is that the user has finished a MOPAC
calculation and later on, when reading the output Ghemical fails
(which could be a GUI problem) or whether it is while
running the simulation that Ghemical fails (which could be a
MOPAC problem).

That it does not happen with other codes is meaningless, as they
use different algorithms and file formats it is normal that their
behavior is different.

And as pointed out, starting from a wrong geometry may yield
absurd results. So, without any knowledge of the starting
geometry it would be difficult to reproduce the bug (not just
in Mopac or Ghemical, in any known QM code).

I've seen similar segfaults sometimes due to problems with the
GL libraries and/or privileges, but this was only on the display
step (which obviously I never reported as this wasn't Ghemical's
problem).

                                j
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