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

[Tommi Hassinen]

Hello Bill,

and thanks for your information and for your positive feedback.  :)

The example file zolmitriptan_3D.mol works OK in my laptop system
(debian lenny/stable). Perhaps this is about fortran compiler (64bit?)
in debian unstable ; the output file ghemical_segfault-2.txt shows that
libmopac7 works quite far until the crash happens. In the text file at line
31 the fortran code starts the output:

 *******************************************************************************
 ** MOPAC FOR LINUX (PUBLIC DOMAIN VERSION)  MTA ATOMKI, Debrecen, 95-JUN-21  **
 *******************************************************************************

Then it says it has read in 42 atoms with a reasonably-looking geometry.
Then symtrz.f prints out some debugging(?) messages like:

 == symtrz.f R00016 ==

followed by more geometry information. Finally at line 452 the crash
happens, and quickly checked it seems that the last values it printed
are OK (my version prints the same numbers).

So what could one do? It's an internal error quite deeply in libmopac7.
Could you try to compile a 32-bit version, or has anybody tried a 32-bit
version of debian unstable? Or could you convert mopac7 in C using
the f2c tool and then use a C compiler (I used to work with mopac7 until
a few years ago)?

Best Regards,
Tommi

________________________________________
From: ghemical-devel-bounces at bioinformatics.org [ghemical-devel-bounces at bioinformatics.org] On Behalf Of Bill Gunn [billggunn at gmail.com]
Sent: Wednesday, May 19, 2010 6:05 AM
To: ghemical-devel at bioinformatics.org
Subject: [ghemical-devel] Fwd: Bug#580828: ghemical: Segmentation fault on      running MOPAC energy calculation

Hello Tommi,

>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.

I am the user that reported the original Debian  Bug#580828: ghemical:
Segmentation fault on running MOPAC energy calculation.

It crashes with any molecular geometry I have tried either imported or
drawn in ghemical.  I attach two example files I have tested.

The calculation that fails is the calculation of energy using MNDO or
any other semi-empirical Hamiltonion.

example:
Compute|Setup - In Setup window All QM|MOPAC/MNDO|OK then Compute|Energy
The program then segfaults.  I have attached the terminal output for the
molecule zolmitriptan_3D.mol in the file ghemical_segfault.txt.

It fails Immediately - the output shows that MOPAC loads the molecule
geometry then segfaults.

The input file "water_mopac.dat" was then submitted to mopac7-bin and
normal output files were returned.

Note, I am running Debian Unstable amd64 installed using sidux on an
Intel Celeron EM64T CPU.

Thank you to Tommi and all the ghemical developers, to whom I am
extremely grateful, for a powerful and useful tool that I have been
using since release 0.8.

Bill Gunn