> [BirdMac:~] % obabel -ig09 Liquids/MOLECULES/G4/water/water-g4.log.gz -osdf
> -O koko.sdf
> Segmentation fault
I mean in this case, you'd want to run inside a debugger and see where the
crash occurs.
> [csb:~] % ~/GG/openbabel-dev/install/bin/obabel -ig09
> Liquids/MOLECULES/G4/water/water-g4.log.gz -osdf -O koko.sdf
> /home/spoel/GG/openbabel-dev/install/bin/obabel: symbol lookup error:
> /home/spoel/GG/openbabel-dev/install/bin/obabel: undefined symbol:
> _ZN9OpenBabel12OBConversion11FullConvertERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERS7_SA_
This is a linking error. My guess is that you have more than one libopenbabel
installed and the dynamic linker is loading an older libopenbabel with your
binary (i.e., the binary interface around OBConversion::FullConvert() changed).
I'd be sure you're doing a 'make install' .. one of those is clearly a Mac and
you can use 'otool -L obabel' to see the list of linked libraries:
/usr/local/bin/obabel:
/usr/local/lib/libopenbabel.6.dylib (compatibility version 6.0.0,
current version 6.0.0)
/usr/local/lib/libcoordgen.1.dylib (compatibility version 1.0.0,
current version 1.3.2)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 1281.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
1.2.11)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
800.7.0)
While there have been changes to the Gaussian parsing, I don't see anything
that would obviously cause a segfault.
(I also suspect i have the same G4 file from your Alexandria archive here and
it parses okay.)
Hope that helps,
-Geoff_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
