> I followed your advise. After editing the CMakeCache.txt and adding the 
> compiler flags OpenMP is working for me. However, I would like to avoid 
> this additional step by adding some conditional compilation lines to the 
> CMakeLists.txt

This seems reasonable, since OMP_NUM_THREADS is needed before the OpenMP 
portion actually runs.

> I tried this lines with a fresh development version of OpenBabel and it 
> seems to be working.  I tried both having a setup with GOMP libraries 
> installed and one without. I also run the ctest for MMFF94 just to be 
> sure everything was working.

Good, thanks. I'll try adding it to the SVN development code and we can see how 
it does on the other test machines:
http://my.cdash.org/index.php?project=Open+Babel&display=project

> run two instances of OBForceFieldMMFF94 are being created. I would like 
> to understand why is that, because I thought only one was necessary and 
> therefore I am confused about this.

I don't know. You'd need to run a debugger or something like Valgrind to figure 
out what part of the code is creating each instance. In this particular code, 
only one instance should be created.

-Geoff
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