Problem with Fortran compilation when numpy.distutils is used

[Peter Danecek]

Hi all,

I am trying to update one of the ports i maintain (py-obspy) and encounter some problem I do not really understand. Maybe someone can help.

Background:
The obspy packages includes compiled extension, both C and Fortran. The C extensions are build with Xcode clang and Fortran with gcc (by variants). This is true for both the version currently available in MacPorts (@ 0.8.4) and the new version, i.e. 0.9.0. One difference is that now the `setup.py` script uses numpy.distutils to be more portable. 

Now when then `python setup.py build` is invoked by Macports, it fails at the linking step of the Fortran extension.

--- snip ---
/opt/local/bin/gfortran-mp-4.8 -Wall -arch x86_64 build/temp.macosx-10.8-x86_64-2.7/build/src.macosx-10.8-x86_64-2.7/build/libtau_Darwin_64bit_py27module.o build/temp.macosx-10.8-x86_64-2.7/build/src.macosx-10.8-x86_64-2.7/fortranobject.o build/temp.macosx-10.8-x86_64-2.7/opt/local/var/macports/build/_Users_petr_sandbox_MyPorts_ports_python_py-obspy-devel/py27-obspy-devel/work/obspy-0.9.0/obspy/taup/src/emdlv.o build/temp.macosx-10.8-x86_64-2.7/opt/local/var/macports/build/_Users_petr_sandbox_MyPorts_ports_python_py-obspy-devel/py27-obspy-devel/work/obspy-0.9.0/obspy/taup/src/libtau.o build/temp.macosx-10.8-x86_64-2.7/opt/local/var/macports/build/_Users_petr_sandbox_MyPorts_ports_python_py-obspy-devel/py27-obspy-devel/work/obspy-0.9.0/obspy/taup/src/ttimes_subrout.o -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin12/4.8.2 -lgfortran -o build/lib.macosx-10.8-x86_64-2.7/obspy/lib/libtau_Darwin_64bit_py27.so
Undefined symbols for architecture x86_64:
  "_PyArg_ParseTupleAndKeywords", referenced from:
      _f2py_rout_libtau_Darwin_64bit_py27_ttimes in libtau_Darwin_64bit_py27module.o
  "_PyCObject_AsVoidPtr", referenced from:
      _initlibtau_Darwin_64bit_py27 in libtau_Darwin_64bit_py27module.o
      _F2PyCapsule_AsVoidPtr in fortranobject.o
[… more symbols …]
--- snap ---

I understand why this command fails (the symbols are from python library). But what puzzles me is what determines this set of flags. When the C extensions are compiled the following flags are used. 

--- snap ---
/usr/bin/clang -bundle -undefined dynamic_lookup -L/opt/local/lib -Wl,-headerpad_max_install_names -L/opt/local/lib/db46 -arch x86_64 -arch x86_64 build/temp.macosx-10.8-x86_64-2.7/opt/local/var/macports/build/_Users_petr_sandbox_MyPorts_ports_python_py-obspy-devel/py27-obspy-devel/work/obspy-0.9.0/obspy/mseed/src/libmseed/fileutils.o [… more object files …] -o build/lib.macosx-10.8-x86_64-2.7/obspy/lib/libmseed_Darwin_64bit_py27.so
--- snip ---

In understand that C (with Clang) and Fortran (with gcc) can have different flags and behave different. But the other think is that when I try to reproduce the build process manually executing in the work directory: 

  sudo env F90=/opt/local/bin/gfortran-mp-4.8 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 setup.py --no-user-cfg build

--- snip ---
/opt/local/bin/gfortran -Wall -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.8-x86_64-2.7/build/src.macosx-10.8-x86_64-2.7/build/libtau_Darwin_64bit_py27module.o build/temp.macosx-10.8-x86_64-2.7/build/src.macosx-10.8-x86_64-2.7/fortranobject.o build/temp.macosx-10.8-x86_64-2.7/opt/local/var/macports/build/_Users_petr_sandbox_MyPorts_ports_python_py-obspy-devel/py27-obspy-devel/work/obspy-0.9.0/obspy/taup/src/emdlv.o build/temp.macosx-10.8-x86_64-2.7/opt/local/var/macports/build/_Users_petr_sandbox_MyPorts_ports_python_py-obspy-devel/py27-obspy-devel/work/obspy-0.9.0/obspy/taup/src/libtau.o build/temp.macosx-10.8-x86_64-2.7/opt/local/var/macports/build/_Users_petr_sandbox_MyPorts_ports_python_py-obspy-devel/py27-obspy-devel/work/obspy-0.9.0/obspy/taup/src/ttimes_subrout.o -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin12/4.8.2 -lgfortran -o build/lib.macosx-10.8-x86_64-2.7/obspy/lib/libtau_Darwin_64bit_py27.so
--- snap ---

The script behaves "correctly" or at least uses a flags set which builds. So I would need to understand what exactly makes the difference here and where the flags are influenced.

Any useful hints here? Thanks!
~petr