[Numpy-discussion] how to compile Fortran using setup.py

Dag Sverre Seljebotn d.s.seljebotn@astro.uio...
Fri Mar 11 02:13:41 CST 2011


On 03/11/2011 07:57 AM, Ondrej Certik wrote:
> On Thu, Mar 10, 2011 at 8:25 PM, Robert Kern<robert.kern@gmail.com>  wrote:
>> On Thu, Mar 10, 2011 at 19:58, Ondrej Certik<ondrej@certik.cz>  wrote:
>>> Hi,
>>>
>>> I spent about an hour googling and didn't figure this out. Here is my setup.py:
>>>
>>> setup(
>>>     name = "libqsnake",
>>>     cmdclass = {'build_ext': build_ext},
>>>     version = "0.1",
>>>     packages = [
>>>         'qsnake',
>>>         'qsnake.calculators',
>>>         'qsnake.calculators.tests',
>>>         'qsnake.data',
>>>         'qsnake.mesh2d',
>>>         'qsnake.tests',
>>>         ],
>>>     package_data = {
>>>         'qsnake.tests': ['phaml_data/domain.*'],
>>>         },
>>>     include_dirs=[numpy.get_include()],
>>>     ext_modules = [Extension("qsnake.cmesh", [
>>>         "qsnake/cmesh.pyx",
>>>         "qsnake/fmesh.f90",
>>>         ])],
>>>     description = "Qsnake standard library",
>>>     license = "BSD",
>>> )
>>>
>>> The qsnake.cmesh extension needs to compile .pyx into .c and later to
>>> .o, it needs to use gfortran to compile fmesh.f90 to fmesh.o, and then
>>> link both things. That's it. In other words, this is what I want
>>> distutils to do:
>>>
>>> $ cython cmesh.pyx
>>> $ gcc -fPIC -o cmesh.o -c cmesh.c -I$SPKG_LOCAL/include/python2.6
>>> -I$SPKG_LOCAL/lib/python2.6/site-packages/numpy/core/include
>>> $ gfortran -fPIC -o fmesh.o -c fmesh.f90
>>> $ gcc -shared -o cmesh.so cmesh.o fmesh.o
>> Difficult if sticking with distutils of any flavor. You would have
>> probably to replace the build_ext command to handle both the Fortran
>> and the Cython. You may want to give David Cournapeau's Bento a try:
>>
>>   http://pypi.python.org/pypi/bento/
> Thanks Robert. I burned most of my today's evening on this, trying to
> replace the command, but so far I didn't figure it out. It is indeed
> difficult, but I wasn't sure, whether it is because I am not so
> familiar with distutils.

Kurt Smith spent much more than an evening on Fortran+distutils for the 
first release of Fwrap, I believe you could find something in the Fwrap 
0.1 release...

BUT, for Fwrap trunk, Kurt ditched all of that in favour of waf. And it 
works much, much better (I can simply export "FC=ifort" and it finds the 
right flags for Intel Fortran). I guess in your case, that means 
sticking with cmake.

> I looked at bento, but I'll simply stick to cmake. I thought that for
> a Python package (that uses cython + C or fortran, which I thought is
> a pretty standard configuration for scientific computing), I would use
> distutils, just like other Python packages.

The point of Bento as I understand it is exactly to seperate packaging 
from building, so that it becomes possible to ditch distutils but still 
have things behave like a Python package more or less.

In theory at least you should be able to plug cmake into Bento (perhaps 
by having Bento generate files included into your cmake scripts, and 
then launching a cmake process).

David is currently working on using Bento and waf together for building 
NumPy.

> With cmake, I have already figured out how to mix fotran, c, c++,
> Cython and Python and everything works nicely together, very robustly.
> So if I have to hack distutils anyway, I would write a simple
> distutils ->  cmake bridge.

Please, write a bento+cmake bridge instead :-) Too much time that could 
have been spent better has gone into distutils already, it's time to 
just stop using it.

Dag Sverre


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