Hi Pearu- Thanks a lot for the quick response! Regarding ignoring wrapping some utility subprograms via a directive:
But I think it would be a useful feature. So I'll add this request to my todo list.
Thanks!
Btw, if you would use scipy_distutils-style setup.py file then you can add the "only: .. :" part to f2py_options
I thought there must be something like this; thanks for spelling it out.
I am not sure if I follow you correctly here but when using f2py from its CVS, all fortran objects have _cpointer attribute that is a C pointer to the actual Fortran or C function.
Well, I'm not sure I've followed you, either. 8-) Here's what I'm trying to do. I have fortran functions and subroutines that need to evaluate special functions as part of what they're doing. E.g., for gamma functions, right now I just define a function "gammaln" that returns the log of a gamma function, within the fortran source of my module. But Scipy already has such a function somewhere (in the Cephes library). Is there a way I can use that Cephes function? For example, could I just figure out the appropriate Cephes call (sorting out the appropriate underscores and pointers) and write a setup.py that will let my fortran routine use the Cephes library that Scipy has installed somewhere? For performance, I'd rather not have to send my fortran module a Python callback; after all, the raw Cephes routine is sitting *somewhere*. There are other examples; another module I have needs a Cholesky decomposition in the middle of a calculation. Right now it's just hard-coded in the C for the module. I should just call the appropriate lapack/atlas routine for this, and I'd love to know how to write the C code and accompanying setup.py file to be able to do this portably without the overhead of a Python callback. Thanks, Tom ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/
On Mon, 13 Dec 2004, Tom Loredo wrote:
I am not sure if I follow you correctly here but when using f2py from its CVS, all fortran objects have _cpointer attribute that is a C pointer to the actual Fortran or C function.
Well, I'm not sure I've followed you, either. 8-) Here's what I'm trying to do. I have fortran functions and subroutines that need to evaluate special functions as part of what they're doing. E.g., for gamma functions, right now I just define a function "gammaln" that returns the log of a gamma function, within the fortran source of my module. But Scipy already has such a function somewhere (in the Cephes library). Is there a way I can use that Cephes function? For example, could I just figure out the appropriate Cephes call (sorting out the appropriate underscores and pointers) and write a setup.py that will let my fortran routine use the Cephes library that Scipy has installed somewhere? For performance, I'd rather not have to send my fortran module a Python callback; after all, the raw Cephes routine is sitting *somewhere*.
Thanks for the explaination. Now I get the problem and using _cpointer is not a solution indeed. A working solution could be figured out from Lib/special/setup_special.py that compiles cephes library sources. Assuming that you have scipy source tree somewhere then in setup.py file use scipy_src_path = '/path/to/scipy/Lib' cephes = glob(os.path.join(scipy_src_path,'special','cephes','*.c')) ext_args = {} dict_append(ext_args, name = 'extname', sources = [...] libraries = ['cephes']) ext = Extension(**ext_args) setup(ext_modules = [ext], libraries = [('cephes',cephes)]) See Lib/special/setup_special.py for details and various aspects making the above example more portable. A better solution (using get_info like below for lapack) has to wait until we have moved various 3rd party libraries in scipy to Lib/lib where get_info could pick up cephes library, for instance, and return appropiate dictionary of libraries and paths to be used when linking your extension module.
There are other examples; another module I have needs a Cholesky decomposition in the middle of a calculation. Right now it's just hard-coded in the C for the module. I should just call the appropriate lapack/atlas routine for this, and I'd love to know how to write the C code and accompanying setup.py file to be able to do this portably without the overhead of a Python callback.
Ok, that problem is easier to solve if you have lapack/atlas libraries installed in you system. In your setup.py file use from scipy_distutils.system_info import get_info, dict_append lapack_opt = get_info('lapack_opt',notfound_action=2) ext_args = {} dict_append(ext_args, name = 'extname', sources = [...]) dict_append(ext_args,**lapack_opt) ext = Extension(**ext_args) to define your Extension module that will be linked against optimized lapack libraries. See Lib/lib/{lapack,blas}/setup_*.py files for more examples. Pearu
participants (2)
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Pearu Peterson -
Tom Loredo