f2py: binding Fortran and Python

I  have recently started using f2py to call Fortran from Python.  I have found this useful for two reasons: speeding up Python scripts by calling compiled Fortran code, and using Python as a unit testing framework for Fortran modules.   Unfortunately, the documentation for f2py is rather sparse, and may not be completely up to date.   In this note, I will hopefully prevent you from wasting a lot of time figuring out how to pass array arguments, and return array results.

Array arguments

Passing array arguments is a critical when working with numerical algorithms.  F2py handles this well, but it is difficult to figure it out how to do it correctly.  Here is a  simple example with some Fortran 90 routines:

module test

contains

subroutine foo (a)
    implicit none

    integer, intent(in) :: a
    print*, "Hello from Fortran!"
    print*, "a=",a
end subroutine foo

function bar (len_a, a)
    implicit none
    integer, intent(in) :: len_a
    real, dimension(len_a), intent(in) :: a

    real, dimension(len_a) :: bar
    !f2py depend(len_a) a, bar

    integer :: i
    real, dimension(len_a) :: b

    do i=1,len_a
        b(i) = 2.0*a(i)
    end do

    bar = b
end function bar

subroutine sub (a, len_a, a_out)
    implicit none

    real, dimension(len_a), intent(in) :: a
    integer, intent(in) :: len_a
    real, dimension(len_a), intent(out) :: a_out

    integer :: i

    do i=1,len_a
        a_out(i) = 2.0*a(i)
    end do

end subroutine sub

end module test

Function “foo” is quite straightforward. Function “bar” is a little more complex, because it accepts an array argument and returns an array. If you’re new to Fortran, it will seem strange to pass the length of the array along with the array, but you need that information to declare the output array. f2py needs to know that the input array a and the output array bar both depend on the argument len_a.  The special comment line

!f2py depend(len_a) a, bar

is mandatory!  It tells f2py that a depends on len_a.  If you omit this comment or the corresponding one for, the function will not work correctly.  You will get strange errors like

ValueError: failed to create intent(cache|hide)|optional array-- must have defined
dimensions but got (0,)

Fortran subroutines

Now look at the subroutine called sub.  On the Fortran side, it has three arguments: two inputs and an output.  However, Python only has functions,  and all non-array arguments are passed by value.  How do you reconcile this?  When the Fortran subroutine is called from Python, the intent(out) variables are returned as a function result, or a tuple of results if there are more than one.  Compare the Fortran code above with the Python call below to see what I mean.

Building

This code can be compiled using the “fast and smart” method described in the docs:

f2py -c -m hello hello.f90

Here is the Python code that calls the Fortran routines:

#!/usr/bin/env python

import hello
from numpy import *
a = arange(0.0, 10.0, 1.0)
len_a = len(a)

print "foo:"
hello.test.foo(len_a)

print "bar:"
a_out = hello.test.bar(len_a, a)
print a_out

print "sub:"
a_out = hello.test.sub(a, len_a)
print a_out

You might also want to check out this rather complicated f2py example.

Advertisements

5 thoughts on “f2py: binding Fortran and Python

  1. My previous comment isn’t correct, since the command as given *does* work. However, putting the module name immediately after -m seems a bit clearer to me, and that is what is suggested in the help given by `f2py -h`.

    Anyway, thanks for your ongoing blog! There’s a lot of very useful stuff here.

    Like

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s