call_py_fort

Call python from Fortran (not the other way around). Inspired by this blog post.

Installation

This library has the following dependencies

1. pfUnit (v3.2.9) for the unit tests
2. python (3+) with numpy and cffi, with libpython built as a shared library.
3. cmake (>=3.4+)

This development environment can be setup with the nix package manager. To enter a developer environment with all these dependencies installed run:

nix-shell

Once the dependencies are installed, you can compile this library using

mkdir build
cd build 
cmake ..
make

Run the tests:

make test

Install on your system

make install

This will usually install the libcallpy library to /usr/local/lib and the necessary module files to /usr/local/include. The specific way to add this library to a Fortran code base will depend on the build system of that code. Typically, you will need to add a flag -I/usr/local/include to any fortran compiler commands letting the compiler find the .mod file for this library, and a -L/usr/local/lib -lcallpy to link against the dynamic library. On some systems, you may need to set LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH at runtime to help the dynamic linker find the library.

Usage

Once installed, this library is very simple to use. For example:

program example
use callpy_mod
implicit none

real(8) :: a(10)
a = 1.0
call set_state("a", a)
call call_function("builtins", "print")
! read any changes from "a" back into a.
call get_state("a", a)

end program example

It basically operates by pushing fortran arrays into a global python dictionary, calling python functions with this dictionary as input, and then reading numpy arrays from this dictionary back into fortran. Let this dictionary by called STATE. In terms of python operations, the above lines roughly translate to

# abuse of notation signifyling that the left-hand side is a numpy array
STATE["a"] = a[:]
# same as `print` but with module name
builtins.print(STATE)
# transfer from python back to fortran memory
a[:] = STATE["a"]

You should be able to compile the above by running

gfortran -I/usr/local/include -Wl,-rpath=/usr/local/lib -L/usr/local/lib main.f90 -lcallpy

Here's what happens when you run the compiled binary:

$ ./a.out 
{'a': array([1., 1., 1., 1., 1., 1., 1., 1., 1., 1.])}

By modifying, the arguments of call_function you can call any python function in the pythonpath.

Currently, get_state and set_state support 4 byte or 8 byte floating point of one, two, or three dimensions.

Examples

See these examples. Most examples pair one fortran driver file (e.g. hello_world.f90) with a python module that it calls (e.g. hello_world.py).

They can be built from the project root like this:

cmake -B build .
make -C build
# need to add the example python modules to the import path
export PYTHONPATH=$(pwd)/examples:$PYTHONPATH
# run the example
./build/examples/hello_world

See the unit tests for more examples.

Troubleshooting

Embedded python does not initialize certain variables in the sys module the same as running a python script via the python command line. This leads to some common errors when using call_py_fort.

Module not found errors

Example of error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'your_module'

Solution: When run in embedded mode, python does not include the current working directory in sys.path. You can fix this in a few ways #. add the current directory to the PYTHONPATH environment variable export PYTHONPATH=$(pwd) #. If you have packaged it you can install it in editable mode pip install -e.

sys.argv is None

Some evil libraries like tensorflow actually look at your command line arguments when they are imported. Unfortunately, sys.argv is not initialized when python is run in embedded mode so this will lead to errors when importing such packages. Fix this by setting sys.argv before importing such packages e.g.

import sys
sys.argv = []
import tensorflow