Adding the iso-c-binding/Cython binding scheme

TestIsoCBinding/README

+This repository illustrates the iso_c_binding-cython way to bind python and fortran.
+It consists in
+- A benchmark_binding.f90 Fortran source code file
+- A benchmark_binding.pyx Cython source code file
+- Files for building the benchmark (build.sh, setup.py)
+- A test script script.py
+
+To build the benchmark, do 
+**source build.sh**
+
+To run the example, do (from the same terminal)
+**python script.py**
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TestIsoCBinding/benchmark_binding.f90

+module test_iso_c_binding
+
+use iso_c_binding, only: c_double, c_int, c_f_pointer, c_loc, c_null_char, c_char, c_ptr
+
+implicit none
+
+public  :: add_function
+
+contains
+
+subroutine add_function(array_length, i_array_1, i_array_2, o_array) bind(C)
+    integer, intent(IN)                              :: array_length
+    real(kind=c_double), dimension(array_length), intent(IN) :: i_array_1, i_array_2
+    real(kind=c_double), dimension(array_length), intent(OUT) :: o_array
+    integer :: i
+    o_array=i_array_1+i_array_2
+end subroutine add_function
+
+end module

TestIsoCBinding/benchmark_binding.pyx

+
+import numpy as np
+cimport numpy  as np
+
+from libc.stdlib cimport malloc
+from libc.string cimport strcpy, strlen
+
+cdef extern:
+    void add_function(bint *length, double *array, double *array, double *array)
+    
+# See https://stackoverflow.com/questions/8215265/passing-python-strings-through-cython-to-c
+def add(np.ndarray[np.double_t,ndim=1] darray, np.ndarray[np.double_t,ndim=1] darray2): #str filename):
+    #cdef double* array = darray
+    cdef bint length = len(darray)
+    cdef np.ndarray[np.double_t,ndim=1] output = np.asarray(np.zeros(len(darray)), dtype=darray.dtype)
+    add_function(&length, &darray[0], &darray2[0], &output[0])
+    return output
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TestIsoCBinding/build.sh

+#!/bin/bash
+#
+
+mkdir shared
+gfortran benchmark_binding.f90 -fPIC -shared -o shared/libFortran.so
+export LD_LIBRARY_PATH=`pwd`/shared:$LD_LIBRARY_PATH
+rm *.mod
+
+python setup.py build gfortran
+cp build/lib.linux-x86_64-2.7/benchmark.so .
+rm *.c
+rm -rf build
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TestIsoCBinding/script.py

+import benchmark
+import numpy as np
+
+print(benchmark.add(np.asarray([1,2,3]).astype(np.float), np.asarray([1,2,3]).astype(np.float)))
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TestIsoCBinding/setup.py

+# Pour compiler:
+#      python setup.py build_ext --inplace
+
+import glob
+import os
+import sys
+
+from Cython.Distutils import build_ext
+
+from distutils.core import setup, Extension
+from distutils.sysconfig import get_config_vars
+
+import numpy
+
+compiler = sys.argv.pop(2)
+
+EXTENSIONS = [Extension('benchmark',
+                        include_dirs=[numpy.get_include()],
+                        library_dirs = ["shared"],
+                        libraries=['Fortran'],
+                        sources = ['benchmark_binding.pyx']
+                        )]
+setup (name = "Benchmark",
+           version = "1.0",
+           ext_modules = EXTENSIONS,
+           package = "Benchmark",
+           package_dir      = {"Benchmark":"."},
+           cmdclass = {'build_ext': build_ext})
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