Using pybind11

The package pybind11 is provides an elegant way to wrap C++ code for Python, including automatic conversions for numpy arrays and the C++ Eigen linear algebra library. Used with the cppimport package, this provides a very nice work flow for integrating C++ and Python:

• Edit C++ code
• Run Python code

! pip install pybind11
! pip install cppimport

Clone the Eigen library if necessary - no installation is required as Eigen is a header only library.

! git clone https://github.com/RLovelett/eigen.git

Resources

• `pybind11 <http://pybind11.readthedocs.io/en/latest/>`__
• `cppimport <https://github.com/tbenthompson/cppimport>`__
• `Eigen <http://eigen.tuxfamily.org>`__

A first example of using pybind11

Create a new subdirectory - e.g. example1 and create the following 5 files in it:

• funcs.hpp
• funcs.cpp
• wrap.cpp
• setup.py
• test_funcs.py

First write the C++ header and implementation files

%mkdir example1
%cd example1

/home/jovyan/work/sta-663-2018/notebooks/example1

%%file funcs.hpp

int add(int i, int j);

Writing funcs.hpp

%%file funcs.cpp

int add(int i, int j) {
    return i + j;
};

Writing funcs.cpp

Next write the C++ wrapper code using pybind11 in wrap.cpp. The arguments "i"_a=1, "j"_a=2 in the exported function definition tells pybind11 to generate variables named i with default value 1 and j with default value 2 for the add function.

%%file wrap1.cpp
#include <pybind11/pybind11.h>
#include "funcs.hpp"

namespace py = pybind11;

using namespace pybind11::literals;

PYBIND11_MODULE(wrap1, m) {
    m.doc() = "pybind11 example plugin";
    m.def("add", &add, "A function which adds two numbers",
          "i"_a=1, "j"_a=2);
}

Overwriting wrap1.cpp

Finally, write the setup.py file to compile the extension module. This is mostly boilerplate.

%%file setup.py
import os, sys

from distutils.core import setup, Extension
from distutils import sysconfig

cpp_args = ['-std=c++11']

ext_modules = [
    Extension(
    'wrap1',
        ['funcs.cpp', 'wrap1.cpp'],
        include_dirs=['pybind11/include'],
    language='c++',
    extra_compile_args = cpp_args,
    ),
]

setup(
    name='wrap1',
    version='0.0.1',
    author='Cliburn Chan',
    author_email='cliburn.chan@duke.edu',
    description='Example',
    ext_modules=ext_modules,
)

Overwriting setup.py

Now build the extension module in the subdirectory with these files

%%bash

python setup.py build_ext -i

running build_ext
building 'wrap1' extension
gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipybind11/include -I/opt/conda/include/python3.6m -c funcs.cpp -o build/temp.linux-x86_64-3.6/funcs.o -std=c++11
gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipybind11/include -I/opt/conda/include/python3.6m -c wrap1.cpp -o build/temp.linux-x86_64-3.6/wrap1.o -std=c++11
g++ -pthread -shared -B /opt/conda/compiler_compat -L/opt/conda/lib -Wl,-rpath=/opt/conda/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/funcs.o build/temp.linux-x86_64-3.6/wrap1.o -L/opt/conda/lib -lpython3.6m -o /home/jovyan/work/sta-663-2018/notebooks/example6/wrap1.cpython-36m-x86_64-linux-gnu.so

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++

And if you are successful, you should now see a new funcs.so extension module. We can write a test_funcs.py file test the extension module:

%%file test_funcs.py

import wrap1

def test_add():
    print(wrap1.add(3, 4))
    assert(wrap1.add(3, 4) == 7)

if __name__ == '__main__':
    test_add()

Writing test_funcs.py

And finally, running the test should not generate any error messages:

%%bash

python test_funcs.py

7

%cd ..

/home/jovyan/work/sta-663-2018/notebooks

Using cppimport

In the development stage, it can be distracting to have to repeatedly rebuild the extension module by running

python setup.py clean
python setup.py build_ext -i

every single time you modify the C++ code. The cppimport package does this for you.

Create a new sub-directory exaample2 and copy the files func.hpp, funcs.cpp and wrap.cpp from example1 over. For the previous example, we just need to add some annotation (between <% and %> delimiters) to the top of the wrap.cpp file

%mkdir example2
%cp example1/funcs.* example2/
%cd example2

mkdir: cannot create directory ‘example2’: File exists
/home/jovyan/work/sta-663-2018/notebooks/example2

%%file wrap2.cpp
<%
cfg['compiler_args'] = ['-std=c++11']
cfg['sources'] = ['funcs.cpp']
setup_pybind11(cfg)
%>

#include "funcs.hpp"
#include <pybind11/pybind11.h>

namespace py = pybind11;

PYBIND11_MODULE(wrap2, m) {
    m.doc() = "pybind11 example plugin";
    m.def("add", &add, "A function which adds two numbers");
}

Overwriting wrap2.cpp

%%file test_funcs.py

import cppimport
funcs = cppimport.imp("wrap2")

def test_add():
    assert(funcs.add(3, 4) == 7)

if __name__ == '__main__':
    print(funcs.add(3,4))
    test_add()

Overwriting test_funcs.py

%%bash

python test_funcs.py

7

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++

Use of cppimport

Note that cppimport.imp is only called once. Once it is called, the shared library is created and can be sued

! ls *so

wrap2.cpython-36m-x86_64-linux-gnu.so

That is, you can import wrap2 and call from notebook

import wrap2

wrap2.add(3, 4)

7

without any need to manually build the extension module. Any updates will be detected by cppimport and it will automatically trigger a re-build.

%cd ..

/home/jovyan/work/sta-663-2018/notebooks

Vectorizing functions for use with numpy arrays

Example showing how to vectorize a square function. Note that from here on, we don’t bother to use separate header and implementation files for these code snippets, and just write them together with the wrapping code in a code.cpp file. This means that with cppimport, there are only two files that we actually code for, a C++ code.cpp file and a python test file.

%mkdir example3
%cd example3

mkdir: cannot create directory ‘example3’: File exists
/home/jovyan/work/sta-663-2018/notebooks/example3

%%file wrap3.cpp
<%
cfg['compiler_args'] = ['-std=c++11']
setup_pybind11(cfg)
%>

#include <pybind11/pybind11.h>
#include <pybind11/numpy.h>

namespace py = pybind11;
double square(double x) {
    return x * x;
}

PYBIND11_MODULE(wrap3, m) {
    m.doc() = "pybind11 example plugin";
    m.def("square", py::vectorize(square), "A vectroized square function.");
}

Overwriting wrap3.cpp

import cppimport

wrap3 = cppimport.imp("wrap3")
wrap3.square([1,2,3])

array([ 1.,  4.,  9.])

Once the shared libary is built, you can use it as a regular Python module.

! ls

wrap3.cpp  wrap3.cpython-36m-x86_64-linux-gnu.so

import wrap3

wrap3.square([2,4,6])

array([  4.,  16.,  36.])

%cd ..

/home/jovyan/work/sta-663-2018/notebooks

Using numpy arrays as function arguments and return values

Example showing how to pass numpy arrays in and out of functions. These numpy array arguments can either be generic py:array or typed py:array_t<double>. The properties of the numpy array can be obtained by calling its request method. This returns a struct of the following form:

struct buffer_info {
    void *ptr;
    size_t itemsize;
    std::string format;
    int ndim;
    std::vector<size_t> shape;
    std::vector<size_t> strides;
};

Here is C++ code for two functions - the function twice shows how to change a passed in numpy array in-place using pointers; the function sum shows how to sum the elements of a numpy array. By taking advantage of the information in buffer_info, the code will work for arbitrary n-d arrays.

%mkdir example4
%cd example4

mkdir: cannot create directory ‘example4’: File exists
/home/jovyan/work/sta-663-2018/notebooks/example4

%%file wrap4.cpp
<%
cfg['compiler_args'] = ['-std=c++11']
setup_pybind11(cfg)
%>

#include <pybind11/pybind11.h>
#include <pybind11/numpy.h>

namespace py = pybind11;

// Passing in an array of doubles
void twice(py::array_t<double> xs) {
    py::buffer_info info = xs.request();
    auto ptr = static_cast<double *>(info.ptr);

    int n = 1;
    for (auto r: info.shape) {
      n *= r;
    }

    for (int i = 0; i <n; i++) {
        *ptr++ *= 2;
    }
}

// Passing in a generic array
double sum(py::array xs) {
    py::buffer_info info = xs.request();
    auto ptr = static_cast<double *>(info.ptr);

    int n = 1;
    for (auto r: info.shape) {
      n *= r;
    }

    double s = 0.0;
    for (int i = 0; i <n; i++) {
        s += *ptr++;
    }

    return s;
}

PYBIND11_MODULE(wrap4, m) {
    m.doc() = "auto-compiled c++ extension";
    m.def("sum", &sum);
    m.def("twice", &twice);
}

Overwriting wrap4.cpp

%%file test_code.py
import cppimport
import numpy as np

code = cppimport.imp("wrap4")

if __name__ == '__main__':
    xs = np.arange(12).reshape(3,4).astype('float')
    print(xs)
    print("np :", xs.sum())
    print("cpp:", code.sum(xs))

    print()
    code.twice(xs)
    print(xs)

Overwriting test_code.py

%%bash

python test_code.py

[[  0.   1.   2.   3.]
 [  4.   5.   6.   7.]
 [  8.   9.  10.  11.]]
np : 66.0
cpp: 66.0

[[  0.   2.   4.   6.]
 [  8.  10.  12.  14.]
 [ 16.  18.  20.  22.]]

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++

%cd ..

/home/jovyan/work/sta-663-2018/notebooks

More on working with numpy arrays

This example shows how to use array access for numpy arrays within the C++ function. It is taken from the pybind11 documentation, but fixes a small bug in the official version. As noted in the documentation, the function would be more easily coded using py::vectorize.

%mkdir example5
%cd example5

mkdir: cannot create directory ‘example5’: File exists
/home/jovyan/work/sta-663-2018/notebooks/example5

%%file wrap5.cpp
<%
cfg['compiler_args'] = ['-std=c++11']
setup_pybind11(cfg)
%>

#include <pybind11/pybind11.h>
#include <pybind11/numpy.h>

namespace py = pybind11;

py::array_t<double> add_arrays(py::array_t<double> input1, py::array_t<double> input2) {
    auto buf1 = input1.request(), buf2 = input2.request();

    if (buf1.ndim != 1 || buf2.ndim != 1)
        throw std::runtime_error("Number of dimensions must be one");

    if (buf1.shape[0] != buf2.shape[0])
        throw std::runtime_error("Input shapes must match");

    auto result = py::array(py::buffer_info(
        nullptr,            /* Pointer to data (nullptr -> ask NumPy to allocate!) */
        sizeof(double),     /* Size of one item */
        py::format_descriptor<double>::value, /* Buffer format */
        buf1.ndim,          /* How many dimensions? */
        { buf1.shape[0] },  /* Number of elements for each dimension */
        { sizeof(double) }  /* Strides for each dimension */
    ));

    auto buf3 = result.request();

    double *ptr1 = (double *) buf1.ptr,
           *ptr2 = (double *) buf2.ptr,
           *ptr3 = (double *) buf3.ptr;

    for (size_t idx = 0; idx < buf1.shape[0]; idx++)
        ptr3[idx] = ptr1[idx] + ptr2[idx];

    return result;
}

PYBIND11_MODULE(wrap5, m) {
    m.def("add_arrays", &add_arrays, "Add two NumPy arrays");
}

Overwriting wrap5.cpp

import cppimport
import numpy as np

code = cppimport.imp("wrap5")

xs = np.arange(12)
print(xs)

print(code.add_arrays(xs, xs))

[ 0  1  2  3  4  5  6  7  8  9 10 11]
[  0.   2.   4.   6.   8.  10.  12.  14.  16.  18.  20.  22.]

%cd ..

/home/jovyan/work/sta-663-2018/notebooks

Using the C++ eigen library to calculate matrix inverse and determinant

Example showing how Eigen vectors and matrices can be passed in and out of C++ functions. Note that Eigen arrays are automatically converted to/from numpy arrays simply by including the pybind/eigen.h header. Because of this, it is probably simplest in most cases to work with Eigen vectors and matrices rather than py::buffer or py::array where py::vectorize is insufficient.

%mkdir example6
%cd example6

mkdir: cannot create directory ‘example6’: File exists
/home/jovyan/work/sta-663-2018/notebooks/example6

%%file wrap6.cpp
<%
cfg['compiler_args'] = ['-std=c++11']
cfg['include_dirs'] = ['../eigen3']
setup_pybind11(cfg)
%>

#include <pybind11/pybind11.h>
#include <pybind11/eigen.h>

#include <Eigen/LU>

namespace py = pybind11;

// convenient matrix indexing comes for free
double get(Eigen::MatrixXd xs, int i, int j) {
    return xs(i, j);
}

// takes numpy array as input and returns double
double det(Eigen::MatrixXd xs) {
    return xs.determinant();
}

// takes numpy array as input and returns another numpy array
Eigen::MatrixXd inv(Eigen::MatrixXd xs) {
    return xs.inverse();
}

PYBIND11_MODULE(wrap6, m) {
    m.doc() = "auto-compiled c++ extension";
    m.def("inv", &inv);
    m.def("det", &det);
}

Overwriting wrap6.cpp

import cppimport
import numpy as np

code = cppimport.imp("wrap6")

A = np.array([[1,2,1],
              [2,1,0],
              [-1,1,2]])

print(A)
print(code.det(A))
print(code.inv(A))

[[ 1  2  1]
 [ 2  1  0]
 [-1  1  2]]
-3.0
[[-0.66666667  1.          0.33333333]
 [ 1.33333333 -1.         -0.66666667]
 [-1.          1.          1.        ]]

%cd ..

/home/jovyan/work/sta-663-2018/notebooks

Using pybind11 with openmp

%mkdir example7
%cd example7

/home/jovyan/work/sta-663-2018/notebooks/example7

Here is an example of using OpenMP to integrate the value of \(\pi\) written using pybind11.

%%file wrap7.cpp
/*
<%
cfg['compiler_args'] = ['-std=c++11', '-fopenmp']
cfg['linker_args'] = ['-lgomp']
setup_pybind11(cfg)
%>
*/
#include <cmath>
#include <omp.h>
#include <pybind11/pybind11.h>
#include <pybind11/numpy.h>

namespace py = pybind11;

// Passing in an array of doubles
void twice(py::array_t<double> xs) {
    py::gil_scoped_acquire acquire;

    py::buffer_info info = xs.request();
    auto ptr = static_cast<double *>(info.ptr);

    int n = 1;
    for (auto r: info.shape) {
      n *= r;
    }

    #pragma omp parallel for
    for (int i = 0; i <n; i++) {
        *ptr++ *= 2;
    }
}

PYBIND11_MODULE(wrap7, m) {
  m.doc() = "auto-compiled c++ extension";
  m.def("twice", [](py::array_t<double> xs) {
      /* Release GIL before calling into C++ code */
      py::gil_scoped_release release;
      return twice(xs);
    });
}

Writing wrap7.cpp

import cppimport
import numpy as np

code = cppimport.imp("wrap7")
xs = np.arange(10).astype('double')
code.twice(xs)
xs

array([  0.,   2.,   4.,   6.,   8.,  10.,  12.,  14.,  16.,   9.])

%cd ..

/home/jovyan/work/sta-663-2018/notebooks