Pybind11: Store pointer to numpy array data in c++ object

Question

I have a c++ class that

stores two pointers to the data of two numpy arrays as members (m_ptrA, m_ptrB)
exposes a function to initialize the pointers (initPtrs)
exposes a function that operates on the pointers (doSomethingWithPtrs)

class Foo
{
public:
  void initPtrs( py::array_t<int32_t  , py::array::c_style>  pyAryA,
                 py::array_t<float32_t, py::array::c_style>  pyAryB
                )
  {
    m_ptrA = (int32_t*)   pyAryA.request().ptr;
    m_ptrB = (float32_t*) pyAryB.request().ptr;
  }
  
  void doSomethingWithPtrs()
  {
     std::cout << m_ptrB[0] << std::endl; //Crashes sometimes here: Pointer m_ptrB is not valid.
  }
  
 private:
   int32_t*   m_ptrA;
   float32_t* m_ptrB;
};

I tried to bind the class and its functions to python using pybind11:

PYBIND11_MODULE(bar,m)
{
py::class_<Foo>(m,"Foo")
  .def(py::init<>())
  .def( "init_ptrs"               , &Foo::initPtrs, py::keep_alive<1,2>(), py::keep_alive<1,3>() )
  .def( "do_something_with_ptrs"  , &Foo::doSomethingWithPtrs );
}

However, when calling do_something_with_ptrs after init_ptrs, the following program crashes sometimes, since the pointer m_ptrB is invalid:

def test( aryA, torchTensorB ):
  my_foo = bar.Foo()
  my_foo.init_ptrs( aryA, torchTensorB.numpy() * 3840 )
  my_foo.do_something_with_ptrs()

aryA is a numpy array of type int32. pyTensorB is a pytorch tensor of type torch.float32.

I'm pretty new to python/pybind. Any help would be appreciated. In particular, I'm not sure if I understood the py::keep_alive statements correctly.

To me, the Foo construction seems off. Are you still interested in a solution? — Dudly01
– Dudly01, Commented Feb 8, 2022 at 23:07
As workaround, I'm just deep copying the arrays now instead of storing the pointers. If you have a solution, I would be happy to hear it. — user16372530
– user16372530, Commented Feb 14, 2022 at 16:21

Dudly01 · Accepted Answer · 2022-08-15 19:35:20Z

IMHO the issue lies somewhere else. I suspect that you are using an uninitialized pointer or going out of bounds.

Without being provided a minimal reproduceable code, I tried to come up with something on my own. I am leaving the sources below for reference. During my testing, everything worked as expected on Windows (with MSVC and Clang). Modifying the array elements in Python showed up in the C++ code. Reassigning the variables in Python and calling the garbage collector manually did not invalidate the C++ class. When removing keep_alive (and multiplying the arrays with 2 at init_ptrs), I also managed to see the same memory being reassigned to the newly initialized array.

Sources

test.py

import torch
import numpy as np
import gc

import foo


if __name__ == "__main__":
    gc.disable()

    my_array = np.array([0, 1, 2, 3], dtype=np.int32)
    my_tensor = torch.tensor([4, 5, 6, 7], dtype=torch.float32)

    my_foo = foo.Foo()
    my_foo.init_ptrs(my_array * 2, my_tensor.numpy() * 2)

    print(gc.get_count())
    gc.collect()
    print(gc.get_count())

    my_foo.do_something_with_ptrs()

    my_array[0] = 71
    my_tensor[0] = 72
    my_foo.do_something_with_ptrs()

    my_array = np.array([10, 11, 12, 13], dtype=np.int32)
    my_tensor = torch.tensor([14, 15, 16, 17], dtype=torch.float)

    print(gc.get_count())
    gc.collect()
    print(gc.get_count())

    my_foo.do_something_with_ptrs()

    del(my_foo)
    print(gc.get_count())
    gc.collect()
    print(gc.get_count())

foo.cpp

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

#include <iostream>

namespace py = pybind11;

class Foo
{
public:
    void initPtrs(py::array_t<int32_t, py::array::c_style> pyAryA,
                  py::array_t<float_t, py::array::c_style> pyAryB)
    {
        auto buffer_info = pyAryA.request();
        m_ptrA = static_cast<int32_t *>(buffer_info.ptr);
        m_sizeA = [&]
        {
            size_t sum = 0;
            for (auto elem : buffer_info.shape)
                sum += elem;
            return sum;
        }();

        std::cout << "Initialized int32 with size: " << m_sizeA << '\n';

        buffer_info = pyAryB.request();
        m_ptrB = static_cast<float_t *>(buffer_info.ptr);
        m_sizeB = [&]
        {
            size_t sum = 0;
            for (auto elem : buffer_info.shape)
                sum += elem;
            return sum;
        }();

        std::cout << "Initialized float with size: " << m_sizeB << '\n';
    }

    void doSomethingWithPtrs()
    {
        std::cout << "int32 idx 0: ";
        for (size_t i = 0; i < m_sizeA /*+ 1*/; ++i)
        {
            std::cout << ' ' << m_ptrA[i];
        }
        std::cout << '\n';

        std::cout << "float idx 0: ";
        for (size_t i = 0; i < m_sizeB /*+ 1*/; ++i)
        {
            std::cout << ' ' << m_ptrB[i];
        }
        std::cout << '\n';
    }

private:
    int32_t *m_ptrA = nullptr;
    size_t m_sizeA = 0;
    float_t *m_ptrB = nullptr;
    size_t m_sizeB = 0;
};

PYBIND11_MODULE(foo, m)
{
    py::class_<Foo>(m, "Foo")
        .def(py::init<>())
        .def("init_ptrs", &Foo::initPtrs, py::keep_alive<1, 2>(), py::keep_alive<1, 3>())
        .def("do_something_with_ptrs", &Foo::doSomethingWithPtrs);
}

setup.py (based on CMake example)

import os
import re
import sys
import platform
import subprocess

from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
from distutils.version import LooseVersion


class CMakeExtension(Extension):
    def __init__(self, name, sourcedir=''):
        Extension.__init__(self, name, sources=[])
        self.sourcedir = os.path.abspath(sourcedir)


class CMakeBuild(build_ext):
    def run(self):
        try:
            out = subprocess.check_output(['cmake', '--version'])
        except OSError:
            raise RuntimeError("CMake must be installed to build the following extensions: " +
                               ", ".join(e.name for e in self.extensions))

        cmake_version = LooseVersion(
            re.search(r'version\s*([\d.]+)', out.decode()).group(1))
        if cmake_version < '3.11.0':
            raise RuntimeError("CMake >= 3.11.0 required")

        for ext in self.extensions:
            self.build_extension(ext)

    def build_extension(self, ext):
        extdir = os.path.abspath(os.path.dirname(
            self.get_ext_fullpath(ext.name)))
        # required for auto-detection of auxiliary "native" libs
        if not extdir.endswith(os.path.sep):
            extdir += os.path.sep

        cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
                      '-DPYTHON_EXECUTABLE=' + sys.executable,
                      '-DPIP_INSTALL=ON',
                      ]

        cfg = 'Debug' if self.debug else 'Release'
        build_args = ['--config', cfg]

        if platform.system() == "Windows":
            cmake_args += [
                '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(cfg.upper(), extdir)]
            if sys.maxsize > 2**32:
                cmake_args += ['-A', 'x64']
            build_args += ['--', '/m']
        else:
            cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
            build_args += ['--', '-j10']

        env = os.environ.copy()
        env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(env.get('CXXFLAGS', ''),
                                                              self.distribution.get_version())
        if not os.path.exists(self.build_temp):
            os.makedirs(self.build_temp)
        subprocess.check_call(['cmake', ext.sourcedir] +
                              cmake_args, cwd=self.build_temp, env=env)
        subprocess.check_call(['cmake', '--build', '.'] +
                              build_args, cwd=self.build_temp)


setup(
    name='Foo',
    version=2022.08,    

    # The list of python packages
    py_modules=['foo'],
    package_dir={'': os.path.join(os.getcwd())},
    # A list of instances of setuptools.Extension providing the list of Python extensions to be built.
    ext_modules=[CMakeExtension('foo')],
    # A dictionary providing a mapping of command names to Command subclasses.
    cmdclass=dict(build_ext=CMakeBuild),
    zip_safe=False
)

CMakeLists.txt

cmake_minimum_required(VERSION 3.5)
project(Foo)


include(FetchContent)

# Fetch pybind11
FetchContent_Declare(
  pybind11
    GIT_REPOSITORY https://github.com/pybind/pybind11
    GIT_TAG        v2.9.1
)

FetchContent_MakeAvailable(pybind11)

pybind11_add_module(foo "")

target_sources(foo
  PUBLIC
    ${CMAKE_CURRENT_LIST_DIR}/foo.cpp
)

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