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xtensor-stack / xtensor

C++ tensors with broadcasting and lazy computing
BSD 3-Clause "New" or "Revised" License
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/home/mona/zephyr/include/numpy_conversions.h:9:10: fatal error: xtensor-python/pyarray.hpp: No such file or directory #2706

Closed monajalal closed 1 year ago

monajalal commented 1 year ago

I get this error in the make step. Please let me know if you can please suggest a fix?

(zephyr) mona@ard-gpu-01:~/zephyr/build$ make
[ 33%] Building CXX object CMakeFiles/zephyr_c.dir/cpp/oriented_features.cpp.o
In file included from /home/mona/zephyr/cpp/oriented_features.cpp:20:
/home/mona/zephyr/include/numpy_conversions.h:9:10: fatal error: xtensor-python/pyarray.hpp: No such file or directory
    9 | #include "xtensor-python/pyarray.hpp"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/zephyr_c.dir/build.make:76: CMakeFiles/zephyr_c.dir/cpp/oriented_features.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/zephyr_c.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

I have installed xtensor using micromamba though.

full log here:

(zephyr) mona@ard-gpu-01:~/zephyr/build$ micromamba install -c conda-forge xtl

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

pytorch/linux-64                                   167.9kB @   2.2MB/s  0.1s
pytorch/noarch                                      10.2kB @ 115.3kB/s  0.1s
pkgs/r/noarch                                        1.3MB @   3.5MB/s  0.3s
pkgs/r/linux-64                                      1.4MB @   3.5MB/s  0.3s
pkgs/main/noarch                                   823.9kB @   1.4MB/s  0.2s
pkgs/main/linux-64                                   5.7MB @   5.3MB/s  1.1s
conda-forge/noarch                                  12.4MB @   4.6MB/s  2.7s
conda-forge/linux-64                                31.8MB @   5.2MB/s  6.4s

Pinned packages:
  - python 3.9.*

Transaction

  Prefix: /home/mona/anaconda3/envs/zephyr

  Updating specs:

   - xtl

  Package  Version  Build       Channel         Size
──────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────

  + xtl      0.7.4  h4bd325d_0  conda-forge     98kB

  Summary:

  Install: 1 packages

  Total download: 98kB

──────────────────────────────────────────────────────

Confirm changes: [Y/n] y

Transaction starting
xtl                                                 98.1kB @   1.2MB/s  0.1s
Linking xtl-0.7.4-h4bd325d_0

Transaction finished

To activate this environment, use:

    micromamba activate /home/mona/anaconda3/envs/zephyr

Or to execute a single command in this environment, use:

    micromamba run -p /home/mona/anaconda3/envs/zephyr mycommand

(zephyr) mona@ard-gpu-01:~/zephyr/build$ cmake .. -DPYTHON_EXECUTABLE=$(python -c "import sys; print(sys.executable)") -DPYTHON_INCLUDE_DIR=$(python -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())")  -DPYTHON_LIBRARY=$(python -c "import distutils.sysconfig as sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- Eigen found (include: /usr/include/eigen3, version: 3.4.0)
-- OpenNI found (version: 1.5.4.0, include: /usr/include/ni, lib: /usr/lib/libOpenNI.so;libusb::libusb)
-- OpenNI2 found (version: 2.2.0.33, include: /usr/include/openni2, lib: /usr/lib/x86_64-linux-gnu/libOpenNI2.so;libusb::libusb)
** WARNING ** io features related to pcap will be disabled
** WARNING ** io features related to png will be disabled
-- Eigen found (include: /usr/include/eigen3, version: 3.4.0)
-- FLANN found (include: /usr/include, lib: /usr/lib/x86_64-linux-gnu/libflann_cpp.so)
-- looking for PCL_COMMON
-- looking for PCL_OCTREE
-- looking for PCL_IO
-- looking for PCL_KDTREE
-- looking for PCL_SEARCH
-- looking for PCL_SAMPLE_CONSENSUS
-- looking for PCL_FILTERS
-- looking for PCL_2D
-- looking for PCL_FEATURES
CMake Error at CMakeLists.txt:31 (find_package):
  By not providing "Findxtensor.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "xtensor", but
  CMake did not find one.

  Could not find a package configuration file provided by "xtensor" with any
  of the following names:

    xtensorConfig.cmake
    xtensor-config.cmake

  Add the installation prefix of "xtensor" to CMAKE_PREFIX_PATH or set
  "xtensor_DIR" to a directory containing one of the above files.  If
  "xtensor" provides a separate development package or SDK, be sure it has
  been installed.

-- Configuring incomplete, errors occurred!
See also "/home/mona/zephyr/build/CMakeFiles/CMakeOutput.log".
(zephyr) mona@ard-gpu-01:~/zephyr/build$ micromamba install -c conda-forge xtensor

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pytorch/linux-64                                            Using cache
pytorch/noarch                                              Using cache
pkgs/r/linux-64                                               No change
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
pkgs/main/linux-64                                            No change

Pinned packages:
  - python 3.9.*

Transaction

  Prefix: /home/mona/anaconda3/envs/zephyr

  Updating specs:

   - xtensor

  Package    Version  Build       Channel          Size
─────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────

  + xtensor   0.24.2  h924138e_0  conda-forge     193kB

  Summary:

  Install: 1 packages

  Total download: 193kB

─────────────────────────────────────────────────────────

Confirm changes: [Y/n] y

Transaction starting
xtensor                                            193.2kB @   2.4MB/s  0.1s
Linking xtensor-0.24.2-h924138e_0

Transaction finished

To activate this environment, use:

    micromamba activate /home/mona/anaconda3/envs/zephyr

Or to execute a single command in this environment, use:

    micromamba run -p /home/mona/anaconda3/envs/zephyr mycommand

(zephyr) mona@ard-gpu-01:~/zephyr/build$ cmake .. -DPYTHON_EXECUTABLE=$(python -c "import sys; print(sys.executable)") -DPYTHON_INCLUDE_DIR=$(python -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())")  -DPYTHON_LIBRARY=$(python -c "import distutils.sysconfig as sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- Eigen found (include: /usr/include/eigen3, version: 3.4.0)
-- OpenNI found (version: 1.5.4.0, include: /usr/include/ni, lib: /usr/lib/libOpenNI.so;libusb::libusb)
-- OpenNI2 found (version: 2.2.0.33, include: /usr/include/openni2, lib: /usr/lib/x86_64-linux-gnu/libOpenNI2.so;libusb::libusb)
** WARNING ** io features related to pcap will be disabled
** WARNING ** io features related to png will be disabled
-- Eigen found (include: /usr/include/eigen3, version: 3.4.0)
-- FLANN found (include: /usr/include, lib: /usr/lib/x86_64-linux-gnu/libflann_cpp.so)
-- looking for PCL_COMMON
-- looking for PCL_OCTREE
-- looking for PCL_IO
-- looking for PCL_KDTREE
-- looking for PCL_SEARCH
-- looking for PCL_SAMPLE_CONSENSUS
-- looking for PCL_FILTERS
-- looking for PCL_2D
-- looking for PCL_FEATURES
-- Performing Test arch_native_supported
-- Performing Test arch_native_supported - Success
-- Found PythonInterp: /home/mona/anaconda3/envs/zephyr/bin/python3 (found suitable version "3.9.16", minimum required is "3.6") 
-- Found PythonLibs: /home/mona/anaconda3/envs/zephyr/lib
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Found pybind11: /home/mona/anaconda3/envs/zephyr/include (found version "2.10.4")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mona/zephyr/build
(zephyr) mona@ard-gpu-01:~$ which cmake
/usr/bin/cmake
(zephyr) mona@ard-gpu-01:~$ cmake --version
cmake version 3.22.1

CMake suite maintained and supported by Kitware (kitware.com/cmake).

(zephyr) mona@ard-gpu-01:~$ gcc --version
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

(zephyr) mona@ard-gpu-01:~$ g++ --version
g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

(zephyr) mona@ard-gpu-01:~$ uname -a
Linux ard-gpu-01 5.19.0-42-generic #43~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Apr 21 16:51:08 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
(zephyr) mona@ard-gpu-01:~$ lsb_release -a
LSB Version:    core-11.1.0ubuntu4-noarch:security-11.1.0ubuntu4-noarch
Distributor ID: Ubuntu
Description:    Ubuntu 22.04.2 LTS
Release:    22.04
Codename:   jammy

https://github.com/r-pad/zephyr/issues/9

also

(zephyr) mona@ard-gpu-01:~/zephyr/build$ python -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())"
/home/mona/anaconda3/envs/zephyr/include/python3.9
(zephyr) mona@ard-gpu-01:~/zephyr/build$ python -c "import sys; print(sys.executable)"
/home/mona/anaconda3/envs/zephyr/bin/python3
(zephyr) mona@ard-gpu-01:~/zephyr/build$ python -c "import distutils.sysconfig as sysconfig; print(sysconfig.get_config_var('LIBDIR'))"
/home/mona/anaconda3/envs/zephyr/lib
monajalal commented 1 year ago

so I installed xtensor-python and that array faded away. Now I get a new error:

(zephyr) mona@ard-gpu-01:~/zephyr/build$ micromamba install -c conda-forge xtensor-python

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pytorch/linux-64                                            Using cache
pytorch/noarch                                              Using cache
pkgs/main/noarch                                              No change
pkgs/main/linux-64                                            No change
pkgs/r/noarch                                                 No change
pkgs/r/linux-64                                               No change

Pinned packages:
  - python 3.9.*

Transaction

  Prefix: /home/mona/anaconda3/envs/zephyr

  Updating specs:

   - xtensor-python

  Package            Version  Build                Channel          Size
──────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────

  + libblas            3.9.0  16_linux64_openblas  conda-forge      13kB
  + libcblas           3.9.0  16_linux64_openblas  conda-forge      13kB
  + libgfortran-ng    12.2.0  h69a702a_19          conda-forge      23kB
  + libgfortran5      12.2.0  h337968e_19          conda-forge       2MB
  + liblapack          3.9.0  16_linux64_openblas  conda-forge      13kB
  + libopenblas       0.3.21  h043d6bf_0           pkgs/main         6MB
  + numpy             1.22.3  py39hc58783e_2       conda-forge       7MB
  + pybind11           2.9.2  py39hf939315_1       conda-forge     165kB
  + pybind11-global    2.9.2  py39hf939315_1       conda-forge     197kB
  + python_abi           3.9  2_cp39               conda-forge       4kB
  + xtensor-python    0.26.1  py39hac2352c_0       conda-forge      20kB

  Summary:

  Install: 11 packages

  Total download: 15MB

──────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y

Transaction starting
libgfortran-ng                                      22.9kB @ 531.8kB/s  0.0s
python_abi                                           4.0kB @  83.9kB/s  0.0s
libcblas                                            12.8kB @ 181.6kB/s  0.0s
libgfortran5                                         1.8MB @  21.7MB/s  0.1s
pybind11                                           165.4kB @   1.8MB/s  0.1s
pybind11-global                                    196.8kB @   2.1MB/s  0.1s
xtensor-python                                      20.1kB @ 202.3kB/s  0.1s
libblas                                             12.9kB @ 126.2kB/s  0.0s
liblapack                                           12.8kB @ 113.1kB/s  0.0s
libopenblas                                          5.7MB @  27.5MB/s  0.1s
numpy                                                7.1MB @  28.7MB/s  0.2s
Linking python_abi-3.9-2_cp39
Linking libgfortran5-12.2.0-h337968e_19
Linking pybind11-global-2.9.2-py39hf939315_1
warning  libmamba [pybind11-global-2.9.2-py39hf939315_1] The following files were already present in the environment:
    - include/pybind11/attr.h
    - include/pybind11/buffer_info.h
    - include/pybind11/cast.h
    - include/pybind11/chrono.h
    - include/pybind11/common.h
    - include/pybind11/complex.h
    - include/pybind11/detail/class.h
    - include/pybind11/detail/common.h
    - include/pybind11/detail/descr.h
    - include/pybind11/detail/init.h
    - include/pybind11/detail/internals.h
    - include/pybind11/detail/type_caster_base.h
    - include/pybind11/detail/typeid.h
    - include/pybind11/eigen.h
    - include/pybind11/embed.h
    - include/pybind11/eval.h
    - include/pybind11/functional.h
    - include/pybind11/gil.h
    - include/pybind11/iostream.h
    - include/pybind11/numpy.h
    - include/pybind11/operators.h
    - include/pybind11/options.h
    - include/pybind11/pybind11.h
    - include/pybind11/pytypes.h
    - include/pybind11/stl.h
    - include/pybind11/stl/filesystem.h
    - include/pybind11/stl_bind.h
    - include/python3.9/pybind11-global/pybind11/attr.h
    - include/python3.9/pybind11-global/pybind11/buffer_info.h
    - include/python3.9/pybind11-global/pybind11/cast.h
    - include/python3.9/pybind11-global/pybind11/chrono.h
    - include/python3.9/pybind11-global/pybind11/common.h
    - include/python3.9/pybind11-global/pybind11/complex.h
    - include/python3.9/pybind11-global/pybind11/detail/class.h
    - include/python3.9/pybind11-global/pybind11/detail/common.h
    - include/python3.9/pybind11-global/pybind11/detail/descr.h
    - include/python3.9/pybind11-global/pybind11/detail/init.h
    - include/python3.9/pybind11-global/pybind11/detail/internals.h
    - include/python3.9/pybind11-global/pybind11/detail/type_caster_base.h
    - include/python3.9/pybind11-global/pybind11/detail/typeid.h
    - include/python3.9/pybind11-global/pybind11/eigen.h
    - include/python3.9/pybind11-global/pybind11/embed.h
    - include/python3.9/pybind11-global/pybind11/eval.h
    - include/python3.9/pybind11-global/pybind11/functional.h
    - include/python3.9/pybind11-global/pybind11/gil.h
    - include/python3.9/pybind11-global/pybind11/iostream.h
    - include/python3.9/pybind11-global/pybind11/numpy.h
    - include/python3.9/pybind11-global/pybind11/operators.h
    - include/python3.9/pybind11-global/pybind11/options.h
    - include/python3.9/pybind11-global/pybind11/pybind11.h
    - include/python3.9/pybind11-global/pybind11/pytypes.h
    - include/python3.9/pybind11-global/pybind11/stl.h
    - include/python3.9/pybind11-global/pybind11/stl/filesystem.h
    - include/python3.9/pybind11-global/pybind11/stl_bind.h
    - share/cmake/pybind11/FindPythonLibsNew.cmake
    - share/cmake/pybind11/pybind11Common.cmake
    - share/cmake/pybind11/pybind11Config.cmake
    - share/cmake/pybind11/pybind11ConfigVersion.cmake
    - share/cmake/pybind11/pybind11NewTools.cmake
    - share/cmake/pybind11/pybind11Targets.cmake
    - share/cmake/pybind11/pybind11Tools.cmake
Linking libgfortran-ng-12.2.0-h69a702a_19
Linking pybind11-2.9.2-py39hf939315_1
Linking libopenblas-0.3.21-h043d6bf_0
Linking libblas-3.9.0-16_linux64_openblas
warning  libmamba [libblas-3.9.0-16_linux64_openblas] The following files were already present in the environment:
    - lib/libblas.so
Linking libcblas-3.9.0-16_linux64_openblas
warning  libmamba [libcblas-3.9.0-16_linux64_openblas] The following files were already present in the environment:
    - lib/libcblas.so
Linking liblapack-3.9.0-16_linux64_openblas
warning  libmamba [liblapack-3.9.0-16_linux64_openblas] The following files were already present in the environment:
    - lib/liblapack.so
Linking numpy-1.22.3-py39hc58783e_2
warning  libmamba [numpy-1.22.3-py39hc58783e_2] The following files were already present in the environment:
    - bin/f2py
    - bin/f2py3
    - bin/f2py3.9
    - lib/python3.9/site-packages/numpy/LICENSE.txt
    - lib/python3.9/site-packages/numpy/__config__.py
    - lib/python3.9/site-packages/numpy/__init__.cython-30.pxd
    - lib/python3.9/site-packages/numpy/__init__.pxd
    - lib/python3.9/site-packages/numpy/__init__.py
    - lib/python3.9/site-packages/numpy/__init__.pyi
    - lib/python3.9/site-packages/numpy/__pycache__/__config__.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/__init__.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/_distributor_init.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/_globals.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/_pytesttester.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/_version.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/conftest.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/ctypeslib.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/dual.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/matlib.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/setup.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/__pycache__/version.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/_distributor_init.py
    - lib/python3.9/site-packages/numpy/_globals.py
    - lib/python3.9/site-packages/numpy/_pytesttester.py
    - lib/python3.9/site-packages/numpy/_pytesttester.pyi
    - lib/python3.9/site-packages/numpy/_version.py
    - lib/python3.9/site-packages/numpy/array_api/__init__.py
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/__init__.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_array_object.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_constants.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_creation_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_data_type_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_dtypes.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_elementwise_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_manipulation_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_searching_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_set_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_sorting_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_statistical_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_typing.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/_utility_functions.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/linalg.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/__pycache__/setup.cpython-39.pyc
    - lib/python3.9/site-packages/numpy/array_api/_array_object.py
    - lib/python3.9/site-packages/numpy/array_api/_constants.py
    - lib/python3.9/site-packages/numpy/array_api/_creation_functions.py
    - lib/python3.9/site-packages/numpy/array_api/_data_type_functions.py
    - lib/python3.9/site-packages/numpy/array_api/_dtypes.py
    - lib/python3.9/site-packages/numpy/array_api/_elementwise_functions.py
    - lib/python3.9/site-packages/numpy/array_api/_manipulation_functions.py
    - lib/python3.9/site-packages/numpy/array_api/_searching_functions.py
    - lib/python3.9/site-packages/numpy/array_api/_set_functions.py
    - lib/python3.9/site-packages/numpy/array_api/_sorting_functions.py
    - lib/python3.9/site-packages/numpy/array_api/_statistical_functions.py
    - lib/python3.9/site-packages/numpy/array_api/_typing.py
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Linking xtensor-python-0.26.1-py39hac2352c_0

Transaction finished

To activate this environment, use:

    micromamba activate /home/mona/anaconda3/envs/zephyr

Or to execute a single command in this environment, use:

    micromamba run -p /home/mona/anaconda3/envs/zephyr mycommand

(zephyr) mona@ard-gpu-01:~/zephyr/build$     micromamba activate /home/mona/anaconda3/envs/zephyr
(zephyr) mona@ard-gpu-01:~/zephyr/build$ cmake .. -DPYTHON_EXECUTABLE=$(python -c "import sys; print(sys.executable)") -DPYTHON_INCLUDE_DIR=$(python -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())")  -DPYTHON_LIBRARY=$(python -c "import distutils.sysconfig as sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- Eigen found (include: /usr/include/eigen3, version: 3.4.0)
-- OpenNI found (version: 1.5.4.0, include: /usr/include/ni, lib: /usr/lib/libOpenNI.so;libusb::libusb)
-- OpenNI2 found (version: 2.2.0.33, include: /usr/include/openni2, lib: /usr/lib/x86_64-linux-gnu/libOpenNI2.so;libusb::libusb)
** WARNING ** io features related to pcap will be disabled
** WARNING ** io features related to png will be disabled
-- Eigen found (include: /usr/include/eigen3, version: 3.4.0)
-- FLANN found (include: /usr/include, lib: /usr/lib/x86_64-linux-gnu/libflann_cpp.so)
-- looking for PCL_COMMON
-- looking for PCL_OCTREE
-- looking for PCL_IO
-- looking for PCL_KDTREE
-- looking for PCL_SEARCH
-- looking for PCL_SAMPLE_CONSENSUS
-- looking for PCL_FILTERS
-- looking for PCL_2D
-- looking for PCL_FEATURES
-- Found pybind11: /home/mona/anaconda3/envs/zephyr/include (found version "2.9.2")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mona/zephyr/build
(zephyr) mona@ard-gpu-01:~/zephyr/build$ make
[ 33%] Building CXX object CMakeFiles/zephyr_c.dir/cpp/oriented_features.cpp.o
In file included from /home/mona/anaconda3/envs/zephyr/include/xtensor-python/pyarray.hpp:22,
                 from /home/mona/zephyr/include/numpy_conversions.h:9,
                 from /home/mona/zephyr/cpp/oriented_features.cpp:20:
/home/mona/anaconda3/envs/zephyr/include/xtensor-python/pycontainer.hpp:30:10: fatal error: numpy/arrayobject.h: No such file or directory
   30 | #include "numpy/arrayobject.h"
      |          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/zephyr_c.dir/build.make:76: CMakeFiles/zephyr_c.dir/cpp/oriented_features.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/zephyr_c.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
monajalal commented 1 year ago

This was the fix in CMakeLists.txt:

include_directories(include)
find_package(Python3 3.9 COMPONENTS Interpreter NumPy REQUIRED)
include_directories(${PYTHON_INCLUDE_DIRS})
pybind11_add_module(zephyr_c MODULE cpp/oriented_features.cpp cpp/numpy_conversions.cpp)
target_link_libraries(zephyr_c PRIVATE Eigen3::Eigen ${PCL_LIBRARIES} ${OpenCV_LIBS})
target_link_libraries(zephyr_c ${PYTHON_LIBRARIES} Python3::NumPy)