MeasureTransport / MeasureTransport/MParT

`Failed building wheel` error for pip install

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Description

Another pip issue brought up by @Ischuler in #342 (possibly related to #326):


  Collecting mpart
    Using cached MParT-2.0.2.tar.gz (1.7 MB)
    Installing build dependencies ... done
    Getting requirements to build wheel ... done
    Preparing metadata (pyproject.toml) ... done
  Building wheels for collected packages: mpart
    Building wheel for mpart (pyproject.toml) ... error
    error: subprocess-exited-with-error
    
   Building wheel for mpart (pyproject.toml) did not run successfully.
    \u2502 exit code: 1
    \u2570\u2500> [171 lines of output]
      
      
      --------------------------------------------------------------------------------
      -- Trying 'Ninja' generator
      --------------------------------
      ---------------------------
      ----------------------
      -----------------
      ------------
      -------
      --
      CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
        Compatibility with CMake < 3.5 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.
      
      Not searching for unused variables given on the command line.
      
      -- The C compiler identification is GNU 10.2.1
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Check for working C compiler: /usr/bin/cc - skipped
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- The CXX compiler identification is GNU 10.2.1
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Check for working CXX compiler: /usr/bin/c++ - skipped
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      -- Configuring done (0.4s)
      -- Generating done (0.0s)
      -- Build files have been written to: /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_cmake_test_compile/build
      --
      -------
      ------------
      -----------------
      ----------------------
      ---------------------------
      --------------------------------
      -- Trying 'Ninja' generator - success
      --------------------------------------------------------------------------------
      
      Configuring Project
        Working directory:
          /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_skbuild/linux-x86_64-3.11/cmake-build
        Command:
          /tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/cmake/data/bin/cmake /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1 -G Ninja -DCMAKE_MAKE_PROGRAM:FILEPATH=/tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/ninja/data/bin/ninja --no-warn-unused-cli -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_skbuild/linux-x86_64-3.11/cmake-install -DPYTHON_VERSION_STRING:STRING=3.11.4 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/u/schuler/.conda/envs/test/bin/python -DPYTHON_INCLUDE_DIR:PATH=/u/schuler/.conda/envs/test/include/python3.11 -DPYTHON_LIBRARY:PATH=/u/schuler/.conda/envs/test/lib/libpython3.11.so -DPython_EXECUTABLE:PATH=/u/schuler/.conda/envs/test/bin/python -DPython_ROOT_DIR:PATH=/u/schuler/.conda/envs/test -DPython_FIND_REGISTRY:STRING=NEVER -DPython_INCLUDE_DIR:PATH=/u/schuler/.conda/envs/test/include/python3.11 -DPython3_EXECUTABLE:PATH=/u/schuler/.conda/envs/test/bin/python -DPython3_ROOT_DIR:PATH=/u/schuler/.conda/envs/test -DPython3_FIND_REGISTRY:STRING=NEVER -DPython3_INCLUDE_DIR:PATH=/u/schuler/.conda/envs/test/include/python3.11 -DCMAKE_MAKE_PROGRAM:FILEPATH=/tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/ninja/data/bin/ninja -DKokkos_ENABLE_THREADS:BOOL=ON -DSKBUILD_LIB_RPATH=/u/schuler/.conda/envs/test/lib -DSKBUILD_SITE_PATH=/u/schuler/.conda/envs/test/lib/python3.11/site-packages/ -DPYTHON_INSTALL_SUFFIX=bindings/python/package/ -DMPART_JULIA:BOOL=OFF -DMPART_MATLAB:BOOL=OFF -DMPART_BUILD_TESTS:BOOL=OFF -DMPART_PYTHON:BOOL=ON -DPYTHON_INSTALL_PREFIX= -DCMAKE_BUILD_TYPE:STRING=Release
      
      Not searching for unused variables given on the command line.
      -- The C compiler identification is GNU 10.2.1
      -- The CXX compiler identification is GNU 10.2.1
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Check for working C compiler: /usr/bin/cc - skipped
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Check for working CXX compiler: /usr/bin/c++ - skipped
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      -- Will install MParT to /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_skbuild/linux-x86_64-3.11/cmake-install
      -- PYTHON_INSTALL_PREFIX was not set by user, defaulting to /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_skbuild/linux-x86_64-3.11/cmake-install/bindings/python/package/
      -- Python packages will be installed to /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_skbuild/linux-x86_64-3.11/cmake-install/bindings/python/package/
      -- JULIA_INSTALL_PREFIX was not set by user, defaulting to /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_skbuild/linux-x86_64-3.11/cmake-install/julia.
      -- Performing Test COMPILER_IS_NVCC1
      -- Performing Test COMPILER_IS_NVCC1 - Success
      -- Performing Test COMPILER_IS_NVCC2
      -- Performing Test COMPILER_IS_NVCC2 - Failed
      -- Found Kokkos!
      -- MParT is not compiled with CUDA support, so CUBLAS and CUSOLVER will not be used.
      -- Found Eigen:
      -- Could not find pybind11. Fetching source.
      CMake Deprecation Warning at _skbuild/linux-x86_64-3.11/cmake-build/_deps/pybind11-src/CMakeLists.txt:8 (cmake_minimum_required):
        Compatibility with CMake < 3.5 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.
      
      
      -- pybind11 v2.10.0
      CMake Warning (dev) at _skbuild/linux-x86_64-3.11/cmake-build/_deps/pybind11-src/tools/FindPythonLibsNew.cmake:98 (find_package):
        Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
        are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
        the cmake_policy command to set the policy and suppress this warning.
      
      Call Stack (most recent call first):
        _skbuild/linux-x86_64-3.11/cmake-build/_deps/pybind11-src/tools/pybind11Tools.cmake:50 (find_package)
        _skbuild/linux-x86_64-3.11/cmake-build/_deps/pybind11-src/tools/pybind11Common.cmake:180 (include)
        _skbuild/linux-x86_64-3.11/cmake-build/_deps/pybind11-src/CMakeLists.txt:200 (include)
      This warning is for project developers.  Use -Wno-dev to suppress it.
      
      -- Found PythonInterp: /u/schuler/.conda/envs/test/bin/python (found suitable version "3.11.4", minimum required is "3.6")
      -- Found PythonLibs: /u/schuler/.conda/envs/test/lib/libpython3.11.so
      -- Performing Test HAS_FLTO
      -- Performing Test HAS_FLTO - Success
      -- Could not find Cereal. Fetching source.
      -- Found NLopt: /usr/lib/x86_64-linux-gnu/cmake/nlopt
      -- Found Doxygen: /usr/bin/doxygen (found version "1.9.1") found components: doxygen dot
      -- Found Sphinx: /ul/logiciels/SPACK/v0.17/spack/opt/spack/linux-debian11-haswell/gcc-10.2.1/anaconda3-2021.05-hs47cjjrjptwrb4hqrbqpiusvnosry2f/bin/sphinx-build
      SPHINX Executable = /ul/logiciels/SPACK/v0.17/spack/opt/spack/linux-debian11-haswell/gcc-10.2.1/anaconda3-2021.05-hs47cjjrjptwrb4hqrbqpiusvnosry2f/bin/sphinx-build
      CMake Warning at cmake/BuildDocs.cmake:94 (message):
        Could not find jupytext, but this is needed to build the examples when
        MPART_DOCKER_EXAMPLES=OFF.  Will not be able to build tutorial
        documentation.
      Call Stack (most recent call first):
        CMakeLists.txt:366 (Include)
      
      
      -- Configuring done (6.2s)
      CMake Error at CMakeLists.txt:256 (target_link_libraries):
        Target "mpart" links to:
      
          Kokkos::kokkos
      
        but the target was not found.  Possible reasons include:
      
          * There is a typo in the target name.
          * A find_package call is missing for an IMPORTED target.
          * An ALIAS target is missing.
      
      
      
      CMake Error at CMakeLists.txt:322 (target_link_libraries):
        Target "PrintKokkosInfo" links to:
      
          Kokkos::kokkos
      
        but the target was not found.  Possible reasons include:
      
          * There is a typo in the target name.
          * A find_package call is missing for an IMPORTED target.
          * An ALIAS target is missing.
      
      
      
      CMake Error at bindings/python/CMakeLists.txt:37 (target_link_libraries):
        Target "pympart" links to:
      
          Kokkos::kokkos
      
        but the target was not found.  Possible reasons include:
      
          * There is a typo in the target name.
          * A find_package call is missing for an IMPORTED target.
          * An ALIAS target is missing.
      
      
      
      -- Generating done (0.0s)
      CMake Generate step failed.  Build files cannot be regenerated correctly.
      Traceback (most recent call last):
        File "/tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/skbuild/setuptools_wrap.py", line 666, in setup
          env = cmkr.configure(
                ^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/skbuild/cmaker.py", line 357, in configure
          raise SKBuildError(msg)
      
      An error occurred while configuring with CMake.
        Command:
          /tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/cmake/data/bin/cmake /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1 -G Ninja -DCMAKE_MAKE_PROGRAM:FILEPATH=/tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/ninja/data/bin/ninja --no-warn-unused-cli -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_skbuild/linux-x86_64-3.11/cmake-install -DPYTHON_VERSION_STRING:STRING=3.11.4 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/u/schuler/.conda/envs/test/bin/python -DPYTHON_INCLUDE_DIR:PATH=/u/schuler/.conda/envs/test/include/python3.11 -DPYTHON_LIBRARY:PATH=/u/schuler/.conda/envs/test/lib/libpython3.11.so -DPython_EXECUTABLE:PATH=/u/schuler/.conda/envs/test/bin/python -DPython_ROOT_DIR:PATH=/u/schuler/.conda/envs/test -DPython_FIND_REGISTRY:STRING=NEVER -DPython_INCLUDE_DIR:PATH=/u/schuler/.conda/envs/test/include/python3.11 -DPython3_EXECUTABLE:PATH=/u/schuler/.conda/envs/test/bin/python -DPython3_ROOT_DIR:PATH=/u/schuler/.conda/envs/test -DPython3_FIND_REGISTRY:STRING=NEVER -DPython3_INCLUDE_DIR:PATH=/u/schuler/.conda/envs/test/include/python3.11 -DCMAKE_MAKE_PROGRAM:FILEPATH=/tmp/pip-build-env-x9wt6se2/overlay/lib/python3.11/site-packages/ninja/data/bin/ninja -DKokkos_ENABLE_THREADS:BOOL=ON -DSKBUILD_LIB_RPATH=/u/schuler/.conda/envs/test/lib -DSKBUILD_SITE_PATH=/u/schuler/.conda/envs/test/lib/python3.11/site-packages/ -DPYTHON_INSTALL_SUFFIX=bindings/python/package/ -DMPART_JULIA:BOOL=OFF -DMPART_MATLAB:BOOL=OFF -DMPART_BUILD_TESTS:BOOL=OFF -DMPART_PYTHON:BOOL=ON -DPYTHON_INSTALL_PREFIX= -DCMAKE_BUILD_TYPE:STRING=Release
        Source directory:
          /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1
        Working directory:
          /tmp/pip-install-1lh613cw/mpart_f16e020889244041929b8b27eec137a1/_skbuild/linux-x86_64-3.11/cmake-build
      Please see CMake's output for more information.
      
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for mpart
Failed to build mpart
ERROR: Could not build wheels for mpart, which is required to install pyproject.toml-based projects

Originally posted by @lschuler1 in https://github.com/MeasureTransport/MParT/issues/342#issuecomment-1667961903

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the failure with the Python wheel build, then inspect CMakeLists.txt:256 and :322 and bindings/python/CMakeLists.txt:37, where the missing Kokkos::kokkos target is linked. Check the surrounding dependency discovery and cmake/BuildDocs.cmake warnings. Done means the CMake configure step completes and pip can build and install the mpart wheel.

Written by the indexing model from the issue text.

Assessment

Tech stack
cmake, cpp, python
Domain
build-system
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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