Compiling with Cython using OpenMP on macOS

Question

I'm on macOS Mojave 10.14.6 and I'm trying to compile some required extensions modules in c and c++ from this repository with:

python setup.py build_ext --inplace

which gives me the following error:

No CUDA runtime is found, using CUDA_HOME='/usr/local/cuda'
running build_ext
/Users/user/miniconda3/envs/torch/lib/python3.8/site-packages/torch/utils/cpp_extension.py:249: UserWarning: 

                               !! WARNING !!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Your compiler (g++) is not compatible with the compiler Pytorch was
built with for this platform, which is clang++ on darwin. Please
use clang++ to to compile your extension. Alternatively, you may
compile PyTorch from source using g++, and then you can also use
g++ to compile your extension.

See https://github.com/pytorch/pytorch/blob/master/CONTRIBUTING.md for help
with compiling PyTorch from source.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

                              !! WARNING !!

  warnings.warn(WRONG_COMPILER_WARNING.format(

and further down:

clang: error: unknown argument: '-i'
clang: error: no such file or directory: 'sysroot'
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang: error: unsupported option '-fopenmp'
ninja: build stopped: subcommand failed.

(this should be the relevant part, most recent tracebacks also show subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. and finally RuntimeError: Error compiling objects for extension)

---

From what I understand and what I tried so far:

• the flag -fopenmp in the setup file is one of the problems, seems like OpenMP is missing
• thus I installed brew install llvm and brew install libomp
• added PATH=\"/usr/local/bin:$PATH\ to my .bash_profile hoping that the newly installed compilers are now used
• added the flag -Xpreprocessor before -fopenmp to the setup file according to here, so that extra_compile_args=['-Xpreprocessor', '-std=c99', '-O3', '-fopenmp']
• I tried CC=gcc python setup.py build_ext --inplace, because of the warning about treating 'c' as 'c++' but since I'm trying to build c and c++ modules, I'm not sure what the variable should actually be set to
• I also tried CC=/usr/local/opt/llvm/bin/clang++ python setup.py build_ext --inplace as suggested here
• trying to build this without -fopenmp (which is not actually an option, because I need the parallel execution which is provided by OpenMP IIRC) results basically in the same error without the error about OpenMP
• Do I also need to set CXXFLAGS and CFLAGS ?
• now I'm doing all this inside a conda environment and it seems that Anaconda comes with their own tools. Should I be using those? and what are the required MacOSX SDK?

I'm sorry for this confusing question, but having no prior knowledge about compilers and trying to solve this is like going down the rabbit hole.... I would be very grateful for any comment shedding light on this situation and I'm happy to provide any missing information!

---

UPDATE:

• cleaning up the .bash_profile and exporting export CC='gcc-10'; export CXX='clang++' got rid of the Pytorch warning, but clang problem remains
• still remains with os.environ['CC'] = 'gcc-10' and os.environ['CXX'] = 'clang++ in the setup.py

The complete error message is:

(torch) [10:48:05] vanessamac: occupancy_networks $ python setup.py build_ext --inplace --verbose
No CUDA runtime is found, using CUDA_HOME='/usr/local/cuda'
running build_ext
building 'im2mesh.utils.libkdtree.pykdtree.kdtree' extension
Emitting ninja build file /Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/build.ninja...
Compiling objects...
Allowing ninja to set a default number of workers... (overridable by setting the environment variable MAX_JOBS=N)
[1/2] clang++ -MMD -MF '/Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/_kdtree_core.o'.d -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/vanessamac/miniconda3/envs/torch/include -arch x86_64 -I/Users/vanessamac/miniconda3/envs/torch/include -arch x86_64 -I/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/numpy/core/include -I/Users/vanessamac/miniconda3/envs/torch/include/python3.8 -c -c '/Users/vanessamac/projects/occupancy_networks/im2mesh/utils/libkdtree/pykdtree/_kdtree_core.c' -o '/Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/_kdtree_core.o' -std=c99 -O3 -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=kdtree -D_GLIBCXX_USE_CXX11_ABI=0
FAILED: /Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/_kdtree_core.o 
clang++ -MMD -MF '/Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/_kdtree_core.o'.d -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/vanessamac/miniconda3/envs/torch/include -arch x86_64 -I/Users/vanessamac/miniconda3/envs/torch/include -arch x86_64 -I/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/numpy/core/include -I/Users/vanessamac/miniconda3/envs/torch/include/python3.8 -c -c '/Users/vanessamac/projects/occupancy_networks/im2mesh/utils/libkdtree/pykdtree/_kdtree_core.c' -o '/Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/_kdtree_core.o' -std=c99 -O3 -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=kdtree -D_GLIBCXX_USE_CXX11_ABI=0
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang: error: unsupported option '-fopenmp'
[2/2] clang++ -MMD -MF '/Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/kdtree.o'.d -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/vanessamac/miniconda3/envs/torch/include -arch x86_64 -I/Users/vanessamac/miniconda3/envs/torch/include -arch x86_64 -I/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/numpy/core/include -I/Users/vanessamac/miniconda3/envs/torch/include/python3.8 -c -c '/Users/vanessamac/projects/occupancy_networks/im2mesh/utils/libkdtree/pykdtree/kdtree.c' -o '/Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/kdtree.o' -std=c99 -O3 -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=kdtree -D_GLIBCXX_USE_CXX11_ABI=0
FAILED: /Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/kdtree.o 
clang++ -MMD -MF '/Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/kdtree.o'.d -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/vanessamac/miniconda3/envs/torch/include -arch x86_64 -I/Users/vanessamac/miniconda3/envs/torch/include -arch x86_64 -I/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/numpy/core/include -I/Users/vanessamac/miniconda3/envs/torch/include/python3.8 -c -c '/Users/vanessamac/projects/occupancy_networks/im2mesh/utils/libkdtree/pykdtree/kdtree.c' -o '/Users/vanessamac/projects/occupancy_networks/build/temp.macosx-10.9-x86_64-3.8/im2mesh/utils/libkdtree/pykdtree/kdtree.o' -std=c99 -O3 -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=kdtree -D_GLIBCXX_USE_CXX11_ABI=0
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang: error: unsupported option '-fopenmp'
ninja: build stopped: subcommand failed.
Traceback (most recent call last):
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1509, in _run_ninja_build
    subprocess.run(
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "setup.py", line 112, in <module>
    setup(
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/setuptools/__init__.py", line 165, in setup
    return distutils.core.setup(**attrs)
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/setuptools/command/build_ext.py", line 87, in run
    _build_ext.run(self)
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 649, in build_extensions
    build_ext.build_extensions(self)
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/distutils/command/build_ext.py", line 449, in build_extensions
    self._build_extensions_serial()
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/distutils/command/build_ext.py", line 474, in _build_extensions_serial
    self.build_extension(ext)
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/setuptools/command/build_ext.py", line 208, in build_extension
    _build_ext.build_extension(self, ext)
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/distutils/command/build_ext.py", line 528, in build_extension
    objects = self.compiler.compile(sources,
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 469, in unix_wrap_ninja_compile
    _write_ninja_file_and_compile_objects(
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1228, in _write_ninja_file_and_compile_objects
    _run_ninja_build(
  File "/Users/vanessamac/miniconda3/envs/torch/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1529, in _run_ninja_build
    raise RuntimeError(message)
RuntimeError: Error compiling objects for extension

Answer 1

Here are a few hints:

• Use gcc instead of llvm or clang for painless openmp-support on macOS. Note that apple's default gcc is just an alias for Apple clang as you'll see with gcc --version. You can install the real gcc with homebrew: brew install gcc.

• Then use export CC='gcc-10' (the newest version should be gcc 10.x) inside the same terminal window to use homebrew's gcc temporarily as your C compiler.

• There's no need to set CXXFLAGS or CFLAGS. The required flags are set by distutils/setuptools inside the setup.py.

• You won't be able to compile dmc_cuda_module on macOS 10.14.6. The latest macOS version nvidia offers cuda drivers for is 10.13.6. So you might uncomment this part of the setup.py and hope for the best you don't need this module...

• Some of the Extensions inside the setup.py aren't including the numpy headers while using the numpy C-API. On macOS it's necessary to include the numpy headers for each Extension, see this comment. So you have to add include_dirs=[numpy_include_dir] to those Extensions.

• Edit: As discussed in the chat: The error was due to the conda env ignoring the CC variable. After installing python+pip via homebrew and the required python packages via pip, this answer's steps worked for the OP.

All in all, here's a setup.py that worked for me (macOS 10.5.7, gcc-10):

try:
    from setuptools import setup
except ImportError:
    from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
from torch.utils.cpp_extension import BuildExtension, CppExtension, CUDAExtension
import numpy


# Get the numpy include directory.
numpy_include_dir = numpy.get_include()

# Extensions
# pykdtree (kd tree)
pykdtree = Extension(
    'im2mesh.utils.libkdtree.pykdtree.kdtree',
    sources=[
        'im2mesh/utils/libkdtree/pykdtree/kdtree.c',
        'im2mesh/utils/libkdtree/pykdtree/_kdtree_core.c'
    ],
    language='c',
    extra_compile_args=['-std=c99', '-O3', '-fopenmp'],
    extra_link_args=['-lgomp'],
    include_dirs=[numpy_include_dir]
)

# mcubes (marching cubes algorithm)
mcubes_module = Extension(
    'im2mesh.utils.libmcubes.mcubes',
    sources=[
        'im2mesh/utils/libmcubes/mcubes.pyx',
        'im2mesh/utils/libmcubes/pywrapper.cpp',
        'im2mesh/utils/libmcubes/marchingcubes.cpp'
    ],
    language='c++',
    extra_compile_args=['-std=c++11'],
    include_dirs=[numpy_include_dir]
)

# triangle hash (efficient mesh intersection)
triangle_hash_module = Extension(
    'im2mesh.utils.libmesh.triangle_hash',
    sources=[
        'im2mesh/utils/libmesh/triangle_hash.pyx'
    ],
    libraries=['m'],  # Unix-like specific
    include_dirs=[numpy_include_dir]
)

# mise (efficient mesh extraction)
mise_module = Extension(
    'im2mesh.utils.libmise.mise',
    sources=[
        'im2mesh/utils/libmise/mise.pyx'
    ],
)

# simplify (efficient mesh simplification)
simplify_mesh_module = Extension(
    'im2mesh.utils.libsimplify.simplify_mesh',
    sources=[
        'im2mesh/utils/libsimplify/simplify_mesh.pyx'
    ],
    include_dirs=[numpy_include_dir]
)

# voxelization (efficient mesh voxelization)
voxelize_module = Extension(
    'im2mesh.utils.libvoxelize.voxelize',
    sources=[
        'im2mesh/utils/libvoxelize/voxelize.pyx'
    ],
    libraries=['m']  # Unix-like specific
)

# DMC extensions
dmc_pred2mesh_module = CppExtension(
    'im2mesh.dmc.ops.cpp_modules.pred2mesh',
    sources=[
        'im2mesh/dmc/ops/cpp_modules/pred_to_mesh_.cpp',
    ]   
)

# dmc_cuda_module = CUDAExtension(
#     'im2mesh.dmc.ops._cuda_ext', 
#     sources=[
#         'im2mesh/dmc/ops/src/extension.cpp',
#         'im2mesh/dmc/ops/src/curvature_constraint_kernel.cu',
#         'im2mesh/dmc/ops/src/grid_pooling_kernel.cu',
#         'im2mesh/dmc/ops/src/occupancy_to_topology_kernel.cu',
#         'im2mesh/dmc/ops/src/occupancy_connectivity_kernel.cu',
#         'im2mesh/dmc/ops/src/point_triangle_distance_kernel.cu',
#     ]
# )

# Gather all extension modules
ext_modules = [
    pykdtree,
    mcubes_module,
    triangle_hash_module,
    mise_module,
    simplify_mesh_module,
    voxelize_module,
    dmc_pred2mesh_module,
    #dmc_cuda_module,
]

setup(
    ext_modules=cythonize(ext_modules),
    cmdclass={
        'build_ext': BuildExtension
    }
)