Building wheel for pykdtree and clang: error: unsupported option '-fopenmp'

[AltynR]

Hi all,

I am trying to install meshparty on my Mac Catalina using pip3 install mesh party but I have an error with building wheel for pykdtree and clang: error: unsupported option '-fopenmp'. I have copied the error message below. When I check the environment with import sys; sys.version, I get: ' \n[Clang 11.0.0 (clang-1100.0.33.17)]' . I checked previous similar issues with pykdtree and it seems like I might not have openmp support. I tried installing llvm from http://openmp.llvm.org but I get zsh: parse error near \n after cmake ../llvm -DLLVM_ENABLE_PROJECTS=openmp -DCMAKE_C_COMPILER=<C compiler> -DCMAKE_CXX_COMPILER=<C++ compiler>. Instead of ../llvm, I put the path to the llvm folder.

Building wheels for collected packages: pykdtree
Building wheel for pykdtree (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-install-0diaq6g4/pykdtree/setup.py'"'"'; file='"'"'/private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-install-0diaq6g4/pykdtree/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-wheel-z43xh9hv
cwd: /private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-install-0diaq6g4/pykdtree/
Complete output (15 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.15-x86_64-3.7
creating build/lib.macosx-10.15-x86_64-3.7/pykdtree
copying pykdtree/test_tree.py -> build/lib.macosx-10.15-x86_64-3.7/pykdtree
copying pykdtree/init.py -> build/lib.macosx-10.15-x86_64-3.7/pykdtree
running build_ext
building 'pykdtree.kdtree' extension
creating build/temp.macosx-10.15-x86_64-3.7
creating build/temp.macosx-10.15-x86_64-3.7/pykdtree
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c pykdtree/kdtree.c -o build/temp.macosx-10.15-x86_64-3.7/pykdtree/kdtree.o -std=c99 -O3 -fopenmp
clang: error: unsupported option '-fopenmp'
error: command 'clang' failed with exit status 1

ERROR: Failed building wheel for pykdtree
Running setup.py clean for pykdtree
Failed to build pykdtree
Installing collected packages: shapely, pykdtree, meshparty
Running setup.py install for pykdtree ... error
ERROR: Command errored out with exit status 1:
command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-install-0diaq6g4/pykdtree/setup.py'"'"'; file='"'"'/private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-install-0diaq6g4/pykdtree/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-record-hhc11pn8/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/pykdtree
cwd: /private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-install-0diaq6g4/pykdtree/
Complete output (15 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.15-x86_64-3.7
creating build/lib.macosx-10.15-x86_64-3.7/pykdtree
copying pykdtree/test_tree.py -> build/lib.macosx-10.15-x86_64-3.7/pykdtree
copying pykdtree/init.py -> build/lib.macosx-10.15-x86_64-3.7/pykdtree
running build_ext
building 'pykdtree.kdtree' extension
creating build/temp.macosx-10.15-x86_64-3.7
creating build/temp.macosx-10.15-x86_64-3.7/pykdtree
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c pykdtree/kdtree.c -o build/temp.macosx-10.15-x86_64-3.7/pykdtree/kdtree.o -std=c99 -O3 -fopenmp
clang: error: unsupported option '-fopenmp'
error: command 'clang' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-install-0diaq6g4/pykdtree/setup.py'"'"'; file='"'"'/private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-install-0diaq6g4/pykdtree/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/z5/d_k3z58543zflpwyrr0ktg4m0000gn/T/pip-record-hhc11pn8/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/pykdtree Check the logs for full command output.

[ceesem]

I think we are going to remove that package, at least as a required install. However, in the meantime I have had more luck with installing it through conda via “conda install -c conda-forge pykdtree”.