macOS build failing @ f652b95

@jnothman, @agramfort, @NicolasHug (#13252)

Description

Build on macOS succeeds at f652b95adad4a54b16d64884adc0d459d7d736b1~1 but fails at f652b95adad4a54b16d64884adc0d459d7d736b1.

Steps/Code to Reproduce

git clone https://github.com/scikit-learn/scikit-learn.git cd scikit-learn pip3 install --user Cython pip3 install --user numpy pip3 install --user .

Actual Results

creating build/temp.macosx-10.14-x86_64-3.7/sklearn/__check_build
compile options: '-I/Users/xxxxx/Library/Python/3.7/lib/python/site-packages/numpy/core/include -I/Users/xxxxx/Library/Python/3.7/lib/python/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.2_2/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-fopenmp'
clang: sklearn/__check_build/_check_build.c
clang: error: unsupported option '-fopenmp'
error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/Users/xxxxx/Library/Python/3.7/lib/python/site-packages/numpy/core/include -I/Users/xxxxx/Library/Python/3.7/lib/python/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.2_2/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c sklearn/__check_build/_check_build.c -o build/temp.macosx-10.14-x86_64-3.7/sklearn/__check_build/_check_build.o -MMD -MF build/temp.macosx-10.14-x86_64-3.7/sklearn/__check_build/_check_build.o.d -fopenmp" failed with exit status 1

[ogrisel]

In particular: https://scikit-learn.org/dev/developers/advanced_installation.html#mac-osx

You have to use a compiler that supports openmp which is not the case of the system default “gcc” alias. You can use homebrew to install the libomp runtime and configure you environment to use the system “clang” / “clang++” compilers with that openmp runtime.

brew install libomp

export CC=/usr/bin/clang
export CXX=/usr/bin/clang++
export CPPFLAGS="$CPPFLAGS -Xpreprocessor -fopenmp"
export CFLAGS="$CFLAGS -I/usr/local/opt/libomp/include"
export CXXFLAGS="$CXXFLAGS -I/usr/local/opt/libomp/include"
export LDFLAGS="$LDFLAGS -L/usr/local/opt/libomp/lib -lomp"
export DYLD_LIBRARY_PATH=/usr/local/opt/libomp/lib

[jeremiedbb]

We could try to compile a test code and if it fails, not set the openmp flag and raise a warning that some parts of sklearn won’t be multithreaded (something similar to what’s done in astropy).