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kiyo-masui / bitshuffle

Filter for improving compression of typed binary data.
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Build on OSX Mavericks #18

Closed telegraphic closed 8 years ago

telegraphic commented 9 years ago

Hi -- checked out the 0.2.1 code on my Mac, and it failed to install with the error

clang: warning: argument unused during compilation: '-fopenmp'
clang -bundle -undefined dynamic_lookup -L/usr/local/lib -L/usr/local/opt/sqlite/lib build/temp.macosx-10.10-x86_64-2.7/bitshuffle/ext.o build/temp.macosx-10.10-x86_64-2.7/src/bitshuffle.o build/temp.macosx-10.10-x86_64-2.7/lz4/lz4.o -L/opt/local/lib -L/usr/local/lib -lgomp -o build/lib.macosx-10.10-x86_64-2.7/bitshuffle/ext.so
ld: warning: directory not found for option '-L/opt/local/lib'
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'clang' failed with exit status 1

Which according to this StackOverflow post is because gcc now symlinks to clang, which does not support OpenMP. This will likely be fixed in the future, there is work toward this effort, but the easiest path for now is probably to use gcc-4.9 (which you can install with homebrew).

The to get it to compile I needed to add a flag -Wa,-q and set the CC/CXX environments, which I did by editing setup.py:

COMPILE_FLAGS = ['-Ofast', '-march=native', '-std=c99', '-fopenmp', '-Wa,-q']
# Cython breaks strict aliasing rules.
COMPILE_FLAGS += ["-fno-strict-aliasing"]
#COMPILE_FLAGS = ['-Ofast', '-march=core2', '-std=c99', '-fopenmp']
os.environ["CC"] = "gcc-4.9" 
os.environ["CXX"] = "g++-4.9"

Not sure what adding this flag would do to other OS environments. I guess there are two options: make mac users use gcc-4.9, or check for macs with clang and disable OpenMP.