build issue on OSX

[djsutherland]

build issue on OSX

[djsutherland]

This looks a lot like #11, though apparently you're on OSX so not precisely the same problem.

• How is flann installed, and what version?
• Can you post the output of pkg-config --libs flann and otool -L /Users/wgmueller/anaconda/envs/py-sdm2/lib/python2.7/site-packages/cyflann/index.so?

[wgmueller1]

I installed flann by brew install flann ... the version is 1.8.4.

pkg-config --libs flann
-L/usr/local/Cellar/flann/1.8.4/lib -lflann_cpp

otool -L /Users/wgmueller/anaconda/envs/py-sdm2/lib/python2.7/site-packages/cyflann/index.so

/usr/local/lib/libflann_cpp.1.8.4.dylib (compatibility version 1.8.0, current version 1.8.4)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1669.0.0)

[djsutherland]

Yeah, okay, it is actually the same problem as #11 then. There hasn't been a flann release since flann-lib/flann@0fba4ec, which fixed this problem. I guess the flann formula doesn't have a HEAD reference either.

The way I have it installed is: I added the line head 'https://github.com/dougalsutherland/flann.git', :branch => 'conditional-openmp' to the initial block of /usr/local/Library/Formula/flann.rb (just after the sha1 line), and installed with brew install flann --HEAD --use-gcc (you may need to brew uninstall flann first). That uses my fork of flann that works around a conflict with py-sdm's use of OpenMP, and compiles with gcc to get OpenMP support in flann (which py-sdm sometimes wants).

You could also use the official repository for flann with head 'https://github.com/mariusmuja/flann.git' instead, and install without --use-gcc (so it uses the system-default clang, which doesn't have OpenMP support at all). py-sdm does sometimes assume flann has multithreading support built in, though, so if you're using non-tiny datasets you'll probably have the best experience with the other approach.

Let me know how your experience with py-sdm goes!

[djsutherland]

Note that this problem can be worked around now in two easier ways:

• set the environment variable FLANN_DIR to eg /usr/local before running setup.py. This avoids using pkg-config and allows flann 1.8.4 to be used (though it doesn't address the OpenMP issues).
• use the conda package manager and follow the instructions in the py-sdm readme to install py-sdm and its dependencies, including flann/cyflann, from a binary distribution. I compiled that with gcc-4.8 so the OpenMP issues are addressed.