Post Amitesh's Mac build fix

[dsteinberg]

To solve the libclusterpy.dylib vs libclusterpy.so issue I found this code snippet which I included in the CMakeLists.txt just after 'library build instructions'. 

if(APPLE)
  set(CMAKE_SHARED_LIBRARY_SUFFIX ".so")
endif(APPLE)

This forced the creation of libclusterpy.so, which python3 was able recognise.

 
Here are the details of the steps I had to take. I am hoping that you can distill some of this information and add to your installation instruction for OSX users. 

1. Installing LLVM (non-Apple): execute: 'brew install --with-toolchain llvm' (comes with clang, check successful installation by executing 'clang --version' or 'which clang')
2. brew install eigen
3. brew install boost

### python3 and numpy
4. brew install python3 
5. pip3 install --upgrade pip setuptools wheels
6. pip3 install numpy
7. brew install boost-python3

### openmp installation
8. cd /Users/me/
9. svn co http://llvm.org/svn/llvm-project/openmp/trunk openmp
10. cd /Users/me/openmp/
11. mkdir build && cd build
12. brew install cmake
12a. cmake path/to/openmp -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
13. make

### editing paths in the .bash_profile for openmp
The dir location for openmp library and header file: '/Users/me/openmp/build/runtime/src' contains both the header file omp.h and libomp.dylib (libomp.so in linux)
13a. Add the following to your .bash_profile:
export DYLD_LIBRARY_PATH="/Users/me/openmp/build/runtime/src"
export LIBRARY_PATH="/Users/me/openmp/build/runtime/src"
export C_INCLUDE_PATH="/Users/me/openmp/build/runtime/src"
export CPLUS_INCLUDE_PATH="/Users/me/openmp/build/runtime/src"
export DYLD_LIBRARY_PATH="/opt/intel/mkl/lib:$DYLD_LIBRARY_PATH"
export DYLD_LIBRARY_PATH="/opt/intel/compilers_and_libraries_2017.*.***/mac/mkl/lib:$DYLD_LIBRARY_PATH"

export PATH="/usr/local/opt/llvm/bin:$PATH"
export PATH="/usr/local/opt/llvm/bin:$PATH"
export PATH="/usr/local/opt/eigen/include/eigen3/:$PATH"
export PATH="/usr/local/opt/llvm/bin:$PATH"
export PATH="/Users/me/openmp/build/runtime/src/:$PATH"

### check installation of OpenMP by compiling hello.c code below using 'clang -fopenmp hello.c -o hello'
#include <omp.h>
#include <stdio.h>
int main() {
#pragma omp parallel
printf("Hello from thread %d, nthreads %d\n", omp_get_thread_num(), omp_get_num_threads());
}

and running ./hello. Should produce no errors.

### Installing libcluster 
14. mkdir build
15. cd build
15a. Makes sure that the following lines of code are present in the CMakeLists.txt

if(APPLE)
  set(CMAKE_SHARED_LIBRARY_SUFFIX ".so")
endif(APPLE)

16. cmake .. -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DUSE_WERROR=ON (the extra flags are different from Linux installation and were needed for openmp)

Should proceed with the following message
----------
----------
-- Found OpenMP_CXX: -fopenmp=libomp
-- Found OpenMP: TRUE
-- Configuring done
----------
----------

17. make

The following error may arise when anaconda python3.6 and python3 are both present.
----------
----------
python/CMakeFiles/clusterpy.dir/flags.make:10: *** multiple target patterns.  Stop.
make[1]: *** [python/CMakeFiles/clusterpy.dir/all] Error 2
make: *** [all] Error 2
----------

To fix this, comment out the anaconda path from the .bash_profile, restart the terminal, delete the contents of the build directory, do a fresh install starting from step 16. If the same error arrises, uninstall python3 
'brew uninstall python3', then follow the instructions here https://stackoverflow.com/questions/3819449/how-to-uninstall-python-2-7-on-a-mac-os-x-10-6-4/3819829#3819829. Remove python3 and python@3 directories from /usr/local/opt and /usr/local/Cellar/. Do a fresh install 'brew install python3', delete the contents of the build directory, do a fresh install starting from step 16.

18. sudo make install

### python interface
19. ccmake. 
set the 'buiild_python_interface' and 'build_use_python3' to ON
and 'eigen_include_dirs' to '/usr/local/opt/eigen/include/eigen3' (or the path to eigen3 )
press [c], [e], and [q]

20. cmake .. -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DUSE_WERROR=ON -BUILD_PYTHON_INTERFACE=ON -BUILD_USE_PYTHON3=ON (note extra flags)
21. make
22. sudo make install

should see the following libcluster.so in the following locations
-- Install configuration: "Release"
-- Installing: /usr/local/lib/libcluster.so
-- Up-to-date: /usr/local/include/libcluster/libcluster.h
-- Up-to-date: /usr/local/include/libcluster/probutils.h
-- Up-to-date: /usr/local/include/libcluster/distributions.h
-- Installing: /usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/libclusterpy.so

to check dependencies of libclusterpy.so 
execute: otool -L /usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/libclusterpy.so

should see no paths pointing to anaconda lib, something similar to:

libclusterpy.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/opt/boost-python3/lib/libboost_python3.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/Python (compatibility version 3.6.0, current version 3.6.0)
	/usr/local/opt/boost-python3/lib/libboost_python3-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
	libcluster.so (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libomp.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.5.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
23. run python3
24. import libclusterpy
should proceed with no errors.