Hi Kimon, I have had similar issues installing graph-tool on the mac. Currently I have it up and running (with a slight gtk+ problem when trying to export animated graphs), but this might be an individual success. However, below I send you the step by step solution that I came up with. At my end this worked at least. Please let me know if it works for you as well. Best, m Step by step instructions on how to install a working copy of graph-tool on OS X (tested with High Sierra) with Python 3.X and OpenMP support. 1) Remove all already installed dependencies (Check with brew info graph-tool) 2) Install llvm, Automarke und libtool: brew install llvm brew install automake brew install libtool 3) Add llvm to environment variables: echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> ~/.bash_profile 4) Reinitialize ENV: source ~/.bash_profile 5) Check if the correct clang is called (not Apple clang): clang --version 6) Install all python3 and all dependencies brew install python3 brew install pkg-config brew install boost brew install boost-python --with-python3 --without-python brew install cairomm brew install cgal brew install py3cairo brew install gnome-icon-theme brew install gtk+3 brew install --force librsvg --with-gtk+3 brew install pygobject3 --with-python3 --without-python brew install google-sparsehash 7) Install python packages with pip3: numpy, scipy, matplotlib pip3 install numpy pip3 install scipy pip3 install matplotlib 7) Clone graph-tool repository: git clone https://git.skewed.de/count0/graph-tool.git 8) Go to the cloned git folder 9) Set correct Python version in file configure.ac: AM_PATH_PYTHON([3.6]) ## Replace 2.7 by the correct version you are using 10) Run ./autogen.sh 11) Modify generated configure file in order to solve a nasty ldflags issue: Replace: if test -z "$PYTHON_EXTRA_LDFLAGS"; then PYTHON_EXTRA_LDFLAGS=`$PYTHON -c "import distutils.sysconfig; \ conf = distutils.sysconfig.get_config_var; \ print (conf('LINKFORSHARED'))"` With: if test -z "$PYTHON_EXTRA_LDFLAGS"; then PYTHON_EXTRA_LIBS=`$PYTHON-config --ldflags` 12) Run ./configure CC=clang CXX=clang++ LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" CPPFLAGS="-I/usr/local/opt/llvm/include -fopenmp" 13) Run make install -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/