Manual Installation on macOS

If you want to use PyNEST, you need to have a version of Python with some science packages installed, see the section Python on Mac for details.

The clang/clang++ compiler that ships with OS X/macOS does not support OpenMP threads and creates code that fails some tests. You therefore need to use GCC to compile NEST under OS X/macOS.

Installation instructions here have been tested under macOS 10.14 Mojave with Anaconda Python 3 and all other dependencies installed via Homebrew. They should also work with earlier versions of macOS.

  1. Install Xcode from the AppStore.

  2. Install the Xcode command line tools by executing the following line in the terminal and following the instructions in the windows that will pop up:

xcode-select --install

  1. Install dependencies via Homebrew:

brew install gcc cmake gsl open-mpi libtool

  1. Create a directory for building and installing NEST (you should always build NEST outside the source code directory; installing NEST in a “place of its own” makes it easy to remove NEST later).

  2. Extract the NEST tarball as a subdirectory in that directory or clone NEST from GitHub into a subdirectory:

mkdir NEST       # directory for all NEST stuff
cd NEST
tar zxf nest-simulator-x.y.z.tar.gz
mkdir bld
cd bld

  1. Configure and build NEST inside the build directory (replacing gcc-9 and g++-9 with the GCC compiler versions you installed with brew):

cmake -DCMAKE_INSTALL_PREFIX:PATH=</install/path> \
      -DCMAKE_C_COMPILER=gcc-9 \
      -DCMAKE_CXX_COMPILER=g++-9 \
      </path/to/NEST/src>

make -j4         # -j4 builds in parallel using 4 processes
make install
make installcheck

To compile NEST with MPI support, add -Dwith-mpi=ON as cmake option.

Troubleshooting

If compiling NEST as described above fails with an error message like

In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/wait.h:110,
                 from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:66,
                 from /usr/local/Cellar/gcc/9.2.0/include/c++/9.2.0/cstdlib:75,
                 from /usr/local/Cellar/gcc/9.2.0/include/c++/9.2.0/bits/stl_algo.h:59,
                 from /usr/local/Cellar/gcc/9.2.0/include/c++/9.2.0/algorithm:62,
                 from /Users/plesser/NEST/code/src/sli/dictutils.h:27,
                 from /Users/plesser/NEST/code/src/sli/dictutils.cc:23:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:443:34: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  443 | int     getiopolicy_np(int, int) __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_2_0);
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~

you most likely have installed a version of XCode prepared for the next version of macOS. You can attempt to fix this by running

sudo xcode-select -s /Library/Developer/CommandLineTools/

If this does not help, you can reset to the default XCode path using

sudo xcode-select -r

Python on Mac

The version of Python shipping with OS X/macOS is rather dated and does not include key packages such as NumPy. Therefore, you need to install Python via a channel that provides scientific packages.

One well-tested source is the Anaconda Python distribution for both Python 2 and 3. If you do not want to install the full Anaconda distribution, you can also install Miniconda and then install the packages needed by NEST by running:

conda install numpy scipy matplotlib ipython cython nose

Alternatively, you should be able to install the necessary Python packages via Homebrew, but this has not been tested.