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Updated/extended macOS install instructions #1297

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Oct 14, 2019
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Updated/extended macOS install instructions #1297

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Updated/extended macOS install instructions, removed untested MacPort…
heplesser Sep 25, 2019
cd171ee
Removed homebrew instructions for macOS and improved formatting.
heplesser Oct 2, 2019
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122 changes: 40 additions & 82 deletions doc/installation/mac_install.rst
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Original file line number Diff line number Diff line change
@@ -1,73 +1,29 @@
Installation on macOS
=========================
Manual Installation on macOS
===============================


On the Mac, you can install NEST either via Homebrew or manually. 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 <python-on-mac>`_ for details.

Installation via Homebrew
--------------------------

The easiest way to install NEST on a Mac is to install it via the Homebrew package manager:

* To install homebrew, follow the instructions at `brew.sh <http://brew.sh/>`_

* Then, in a terminal

* Add the homebrew/science tap by running:

.. code-block:: sh

brew tap brewsci/science

* For information on what options NEST has and what will be installed, run:

.. code-block:: sh

brew info nest

* To install nest, execute

.. code-block:: sh

brew install nest

Options have to be appended, so for example, to install NEST with PyNEST run:

.. code-block:: sh

brew install nest --with-python

This will install the most recent release version of NEST. To build
NEST from the most recent sources on Github, use:

.. code-block:: sh

brew install nest --HEAD

Manual installation
--------------------
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 <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 OS X 10.11 *El Capitan* and macOS 10.12 *Sierra* with `Anaconda Python 2 and 3 <https://www.continuum.io/anaconda-overview>`_ and all other dependencies installed via `Homebrew <http://brew.sh>`_. See below for `Manual installation with dependencies from MacPorts`_.
Installation instructions here have been tested under macOS 10.14 *Mojave* with `Anaconda Python 3 <https://www.continuum.io/anaconda-overview>`_ and all other dependencies installed via `Homebrew <http://brew.sh>`_. They should also work with earlier versions of macOS.
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@heplesser Can you be more explicit here in the steps you took to create this environment?
What about the PyNEST dependencies like numpy, scipy, and matplotlib?
which order did you use (brew install then conda install) ? Do you create a conda environment before installing the dependencies?

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I have tried different approaches at different times, both with the full Anaconda package and miniconda plus the conda install line shown in the Python section. I did not explicitly create conda environments in all cases I tested, it worked with and without for me. Therefore I have't been more specific here.


* Install Xcode from the AppStore.
#. Install Xcode from the AppStore.

* 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:
#. 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:

.. code-block:: sh

xcode-select --install

* Install dependencies via Homebrew:
#. Install dependencies via Homebrew:

.. code-block:: sh

brew install gcc cmake gsl open-mpi libtool

* 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).
#. 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).

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

.. code-block:: sh

Expand All @@ -77,13 +33,13 @@ Installation instructions here have been tested under OS X 10.11 *El Capitan* an
mkdir bld
cd bld

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

.. code-block:: sh

cmake -DCMAKE_INSTALL_PREFIX:PATH=</install/path> \
-DCMAKE_C_COMPILER=gcc-6 \
-DCMAKE_CXX_COMPILER=g++-6 \
-DCMAKE_C_COMPILER=gcc-9 \
-DCMAKE_CXX_COMPILER=g++-9 \
</path/to/NEST/src>

.. code-block:: sh
Expand All @@ -94,34 +50,37 @@ Installation instructions here have been tested under OS X 10.11 *El Capitan* an

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

Manual installation with dependencies from MacPorts
"""""""""""""""""""""""""""""""""""""""""""""""""""

The following should work if you install dependencies using MacPorts (only steps that differ from the instructions above are shown):

* Install dependencies via MacPorts::
Troubleshooting
.................

sudo port install gcc6 cmake gsl openmpi-default libtool \
python27 py27-cython py27-nose doxygen

* Configure and build NEST inside the build directory
If compiling NEST as described above fails with an error message like

.. code-block:: sh

cmake -DCMAKE_INSTALL_PREFIX:PATH=</install/path> \
-DPYTHON_LIBRARY=/opt/local/lib/libpython2.7.dylib \
-DPYTHON_INCLUDE_DIR=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 \
-DCMAKE_C_COMPILER=/opt/local/bin/gcc-mp-6 \
-DCMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-6 \
</path/to/NEST/src>

.. code-block:: sh

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.

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

.. code-block:: sh

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

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

.. code-block:: sh

sudo xcode-select -r




Python on Mac
Expand All @@ -134,4 +93,3 @@ One well-tested source is the `Anaconda <https://www.continuum.io/anaconda-overv
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.