Compilation Options

NEST is installed with cmake (at least v2.8.12). In the simplest case, the commands:

cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir> </path/to/NEST/src>
make
make install

should build and install NEST to /install/path, which should be an absolute path.

Choice of CMake Version

We recommend to use cmake v3.4 or later, even though installing NEST with cmake v2.8.12 will in most cases work properly. For more detailed information please see below: Python Binding (PyNEST)

Choice of compiler

The default compiler for NEST is GNU gcc/g++. Version 7 or higher is required due to the presence of bugs in earlier versions that prevent the compilation from succeeding. NEST has also successfully been compiled with Clang 7 and the IBM XL C++ compiler.

To select a specific compiler, please add the following flags to your cmake line:

-DCMAKE_C_COMPILER=<C-compiler> -DCMAKE_CXX_COMPILER=<C++-compiler>

Options for configuring NEST

NEST allows for several configuration options for custom builds:

Change NEST behavior:

-Dtics_per_ms=[number]     Specify elementary unit of time. [default 1000.0]
-Dtics_per_step=[number]   Specify resolution. [default 100]
-Dwith-ps-arrays=[OFF|ON]  Use PS array construction semantics. [default=ON]

Add user modules:

-Dexternal-modules=[OFF|<list;of;modules>]  External NEST modules to be linked
                                            in, separated by ';'. [default=OFF]

Connect NEST with external projects:

-Dwith-libneurosim=[OFF|ON|</path/to/libneurosim>]  Request the use of libneurosim.
                                                    Optionally give the directory,
                                                    where libneurosim is installed.
                                                    [default=OFF]
-Dwith-music=[OFF|ON|</path/to/music>] Request the use of MUSIC. Optionally
                                       give the directory, where MUSIC is installed.
                                       [default=OFF]

Change parallelization scheme:

-Dwith-mpi=[OFF|ON|</path/to/mpi>]  Request compilation with MPI. Optionally
                                    give directory with MPI installation.
                                    [default=OFF]
-Dwith-openmp=[OFF|ON|<OpenMP-Flag>]  Enable OpenMP multi-threading.
                                      Optional: set OMP flag. [default=ON]

Set default libraries:

-Dwith-gsl=[OFF|ON|</path/to/gsl>]           Find a gsl library. To set a specific
                                             library, set install path.[default=ON]
-Dwith-readline=[OFF|ON|</path/to/readline>] Find a GNU Readline library. To set
                                             a specific library, set install path.
                                             [default=ON]
-Dwith-ltdl=[OFF|ON|</path/to/ltdl>]         Find an ltdl library. To set a specific
                                             ltdl, set install path. NEST uses the
                                             ltdl for dynamic loading of external
                                             user modules. [default=ON]
-Dwith-python=[OFF|ON]                       Build PyNEST. [default=ON]
-Dcythonize-pynest=[OFF|ON]                  Use Cython to cythonize pynestkernel.pyx.
                                             If OFF, PyNEST has to be build from
                                             a pre-cythonized pynestkernel.pyx.
                                             [default=ON]

Change compilation behavior:

-Dstatic-libraries=[OFF|ON]     Build static executable and libraries. [default=OFF]
-Dwith-optimize=[OFF|ON|<list;of;flags>]       Enable user defined optimizations. Separate
                                               multiple flags by ';'.
                                               [default OFF, when ON, defaults to '-O3']
-Dwith-warning=[OFF|ON|<list;of;flags>]        Enable user defined warnings. Separate
                                               multiple flags by ';'.
                                               [default ON, when ON, defaults to '-Wall']
-Dwith-debug=[OFF|ON|<list;of;flags>]          Enable user defined debug flags. Separate
                                               multiple flags by ';'.
                                               [default OFF, when ON, defaults to '-g']
-Dwith-intel-compiler-flags=[<list;of;flags>]  User defined flags for the Intel compiler.
                                               Separate multiple flags by ';'.
                                               [defaults to '-fp-model strict']
-Dwith-libraries=<list;of;libraries>           Link additional libraries. Give full path.
                                               Separate multiple libraries by ';'.
                                               [default OFF]
-Dwith-includes=<list;of;includes>             Add additional include paths. Give full
                                               path without '-I'. Separate multiple include
                                               paths by ';'. [default OFF]
-Dwith-defines=<list;of;defines>               Additional defines, e.g. '-DXYZ=1'.
                                               Separate multiple defines by ';'. [default OFF]

NO-DOC option

On systems where help extraction is slow, the call to make install can be replaced by make install-nodoc to skip the generation of help pages and indices. Using this option can help developers to speed up development cycles, but is not recommended for production use as it renders the built-in help system useless.

Configuring NEST for Distributed Simulation with MPI

NEST supports distributed simulations using the Message Passing Interface (MPI). Depending on your setup, you have to use one of the following steps in order to add support for MPI:

1. Try -Dwith-mpi=ON as argument for cmake.

2. If 1. does not work, or you want to use a non-standard MPI, try -Dwith-mpi=/path/to/my/mpi. The mpi directory should contain the include, lib and bin subdirectories of the MPI installation.

3. If 2. does not work, but you know the correct compiler wrapper for your installation, try adding the following to the invocation of cmake:

   -DMPI_CXX_COMPILER=myC++_CompilerWrapper
   -DMPI_C_COMPILER=myC_CompilerWrapper -Dwith-mpi=ON
   

When running large-scale parallel simualations and recording from many neurons, writing to ASCII files might become prohibitively slow due to the large number of resulting files. By installing the SIONlib library and supplying its installation path to the -Dwith-sionlib=<path> option when calling cmake, you can enable the recording backend for binary files, which solves this problem.

If you compiled NEST with support for MPI and also want to run the corresponding tests, you have to tell it about how your mpirun/mpiexec command works by defining the mpirun function in your ~/.nestrc file. The file already contains an example implementation that should work with the OpenMPI implementation. For more details, see the documentation on the Configuration Options.

See the Guide to parallel computing to learn how to execute threaded and distributed simulations with NEST.

Disabling the Python Bindings (PyNEST)

To disable Python bindings use:

-Dwith-python=OFF

as an argument to cmake.

Please see the README for details.

Python Binding (PyNEST)

Note that since NEST 3.0, support for Python 2 has been dropped. Please use Python 3 instead.

cmake usually autodetects your Python installation. In some cases cmake might not be able to localize the Python interpreter and its corresponding libraries correctly. To circumvent such a problem following cmake built-in variables can be set manually and passed to cmake:

 PYTHON_EXECUTABLE ..... path to the Python interpreter
 PYTHON_LIBRARY ........ path to libpython
 PYTHON_INCLUDE_DIR .... two include ...
 PYTHON_INCLUDE_DIR2 ... directories

e.g.: Please note ``-Dwith-python=ON`` is the default::
 cmake -DCMAKE_INSTALL_PREFIX=<nest_install_dir> \
       -DPYTHON_EXECUTABLE=/usr/bin/python3 \
       -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython3.4m.so \
       -DPYTHON_INCLUDE_DIR=/usr/include/python3.4 \
       -DPYTHON_INCLUDE_DIR2=/usr/include/x86_64-linux-gnu/python3.4m \
       </path/to/NEST/src>

Compiling for Apple OSX/macOS

NEST can currently not be compiled with the clang/clang++ compilers shipping with macOS. Therefore, you first need to install GCC 6.3 or later. The easiest way to install all required software is using Homebrew (from http://brew.sh):

brew install gcc cmake gsl open-mpi libtool

will install all required prequisites. You can then configure NEST with

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

For detailed information on installing NEST under OSX/macOS, please see the “macOS” section of https://www.nest-simulator.org/installation.

Choice of compiler

Most NEST developers use the GNU gcc/g++ compilers. We also regularly compile NEST using the IBM xlc/xlC compilers. You can find the version of your compiler by, e.g.:

g++ -v

To select a specific compiler, please add the following flags to your cmake line:

-DCMAKE_C_COMPILER=<C-compiler> -DCMAKE_CXX_COMPILER=<C++-compiler>

Compiler-specific options

NEST has reasonable default compiler options for the most common compilers.

When compiling with the Portland compiler:

Use the -Kieee flag to ensure that computations obey the IEEE754 standard for floating point numerics.

When compiling with the Intel compiler:

To ensure that computations obey the IEEE754 standard for floating point numerics, the -fp-model strict flag is used by default, but can be overridden with

-Dwith-intel-compiler-flags="<intel-flags>"