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CMake Options for NEST¶
NEST is installed with
cmake (at least v3.12). In the simplest case, the commands:
cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir> <nest_source_dir> make make install
should build and install NEST to
/install/path, which should be an absolute
Choice of compiler¶
We systematically test NEST using the GNU gcc and the Clang compiler suites. Compilation with other up-to-date compilers should also work, but we do not regularly test against those compilers and can thus only provide limited support.
To select a specific compiler, please add the following flags to your
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]
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-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]
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:
-Dwith-mpi=ONas argument for
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.
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
mpiexec command works by defining the
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.
Support for libneurosim¶
In order to allow NEST to create connections using external libraries,
it provides support for the Connection Generator Interface from
libneurosim. To request the use of libneurosim, you have to use the
follwing switch for the invocation of
cmake. It expects either
ON or OFF, or the directory where libneurosim is installed:
For details on how to use the Connection Generator Interface, see the guide on connection management.
Disabling the Python Bindings (PyNEST)¶
To disable Python bindings use:
as an argument to
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
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 \ <nest_source_dir>
NEST has reasonable default compiler options for the most common compilers.
To ensure that computations obey the IEEE754 standard for floating point
-fp-model strict flag is used by default, but can be
-Kieee flag to ensure that computations obey the IEEE754 standard for floating point numerics.