Compiled C code can be used in several places in Brian to get speed improvements in cases where performance is the most important factor.
Weave is a SciPy module that allows the use of inlined C++ code. Brian by default doesn’t use any C++ optimisations for maximum compatibility across platforms, but you can enable several optimised versions of Brian objects and functions by enabling weave compilation. See Preferences for more information.
See also Vectorisation for some information on writing your own inlined C++ code using Weave.
For maximum compatibility, Brian works with pure Python only. However, as well as the optional
weave optimisations, there are also objects can run with a pure C++ version for a considerable speedup.
For this to work, you need a copy of the
gcc compiler installed (either on Linux, Mac or through cygwin on Windows)
to build them. During installation (via
pip or with
python setup.py install), two objects
are compiled automatically: brian.utils.fastexp.fastexp (providing a fast, approximate exponential function) and
brian.utils.ccircular.ccircular (a circular array data structure). If the compilation fails, a warning message
will be displayed and the pure Python versions used instead.
In addition, it is possible to compile a C++ version of a more recent datastructure underlying the Synapses object, the SpikeQueue. To compile this object, follow these instructions:
In a command prompt or shell window, go to the directory where Brian is installed. On Windows this
will probably be
go to the
experimental/cspikequeue folder. If you’re on Linux (and this may also work for Mac) run
python setup.py build_ext --inplace. If you’re on Windows you’ll need to have cygwin with gcc
installed, and then you run
setup.py build_ext --inplace -c mingw32 instead. You should see some
compilation, possibly with some warnings but no errors.
If all works OK, you should see a UserWarning when importing Brian. You can uninstall (and effectively switch off) the use of the C++ SpikeQueue by removing the
*.so file in the
experimental/cspikequeue/ directory. Repeating the steps above (i.e. recompiling the object) will re-enable the C SpikeQueue.
The same steps can also be used for compiling the ccircular or fastexp if they were not already compiled automatically during installation, just navigate to the respective directory.