From NEST

[ Software:Documentation ]

NEST2 has a modular architecture which allows you to add your own elements to the NEST simulator without any need to modify the NEST software itself. To extend NEST, you simply write a new module. You can then either load this module dynamically at runtime (preferred) or you can link NEST against your module.

By writing a new module, you can add

• your own neuron models
• your own synapse types
• your own connection (or other) functions

to NEST. For the benefit of the NEST Community at large, we would encourage you to share your modules with other NEST users. We will soon create web resources that will allow you to do so.

On this page, you will find a (brief) overview over how to create your own module, based on the example MyModule. For information about how to write new neuron or synapse models or functions as part of your module, please see Developing Models, Developing Synapse Types and Writing SLI Functions.

External modules are rather new in NEST, and we are very interested in your feedback. Please join the mailing list to share your experience with us and other users.

Contents 1 Compilation and Installation 1.1 Prerquisites 1.2 Building MyModule 1.3 Using MyModule 1.4 Creating your own module 1.5 Linking MyModule into NEST

Compilation and Installation

Prerquisites

1. Download, build and install NEST. NEST should be built outside the source code directory.
2. GNU Autotools, we recommended at least:
   • m4-1.4.11
   • libtool-2.2.6
   • autoconf-2.62
   • automake-1.11
3. The NEST source code and installation directory must be accessible for building modules.
4. Define the environment variable NEST_INSTALL_DIR to contain the path to which you have installed NEST, e.g. using bash,

export NEST_INSTALL_DIR=/Users/plesser/NEST/ins

This environment variable is not strictly necessary, but saves you typing later.

Building MyModule

As a starting point, try to build MyModule as follows:

1. From the NEST source directory, copy directory examples/MyModule to somewhere outside the NEST source, build or install directories.

2. Change to the new location of MyModule and prepare by issuing

imt-b23010408:MyModule plesser$ ./bootstrap.sh 
Bootstrapping MyModule
  -> Removing old automake cache ...
  -> Running aclocal ...
  -> Installing libtool components ...
  -> Running autoheader ...
  -> Running automake ...
  -> Running autoconf ...
Done.

You may see some more output.

3. Leave MyModule and create a build directory for it, e.g., mmb next to it

 cd ..
 mkdir mmb
 cd mmb

4. Configure. The configure process uses the script nest-config.sh to find out where NEST is installed, where the source code resides, and which compiler options were used for compiling NEST. If nest-config.sh is not in your path, you need to provided it explicitly like this

 ../MyModule/configure --with-nest=${NEST_INSTALL_DIR}/bin/nest-config

MyModule will then be installed to ${NEST_INSTALL_DIR}. This ensures that NEST will be able to find initializing SLI files for the module. You should not use the --prefix to select a different installation destination. If you do, you must make sure to use addpath in SLI before loading the module to ensure that NEST will find the SLI initialization file for your module.

5. Compile.

 make
 make install

6. The previous command installed MyModule to the NEST installation directory, including help files generated from the source code.

Using MyModule

1. Set your LD_LIBRARY_PATH to include $NEST_INSTALL_DIR/lib/nest, where $NEST_INSTALL_DIR is the root of the NEST installation directory tree. On OSX, set DYLD_LIBRARY_PATH.
2. Start NEST.
3. Load the module using

SLI ] (mymodule) Install

Apr 30 17:06:11: *** Info: Install
Apr 30 17:06:11: loaded module My NEST Module

1. You should now see pif_psc_alpha in the modeldict and drop_odd_spike in the synapsedict. You can learn more about these models and the additional (meaningless) connection function supplied by the model by typing

 /pif_psc_alpha help
 /drop_odd_spike help
 /StepPatternConnect help

1. In PyNest, use

 nest.Install("mymodule")

This is available under Linux and OSX from r8497 and later. Link the module into NEST if you run into problems.

Creating your own module

1. Start with the code from MyModule, replace anything called "mymodule" in any form of camelcasing by the name of your module, and proceed as above.
2. When you change names of source code files or add/remove files, you need to update Makefile.am.
3. make dist will roll a tarball of your module for distribution to others.
4. mymodule.cpp and sli/mymodule.sli contain versioning information that you may want to update. It helps to keep the C++ code and SLI wrapper of your module in sync.

Linking MyModule into NEST

1. Build NEST and MyModule as described above.
2. Change back to the NEST build directory.
3. Reconfigure NEST informing it about your MyModule. Note that the module MUST be installed in the NEST installation directory tree!

 ../src/configure --with-modules="mymodule"

Several modules can be given, separated by spaces.

1. Recompile and install NEST.
2. The module should now be available as soon as NEST has started up. It will also be available in PyNEST.
3. When you make any change to your module, you must first re-compile and re-install your module.
4. Then move to the NEST build directory and issue

 make -C nest clean
 make  
 make install-exec

This rebuilds only the NEST executable.