mozaik 0.1.0

Virtual env

We recommend to install mozaik using the virtualenv python environment manager (http://pypi.python.org/pypi/virtualenv/) , to prevent potential conflicts with standard versions of required libraries. Users can follow for example http://simononsoftware.com/virtualenv-tutorial tutorial or just do the following steps:

• Install virtualenv

• Create (for example in your home directory) a directory where all virtual environments will be created home/virt_env

• Create the virtual environment for mozaik:

  virtualenv virt_env/virt_env_mozaik/ --verbose --no-site-packages

• Load the virtual environment for mozaik by:

  source virt_env/virt_env_mozaik/bin/activate

Your shell should look now something like:

(virt_env_mozaik)Username@Machinename:~$

You can use pip to view the installed packages:

pip freeze

Dependencies

Note that if the installation is done in your virtualenv environment, it doesn’t require any root privilege.

• scipy

• numpy

• mpi4py

• matplotlib (1.1 and higher)

• quantities

• PyNN:

  git clone https://github.com/NeuralEnsemble/PyNN.git

  • Then, in your virtual environment:

    python setup.py install

• Neo:

  git clone https://github.com/apdavison/python-neo python-neo
  cd python-neo
  python setup.py install

• imagen:

  pip install --user imagen

• parameters:

  git clone https://github.com/apdavison/parameters.git parameters
  cd parameters
  python setup.py install

• NeuroTools:

  svn co https://neuralensemble.org/svn/NeuroTools/trunk NeuroTools
  python setup.py install

For mozaik itself, you need to clone with the help of git:

git clone https://github.com/antolikjan/mozaik.git
python setup.py install

VIRTUALENV NOTE: You might already have some of the above packages if you’ve used the option –system-site-packages when creating the virtual environment for mozaik. You can list the packages you have e.g. with the help of yolk): If you’ve set up the virt_env with the option –system-site-packages and you’re using scipy, numpy, matplotlib anyway you don’t have to install those in your virt_env.

Virtual env

Then python virtualenv and virtualenvwrapper (an handy way to manage python virtual environments):

$ sudo pip install virtualenv
$ sudo pip install virtualenvwrapper

To setup virtualenvwrapper add the following lines at the top of ~/.bash_profile (create it if you don’t have one):

# virtualenvwrapper
export WORKON_HOME=~/.virtualenvs
source /usr/local/bin/virtualenvwrapper.sh
export PIP_VIRTUALENV_BASE=$WORKON_HOME
export PIP_RESPECT_VIRTUALENV=true

For the first time, run bash_profile (the next times it will be loaded by your terminal):

$ source .bash_profile

To create a new managed virtualenv you just need to:

$ mkvirtualenv --no-site-packages mozaik
$ workon mozaik
(mozaik)$>

To produce a requirement file (it will list all the installed package in the virtual environment, so that pip can reinstall the same set of packages):

(mozaik)$> pip freeze > requirements.txt

Then you can use it to replicate installation:

(mozaik)$> pip install -r requirements.txt

To exit the environment:

(mozaik)$> deactivate

Dependencies

Now you can install in this protected environment all other dependencies:

pip install --upgrade distribute
pip install numpy mpi4py
pip install scipy matplotlib quantities lazyarray
pip install imagen interval PIL

Now we can install Nest (always in the virtual environment):

• download the latest version from their website

• untar and cd into it:

  tar xvfz nest-2.2.2.tar.gz
  cd nest-2.2.2

• then configure, choose if you want mpi. And, if you decide to have nest installed somewhere else from normal places add it with a prefix, then you also need to specify the pynest prefix. So if ‘mozaik’ is your virtual environment, and if the directory of all the virtual environments is virt_env, then the configure line should look like:

  (mozaik)$ ./configure --with-mpi --prefix=$HOME/opt/nest --with-pynest-prefix=$HOME/virt_env/mozaik

• finally, by launching make and install, it installs PyNest in

  (mozaik)$ make
  (mozaik)$ make install

• in the ./~nestrc, uncomment the lines regarding mpirun, and check that the mpirun executables are installed. Then:

  make installcheck

• nest will reside in $HOME/virt_env/mozaik/lib/python2.7/site-packages. Check that the package is seen by python using:

  python -c 'import nest'

Install PyNN:

git clone https://github.com/NeuralEnsemble/PyNN.git
cd PyNN/
python setup.py install

that will reside in $HOME/virt_env/mozaik/lib/python2.7/site-packages/PyNN-0.8dev-py2.7.egg-info. Check:

python -c 'import pyNN'

Install NEO:

git clone https://github.com/apdavison/python-neo python-neo
cd python-neo/
python setup.py install

Install Parameters package:

git clone https://github.com/apdavison/parameters.git parameters
cd parameters/
python setup.py install

Install NeuroTools:

svn co https://neuralensemble.org/svn/NeuroTools/trunk NeuroTools
cd NeuroTools/
python setup.py install

Install TableIO (not always necessary). Download it from http://kochanski.org/gpk/misc/TableIO.html:

tar xvzf TableIO-1.2.tgz
python setup.py install

And, finally, Mozaik:

git clone https://github.com/antolikjan/mozaik.git
cd mozaik/
python setup.py install