mozaik 0.1.0

Python package mozaik is an integrated workflow framework for large scale neural simulations.

Dependencies

• python 2.7

• scipy/numpy

• nest (latest release, compiled with mpi)

• mpi4py

• pyNN (neo_output branch)

• imagen

• parameters

• quantities

• neo

Installation

Instructions:

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

Please see below:

• the installation of the dependencies.

• the installation on Ubuntu Linux

• how to run the examples

Detailed instructions

Mozaik requires currently some “non-standard” branches of software like the pyNN which will be resolved in the future. Therefore more detailed installation instructions follow.

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.

Ubuntu

Following these instruction should give you a working copy of mozaik on a fresh installation of Ubuntu (at the time of the writing the version was 12.04)

First the list of ubuntu package dependencies:

sudo apt-get install python2.7 python-dev python-pip python-nose subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin

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

Running examples

If you use mpi and mpirun, you should install first the mpi executables if not already done:

sudo apt-get install openmpi-bin

Then, you go to the examples directory in the mozaik loaded from github (see above) and launch the model VogelsAbbott2005:

cd examples
cd VogelsAbbott2005
mpirun python run.py nest 2 param/defaults 'test'

This will launch the example with the nest simulator, on 2 nodes, using the parameter param/defaults. Last, ‘test’ is the name of this run.

copyright:

Copyright 2011-2013 by the mozaik team, see AUTHORS.

license:

CECILL, see LICENSE for details.