This version of mozaik (with models LSV1M and VogelsAbbott) is modified to run on the SpiNNaker Neuromorphic Platform.

In a Collab of the HBP Neuromorphic Computing Platform, for running the V1 model, sending a job requires:

Code (url to repository):

https://github.com/aopy/mozaik

Command:

examples/LSV1M/run.py spiNNaker 2 examples/LSV1M/param/defaults 'test'

Hardware Config:

{

"extra_git_repositories": [

"https://github.com/aopy/imagen"

], "extra_pip_installs": [

"numpy", "scipy", "parameters", "param==1.9.3", "quantities", "psutil"

], "extra_python_setups": [

".", "imagen"

], "spynnaker_version": "master"

}

Installation intructions

Dependencies

• python 2.7
• scipy/numpy
• nest (latest release, compiled with mpi)
• mpi4py
• pyNN
• imagen
• param
• 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

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:~$

Dependencies

Note that if the installation is done in your virtualenv environment, it doesn't require any root privilege. Unless specified otherwise all dependencies should be installed via pip.

• scipy
• numpy
• mpi4py
• matplotlib (1.1 and higher)
• quantities
• imagen
• PyNN
• Neo
• parameters
• param

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 16.04)

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 python-tk cmake

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 ~/.bashrc

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

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

$ source .bashrc

To create a new managed virtualenv you just need to:

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

Dependencies

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

pip install --upgrade distribute
pip install numpy scipy mpi4py matplotlib==2.1.1 quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.5.2 cython pynn psutil

Now we will manually install several packages. It is probably the best if you create a separate directory in an appropriate place, where you will download and install from the packages.

First we will install imagen package:

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

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

• download the latest version from their website

  wget https://github.com/nest/nest-simulator/archive/v2.18.0.tar.gz

• untar and cd into it:

  tar xvfz v2.18.0.tar.gz
  cd nest-simulator-2.18.0
  

• then configure, choose if you want mpi:

  (mozaik)$ cmake -Dwith-mpi=OFF -Dwith-boost=ON -DCMAKE_INSTALL_PREFIX:PATH=$HOME/virt_env/mozaik -Dwith-optimize='-O3' ./
  

• finally, by launching make and install, it installs PyNest in the activated virtual environment mozaik:

  (mozaik)$ make
  (mozaik)$ make install
  

• 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'

And, finally, Mozaik:

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

Running examples

Go to the examples directory in the mozaik cloned from github (see above) and launch the model VogelsAbbott2005:

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

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

Simple Installation with Docker

Run the following commands to build a Docker container with Mozaik:

git clone https://github.com/antolikjan/mozaik.git
cd mozaik
docker build --tag antolikjan/mozaik --target prod .

To run the examples:

cd examples
cd VogelsAbbott2005
docker run --rm -v "`pwd`:/app" antolikjan/mozaik run.py nest 2 param/defaults 'test'

To build a development container:

docker build --tag antolikjan/mozaik:dev --target dev .

To run tests:

docker run --rm -v "`pwd`:/app" antolikjan/mozaik:dev pytest

copyright:	Copyright 2011-2013 by the mozaik team, see AUTHORS.
license:	CECILL, see LICENSE for details.