• python 2.7 or later
• scipy/numpy
• nest (latest release, compiled with mpi)
• mpi4py
• pyNN
• imagen
• param
• parameters
• quantities
• neo

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

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:~$

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.

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 python3 python3-dev python3-pip python3-setuptools python3-tk 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

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

$ sudo pip3 install virtualenv
$ sudo pip3 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 --python=/usr/bin/python3 mozaik
$ workon mozaik
(mozaik)$>

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

pip3 install numpy scipy mpi4py matplotlib==2.1.1 quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.8.0 cython pynn psutil future requests libboost-all-dev

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/CSNG-MFF/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/v2.20.1.tar.gz

• untar and cd into it:

  tar xvfz v2.20.1.tar.gz
  cd nest-simulator-2.20.1

• 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/python3.*/site-packages. Check that the package is seen by python using::

  python -c 'import nest'

And, finally, Mozaik:

git clone https://github.com/CSNG-MFF/mozaik.git
cd mozaik
python setup.py install

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.

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

git clone https://github.com/CSNG-MFF/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

In case you want to contribute to the project, you need to make sure your code passes all unit tests and is formatted with the Black autoformatter. You can make sure this is the case by running from the project directory:

pytest && black --check .

This command will run all tests that it can find recursively under the current directory, as well as check all non-blacklisted files for formatting. Travis-CI will run the same steps for your pull request once you submit it to the project. To install pytest and black:

pip3 install pytest pytest-cov pytest-randomly coverage black

There are additional useful options for pytests that you can use during development:

• You may exclude tests running the model by adding the option:

  pytest -m "not model"

• You can run the tests in a single file by:

  pytest path/to/file

• Pytest doesn't, print to stdout by default, you can enable this by:

  pytest -s

copyright

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

license

CECILL, see LICENSE for details.