Mozaik
Computational neurosceince is shifting towards more heterogeneous models of neuronal circuits, and application of complex experimental protocols. This escalation of complexity is not sufficiently met by existing tool chains. Mozaik is a workflow system for spiking neuronal network simulations written in Python that integrates model, experiment and stimulation specification, simulation execution, data storage, data analysis and visualization into a single automated workflow. This way, Mozaik increases the productivity of running virtual experiments on complex heterogenous spiking neuronal networks.
You can read more about Mozaik here.
Currently, Mozaik is being fully tested only on Ubuntu Linux distribution.
Ubuntu installation instructions
Following these instruction should give you a working copy of mozaik on a fresh installation of current Ubuntu system.
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 libboost-all-dev
Virtual env
Then python virtualenv and virtualenvwrapper (a 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 (in the future 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)$>
Dependencies
Now you can install all other dependencies in this protected environment:
pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
Next we will manually install several packages. It is probably the best if you create a separate directory in an appropriate place, where you will download and install the packages from.
First install the imagen package:
git clone https://github.com/CSNG-MFF/imagen.git cd imagen python setup.py install
Then install the PyNN package from the PyNNStepCurrentModule branch:
git clone https://github.com/CSNG-MFF/PyNN.git cd PyNN git checkout PyNNStepCurrentModule python setup.py install
Next install the Nest simulator (always in the virtual environment):
download the latest version from their website:
wget https://github.com/nest/nest-simulator/archive/refs/tags/v3.4.tar.gzuntar and cd into it:
tar xvfz v3.4.tar.gz cd nest-simulator-3.4then configure (change path to wherever you installed your virtual environemnt):
(mozaik)$ cmake -Dwith-mpi=ON -Dwith-boost=ON -DCMAKE_INSTALL_PREFIX:PATH=$HOME/virt_env/mozaik -Dwith-optimize='-O3' ./finally, by launching make and install, it installs PyNest in the activated virtual environment mozaik. If you're using Slurm, run these commands through
srun
(mozaik)$ make (mozaik)$ make installThen:
(mozaik)$ make installcheckor if you are using Slurm:
(mozaik)$ salloc -n8 make installchecknest will reside in $HOME/virt_env/mozaik/lib/python3.*/site-packages. Check that the package is seen by python using:
(mozaik)$ python -c 'import nest'
Then install the stepcurrentmodule Nest module:
get the module from github and cd into it:
git clone https://github.com/CSNG-MFF/nest-step-current-module.git cd nest-step-current-modulethen, in the following command, replace NEST_CONFIG_PATH by your nest-config installation path (should reside in $HOME/virt_env/mozaik/bin/nest-config) and run it:
(mozaik)$ cmake -Dwith-mpi=ON -Dwith-boost=ON -Dwith-optimize='-O3' -Dwith-nest=NEST_CONFIG_PATH ./finally, by launching make and install, it installs the nest module in the activated virtual environment mozaik. If you're using Slurm, run these commands through
srun
(mozaik)$ make (mozaik)$ make installCheck that the package is seen by python using:
(mozaik)$ python -c 'import nest; nest.Install("stepcurrentmodule")'
And, finally, Mozaik:
git clone https://github.com/CSNG-MFF/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 running 2 MPI processes, each process running 2 threads, using the parameterization of the model rotted in param/defaults. Finally, 'test' is the name of this run.
Testing, Autoformat, Continuous Integration
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 following from the project directory:
pytest && black --check .
- Note that the mpi tests are currently not working when invoking pytest in this manner. You can run these specific tests the following way::
- pytest tests/full_model/test_models_mpi.py
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/filePytest doesn't, print to
stdout
by default, you can enable this by:pytest -s
Due to the impossibility of using more than 2 cores in Github actions, the test test_mozaik_rng_mpi7
invoking 7 MPI processes cannot be ran there. It is therefore necessary to run it locally, by following these steps:
Modify the sbatch_test_RNG_MPI7.sh sbatch script to include your virtual environment after the
source
command.Using the following command to run it locally if using slurm:
sbatch sbatch_test_RNG_MPI7.shCheck the slurm output file to verify whether the test passed
copyright: | Copyright 2011-2013 by the mozaik team, see AUTHORS. |
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license: | CECILL, see LICENSE for details. |