Cortix

A Python library for network dynamics modeling and HPC simulation.

• Cortix on Jupyter notebook examples
• Documentation on the web

What is Cortix?

• Cortix is a massively parallel Python library for system-level module coupling, execution, and analysis of dynamical system models that exchange time-dependent data.
• Cortix takes as input a collection of computational modules and provides an environment for the coupling of these modules into a single simulation.
• Cortix supports:
  • Module decoupling
  • Communication between modules
  • Data visualization
• Cortix runs on top of MPI and scales across many cores.

Installation: start by installing MPI

Installing via PyPI

pip install --user cortix

if updating to a new version, you may need to specify the version

pip install --user cortix=="<version>"

NB: this will not install the GraphViz executables but only the python wrapper. Install the GraphViz library on your system by yourself.

Installing via Conda

In a Anaconda environment (MacOS terminal conda, or Windows Anaconda powershell) do:

pip install cortix
conda install graphviz

if updating to a new version, you may need to specify the version

pip install cortix=="<version>"

Installing from source

1. Clone this repository to install the latest version of Cortix

git clone https://github.com/dpploy/cortix.git

2. Install the required dependencies listed in requirements.txt

pip install --user -r cortix/requirements.txt

3. Add cortix's parent path to your $PYTHONPATH variable

export PYTHONPATH=$PYTHONPATH:$(pwd)

Note: you may want to add this line to your .bashrc in order for it to be persistent

Verify your Cortix install by running the Droplet example

mpiexec -n xx examples/run_droplet_swirl.py

where xx is the number of MPI processes which must match the number of modules plus 1. If there are 10 droplets and 1 vortex, use $xx = 12$.

Testing

Testing is facilitated by PyTest. Tests can be run locally from within the tests directory

cd tests && py.test

Using Cortix

Please refer to the documentation for more on getting started!

Team

• Valmor F. de Almeida: [email protected]
• Taha M. Azzaoui: [email protected]
• Seamus D. Gallagher: [email protected]
• Austin Rotker: [email protected]
• Gilberto E. Alas: [email protected]

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

Location

Cortix Group

c/o UMass Innovation Hub

110 Canal St., 3rd Floor

Lowell, MA 01852