cortix 0.0.2

Cortix is a Python library for system-level module coupling, execution, and analysis.

Cortix

What is Cortix?

• Cortix is a Python library for system-level module coupling, execution, and analysis.
• Cortix takes as input a collection of computational modules and provides an environment for the coupling of those modules into a single simulation.
• Cortix handles:
  • Communication between the modules
  • Numerical integration
  • Data visualization

The basic concepts in Cortix are the creation of an Application and a Simulation involving Tasks.

Dependencies

• Core

  • python >= 3.6.5
  • mpi4py >= 3.0.0 (use openmpi >= 3.1.1)
  • networkx >= 1.11
  • numpy >= 1.10.4
  • matplotlib >= 2.2.2
  • sphinx >= 1.6.5
  • pandoc >= 1.19
  • pytest==3.7.2

• Support

  • pandas >= 0.19

• Modulib

  • pandas >= 0.19
  • scikits.odes==2.4.0.dev0
  • sundials >= 2.7

Usage

Cortix is a library and it is best used when copied to its own directory, say inside a project directory of your choice, e.g., /somepath/myproject/cortix/, or anywhere else in your system, e.g., /somepath/cortix. Then add either /somepath/myproject to $PYTHONPATH or /somepath to $PYTHONPATH, respectively.

Cortix has a directory (examples/) that contains examples for input files, and a driver file. At the moment these input files are past files used in the development of Cortix. A driver file is needed to run Cortix. There is an example (examples/driver-cortix.py) that can be copied to say: /somepath/driver-test.py or /somepath/myproject/driver-test.py. An input configuration (xml) file is also needed. An example is provided in the examples/input/ directory (cortix-config.xml). Then to run Cortix, enter the directory of the driver and run the driver ./driver-test.py which will run an MPI process for Cortix and an additional MPI process for each launched module as a single MPI process or as a pool of processes. To capture the Cortix screen output of log messages (and other standard output messages), issue the bash command /driver-cortix.py >& screen.out under Linux (inspect the output file screen.out when the run is finished). Extensive logging of runtime information is stored in the <work_dir> directory specified in the cortix-config.xml input file.

Testing

Testing is facilitated through PyTest. To execute the tests, run the py.test command from the tests directory.

Linux

Most Linux distros will provide an evironment with the needed dependencies.

Mac OS X

Developers

• Valmor F. de Almeida: [e-mail]
• Taha M. Azzaoui: [e-mail]

Documentation

• Gilberto E. Alas: [e-mail]