channel-validation-framework

CVF aims to validate nmodl comparing its results with mod2c traces. The general scheme is presented below:

• run_config.yaml is read: this gives us the setups for all the simulators that are going to be tested. Check the file for more info.
• For each simulator we compile (in its appropriate tmp_* folder) all the mod files (default in mod/local; you can add folders)
• For each mod file CVF automatically (it is magic!) generates a config object that dictates how the simulations for that mod file must be done: how many cells, what stimuli, on which cells etc. If you prefer to specify how the mod file must be tested you can add a config file in config/<mod_file_name>.yaml (it must have the same name as the mod file). You can check the other files present in config/ for inspiration
• Simulations are run and compared (numerically and, possibly, visually)

Installation

In order to use CVF you need the various neuron and coreneurons that you are going to use (specified in run_config .yaml) installed with spack. For the standard cvf you need to do:

spack install neuron@develop~mpi
spack install coreneuron@develop~mpi~report ^bison@3.4.2
spack install coreneuron@develop+nmodl~mpi~report ^nmodl@develop ^bison@3.4.2

How to run CVF

CVF can be run in 2 ways:

• Install cvf and run cvf_stdrun to do a standard check

  • Load libraries module load neuron/develop nmodl/develop
  • Create a python virtual env python -m venv venv
  • Activate it source venv/bin/activate
  • Install cvf python3 setup.py install
  • Call the standard run cvf_stdrun

• SUGGESTED:

  • Load the libraries module load neuron/develop nmodl/develop
  • Add your mod files in mod/local
  • Modify run_config.yaml to set up the various run configurations
  • Run your own python script (check example.py for inspirations). The functions exposed to public (in channel -validation-framework/commands) have python docstring to describe their functionalities

License

See the LICENSE file.

Funding and Acknowledgments

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2023-2024 Blue Brain Project/EPFL