TVB-NEST-demo

temporary repo for a TVB-NEST demonstrator

Topic

This repository is a demonstration for the co-simulation between TVB, NEST and Elephant. It should be flexible and scalable to adapt to any networks simulation and run in supercomputers.
It's a demonstration of a work underdevelopment: https://github.com/multiscale-cosim/TVB-NEST

Table of Contents

1. Installation
2. Example
3. Files

Installation and update :

For the installation, you should look at the script in the folder install. The docker file is a good example of finding of the missing dependency.
The ubuntu_installation.sh is an incomplete script to install all the tools.

Example

This demonstration is based on the example of NEST and TVB. It can help you to develop your own co-simulation but it is not optimized and it can miss some functionalities.
For running the example, run the script nest_elephant_tvb/launcher/run.py

Files

• install: Documentation of the project
• nest_elephant_tvb: file which contains all the kernel of the simulation
  • launcher:
    • run.py: main script of the simulation on one simulator or the co-simulation.
  • nest: folder contains all the file to configure and launch Nest
    • Balanced_network_reduce_co-sim.sh: run the NEST example
    • utils_function.py: function used for the Nest simulation
  • transformation: folder contains the transformer between TVB and Nest using Elephant
    • communication: functions for internal ad external communication
      • internal.py: abstract classes for the internal communication/ the communication between component of the transformer
      • internal_mpi.py: implementation with MPI communication
      • internal_thread.py: implementation with thread communication
      • mpi_io_external.py: management the mpi communication with the simulator
    • simulator: Communication with simulator
      • Nest_IO: communication with NEST simulator
      • TVB_IO: communication with TVB simulator
    • transformation_function: function for the transformation
      • abstract_transformation_function.py: Management communication with the other components of the transformer
      • transformation_function.py: implementation of the transformation function
    • nest_to_tvb: launcher of the component of the transformer between NEST to TVB
    • tvb_to_nest: launcher of the component of the transformer between TVB to NEST
  • TVB
    • TVB_simple_example_co_sim.sh: run the TVB example
    • wrapper_TVB_mpi.py: wrapper of TVB for management of the MPI communication. *utils.py: functions shared by all the modules