ARBOR NEST Cosimulation usecase

WIP

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Get repositories and install everything

• For VM it is the same process as for TVB-NEST usecase: https://github.com/multiscale-cosim/TVB-NEST-usecase1/blob/main/INSTALL.md
  • updated bootstrap.sh and Vagrantfile in https://github.com/multiscale-cosim/ARBOR-NEST-usecase1/tree/main/installation/local

Short description:

• Have virtualbox and vagrant installed
• get the bootstrap.sh and Vagrantfile from the installation folder
  • create a VM directory on the host-system with the bootrap.sh, Vagrantfile and a shared firectory
• run vagrant up to start the VM with ARBOR and NEST installed
• run vagrant ssh to log in to the VM
• test the installation:
  • cd multiscale-cosim
  • source ARBOR-NEST-usecase1.source
  • python3 ARBOR-NEST-usecase1/installation/tests/nest_test.py
  • sh ARBOR-NEST-usecase1/installation/tests/arbor_test.sh

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Next steps / TODOs:

Action Adapters

• Interscalehub (copied from TVB-Nest usecase)
• Nest (copied from TVB-Nest usecase): new adapter / edit current one to fit this usecase
• Arbor: new adapter

Model and Parameters

• add models adn parameters for NEST and ARBOR in userland/modles which is then loaded by adpater(s) for configuration and simulation
• For ref -- NEST adapter https://github.com/multiscale-cosim/Cosim-LFPy/blob/main/action_adapters/nest_simulator/nest_adapter.py -- model at https://github.com/multiscale-cosim/Cosim-LFPy/tree/main/userland/models/Potjans -- parameters at https://github.com/multiscale-cosim/Cosim-LFPy/tree/main/userland/parameters

InterscaleHUB endpoints

• Add a Manager class for setup and steering at https://github.com/multiscale-cosim/EBRAINS_InterscaleHUB/tree/main/managers/usecase_specific
• Communication class for ARBOR at https://github.com/multiscale-cosim/EBRAINS_InterscaleHUB/tree/main/communicators

Configurations files

• see sample files in userland/configs i.e. https://github.com/multiscale-cosim/ARBOR-NEST-usecase1/tree/main/userland/configs