Docker Installation for NEST Simulator and Felix Module

🐳 Run with Docker (Recommended)

To quickly set up and run the NEST Simulator with the Felix Module, use the provided Docker image.

1️⃣ Pull the Docker Image

docker pull maxc93/cogninest

2️⃣ Run the Container

docker run --rm -it maxc93/cogninest

If the application runs a web service, use:

docker run -d -p 8080:80 maxc93/cogninest

Then access it at http://localhost:8080.

3️⃣ Enter the Container (Optional Debugging Mode)

To explore the environment:

docker run --rm -it maxc93/cogninest /bin/bash

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Manual Installation Guide for NEST Simulator and Felix Module

📌 Prerequisites

Ensure your system is up to date and has the required dependencies installed:

sudo apt update && sudo apt upgrade -y
sudo apt install -y build-essential cmake git libtinfo-dev wget

📥 Install Miniconda

Download and install Miniconda for managing Python environments:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3

Add Miniconda to the system PATH:

export PATH="$HOME/miniconda3/bin:$PATH"
echo 'export PATH="$HOME/miniconda3/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc  # Reload shell configuration

🛠 Install and Build NEST Simulator

Clone the NEST repository and switch to the desired branch:

git clone --branch 3.6-develop https://github.com/nest/nest-simulator.git

Create and activate a Conda environment for NEST:

conda env create --name nest --file=nest-simulator/environment.yml  
conda activate nest

🔧 Build and Install NEST

Create a build directory:

mkdir -p ~/nest_build && cd ~/nest_build

Ensure a clean build by removing old files:

rm -rf CMakeCache.txt CMakeFiles

Configure the NEST build:

CMAKE_PREFIX_PATH=${CONDA_PREFIX} cmake -DCMAKE_INSTALL_PREFIX:PATH=`pwd`/install ~/nest-simulator

Compile and install NEST:

make -j$(nproc) install
make installcheck

Set NEST environment variables:

source install/bin/nest_vars.sh
echo 'source ~/nest_build/install/bin/nest_vars.sh' >> ~/.bashrc
source ~/.bashrc  # Apply changes

🔧 Build and Install Felix

Create and enter the Felix build directory:

mkdir -p ~/felix_build && cd ~/felix_build

Remove any old build files:

rm -rf ~/felix_build/*

Configure the Felix module:

CMAKE_PREFIX_PATH=${CONDA_PREFIX} cmake -Dwith-nest=../nest_build/install/bin/nest-config ../nest_test

Compile and install Felix:

make -j$(nproc)
make install

🏗 Install Cogninest

Clone the Cogninest repo:

git clone https://github.com/MaximeCarriere/cogninest.git

Install additional dependencies:

cd cogninest
pip install -r requirements.txt

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✅ Final Checks

1. Verify NEST Installation:

   nest --version

2. Test Felix Module:

   import nest
   nest.Install('felixmodule')

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🌟 Running a Simulation

To run a simulation, navigate to the correct directory and execute the Python script:

cd ~/cogninest/training_testing/main/
python main_training.py

🚀 You're now ready to use NEST and Cogninest!