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Installation

Quick Start Guide for NERDSS Setup

Note:

If you prefer using Docker for environment setup (it might be slow), jump directly to Step 4.

Windows OS: It's recommended to use either Windows Subsystem for Linux (WSL) or Docker.

Step 1: Clone the Repository

git clone https://github.com/mjohn218/NERDSS.git

Step 2: Install Dependencies

  • For Ubuntu or WSL:
sudo apt-get update && sudo apt-get install -y build-essential libgsl-dev
  • For macOS:

Install Homebrew:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install GCC and GSL:

brew update
brew install gcc gsl

Step 3: Compile NERDSS

Navigate to the NERDSS directory and compile:

cd NERDSS
make serial

The resulting executable will be located in the bin folder.

Install ioNERDSS library from PyPi

Install Anaconda, then

conda create --name ionerdss
conda activate ionerdss
conda install pip
pip install ioNERDSS
pip install jupyter

Step 4: Using Docker for Environment Setup (Optional)

If you'd rather not install the required tools directly on your machine, you can use Docker:

  • Install Docker

  • Pull the pre-configured Docker image:

Intel Chip:

docker pull sikaoguo/nerdsstutorial:latest

Mac M1 Chip:

docker pull sikaoguo/nerdsstutorial:m1
  • Launch the Docker image:

To run nerdss with the .inp file in the current folder and start Jupyter for analyze after the simulation done:

docker run -e RUN_NERDSS=true -e ANALYZE_OUTPUT=true -p 8888:8888 -v $(pwd):/SIMULATION -it sikaoguo/nerdsstutorial:latest

To run only nerdss:

docker run -e RUN_NERDSS=true -v $(pwd):/SIMULATION -it sikaoguo/nerdsstutorial:latest

To start only Jupyter:

docker run -e ANALYZE_OUTPUT=true -p 8888:8888 -v $(pwd):/SIMULATION -it sikaoguo/nerdsstutorial:latest

To run Container only:

docker run -v $(pwd):/SIMULATION -it sikaoguo/nerdsstutorial:latest

Note: Replace $(pwd) with ${PWD} in Windows powershell.

When you do the above, any changes you make to current folder on your local machine will be reflected in /SIMULATION in the Docker container, and vice versa.

  1. Copying files from host to container: bash docker cp <path-on-host> <container-id-or-name>:<path-in-container>

  2. Copying files from container to host: bash docker cp <container-id-or-name>:<path-in-container> <path-on-host>