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INSTALLATION.md

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Installation Instructions

Table of Contents

  1. PIP Install (Recommended)
  2. Manual Install
  3. Conda Install
  4. Install Graphviz (Optional)
  5. Test NeuroMANCER Installation

PIP Install (Recommended)

Using pip is the simplest way to install NeuroMANCER. It's recommended to use a dedicated virtual environment (e.g., conda, venv) with Python 3.9+.

Since PyTorch doesn't officially publish CUDA wheels to PyPI (due to size), to use CUDA, you need to manually reinstall pytorch in your local environment via:

pip uninstall torch -y
pip install torch --index-url https://download.pytorch.org/whl/cu121

Manual Install

Clone the Repository

First clone the neuromancer package. A dedicated virtual environment (conda or otherwise) is recommended.

Note: If you have a previous neuromancer env it would be best at this point to create a new environment given the following instructions.

git clone -b master https://github.com/pnnl/neuromancer.git --single-branch

Create and Activate Virtual Environment

conda create -n neuromancer python=3.10.4
conda activate neuromancer

Install Neuromancer and All Dependencies.

From top level directory of cloned neuromancer run:

pip install -e.[docs,tests,examples]

OR, for zsh users:

pip install -e.'[docs,tests,examples]'

See the pyproject.toml file for reference.

[project.optional-dependencies]
tests = ["pytest", "hypothesis"]
examples = ["casadi", "cvxpy", "imageio", "cvxpylayers"]
docs = ["sphinx", "sphinx-rtd-theme"]

Notes for MacOS (Apple M1)

Before CVXPY can be installed on Apple M1, you must install cmake via Homebrew:

brew install cmake

See CVXPY installation instructions for more details.

Conda install

Conda install is recommended for GPU acceleration.

❗️Warning: linux_env.yml, windows_env.yml, and osxarm64_env.yml are out of date. Manual installation of dependencies is recommended for conda.

Create Environment and Install Dependencies

Ubuntu

conda env create -f linux_env.yml
conda activate neuromancer

Windows

conda env create -f windows_env.yml
conda activate neuromancer
conda install -c defaults intel-openmp -f

MacOS (Apple Silicon)

conda env create -f osxarm64_env.yml
conda activate neuromancer

Other (manually install all dependencies)

!!! Pay attention to comments for non-Linux OS !!!

conda create -n neuromancer python=3.10.4
conda activate neuromancer
conda install pytorch pytorch-cuda=11.6 -c pytorch -c nvidia
## OR (for Mac): conda install pytorch -c pytorch
conda config --append channels conda-forge
conda install scipy numpy"<1.24.0" matplotlib scikit-learn pandas dill mlflow pydot=1.4.2 pyts numba
conda install networkx=3.0 plum-dispatch=1.7.3 
conda install -c anaconda pytest hypothesis
conda install cvxpy cvxopt casadi seaborn imageio
conda install tqdm torchdiffeq toml
conda install lightning wandb -c conda-forge
## (for Windows): conda install -c defaults intel-openmp -f

Install NeuroMANCER package

From the top level directory of cloned neuromancer (in the activated environment where the dependencies have been installed):

pip install -e . --no-deps

Install Graphviz (optional)

In order to use the Problem graph plots, we recommend installing Graphviz system-wide. Note that this feature is optional.

For Windows:

Package must be installed manually: Graphviz website

For Linux (Debian, Ubuntu)

sudo apt install graphviz

For MacOS

brew install graphviz

Test NeuroMANCER install

Run pytest on the tests folder. It should take about 2 minutes to run the tests on CPU. There will be a lot of warnings that you can safely ignore. These warnings will be cleaned up in a future release.