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Installation

ALIGNN supports Linux, macOS, and Windows with Python 3.10.

Prerequisites

Install Miniconda from https://conda.io/miniconda.html. Pick the installer matching your OS:

bash Miniconda3-latest-Linux-x86_64.sh      # Linux
bash Miniconda3-latest-MacOSX-x86_64.sh     # macOS

On Windows, use the 64-bit Python 3.10 Miniconda installer.

Method 1 — conda (recommended)

conda create --name my_alignn python=3.12 -y
conda activate my_alignn
conda install -c dglteam/label/th24_cu124 dgl
conda install alignn -y

Method 2 — from GitHub (development install)

conda create --name my_alignn python=3.12 -y
conda activate my_alignn
conda install -c dglteam/label/th24_cu124 dgl
git clone https://github.com/atomgptlab/alignn
cd alignn
python -m pip install -e .

Method 3 — pip

If you prefer pip, install DGL first from the wheel index that matches your CUDA/PyTorch version (see https://www.dgl.ai/pages/start.html).

PyTorch 2.1 + CUDA 12.1 (Windows/Linux):

conda install -c dglteam/label/th24_cu124 dgl
pip install alignn

CPU only:

conda install -c dglteam/label/th24_cu124 dgl
pip install alignn

Verifying your install

train_alignn.py -h
pretrained.py -h
run_alignn_ff.py -h

All three are Python executable scripts installed to your environment's bin/ directory — you do not need to provide an absolute path.

Common issues

!!! warning "DGL + CUDA mismatches" The most common install problem is a DGL build that does not match your CUDA version. If you see import errors about libtorch_cuda.so or similar, reinstall DGL from the wheel index matching your CUDA driver.

  • Use batch_size of 32 or 64 for real trainings (the examples ship with batch_size: 2).
  • Complex .cif and .pdb files may require cif2cell==2.0.0a3 and pytraj respectively.
  • pandas >= 1.2.3 is required.
  • From March 2024, pytorch-ignite is no longer required (removed for conda-forge compatibility).

See the Notes & FAQ for more tips.