Environment Setup

Important setup:

torch, torch_geometric and their dependencies: torch_scatter and torch_cluster

  1. conda create -n plienv python=3.9.18

  2. nvcc -V

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2024 NVIDIA Corporation
Built on Thu_Sep_12_02:18:05_PDT_2024
Cuda compilation tools, release 12.6, V12.6.77
Build cuda_12.6.r12.6/compiler.34841621_0
  1. python
Python 3.9.18 (main, Sep 11 2023, 13:41:44)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>
  1. https://pytorch.org/get-started/previous-versions/
pip install torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --index-url https://download.pytorch.org/whl/cu124
  1. https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html
pip install torch_geometric

pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.5.0+cu124.html

IMPORTANT:

  1. Both PyG and PyTorch must be installed via pip

  2. PyTorch and CUDA version must be same.

  3. PyTorch installation must be through Wheel not Conda.

  4. PyTorch 2.5.1 doesn't work with PyG 2.5.0.

  1. pip install e3nn
  2. pip install fair-esm
  3. pip install rdkit-pypi
  4. pip install biopython
  5. pip install ProDy
  6. pip install matplotlib
  7. pip install pandas
  8. pip install PyYAML