DipGNNome/environment_gpu.yml at main · lbcb-sci/DipGNNome · GitHub

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name: dipgnnome_gpu
channels:
  - conda-forge
  - pytorch
  - nvidia
  - bioconda

dependencies:
  # Python version
  - python=3.9

  # Core scientific computing
  - numpy>=1.21.0
  - scipy>=1.7.0
  - pandas>=1.3.0
  - scikit-learn>=1.0.0

  # Machine learning and deep learning (GPU versions)
  - pytorch>=1.12.0
  - torchvision>=0.13.0
  - torchaudio>=0.12.0
  - pytorch-cuda=11.8  # Adjust based on your CUDA version

  # Graph processing
  - networkx>=2.6.0

  # Bioinformatics
  - biopython>=1.79
  - edlib>=1.3.9
  - pyliftover>=0.4

  # Utilities
  - tqdm>=4.62.0
  - pyyaml>=6.0

  # Experiment tracking
  - wandb>=0.12.0

  # System tools
  - git
  - make
  - gcc_linux-64  # For Linux
  - gxx_linux-64  # For Linux
  - clang_osx-64  # For macOS
  - clangxx_osx-64  # For macOS

  # Pip packages (for packages not available in conda)
  - pip
  - pip:
    - dgl>=1.0.0  # Deep Graph Library
    - argparse  # Usually included in Python 3.2+

# Environment variables for GPU support
variables:
  CUDA_VISIBLE_DEVICES: "0"  # Adjust based on your GPU setup
  PYTORCH_CUDA_ALLOC_CONF: "max_split_size_mb:128"