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Python Environment

Conda Create and Activate Environment

conda create --name MolTran_CUDA11 python=3.8.10
conda activate MolTran_CUDA11

Conda Install Packages

conda install pytorch==1.7.1 cudatoolkit=11.0 -c pytorch
conda install numpy=1.22.3 pandas=1.2.4 scikit-learn=0.24.2 scipy=1.6.2
conda install rdkit==2022.03.2 -c conda-forge

Pip install Packages

pip install transformers==4.6.0 pytorch-lightning==1.1.5 pytorch-fast-transformers==0.4.0 datasets==1.6.2 jupyterlab==3.4.0 ipywidgets==7.7.0 bertviz==1.4.0

Compile Apex from source

Due to the use of Apex Optimizers, Apex must be compiled with CUDA and C++ extensions via

git clone https://github.com/NVIDIA/apex
cd apex
git checkout tags/22.03 -b v22.03
export CUDA_HOME='Cuda 11 install'
pip install -v --disable-pip-version-check --no-cache-dir --no-build-isolation --config-settings "--build-option=--cpp_ext" --config-settings "--build-option=--cuda_ext" ./