scvi-tools
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mamba receipt to use gpu for scvitools
Is your feature request related to a problem? Please describe. To make scvitools utilize gpus, Jax, cudatoolkit and torch all have to be installed without conflicts.
Describe the solution you'd like Here is the receipt we used on our cluster, might save others some time:
mamba create -n scvi-env python=3.9
mamba activate scvi-env
# install cudatoolkit/11.8 with jax
pip install -U "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
mamba install cudatoolkit
# install torch
pip install torch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0 --index-url https://download.pytorch.org/whl/cu121
# install scvi-tools with scanpy
pip install "scvi-tools[tutorials]"