Dictys refuses to use CUDA supported pytorch during installation

Question

[zwjiang]

I'm trying to install the tool Dictys to do some GRN inference. The platform I am working on is a HPC cluster. I followed the installation tutorial on their Github page at github.com/pinellolab/dictys/tree/master. To be more specific, I went for the option 1: with Anaconda, GPU computation for PyTorch. The code I used to create the conda environment was:

conda create -y -p /project/spott/zwjiang/conda_envs/dictys -c conda-forge python=3.9 mamba 
conda activate /project/spott/zwjiang/conda_envs/dictys 
mamba install -y -c lingfeiwang -c bioconda -c conda-forge -c pytorch -c nvidia dictys pytorch torchvision torchaudio pytorch-cuda=11.7

The installation looked fine, but when I later tried to execute the part of dictys that requires a GPU, it said that the pytorch I was using did not have CUDA support. So I started an interactive session with one GPU node and confirmed it.

[zwjiang@midway3-0285 ~]$ conda activate /project/spott/zwjiang/conda_envs/dictys 
(/project/spott/zwjiang/conda_envs/dictys) [zwjiang@midway3-0285 ~]$ python
Python 3.9.23 | packaged by conda-forge | (main, Jun  4 2025, 17:57:12) 
[GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> torch.cuda.is_available()
False

I did some research about that, and had seen people fixing it by uninstalling and reinstalling the torch. So I tried to uninstall pytorch and related packages with:

conda remove pytorch torchvision torchaudio
pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu117

Then I tried again the a gpu node, where torch.cuda.is_available() now returned True for this conda environment. However, I seemed to have removed the dictys package itself somehow during the installation, as which dictys now returned /usr/bin/which: no dictys in .... I tried to install dictys with

mamba install -y -c lingfeiwang -c conda-forge -c bioconda dictys

But got another error critical libmamba filesystem error: cannot remove: Directory not empty [/project/spott/zwjiang/conda_envs/dictys_GPU/lib/python3.9/site-packages/torch/include/ATen].

Is there anyone who was able to successfully install dictys and run through the part requiring a GPU? Could you kindly provide some advice on this issue? Thanks!

Answer 1

[zwjiang]

I fixed my problem by

conda create -y -p /project/spott/zwjiang/conda_envs/dictys_gpu -c conda-forge python=3.9 mamba
conda activate /project/spott/zwjiang/conda_envs/dictys_gpu
mamba install -y -c lingfeiwang -c bioconda -c conda-forge dictys 
export PYTHONNOUSERSITE=True # prevent environment contamination 
pip install --no-cache-dir --no-user --upgrade --force-reinstall torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117