[BUG] Installation fails with PyTorch ImportError: undefined symbol: iJIT_NotifyEvent

[GianlucaMattei]

Hello,

I am having trouble installing robin. I've followed the instructions and have tried extensive troubleshooting, but I consistently get a low-level PyTorch error.

Traceback (most recent call last): File "/data/home/user/miniforge3/envs/robin/bin/robin", line 3, in <module> from robin.main import package_run ... File "/data/home/user/miniforge3/envs/robin/lib/python3.9/site-packages/torch/__init__.py", line 202, in <module> from torch._C import * # noqa: F403 ImportError: /data/home/user/miniforge3/envs/robin/lib/python3.9/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent

Environment Details:

OS: Linux RHEL

Conda: Miniforge

Python: 3.9

PyTorch Version: 1.12.1 (as required)

Installation Steps:
I tried to create a Conda environment using the provided .yml file, and also attempted to build a custom environment to resolve dependency conflicts. The error seems to stem from an incompatibility between pytorch==1.12.1 and its underlying MKL dependencies when installed with modern Conda channels.

Could you please provide guidance on a known working set of dependencies or suggest a workaround? It seems the current requirements are no longer compatible.

conda create --name robin -c pytorch -c conda-forge -c bioconda python=3.9 pytorch=1.12.1 torchvision torchaudio cudatoolkit=11.3 "numpy<2.0" "protobuf<=3.20.1" h5py numba patsy statsmodels llvmlite opencv anndata scanpy icecream ruptures "prompt-toolkit<3.1"

conda activate robin

pip install docker cnv-from-bam pywebview zxing-cpp flet "minknow-api==4.5.0" alive-progress git+https://github.com/mattloose/methylartist.git psutil watchdog reportlab click "nicegui<=2.0.0" dna-features-viewer gff3-parser readfish yappi

# in robin path I run:

pip install --no-deps .

# then in sturgeon path I run:

pip install --no-deps .

Thank you.