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ikalvet / heme_binder_diffusion

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how to run rf_se3_diffusion.sif? #1

Open xingbanbin opened 4 months ago

xingbanbin commented 4 months ago

cd 7o2g_HBA ; /backup/weizg/xingbb/SOFT/rf_diffusion_all_atom/rf_se3_diffusion.sif /backup/weizg/xingbb/SOFT/rf_diffusion_all_atom/run_inference.py --config-dir=../ --config-name=config.yaml inference.input_pdb=/backup/weizg/xingbb/SOFT/heme_binder_diffusion/input/7o2g_HBA.pdb inference.output_prefix='./out/7o2g_HBA_dif' > output.log ; cd ..

The above command is generated from the Jupyter notebook. When I ran this command, I encountered the following error: /backup/weizg/xingbb/SOFT/rf_diffusion_all_atom/rf_se3_diffusion.sif: Permission denied

What should I do? My server does not have apptainer installed. Looking forward to your reply, thank you.

ikalvet commented 4 months ago

One solution would be to set up a conda environment with these instructions:

conda create -n "diffusion" python=3.9
conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
conda install -c conda-forge omegaconf hydra-core=1.3.2 scipy icecream openbabel assertpy opt_einsum pandas pydantic deepdiff e3nn prody pyparsing=3.1.1
conda install dglteam/label/cu118::dgl
conda install pytorch::torchdata

And then run these scripts just as /condapath/envs/diffusion/bin/python /path/to/script.py

The other option would be to try to install/build Apptainer yourself, but that seems to be difficult without root access.