To run on singularity/amulet, make sure you have already downloaded the CATH dataset (see instructions above). If you do not have amulet installed, folow the instructions at https://amulet-docs.azurewebsites.net/main/setup.html. This should leave you with a conda environment named amlt8. Note that this environment should be separate from the environment for the diffusion model itself. Note that you do not need to create the given environment.yml to submit to amulet/singularity; the environment for running the code is separately set up within the Singularity compute cluster.

With these two requirements, to run training on singularity, run:

conda activate amlt8  # Activate the conda env.
amlt run -y scripts/amlt.yaml -o results

Within this amlt.yaml file, the python command contains a pointer to a config json file. Edit the path indicated here to use a different configuration for training.

Note rearding the structure of the amlt.yaml file: installing packages via conda is very slow on the Singularity cluster, so we recreate the same set of packages installed via pip instead of relying on conda.