Troubleshooting & FAQ

The installer finished but moldesk says "command not found"

Open a new terminal window: the installer adds moldesk to your shell profile, and already-open terminals do not see the change. To use it in the current window, run export PATH="$HOME/.moldesk/bin:$PATH". If you installed with MOLDESK_NO_MODIFY_PATH=1, add that folder to your PATH yourself.

The installer says my system is not supported

The installer supports macOS and Linux on 64-bit Intel/AMD or ARM processors. On Windows, use WSL2 and run the install command in the Ubuntu terminal. Alpine Linux (musl) is not supported yet. If curl or wget is missing on Ubuntu or Debian, run sudo apt-get install -y curl first.

How do I update or remove MoleculeDesk itself?

See Update and Remove on the installation page. Updating is re-running the install command.

Do I need a GPU?

It depends on the model. moldesk doctor reports whether an NVIDIA GPU/CUDA is required or just recommended for each model, based on its manifest. Some models can run on CPU, just more slowly.

Where are models installed?

By default under ~/.moldesk. Set MOLDESK_HOME before installing to use a different location for managed models, state, locks, and caches.

How do I check what's installed?

moldesk list --installed

How do I reinstall a model cleanly?

moldesk install <model> --reinstall --yes

Reinstallation is staged and promoted atomically — if it fails partway through, your previous working installation is left intact.

How do I remove a model?

moldesk uninstall <model> --yes

This removes the model's environment and state but keeps shared cached downloads (like checkpoints), so reinstalling later — or installing a different model that shares an asset — doesn't require redownloading.

A model shows as "planned" or "beta" — can I use it?

planned means installation/run support isn't finished yet. beta means install and run both work, but broader verification is still in progress before promotion to available. See Model compatibility & registry for what each status means.

Where can I ask for help or report a bug?

Open an issue on the MoleculeDesk GitHub repository.