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rfd4-proteina-setup

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Updated 10-21 19:19

About this skill

RFD4-Proteína Setup

Purpose

Install the RFD4-Proteína model runtime and released checkpoint pair, then prove readiness with preflight and one generated monomer. Use this for native model setup and troubleshooting; an already-running NIM has a different deployment workflow.

Prerequisites

The RFD4-Proteína model checkout, its documented host/GPU platform, and storage for the environment and checkpoints. The skill catalog contains instructions and helpers, not the model source. A skill being installed does not imply that the model or a GPU is installed.

Inputs

Use the supplied model checkout at RFPROTEINA_ROOT, or the supplied source URL and revision when a clone is needed. Reuse known paths and access information. Optional inputs are DATA_PATH, RFPROTEINA_PYTHON for an existing model interpreter, and oracle or scheduler settings. Exported values take precedence over configuration-file defaults.

Instructions

1. Locate the model and preserve the workspace

  • Resolve the loaded skill directory to an absolute path and keep it in RFD4_SETUP_SKILL before changing directory. Its helpers belong to the skill installation; setup.sh, configs, and benchmark inputs belong to the model.
  • Inspect the supplied RFPROTEINA_ROOT, or the current project if no path was supplied. A model checkout has .project-root, pyproject.toml, and configs/inference.yaml. Read its installation manual and setup entry point. A missing scripts/rfproteina_exec.sh alone does not mean the model is absent: native installations can use .venv/bin/python directly.
  • If the source is missing, use an already-supplied repository URL and revision to clone into a new, unused directory. Otherwise request that missing source information. Do not guess a similarly named Proteina repository or substitute the NIM for this model. A 404 can mean unavailable or private source.
  • Preserve existing files, Git metadata, environments, and data. Never clear or reset a workspace to make a clone fit. If the destination exists, inspect it and reuse a valid checkout or select an unused destination. A failed clone does not authorize deleting its destination or unrelated files.

Set RFPROTEINA_ROOT to the verified absolute model path and execute RFProteína commands there. Use the absolute skill path for its helpers. For revision-specific setup and safe environment-file handling, read environment.

2. Check the host, then install

Check the selected execution host's GPU visibility (for example nvidia-smi -L), storage, and required platform against its installation manual. On a cluster, inspect the requested GPU allocation rather than treating a login node as the inference host. Distinguish a missing driver utility from a failed CUDA check. If GPU access is unavailable, report that inference is blocked; perform an explicitly requested environment-only installation without claiming readiness.

From the verified model checkout, use its maintained installation recipe:

cd "$RFPROTEINA_ROOT"
make setup
source .venv/bin/activate

If the user selected an existing model environment, reuse it and install only missing dependencies. Run the later rfd4-generate command from the same environment that preflight checks.

The documented native setup creates .venv and installs AtomWorks at the revision pinned in pyproject.toml. It preserves existing environment files and does not edit shell startup files. Inspect the chosen revision's manual before adapting these commands. Diagnose installation failures from their logs; do not disable TLS verification, substitute import stubs, or patch model code to manufacture a successful preflight.

3. Resolve data paths and checkpoints

The documented setup downloads both released checkpoints into DATA_PATH, defaulting to ./data_path, and reuses existing files. Set a custom DATA_PATH before setup. bash setup.sh --skip-weights installs only the environment. A missing checkpoint is a download/configuration problem, not evidence that the checkout is absent.

Read the checkpoint names from configs/inference.yaml and check the selected data directory. Exported DATA_PATH takes precedence over .env.local, with .env used only when .env.local is absent. Treat these files as data, never shell-source them or print credentials. See checkpoints for the release files and downloader. Keep optional refolding setup separate; plain monomer generation needs no oracle.

For native preflight, export the actual data directory selected during setup, or pass it explicitly with --data-path. The checker uses this supplied path; it does not load credential files. Preserve the existing configuration rather than replacing it with a guessed default.

4. Run preflight in that model's runtime

bash "$RFD4_SETUP_SKILL/scripts/preflight.sh" --repo-root "$RFPROTEINA_ROOT"

The helper uses explicit RFPROTEINA_PYTHON when supplied, otherwise the checkout's executable dispatcher if present, otherwise its native .venv/bin/python. It checks imports, CUDA, and nonempty released checkpoint files. --data-path overrides exported DATA_PATH; relative data paths resolve against the model root. A nonzero exit blocks the smoke test. Report the actual failed check and remedy instead of replacing the checkout or calling setup complete.

5. Generate and verify one smoke result

After preflight exits 0 with PREFLIGHT PASSED, run:

rfd4-generate inputs=data/benchmarks/monomer \
    subset_to_examples=monomer-short num_replicates=1 out_dir=./runs/smoke

Use an unused output directory; preserve earlier runs if runs/smoke already contains results. Confirm command success and a nonempty annotated CIF under the actual output directory's inference_samples/. Report the checkout, interpreter, checkpoint pair, preflight result, and resulting CIF path. A passing preflight alone does not establish successful generation. Hand off to rfd4-proteina-generate for larger design requests.

Troubleshooting

  • Skill present but model source unavailable: report which candidate paths were checked and request the approved checkout or source URL/revision. Stop source guessing after an access failure; preserve the workspace.
  • Checkout found but runtime missing: run its installer or select its existing interpreter with RFPROTEINA_PYTHON.
  • Missing data/checkpoints: check the selected DATA_PATH and repeat the documented download for that directory; preserve existing settings.
  • No usable CUDA device: fix the requested host/allocation before generation.
  • Refolding failures: check the separate oracle image, weights, cache, and host runtime. Do not add refolding to this plain generation smoke test.

Limitations

A checkout, GPU, and checkpoint access must exist in the execution environment. Preflight checks dependencies, CUDA, and release files; it does not validate every design task, checkpoint checksum, custom checkpoint override, or optional oracle.

Examples

For a separately installed skill and model, set RFD4_SETUP_SKILL to the loaded skill directory and RFPROTEINA_ROOT to the model checkout, then follow steps 2–5. On a host without a GPU, a useful result is an accurate blocker diagnosis; it is not a completed inference installation.

Available Scripts

Script Purpose Arguments
scripts/preflight.sh Check the selected model runtime --repo-root PATH or RFPROTEINA_ROOT; --data-path PATH or DATA_PATH; optional RFPROTEINA_PYTHON
scripts/preflight.py Run checks directly in an installed model interpreter --repo-root PATH or RFPROTEINA_ROOT; --data-path PATH or DATA_PATH