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setup-protenix_v1-remote-tool

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Set up, launch, validate, and troubleshoot the Protenix ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

skills/setup-protenix_v1-remote-tool/SKILL.md

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# Set up Protenix as a remote tool

> Validation status (2026-10-01): Protenix 1.1.0 (ByteDance's AlphaFold3 reproduction) ran on the NVIDIA GB10 (aarch64, cc 12.1) with the optimization kit **OFF** — its one prebuilt object is x86-64 and `kit_foreign_objects` refuses per directory, so the kit mode is unreachable here. Verified on FOUR CONSECUTIVE IDENTICAL REQUESTS plus a mixed-shape sequence and an ascending ladder: 4.4-5.1 s per 35-residue fold, peak reserved ~1.9 GiB at 100 residues rising to 9.65 at 800 — about 5.1x, the same shape protenix_v1 measures (5.3x) for the same architecture through a different reimplementation. **One thing to know before deploying: stock's fast-LayerNorm extension cannot run on this card and fails LATENTLY.** It emits SASS for sm_70..sm_100 with no PTX, so on sm_121 the call returns, `torch.cuda.synchronize()` passes, and the NEXT unrelated torch operation raises `no kernel image is available for execution on the device` — with a LayerNorm output in hand that was never written. `[kit.env] LAYERNORM_TYPE = "torch"` is upstream's own switch and is load-bearing; the worker refuses to start if an operator overrides it back on a card outside the extension's built set. Public publication, cross-user isolation, concurrency, recovery and structural accuracy are untested; keep this deployment private.

## Prerequisites

- Run from the ToolUniverse repository root on Linux with Python 3.12.3.
- A CUDA GPU is required. This provider holds its model resident between requests; CPU is not a target.
- Keep provider data, weights, caches, and credentials outside Git.
- Bind to loopback. A non-loopback bind requires TOOLUNIVERSE_API_TOKEN; never put it in arguments or results.

Run the standard-library contract check before downloading large dependencies:

~~~bash