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setup-bioemu2-remote-tool

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Set up, launch, validate, and troubleshoot the BioEmu-2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

skills/setup-bioemu2-remote-tool/SKILL.md

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# Set up BioEmu-2 as a remote tool

> Validation status (2026-10-25): BioEmu-2 ran on the NVIDIA GB10 (aarch64, cc 12.1, 128 GB unified), driver 580.173.02, through this provider's own path. `tu remote setup` completed all four steps: weights 2/2 at their pins after an independent fetch, and the smoke OK in 89 s at 2.06 GiB peak reserved with both declared outputs matched by the manifest's globs. Four socket requests exercised the one-entry session cache in both directions; 428- and 642-token multi-chain systems ran on the same socket with real ColabFold queries, every frame passing physicality; a three-shape session at and below the 448-token ceiling held peak reserved flat at 12.38 GiB. The live MCP endpoint on 8063 returned correct results for three calls and named refusals for six malformed ones, four from the tool and two from the published schema, with no traceback reaching a caller. The orphan watchdog was observed releasing the card 122 s after the server stopped. Every wall-clock figure is an upper bound measured under a host load average of 26-45 and is not the model's speed; no saving from trunk reuse is established, because an identical repeat ran 15.4 s then 11.1 s through the socket but 22.3 s then 23.6 s through MCP -- opposite signs, both inside the noise at 20 tokens. Propagation is not exposed. Only protein chains have gone through the worker; ligands, RNA, DNA, contact conditioning, steering samplers and every physicality mode but high_quality are unexercised. Ensemble accuracy is unvalidated and nothing here checks it: the physicality report is geometry, and sampling frequency is not a calibrated Boltzmann probability. Public publication, cross-user isolation, concurrency, recovery and long inputs 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. Upstream supports Linux and NVIDIA only.
- 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
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