fix: use remote-safe Gromacs model path

[njzjz-bot]

Summary

• write the staged relative model path into DP-Gromacs input.json
• avoid leaking a local absolute training path into remotely dispatched tasks
• assert the generated graph path in the Gromacs model-deviation test

The login-shell discussion in the issue is cluster/DPDispatcher configuration, while the nopbc behavior depends on the physical Gromacs setup. This PR fixes the actionable DP-GEN path defect.

Testing

• /tmp/dpgen-test-env/bin/python -m unittest tests.generator.test_gromacs_engine -v
• ruff check dpgen/generator/run.py tests/generator/test_gromacs_engine.py
• ruff format --check dpgen/generator/run.py tests/generator/test_gromacs_engine.py

Fixes #880

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

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📥 Commits

Reviewing files that changed from the base of the PR and between d5ce577 and 57ff844.

📒 Files selected for processing (2)

• dpgen/generator/run.py
• tests/generator/test_gromacs_engine.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 49.80%. Comparing base (d5ce577) to head (57ff844).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1962   +/-   ##
=======================================
  Coverage   49.80%   49.80%           
=======================================
  Files          83       83           
  Lines       14986    14986           
=======================================
  Hits         7464     7464           
  Misses       7522     7522           

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[njzjz-bot]

Independent review C

I found no blocking correctness, regression, security, or API issue in this change. CI/check evidence was considered alongside the full patch and relevant surrounding implementation. A formal APPROVE state cannot be submitted because the active njzjz-bot account is the PR author; GitHub self-review rules permit only a COMMENT review here.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent review B

No blocking findings. I reviewed the full diff, relevant surrounding behavior, tests, and current check status. GitHub does not permit njzjz-bot to APPROVE or REQUEST_CHANGES on its own pull request, so this review is recorded as COMMENT only.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent review A

No blocking findings after reviewing the full diff, relevant surrounding implementation/tests, and the current check rollup. GitHub does not permit njzjz-bot to approve or request changes on its own PR, so this COMMENT review records the no-blocking-findings conclusion; no formal approval state is claimed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh