cbbef10e5d
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
61 lines
2.8 KiB
Markdown
61 lines
2.8 KiB
Markdown
# NP Replica
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This project provides a local Chinese web replica of the core NUPACK `analysis/input` workflow.
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## Run
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```bash
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docker compose up --build -d
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```
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Open `http://127.0.0.1:18765`.
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## Reverse Proxy
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The service listens on port `18765`. You can later reverse proxy `np.lihato.icu` to this port from your public server.
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## Endpoints
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- `GET /`
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- `GET /health`
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- `GET /api/example`
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- `POST /api/analyze`
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- `POST /api/jobs`
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- `GET /api/jobs/<job_id>`
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## Persistent Shares
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Shared result links are stored in Redis when `NP_REDIS_URL` is enabled. The compose file maps Redis data to `./runtime/redis` and enables AOF/RDB persistence, so shares survive container recreation and service restarts. Back up or migrate `./runtime/redis` if you move the deployment.
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## Notes
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- `tube` mode supports strand concentrations and `SetSpec(max_size=...)`.
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- `complex` mode supports explicit complex definitions such as `A+B`.
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- Pair matrices are returned as a preview block to keep responses manageable.
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- The Docker image compiles ViennaRNA `RNAplot` from `rna/ViennaRNA-2.7.2.tar.gz` and embeds SVG structure plots into MFE results.
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- Multistrand MFE plots now use a split-strand layout by default when a structure contains `+`, with `RNAplot` retained as the fallback path.
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- The web UI now supports Chinese and English switching, browser-side history, result export, and async polling for submitted jobs.
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- Docker now starts three services: `np-replica`, `np-worker`, and `redis`.
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- Async jobs use Redis-backed storage and queueing when `NP_REDIS_URL` is configured; otherwise the app falls back to the older in-memory mode.
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- The browser-facing API and page behavior stay the same after enabling Redis-backed jobs.
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- Worker concurrency is controlled by `NP_WORKER_CONCURRENCY` and defaults to `2`.
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- Per-job native thread usage is capped by `NP_PER_JOB_THREAD_LIMIT` and defaults to `1` to prevent a single analysis from monopolizing the machine.
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- `NP_STRUCTURE_PLOT_MODE` supports `auto` (default), `split`, and `rnaplot`.
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- Static pages are served with ETag-based browser caching; JSON API responses remain uncached.
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- The force-directed structure viewer lazy-loads D3 only when that view is opened, so the initial page load is not blocked by the external CDN.
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- `/health` uses Redis queue length plus a running-job set instead of scanning every historical job on each poll.
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现在 `docker-compose.yml` 面向 64 核 / 64G WSL 服务器的并发策略是：
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- 最多同时跑 16 个任务
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- 每个任务最多用 4 个计算线程
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- 后续任务进入队列等待
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- 理论上最多占用约 64 个 native 计算线程，避免 16 × 8 这类过度超卖
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如果后面你发现机器还会被压满，最直接的调法就是在 docker-compose.yml 里继续压：
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- 把 NP_WORKER_CONCURRENCY 改小
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- 或保持并发不变，把 NP_PER_JOB_THREAD_LIMIT 改成 2 或 1
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