Optimize nupack service startup and compute

README.md

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+# NP Replica
+
+This project provides a local Chinese web replica of the core NUPACK `analysis/input` workflow.
+
+## Run
+
+```bash
+docker compose up --build -d
+```
+
+Open `http://127.0.0.1:18765`.
+
+## Reverse Proxy
+
+The service listens on port `18765`. You can later reverse proxy `np.lihato.icu` to this port from your public server.
+
+## Endpoints
+
+- `GET /`
+- `GET /health`
+- `GET /api/example`
+- `POST /api/analyze`
+- `POST /api/jobs`
+- `GET /api/jobs/<job_id>`
+
+## Notes
+
+- `tube` mode supports strand concentrations and `SetSpec(max_size=...)`.
+- `complex` mode supports explicit complex definitions such as `A+B`.
+- Pair matrices are returned as a preview block to keep responses manageable.
+- The Docker image compiles ViennaRNA `RNAplot` from `rna/ViennaRNA-2.7.2.tar.gz` and embeds SVG structure plots into MFE results.
+- Multistrand MFE plots now use a split-strand layout by default when a structure contains `+`, with `RNAplot` retained as the fallback path.
+- The web UI now supports Chinese and English switching, browser-side history, result export, and async polling for submitted jobs.
+- Docker now starts three services: `np-replica`, `np-worker`, and `redis`.
+- 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.
+- The browser-facing API and page behavior stay the same after enabling Redis-backed jobs.
+- Worker concurrency is controlled by `NP_WORKER_CONCURRENCY` and defaults to `2`.
+- 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.
+- `NP_STRUCTURE_PLOT_MODE` supports `auto` (default), `split`, and `rnaplot`.
+- Static pages are served with ETag-based browser caching; JSON API responses remain uncached.
+- 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.
+- `/health` uses Redis queue length plus a running-job set instead of scanning every historical job on each poll.
+
+
+
+  现在 `docker-compose.yml` 面向 64 核 / 64G WSL 服务器的并发策略是：
+
+  - 最多同时跑 16 个任务
+  - 每个任务最多用 4 个计算线程
+  - 后续任务进入队列等待
+  - 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
+
+  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：
+
+  - 把 NP_WORKER_CONCURRENCY 改小
+  - 或保持并发不变，把 NP_PER_JOB_THREAD_LIMIT 改成 2 或 1