69 lines
3.9 KiB
Markdown
69 lines
3.9 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`. The current local deployment is reverse proxied as `npt.lihato.icu`.
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Traefik only performs TLS termination, compression, and reverse proxying for `npt`; authentication is enforced by this application.
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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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Live jobs and sessions are stored in Redis when `NP_REDIS_URL` is enabled. Account history and share links are stored in `./runtime/account/np-replica.sqlite3`; back up both runtime directories when moving 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 supports Chinese and English switching, account-scoped cloud history, result export, share controls, 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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- Application login uses the public Authentik issuer at `https://auth.lihato.icu/` with Authorization Code + PKCE.
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- The current `npt` instance uses issuer `/application/o/nupack-account-npt/`, client `npt-replica-web`, callback `https://npt.lihato.icu/auth/callback`, and logout return `https://npt.lihato.icu/`.
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- For the independent `np` deployment on `100.64.0.11`, set `NP_OIDC_ISSUER=https://auth.lihato.icu/application/o/nupack-account/`, `NP_OIDC_CLIENT_ID=np-replica-web`, `NP_OIDC_REDIRECT_URI=https://np.lihato.icu/auth/callback`, and `NP_OIDC_POST_LOGOUT_URI=https://np.lihato.icu/`.
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- Redis stores the live queue and login sessions. SQLite WAL at `/data/np-replica.sqlite3` stores users, owned jobs, compressed inputs/results/errors, usage totals, and durable share links.
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- History and job APIs enforce ownership by the Authentik OIDC subject. Public share links expose only the selected record and can be disabled or given an expiry by its owner.
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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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- 每个任务的 NUPACK 缓存上限为 8 GB
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- 理论上最多占用约 64 个 native 计算线程
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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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