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np_app/README.md

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NP Replica

This project provides a local Chinese web replica of the core NUPACK analysis/input workflow.

Run

docker compose up --build -d

Open http://127.0.0.1:18765.

Reverse Proxy

The service listens on port 18765. The current local deployment is reverse proxied as npt.lihato.icu.

Traefik only performs TLS termination, compression, and reverse proxying for npt; authentication is enforced by this application.

Deploying the independent np instance

np.lihato.icu runs independently on 100.64.0.11. Do not copy the npt OIDC values unchanged. In the np-replica service of the docker-compose.yml deployed on .11, use:

ports:
  - "100.64.0.11:18765:18765"
environment:
  NP_AUTH_REQUIRED: 1
  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
  NP_OIDC_POST_LOGOUT_URI: https://np.lihato.icu/

The NP_OIDC_* variables belong on the web service (np-replica); the worker does not perform browser login. Preserve the existing calculation settings, including NP_WORKER_CONCURRENCY=16, NP_PER_JOB_THREAD_LIMIT=4, and NP_NUPACK_CACHE_GB=8.0.

After editing the Compose file on .11, recreate the web container:

docker compose up -d --force-recreate np-replica

If the deployed image predates the account/OIDC changes, rebuild both application containers instead:

docker compose up -d --build --force-recreate np-replica np-worker

Verify the result:

curl -I https://np.lihato.icu/
curl -I 'https://np.lihato.icu/auth/login?next=%2F'

The first response should redirect to /auth/login?next=%2F. The second Location header must contain all of the following:

  • client_id=np-replica-web
  • redirect_uri=https%3A%2F%2Fnp.lihato.icu%2Fauth%2Fcallback
  • code_challenge_method=S256

If it contains npt-replica-web or npt.lihato.icu, the .11 container is still running with the wrong environment and must be recreated.

容器资源配置

当前 docker-compose.yml 面向 64 核 / 64 GB 级别的服务器配置，服务拆成三个容器：

  • redis：只保存实时队列、运行状态和会话缓存，限制为 mem_limit: 3g。Redis 开启 AOF，数据写入 ./runtime/redis。
  • np-replica：Web/API 容器，限制为 mem_limit: 4g，负责页面、登录、历史记录、任务提交和状态查询。它不应该承担大规模计算。
  • np-worker：后台计算容器，限制为 mem_limit: 56g，负责实际 NUPACK 计算。大任务应该由这个容器消耗 CPU 和内存。

计算相关环境变量需要在 np-replica 和 np-worker 中保持一致：

  • NP_WORKER_CONCURRENCY=16：最多同时执行 16 个后台任务，超过后进入 Redis 队列等待。
  • NP_PER_JOB_THREAD_LIMIT=4：单个任务最多使用 4 个 native 计算线程，同时写入 OMP_NUM_THREADS、OPENBLAS_NUM_THREADS、MKL_NUM_THREADS、NUMEXPR_NUM_THREADS、VECLIB_MAXIMUM_THREADS、GOTO_NUM_THREADS，并设置 nupack.config.threads。
  • NP_NUPACK_CACHE_GB=8.0：单个 NUPACK 进程可使用的缓存上限。
  • NP_JOB_TTL_SECONDS=3600：Redis 中实时任务状态的保留时间；长期历史记录写入 SQLite。

理论上当前峰值为 16 * 4 = 64 个 native 计算线程。若机器被压满，优先把 NP_WORKER_CONCURRENCY 从 16 降到 8 或 4；如果单任务仍过重，再把 NP_PER_JOB_THREAD_LIMIT 从 4 降到 2 或 1。np-replica 的内存不建议调高来跑计算，应该把计算压力留给 np-worker。

设计任务默认使用官方行为：固定序列 target 也参与 tube_design / complex_design。如果确认某些 target 完全固定、只需要展示结果、不需要参与优化，可在页面中把 “固定目标策略” 改为 “剥离固定目标以提速”，这样会减少 off-target 集合和优化搜索量。

Endpoints

  • GET /
  • GET /health
  • GET /api/example
  • POST /api/analyze
  • POST /api/jobs
  • GET /api/jobs/<job_id>

Persistent Shares

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.

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 supports Chinese and English switching, account-scoped cloud history, result export, share controls, 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.
  • Application login uses the public Authentik issuer at https://auth.lihato.icu/ with Authorization Code + PKCE.
  • 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/.
  • 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/.
  • 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.
  • 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.