From eb7033c49695fd6841405f6882e71c619b1f10da Mon Sep 17 00:00:00 2001
From: Lihatoo <1747565629@gmail.com>
Date: Sun, 26 Jul 2026 17:14:19 +0800
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---
 README.md          | 86 ++++++++++++++++++++++++++++++++++++++--------
 docker-compose.yml |  2 +-
 service/index.html | 17 +++++----
 service/server.py  |  6 ++--
 4 files changed, 85 insertions(+), 26 deletions(-)

diff --git a/README.md b/README.md
index 3c5042c..41f1606 100644
--- a/README.md
+++ b/README.md
@@ -16,6 +16,77 @@ The service listens on port `18765`. The current local deployment is reverse pro
 
 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:
+
+```yaml
+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:
+
+```bash
+docker compose up -d --force-recreate np-replica
+```
+
+If the deployed image predates the account/OIDC changes, rebuild both
+application containers instead:
+
+```bash
+docker compose up -d --build --force-recreate np-replica np-worker
+```
+
+Verify the result:
+
+```bash
+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 /`
@@ -52,18 +123,3 @@ Live jobs and sessions are stored in Redis when `NP_REDIS_URL` is enabled. Accou
 - 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.
-
-
-
-  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
-  - 每个任务的 NUPACK 缓存上限为 8 GB
-  - 理论上最多占用约 64 个 native 计算线程
-
-  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
diff --git a/docker-compose.yml b/docker-compose.yml
index 3232cf3..d06382d 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -3,7 +3,7 @@ services:
     image: redis:7.4.8-bookworm
     container_name: np-redis
     restart: always
-    mem_limit: 2g
+    mem_limit: 3g
     command: ["redis-server", "--appendonly", "yes", "--appendfsync", "everysec", "--save", "60", "1"]
     volumes:
       - ./runtime/redis:/data
diff --git a/service/index.html b/service/index.html
index d6257f4..2990eb5 100644
--- a/service/index.html
+++ b/service/index.html
@@ -1687,6 +1687,7 @@ A+B</textarea>
                 <label>
                   <span data-i18n="design_stop_condition"></span>
                   <input id="designStopCondition" type="number" value="0.02" min="0.001" max="0.99" step="0.01" />
+                  <small class="minor-note" data-i18n="design_stop_condition_hint"></small>
                 </label>
                 <label>
                   <span data-i18n="design_max_time_hours"></span>
@@ -1706,8 +1707,8 @@ A+B</textarea>
                 <label>
                   <span data-i18n="design_fixed_target_policy"></span>
                   <select id="designFixedTargetPolicy">
-                    <option value="exclude_from_optimization" data-i18n="design_fixed_target_exclude"></option>
                     <option value="include" data-i18n="design_fixed_target_include"></option>
+                    <option value="exclude_from_optimization" data-i18n="design_fixed_target_exclude"></option>
                   </select>
                 </label>
               </div>
@@ -2223,14 +2224,15 @@ A+B</textarea>
           design_help: "Design 按 NUPACK 的 `Domain -> TargetStrand -> TargetComplex/TargetTube` 关系组织。可先定义 domain 约束，再在链输入中用空格分隔的 domain composition 组装链；也可让某条链继续直接使用整链 IUPAC 约束。",
           design_guide_btn: "打开 Design 教学",
           design_stop_condition: "停止条件 f_stop",
+          design_stop_condition_hint: "f_stop 越小越严格，可能极慢；若长时间无法达到该缺陷阈值，设计会持续搜索。",
           design_max_time_hours: "最大设计时间 (小时)",
           design_seed_label: "随机种子",
           design_wobble_label: "Wobble mutations",
           design_wobble_allow: "允许",
           design_wobble_prohibit: "禁止",
           design_fixed_target_policy: "固定目标策略",
-          design_fixed_target_exclude: "剥离出优化",
-          design_fixed_target_include: "参与优化",
+          design_fixed_target_exclude: "剥离固定目标以提速",
+          design_fixed_target_include: "参与优化（官方默认）",
           design_tab_targets: "Target Tubes",
           design_tab_hard: "Hard Constraints",
           design_tab_soft: "Soft Constraints",
@@ -2574,14 +2576,15 @@ A+B</textarea>
           design_help: "Design follows the NUPACK `Domain -> TargetStrand -> TargetComplex/TargetTube` hierarchy. You can define domains first and then compose strands from domain tokens, while still allowing any strand to stay as a whole-strand IUPAC constraint when needed.",
           design_guide_btn: "Open Design Guide",
           design_stop_condition: "Stop Condition f_stop",
+          design_stop_condition_hint: "Smaller f_stop values are stricter and can be extremely slow; design keeps searching until this defect threshold is reached.",
           design_max_time_hours: "Max Design Time (hours)",
           design_seed_label: "Random Seed",
           design_wobble_label: "Wobble Mutations",
           design_wobble_allow: "Allow",
           design_wobble_prohibit: "Prohibit",
           design_fixed_target_policy: "Fixed Target Policy",
-          design_fixed_target_exclude: "Exclude from Optimization",
-          design_fixed_target_include: "Include in Optimization",
+          design_fixed_target_exclude: "Exclude Fixed Targets for Speed",
+          design_fixed_target_include: "Include in Optimization (Official Default)",
           design_tab_targets: "Target Tubes",
           design_tab_hard: "Hard Constraints",
           design_tab_soft: "Soft Constraints",
@@ -4070,7 +4073,7 @@ A+B</textarea>
         document.getElementById("designSeed").value = payload.design?.seed ?? 0;
         document.getElementById("designWobble").value = String(payload.design?.wobble_mutations ?? false);
         document.getElementById("designMaxTimeHours").value = ((payload.design?.max_time_seconds ?? 0) / 3600);
-        document.getElementById("designFixedTargetPolicy").value = payload.design?.fixed_target_policy ?? "exclude_from_optimization";
+        document.getElementById("designFixedTargetPolicy").value = payload.design?.fixed_target_policy ?? "include";
         const payloadCompute = Array.isArray(payload.compute) ? payload.compute : [];
         document.querySelectorAll(".check input").forEach((input) => {
           input.checked = payloadCompute.includes(input.value);
@@ -6176,7 +6179,7 @@ A+B</textarea>
         document.getElementById("designSeed").value = example.design?.seed ?? 0;
         document.getElementById("designWobble").value = String(example.design?.wobble_mutations ?? false);
         document.getElementById("designMaxTimeHours").value = ((example.design?.max_time_seconds ?? 0) / 3600);
-        document.getElementById("designFixedTargetPolicy").value = example.design?.fixed_target_policy ?? "exclude_from_optimization";
+        document.getElementById("designFixedTargetPolicy").value = example.design?.fixed_target_policy ?? "include";
         document.getElementById("complexesText").value = example.complexes_text;
         const exampleCompute = Array.isArray(example.compute) ? example.compute : [];
         document.querySelectorAll(".check input").forEach((input) => {
diff --git a/service/server.py b/service/server.py
index fefc7bf..8b3675f 100644
--- a/service/server.py
+++ b/service/server.py
@@ -371,7 +371,7 @@ def parse_design_options(payload):
         "seed": int(raw.get("seed", 0)),
         "wobble_mutations": bool(raw.get("wobble_mutations", False)),
         "max_time_seconds": int(raw.get("max_time_seconds", 0)),
-        "fixed_target_policy": str(raw.get("fixed_target_policy", "exclude_from_optimization")).strip().lower(),
+        "fixed_target_policy": str(raw.get("fixed_target_policy", "include")).strip().lower(),
     }
     if options["trials"] < 1 or options["trials"] > 8:
         raise ValueError("design trials must be between 1 and 8.")
@@ -2245,7 +2245,7 @@ EXAMPLE_PAYLOAD = {
         "seed": 0,
         "wobble_mutations": False,
         "max_time_seconds": 0,
-        "fixed_target_policy": "exclude_from_optimization",
+        "fixed_target_policy": "include",
     },
     "design_domains": [
         {"name": "a", "sequence": "N10"},
@@ -2307,7 +2307,7 @@ DESIGN_TUBE_EXAMPLE_PAYLOAD = {
         "seed": 1,
         "wobble_mutations": False,
         "max_time_seconds": 0,
-        "fixed_target_policy": "exclude_from_optimization",
+        "fixed_target_policy": "include",
     },
     "design_domains": [
         {"name": "a", "sequence": "N10"},