Jupyter保存报错sqlite3.DatabaseError：数据库镜像损坏，求解及续算风险

通过SSH连接两台由AFS共享存储的计算机，同时在两台设备上运行Jupyter Notebook，保存第一个笔记本时出现错误：Unexpected error while saving file: Untitled.ipynb database disk image is malformed。怀疑是对nbsignatures.db的并发写入导致，完整错误日志如下：

[W YYYY-MM-DD HH:MM:SS.SSS ServerApp] 500 PUT /api/contents/Untitled.ipynb?########## (127.0.0.1): Unexpected error while saving file: Untitled.ipynb database disk image is malformed
[W YYYY-MM-DD HH:MM:SS.SSS ServerApp] wrote error: 'Unexpected error while saving file: Untitled.ipynb database disk image is malformed'
    Traceback (most recent call last):
      File "/nobackup/username/env_name/lib/python3.10/site-packages/jupyter_server/services/contents/filemanager.py", line 911, in save
        self.check_and_sign(nb, path)
      File "/nobackup/username/env_name/lib/python3.10/site-packages/jupyter_server/services/contents/manager.py", line 713, in check_and_sign
        self.notary.sign(nb)
      File "/nobackup/username/env_name/lib/python3.10/site-packages/nbformat/sign.py", line 477, in sign
        self.store.store_signature(signature, self.algorithm)
      File "/nobackup/username/env_name/lib/python3.10/site-packages/nbformat/sign.py", line 214, in store_signature
        if not self.check_signature(digest, algorithm):
      File "/nobackup/username/env_name/lib/python3.10/site-packages/nbformat/sign.py", line 241, in check_signature
        r = self.db.execute(
    sqlite3.DatabaseError: database disk image is malformed
    
    The above exception was the direct cause of the following exception:
    
    Traceback (most recent call last):
      File "/nobackup/username/env_name/lib/python3.10/site-packages/tornado/web.py", line 1786, in _execute
        result = await result
      File "/nobackup/username/env_name/lib/python3.10/site-packages/jupyter_server/services/contents/handlers.py", line 266, in put
        await self._save(model, path)
      File "/nobackup/username/env_name/lib/python3.10/site-packages/jupyter_server/services/contents/handlers.py", line 191, in _save
        model = await ensure_async(self.contents_manager.save(model, path))
      File "/nobackup/username/env_name/lib/python3.10/site-packages/jupyter_core/utils/__init__.py", line 189, in ensure_async
        result = await obj
      File "/nobackup/username/env_name/lib/python3.10/site-packages/jupyter_server/services/contents/largefilemanager.py", line 133, in save
        return await super().save(model, path)
      File "/nobackup/username/env_name/lib/python3.10/site-packages/jupyter_server/services/contents/filemanager.py", line 927, in save
        raise web.HTTPError(500, f"Unexpected error while saving file: {path} {e}") from e
    tornado.web.HTTPError: HTTP 500: Internal Server Error (Unexpected error while saving file: Untitled.ipynb database disk image is malformed)
[E YYYY-MM-DD HH:MM:SS.SSS ServerApp] {
      "Host": "localhost:8080",
      "Accept": "*/*",
      "Referer": "http://localhost:8080/notebooks/Untitled.ipynb",
      "User-Agent": "Mozilla/5.0 (OS; CPU; rv:##.0) Gecko/######## Firefox/###.0"
    }
[E YYYY-MM-DD HH:MM:SS.SSS ServerApp] 500 PUT /api/contents/Untitled.ipynb?########## (user_hash@127.0.0.1) ###.##ms referer=http://localhost:8080/notebooks/Untitled.ipynb

请问如何解决该问题？若我不保存该Jupyter Notebook，继续在其中进行计算是否会有问题？

解决方法 #

• 删除损坏的签名数据库：找到nbsignatures.db文件（通常路径为~/.local/share/jupyter/nbsignatures.db），直接删除该文件。下次启动Jupyter时会自动重建新的数据库，可快速解决当前错误。
• 禁用笔记本签名功能：在Jupyter配置文件（jupyter_server_config.py或jupyter_notebook_config.py）中添加以下配置，彻底关闭签名机制，从根源避免并发写入冲突：

  c.ContentsManager.signatures_enabled = False
  

  若没有配置文件，可执行jupyter server --generate-config生成后再修改。
• 隔离签名数据库存储：确保两台机器的Jupyter使用独立的nbsignatures.db文件，不要将该文件放在AFS共享目录下。可通过设置环境变量JUPYTER_DATA_DIR指向本地目录，让Jupyter将数据文件存储在本地而非共享存储中。

不保存继续计算的风险 #

• 短期计算不受影响：当前计算过程不会被保存错误干扰，Jupyter会将运行状态暂存于内存，只要服务器不重启、连接不中断，计算可正常进行。
• 数据丢失风险极高：一旦出现网络中断、服务器崩溃、Jupyter进程意外退出等情况，所有未保存的代码、运行结果、变量都会直接丢失，无法恢复。
• 工作进度无持久化记录：不保存的话，代码修改、分析步骤等内容没有持久化存储，后续回溯或继续工作会非常困难。

内容的提问来源于stack exchange，提问作者olivarb