Question

我正在使用分布式文件系统的计算机集群上运行Jupyter笔记本电脑。

一段时间后，由于出现错误，我无法打开新笔记本：

Close without saving?
File "XXX.ipynb" has unsaved changes, close without saving?

查看Jupyter日志，我发现由于nbsignatures.db数据库被锁定而导致了该错误。

[E 15:58:01.190 LabApp] Uncaught exception GET /api/contents/workspace/proteinsolver/notebooks/XXX.ipynb?type=notebook&content=1&1572638276143 (10.74.73.2)
    HTTPServerRequest(protocol='http', host='localhost:9416', method='GET', uri='/api/contents/workspace/proteinsolver/notebooks/04_sudoku_train-01-Copy8.ipynb?type=notebook&content=1&1572638276143', version='HTTP/1.1', remote_ip='10.74.73.2')
    Traceback (most recent call last):
      File "/home/username/miniconda3/lib/python3.7/site-packages/tornado/web.py", line 1699, in _execute
        result = await result
      File "/home/username/miniconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
        yielded = next(result)
      File "/home/username/miniconda3/lib/python3.7/site-packages/notebook/services/contents/handlers.py", line 112, in get
        path=path, type=type, format=format, content=content,
      File "/home/username/miniconda3/lib/python3.7/site-packages/notebook/services/contents/filemanager.py", line 433, in get
        model = self._notebook_model(path, content=content)
      File "/home/username/miniconda3/lib/python3.7/site-packages/notebook/services/contents/filemanager.py", line 392, in _notebook_model
        self.mark_trusted_cells(nb, path)
      File "/home/username/miniconda3/lib/python3.7/site-packages/notebook/services/contents/manager.py", line 508, in mark_trusted_cells
        trusted = self.notary.check_signature(nb)
      File "/home/username/miniconda3/lib/python3.7/site-packages/nbformat/sign.py", line 439, in check_signature
        return self.store.check_signature(signature, self.algorithm)
      File "/home/username/miniconda3/lib/python3.7/site-packages/nbformat/sign.py", line 232, in check_signature
        """, (algorithm, digest)).fetchone()
    sqlite3.OperationalError: database is locked

对我来说，最简单的解决方法是什么？

Answer 1

笔记本是否有可能被保存在git中并且存在合并冲突？查看此解决方案：https://stackoverflow.com/a/61031136/4001214修复了我遇到的问题。

当git无法解决文本文件中的冲突时，它将其合理的差异想法放入文件中。这会破坏.ipynb的JSON结构，并使它在jupyter中不可读。在链接的解决方案中，作者显示

<<<<<<< HEAD
  },
  {
   <CONTENTS OF MY CELL>
   ]
=======
>>>>>>> a23f8f8f9db0974b7de90c6e7ed8599fa04d53cc

，并注意到使用文本编辑器从文件中删除有问题的行可以解决此问题。就我而言，我在git中有一个已知的好文件，因此我删除了本地副本并重新拉了。

Answer 2

Jupyter使用SQLite数据库编写笔记本签名，as reported previously表示SQLite在分布式文件系统上表现不佳。

首先，我们需要生成一个Jupyter配置文件（默认情况下未创建）：

jupyter notebook --generate-config

然后，我们需要编辑此配置文件（jupyter_notebook_config.py），以将默认SQLite存储引擎设置为:memory:：

c.NotebookNotary.db_file = ':memory:'

打开新笔记本将不再需要调用数据库！

Jupyter无法打开笔记本，出现错误：“文件“ XX”具有未保存的更改，没有保存就关闭了吗？”

2 个答案: