如何使用Singularity镜像运行Jupyter笔记本？

Question

我已经创建了一个包含最新的Anaconda版本的Singularity镜像（jupyter.sif），我想使用它来运行Jupyter笔记本。

我希望运行类似于以下命令：

singularity exec \
  --bind /path/outside/image/:/path/inside/image/ \
  jupyter.sif jupyter notebook \
    --notebook-dir=/path/to/dir --no-browser --ip=127.0.0.1

基本上，只需启动一个普通的Jupyter Notebook，它将使用安装在Singularity镜像中的Python版本和软件包。理想情况下，Notebook将读取和写入图像之外的文件（因此我指定了绑定路径）。

然而，当我运行上述命令时，我会得到以下错误：

> Traceback (most recent call last):   File
> "/opt/conda/lib/python3.7/site-packages/traitlets/traitlets.py", line
> 528, in get
>     value = obj._trait_values[self.name] KeyError: 'runtime_dir'
> 
> During handling of the above exception, another exception occurred:
> 
> Traceback (most recent call last):
> 
>   File "/opt/conda/bin/jupyter-notebook", line 11, in <module>
>     sys.exit(main())
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/jupyter_core/application.py",
> line 266, in launch_instance
>     return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/traitlets/config/application.py",
> line 657, in launch_instance
>     app.initialize(argv)
> 
>   File "<decorator-gen-7>", line 2, in initialize
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/traitlets/config/application.py",
> line 87, in catch_config_error
>     return method(app, *args, **kwargs)
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/notebook/notebookapp.py", line
> 1626, in initialize
>     self.init_configurables()
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/notebook/notebookapp.py", line
> 1319, in init_configurables
>     connection_dir=self.runtime_dir,
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/traitlets/traitlets.py", line
> 556, in __get__
>     return self.get(obj, cls)
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/traitlets/traitlets.py", line
> 535, in get
>     value = self._validate(obj, dynamic_default())
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/jupyter_core/application.py",
> line 99, in _runtime_dir_default
>     ensure_dir_exists(rd, mode=0o700)
> 
>   File
> "/opt/conda/lib/python3.7/site-packages/jupyter_core/utils/__init__.py",
> line 13, in ensure_dir_exists
>     os.makedirs(path, mode=mode)
> 
>   File "/opt/conda/lib/python3.7/os.py", line 211, in makedirs
>     makedirs(head, exist_ok=exist_ok)
> 
>   File "/opt/conda/lib/python3.7/os.py", line 211, in makedirs
>     makedirs(head, exist_ok=exist_ok)
> 
>   File "/opt/conda/lib/python3.7/os.py", line 221, in makedirs
>     mkdir(name, mode)
> 
> OSError: [Errno 30] Read-only file system: '/run/user'

我猜这是因为笔记本试图在镜像内部写东西，由于我不以sudo身份运行镜像（我不想这样做），并且在执行镜像时也没有指定--writable选项（也不想这样做），它会抱怨无法在镜像内部进行写操作。

有没有一种方法可以“告诉”镜像读写我的主目录中的文件，而不是镜像内部的文件？

谢谢。

- maos.a

Answer 1

我刚碰到了同样的问题，这似乎为我解决了：将容器内的/run/user映射到您外部的工作目录（或您选择的目录）。对于您的情况，可能意味着这样：

singularity exec --bind /path/outside/image/:/path/inside/image/ --bind $PWD:/run/user jupyter.sif jupyter notebook --notebook-dir=/path/to/dir --no-browser --ip=127.0.0.1

运行时，我的情况下创建了一个文件夹1000

- Lex Nederbragt

Answer 2

这在使用 singularity 实例时效果很好，例如：

   singularity instance.start --writable --contain --bind shared:/shared sandbox/ jupyter

- chrishmorris

Answer 3

接受的答案是有效的，但是这里有另外一种不需要绑定挂载的解决方案。在运行jupyter笔记本之前可以运行unset XDG_RUNTIME_DIR，然后这个错误就会消失。

- jkr