How to run a jupyter notebook using a singularity image?

Question

I have built a singularity image (jupyter.sif) that contains the latest anaconda version and I want to use that to run a jupyter notebook.

I would like to run something like this:

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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

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Essentially, just launch a normal jupyter notebook that will use the python version and packages installed in the singularity image. Ideally the notebook will read and write files outside the image (hence why I specify a bind path).

However, when I run the above command I get the following error:

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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 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 "", 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'

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I assume this is because the notebook is trying to write stuff inside the image and since i don't run the image as sudo (i don't want to do this) and i also do not specify --writable when executing the image (also don't want to do this), it complains about not being able to write within the image.

Is there a way of "telling" the image to read and write files in my home directory and not inside the image?

Thanks

Answer 1

I just came across the same problem and this seems to have solved it for me: map /run/user inside to container to your working directory outside (or a directory of your choosing). For your case, would mean probably this:

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

When running like this, in my case a folder 1000 was created

Answer 2

这适用于奇点实例，例如：

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

Answer 3

The accepted answer works, but here is another solution that does not require bind mounts. One can run unset XDG_RUNTIME_DIR before running the jupyter notebook, and this error will disappear.