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:
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
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:
> 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'
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
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
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