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
