Question on: https://github.com/vsoch/lessons/tree/master/_posts/hpc/2018-07-10-sherlock-jupyter.md#21-jupyter-notebook

After following prompts to enter and verify password, I receive an error message and the step apparently fails. Any idea why this problem occurs and what can be done to fix it?

The error message in question:
Traceback (most recent call last): File "/share/software/user/open/py-jupyter/1.0.0_py36/bin/jupyter-notebook", line 11, in <module> sys.exit(main()) File "/share/software/user/open/py-jupyter/1.0.0_py36/lib/python3.6/site-packages/jupyter_core/application.py", line 267, in launch_instance return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs) File "/share/software/user/open/py-jupyter/1.0.0_py36/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance app.start() File "/share/software/user/open/py-jupyter/1.0.0_py36/lib/python3.6/site-packages/notebook/notebookapp.py", line 1362, in start super(NotebookApp, self).start() File "/share/software/user/open/py-jupyter/1.0.0_py36/lib/python3.6/site-packages/jupyter_core/application.py", line 256, in start self.subapp.start() File "/share/software/user/open/py-jupyter/1.0.0_py36/lib/python3.6/site-packages/notebook/notebookapp.py", line 345, in start set_password(config_file=self.config_file) File "/share/software/user/open/py-jupyter/1.0.0_py36/lib/python3.6/site-packages/notebook/auth/security.py", line 148, in set_password config.NotebookApp.password = hashed_password File "/share/software/user/open/python/3.6.1/lib/python3.6/contextlib.py", line 89, in __exit__ next(self.gen) File "/share/software/user/open/py-jupyter/1.0.0_py36/lib/python3.6/site-packages/notebook/auth/security.py", line 131, in persist_config with io.open(config_file, 'w', encoding='utf8') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/users/jazam/.jupyter/jupyter_notebook_config.json'

Hi,
I tried to run an slurm job through sbatch with a python script inside. The script does not run and it can be seen the following message instead:
QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/9980', please create it with 0700 permissions.
qt.qpa.screen: QXcbConnection: Could not connect to display localhost:12.0
Could not connect to any X display.

Now:

• I know the problem is that I am importing the matplotlib module since my final results are some figures.
• I also know that the same script runs well when I run it in the login node which I remotely accessed via ssh -X
• I believe that the compute nodes don't have permission to access any X display because perhaps the communication between the login node and the compute node was automatically made by slurm without this feature enabled
• I confirmed that /run/user/9980, accessed from the login node, does exist and has proper permissions assigned.
  So, my real question is: How do I solve my problem????

Any help or ideas please

• python
• R

and for both, include example files to download

Hello! I am using Jupyter notebooks on Sherlock by following the steps detailed here (with your default container): https://vsoch.github.io/lessons/sherlock-jupyter/

But I am running into issues as I am unable to use the modules that I have loaded on the interactive terminal of my Sherlock login outside of this jupyter notebook. This screenshot in black is from my terminal, where I have listed the modules using module list. This other screenshot is from my jupyter notebook where I am trying to list modules the same way as in the terminal but getting a different list. Additionally, for some reason I am also unable to see the latest version of Python in the notebook using !python --version. Can you please help with what's going wrong?