Issues activating new login
Activation link expired
To activate your login, you get a link that is only valid for 12 hours. However, you can generate a new link to pick your password by following the instructions here.
Issues logging in or starting a Notebook Server
I cannot login: invalid username or password
Your original password was sent to you by e-mail (see User Manual - Student#Receivelogincredentials). In this e-mail you were also urged to change it. Assuming you changed it, the original password from the e-mail no longer works. If you really cannot remember your password, ask your teacher to contact the SURF helpdesk.
I cannot start a Notebook Server: "Server failed: Timeout"
There are two possible reasons for this.
- You did not accept the usage agreement. In this case, after pressing 'spawn' in the Jupyter Notebook interface, you should see "Pending in the queue", then "Cluster job running, waiting to connect". The latter message will just stay there, until the spawning times out. To resolve, please accept the usage agreement at https://portal.cua.surf.nl/ . If you own multiple logins, we advice to do so in an incognito window, to avoid confusion about which login accepted the usage agreement.
- The scheduler that is responsible for starting a Notebook Server for you, is slow to respond. Please retry to launch your server one or two times, and/or wait a minute and try again. This usually resolves the issue. If you are submitting in the outside course hours profile, this error may also be given when many other users (of your course) are already logged in. In that case, you'll have to wait until a slot opens up again (simply retry every so 10 or so minutes). If the problem persists, and you are sure it is not because too many students from your course are already logged in, please ask the course teacher to contact us through the servicedesk.
I cannot start a Notebook Server: "Spawn failed: sbatch: error: Batch job submission failed: Requested reservation is invalid"
You get this error when trying to submit to the course hours profile outside of your course hours. You probably should have selected the outside course hours profile. See also User Manual - Student#Profileselection. If you are sure you selected the correct profile, have your teacher contact the SURF helpdesk.
I cannot start a Notebook Server: "Spawn failed: sbatch: error: Batch job submission failed: Invalid qos specification"
If you have access to multiple JupyterHubs (e.g. because you participate in multiple courses), make sure that you use the right login credentials with the right JupyterHub URL. If you are sure those match, please ask your teacher to contact the SURF helpdesk.
The Jupyter Notebook is stuck in the 'pending spawn' step. If I click 'stop server' I get an API error.
The JupyterHub sends a command to start a Notebook once you press 'start'. It then repeatedly queries to see if the Notebook Server has come online. In some rare cases, the Notebook Server starts, but the JupyterHub is not notified properly, and gets stuck in this 'pending spawn' phase. Your teacher can solve this by logging in to the JupyterHub, going to the admin panel, and clicking 'Delete User'. Note that this does NOT delete any data from your home directory: it just resets the JupyterHub 'state' for your login, so it will no longer wait for a notebook to spawn. After your teacher has done this, you should relogin, and try to spawn a Jupyter Notebook Server again.
Issues running a Notebook
After opening a notebook, it says 'Kernel starting, please wait' but doesn't proceed and my cells won't run any code.
First, try to restart the kernel. Go to "Kernel => Restart".
If that doesn't help, there are two possibilities.
- Something broke the kernel. This can for example happen if you installed or upgraded software packages that the kernel also uses. The kernel than picks up on your installations, rather than the one from the system. If there proves to be a problem with what you installed, the kernel will fail to start.
- You are running into a known issue with the Safari browser (see e.g. https://discussions.apple.com/thread/251226403). Please switch to Firefox and Google Chrome, these have been shown to work on MacOS.
I'm getting a 500: Internal Server Error when opening any notebook
There is a known issue with the nbconvert package, which causes file permission issues on templates that are generated for nbconvert (see https://github.com/jupyter/nbconvert/issues/1430). This should be resolved with nbconvert version 6.4.0 (which we are running), but we are still seeing issues sometimes. To resolve this, first check which user owns the template directory:
ls -ald $TEACHER_DIR/JHS_installations/Python/share/sjupyter/nbconvert/templates
The 'lcurXXXX' user that is listed there should execute the following command:
find ~/JHS_installations/Python -not -perm -g=rX -exec chmod g+rwX {} \;
Then, notebooks should open again without issues.
How to monitor the amount of CPU /memory used by my Jupyter Notebooks
In your Jupyter Notebook Server, click 'new' and then 'terminal'. In this terminal session, you can run the command htop -u <username>, where <username> is your login name. This shows, for each of your running processes, the CPU usage (100% = 1 CPU core) and memory usage (the 'RES' column).
An image is not being displayed in my Markdown cell
Markdown doesn't support hardcoded paths, e.g. referring to /home/<loginname>/images/my_image.png in a Markdown cell wouldn't work. Thus, specify a relative path instead. E.g. if the notebook is in /home/<loginname>/notebooks/my_notebook.ipynb, the relative path to the image would be ../images/my_image.png (where the '..' means 'one directory up' in the hierarchy).
Error when creating a plot with Matplotlib: "Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure"
You'll need to insert the '%matplotlib notebook' magic in your code before plotting. See Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure
Plots made using the R kernel have poor resolution axes labels / don't respect the selected font family
This is a known issue. See Plotting with the R kernel.
Issues specific to the teacher
My notebooks are not synchronized to the students
Notebooks are synchronized whenever a student starts a Jupyter Notebook Server. Thus, try to shutdown the Jupyter Notebook Server and restart it first (the Student Manual explains how to shutdown and start a Jupyter Notebook Server). If that doesn't help, see Notebooks are not synchronized to students
I have installed additional Python or R packages. I can use them, but my students cannot.
See Python or R packages not available to students
How to enable a notebook extension
See How to enable a notebook extension.
I already have existing notebooks and a data folder that they refer to. Can't I just put all of that in JHL_notebooks?
See subtopic Separate notebooks and data for existing course material