Notebook keeps crashing

Post author
Kate Augustyn

Everytime I try to open my notebook for the past 3 days it eventually crashes and gives me this image. It is not an issue with my internet connection because everything else works fine. Does anybody know why this keeps happening? My other notebooks seem to run fine, it is only one of them that I am having trouble with. I also get an error message when trying to preview this same notebook.

Comments

4 comments

  • Comment author
    Josh Evans

    Hi Kate,

    Thanks for writing in! I have a few follow up questions that should help me troubleshoot this issue:

    • Are the other notebooks in the same workspace? 
    • Can you please share a screenshot of the configurations you use for the Cloud Environment these notebooks work with? (You can find this information on the configuration pane that displays before running the environment.)
    • Can you share the workspace you're seeing this issue in with Support? (You can do so by clicking on the three dots in the upper right, selecting share, and then clicking the Share with Support toggle. Please provide a link to your workspace.) 
    • What is the name of the notebook file that you are seeing this issue with? 

    Once we have the answers to these questions, we'll take a look as soon as we can.

    Please let me know if you have any questions.

    Best,

    Josh

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  • Comment author
    Kate Augustyn

    Hi Josh,

    I have two other notebooks in the same workspace. Here is a link to the workspace, and the name of the notebook I am having trouble with is annotation_epithelial.ipynb : https://app.terra.bio/#workspaces/shalek-lab-firecloud/augustyn_PREDICT

    Here is a screenshot of the cloud environment configurations:

     

    Thank you,

    Kate

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  • Comment author
    Josh Evans

    Hi Kate,

    Thanks for the reply! I've taken a look at your workspace and I'm getting the error too when I preview the notebook.  This leads me to believe that the issue could be with the file itself.  I've already opened a request with our engineering team to take a look and see if we can determine the cause.  I'll contact you once we have any updates.

    Please let me know if you have any questions.

    Best,

    Josh

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  • Comment author
    Josh Evans

    Hi Kate,

    I'd like to give you an update on this request. Our engineers took a look and it appears that this file has gotten too large for the system to display it correctly.  We have a few suggestions for how to prevent this moving forward:

    • Download the notebook file onto your computer and remove some of the data that has been added to it.  You can then upload this to the application as either the same or new file name.  If you use the old file name, the existing file will be over written.
    • Create a new file with this code, but have code limit how much output it writes to the file.  This will keep the size down.
    • Create a new file with this code but have it write all of it's output to a secondary file.  This will allow you to retain all of the output without the actual notebook size being affected.

    Please let me know if that information was helpful or if you have any questions.

    Best,

    Josh

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