Error modifying cloud environment - Terra notebook not able to be used

Post author
Sabrina Camp

Hi,

I was trying to start a python 3 kernel jupyter notebook with the "Python" application configuration (us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.4), and the kernel would never start. I then tried to recreate the cloud environment the newer "Python" configuration from the Terra Docker base images github repo (us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.5) and the creation of the environment timed out. Now, whether I try to delete the environment or update to a new configuration, it throws this error. I unfortunately can't use Terra notebooks until this is resolved.

All the best,

Sabrina

Terra account email: scamp@broadinstitute.org

Google Project ID: nci-mxhe-bi-org

Cluster ID: saturn-8131a0f9-0bca-44c9-bc33-6667c68bdefb

Time first occurred: 3:30 PM

The workspace is already shared with support. 

Comments

7 comments

  • Comment author
    Sabrina Camp
    • Edited

    Update: I was able to change the environment by entering a new path to a base image in the Custom Environment container image section.

    However, my issue of the kernel not starting still remains. Here is the configuration! 

    When I switch to the default environment, notebooks with an R kernel work fine. However, the notebooks with a python kernel fail to start

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  • Comment author
    Josh Evans

    Hi Sabrina,

    Thanks for writing in! We were having a known issue with Cloud Environments not deleting correctly after they experienced an error.  This might have been causing some of the issues you're seeing.  My suggestion would be to try to create the environment now, and I'll keep investigating things on my end as well.

    Let me know how that goes.

    Best,

    Josh

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  • Comment author
    Sabrina Camp

    Hi Josh, 

    The kernel for my R Terra notebooks have not been able to start Friday or Today. Is this a known issue or is there a workaround?

     

    Terra account email: scamp@broadinstitute.org

    Google Project ID: nci-mxhe-bi-org

    Cluster ID: saturn-2cc6964d-9e5f-4c51-97ed-53ee14617a6c

    Time first occurred: Friday 2:00 PM

    The workspace is already shared with support. 

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  • Comment author
    Sabrina Camp

    Here is the environment configuration

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  • Comment author
    Josh Evans

    Hi Sabrina,

    Thanks for getting back to me. I have a few follow up questions that will help me find a solution to this issue:

    • Are you getting an error message when you try to start the Cloud Environment? 
    • If this is a pre-existing Cloud Environment, when was it first created?
    • Could you please provide a link to the workspace you've shared with support?

    Please let me know if you have any questions.

    Best,

    Josh

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  • Comment author
    Sabrina Camp

    No problem!

    Its not an error message when I try to start the environment, but when I've copied the notebook into the environment and want to start editing the notebook. It will have a message next to the kernel busy/not busy indicator saying "kernel is starting..." and then it will never start.

    It is working now, so I'm not sure what was happening. 

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  • Comment author
    Josh Evans

    Hi Sabrina,

    I'm glad the Environment is working for you now.  I did some testing by replicating your configuration in by own Workspace, but didn't run into any issues.  Can you provide a link to your workspace and which notebook you were seeing the issue with? I'd like to take a look and see if they are connected.

    Please let me know if you have any questions.

    Best,

    Josh

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