Unable to create cloud environment for jupyter notebook

Post author
Sabrina Camp

Hi!

This morning I have been unable to create a new cloud environment to use for a Terra jupyter notebook. The environment shows it is being created for 10 minutes, and then it times out. I have tried deleting the environment along with the persistent disk and trying again, but I come across the same issue! Cloud environments I created yesterday are still running fine. 

Appreciate any guidance on this,

Sabrina 

Comments

7 comments

  • Comment author
    Samantha (she/her)

    Hi Sabrina Camp,

    Thanks for reaching out. Can you please share a screenshot of the error you are receiving and provide the following details so we can take a closer look at your issue?

    • Terra account email address

    • Google Project ID for workspace, found on the right side of the workspace dashboard
      ​​

    • Cluster ID (visit https://app.terra.bio/#clusters, click Details, and see Name field)

    • Screenshot of your cloud environment configuration (gear icon at the top-right of workspace)

    • Approximate time issue first occurred


    Best,
    Samantha​

     

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  • Comment author
    Sabrina Camp

    Issue started around 10 AM

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  • Comment author
    Samantha (she/her)

    Hi Sabrina,

    It looks like you are using an older version of the terra-jupyter-bioconductor image. I would suggest using the most recent version, which is us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.0.3. You can also just select the R/Bioconductor environment in the dropdown menu:

    Custom environments that extend from an older base image fail to start in time, but using custom dockers that extend from the latest base image version create successfully. The reason being that the latest images are cached so Terra isn't trying to build the environment from scratch.

    Best,

    Samantha

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  • Comment author
    Sabrina Camp

    Hi Samantha,

    I'm using an older base image intentionally. If I always use the most recent image, the packages installed would be newer/different versions which hurts the reproducibility in my research.

    I may be misunderstanding, but are you saying if I use a custom environment from an older base image version it will always time out and be unusable? Is there a workaround for this?

    Best,

    Sabrina

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  • Comment author
    Samantha (she/her)

    Hi Sabrina Camp,

    Sorry for the delayed response.

    I may be misunderstanding, but are you saying if I use a custom environment from an older base image version it will always time out and be unusable?

    Not necessarily - for older images, it depends on how big the difference is from the current cached version. If there is not much of a difference, the cloud environment will get created successfully since it doesn't need to do any extra docker pull. If there is a bigger difference between the versions, there will be more layers to docker pull which can take much longer.

    That said, your concern around reproducibility is very valid and I will bring this up with our engineers to find a solution for. I'll let you know once I have an update.

    Best,

    Samantha

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  • Comment author
    Sabrina Camp

    Hi Samantha,

    This issue did resolve itself last week. However, I am coming across this issue again this week where the environment creation times out. This happens using any custom environment. 

    Is this a known issue?

    Sabrina

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  • Comment author
    Samantha (she/her)

    Hi Sabrina,

    Can you share a screenshot of the error? Have you tried manually deleting your cloud environment/persistent disk and creating a new one?

    Best,

    Samantha

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