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03-Auth-Notebooks-and-Web-Console.md

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Jupyter environment

Custom Kernels

Your Jupyter server has multiple kernels available for use right away. We have preconfigured them with several useful libraries and tools to help users get up and running with common tasks easier. Additionally, we have bundled in Agave CLI and Python SDK into the Bash and Python2 kernels respectively. Both kernels are pre-authenticated with valid Agave auth tokens that you can use to begin interacting with the Agave Platform right away.

Shared file system

Your home directory on the Jupyter server is shared with your sandbox, so you can safely copy data between the two environments quickly and easily.

Web console

Jupyter contains a web terminal that can be used to access your sandbox environment or interact with the Jupyter container itself. To login to your sandbox from the Jupyter web terminal, simply run the following command:

ssh sandbox

Pre-authenticated API access

A valid Agave auth token has been placed on your system for you. If you are using the Bash or Python2 kernels, this token will be picked up automatically and refreshed as needed

Tutorial notebooks

Extras

Inside of the examples directory, you will find several notebooks to help you learn more about the Agave platform, containers, and SciOps. We leave these for you to follow after the tutorial.

Sandbox environment

The sandbox has the following pre-installed:

  • build-essential
  • gfortran

Sample application code

The sample code for this project is already present in ~/funwave-tvd.

Container runtimes

Docker and Singularity are both preinstalled in the Sandbox. Private registries for both container runtimes are hosted on build.tutorial.public.agaveplatform.org. You may authenticate with your Agave credentials.

Agave CLI

The Agave CLI is available in your sandbox ~/src/agave-cli directory. The commands are already present in your environment $PATH.

Shared file system

Your home directory on the Jupyter server is shared with your sandbox, so you can safely copy data between the two environments quickly and easily.

Accessibility

To login to the sandbox from outside the Jupyter server, use the fully qualified domain name. You can obtain valid ssh keys from the ~/.ssh director of your Jupyter server.

ssh -i /path/to/private/key.pem -p 10022 jovyan@$VM_IPADDRESS