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Getting started with the CESM Lab container

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will wieder edited this page Sep 24, 2021 · 13 revisions

The following instructions describe how to download docker, get the CESM-Lab container, and run the CESM-Lab for NEON tower sites.

If you prefer to see a slide deck with more images, see this Docker Tutorial.

Container Basics

CESM-Lab: A containerized environment with CESM + Jupyter Lab

CTSM and CESM typically require computing resources that can be complicated to set up on a personal computer. Now you can easily run CTSM using a container. A container is preconfigured, portable application that can reliably run on any computing infrastructure.

  • How do I get started? The software is available through a Docker container. This tutorial will guide you through setting up the CTSM container, where you will find a separate tutorial on running CTSM at NEON tower sites.
  • Before diving in, we’ll need to install Docker, which we’ll cover next.
  • Some of the instructions also in this tutorial also use basic Linux commands, which you can run on Macs using the Terminal application (in the Utilities folder) or a similar application for PCs, like Windows Command Prompt.
  • Knowledge of Linux is not required for this tutorial. If you are unfamiliar with Linux and would like to know more, there are several online tutorials

1   Download & Install Docker

Docker is available from this website

Follow the instructions to install the Docker Desktop App

  • To access the container, you can interface with Docker using the Desktop App or using a command line
  • Note If you have trouble installing the latest Docker, please try Docker 3.x. Some newer versions of Docker may be incompatible with your operating system.

2   Download the CESM-Lab Container

This only needs to be done one time -- you can keep using this container any time you run NEON simulations. Please note that this step can take a little time as it will download ~5GB of data (time will vary based on internet speed).

2.1   Getting CESM-Lab: using a Linux command-line

  • Mac: find “Terminal” in your Utilities
  • Windows: Run the ‘PowerShell’ from the Start menu

2.2   Download the CTSM Docker Container

In your Terminal or PowerShell window, type:

docker pull escomp/ctsm-lab-2.3-preview

3   Set up a directory for your simulations

These instructions create a new folder 'Simulations' (or whatever name you choose) on your desktop. You may customize the location of the folder.

In your terminal or PowerShell window, type:

mkdir $HOME/Desktop/Simulations

4   Running CESM-Lab on the command line

There are two options for running the container.

The example below walks through the command line option (recommended), but this `Docker Tutorial <https://drive.google.com/file/d/1Zs_SrlpGVlS3KHvFDUVyCGPXOfKgG4_c/view`__ also walks trough using the GUI interface within the Docker App.

This runs the container using an interactive session. Descriptions are included below the command line to help understand what it’s doing.

In your terminal or PowerShell window, type:

docker run -it --rm -p 9999:8888 -v $HOME/Desktop/Simulations:/home/user escomp/ctsm-lab-2.3-preview
  • -it --rm = 'Ease-of-use’ options: interactive & clean-up
  • -p = Port number
  • -v = Directory to mount into the container (first half), and the container’s mount location
  • "escomp/ctsm-..." = Container Image Name

Your terminal screen will show the some text

5   Connecting to CESM-Lab using a browser

Open a new web browser window.

In the search bar type:

localhost:9999

This connects to an interface. Note the ‘9999’ at the end of this number is the same as the beginning of the port in step 4 above. If you launch more than one container at a time, you will need to change the port number

6   Accessing the NEON Tower Simulation Tutorial

Your browser window will open a Jupyter Notebook environment

  • Click on the “tutorials” folder on the left, then
  • Click on the “notebooks” folder.
  • Open the ‘NEON_Tower_Simulation_Tutorial’

Follow the tutorial instructions to run a NEON tower site simulation & explore the data

Note:

  • If you want to access the container again in the future and do not end your session, you can open a web browser and point to the container (Step 5).
  • If you end your session (Step 7) or restart your computer, you can restart the container from Step 4

7   Ending your session

When you are ready to close your session

Identify active sessions by typing the following into terminal. (Note, you may need to open a new terminal window to do this):

docker ps

Once the container ID has been identified, kill the job by typing the following into terminal:

docker kill <session ID>

If the `docker run` command was not run in the background, you might find that you cannot type anything into the open terminal window. Either open a new terminal window to identify and kill sessions, or you can use `ctrl + c` to kill all active sessions.

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