Welcome to the EMBER Tutorial 2025

This tutorial will be used as a resource during the 2025 EMBER bootcamp tutorial.

The materials and notebooks in this tutorial is published as a Jupyter book here.

These tutorials are designed as an introduction to running the Community Terrestrial Systems Model (CTSM). Users can begin with the notebooks in the Getting Started directory, which contains:

1. An introduction to CTSM, CESM-Lab, and Git

2. Running CTSM simulations at NEON tower sites

3. Evaluating CTSM at NEON tower sites

We’ll also have opportunities to explore more ProjectExamples which describe how to:

• Plot data

• Make simple code modifications

• Change simulated plant type

• Change model options (eg, FATES)

• Identify how to change model output

Quick Start

Step 1: Open up CESM-Lab

• In your web browser go to https://ctsm-jhub.k8s.ucar.edu

  It will automatically open up a portal to connect to the cloud:

  

• Enter your username and password provided with your tutorial registration

• This should launch a JupyterLab window in your browser.

Step 2: Navigate to tutorials directory

• Click on the EMBER_Tutorial_2025 directory

• Click on the notebooks directory

• Click on the GettingStarted directory

• Click on the 1_GitStarted.ipynb notebook in the sidebar of your JupyterLab window.

Now you’re ready to get started with the first. Let’s get started by following along in the first notebook.

We’ll likely need to update your tutorial repository. To do this

• Click on the Terminal icon to open a terminal window.

Move into the tutorial reopsitory and pull in the updates

cd ~/tutorials/EMBER_Tutorial_2025
git pull

IF you need to get the tutorial repository, you can clone CTSM Tutorial Repository:

• Click on the Terminal icon to open a terminal window (see above).

• If the directory does not already exist (everything should be pre-staged, so you shouldn’t have to do this), run the following command to clone this repository. (Just copy and paste the text below into the terminal window that opens in JupyterLab)

git clone -b EMBER_Tutorial_2025 https://github.com/NCAR/CTSM-Tutorial

Then, run the following command from within CTSM-Tutorial to update.

git pull

This gives you an updated local copy of the material you’ll need for the tutorial

Can you see a new directory on your navigation sidebar called CTSM-Tutorial? (See the left sidebar of your JupyterLab window)

Notebook Table of Contents

• GettingStarted: These notebooks are the building blocks for all additional notebooks.

  • 1_NEON_Simulation_Tutorial.ipynb : This notebook shows how to run a NEON simulation

  • 2_NEON_Simulation_Visualization.ipynb : This notebook shows how to visualize NEON simulation output

• ProjectExamples: These notebooks are project-specific and build upon the GettingStarted notebooks

  • Basic_CTSM-NEON_Plots.ipynb : This notebook shows how to create plots from NEON data, as well as perform time averaging, etc

  • CTSMsp_NEON_fromScratch.ipynb : This notebook focuses on using CTSM with satellite phenology

  • Clone_Case.ipynb : This notebook shares how to clone a case

  • FATES_NEON_fromScratch.ipynb : This notebook works on creating a FATES case from scratch with NEON

  • Plot_flux_climatology.ipynb : This notebook provides climatology plotting examples

  • QuickPlot_CTSM-FATESsp.ipynb : This notebook provides plotting tools for use with FATES run with satellite phenology

  • QuickPlot_CTSM_h0.ipynb : This plots monthly CTSM data

  • QuickPlot_CTSM_spinup.ipynb : This plots CTSM cases that have been spun up

  • customizeCase_PRISM.ipynb : This customizes a case to use PRISM precipitation input data

  • customizeCase_modelFeatures.ipynb : This customizes various model features

  • customizeCase_parameterModifications.ipynb : This notebook provides tools for parameter modifications and takes input that is generated from modifyParameterFile.ipynb

  • modifyParameterFile.ipynb : This notebook modifies a parameter file that can then be used by customizeCase_parameterModifications.ipynb

  • modifySurfdataFile.ipynb : This notebook modifies a surface data file that can then be used by customizeCase_modelFeatures.ipynb

• ContributedNotebooks: These notebooks are contributed by workshop participants who dove further into a particular project.

📚 Resources

CTSM Repository which includes the CTSM Wiki page that has lots of resources, including much of the following:

• CTSM Technical Documentation

• CTSM User’s Guide

• Quickstart Guide for Various Model Configuraions

• Running single-point cases other than NEON

• Running NEON cases with a container – Running CTSM for NEON cases on a laptop

NCAR-NEON paper that overviews this system hand has nice samples of plots. Lombardozzi and Wieder et al 2024 GMD.

CLM5 Overview Paper Lawrence et al. 2019 JAMES

CLM5 Diagnostic plots, from the overview paper.

CLM5 ILAMB page, also from the overview paper.

❓ Questions

For questions about running simulations, please use DiscussCESM Forums:

Containers & Cloud Platforms Forum

CTSM Forum

👍 Acknowledgements

A number of people have been critical to this effort, including:

• Adrianna Foster, Negin Sobhani, Danica Lombardozzi, Will Wieder, Gordon Bonan, & Teagan King who put together tutorial materials.

• Brian Dobbins, who put together the AWS configuration of CESM-Lab;

• Jackie Shuman, Polly Buotte, & Keith Oleson, who tested tutorial materials;

• Erik Kluzek & Bill Sacks, who made CTSM tags needed for running simulations.

• Elizabeth Faircloth and Ryan Johnson who helped with tutorial registration, logistics and webpages; and finally the rest of the

• TSS staff who provided lecture materials and helped answer questions during the tutorial.

This material is based upon work supported by the National Center for Atmospheric Research (NCAR), which is a major facility sponsored by the National Science Foundation (NSF) under Cooperative Agreement No. 1852977. Staff time on this project was also supported by NSF award numbers 2039932, 2031238, 1926413, and 2120804.