Using Virtualizarr, Dask and Holoviz to explore NODD data

Author: Rich Signell (Open Science Computing)

We will use the notebook here to explore NODD data using holoviz, then create a virtual dataset using Virtualizarr, and then run an embarrassingly parallel job (construction of references for each file) using Dask, and then also use Dask for parallel data access in Xarray.

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To allow folks to try Coiled, but without signing up, you can use a token I created that expires in one day. To use the token to run COILED, login to the NMFS OpenSpaces 2i2c JuptyerHub with the default environment, open a terminal and type:

coiled login --token af791b1a879e4c0b99a8b7bec850e9a1-1e7144a190114be06abf273052d98640b62cb5fa

I created the named coiled environment by creating a conda environment file that matched the package versions in the JupyterHub default environment, as of 2025-03-21, via this command:

coiled env create --name hackhours-arm --workspace esip-lab --conda hackhours_coiled_env.yml --architecture aarch64

How to download and open the tutorials

Jupyter Hub

  1. Start the Jupyter Hub server <nmfs-openscapes.2i2c.cloud>
  2. Click the orange Open in Jupyter Hub button

Colab

  1. Click the Open in Colab button

Download

  1. Download to your local computer
  2. You will need to have Python and Jupyter Lab installed
  3. Install any needed packages

How to clone the git repository

After cloning, you will need to navigate to the tutorials in the topics-2025 directory.

Never cloned the NMFSHackDays-2025 repo?

cd ~
git clone https://github.com/nmfs-opensci/NMFSHackDays-2025

Have cloned it but need to update? This is going to destroy any changes that you made to the repo to make it match the current state of the repo on GitHub.

cd ~/NMFSHackDays-2025
git fetch origin
git reset --hard origin/main