March '23: The notebooks in this repo are no longer supported with the latest OceanSpy version. To see working, supported versions of these notebooks visit: https://github.com/hainegroup/Poseidon-share

Ocean Sciences 2022 Poseidon tutorial

Repository containing the tutorial notebook run during the Townhall Sesion

TH11 - Open Science Analysis of Petabyte Scale Ocean and Ocean-Atmosphere Models with Open Source Cloud Tools

How to:

You can download the contents of this repository into any machine with internet access and git installed, by executing the following in the command line:

git clone https://github.com/hainegroup/OceanSciences2022.git

To reproduce the results of the tutorial notebooks, they need to be downloaded and executed within Sciserver to access the model data and correct (conda) environment. Furthermore, within Sciserver, the notebooks must run within a container created with the Oceanography 2.3 Compute image, along with access to either the Poseidon (for llc4320) or Ocean Circulation (for ECCO) data volumes.

The folder img/ contains static images used in the notebooks for model-data comparison. The folder needs to be added within the (local) directory as to where the tutorial notebooks are stored, so that within the notebooks img/figure.png sucessfully loads the static images.

LLC90 Tutorial

To run the notebook :

1. Make sure you create a container with Oceanography 2.3 compute image along with Ocean Circulation data volume. You will be redirected into a jupyter lab environment. Navigate to Temporary/user/scratch. This is where you will run the notebook. You can do this simply by clicking and opening these folders. If you're comfortable with working on a terminal , you will have to go to /scratch using the following command
   

cd /home/idies/workspace/Temporary/your_username/scratch/

2. You should have the notebook LLC_90_Sciserver_tutorial.ipynb along with the folders /img and /test_data to successfully reproduce the Ocean Sciences tutorial. If you are comfortable using git you can clone this repo into your /scratch folder. If you have no prior experience with git, simply download this repo and upload the folders into your jupyter lab environment on SciServer. The jupyter lab interface gives you the option to upload files and folders from your local system.

LLC4320 Tutorial

1. Follow the same steps as for the LLC90 tutorial, except make sure that when you create your container, you additionally select the Poseidon data volume.