Specialised Environments

Page tree

The following UATs are designed to test some selected libraries contained within the NCI-geophys/23.04 environment.

To run these tests, you will first need to join the following NCI project codes via the mynci portal ( https://my.nci.org.au ):

my80: https://my.nci.org.au/mancini/project/my80

up99: https://my.nci.org.au/mancini/project/up99

qt52: https://my.nci.org.au/mancini/project/qt52

rt52: https://my.nci.org.au/mancini/project/rt52

dk92: https://my.nci.org.au/mancini/project/dk92

iv65: https://my.nci.org.au/mancini/project/iv65

Once you are approved as a member of these projects, you can next log on to Gadi and run the following commands:

$ module use /g/data/up99/modulefiles
$ module load NCI-geophys/23.04
$ cp -r ${NCI_GEOPHYS_ROOT}/UAT ~/

The above commands will copy four Jupyter notebooks to your home directory. To check that these notebooks are available, run:

$ cd ~/UAT
$ ls

and you should see the following Jupyter Notebooks:

Julia_examples.ipynb
Python_examples.ipynb
R_examples.ipynb
Geophysics_data_indexing.ipynb

Now we can exit Gadi and launch a JupyterLab session on the Australian Research Environment (ARE - https://are.nci.org.au ). For more information on ARE, please refer to the ARE User Guide.

First log in to ARE using your NCI user name and password:

Next, click on the JupyterLab app:

To run these examples, let's request:

Walltime (hours): 2
Queue: normalbw
Compute Size: xlarge
Project: <insert a compute project code that you are a member of>
Storage: gdata/my80+gdata/up99+gdata/qt52+gdata/rt52+gdata/dk92+gdata/iv65

Under the “Advanced options…” tab, add in the following Module:

Module directories: /g/data/up99/modulefiles
Modules: NCI-geophys/23.04

Now click the “Launch” tab and your JupyterLab job will join the queue:

Once the JupyterLab is running, click the “Open JupyterLab” tab:

On the left filesystem pane of the JupyterLab session, you will need to navigate to the directory containing the four Jupyter Notebooks that were copied over. Click on the /home folder and search for the UAT subfolder:

This is where you should find the four test Jupyter Notebooks:

Open up Python_examples.ipynb and start running through this Jupyter notebook by clicking the “run selected cells” button in the top panel:

Note that after Cell 21, there is a step that requires you to run an Occam inversion either on Gadi or using JupyterLab. To do this within JupyterLab, open up a Launcher Tab and click on the “Terminal” app:

 

Then follow the steps in the notebook to run the example Occam inversion:

Once this Occam inversion is complete (it should only take a few minutes), please continue running the remaining cells in the Python_examples notebook.

Finally, you can also try running through the R_examples, Julia_examples and Geophysics_data_indexing notebooks:



  • No labels