Software

Conda

You can install miniconda under your user according to the instructions on the conda site (either with the bootstrap script or pip), or alternatively initialise your shell using the preinstalled Spack-provided miniconda:

spack load miniconda3
conda init bash
printf "if [ -s ~/.bashrc ]; then\n\tsource ~/.bashrc;\nfi\n" >> ~/.bash_profile

Then re-open a shell as instructed. This should initialise conda, making it available from that point on without the need for a spack load.

It is recommended to install related conda packages for a particular project within their own dedicated conda environment.

GLOBE Claritas

To start the Claritas GUI (in an Apptainer container):

claritas-7.4.1.sif

MATLAB

In a non-graphical environment, matlab will start the commandline interface. e.g. to run a script: .. code-block:: bash

matlab -nodisplay < MATLAB_job.m

The MATLAB GUI can be remotely started with matlab from within the terminal of a FastX, X2Go or otherwise X-enabled session. To force the MATLAB commandline without the GUI, run matlab -nodisplay;

Additional MATLAB Toolboxes are managed centrally and can be requested to be installed.

MATLAB with the relevant toolboxes on klima.uod.otago.ac.nz is also available as an Apptainer container image, for a more self-contained and portable workflow.

MATLAB-R2023a-klima-0.1.sif

NCSTAT

NCSTAT is made available as an Apptainer container.

To run any operators in the NCSTAT suite, prepend the operator and its arguments with the container name, e.g.:

NCSTAT-2.1.sif comp_clim_3d -f=ST7_1m_00101_20012_grid_T_sosstsst.nc -v=sosstsst ....

Not specifying an operator will open a shell within the container.

NCO

spack load nco
nc...

Jupyter

JupyterHub is available at: https://klima.uod.otago.ac.nz/jupyter

Use your University credentials to login.

Jupyter can also be started from within a customised environment (conda, Spack, etc).

In an X session (FastX, X2Go), open a terminal window, and activate the respective environent.

conda activate foo
conda install ipykernel
jupyter notebook

Your Jupyter Notebook instance should open in a browser window. If not, take note of the URL, eg http://localhost:8888/?token=… and copy-paste this in the browser within your X2Go session.

Then when creating a new notebook, make sure to select the conda environment in the ‘kernel’ dropdown.

OpenGrADS

OpenGrADS is distributed as an Apptainer container. To start the container, run:

opengrads_v2.2.1.oga.1.sif

The prompt will change to Apptainer>; You’re now in a shell within the container, where you can run the GrADs binaries. e.g.: grads

Python

By default the system Python will be used; python -V.

spack find python will show you additional installed versions that can be loaded with Spack:

spack load python@<version>
python -V

While you can install pip or conda packages in your local home directory as usual, several optimised python packages may already be installed and available for use via Spack.

spack find ^python@<version> | grep py- will show the list of Spack-installed pip packages available for the given Python version. These can be loaded in a similar way to make them available in python. e.g.

spack load py-numpy ^python@3.9

R

spack load r
R

While you should be able to download additional CRAN packages from within R, several common packages are already installed and available to be loaded with Spack before starting R. See spack find | grep r- to get a list of the installed R packages. These additional packages can be spack-loaded at the same time. e.g.:

spack load r r-units r-sp
R

RStudio Server

RStudio Server can be accessed at https://klima.uod.otago.ac.nz . Use your University credentials to login.

For more flexibility, R Studio can also be launched as a container.