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Python, R, conda, Jupyter

Python

We provide Python modules (currently only 3.10) with a series of useful packages pre-installed. This python module is actually a conda environment which simply sets the correct shell variables for you. You can also use it as a starting location to create your own environments. The definition file may be found here: /albedo/soft/install_templates/conda/plotting/requirements.yml

If you would like additional globally available python environments, just ask!

R

Similar to the Python, the R modules are also conda environments. The module r/4.2 also includes r-studio, which you can open from the terminal and then use via X.

Conda

Conda is a package manager for Python, R, and Julia software. You can use it on our HPC system by:

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Note that this allows you to install both Python as well as R packages. Full documentation for conda is provided here: https://docs.conda.io/en/latest/ 

A useful cheat sheet for using conda can be found here: https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf

Jupyter

Jupyter is an interactive computing environment which lets you execute notebooks which can mix code, text, graphics, and LaTeX all in a single document. To start a local Jupyter server, ensure that you have Jupyter installed in your currently activated conda environment, and then run:

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The printed output will direct you to a website where you can then open up the Jupyter interface. We  

Singularity

Singularity (now renamed Apptainer) is a containerization software similar to Docker but with several additional security features which make it feasible to use on HPC systems. You can find more information about the software here: https://apptainer.org/docs/user/main/

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