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Clarified conda usage #412

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Clarified conda usage #412

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17 changes: 13 additions & 4 deletions docs/user-guide/python.md
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Expand Up @@ -122,7 +122,7 @@ srun --distribution=block:block --hint=nomultithread python myvenv-script.py

You can check a module's install location and its dependencies with `pip show`, for example `pip show matplotlib`. You may then run `pip uninstall matplotlib` while no virtual environment is active to uninstall it from `$HOME/.local`, and then re-run `pip install matplotlib` while your virtual environment on `/work` is active to reinstall it there. You will need to do this for any modules installed on `/home` that will use either directly or indirectly. Remember you can check all your installed modules with `pip list`.

## Conda on ARCHER2
## Conda on Cirrus

Conda-based Python distributions (e.g. Anaconda, Mamba, Miniconda) are an extremely popular way of installing and
accessing software on many systems, including Cirrus. Although conda-based distributions can be used on Cirrus,
Expand Down Expand Up @@ -182,8 +182,8 @@ contact the [Cirrus Service Desk](mailto:support@cirrus.ac.uk)

#### Install conda on the work file system

To do this, specify an install location
in your directories on the work file system when prompted in the conda installation process.
To do this, specify an install location in your directories on the work file system when
prompted in the conda installation process.

### Conda additions to shell configuration files

Expand Down Expand Up @@ -225,6 +225,11 @@ unset __conda_setup
# <<< conda initialize <<<
```

The effect of not having this section in your `~/.bashrc` is that conda must be initialised
manually and the specific conda environment must be activated before it can be used. The
submission script below shows how this can be done. It can also be done with the same commands
in an interactive shell.


## Running Python

Expand All @@ -245,8 +250,12 @@ unset __conda_setup
# Load the Python module, ...
module load cray-python

# ..., or, if using local virtual environment
# ..., or, if using a python venv with user-installed packages
source <<path to virtual environment>>/bin/activate

# ..., or, if using a conda environment installed on the /work filesystem
eval "$('/work/t01/t01/auser/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
conda activate mycondaenv

# Run your Python program
python python_test.py
Expand Down