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Recommendations

  1. Use environments (e.g. conda)

  2. Use the parallel file system (i.e. /scratch/<group>/<username>/)

Note that HOME is not a good choice for storing Python packages since

  1. it is not designed for parallel use,

  2. it will very likely lead to quota issues (HOME is limited to 20 GB), and

  3. it causes unnecessary backups of reproducible data.

Self-Learning Mini-Tutorials

Conda

which python

# load module

ml lang

ml Anaconda3

which python

conda create --name myenv python=3.9.5

conda activate myenv # won't work if shell integration hasn't been set up already

# shell integration

conda init

. $HOME/.bashrc # update shell

# or `source $(conda info --base)/etc/profile.d/conda.sh` for immediate + non-permanent

conda activate myenv # works now

which python

conda list

conda install numpy

# so far so good, but where is our environment (and the packages etc.) located?

conda env list

# it shouldn't live in $HOME but on the parallel FS

# how to resolve this?

#     1) provide `--prefix <path>` to `conda create` (and then full path to `conda activate`)

#     2) conda config --add envs_dirs /scratch/<group>/<username>/.conda/envs

#        conda config --add pkgs_dirs /scratch/<group>/<username>/.conda/pkgs

# let's recreate it properly...

conda deactivate myenv

# conda env remove --name myenv .... but let's just rm -rf $HOME/.conda

conda config --add envs_dirs /scratch/pc2-mitarbeiter/bauerc/.conda/envs

conda config --add pkgs_dirs /scratch/pc2-mitarbeiter/bauerc/.conda/pkgs

cat $HOME/.condarc

# (potentially) redo the above....

# then `which python`

Pip (global)

which python

pip # command not found

# load module

ml lang

ml Python/3.9.5

which python

which pip

# note that the default path for global packages etc. is $HOME/.local/lib/python<ver>/site-packages

# to change it we can put the following into our .bashrc

#   export PYTHONUSERBASE=/scratch/<group>/<username>/.local

export PYTHONUSERBASE=/scratch/pc2-mitarbeiter/bauerc/.local

# you might also want to add

export PATH=/scratch/pc2-mitarbeiter/bauerc/.local/bin:$PATH

pip install numpy

ls /scratch/pc2-mitarbeiter/bauerc/lib/python3.9/site-packages

However, if you want/need to use it, we generally recommend to use `pip` within a conda environment!

Poetry

export POETRY_CACHE_DIR=/scratch/pc2-mitarbeiter/bauerc/.pypoetry

# or `poetry config cache-dir /scratch/pc2-mitarbeiter/bauerc/.pypoetry` (config file is here: `$HOME/.config/pypoetry/config.toml`)

poetry new myproject

cd myproject

poetry show # list installed packages

poetry add numpy

poetry show

# how to run something in the environment or use it interactively?

which python # still points to the general one.... WHY?!

python

    import numpy # fails.... WHY?!

poetry run which python

poetry shell

    which python

    python

        import numpy # works within the poetry shell

    exit # leave the shell

# where is the actual virtualenv: `poetry env list --full-path`

Virtualenv (this is not `python -m venv`!)

#virtualenv --python="/usr/bin/python2.6" "/path/to/new/virtualenv/"

virtualenv venv

source venv/bin/activate # activate local virtual environment

which python

pip list

pip install numpy

python

    import numpy # works

    

deactivate # deactivates local virtual environment

python

import numpy # fails (as expected)

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