Conda init problems

Technical
5

Hi @dkhutch,

On Gadi is preferrable not to run conda init, but rather use an already available conda/micromamba executable and setup (similar to what the conda init command would do). Then add a ~/.condarc file for its configuration.

I would strongly suggest switching to micromamba, which is much faster and has pretty much all the conda functionalities a general user would need.

My suggestion (and my setup on Gadi) is the following:

Micromamba executable

In my ~/.bash_profile I have the following lines:

# >>> mamba initialize >>>
export MAMBA_EXE='/g/data/vk83/apps/base_conda/bin/micromamba';
echo "Initializing 'micromamba' using $MAMBA_EXE"
export MAMBA_ROOT_PREFIX='/scratch/$PROJECT/$USER/micromamba';
__mamba_setup="$($MAMBA_EXE shell hook --shell bash --root-prefix $MAMBA_ROOT_PREFIX 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__mamba_setup"
else
    alias micromamba="$MAMBA_EXE"  # Fallback on help from mamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<

This runs the setup for mircomamba, setting its exe to /g/data/vk83/apps/base_conda/bin/micromamba and its root prefix to /scratch/$PROJECT/$USER/micromamba.

Configuration

micromamba can be configured with a ~/.condarc file.
I suggest something similar to:

auto_activate_base: false
envs_dirs:
  - $MAMBA_ROOT_PREFIX/envs
pkgs_dirs:
  - $MAMBA_ROOT_PREFIX/pkgs
conda-build:
  root-dir: $MAMBA_ROOT_PREFIX/bld
channels:
  - accessnri
  - conda-forge
  - nodefaults
changeps1: true

Micromamba alias (optional)

If you want to alias micromamba with something different or shorter, you can add an alias in your ~/.bashrc file. For example, I have it aliased to mamba:

alias mamba='micromamba'

Conda

A very similar approach could be done with conda if needed. The only reason to also need conda I think is being able to build conda packages using conda build.
In this case, the following can be added to the ~/.bash_profile after the micromamba setup above:

# >>> conda initialize >>>
export CONDA_EXE=/g/data/xp65/public/apps/med_conda/bin/conda
echo "Initializing 'conda' using $CONDA_EXE"
__conda_setup="$($CONDA_EXE shell.bash hook --root-prefix $MAMBA_ROOT_PREFIX 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "$CONDA_EXE" ]; then
        . "$(dirname $(dirname $CONDA_EXE))/etc/profile.d/conda.sh"
    else
        export PATH="$(dirname $CONDA_EXE):$PATH"
    fi
fi
# <<< conda initialize <<<

In this case, I would keep the same ~/.condarc configuration and make sure to only use conda to build packages, and micromamba for all the rest.

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