# conda and mamba on Rackham@UPPMAX, Dadel@PDC

:::danger
**Note: the following instructions do not apply for Bianca!**
:::

In case you insist using conda from the module system, please follow these instructions. [Conda - best practices @ UPPMAX](/yfd4YuTEQWGvZsanzFUbsw)

If you experience unexpected problems with the `conda` provided by the module system on Rackham or `anaconda3` on Dardel, you can easily install your own and maintain it yourself.

:exclamation:**Important: Please, install `miniforge3` or `miniconda3` in your project folder!**:exclamation:

Home folders at UPPMAX have 32GB (25GB on Dardel) which is rather limited storage space for most common conda installations.

:exclamation:**Important: Please, install `miniforge3` or `miniconda3` in your project folder!**:exclamation:

1. Take some precautions by (re)moving the `.conda` directory and `.condarc` in your home folder if you had ones from previous use. Look in your `~/.bashrc` and remove leftovers from other conda installations. Delete everything between `## >>> conda initialize >>>` and `## <<< conda initialize <<<` including these two lines. Remove any exports related to conda i.e. VARIABLES starting with `CONDA_`
2. Install `miniforge3` https://github.com/conda-forge/miniforge
Download the installation media, run the installation, read and accept the user agreement, and redirect the installation to your project folder, preferably in `/proj/naiss2023-XXX-XX/nobackup/miniforge3`. **Choose to initialize the shell.**

    # Navigate to your project folder
    cd /proj/naiss2023-XXX-XX/nobackup
    
    # Download the installation file
    wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
    
    # Start the interactive installation
    sh Miniforge3-Linux-x86_64.sh
    
    # ... or non-interactive  
    # sh Miniforge3-Linux-x86_64.sh        -b -p /proj/naiss2023-XXX-XX/nobackup/miniforge3
    ...

- Logout and login again to pickup the new `conda` setup, then disable the auto activation of the base environment. Working from the conda base environment might interfere with the software modules provided by the computer center.

    (base) conda config --set auto_activate_base false

- Logout and login again to get the final setup active.
3. Check that `conda` works

    # Check where is conda
    which conda
    /proj/naiss2023-XXX-XX/nobackup/miniforge3/condabin/conda
    
    # Activate base environment
    conda activate
    
    # Display a health report for your environment.
    (base) conda doctor
    Environment Health Report for: /proj/naiss2023-XXX-XX/nobackup/miniforge3
    1. Missing Files:
    ✔ There are no packages with missing files.
    2. Altered Files
    ✔ There are no packages with altered files.

4. Check

    # Activate base environment
    conda activate
    
    # Check the output from mamba -V
    (base) mamba -V
    mamba 1.5.0
    conda 23.7.3
    
    (base) mamba info

5. OPTIONAL: Define `CONDA_ENVS_PATH` if you want to specify different location than the default miniconda3/miniforge3 sub-folder for the new conda environments.

    # Add the line bellow in your $HOME/.bashrc
    export CONDA_ENVS_PATH=/proj/naiss2023-XXX-XX/user/CONDA_ENVS
    mkdir -p $CONDA_ENVS_PATH  

## Advantages and disadvantages of user/project installation
### Advantages:
- **Full control over the installation**.
- **No specific setup** i.e. one can follow the regular installation instructions provided by developers.
- Environments will be installed in subfolder of the installation i.e. in your project folder.
- **Faster solutions** for installations - conda does not have to search through all available indexes Rackham but only the one you provide.
- You can install in the `(base)` environment (although not a good practice).

### Disadvantages
- **:point_right: You need to maintain the installation** - setup, cleaning cache, update, etc.
- Not applicable solution for isolated clusters like Bianca.

## If you insist on using conda from the module system

[Conda - "best practices" - UPPMAX](https://hackmd.io/@pmitev/module_conda_Rackham)

## Beyond conda and mamba
- Alternatively, this might be more than enough to get you working - [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html)
- Tired of conda - try [pixi](https://pixi.sh/latest/) - faster, python independent package manager and more utilizing the conda packaging ecosystem.
- [7 Reasons to Switch from Conda to Pixi](https://prefix.dev/blog/pixi_a_fast_conda_alternative)
- [What is the difference with `conda`, `mamba`, `poetry`, `pip`](https://pixi.sh/latest/FAQ/#what-is-the-difference-with-conda-mamba-poetry-pip)
- > just my personal opinion 🤏🧂: I hope this or similar project becomes more popular or standard...

## Troubleshooting conda provided on Rackham
- If it complains - it is time to clean the mess.
- Look in your `~/.bashrc` for conda configuration and remove these lines - if uncertain - copy them in another file, for safety...

  # >>> conda initialize >>>
  # !! Contents within this block are managed by 'conda init' !!
  __conda_setup="$('/xxxxx/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
  if [ $? -eq 0 ]; then
      eval "$__conda_setup"
  else
      if [ -f "/xxxxx/conda.sh" ]; then
          . "/xxxx/etc/profile.d/conda.sh"
      else
          export PATH="/xxx/bin:$PATH"
      fi
  fi
  unset __conda_setup
  # <<< conda initialize <<<

- **run `conda init --reverse` to reverse the damage. This is problematic only on Rackham and Bianca, where this is not the correct way to activate conda.**
- logout and login again.

## Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uppmax.uu.se/)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)

###### tags: `UPPMAX`, `PDC`, `conda`, `mamba`