Optional: Conda

Table of Contents

• • Installing Mamba (Conda)
  • Creating the PUEO environment
  • Installing cmake
  • Done

• Last tested: Thursday July 3, 2025 on OSC: Cardinal Cluster
  

  Deprecated

  Seems like environment variables can no longer be set through conda-devenv as promised in the old README, so you should still follow Step 1: install location to set $PUEO_UTIL_INSTALL_DIR. If you figure out how to solve this issue, please submit a PR to edit this page accordingly.

• You can safely ignore Step 2: dependencies if you choose to follow the instructions on this page. That said, Conda is probably more difficult to set up and will incur overhead each time you log in.
• The instruction below is ported from here, which in turn is modified from the old README.

Installing Mamba (Conda)

Remarks

We use Mamba to manage packages and environments instead of Conda to save some disk space, also because it is way faster. It is possible to install Mamba through an existing Anaconda (or Miniconda) installation, but this method is not recommended by Mamba. Consider checking out the Mambaforge (aka Miniforge) distribution to learn more.

1. Download the Mamba installation script through

   wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"

   and install with

   bash Miniforge3-Linux-x86_64.sh

2. Press Enter to proceed to the license page, when prompted with

   ‍Do you accept the license terms? [yes|no]

   Enter yes to agree to the license terms.
3. Press Enter again to install Miniforge to the default location (probably your home directory)
4. When prompted with

   ‍installation finished.
   Do you wish to update your shell profile to automatically initialize conda?
   This will activate conda on startup and change the command prompt when activated.
   If you'd prefer that conda's base environment not be activated on startup,
   run the following command when conda is activated:

   conda config --set auto_activate_base false

   You can undo this by running conda init --reverse $SHELL? [yes|no]

   
   Answer no to finish the installation.
5. Next, follow the prompt on your terminal and activate conda. Assuming that you installed to ${HOME}/ and that you are using the bash shell, you'd enter

   eval "$(${HOME}/miniforge3/bin/conda shell.bash hook)"

   and then you should see (base) popping up in front of your username prompt:

   ‍[jason@cardinal-login03 ~]$ eval "$(${HOME}/miniforge3/bin/conda shell.bash hook)"
   (base) [jason@cardinal-login03 ~]$

   This means the "base" environment has been activated.
6. Next, make mamba available through

   eval "$(mamba shell hook --shell bash)"

7. Next, enter (assuming you installed Miniforge to home)

   mamba shell init --shell bash --root-prefix=~/miniforge3

   in your terminal. You should see a prompt similar to

   ‍Running shell init, which:

   • modifies RC file: "/users/PAS2137/unmovingcastle/.bashrc"
   • generates config for root prefix: "/users/PAS2137/unmovingcastle/miniforge3"
   • sets mamba executable to: "/users/PAS2137/unmovingcastle/miniforge3/bin/mamba"

   The following has been added in your "/users/PAS2137/unmovingcastle/.bashrc" file ...

   This means that mamba has modified your ~/.bashrc.
   Next time you log in, mamba would automatically activate.
8. You can confirm that you have an environment called "base" by entering the command

   conda info --env

   Miniforge also comes with a Python installation, type

   which python

   and you should see a path pointing to miniforge3/bin/python3.
9. Finally, you would want to install conda-devenv through

   mamba install conda-devenv

   You can find the documentation for conda-devenv here.

Creating the PUEO environment

1. We will first create an empty environment:

   mamba create -n pueo_env

   Using vim or any editor, create a text file called pueo.devenv.yml that contains the following:

   name: pueo_env
   channels:
     - conda-forge
     - defaults
    
   dependencies:
     - fftw
     - root

2. Make sure that (base) is active. If not, run

   conda activate base

   Then, create a new environment called pueo_env through

   mamba-devenv -f pueo.devenv.yml

   Attention

   For OSC: Pitzer users:

   • Consider using Cardinal.
   • If you want to run on Pitzer, it is important that you run

     mamba-devenv

     and not conda-devenv or mamba devenv.
     Anything that is not mamba-devenv seems to be exceedingly slow on Pitzer.

   Bug

   You might see a KeyError: envs_dirs. I think it's fine?

3. Activate this new environment pueo_env through

   conda activate peuo_env

   (or mamba activate pueo_env)

Installing cmake

If you are doing this on your own Linux machine, you likely already have cmake; If not, you can usually easily obtain it through your distro's package manager (eg. dnf).

On OSC, cmake is also already installed. To use cmake version 3.25.2, run

module load cmake/3.25.2

and check that the version is activated through

cmake --version

Done

Make sure that the pueo_env environment is actived, and make sure that you cmake is loaded. Next, follow Installing All Things PUEO.