The behavior you're observing with apptainer run and your custom PS1 in ~/.bashrc is likely due to how Apptainer (formerly Singularity) handles shell initialization and the type of shell it invokes by default.

Here’s why this happens and how to fix it:

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Why PS1 is Not Applied

1. Non-Interactive Shell by Default When you run apptainer run my_debian.sif, Apptainer typically starts a non-interactive, non-login shell inside the container. In such shells, ~/.bashrc is not automatically sourced. However, some parts of your ~/.bashrc (e.g., aliases, functions, or environment variables) may still be applied if they are set in a way that Bash reads them even in non-interactive mode (e.g., via BASH_ENV or explicitly sourced).

2. PS1 is for Interactive Shells The PS1 variable (your shell prompt) is only used by interactive shells. Since Apptainer’s default shell is non-interactive, PS1 is ignored.

3. Login vs. Non-Login Shells

   • If you use apptainer shell my_debian.sif, it starts an interactive shell, and ~/.bashrc (and thus PS1) will be applied.
   • apptainer run does not start an interactive shell by default, so PS1 is not loaded.

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How to Fix It

Option 1: Force an Interactive Shell

If you want your custom PS1 to appear, use apptainer shell instead of apptainer run:

bash
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apptainer shell my_debian.sif

This will give you an interactive shell inside the container, and ~/.bashrc (including PS1) will be sourced.

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Option 2: Explicitly Source ~/.bashrc in apptainer run

If you must use apptainer run, you can force Bash to source ~/.bashrc by passing a command that starts an interactive shell:

bash
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apptainer run --shell /bin/bash my_debian.sif

Or, explicitly source it in your command:

bash
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apptainer exec my_debian.sif bash -c "source ~/.bashrc; your_command"

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Option 3: Set PS1 in a File Sourced by Non-Interactive Shells

If you want PS1 to work even in non-interactive shells (uncommon, but possible), you can set it in a file that Bash reads for non-interactive shells, such as:

• The BASH_ENV environment variable (point it to a file containing PS1).
• The --nv flag in Apptainer to pass your host’s environment.

Example:

bash
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export BASH_ENV=~/.bashrc
apptainer run my_debian.sif

But this is not recommended, as PS1 is meant for interactive use.

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Summary Table

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Key Takeaway: PS1 is for interactive shells. Use apptainer shell or explicitly start an interactive shell if you want your custom prompt. For apptainer run, the shell is non-interactive by design, so PS1 is ignored.