8  Bonus: Customizing your shell

Learning Objectives:
Customize your shell

There are a number of ways you can customize your shell to make working at the command line easier. These involve editing two hidden files that reside in your home directory: .bashrc and .bash_profile

If you went through the chapter on software installation and installed conda, you will already have .bashrc, but you may not have .bash_profile.

Log in to Xanadu and check to see if either exist with ls -a to list all files (including hidden ones) in your home directory. If you don’t have them, create them with:

touch .bashrc .bash_profile

If you’ve installed conda, you will already have this mess in your .bashrc (it initializes conda on login):

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/FCAM/nreid/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/FCAM/nreid/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/FCAM/nreid/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/FCAM/nreid/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

Don’t touch this. You can add any of the things we discuss above that section.

8.0.1 Customizing your prompt

Probably at the moment when you log in your prompt looks like this:

-bash-4.2$

But you can change this. My prompt looks like this (but with some color and bolding added):

[ username@hostname ] ~ [ current working directory ] $

Or specifically on login:

[ nreid@hpc-ext-1 ] : [ ~ ] $

I like this because it tells me which node I’m on (login node 1) and which directory I’m working in (my home directory). If I have a few terminal windows open, it helps keep me oriented.

To create a custom prompt, you simply need to set an environment variable called PS1. This variable is read by the shell as the prompt configuration. To get the prompt above, add the following line to .bashrc:

PS1="\[\033[01;32m\][ \u@\h ]\[\033[37m\] : \[\033[01;36m\][ \W ] \[\033[01;37m\]\$\[\033[00m\] "

If you want to get rid of the color and bolding:

PS1="[ \u@\h ] : [ \W ] \$ "

If you want to get crazy with emojis, all unicode characters are available.

For more details on customizing your prompt, check this website

NOTE: To test any of these modifications, simply paste them in at the prompt and hit enter. They will take effect immediately, but will not persist when you kill this shell.

8.0.2 Aliasing common commands

There may be commands you find yourself typing out many, many times. You can create aliases for these commands to ease the typing burden.

The syntax is:

alias shortcommand='longcommand --option1 --option2 --option3'

I use a few. This gives the long directory listing with file sizes in human readable format:

alias ll='ls -lh'

This does the same thing, but sorts by modification time and prints the first N lines (you must supply N):

alias lth='ls -lth | head -n'

Used like lth 20.

I use these for navigation:


alias ..='cd ..'
alias ...='cd ../../'
alias ....='cd ../../../'

I alias a few directories like this:

alias ebp="cd /core/projects/EBP/CBC/"

And I have a few slurm commands aliased:

# for more detailed node status info:
alias sf='sinfo --format="%10P %6t %15O %15C %15F %10m %10e %15n %30E %10u"'
# to do squeue, but print *only* my jobs:
alias sqm="squeue -u ${USER} -o \"%.12i %.9P %.30j %.8u %.2t %.10M %.6D %R\" -S i"

Two cautions about aliases:

  1. They won’t be present on other machines or accounts. If you get used to them and they aren’t there, it can be an irritation.
  2. Don’t use them in code that other people might need to run. They won’t have your peculiar aliases.

8.0.3 .bash_profile

The above edits to .bashrc will change the prompt in interactive sesssions, but not in login sessions or batch jobs, so we also need to add the following lines to .bash_profile (which you should create if you don’t have):

if [ -f $HOME/.bashrc ]; then
        source $HOME/.bashrc
fi

Now, if you log out and log back in, you should see your changes take effect.

8.0.4 Your local machine

You can make all these changes on your local machine as well (though some of them will only make sense on the cluster).