Bash Quick Start

This page introduces core Bash configuration practices to help users customize their environment effectively. You’ll learn how to manage startup files, use aliases, extend your PATH, and improve your shell productivity with built-in tools.

Understanding Bash Startup Files

When you connect to the cluster, your shell session is initialized based on whether it’s a login or interactive shell:

Login shells (like SSH): Bash looks for and loads the first of these files: ~/.bash_profile, ~/.bash_login, or ~/.profile.
Interactive non-login shells (like opening a terminal or launching bash): Bash loads ~/.bashrc.

To ensure consistent behavior across environments, your .bash_profile should source .bashrc. This is already set by default for users:

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

Because .bashrc is sourced in every interactive shell, place all your personal configurations there — aliases, environment variables, $PATH, and module loads.

Protecting Your $PATH

When adding directories to your PATH, avoid doing so repeatedly in nested shells by using a guard variable:

if [ -z "$CLUSTER_ENV" ]; then
    export CLUSTER_ENV=1
    export PATH="$HOME/bin:$PATH"
fi

This ensures your custom paths are added only once per session.

Aliases: Quick Commands

Aliases are shorthand for longer commands, helping you work more efficiently. For example:

alias ll='ls -lFh'
alias usage='quotas.py'
alias la='ls -a'
alias gpustat='nvidia-smi'

To make these available every time you log in, define them in your ~/.bashrc.

Helpful Customizations

Other useful customizations — like loading modules or setting environment variables — should also go in ~/.bashrc. For example:

module load intel/2020.2
module load gcc/11.2.0

export EDITOR=vim
export PROJECT_SCRIPTS=$HOME/projects/scripts

Example .bashrc Template

# Source system-wide defaults
if [ -f /etc/bashrc ]; then
    . /etc/bashrc
fi

# Prevent re-initializing environment on every subshell
if [ -z "$CLUSTER_ENV" ]; then
    export CLUSTER_ENV=1

    # Extend PATH for custom scripts
    export PATH="$HOME/bin:$PATH"

    # Load frequently used modules
    module load module_xyz

    # Set environment variables
    export EDITOR=vim
    export PROJECT_SCRIPTS=$HOME/projects/scripts

    # Define helpful aliases
    alias ll='ls -lFh'
    alias la='ls -a'
    alias gpustat='nvidia-smi'
    alias usage='quotas.py'
fi

Useful Bash Tricks for HPC Users

History Expansion and Reuse

Repeat the last command:
```
!!
```
Search your command history:
```
history | grep slurm
```

Timing and Logging

Measure how long a command takes:
```
time ./my_script.sh
```
Redirect standard output and error to a single file:
```
./script.sh > script.out 2>&1
```
Append to an existing output log:
```
./script.sh >> script.out 2>&1
```

Monitoring and Usage

Check your running processes:
```
top -u $USER
```
Watch GPU usage in real time:
```
watch -n 2 nvidia-smi
```

Show job efficiency stats (Slurm):

seff <jobid>
reportseff <jobid>
jobstats <jobid>

File Inspection

Preview the top or bottom of a file:

head -n 20 logfile.txt
tail -n 20 logfile.txt

Follow a growing log file in real time:
```
tail -f logfile.txt
```

Testing Your Configuration

To apply changes without logging out:

Use source ~/.bashrc in an active terminal
Open a second terminal to test changes independently

Copy Default Bash Files

If you don’t have a .bashrc or .profile, you can copy the cluster defaults from:

cp /etc/skel/.bashrc ~/.bashrc
cp /etc/skel/.profile ~/.profile

Customize these as needed with your preferred modules, aliases, and paths.

Troubleshooting

Q: Why isn’t my `.profile` being read? Bash loads the first available of the following: .bash_profile, .bash_login, or .profile. Use only one, and ensure it sources .bashrc.

Q: Why is my `$PATH` getting longer and longer? You’re likely appending to it every time .bashrc is sourced. Use a guard variable like CLUSTER_ENV to prevent that.