4. Bash Basics

Bash is the shell—the command-line interface you use to interact with your computer or remote systems like Falcon. This guide covers the most common and useful bash commands you’ll need for scientific computing and file management.

4.1. Directory Navigation

pwd — Print Working Directory Shows the full path of the directory you’re currently in.

pwd

This is useful when you get lost and need to know where you are.

cd — Change Directory Move to a different directory.

cd /path/to/directory      # Navigate to an absolute path
cd subfolder               # Navigate to a subfolder in current directory
cd ..                      # Go up one directory level
cd ../..                   # Go up two levels
cd ~                       # Go to your home directory
cd -                       # Go back to the previous directory

ls — List Directory Contents Show what’s in a directory. This command has many useful flags:

ls                         # List files and folders (basic listing)
ls -l                      # Long format (shows permissions, size, date, etc.)
ls -a                      # Show all files (includes hidden files starting with .)
ls -h                      # Human-readable file sizes (KB, MB, GB)
ls -lah                    # Combine flags: long, all, human-readable
ls -lah /path/to/dir       # List contents of a specific directory
ls -lt                     # Sort by modification time (newest first)
ls -lS                     # Sort by file size (largest first)
ls -1                      # List one file per line
ls *.txt                   # List only files matching a pattern

The permissions shown in ls -l look like -rw-r--r--. The first character is the file type (- for file, d for directory), followed by three groups of three characters for owner, group, and others (read/write/execute).

4.2. File Operations

mkdir — Make Directory Create new directories.

mkdir foldername           # Create a single directory
mkdir -p path/to/nested    # Create nested directories (creates parent directories if needed)
mkdir dir1 dir2 dir3       # Create multiple directories at once

cp — Copy Copy files and directories.

cp file1.txt file2.txt     # Copy a file
cp -r folder1 folder2      # Copy a directory and its contents (recursive)
cp file.txt /path/to/dest  # Copy to a different directory
cp *.txt backup/           # Copy all .txt files to a folder

mv — Move or Rename Move files/folders or rename them.

mv old_name.txt new_name.txt    # Rename a file
mv file.txt /path/to/new/location  # Move a file to another directory
mv -i old.txt new.txt            # Ask before overwriting (interactive)
mv folder1 folder2                # Rename a folder

rm — Remove Delete files. Be careful—deletion is permanent!

rm file.txt                # Delete a single file
rm file1.txt file2.txt     # Delete multiple files
rm -i file.txt             # Ask before deleting (interactive/safe)
rm -r folder/              # Delete a folder and all contents (recursive)
rm -rf folder/             # Force delete without asking (be very careful!)

touch — Create an Empty File or Update Timestamp

touch newfile.txt          # Create an empty file
touch existing_file.txt    # Update the modification time without changing content

cat — Concatenate and Display Show file contents or combine files.

cat file.txt               # Display a file's contents
cat file1.txt file2.txt    # Display multiple files
cat file1.txt > combined.txt  # Combine files into a new file
cat file.txt | head -20    # Show first 20 lines (more on pipes later)

head and tail — View Start or End of Files

head file.txt              # Show first 10 lines
head -20 file.txt          # Show first 20 lines
tail file.txt              # Show last 10 lines
tail -f file.txt           # Follow the file (useful for monitoring logs)

4.3. File Search and Filtering

grep — Search Text Find lines matching a pattern.

grep "search_term" file.txt         # Find lines containing search_term
grep -n "term" file.txt             # Show line numbers
grep -i "term" file.txt             # Case-insensitive search
grep -v "term" file.txt             # Invert match (show lines NOT matching)
grep "^start" file.txt              # Lines starting with "start"
grep -r "term" folder/              # Recursive search in folder
grep "pattern" *.txt                # Search multiple files

sed — Stream Editor Edit text in files (or streams). Common uses:

sed 's/old/new/g' file.txt          # Replace all "old" with "new" (s = substitute, g = global)
sed 's/old/new/' file.txt           # Replace only first occurrence per line
sed '5d' file.txt                   # Delete line 5
sed '1,10d' file.txt                # Delete lines 1-10
sed -n '5,10p' file.txt             # Print only lines 5-10
sed -i 's/old/new/g' file.txt       # Edit file in-place (saves changes)
sed 's/old/new/g' file.txt > new.txt # Save to new file instead

wc — Word Count Count lines, words, and characters.

wc file.txt                # Show lines, words, characters
wc -l file.txt             # Count lines only
wc -w file.txt             # Count words only
wc -c file.txt             # Count characters only
wc -l *.txt                # Count lines in all .txt files

find — Search for Files Locate files by name, type, size, etc.

find . -name "*.txt"       # Find all .txt files in current directory and subdirectories
find / -name "file.txt"    # Search entire system (slow!)
find . -type f -name "*.py"  # Find files (-f) with .py extension
find . -type d -name "folder"  # Find directories (-d)
find . -size +10M          # Find files larger than 10MB
find . -mtime -7           # Find files modified in last 7 days

4.4. Text Editors

On remote systems, you’ll often use a terminal text editor. The most common are vi/vim and sometimes emacs or nano. We’ll focus on vim since it’s nearly universal.

Opening Files

vim filename.txt           # Open or create a file
vi filename.txt            # vi (older version of vim)
nvim filename.txt          # neovim (modern vim variant)

Understanding Vim Modes

Vim has two main modes:

Normal mode (command mode): You use keys to navigate and execute commands. This is where you start when you open a file.
Insert mode: You can type text. Press i to enter this mode, Esc to exit.

Essential Vim Commands

Navigate and View:

h, j, k, l          Arrow keys: left, down, up, right
w                   Jump to next word
b                   Jump to previous word
e                   Jump to end of word
0                   Jump to start of line
$                   Jump to end of line
gg                  Jump to start of file
G                   Jump to end of file
nG                  Jump to line n (e.g., 5G goes to line 5)
Ctrl+u              Scroll up half page
Ctrl+d              Scroll down half page
:n                  Go to line n (e.g., :42)

Editing:

i                   Enter insert mode at cursor
I                   Enter insert mode at start of line
a                   Enter insert mode after cursor
A                   Enter insert mode at end of line
o                   Create new line below and enter insert mode
O                   Create new line above and enter insert mode
Esc                 Exit insert mode (back to normal mode)
x                   Delete character at cursor
dw                  Delete word
d$                  Delete from cursor to end of line
dd                  Delete entire line
5dd                 Delete 5 lines
D                   Delete from cursor to end of line (same as d$)
u                   Undo last change
Ctrl+r              Redo (undo the undo)

Copy and Paste (Yank in Vim terminology):

yy                  Yank (copy) entire line
5yy                 Yank 5 lines
yw                  Yank word
p                   Paste after cursor
P                   Paste before cursor

Search and Replace:

/search_term        Search forward for term
?search_term        Search backward for term
n                   Go to next match
N                   Go to previous match
:%s/old/new/g       Replace all "old" with "new" in file
:s/old/new/g        Replace in current line only
:5,10s/old/new/g    Replace in lines 5-10 only

Saving and Exiting:

:w                  Write (save) file
:q                  Quit (only if no unsaved changes)
:q!                 Quit without saving (discard changes)
:wq                 Write and quit
:x                  Write and quit (alternative to :wq)
ZZ                  Write and quit (no colon needed)

A Simple Vim Workflow

Open file: vim myfile.txt
Press i to enter insert mode
Type or edit your text
Press Esc to exit insert mode
Type :wq to save and quit
Press Enter

If you get stuck in Vim:

Press Esc multiple times to ensure you’re in normal mode
Type :q! and press Enter to quit without saving

Other Editors

If vim feels overwhelming, here are alternatives:

nano: Simpler but less powerful. Press Ctrl+X to exit, y to save.
emacs: More complex but very powerful. Press Ctrl+X Ctrl+C to exit.
nvim (neovim): Modern version of vim with better defaults. Most commands are the same.

4.5. Advanced Bash Concepts

Pipes — Chain Commands Together The pipe operator | sends the output of one command as input to another.

cat file.txt | grep "search_term"        # Find lines in a file
cat file.txt | wc -l                     # Count lines in a file
ps aux | grep python                     # Find running Python processes
ls -lah | grep "Jan"                     # List files from January

Redirection — Save Output to Files

command > file.txt                       # Overwrite file with output
command >> file.txt                      # Append output to file
command < input.txt                      # Use file as input
command 2> errors.txt                    # Redirect errors to file
command &> all.txt                       # Redirect output and errors

Wildcards — Match Multiple Files

*.txt                                    # All .txt files
file?.txt                                # file with one character (file1.txt, file2.txt)
file[0-9].txt                           # file with a digit
file[abc].txt                           # file followed by a, b, or c

source — Run Commands from a File Execute a shell script or configuration file.

source ~/.bashrc                         # Load bash configuration
. ~/.bashrc                              # Same as source (dot notation)
source /path/to/script.sh                # Run all commands in a script

This is useful when you change your dotfiles and want to reload them without restarting your terminal.

chmod — Change File Permissions Control who can read, write, and execute files.

chmod u+x script.sh                      # Add execute permission for user
chmod +x script.sh                       # Add execute permission for all
chmod 755 script.sh                      # rwxr-xr-x (common for scripts)
chmod 644 file.txt                       # rw-r--r-- (common for text files)

which and whereis — Find Commands Locate where a command or program is installed.

which python                             # Show path to python executable
which vim                                # Show path to vim
whereis python                           # Show multiple locations

man — Manual Pages Read documentation for commands.

man ls                                   # Read manual for ls
man grep                                 # Read manual for grep
man -k search_term                       # Search manual pages

Press q to exit a manual page.

alias — Create Command Shortcuts Make shortcuts for long commands (usually in your dotfiles).

alias ll='ls -lah'                       # Create shortcut
alias rm='rm -i'                         # Confirm before deleting (safer)
alias mypy='python3'                     # Create alternative name

4.6. Tips for Efficient Bash Usage

Tab completion: Press Tab to auto-complete file names and commands. Press twice to see all options.
Command history: Press Up and Down arrows to recall previous commands.
Search history: Press Ctrl+R and type to search your command history. Press Ctrl+R again to find next match.
Clear screen: Type clear or press Ctrl+L
Stop a running command: Press Ctrl+C
Suspend a process: Press Ctrl+Z (you can resume with fg)
Comment: Lines starting with # are comments and won’t execute

4.7. Common Bash Gotchas

Spaces matter: cd my folder is different from cd myfolder. Use quotes: cd "my folder" or escapes: cd my\ folder

Case sensitive: File.txt and file.txt are different files on Unix/Linux.

Wildcards don’t work in quotes: ls "*.txt" looks for a file literally named *.txt, not all .txt files. Use ls *.txt instead.

The dot is important: ./script.sh runs a script in the current directory. script.sh without ./ searches your PATH.

Quotes matter for variables: echo $VAR expands the variable. echo '$VAR' prints $VAR literally.

4.8. Practice

Try these commands to get comfortable:

mkdir test_folder                        # Create a test folder
cd test_folder                           # Enter it
touch file1.txt file2.txt               # Create two files
echo "Hello world" > file1.txt           # Add content
cat file1.txt                            # View content
cp file1.txt file3.txt                   # Copy it
ls -lah                                  # See all files with details
rm file2.txt                             # Delete one file
cd ..                                    # Go back up
rm -r test_folder                        # Delete the test folder

4.9. Need Help?

Use man command to read documentation
Google the error message
Ask Omar or a colleague
Check your dotfiles for examples of how others use bash