logging-on-linux-slides.qmd

---
title: "Linux Command Line Essentials"
subtitle: "Getting comfortable with the CLI on HPC systems"
format: 
  revealjs:
    theme: [default, slides-custom.scss]
    logo: assets/img/logo/logo.png
    footer: "HPC1: Introduction to High Performance Computing | University of Leeds"
    slide-number: true
    show-slide-number: all
    background-transition: fade
---

## Command Line Interface (CLI)

Aire does not have a GUI (Graphical User Interface) and so you need to interact with it through a CLI.

::: {.fragment}
- CLIs allow us to interact with a computer through text-based commands typed into the command-line
- While GUIs can be simple and intuitive to use, they can make it difficult to reproduce workflows
:::

---

## Why CLI for HPC?


**Reproducibility Issues with GUIs:**

- Sometimes you have to record by hand (or with a screen recording) what sub-options from different menus you used
- Updates to GUIs can make it difficult to find the same menu options
- A workflow with multiple steps can be tedious to repeat for multiple datasets (having to click through multiple layers of menu options for each dataset)


## Why CLI for HPC?

**CLI Benefits:**

- Scriptable and repeatable
- Faster for experienced users
- Works better over remote connections
- Can be automated


---

## Bash Shell

Bash is the default shell on Unix systems like Linux or Mac

::: {.fragment}
**Key Concepts:**

- Shell interprets and executes commands
- Commands follow pattern: `command [options] [arguments]`
- Case sensitive
- Use `man command` to get help
:::

---

## File Systems on Linux

::: {.fragment}
**Navigation Basics:**

- Navigate to your home directory with `cd`
- List the files and directories present with `ls`
- Change to a different directory with `cd path/to/directory`
:::

::: {.fragment}
**Path Types:**

- Absolute path: `/home/username/data`
- Relative path: `../data` or `./scripts`
- Home directory: `~`
:::

---

## Essential Commands

- We don't expect you to memorise these!
- We have included them here for quick and easy reference.

## Essential Commands - Navigation

```bash
pwd          # Print working directory - where am I?
ls           # List files and directories
ls -la       # List with details and hidden files
cd           # Change to home directory
cd /path     # Change to specific directory
cd ..        # Go up one directory level
cd -         # Go back to previous directory
```

::: {.fragment}
**Try it:** Navigate around the file system and see where you are. You might not have any files or folders if you've just created your account!
:::

---

## Essential Commands - Files

```bash
mkdir newdir     # Create directory
cp file1 file2   # Copy file1 to file2
mv oldname new   # Move/rename file
rm filename      # Remove file (be careful!)
rm -r dirname    # Remove directory and contents
```

::: {.fragment}
::: {.callout-warning}
## Be Careful with rm!
The `rm` command permanently deletes files - there's no "recycle bin" on Linux!
:::
:::

---

## Essential Commands - Viewing Files

```bash
cat filename     # Display entire file contents
less filename    # View file page by page (q to quit)
head filename    # Show first 10 lines
tail filename    # Show last 10 lines
head -20 file    # Show first 20 lines
tail -f logfile  # Follow a log file in real time
```

---

## Essential Commands - System Info

```bash
whoami           # Current username
df -h            # Disk usage (human readable)
free -h          # Memory usage
ps               # Running processes
top              # Real-time process viewer
which command    # Location of a command
```

---

## Exercise: Command Practice {.center}

What do the following Linux commands do? How might they be used on the HPC service?

---

## Exercise Questions

::: {.fragment}
- `ls` - ?
:::

::: {.fragment}
- `pwd` - ?
:::

::: {.fragment}
- `mkdir` - ?
:::

::: {.fragment}
- `cp` - ?
:::

::: {.fragment}
- `wget` - ?
:::

::: {.fragment}
- `rm` - ?
:::

---

## Exercise Answers

- `ls` - **List files and directories** (see what's available)
- `pwd` - **Print working directory** (know where you are)
- `mkdir` - **Make directory** (organize your work)
- `cp` - **Copy files** (backup important data)
- `wget` - **Download files from web** (get datasets, software)
- `rm` - **Remove files** (clean up files)

---

## Getting More Help

::: {.fragment}
- `man command` - Manual pages for any command
- `command --help` - Quick help for most commands
- [Linux Cheat Sheet](https://arctraining.github.io/rc-slides/linux101#/cheat-sheet)
- [Introduction to Linux for HPC](https://arctraining.github.io/rc-slides/linux101#/section)
:::

---

## Next Steps {.center}

Now you're ready to work on the command line!

Let's learn about [storage systems on HPC](storage.html)