MonashDeepNeuron · oraqlle · Apr 16, 2023 · Mar 18, 2023 · Mar 19, 2023 · Mar 20, 2023
diff --git a/README.md b/README.md
@@ -27,8 +27,11 @@ $ mdbook serve --open
 
 - Tyler Swann
 - Ankita Gosavi
-- Nikhil Kannachel
 - Mitchell Mibus
+- Nikhil Kannachel
+- Jaspar Martin
+- Yuki Kume
+- Osman Haji
 
 ## Code of Conduct, License & Contributing
 

diff --git a/src/SUMMARY.md b/src/SUMMARY.md
@@ -2,47 +2,48 @@
 
 [Welcome](home.md)
 
-- [Getting Started](./chapter1/chapter1.md)
+- [Getting Started](./chapter1/getting-started.md)
+  - [GitHub](./chapter1/github.md)
   - [Windows](./chapter1/windows.md)
   - [Mac](./chapter1/mac.md)
   - [Linux](./chapter1/linux.md)
   - [WSL](./chapter1/wsl.md)
-  - [GitHub](./chapter1/github.md)
-  - [M3](./chapter1/m3.md)
+  - [Challenges](./chapter1/challenges.md)
 
 - [Brief Introduction to C](./chapter2/intro-to-c.md)
   - [Hello World](./chapter2/helloworld.md)
-  - [Header & Source Files](./chapter2/files.md)
-  - [Compilers & Linkers](./chapter2/compiler.md)
+  - [Compilation](./chapter2/compilation.md)
   - [Types & Variables](./chapter2/vars.md)
+  - [Printing](./chapter2/printing.md)
+  - [Arrays & Strings](./chapter2/array.md)
   - [Control Flow](./chapter2/ctrl-flow.md)
   - [Loops](./chapter2/loops.md)
   - [Functions](./chapter2/functions.md)
-  - [Arrays & Strings](./chapter2/array.md)
-  - [Pointers & Memory](./chapter2/memory.md)
+  - [Pointers](./chapter2/pointers.md)
+  - [Dynamic Memory](./chapter2/memory.md)
   - [Structures](./chapter2/structs.md)
   - [Macros & The Preprocessor](./chapter2/macros.md)
-  - [The Standard Library](./chapter2/stdlib.md)
   - [Challenges](./chapter2/challenges.md)
 
 - [M3](./chapter3/chapter3.md)
+  - [Getting Started](./chapter3/start.md)
   - [Logging In](./chapter3/login.md)
   - [Linux Commands](./chapter3/linux-cmds.md)
-  - [Compiling](./chapter3/compiling.md)
   - [M3's Shared Filesystem](./chapter3/shared-fs.md)
+  - [Software and Tooling](./chapter3/software-tooling.md)
   - [Bash Scripts](./chapter3/bash.md)
   - [Job batching & SLURM](./chapter3/slurm.md)
   - [Challenges](./chapter3/challenges.md)
 
 - [Parallel Computing](./chapter4/chapter4.md)
   - [What is Parallel Computing?](./chapter4/parallel-computing.md)
-  - [Shared Memory Resources](./chapter4/shared-memory.md)
   - [Multithreading](./chapter4/multithreading.md)
   - [OpenMP](./chapter4/openmp.md)
   - [Challenges](./chapter4/challenges.md)
 
 - [Distributed Computing](./chapter5/chapter5.md)
-  - [What is Distributed Computing](./chapter5/distrubuted-computing.md)
+  - [Refresher on Parallelism](./chapter5/parallel-refresher.md)
+  - [What is Distributed Computing](./chapter5/distributed-computing.md)
   - [Message Passing](./chapter5/message-passing.md)
   - [OpenMPI](./chapter5/openmpi.md)
 

diff --git a/src/acknowledgements.md b/src/acknowledgements.md
@@ -1 +1,15 @@
 # Acknowledgements
+
+This book is part of Monash DeepNeurons collection information and training resources. It is built and maintained internally by members of Monash DeepNeuron.
+
+## Authors
+
+- [Tyler Swann](https://github.com/oraqlle)
+- [Osman Haji](https://github.com/Ozzywap)
+- [Yuki Kume](https://github.com/UnciaBit)
+- [Jaspar Martin](https://github.com/jasparm)
+
+## Contributors
+
+- [Mitchell Mibus](https://github.com/mmib0001)
+- [Ankita Gosavi](https://github.com/ankitaagosavi)
diff --git a/src/chapter1/challenges.md b/src/chapter1/challenges.md
@@ -0,0 +1,35 @@
+# Challenges
+
+As you progress through each chapter you will be given a small set of challenges to complete. In order to complete the challenges there is a complementary GitHub template repository found on the Monash DeepNeuron GitHub organisation called [HPC Training Challenges](https://github.com/MonashDeepNeuron/HPC-Training-Challenges). As a template you are able to create your own copy of the repository and complete the challenges completely independent of the other recruits.
+
+## Setting Up Challenges Repository
+
+To get setup:
+
+- Click the link above to go to the repository on GitHub.
+- Click 'Use this template' button (green) and select 'Create a new repository'.
+- Give it a name and make sure it is private.
+- Click 'Create repository from template'.
+- This will open the page for the repository. Click the '<> Code' button (green), make sure you are in the HTTPS tab and copy the link.
+- Open a terminal in your dev directory.
+- Run:
+
+```sh
+git clone <repo-link>
+code <repo-name>
+```
+
+And thats it, you can now edit any of the files and complete the challenges. When you want to save your changes to GitHub simply add them and push to them to GitHub.
+
+```sh
+git add .  # Add any untracked or modified files
+git push origin  # Push to GitHub
+```
+
+> **Note:** Look at the README.md of the repo for the for more instructions.
+
+## Challenges Repository
+
+The challenges repository is broken down into different directories for each chapter. For each chapter their will be a series of additional directories corresponding to the specific challenge. These will contain any and all the resources needed for the challenge except programs that you are required to complete.
+
+<!-- For some of the challenges, GitHub will have some automatic tests that run when you push your changes back up to GitHub. -->
diff --git a/src/chapter1/chapter1.md b/src/chapter1/chapter1.md
diff --git a/src/chapter1/getting-started.md b/src/chapter1/getting-started.md
@@ -0,0 +1,3 @@
+# Getting Started
+
+In this chapter you'll setup some essential software tools that you will be using throughout your training. Note that some sections are specific to particular platform and devices. Only complete the section that is specific to your platform. The GitHub section you must complete no matter which platform you are on.
diff --git a/src/chapter1/github.md b/src/chapter1/github.md
@@ -1 +1,23 @@
 # GitHub
+
+## Git. What is it?
+
+Git is a Source Control Management tool (SCM). It keeps a history of multiple files and directories in a bundle called a repository. Git tracks changes using save points called commits. Commits use `.diff` files to track the difference in files between commits. Repositories can have multiple branches allow many different developers to create new changes and fixes to a codebase that are separate from each other. You can also switch between branches to work on many different changes at once. These branches can then later be merged back together to a `main` branch, integrating the various changes.
+
+## What is GitHub?
+
+GitHub is a remote Git service. This allows you to store Git repositories online so that individuals and teams can access and work on Git repositories and projects remotely. It offers many features on top of basic version control such as branch, issue and feature tracking, releases, CI/CD pipelines, project management and more. Its predominately used through its website which offers control of these features through a simple GUI. Throughout your time at Monash DeepNeuron, university and probably for the rest of your career (if in a software based role), you will use service like GitHub to help management the development of projects.
+
+Your first task is to sign up for a GitHub account, if you haven't already. I would highly recommend using a personal email address (not a university one) as you will most likely want access to your account after university.
+
+[GitHub - Join](https://github.com/join)
+
+It is also a good idea to install the GitHub mobile app. This allows you track and manage projects and reply to messages and issues from your phone.
+
+## Joining Monash DeepNeuron's GitHub Organisation
+
+Once you have signed up for GitHub, you will need to provide your instructors with your GitHub username. This is so we can invite you as a member of the Monash DeepNeuron's organisation on GitHub. This will give you access to projects and allow you to communicate with other members. This will also allow you to gain specific privileges for your future projects at Monash DeepNeuron. You're invitation to the organisation will be sent via the email used for your account.
+
+## Watching Repositories
+
+GitHub allows you 'watch' repositories. This means you'll be notified of changes to the repository so that you can keep on top of is happening with various projects. You'll be using this later in your training.
diff --git a/src/chapter1/linux.md b/src/chapter1/linux.md
@@ -1 +1,56 @@
 # Linux Setup
+
+For your training you will need a few tools. Namely:
+
+- Git
+- C compiler toolchain (GCC)
+- A text editor (VSCode)
+
+ For this section I will be assuming a Debian system, namely Ubuntu. Replace `apt` commands with your distributions relevant package manager.
+
+## Installing Packages
+
+To begin, you will need to install some packages. This will be done using `apt`, Ubuntu's system package manager. Run the commands in the shell.
+
+```sh
+# `sudo` represents 'super user do'.
+
+# This runs a command with admin. privileges.
+# Update apt's local package index.
+sudo apt update
+
+# The `-y` flag means upgrade yes to all.
+# This bypasses confirming package upgrades.
+# Upgrade packages with new versions
+sudo apt upgrade -y
+
+# Installs specified packages (separated by spaces).
+sudo apt install git curl wget build-essential
+```
+
+And that's it. Linux is setup and installed.
+
+## Connect Git & GitHub
+
+Next we will link your GitHub account to you local Git install. Run the following commands, replacing the username and email section with your details (keeping the quotation marks).
+
+```sh
+git config --global user.name "<github-username>"
+git config --global user.email "<github-email>"
+```
+
+## VSCode Installation and Setup
+
+Now that GCC is installed and setup we will want to setup a text editor so we can easily edit and build our programs. For your training, I recommend using VSCode as it allows you to customize you developer environment to your needs. If you prefer another editor such as Vim, Emacs or Neovim, feel free to use them as you please.
+
+First download VSCode for Linux [VSCode Download](https://code.visualstudio.com/download)
+
+Once installed, open the app and navigate to the extensions tab (icon on the left size made of four boxes). Using the search bar, install the following extensions.
+
+- C/C++
+- GitLens
+- Git Graph
+- GitHub Pull Requests and Issues
+- Sonarlint
+
+And thats it, you are all setup.
diff --git a/src/chapter1/m3.md b/src/chapter1/m3.md
diff --git a/src/chapter1/mac.md b/src/chapter1/mac.md
@@ -1 +1,45 @@
 # Mac Setup
+
+For your training you will need a few tools. Namely:
+
+- Xcode
+- Git
+- C compiler toolchain (GCC)
+- A text editor (VSCode)
+
+## Installing Xcode, Git & GCC
+
+First, we will need Xcode command line tool utilities, to do so, open the 'Terminal' app and run the following command:
+
+```sh
+xcode-select --install
+```
+
+This will prompt you to accept the install and will download Git and GCC onto your device. To verify installation was successful, run:
+
+```sh
+$ xcode-select -p
+
+# Should print this
+/Library/Developer/CommandLineTools
+```
+
+> **Note:**
+>
+> Here, `$` indicates the prompt of the terminal. Do not include it in the command. This may be a different symbol on your device.
+
+## VSCode Installation and Setup
+
+Now that Homebrew, Xcode and GCC are installed and setup we will want to setup a text editor so we can easily edit and build our programs. For your training, I recommend using VSCode as it allows you to customize you developer environment to your needs. If you prefer another editor such as Neovim, feel free to use them as you please.
+
+First download VSCode for Mac [VSCode Download](https://code.visualstudio.com/download)
+
+Once installed, open the app and navigate to the extensions tab (icon on the left size made of four boxes). Using the search bar, install the following extensions.
+
+- C/C++
+- GitLens
+- Git Graph
+- GitHub Pull Requests and Issues
+- Sonarlint
+
+And thats it, you are all setup.
diff --git a/src/chapter1/taskmanager.png b/src/chapter1/taskmanager.png
diff --git a/src/chapter1/windows.md b/src/chapter1/windows.md
@@ -1 +1,50 @@
 # Windows Setup
+
+For your training you will need a few tools. Namely:
+
+- Git
+- C compiler toolchain (MSVC)
+- A text editor (VSCode)
+
+## Installing Git
+
+First, you will need to install Git. This allows you to use Git from the terminal and also gives you access to a bash shell environment. While following the install wizard, make sure to select the option that adds Git to your `PATH`. This important as it allows you to use Git in 'PowerShell'. Keep the other default operations. Git may require you to restart you machine.
+
+[Git Download](https://git-scm.com/downloads)
+
+### Connect GitHub
+
+Once Git has installed, open a new 'Git Bash' that was installed. This can be found in the Windows 'Start' menu. Once it is open, run the following commands, replacing the username and email section with your details (keeping the quotation marks).
+
+```sh
+git config --global user.name "<github-username>"
+git config --global user.email "<github-email>"
+```
+
+## Installing MSVC
+
+Next we will need to install a C compiler toolchain. There a many different environments such as CygWin, MinGW but the most ideal environment is Microsoft's official development environment, MSVC. Download the Community Edition of Visual Studio and launch the installer. Under the 'Workloads' tab of the installer select the 'C++ Build Tools' bundle and click install. This may take a while. Once installed (may require restart) open the 'Start' menu and navigate to the 'Visual Studio' folder. There should a variety of different terminal environment applications. This is because Windows has slightly different toolchains and environments for x86 (32-bit) and x86_64 (64-bit). Select the 'Developer Command Prompt for VS 2022' app. In the terminal that spawns, run the command.
+
+```cmd
+cl
+```
+
+This will display the help options for `cl`, Window's C compiler.
+
+[Download MSVC](https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019)
+
+## VSCode Installation and Setup
+
+Now that MingW and GCC are installed and setup we will want to setup a text editor so we can easily edit and build our programs. For your training, I recommend using VSCode as it allows you to customize you developer environment to your needs. If you prefer another editor such as Neovim, feel free to use them as you please.
+
+First download VSCode for Windows [VSCode Download](https://code.visualstudio.com/download)
+
+Once installed, open the app and navigate to the extensions tab (icon on the left size made of four boxes). Using the search bar, install the following extensions.
+
+- C/C++
+- GitLens
+- Git Graph
+- GitHub Pull Requests and Issues
+- Sonarlint
+
+And thats it, you are all setup.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		# Getting Started

		In this chapter you'll setup some essential software tools that you will be using throughout your training. Note that some sections are specific to particular platform and devices. Only complete the section that is specific to your platform. The GitHub section you must complete no matter which platform you are on.