MonashDeepNeuron · linton2000 · Apr 7, 2024 · Mar 14, 2024 · Mar 19, 2024 · Mar 20, 2024
diff --git a/src/SUMMARY.md b/src/SUMMARY.md
@@ -3,18 +3,16 @@
 [Welcome](home.md)
 
 - [Installation & Set-up](./chapter1/getting-started.md)
-
   - [GitHub](./chapter1/github.md)
   - [Windows](./chapter1/windows.md)
   - [Mac](./chapter1/mac.md)
   - [Linux](./chapter1/linux.md)
   - [WSL](./chapter1/wsl.md)
-  - [M3 MASSIVE]()
-  - [Nectar Cloud]()
+  - [M3 MASSIVE](./chapter1/m3.md)
+  - [Nectar Cloud](./chapter1/nectar.md)
   - [Challenges](./chapter1/challenges.md)
 
 - [Intro to C](./chapter2/intro-to-c.md)
-
   - [Hello World](./chapter2/helloworld.md)
   - [Compilation](./chapter2/compilation.md)
   - [Types & Variables](./chapter2/vars.md)
@@ -27,15 +25,13 @@
   - [Challenges]()
 
 - [Operating Systems]()
-
   - [Components of Linux]()
   - [Memory & IO]()
   - [Processes & Scheduling]()
   - [Threading & Concurrency]()
   - [Inter-Process Communication]()
 
 - [More C]()
-
   - [Pointers](./chapter2/pointers.md)
   - [Dynamic Memory](./chapter2/memory.md)
   - [Structures](./chapter2/structs.md)
@@ -44,50 +40,26 @@
   - [Spawning Processes & Threads]()
   - [Challenges](./chapter2/challenges.md)
 
-- [M3 & SLURM](./chapter3/chapter3.md)
+- [M3 & SLURM](./chapter5/chapter5.md)
 
-  - [Login - SSH & Strudel](./chapter3/login.md)
-  - [Batch vs. Stream Processing]()
-  - [Cluster Architectures]()
-  - [Schedmd's SLURM]()
-  - [M3 Interface & Usage]()
-  - [Job Scripting]()
+  - [Batch Processing vs. Cloud Computing](./chapter5/batch-cloud.md)
+  - [Parallel & Distributed Computing](./chapter5/parallel-distributed.md)
+  - [M3 Login - SSH & Strudel](./chapter5/login.md)
+  - [Schedmd's SLURM](./chapter5/slurm.md)
+  - [M3 Interface & Usage](./chapter5/m3-interface.md)
+  - [Job Scripting](./chapter5/job-scripting.md)
   - [Advanced SLURM]()
-  - [Challenges](./chapter3/challenges.md)
-
-- [Virtualisation & DevOps]()
+  - [Challenges](./chapter5/challenges.md)
 
-  - [VMs & Hypervisors]()
-  - [Containers]()
-  - [Virtual Environments]()
-  - [Application Deployments]()
-  - [DevOps]()
-  - [Configuration Management]()
-
-- [Networking]()
-
-  - [TCP/IP Stack & OSI Model]()
-  - [Application Layer]()
-  - [Transport Layer]()
-  - [Internet & other Layers]()
-  - [Socket Programming]()
-  - [Cyber Security]()
-
-- [Intro to Parallel Computing]()
-
-  - [Concurrent Execution]()
-  - [Driver-Worker Architecture]()
-  - [Global & Local Phases]()
-  - [Data Parallelism]()
-  - [Model Parallelism]()
-  - [Pipeline Parallelism]()
-  - [Synchronisation Issues]()
-  - [Deadlocks]()
-  - [Mutexes & Semaphores]()
-  - [Thread Safety]()
+- [Introduction to Parallel Computing](./chapter8/chapter8.md)
+  - [Multithreading](./chapter8/multithreading.md)
+  - [Synchronisation](./chapter8/synchronisation.md)
+  - [Locks](./chapter8/locks.md)
+  - [Message Passing](./chapter8/message-passing.md)
+  - [Types of Parallelism](./chapter8/parallelism.md)
+  - [Challenges](./chapter8/challenges.md)
 
 - [Parallellisation of Algorithms]()
-
   - [Distributed Databases]()
   - [Parallel Search]()
   - [Parallel Sort]()
@@ -102,10 +74,10 @@
   - [Job Batching](./chapter10/job-batching.md)
   - [Challenges](./chapter10/challenges.md)
 
-- [Being a HPC Member]()
+- [Being a HPC Member](./chapter11/chapter11.md)
 
-  - [Expectations & Leadership]()
-  - [Project Workflow]()
-  - [Academic Supervisors & Papers]()
+  - [Expectations & Leadership](./chapter11/expectations-leadership.md)
+  - [Project Workflow](./chapter11/project-workflow.md)
+  - [Academic Supervisors & Papers](./chapter11/supervisors-papers.md)
 
 [Acknowledgements](./acknowledgements.md)
diff --git a/src/chapter1/aaf.png b/src/chapter1/aaf.png
diff --git a/src/chapter1/hpcid.png b/src/chapter1/hpcid.png
diff --git a/src/chapter1/join_project.png b/src/chapter1/join_project.png
diff --git a/src/chapter3/start.md → src/chapter1/m3.md b/src/chapter3/start.md → src/chapter1/m3.md
@@ -1,22 +1,29 @@
-# Getting Started
+# M3 MASSIVE
+
+MASSIVE (Multi-modal Australian ScienceS Imaging and Visualisation Environment) is a HPC supercomputing cluster that you will have access to as an MDN member. In this page we will set you up with access before you learn how to use it in Chapter 5. Feel free to go through the docs to learn about the [hardware config](https://docs.massive.org.au/M3/m3users.html) of M3 (3rd version of MASSIVE) and it's [institutional governance](https://massive.org.au/about/about.html#governance).
 
 ## Request an account
 
-In order to access M3, you will need to request an account. To do this, follow this link: [HPC ID](https://hpc.erc.monash.edu.au/karaage/aafbootstrap). This should take you to a page this this: 
+In order to access M3, you will need to request an account. To do this, follow this link: [HPC ID](https://hpc.erc.monash.edu.au/karaage/aafbootstrap). This should take you to a page this this:
+
 
-![HPC ID](./imgs/aaf.png)
+![HPC ID](./aaf.png)
 
 Type in Monash, as you can see here. Select Monash University, and tick the Remember my organisation box down the bottom. Once you continue to your organisation, it will take you to the Monash Uni SSO login page. You will need to login with your Monash credentials.
 
-You should now see something like this: ![HPC ID System](./imgs/hpcid.png)
+You should now see something like this: 
+
+![HPC ID System](./hpcid.png)
 
 Once you are here, there are a couple things you will need to do. The first, and most important is to set your HPC password. This is the password you will use to login to M3. To do this, go to home, then click on Change Linux Password. This will take you through the steps of setting your password.
 
 Once you have done this, you can move on to requesting access to the MDN project and getting access to gurobi.
 
 ## Add to project
 
-To request to join the MDN project, again from the Home page click on Join Exiting Project. You should see a screen like this: ![Join Project](./imgs/join_project.png)
+To request to join the MDN project, again from the Home page click on Join Exiting Project. You should see a screen like this: 
+
+![Join Project](./join_project.png)
 
 In the text box type `vf38` and click search. This is the project code for MDN. Then select the project and click submit. You will now have to wait for the project admins to approve your request. Once they have done this, you will be able to access the project. This should not take longer than a few days, and you will get an email telling you when you have access.
 
@@ -47,4 +54,4 @@ cat ~/.ssh/id_ed25519.pub
 
 Then, go to your github account, go to settings, and click on the SSH and GPG keys tab. Click on New SSH key, and paste the key into the box. Give it a name, and click Add SSH key.
 
-You should now be able to clone repos using SSH. To do this, go to the repo you want to clone, but instead of copying the HTTP link, copy the SSH link, and then its regular git cloning.
+You should now be able to clone repos using SSH. To do this, go to the repo you want to clone, but instead of copying the HTTP link, copy the SSH link, and then its regular git cloning.
diff --git a/src/chapter1/nectar-login.png b/src/chapter1/nectar-login.png
diff --git a/src/chapter1/nectar.md b/src/chapter1/nectar.md
@@ -0,0 +1,16 @@
+# Nectar Cloud
+
+The ARDC Nectar Research Cloud (Nectar) is Australia’s national research cloud, specifically designed for research computing. Like with M3, we will set you up with access now before you learn about it in later chapters. [This webpage](https://ardc.edu.au/services/ardc-nectar-research-cloud/) explains what it is if you're curious.
+
+## Connect Monash Account to Nectar Cloud
+To create an [identity](https://medium.com/@ciente/identity-and-access-management-iam-in-cloud-computing-2777481525a4) (account) in Nectar Cloud, all you have to do is login using your Monash student account. Click [this link](https://dashboard.rc.nectar.org.au) to access Nectar's landing page.
+
+You will see the following. Make sure to click "Login via AAF (Australia)".
+
+![nectar](./nectar-login.png)
+
+You will be redirected to enter your Monash credentials after which you will see the Nectar Cloud dashboard for your trial project (your project name will be pt-xxxxx).
+
+## Cloud Starter Series
+
+ARDC has provided [this cloud starter tutorial series](https://tutorials.rc.nectar.org.au/cloud-starter/01-overview) for people new to Nectar Cloud. You should be able to follow these tutorials using your trial project. If you need more SUs (service units aka. cloud credits) in order to provision more cloud resources for MDN-related work, you should message your HPC Lead with that request.
diff --git a/src/chapter11/chapter11.md b/src/chapter11/chapter11.md
@@ -0,0 +1,6 @@
+# Being a HPC Member
+
+Congratulations! You've completed all your technical new recruit training! 
+
+At this point it's important to remember that technical skills are only a part of what's required to succeed as a HPC member. 
+Without good teamwork skills and collaboration practices we will not be able to work together effectively and achieve our goals. To that end, this chapter outlines some basic expectations required of all HPC members along with other non-technical information that you might find useful.
diff --git a/src/chapter11/expectations-leadership.md b/src/chapter11/expectations-leadership.md
@@ -0,0 +1 @@
+# Expectations & Leadership
diff --git a/src/chapter11/project-workflow.md b/src/chapter11/project-workflow.md
@@ -0,0 +1 @@
+# Project Workflow
diff --git a/src/chapter11/supervisors-papers.md b/src/chapter11/supervisors-papers.md
@@ -0,0 +1 @@
+# Academic Supervisors & Papers
diff --git a/src/chapter3/chapter3.md b/src/chapter3/chapter3.md
diff --git a/src/chapter3/imgs/hpcid.png b/src/chapter3/imgs/hpcid.png
diff --git a/src/chapter3/imgs/join_project.png b/src/chapter3/imgs/join_project.png
diff --git a/src/chapter3/linux-cmds.md b/src/chapter3/linux-cmds.md
diff --git a/src/chapter3/shared-fs.md b/src/chapter3/shared-fs.md