Merge pull request #87 from MonashDeepNeuron/dev

Dev

Author: linton2000

README.md

@@ -34,6 +34,8 @@ $ mdbook serve --open
 - Jaspar Martin
 - Yuki Kume
 - Osman Haji
+- Duc Thanh Vinh Nguyen
+- Linton Charles
 
 ## Code of Conduct, License & Contributing
 

src/.chapter7/challenges.md

@@ -0,0 +1 @@
+# Challenges

src/SUMMARY.md

@@ -2,15 +2,17 @@
 
 [Welcome](home.md)
 
-- [Getting Started](./chapter1/getting-started.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](./chapter1/m3.md)
+  - [Nectar Cloud](./chapter1/nectar.md)
   - [Challenges](./chapter1/challenges.md)
 
-- [Brief Introduction to C](./chapter2/intro-to-c.md)
+- [Intro to C](./chapter2/intro-to-c.md)
   - [Hello World](./chapter2/helloworld.md)
   - [Compilation](./chapter2/compilation.md)
   - [Types & Variables](./chapter2/vars.md)
@@ -20,34 +22,55 @@
   - [Control Flow](./chapter2/ctrl-flow.md)
   - [Loops](./chapter2/loops.md)
   - [Functions](./chapter2/functions.md)
-  - [Pointers](./chapter2/pointers.md)
-  - [Dynamic Memory](./chapter2/memory.md)
-  - [Structures](./chapter2/structs.md)
-  - [Macros & The Preprocessor](./chapter2/macros.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)
-  - [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)
-  - [Strudel](./chapter3/strudel.md)
+- [Operating Systems](./chapter3/chapter3.md)
+  - [Computer Architecture](./chapter3/computer-architecture.md)
+  - [Pointers & Memory](./chapter3/memory-pointers.md)
+  - [Intro to Linux](./chapter3/linux-intro.md)
+  - [Threading & Concurrency](./chapter3/threads-concurrency.md)
+  - [Processes](./chapter3/processes.md)
+  - [Scheduling Algorithms](./chapter3/scheduling.md)
   - [Challenges](./chapter3/challenges.md)
 
-- [Parallel Computing](./chapter4/chapter4.md)
-  - [What is Parallel Computing?](./chapter4/parallel-computing.md)
-  - [Multithreading](./chapter4/multithreading.md)
-  - [OpenMP](./chapter4/openmp.md)
+- [More C](./chapter4/chapter4.md)
+  - [Dynamic Memory](./chapter4/memory.md)
+  - [Structures](./chapter4/structs.md)
+  - [Macros & The Preprocessor](./chapter4/macros.md)
+  - [System Calls](./chapter4/syscalls.md)
+  - [Spawning Processes & Threads](./chapter4/spawn-procs.md)
   - [Challenges](./chapter4/challenges.md)
 
-- [Distributed Computing](./chapter5/chapter5.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)
+- [M3 & SLURM](./chapter5/chapter5.md)
+
+  - [Batch Processing vs. Cloud Computing](./chapter5/batch-cloud.md)
+  - [Parallel & Distributed Computing](./chapter5/parallel-distributed.md)
+  - [M3 Login - SSH & Strudel](./chapter5/login.md)
+  - [Intro to SLURM](./chapter5/slurm_intro.md)
+  - [M3 Interface & Usage](./chapter5/m3-interface.md)
+  - [Software & Tooling](./chapter5/software-tooling.md)
   - [Challenges](./chapter5/challenges.md)
 
-[Acknowledgements](./acknowledgements.md)
+- [Introduction to Parallel Computing](./chapter6/chapter6.md)
+  - [Multithreading](./chapter6/multithreading.md)
+  - [Synchronisation](./chapter6/synchronisation.md)
+  - [Locks](./chapter6/locks.md)
+  - [Message Passing](./chapter6/message-passing.md)
+  - [Challenges](./chapter6/challenges.md)
+
+- [Parallellisation of Algorithms](./chapter7/chapter7.md)
+  - [Parallel Search](./chapter7/parallel-search.md)
+  - [Parallel Sort](./chapter7/parallel-sort.md)
+  - [Other Parallel Algorithms](./chapter7/other-parallel-algos.md)
+  - [Machine Learning & HPC](./chapter7/machine-learning-and-hpc.md)
+  - [Optimisation Algorithms](./chapter7/optim-algos.md)
+  - [Challenges](./chapter7/challenges.md)
+
+- [Apache Spark](./chapter8/chapter8.md)
+  - [Installation & Cluster Set-up](./chapter8/set-up.md)
+  - [Internal Architecture](./chapter8/internals.md)
+  - [Data Processing](./chapter8/data-processing.md)
+  - [Job Batching](./chapter8/job-batching.md)
+  - [Challenges](./chapter8/challenges.md)
+
+[Acknowledgements](./acknowledgements.md)

src/acknowledgements.md

@@ -8,6 +8,8 @@ This book is part of Monash DeepNeurons collection of technical information and
 - [Osman Haji](https://github.com/Ozzywap)
 - [Yuki Kume](https://github.com/UnciaBit)
 - [Jaspar Martin](https://github.com/jasparm)
+- [Duc Thanh Vinh Nguyen](https://github.com/VincentNguyenDuc)
+- [Linton Charles](https://github.com/linton2000)
 
 ## Contributors
 

src/chapter1/aaf.png

@@ -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.

src/chapter1/hpcid.png

@@ -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.