Merge pull request #159 from chpc-tech-eval/tut4/release

Tut4/release
chpc-tech-eval · Jul 11, 2024 · fccdcb8 · fccdcb8
2 parents a37d029 + 1ceba8b
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diff --git a/README.md b/README.md
@@ -198,8 +198,7 @@ You will be evaluated on your overall progress in the tutorials. Below you will
 1. [WirGuard VPN Cluster Access](tutorial2/README.md#wirguard-vpn-cluster-access)
 1. [ZeroTier](tutorial2/README.md#zerotier)
 
-**Tutorial 3** will demonstrate how to configure, build, compile and install a number of applications. You will also be building these applications with different tools. Finally, you will learn how to run applications across your cluster.
-
+**Tutorial 3** will demonstrate how to configure, build, compile and install a number of various system software and applications. You will also be building these applications with different tools. Finally, you will learn how to run applications across your cluster.
 
 1. [Checklist](tutorial3/README.md#checklist)
 1. [Managing Your Environment](tutorial3/README.md#managing-your-environment)
@@ -221,39 +220,67 @@ You will be evaluated on your overall progress in the tutorials. Below you will
 1. [Application Benchmarks and System Evaluation](tutorial3/README.md#application-benchmarks-and-system-evaluation)
     1. [GROMACS (ADH Cubic)](tutorial3/README.md#gromacs-adh-cubic)
     1. [LAMMPS (Lennard-Jones)](tutorial3/README.md#lammps-lennard-jones)
-    1. [Qiskit (Quantum Volume)](tutorial3/README.md#qiskit-quantum-volume)
-
-
+    1. [Qiskit (Quantum Volume)](tutorial3/README.md#qiskit-quantum-volume**
+
+**Tutorial 4** demonstrates how to configure docker containers to deploy a monitoring stack, comprising of a metrics database service, an exporting / scraping service and a metric visualization services. You will then learn the very basics of how to visualize and interpret data. You will then learn how to automate the deployment of your Sebowa OpenStack infrastructure. Lastly, you'll deploy a scheduler and submit a job to it.
+
+1. [Checklist](tutorial4/README.md#checklist)
+1. [Cluster Monitoring](tutorial4/README.md#cluster-monitoring)
+    1. [Install Docker Engine, Containerd and Docker Compose](tutorial4/README.md#install-docker-engine-containerd-and-docker-compose)
+    1. [Installing your Monitoring Stack](tutorial4/README.md#installing-your-monitoring-stack)
+    1. [Startup and Test the Monitoring Services](tutorial4/README.md#startup-and-test-the-monitoring-services)
+    1. [SSH Port Local Forwarding Tunnel](tutorial4/README.md#ssh-port-local-forwarding-tunnel)
+    1. [Create a Dashboard in Grafana](tutorial4/README.md#create-a-dashboard-in-grafana)
+    1. [Success State, Next Steps and Troubleshooting](tutorial4/README.md#success-state-next-steps-and-troubleshooting)
+1. [Configuring and Connecting to your Remote JupyterLab Server](tutorial4/README.md#configuring-and-connecting-to-your-remote-jupyterlab-server)
+    1. [Visualize Your HPL Benchmark Results](tutorial4/README.md#visualize-your-hpl-benchmark-results)
+    1. [Visualize Your Qiskit Results](tutorial4/README.md#visualize-your-qiskit-results)
+1. [Automating the Deployment of your OpenStack Instances Using Terraform](tutorial4/README.md#automating-the-deployment-of-your-openstack-instances-using-terraform)
+    1. [Install and Initialize Terraform](tutorial4/README.md#install-and-initialize-terraform)
+    1. [Generate `clouds.yml` and `main.tf` Files](tutorial4/README.md#generate-cloudsyml-and-maintf-files)
+    1. [Generate, Deploy and Apply Terraform Plan](tutorial4/README.md#generate-deploy-and-apply-terraform-plan)
+1. [Continuous Integration Using CircleCI](tutorial4/README.md#continuous-integration-using-circleci)
+    1. [Prepare GitHub Repository](tutorial4/README.md#prepare-github-repository)
+    1. [Reuse `providers.tf` and `main.tf` Terraform Configurations](tutorial4/README.md#reuse-providerstf-and-maintf-terraform-configurations)
+    1. [Create `.circleci/config.yml` File and `push` Project to GitHub](tutorial4/README.md#create-circleciconfigyml-file-and-push-project-to-github)
+    1. [Create CircleCI Account and Add Project](tutorial4/README.md#create-circleci-account-and-add-project)
+1. [Slurm Scheduler and Workload Manager](tutorial4/README.md#slurm-scheduler-and-workload-manager)
+    1. [Prerequisites](tutorial4/README.md#prerequisites)
+    1. [Head Node Configuration (Server)](tutorial4/README.md#head-node-configuration-server)
+    1. [Compute Node Configuration (Clients)](tutorial4/README.md#compute-node-configuration-clients)
+1. [GROMACS Application Benchmark](tutorial4/README.md#gromacs-application-benchmark)
+    1. [Protein Visualization](tutorial4/README.md#protein-visualization)
+    1. [Benchmark 2 (1.5M Water)](tutorial4/README.md#benchmark-2-15m-water)
 # Lecture Recordings
 
 In this section you will finds links to all of the livestreams of the lectures (Teams Meetings) and subsequent recordings for you to refer back to.
 
-1. Day 1 - Welcome, Introduction and Getting Started
-   * **08:30 - 09:30**: [Welcome and Introduction](https://youtu.be/T68pHDdZW3s)
-   * **09:30 - 10:30**: [Getting Started](https://youtu.be/cIB9Gtpifpk)
-   * **11:00 - 12:00**: [Intro to Linux & Services](https://youtu.be/pbpjAw9eVcM)
-   * **12:00 - 13:30**: [Intro to Tools for the Modern IT Engineer](https://youtu.be/t4hD6NMw9Xg)
-
-2. Day 2 - HPC Hardware, HPC Networking and Systems Administration
-   * **08:30 - 09:30**: [HPC Hardware]()
-   * **09:30 - 10:30**: [HPC Networking]()
-   * **11:00 - 12:00**: [System Administration & Configuration Management]()
-   * **12:00 - 13:30**: [Standing up a Compute Node]()
-
-3. Day 3 - Benchmarking, Compilation and Parallel Computing
-   * **08:30 - 09:30**: [HPC Benchmarking]()
-   * **09:30 - 10:30**: [Code Compilation]()
-   * **11:00 - 12:00**: [Parallel Computing and Intro to QC]()
-   * **12:00 - 13:30**: [Applications: LAMMPS & Qiskit]()
-
-4. Day 4 - HPC Administration and Application Visualization
-   * **08:30 - 09:30**: [Cluster Admin, Ansible & Containers]()
-   * **09:30 - 10:30**: [Monitoring]()
-   * **11:00 - 12:00**: [Schedulers]()
-   * **12:00 - 13:30**: [Data Visualization & Jupyter Lab]()
-
-5. Day 5 - Career Guidance
-   * **08:30 - 10:30** [HPC Career Panel]()
+1. Welcome, Introduction and Getting Started
+   * [Welcome and Introduction](https://youtu.be/T68pHDdZW3s)
+   * [Getting Started](https://youtu.be/cIB9Gtpifpk)
+   * [Intro to Linux & Services](https://youtu.be/pbpjAw9eVcM)
+   * [Intro to Tools for the Modern IT Engineer](https://youtu.be/t4hD6NMw9Xg)
+
+2. HPC Hardware, HPC Networking and Systems Administration
+   * [HPC Hardware](https://youtu.be/gkZCrdTuvrc)
+   * [HPC Networking](https://youtu.be/pGzQutsk2-A)
+   * [System Administration & Configuration Management](https://youtu.be/YY6D-0e5iHw)
+   * [Standing up a Compute Node](https://youtu.be/V6bx86qJwHE)
+
+3. Benchmarking, Compilation and Parallel Computing
+   * [HPC Benchmarking]()
+   * [Code Compilation]()
+   * [Parallel Computing and Intro to QC]()
+   * [Applications: LAMMPS & Qiskit]()
+
+4. Administration and Application Visualization
+   * [Cluster Admin, Ansible & Containers]
+   * [Monitoring]()
+   * [Schedulers]
+   * [Data Visualization & Jupyter Lab]
+
+5. Career Guidance
+   * [HPC Career Panel]()
 
 # Contributing to the Project
 

diff --git a/tutorial3/README.md b/tutorial3/README.md
@@ -1,4 +1,4 @@
-# Student Cluster Competition - Tutorial 3
+Student Cluster Competition - Tutorial 3
 
 ## Table of Contents
 
@@ -43,7 +43,7 @@ In this tutorial you will:
 - [ ] Understand the pros and cons of compiling libraries from source.
 - [ ] Install and make use of Intel's oneAPI framework to run HPL.
 - [ ] Understand theoretical system peak performance.
-- [ ] Appreciate the significance of the Top500 list and bencmarking.
+- [ ] Appreciate the significance of the Top500 list and benchmarking.
 - [ ] Standup and Configure a Second Compute Node, and running applications across a cluster.
 - [ ] Download and compile the High Performance Computing Challenge (HPCC) benchmark.
 - [ ] Understand that scientific computer applications are primarily used to conduct scientific research, and can also evaluate system performance.
@@ -131,7 +131,7 @@ In this section, you are going to be building and compiling Lmod from source. Lm
      sudo dnf install -y epel-release
      sudo dnf install -y tcl-devel tcl tcllib  bc
      sudo dnf install -y lua lua-posix lua-term
-     sduo dnf --enable-repo=devel install lua-devel
+     sudo dnf --enable-repo=devel install lua-devel
      ```
    * APT
      ```bash
@@ -526,7 +526,7 @@ After you've successfully completed the previous section, you will be ready to r
    cp setup/Make.Linux_Intel64 ./
 
    # Edit the configuration file to make use of your Intel oneAPI Toolkit
-   nano Make.Linux64
+   nano Make.Linux_Intel64
    ```
 
 1. Configure your `Make.Linux_Intel64`
@@ -592,7 +592,6 @@ The [TOP500 list](https://top500.org/lists/top500/2024/06/) is a project that ra
 |      | Compute node using custom compiled MPI and BLAS |           |                       |                          |
 |      | Compute node using Intel oneAPI Toolkits        |           |                       |                          |
 |      | Across two compute nodes                        |           |                       |                          |
-|      |                                                 |           |                       |                          |
 
 > [!IMPORTANT]
 > You do **NOT** need to try and Rank you VM's HPL performance. Cores and threads are used interchangeably in this context. Following the recommended configuration and guides, your head node has one CPU package with two compute cores (or threads). Continuing this same analogy, your compute node has one CPU with six cores (or threads).