HPC Introduction 09/2021

Introduction to HPC at the University Oldenburg

Due to the anti-Corona measures, the course will be given online in a web conference. See Video Conference below.

Description

This 3-day course is aimed at HPC beginners as well as experienced users who wish to learn about HPC and the use of the local clusters CARL and EDDY. The course will cover the following topics:

• General Introduction to HPC and the use of CARL and EDDY
• Introduction to the Job Scheduler SLURM
• Programming in an HPC Environment
• Introduction to Parallel Programming (MPI, OpenMP, OpenACC)
• Introduction to Matlab Distributed Compute Server (MDCS)

The course will consist of lectures and hands-on practical parts. Special topics may be covered if requested.

Date, Time and Registration

The course will be held by Stefan Harfst and Wilke Trei:

• Date: September 20 – 22, 2021
• Time: 10:00 to 17:00
• Room: online, Meeting in Stud.IP

The schedule for the course can be found here.

We kindly ask you to register for the course in Stud.IP (look for course No. 5.WR.1037 in case the link does not work). If you have problems please send us an e-mail.

Web Conference

This time, the course is given in the form of a web conference again. If you want to participate, you should make the following preparations":

• sign up for the course as mentioned above
• if you do not have one yet, request an HPC account (if you have problems contact Scientific Computing)
• have a computer connected to the internet available during the time of the course
• you also need speakers or headphones, a microphone is not needed (if you have one, please use headphones to avoid feedback loops). A webcam should not be used as it takes up too much bandwidth.
• your computer should also be able to connect to the HPC cluster, for this you need to install and use the GlobalProtect client to establish a VPN.
• on Windows computers use MobaXterm to login to the cluster, Linux and Mac users can use ssh in a terminal

On Monday, a little before the course starts at 10:15 am, go to the course page in Stud.IP, select the Meetings tab and join the web conference (or use the link before). In the web conference, we will show slides and use audio for the lecturers, you can ask questions in the text chat.

Lecture Slides and Materials

Day 1 - Monday, September 20th

• Session 1: Introduction to High-Performance Computing (10:15-11:15am)
  • lecture slides [pdf]
• Session 2: Basic HPC Clusters Usage (11:30-13:00pm)
  • lecture slides [pdf]
  • example: SLURM HelloWorld [tgz]
• Session 3: HPC Cluster Environment (13:45-17:00pm)
  • lecture slides [pdf]
  • example: RandomWalk [tgz]
  • example: Matrix-Matrix Multiplication [tgz]
  • example: Array Job [tgz]

Day 2 - Tuesday, September 21st

• Session 4: Introduction to Parallel Computing (10:15-11:30am)
  • lecture slides [pdf]
  • example: MPI_HelloWorld [tgz]
• Session 5: Introduction to OpenMP (11:45-13:00pm)
  • lecture slides [pdf]
  • example: OMP_HelloWorld [tgz]
• Session 6: Introduction to OpenMP (13:45-15:15pm)
  • lecture slides [pdf]
  • example: Work Sharing Directives [tgz]
  • example: Parallelizing Program Random [tgz]
  • excercise: Pi Calculation Exercise [tgz]
• Session 7: Performance Optimization (15:30-17:00pm)
  • lecture slides [pdf]
  • example: Stencil code [tgz]

Day 3 - Wednesday, September 22nd

• Session 8: Introduction to MDCS (I) (10:15-13:00pm)
  • lecture slides [pdf]
  • Basic Parfor example: Parameter Sweep [zip]
• Session 9: Introduction to MDCS (II) (13:45-16:00pm)
  • lecture slides [pdf]
  • SPMD example: Noise Reduction [zip]
  • SPMD example: Contrast Adjustment [zip]
  • heat exercise [zip]