HPC and NIRD toolkit user course November 2021
In November 2021, the Norwegian Research Infrastructure Services NRIS (formerly known as the Metacenter) partners Sigma2, UiB, UiO & UiT are jointly offering a hands-on course for current and future users of national HPC systems (Saga, Fram, Betzy) and the NIRD Toolkit. The course is open to all users and free of charge.
For individual sessions we list recommended prerequisites. The participants can choose which session they want to attend and you’re certainly welcome to just attend all sessions you are interested in. On each course day, we will start at 09:00 and conclude at around 13:00. Each “morning” will include presentations and hands-on time on one of the actual HPC systems or the NIRD Toolkit. We recommend that participants use the afternoon on each day to repeat examples from the morning to get more experience on the systems.
Note
The video recordings and notes can be found here
Practical Information
This is an online course via zoom. Participants require access to a computer (not provided by the course organisers) with internet connectivity and pre-installed programs to participate in the video meeting of the course (zoom, might work from a browser), to access the HPC systems (e.g., ssh or Putty), to transfer data to/from an HPC system (e.g., scp or WinSCP) and to access the NIRD Toolkit (web browser).
Note
Those who do not have an account on one of the HPC machines or NIRD (storage, Toolkit, …) yet need to apply for an account. The application page is available here and documentation for the application procedure is available here. You are applying for an HPC account. For the project, please select “NN9987K: Course Resources as a Service #3” (the Project manager will be filled in automatically), choose Saga under Resources, set the Account start date to 2021-10-26 and the Account end date to one week after the course, that is 2021-11-12.
In order to use the NIRD Toolkit during the course you will need either a Feide account or a Feide OpenIDP guest account. You can create a Feide OpenIDP guest account at https://openidp.feide.no/. See your eduPersonPrincipalName (eduPPN) at http://innsyn.feide.no . Those who are using Feide openidp guest account should go to minside.dataporten.no to find eduppn, and it is the field called “Secondary user identifiers”.
You can always contact us by sending an email to support@nris.no.
If you want to receive further information about training events, and other announcements about IT resources and services for researchers, there are a couple of information channels you can subscribe to:
users at University of Bergen and affiliated institutes: register to hpcnews@uib.no
users of Sigma2 services: subscribe to Sigma2’s newsletter
Dates: 2021 November 2, 3, 4 and 5 Time: each day 09:00-13:00 with short breaks Location: Video meeting (zoom), we use HackMD for asking questions (information will be send to registered participants via email). Note, sessions will be recorded and made publicly available after the course!
Participants may choose the lectures which they are interested in.
Registration
The course is free of charge and is organised by the NRIS partners Sigma2, UiB, UiO & UiT. Registration is closed
Code of Conduct
All participants in our course are expected to show respect and courtesy to others. We follow carpentry code of conduct. If you believe someone is violating the Code of Conduct, we ask that you report it to the training team.
Agenda
Day 1: 02-11.2021: Welcome, Introduction to High Performance Computing
Get ready: 08:50-09:00 Connect to zoom meeting
Prerequisites: Command line experience is necessary for this lesson. We recommend the participants to go through shell-novice, if new to the command line (also known as terminal or shell)
Course material here
Session 1: 09:00-09:55 Welcome, What is HPC, working on HPC System, Scheduling Jobs
Break for 10 minutes
Session 2: 10:05-11:00 Accessing Software, transferring files
Break for 10 minutes
Session 3: 11:10-12:05 Running a parallel job, Using resources effectively
Break for 10 minutes
Session 4: 12:15-12:45 HPC through a web browser
Session Q&A: 12:45-13:00 Questions & Answers
Day 2: 03-11-2021: Optimization of codes and Resource Management
Prerequisites: Basic HPC knowledge, we recommend participants to attend Day1 sessions
Get ready: 08:50-09:00 Connect to zoom meeting
Session 1: 09:00-09:45 Effective use of HPC resources part I (basic) (O. W. Saastad)
Break for 10 minutes
Session 2: 09:55-10:30 Effective use use of HPC resources part II (intermediate) (O. W. Saastad)
Break for 10 minutes
Session 3: 10:40-11:20 How to choose memory and number of cores (part I) (R. Bast)
Break for 10 minutes
Session 4: 11:30-12:10 How to choose memory and number of cores (part II) (R. Bast)
Break for 10 minutes
Session 5: 12:20-12:50 Optimization of codes: Usecase
Session Q&A: 12:50-13:00 Questions & Answers
Day 3: 04-11-2021: Containers on HPC and NIRD Toolkit
Get ready: 08:50-09:00 Connect to zoom meeting
Session 1: 09:00-10:20 Containers on HPC (part I)
Break for 10 minutes
Session 2: 10:35-11:30 NIRD Toolkit (part I)
Break for 10 minutes
Session 3: 11:40-12:40 NIRD Toolkit (part II)
Break for 10 minutes
Session Q&A: 12:40-13:00 Questions & Answers
Day 4: 05-11-2021: GPU Computing
Get ready: 08:50-09:00 Connect to zoom meeting
Session 1: 09:00-09:45 Introduction to GPU computing (J. Nordmoen)
Break for 15 minutes
Session 2: 10:00-10:45 Using GPUs at NRIS (J. Nordmoen)
Break for 15 minutes
Session 3: 11:00-11:45 Practical introduction to using GPUs (S.R. Jensen)
Course material:
Prerequisites:
GPU fundamentals, e.g. from the previous session
Break for 15 minutes
Session 4: 12:00-12:45 Containers on HPC (part II): MPI and GPU (S.R. Jensen)
Course material:
Prerequisites:
running Singularity containers, e.g. from Day 3
running MPI jobs using Slurm scripts, e.g. from Day 2
running GPU jobs using Slurm scripts, e.g. from the previous session
Session Q&A: 12:45-13:00 Questions & Answers
Preparing your machine for the course
We assume you have the necessary tools installed on your machine and are able to use them. You need tools to login into a remote machine (e.g., ssh or PuTTY) and to transfer data to/from a remote machine (e.g., scp or WinSCP). If you need to install such tools, please see prepare your machine section.
Previous Course
Our previous course page can be found here and video recording of the course will be updated soon.