HPC for research training course November 2018

Training in using High-performance Computing (HPC) efficiently, for Abel users. The course is also open for all users of Notur systems, but examples and specifics will pertain to Abel.

This time we have a  research computing training week in collaboration with the software carpentry initiative, to be held in November 2018

This course is designed for Notur as well as local users. This event is especially suitable for scientists who wish to learn more about how they can use  Abel computer cluster for their research.

*Please note that it is not possible to get credit points for this course.

Session 0 : UNIX basics Register for this course

Session 1 : HPC for beginners Register for this course 

Session 2 : HPC for advanced users Register for this course

 

Software carpentry - UNIX terminal basics

The HPC training course requires a working knowledge of the UNIX terminal (also know as as "the command line" or "the bash shell". We are collaborating with the University of Oslo software carpentry to provide our users with this knowledge.  Please note that if you do not have a working knowledge of the terminal it will be impossible to follow the HPC lessons.

Carpentry@UiO : https://www.ub.uio.no/english/courses-events/courses/other/Carpentry/software-carpentry/

Please use the following link to find carpentry lesson that suits you : https://www.ub.uio.no/english/courses-events/courses/other/Carpentry/software-carpentry/time-and-place/

* There will be at least two "Unix Bash Shell workshops" before the HPC course week. 

 

  HPC for beginners  (Wednesday 14-11-2018) 

Room : Ole-Johan Dahls hus,  Seminarrom Python

Register for this course 
This session is for users starting to use Abel and provides basic training on how to run a job. The lessons marked with requires a laptop with a UNIX terminal.
Time and place Title Lecturer Description
09:15 - 10:00 Connect to Abel Sabry Razick

Description: How to access Abel. This lesson is for the first time Abel users and for Abel new comers. We have allocated this slot so participants get help connecting to a WI-FI network and to Abel so we do not waste any time during the next lessons.

Target audience: User who want to use Abel for computational  needs in research. 

Prerequisites: Working knowledge of UNIX (At least first three modules of the course https://swcarpentry.github.io/shell-novice/ )

Equipment: The participants are required to bring their own laptop. The laptops should run one of the following OS versions. any UNIX flavour including Ubuntu and RedHat , Chrome OS,  Mac OS, Windows 8.1, Windows 10. We do not support Windows 7 or any of the earlier windows versions.

  PDF1

10:15 - 12:00 Abel for beginners Sabry Razick

Description: Introduction to the high performance computer cluster Abel at the University of Oslo. By the end of the lecture you will have a basic working knowledge of Abel and will be able to submit simple jobs.  

Target audience: User who want to use Abel for computational  needs in research. 

Prerequisites: Working knowledge of UNIX (At least first three modules of the course https://swcarpentry.github.io/shell-novice/ ) and knowledge on how to connect to Abel.

Equipment: The participants are required to bring their own laptop. The laptops should run one of the following OS versions. Ubuntu , RedHat, Mac OS, Windows 8.1, Windows 10. We do not support Windows 7 or any of the earlier windows versions.

Slides: PDF1, PDF2

13:15 - 15:00 Abel hands-on Sabry Razick

Description: Introduction to the high performance computer cluster Abel at the University of Oslo. By the end of the lecture you will have a basic working knowledge of Abel and will be able to submit simple jobs.  

Target audience: User who want to use Abel for computational  needs in research. 

Prerequisites: Working knowledge of UNIX (At least first three modules of the course https://swcarpentry.github.io/shell-novice/ ) and knowledge on how to connect to Abel.

Equipment: The participants are required to bring their own laptop. The laptops should run one of the following OS versions. Ubuntu , RedHat, Mac OS, Windows 8.1, Windows 10. We do not support Windows 7 or any of the earlier windows versions.

Slides: PDF1, PDF2

15:15 - 16:00 How to ask for help or software  Bjørn-Helge Mevik

Description: Where can you get help or ask for software on Abel or Colossus? What should you do before sending in a help request? How do you write an email that is likely to get a good reply, and what should you include?  

Target Audience: All Abel or Colossus users  

Prerequisites: Basic knowledge of Abel or Colossus

Slides :Slides

 

 HPC for advanced users (Thursday 15-11-2018)

Room : Ole-Johan Dahls hus,  Seminarrom Python

Register for this course 
This session is for experienced Abel users and provide training on how to install software and best practices.
09:15 - 10:00

How to run jobs efficiently on Abel

Ole W. Saastad

Description: Different subsystems, queue tips, scheduling, storage,  staging of data, MPI, big data, think parallel - as next generation hardware will force you to so and some more goodies for the computer minded. In addition there will be an introduction to the Intel tuning tools.

Target Audience: Users who take performance seriously and are willing to invest to do something with it.

Prerequisites: Basic knowledge of Abel or Colossus

Slides: PDF

10:15 - 12:00 Introduction to shell scripting Dmytro Karpenko

Description: Very first steps; what (shell) scripting is useful for, invocation, variables, if-then-else. loops, expansion and a few tricks  

Target audience: New comers to shell scripting.

Prerequisites: Knowledge of one other programming language and Unix command line

Equipment: The participants are welcome to use their own laptops for exercises.

Slides :Slides

13:15 - 15:00 How to install software on Abel Bjørn-Helge Mevik

Description: How to install R packages, Perl modules, Python modules and general software packages on Abel.

Target Audience: Abel or Colossus users.

 Prerequisites: Basic knowledge of Abel/Colossus and Unix

Slides :Slides

15:15 - 16:00 HPC best practices Ole W. Saastad

Description:Job analysis and best practices

  • HPC best practices.
  • Different nodes, login, compute, hugemem, GPU
  • Monitor jobs
  • Monitor queue
  • Monitor job status
  • Plan disk I/O and minimize metadata generation. How to anticipate and monitor
  • Different mounts and there properties.

Target Audience: All Abel or Colossus users  

Prerequisites: Basic knowledge of Abel or Colossus

Slides: Slides Slides2

 

Organizer

Sabry Razick
Tags: Abel, HPC
Published June 10, 2018 9:06 PM - Last modified Nov. 15, 2018 11:26 AM