HPC for research training course November 2017

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

This November we have a  research computing training week in collaboration with the software carpentry initiative, to be held in November 02 - 03 , 2017.

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 and  Tjenester for Sensitive Data (TSD) for their research.

Please make sure that you have a functioning Abel account before the start of the course. Visit the Abel access webpages  to obtain an account. Please note that registering to the course does not provide you with an account automatically. However, if you want to test our services or if you have only a TSD account  or if you are a student from another University than University of Oslo, please indicate this during registration so we can make some temporary arrangements.

The courses are held on November 02 - 03 in the    the event is free of charge but requires registration.The lectures are held in English.

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

Section 0 : Unix basics  (will be arranged before 02,11 only if required)

Section 1 : HPC for beginners   - 02-11-2017

Section 2 : HPC for advanced users   - 03-11-2017


Registration (Deadline 25-10-2017 or course is full) : Registration form

Time and place





 Software carpentry

There will be several workshops before the start of the course and participants can select any one of these (Not mandatory if you have enough UNIX knowledge). Please contact Sabry if you could not find a date suits you and we will try to arrange something for you.

More courses :



**Last Unix training workshop before the HPC training week October 27 Register:  http://www.ub.uio.no/english/courses-events/courses/other/Carpentry/software-carpentry/time-and-place/171027_unixshell


Session 1 - HPC for beginners   - 02.11.2017 (Thursday- 12:00-16:00)

This session is for users starting to use Abel or Colossus and provides basic training on how to run a job.

12:00 - 15:00

 Aud Smalltalk

Abel/Colossus  for beginners

Sabry Razick

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

Target audience: User who want to use Abel or Colossus 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. Ubuntu , RedHat, Mac OS, Windows 8.1, Windows 10. We do not support Windows 7 or any of the earlier windows versions.

Download :Slides1  Slides2,


 Aud Smalltalk

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

Download :Slides

Section 2 : HPC for advanced users   - 03.11.2017

This session is for experienced Abel and Colossus users and provide training on how to install software and best practices.


 Aud Smalltalk

Introduction to shell scripting Andreas Buzh

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.

Download :Slides


 Aud Smalltalk

Practice shell scripting Andreas Buzh

Description: Hands-on exercises on shell scripting.  

Target audience: New comers to shell scripting.

Prerequisites: Posses basic shell scripting knowledge and Unix command line

 Equipment: The participants are required to bring their own laptop.

Download: Slides

11:15 -  12:00 TBA    

12:15 - 14:00

 Aud Smalltalk

How to install software on Abel and Colossus 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

Download :Slides

14:15 - 15:00

 Aud Smalltalk

How to run jobs efficiently on Abel and Colossus 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


15:15 - 16:00

 Aud Smalltalk

HPC best practices

Ole W. Saastad/

Marcin Krotkiewski

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




Published June 22, 2017 12:45 PM - Last modified Jan. 24, 2018 12:51 PM