HPC for research training course March 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 March we have a  research computing training week in collaboration with the software carpentry initiative, to be held in March 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.

Section 1 : HPC for beginners (21.03.2018,Wednesday-09:00 to 22.03.2017,Thursday-10:00)

Section 2 : HPC for advanced users (22.03.2017,Thursday-10:15 to 23.03.2017,Friday- 13:00)

 

Registration: (Deadline 18-03-2018 or the course is full) :Registration https://nettskjema.uio.no/answer/93489.html (all seats taken)

Location: Aud Smalltalk, Ole-Johan Dahls hus (https://goo.gl/maps/KRTj1nbvHHQ2)

Time and place

Title             

Lecturer 

Description     

 

 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 :

uio.no/carpentry

https://www.ub.uio.no/english/courses-events/courses/other/Carpentry/CarpentryWorkshops/


 

Session 1 - HPC for beginners   - 21.03.2018 (Wednesday- 09:00-12:00)

This session is for users starting to use Abel and provides basic training on how to run a job.
09:15 -10:00 Connect to Abel.  Practice Unix 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/ )

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 : https://swcarpentry.github.io/shell-novice/, PDF

10:15 - 12:00

 Aud Smalltalk

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/ )

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

Section 1: continued  : HPC for beginners  - 22.03.2017 (Thursday- 09:15-10:00)

09:15-10:00

 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

Slides :Slides

Section 2 : HPC for advanced users - 22.03.2017 (Thursday- 10:15-16:00)

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

10:15-11:00

 Aud Smalltalk

Introduction to shell scripting

Andreas Skau

Trond Thorbjørnsen

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

11:15-12:00

 Aud Smalltalk

Practice shell scripting

Andreas Skau

Trond Thorbjørnsen

Prerequisites: Introduction to shell scripting

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

Slides :Slides

12:15 -  13:00 Break

13:15 - 15:00

 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

Slides :Slides

15:15 - 16:00

 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

Slides: PDF

Section 2 continued  : : HPC for advanced users - 23.03.2017 (Friday- 09:15-13:00)

09:15 - 10:00

 Aud Smalltalk

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:Pdf 

10:15 - 12:00 Containers in HPC Abdulrahman Azab

Description: Linux containers, with the build-once-run-anywhere approach, are becoming popular among scientific communities for software packaging and sharing. Docker is the most popular and user friendly platform for running and managing Linux containers. Singularity is a platform for deploying light-weight containers for HPC systems, and is now supported on both Abel and Colossus.

This hands-on tutorial is organized as follows:

  • Overview of the Linux containers technology
  • Docker: Installation, building and managing Docker containers
  • Singularity: Building singularity containers, converting Docker containers to singularity, and running singularity containers on Abel

 

Target audience: All Abel or Colossus users

Prerequisites: Basic Linux knowledge, and a user on Abel

Equipment: Own laptop with SSH access (Install Putty for windows)

 

Requires own laptop.

 

 

Published Dec. 5, 2017 10:14 AM - Last modified Aug. 16, 2018 4:40 PM