HPC basics for research training course 08-10, November 2016

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

This November  we have a shorter research computing training week in collaboration with the software carpentry initiative., to be held in November 8-10, 2016. 

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 or a TSD account before the start of the course. Visit /english/services/it/research/hpc/abel/help/access/  or/english/services/it/research/sensitive-data/use-tsd/ 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 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 08-10 in the Ole-Johan Dahls hus and Kristen Nygaards hus  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.

Registration:

For Registration please use the web.form https://nettskjema.uio.no/answer/73724.html  (starts 01 August 2016, Deadline for registration until course is full (32 participants maximum) or 21  October 2016, which ever reached first.

 

Time and place

Title             

Lecturer 

Description     

 

 Software carpentry

There will be two or three workshops before the start of the course and participants can select any one of these.

First course is arranged on Aug 23rd, 2016: https://uio-carpentry.github.io/2016-08-23-unix/

Second  course is arranged on Oct 12th, 2016: https://uio-carpentry.github.io/2016-10-12-unix/

More courses : http://www.ub.uio.no/english/courses-events/courses/other/Carpentry/

 Introduction 08-11-2016 (Tuesday)

09:15 - 10:00

Seminarrom-C

Ole-Johan Dahls hus

3437 Seminarrom C

Preparation

Sabry Razick

Prepare your computers to connect to Abel. By the end of this session, all participants must have command line access to Abel.

Target audience:All  

Prerequisites: None

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. If you must use Chrome OS or Android you must inform us well in advanced.

Slides

10:15 - 11:00

Seminarrom-C

Ole-Johan Dahls hus

3437 Seminarrom C

Practice Unix on Abel/Colossus

 

Sabry Razick

 

Description: Practice Unix command on Abel.

Target:  audience:All  

Prerequisites: Participated in the Software Carpentry' workshop or have a working knowledge of UNIX

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

Slides

11:15 -12:00

Seminarrom-C

Ole-Johan Dahls hus

3437 Seminarrom C

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.

Slides

13:15 -14:00

Seminarrom-Logo

Ole-Johan Dahls hus

2438 Seminarrom Logo

(Room open from 12:00))

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.

Slides

15:00-16:00

Seminarrom-pascal

No lecture on this slot

Abel/Colossus  for beginners

This lecture is merged with First steps on Abel - hands on tutorial (Wednesday)

Sabry Razick

Description: Introduction to the computer cluster Abel that is the principal scientific computational resource at the University of Oslo. By the end of the lecture you will have a basic working knowledge of Abel.

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

Prerequisites: Working knowledge of UNIX

Equipment: None, but Welcome to bring own laptops

Download:

HPC 09-11-2016 (Wednesday)

09:15 - 11:00

Seminarrom Logo

Ole-Johan Dahls hus

2438 Seminarrom Logo

First steps on Abel - hands on tutorial Sabry Razick

Description: Hands on introduction to the computer cluster Abel.  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: Knowledge of Unix and shell scripting

Equipment: The participants required to bring own laptops for exercises.

Download : Slides, Slides

11:15-12:00

Seminarrom Logo

Ole-Johan Dahls hus

2438 Seminarrom Logo

How to ask for help or software  Bjørn-Helge Mevik

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

13:15-15:00

Seminarrom-Logo

Ole-Johan Dahls hus

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

15:00- 17:00

Seminarrom-Shell

Ole-Johan Dahls hus

1456 Seminarrom Shell

Social event with Pizza

 10-11-2016(Thursday)

09:15 -11:00

Store-auditorium  

Kristen Nygaards hus    

Introduction to TSD

 

Francesca/Nihal

Description: Introduction to UiO's service for sensitive data and first steps:

  1. TSD in a nutshell
  2. Log in TSD
  3. File structure in TSD and backup
  4. Nettskjema in TSD

Target Audience: Current and potential TSD users

Prerequisites: None

Equipment: The participants required to bring own laptops for exercises.

Slides   

Slides 2

11:15 -12.00

Store-auditorium

Kristen Nygaards hus      

Lifeportal Nikolay Vazov

Description: Learn about lifeportal (portal for life sciences) that enables entry level users to start large computations on the Abel computer cluster.  This module explains the basic operations of the Lifeportal, submit jobs upload download files and get help

Target Audience: All welcome  

Prerequisites: None

Slides

13:15 - 14:00

Seminarrom-Java

Ole-Johan Dahls hus

2423 Seminarrom Java

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

14:15-15:00

Seminarrom-Perl 

Ole-Johan Dahls hus

2453 Seminarrom Perl

 

HPC best practices

Ole W. Saastad/

Marcin Krotkiewski

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

 

Lecture rooms:

Seminar room C: Ole-Johan Dahls hus (3rd floor)

Seminar room Logo Ole-Johan Dahls hus

Seminar room Shell Ole-Johan Dahls hus

Seminar room shell:Ole-Johan Dahls hus

Store auditorium:  Kristen Nygaards hus 

: For these modules you need to bring your own laptop.

 

Organizer

Research Computing Services

Contact : Sabry Razick (email, mobile:93870788)

Published June 8, 2016 10:22 AM - Last modified Mar. 2, 2017 10:59 AM