HPC basics for research, certification course 04-07, April 2016

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

This spring we have a slightly modified version of our research computing training week, to be held in April 4-7, 2016.  The plan is to provide a thorough training on the basics of research computing, with more interactive and hands-on exercises. The course-week we are planning later this year (November) will cover more advanced topics.

To encourage the systematic learning experience we will provide a certificate for participants who complete a minimum number of modules!

This course is designed for Notur as well as local users. This event is especially suitable for scientists who wish to learn more about programming and using the Abel computer cluster and Tjenester for Sensitive Data (TSD).

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 http://www.uio.no/tjenester/it/forskning/sensitiv/ta-i-bruk/index.html 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 April 04-07 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.

Certificate

Minimum of 8 modules+user presentation needs to be completed to qualify for the certificate.

Registration:

Registration closed as we have received more applications than we could accommodate. For Registration please use the web.form https://nettskjema.uio.no/answer/70238.html  (starts 01 February 2016, Deadline for registration 15, March 00:00)

 

Time and place

Title             

Lecturer 

Description     

Schedule

Monday April 04, Introduction

09:15 - 10:00

Seminarrom-Shell

Preparation

Sabry Razick,

Marcin Krotkiewski

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.

10:15 - 11:00

Seminarrom-Shell

Introduction to Unix

(Module 1)

Thierry Toutain

Description:Command line for complete novices  

Target audience:All  

Prerequisites: Must have a laptop with terminal access to Active Abel account.

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

Slides

12:15 - 14:00

Seminarrom-Shell

Do more with Unix

(Module 2)

Sabry Razick

Marcin Krotkiewski

Milen Kouylekov

Description:

  1. Learn to use basic commands and scripts to perform tasks.
  2. The system PATH and other variables
  3. Copy and move files locally and between local computer and server (scp, rsync)
  4. We will learn to use grep, sed, awk,
  5. Basic Python,

Target audience:All  

Prerequisites: Basic Unix knowledge or completed the module 1 or have participated in the Software Carpentry' workshop

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

Slides: Unix, Python 1, Python 2

14:15 - 15:00

Seminarrom-Shell

Practice Unix

(Module 3)

Sabry Razick

Marcin Krotkiewski

Milen Kouylekov

Description:Practice what was learned in Module 2

Target audience:All  Prerequisites: Completed the Module 2 or have participated in the Software Carpentry' workshop

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

15:15 -16:00

Seminarrom-Shell

Abel for beginners

(Module 4)

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: some knowledge of command line or have completed Module 3  or have participated in the Software Carpentry' workshop

Equipment: None, but Welcome to bring own laptops

Download: Slides

Tuesday April 05, Introduction

09:15-10:00

Seminarrom-Shell

Advanced python on Abel

(Module 17)

Description: an overview and usage examples of numpy, scipy, and matplotlib, popular Python packages for scientific computing and plotting. 

Target audience: Researchers that use Python in their work.

Prerequisites: Knowledge of Python and modules usage.

Equipment: The participants need their laptops if they want to try the packages during the lecture.

Slides

10:15 - 11:00

Seminarrom-Shell

Introduction to shell scripting

(Module 5)

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

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

Slides

11:15-12:00

Seminarrom-Shell

Practice shell scripting

(Module 6)

Andreas Buzh

Thomas Röblitz

Sabry Razick,

Description: Hands-on exercises on shell scripting.  

Target audience: New comers to shell scripting.

Prerequisites: Posses basic shell scripting knowledge or have completed the module (Module 5)

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

 

Slides

13:15-15:00

Seminarrom-Shell

First steps on Abel - hands on tutorial

(Module 7)

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: Users with basic knowledge on Abel or have completed the module Module 4

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

Download : Slides

15:15 - 16:00

Seminarrom-Shell

Work-flows and pipelines - hands on tutorial

(Module 8)

Abdulrahman Azab

Description:: How to write a workflow description for workflows and nested workflows, How to submit and monitor workflow execution

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

Prerequisites: Users with basic knowledge on Abel or have completed the module Module 7

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

Download : Slides

Wednesday, 06 April

09:15 -11:00

Lille-auditorium     

How to install software on Abel 

(Module 9)

Ole W. Saastad

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 and Unix

Slides

11:15 -12.00

Lille-auditorium     

How to ask for help or software 

(Module 10)

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 - 14:00

Seminarrom-Perl 

How to run jobs efficiently on Abel and Colossus

(Module 11)

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: Module 7 or Working knowledge of Abel.

Slides

14:15-15:00

Seminarrom-Perl 

Lifeportal -1

(Module 12)

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

15:15-16:00

Seminarrom-Perl 

Lifeportal 2

(Module 13)

Kidane M. Tekle

Description: *Please note this module has been modified on Feb,17.  Introduction to the Norwegian e-Infrastructure for Life Sciences (NeLS ) . Get an introduction of how the NeLS system can foster collaborative research and assist in flexible management of data across multiple accessibility means including web-based access, Galaxy integration, TSD integration, Storebioinfo integration, SSH access and programmatic API access.

Target Audience: All welcome  

Prerequisites: Have a working knowledge on Lifeportal or completed Module 12

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

Slides

Thursday 7th April

09:15- 10:00

Seminarrom-Shell

Introduction to TSD

(Module 14)

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

10:15 - 11:30

Seminarrom-Shell

TSD hands-on

(Module 15)

Francesca/Sabry

Description: Using TSD:

  1. File import/export
  2. Install software without internet.
  3. Submitting jobs to cluster

Target Audience: Current and potential TSD users

Prerequisites: Basic UNIX and Abel knowledge or completed Module 4 (Module 7 recommended).

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

Slides,  Slides 2

12:15-14:00

Seminarrom-Pascal  

Code and data management with version control on Abel

(Module 16)

Leon du Toit

Description:    How can GIT help you when working on Abel. Avoid keeping multiple copies of data and instead keep versions that you can switch between. Collaboration when writing a research article.

Target audience:  Researchers who work on collaborative projects; those interested in effective code and data (files) management.

Preparation: you need to have git installed and have access to a terminal application running bash. You can follow the instructions provided in the course notes below.

Course notes and instructions for preparation.

Slides , Slides2

14:00 -16:00
Seminarrom-Shell
 

Thomas Röblitz

Sabry Razick

User presentations.

Available topics :

  1. How I use/plan to use Abel
  2. Efficient programs vs inefficient programs on HPC
  3. Lifeportal vs the terminal
14:00 -16:00
Seminarrom-Pascal
 

Milen Kouylekov

Sabry Razick

User presentations.

Available topics :

  1. How I use/plan to use Abel/TSD in my research

 

Lecture rooms:

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

Seminar room shell:Ole-Johan Dahls hus

Lille auditorium:  Kristen Nygaards hus 

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

 

Organizer

Research Computing Services

Contact : Sabry Razick (email, mobile:93870788)

Organizer

Research Computing Services
Tags: HPC, Python, Abel, command line, shell scripting, TSD, Lifeportal
Published Jan. 8, 2016 3:30 PM - Last modified Dec. 23, 2016 8:38 AM