Research Computing Services tutorial and courses November 02-06, 2015

The courses and tutorials are centered around UiO's computing facility - the compute cluster Abel. This is a national resource also available to local researchers and students who have need for extra computing resources.

Twice a year, the USIT Research Computing department organizes training week for all Notur and local users. This event is especially suitable for scientists who wish to learn more about programming and using the Abel computer cluster.  The topics range from beginner introduction to command line, shell scripting and programming to advanced cluster usage, installing software and high-performance computing.

The courses are held on November 02-06 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.

 

Registration starts 15 September. Course registration page . (Deadline for registration 20, October 00:00)

*Please note the change in timetable (Changed 02-11-2015)

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

 

Time/Place

Title

     lecturer

Description

Timetable
Monday, November 02

Introduction

12:15-13:00

Room-Pascal

Introduction to the Linux command line.

Sabry Razick, George Magklaras

 

Description:Command line for complete novices

Target audience:All

Prerequisites: None

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

Slides : Download

13:15 - 14:00

Room-Pascal

Abel for beginners

Sabry Razick, Marcin Krotkiewski

Postponed to 3rd November

 

14:15-16:00  

Room-JAVA

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: Never done shell scripting before

Prerequisites: Knowledge of one other programming language

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

Slides: Download

Tuesday, November 03

High performance computing

12:15 - 13:00 Room-Logo Abel for beginners

Sabry Razick

Description: Introduction to the computer cluster Abel that is the principal scientific computational resource at the University of Oslo. The course is aimed at people with little background in UNIX and parallel computing and includes simple examples. By the end of the lecture you will have a basic working knowledge of Abel and will be able to submit simple jobs using the SLURM job manager.

Target audience: Users with minimal background in UNIX and parallel computing

Prerequisites: some knowledge of command line and shell scripting

Slides: Download

13:15 - 14:00 Room-Logo First steps on Abel - hands on tutorial Laptop 

Sabry Razick

Description: Hands on introduction to the computer cluster Abel. The course is aimed at people with little background in UNIX and parallel computing and includes simple examples. 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: Users with modest background in UNIX and parallel computing

Prerequisites: some knowledge of command line and shell scripting, e.g. participation in the "The Linux command line for novices", "Introduction to shell scripting" and "Abel for beginners".

Equipment: The participants are required to bring their own laptop to participate in the tutorial.  The UiO participants who signed up before Thursday April 16, 14:00 will have Abel account created for them.  Participants who sign up later (or are not from UiO) will have access to guest accounts only.

Slides: Download

14:15 - 15:00 Room-Lille_auditorium How to install software on Abel  Laptop Bjørn-Helge Mevik

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

Target Audience: All welcome.

Prequisites: None.

Slides : Download

15:15 - 16:00,  Room-Lille_auditorium How to get help or ask for 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: None

Slides : Download

Wednesday, 04

Services

09:15- 10:00, Room-Store_auditorium TSD1

Nihal Perera, Maria Francesca

Description: Introduction to UiO's service for sensitive data.

Target Audience: All welcome, specially for new comers

Prerequisites: None

Slides : Download

10:15- 11:00, Room-Store_auditorium TSD2

Maria Francesca,Nihal Perera

Description: Introduction to UiO's service for sensitive data.

Target Audience: TSD users

Prerequisites: Basic knowledge of TSD or attend the TSD1 lecture

Slides : Download

11:15 - 12:00, Room-Store_auditorium Lifeportal-1

Nikolay Vazov

Description: Learn about our portal for life sciences that enables entry level users to start large computations on the Abel computer cluster.

Target Audience: All welcome

Prerequisites: None

Slides : Download

12:00 - 13:00 Lunch break

13:15 - 14:00 Room-SmallTalk

14:15 - 16:00                    Store auditorium

Python Jon Kerr Nilsen,Dmytro Karpenko

Description: Introduction to Programming, What is Python, Python as a calculator, Tuples and Lists, Control Flow, Dictionaries, Input and Output, Modules, Errors and Exceptions, Classes. Bring your laptop to participate in code exercises. Note: There will be breaks.

Target audience: Beginners.

Prerequisites: None.

Equipment: The participants must bring their own laptop with Python installed.

slides, my_file.py

advanced_slides, extra exercises

Thursday, 05

Programming

09:15 -10:00

Seminarroom-C

Efficient Usage of R

Bjørn-Helge Mevik

Description: How to optimize R code for speed, including general tips for speed improvement, timing R code to compare different versions, profiling R code to find out where time is spent.

Target Audience: R users on Abel

Prerequisites: The participants should know how to program in R.

Slides: Dowload

10:15-12:00

Seminarroom-C

Code and data management with version control

Leon du Toit

Description: 

Most people have used Dropbox and/or Word with 'track changes' and similar solutions to manage project collaboration. Although this can work for extremely simple workflows it quickly becomes painful when multiple people need to edit the same files, when you need the ability to track changes over time and when you want the ability to go back in time to revisit earlier versions of your document.

Git is a version control program designed to address all these collaborative concerns. It provides well defined ways to collaborate on the same set of files and gives you the ability to track changes without losing access to previous project states. Embracing version control will increase your productivity and make collaboration a pleasure.

 

Target audience:

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

 

Prerequisites:

Follow the simple setup instructions here.

Sildes.

12:00-13:00 Lunch break

13:15 - 14:00

Room-Prolog

How to run jobs efficiently on Abel

Ole Widar 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.

Target Audience: Users who take performance seriously.

Prerequisites: Working knowledge of Abel.

14:15 - 16:00

Room-Prolog

Workflows and pipelines - hands on tutorial

 

Abdulrahman Azab

Description: Researchers collaborate on conducting large scale scientific experiments and knowledge discovery applications using workflow systems. The lecture and tutorial will cover: 

  • How to write a workflow description for workflows and nested workflows 
  • How to submit and monitor workflow execution

Target audience: All are welcome.

Prerequisites: Basic knowledge of Abel, e.g. participation in "First steps on Abel"

Equipment: The participants are required to bring their own laptop to participate in the tutorial.  The UiO participants who signed up before Thursday April 16, 14:00 will have Abel account created for them.  Participants who sign up later (or are not from UiO) will have access to guest accounts only.

Slides: Download

Friday, 06

User experience

09:15 -12:00, Room-Lille_auditorium User community

Sabry Razick

*This course will only be arranged after considering interest of the participants (could request during registration)

Participants will get a chance to talk about there experience using Abel, TSD and Lifeportal. How they use it, what problems they face and suggestions. 

Lecture rooms:

CAML: Ole-Johan Dahls hus

PASCAL: Ole-Johan Dahls hus, second floor

LOGO: Ole-Johan Dahls hus

SmallTalk:Ole-Johan Dahls hus

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

JAVA:Ole-Johan Dahls hus, second floor

PROLOG:Ole-Johan Dahls hus

Lille auditorium:  Kristen Nygaards hus 

Store_auditorium:  Kristen Nygaards hus 

: Need to bring own laptop.

 

Organizer

Research Computing Services

Contact : Sabry Razick (email, mobile:93870788)

Organizer

Research Computing Services
Tags: HPC, Python, TSD, Lifeportal, Abel, command line, shell scripting
Published Aug. 21, 2015 6:31 PM - Last modified Feb. 11, 2016 10:13 AM