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Getting started with high-performance computing

Cluster Research and Valorization

Target group

Members of the Doctoral Schools

Level

Part 1 of this course is intended for researchers that are new to working in a Unix/Linux environment.

Part 2 of this course is intended for researchers that are already familiar with working at the Unix command line and who are entitled to request an account for the HPC infrastructure of the Vlaams Supercomputer Center (VSC).

Coordinators

Prof Dr Peter Dawyndt (Department of Applied Mathematics and Computer Science, Faculty of Sciences, Ghent University), Dr Ewald Pauwels (Vlaams Supercomputer Centrum) and Dr Kenneth Hoste (Information and Communication Technology Department, Ghent University).

Content

Computers have played an increasingly important role in science for 50 years, and in particular the past decade and a half, and will continue to do so. Scientists today need to be completely computationally literate, as it simply becomes almost impossible to do competitive science without such literacy.

This course provides an introduction to the Unix command line, scripting and high-performance computing (HPC) as a stepping stone towards the use of computer clusters for solving advanced computation problems.

Added value for doctoral students

Computational skills are an essential underpinning for scientists that wish to perform competitive research at an international level. Computer clusters therefore are no longer to sole playground of computer scientists. With the installation of its own high-performance computer, Ghent University has chosen to bundle efforts into a centrally managed computing infrastructure.

In offering a technical toolkit of basic computational skills, this course aims at lowering the threshold for doctoral researchers in different scientific domains to start making use of this HPC cluster. This must enable them to give birth to new kinds of science and possibly a new economic era of science-based innovation that could create new kinds of high-tech sectors that we can barely imagine today.

Programme

Part 1. Unix command line & shell scripting

  • working interactively with the shell command line
  • consulting technical information
  • interactive text editing
  •  file management
  • fi les and fi lters
  • protections and privileges
  • IO-redirection en pipes
  • regular expressions
  • process and job management
  • computer networks, X Window System
  • version control systems (http://github.ugent.be)
  • shell scripting basics
    • shell variables
    • processing command line arguments
    • control structures
    • fi le descriptors
    • shell functions

Part 2. HPC basics & python scripting

  • HPC basics
    • submitting jobs
    • submitting array jobs
    • monitoring and managing submitted jobs
    • HPC environment variables
    • checkpointing
  • Python scripting
    • introduction to Python
    • scientific computing with pylab: numpy, scipy and matplotlib

Format

Part 1 and part 2 comprise (each) three full days of hands-on sessions where newly acquired skills will immediately be brought into practice.

Time schedule

  • Part 1: FULL !! Mon-Wed 26, 27 & 28 May 2014, 9:00-18:00
  • Part 2: FULL !! Mon-Wed 2, 3 & 4 June 2014, 9:00-18:00

References

  • E. Nemeth, G. Snyder, T.R. Hein, B. Whaley, UNIX and Linux System Administration Handbook (4th Edition), Prentice Hall, 2010.
  • A. Afzal, UNIX Unbounded: A Beginning Approach, fourth edition, Pearson Education, 2003.
  • D. Barron, The World of Scripting Languages, John Wiley & Sons, 2000.
  • R. Blum, Linux Command Line and Shell Scripting Bible, Wiley, 2008.
  • S.M. Sarwar, R. Koretsky, S.A. Sarwar, UNIX the textbook, second edition, Pearson Education, 2005.

Course material

Each participant will receive:

  • Part 1: Mark G. Sobell, A Practical Guide to Linux Commands, Editors, and Shell Programming, Prentice Hall, 2009 (2nd edition).
  • Part 2: Mark Lutz, Learning Python: Powerful Object-Oriented Programming, O‚ÄôReilly Media, 2009 (4th edition).

Other course material will be made available through Zephyr.Textbooks will be complemented with additional printed tutorials, exercises and solutions. Participants will receive alive-DVD of Ubuntu Linux.

Number of participants

  • Part 1: 50
  • Part 2: 50

For the second part of the course, priority will be given to students that have subscribed to the first part of the course.

Venue

Multimedia-room, Information and Communication Technology Department (DICT), S9, Krijgslaan 281, Gent

Registration fee

Free of charge for members of the Doctoral Schools

Registration procedure

To register or add your name to the waiting list, send an e-mail to doctoralschools@UGent.be (mentioning your name, first name, student number, Doctoral School, Department, course title and course code/group). Your registration will be confirmed by e-mail. For the second part of the course, priority will be given to students that have subscribed to the first part of the course.