Getting Started with High-Performance Computing Part I (HPC basics) and Part II (Python scripting)

Cluster Research and Valorization

Target group

Members of the Doctoral Schools

Target audience

  • Part 1 of this course (three full days) is intended for researchers that are new to working in a Unix/Linux environment. It comprises three full days of hands-on sessions where newly acquired skills will immediately be brought into practice. Participants must be entitled to request an account for the HPC infrastructure of the Vlaams Supercomputer Center (VSC). The number of participants for these sessions is restricted to 50.
  • Part 2 of this course (three full days) is intended for researchers that are new to programming or new to Python programming. It comprises three full days of hands-on sessions where newly acquired skills will immediately be brought into practice through a series of case studies. The number of participants for these sessions is restricted to 50.

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.

Time schedule

  • Part I: 31 May-1-2 June 2017 (Wednesday till Friday) 9:00-17:00    (Sandwich lunch is provided)
  • Part II: 7-8-9 June 2017 (Wednesday till Friday) 9:00-17:00     (Sandwich lunch is provided)

Venue: Multimedia-room (ground floor), Building S9, Information and Communication Technology Department (DICT), Krijgslaan 281, Ghent

Other course material will be made available through the electronic learning environment of Ghent University (http://zephyr.ugent.be)

Number of participants

  • Part 1: maximum 50
  • Part 2: maximum 50

Registration procedure

Please follow this link: https://webapps.ugent.be/eventManager/events/GSHPC Your registration will be confirmed by e-mail from the Doctoral Schools.

    Programme

    Part 1. Unix command line, shell scripting and HPC basics

    • working interactively with the shell command line
    • consulting technical information
    • interactive text editing
    • file management
    • files and filters
    • 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
      • file descriptors
      • shell functions
    • HPC basics
      • submitting jobs
      • submitting array jobs
      • monitoring and managing submitted jobs
      • HPC environment variables
      • checkpointing

      Part 2. Python scripting

        • Python scripting
          • introduction to Python
          • scientific computing with pylab: numpy, scipy and matplotlib and Jupyter Notebook

        Evaluation criteria

        Each part (part I and part II) counts as 1 transferable skills training after 100% participation

        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’Reilly Media, 2009 (4th edition).

        Registration fee

        Free of charge for members of the Doctoral Schools

        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.