Topic outline

  • General

    High Performance Computing (HPC) in Life Sciences: Vital-IT & UniFr-UniBe Infrastructure Training

    Fribourg, 3 December 2015

    Trainers: Vassilios Ioannidis, Grégoire Rossier
    Venue: Room 2.225, Building DOKPE-Geographie 14 (PER14), University of Fribourg
    ECTS: 0.25 (given a passed exam)
    Fee: no
    Application deadline:
    1 December 2015
    Application status: closed


    Several scientific applications require computing and/or storage resources that go beyond the processing power of a single multi-core machine. High performance computing (HPC) clusters provide the necessary hardware and software infrastructure to efficiently run computing and data intensive applications. The course provides detailed information on how to efficiently use Vital-IT's compute and storage infrastructure for life science applications.


    This course is reserved for people wanting to use the Vital-IT cluster. People using the UBELIX infrastructure are welcome too.

    Learning Objectives

    • Obtain basic knowledge on high throughput and high performance computing
    • Learn how to use Vital-IT's infrastructure for scientific applications (including hands-on exercises)
    • Tips and tricks for effective and efficient cluster usage (incl. compute and storage usage guidelines)
    • Discuss particular computing needs and requirements of course participants


    Knowledge / competencies:

    • Basic understanding of working with command line tools on Linux or Windows-based operating systems. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module.

    • Scripting language such as bash or Perl is an asset


    • Please bring your own laptop with WIFI Eduroam activated (Windows with Putty application installed or a Linux or Mac with a Terminal application)

    • Complete the exercise 'UNIX evalutation' at least 4 days before the course - see below


    Application is closed


    Beware, location has changed!

    University of Fribourg, Building DOKPE-Géographie 14 (PER14 on the linked map), room 2.225

    Additional information

    The course will be taught by Vassilios Ioannidis and Grégoire Rossier, with the assistance of Ivan Topolsky for the practicals.

    We will recommend 0.25 ECTS credits for this course (given a passed oral exam at the end of the session and a written exercise).

    You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

  • Programme

    Grégoire Rossier (Training and Outreach, Vital-IT), Vassilios Ioannidis (SIB Technology, Vital-IT), Ivan Topolsky (Vital-IT),

    09h15 -10h45
    Introduction to HPC and Basic Infrastructure Usage

    11h30 - 12h30
    Exercises I

    13h30 - 14h45
    Advanced Infrastructure Usage and Use Case Discussion

    15h00 - 16h30
    Exercises II

    16h30 - 17h00
    Optional exam