Topic outline

  • General

    High Performance Computing (HPC) in Life Sciences - UBELIX oriented

    Bern, 2 June 2015


    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 UBELIX compute and storage infrastructure for life science applications.


    • Obtain basic knowledge on high throughput and high performance computing
    • Learn how to use UBELIX 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


    • Basic understanding of working with command line tools on Linux or Windows-based operating systems (Link to our UNIX Fundamentals self-learning module).
    • Scripting language such as bash or Perl is an asset
    • Please bring your own PC with WIFI Eduroam activated (Windows with Putty application installed or a Linux or Mac with a Terminal application)
    • If you attended UNIX First step course, please skip this step. Else, please complete the exercise 'UNIX evalutation' before the course - see below


    Application is closed.


    This one-day course is held in at the University of Bern.

    • University of Bern, Hochschulstrasse 4
    • Seminar room Nr. 331/ 3rd floor West

    Sessions run from 9:00 to 17:00 approximately, with a lunch break.

    Additional information

    The course will be taught by Walid Gharib.

    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.

    • Schedule

      09h00 -10h30

      Introduction to HPC and Basic Infrastructure Usage

      11h00 - 12h30
      Exercises I

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

      15h00 - 17h30
      Exercises II