DCSR, Running Python and R applications on the clusters


 

A lot of scientific applications at UNIL are based on Python or R. Running such applications on HPC clusters can be complex regarding the constraints induced by the use of shared facilities with no administrative rights (and no Internet access in the case of Jura cluster). This course provides information on how to be autonomous regarding installation/run of Python and R applications on all the DCSR clusters.

 

Objectives   Learn how to install and run in a clean way Python and R applications on the UNIL HPC clusters. The purpose is NOT to learn Python or R programming.
Target audience   Any PhD students, post-docs, researchers of UNIL and CHUV who need to  use (their own/open source) Python or R applications  on the UNIL HPC clusters.
Content  

At the end of the course, the participants are expected to:

  • Be able to install and run Python applications on HPC clusters (including Jura) from:
    • the DCSR software stack
    • Pypi repository
    • Conda repository
    • Sources
  • Understand the interest Python/Conda virtual environments
  • Be able to install and run R applications on HPC clusters (including Jura) from:
    • CRAN
    • Bioconductor
  • Be able to properly organize the installed applications in the storage facility.
Length   1 half-day
Organization   On a quarterly basis
Location   To be defined or remotely
Prerequisites  
  • Basic knowledge of working with command line tools on Linux based operating systems. If you do not feel comfortable with UNIX commands, please take a UNIX fundamentals e-learning module or attend the SIB 'First Steps with UNIX' course for example.
  • Basic knowledge of bash is an asset.
  • Be comfortable with all the topics addressed in the introduction course "DCSR, Introduction to using the clusters".
  • Please bring your own laptop with WIFI eduroam activated. You will need a SSH client to connect to the clusters. Windows users can install e.g. Putty or MobaXterm or a Linux virtual machine or use the Windows Subsystem for Linux (WSL) if available (Windows 10).

 

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