Software and tools


  • We’ll briefly get overviews over

    • software tools on UPPMAX

    • databases

  • Introduction quide for installing own software or packages

  • Very short introduction to developing old programs

  • 800+ programs and packages are installed.

  • To avoid chaos and collisions, they are managed by a module system.

  • This system keeps installed software hidden by default, and users have to explicitly tell their terminal which version of which software they need.

  • The modules are most often available across cluster (except for Miarka)


  • Bioinformatics tools require loading the “bioinfo-tools” module first.


Some commands

  • list all available modules (also bio-informatics if bioinfo-tools is loaded)

    • module avail or ml av

  • Search for modules (full name not needed and case insensitive)

    • module avail <part of tool name> or ml av <part of toolname>

  • Load a module

    • module load <module name> or ml <module name>

  • Unload a module

    • module unload <module name> or ml -<module name>

  • List loaded modules

    • module list or ml

  • Display a brief module-specific help (not available for all modules)

    • module help <module name> or ml help <module name>

  • Search (like avail) but otherwise hidden modules (bioinfo-tools and Easybuild modules)

    • module spider <part of tool name> or ml spider <module name>

Installed software

Installed databases

Hands on using a tool

  1. use matlab

$ matlab &
  • Does not work!

  • Load module first

$ module avail matlab
  • module load matlab will start Default version (often latest) demarked with a D in the list

  • Let’s load a specific version, often good for reproducibility.

$ module load matlab/R2020b

$ matlab &
  • Matlab starts (if X11 is active)

  1. use Samtools

$ module load samtools

        "These module(s) or extension(s) exist but cannot be loaded as requested: "samtools""
$ module load bioinfo-tools samtools
  • Bioinformatic tools are hidden by default

Install software yourself

  • You can install in your home directory.

    • This is handy for personal needs, low numbers of files (i.e. not Conda).

  • Usually better to install in project directory.

    • This way the project contains both data and software — good for reproducibility, collaboration, and everyone’s general sanity.

Python packages





  • Docker will unfortunately not work on the clusters, since it requires root permission.

Build from source


  • The UPPMAX staff has already other ways to install most software applications.

  • Please use Spack only if other ways to install your tool is not possible or very difficult, e.g. requiring very many dependencies and it is not available through, e.g. Easybuild.

  • Spack user guide at UPPMAX

Own development…

Run own scripts or programs

  • Unless your script or program is in the active path, you run it by the full path or ./<file> if you are in the present directory.

Demo: Run a Fortran program

  • Run the program “sunray” located in: /proj/introtouppmax/labs/sunray


  • Centrally installed software are reached through the module system and available throughout all nodes.

  • Your own installed software, scripts, python packages etcetera are available from their paths.