Software and tools
We’ll briefly get overviews over
software tools on UPPMAX
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.
list all available modules (also bio-informatics if
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
Display a brief module-specific help (not available for all modules)
module help <module name>or
ml help <module name>
avail) but otherwise hidden modules (
bioinfo-toolsand Easybuild modules)
module spider <part of tool name>or
ml spider <module name>
You can also find (almost) all installed software at: https://www.uppmax.uu.se/resources/software/installed-software/
Hands on using a tool
$ matlab &
Does not work!
Load module first
$ module avail matlab
module load matlabwill 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)
$ 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.
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.
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 cd /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.