Software and tools

Objectives

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)

Note

Modules

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>

Hands on using a tool

$ matlab &

$ 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 &

$ module load samtools

        "These module(s) or extension(s) exist but cannot be loaded as requested: "samtools""

$ module load bioinfo-tools samtools

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.

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

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

Solution

 /proj/introtouppmax/labs/sunray
 
 cd /proj/introtouppmax/labs/
 ./sunray

Keypoints

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.