04_modules.md

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Modules and pre-installed software {.title}

The module system and how to use it on CSC supercomputers. The same information can be found in the module section of Docs CSC.


All materials (c) 2020-2025 by CSC – IT Center for Science Ltd. This work is licensed under a **Creative Commons Attribution-ShareAlike** 4.0 Unported License, [http://creativecommons.org/licenses/by-sa/4.0/](http://creativecommons.org/licenses/by-sa/4.0/)

Module systems in supercomputers

• A variety of software with different (possibly conflicting) requirements are needed on a supercomputer

• The solution for managing this situation: separating the applications into modules

• Environment modules set up everything required by a particular application:

  • Load libraries, adjust paths, set environment variables

• CSC uses Lmod environment modules

How to access pre-installed software on CSC supercomputers

• You can check the available applications and their respective modules in the application list

  • Each application page in Docs CSC contains information on basic usage

• You can use module spider to search for an application

  • On LUMI you need to first run module use /appl/local/csc/modulefiles to see modules installed by CSC

• Use the software by loading the module: module load modulename

  • For example: module load gromacs-env

How to use modules

• The general syntax is simple: module command modulename

  • List of the most common commands

• These modules are used both in interactive sessions and batch jobs

  • Include module purge and module load modulename in your batch scripts to always get the same modules in consecutive jobs

• You can't just load all the modules because of possibly conflicting dependencies

Useful commands for the module environment

• These commands will help you navigate the module environment:

  • module list: See a list of the currently loaded modules

  • module avail: Modules currently available for loading (hides modules that can't be loaded at the moment due to dependencies)

  • module spider modulename: Search for an application in the list of all existing modules

  • module spider modulename/version: Gives information on how to load a specific version of a module (prerequisites etc.)

• If you try to load a module that is unavailable, you will get an error message

Various kinds of modules

• Some modules contain software that have a graphical user interface

  • For example, the chemistry visualization software VMD

  • Use the Puhti or Mahti web interface, or another method to open the GUI

• Some modules contain software that only provide a command-line interface

  • For example, the OpenBabel module

• A module might contain only one program (e.g. gromacs-env), while some provide a collection of applications (e.g. Python or R packages)

  • For example, Geoconda and Python Data

Conda, Python and R packages

• Some pre-installed software are distributed through the Conda package management tool

  • Do not install Conda environments directly on the Lustre parallel file system, containerize them instead using e.g. Tykky

  • See the usage policy for further details

• Pre-installed Python packages are available in Python-related modules

  • Check Docs CSC for the available packages and usage instructions

  • It is not possible to load multiple modules with Python packages at once

  • pip list shows a list of packages installed in the current environment

• Instructions on how to check installed R libraries

  • RStudio shows available packages in the sidebar

Customizing your own environment

• If you "always" use certain modules, it is possible to load them in your .bashrc, but we do not recommend this

  • This causes the modules to be always loaded, also in batch jobs which may cause hard-to-spot issues

  • If you already did this, see the csc-env command

• If it feels cumbersome to run multiple module load modulenames at the start of each session, you can define an alias for these in your .bashrc

  • Add this line to your .bashrc: alias mods="module load modulenames"

  • Now you can load all those modules easily with mods (after sourcing your .bashrc or logging out and in again)

Advanced module use

• You can save your current set of modules with module save filename and load it later with module restore filename

• You can also write your own module files:

  1. Add them to your home directory ($HOME/modulefiles)

  2. Add this path to the module search path (module use $HOME/modulefiles)

• To see the parameters of a module file, use the command module show modulename