Introduction to the module system

Objectives

  • Learn the basics of the module system which is used to access most of the software at the majority of the HPC centres in Sweden
  • Learn about some of the most used commands for the module system
  • Find existing modules

Most programs are accessed by first loading them as a ‘module’. Thus, knowing about modules is necessary for you to be able to access the majority of the installed software at a centre!

Modules are:

  • used to set up your environment (paths to executables, libraries, etc.) for using a particular (set of) software package(s)
  • a tool to help users manage their Unix/Linux shell environment, allowing groups of related environment-variable settings to be made or removed dynamically
  • allows having multiple versions of a program or package available by just loading the proper module
  • are installed in a hierarchial layout. This means that some modules are only available after loading a specific compiler and/or MPI version, etc.
    • that is, the modules have prerequisites that needs to be loaded before they can be loaded.
    • Whether or not modules have prerequisites vary by center. More on this later!

Many of the centres in Sweden are using the Lmod module system. It is an environment module system that is Lua based.

Many, but not all, of the centres in Sweden are using the EasyBuild framework for building and installing software modules.

Important

Take care not to use any system-installed versions of gcc, python, etc. Always use the module instead, when available!

Always check if there is a module instead of just building the software/package yourself!

If there is a software missing that you need, then ask if it can be installed.

Useful commands

This is a list of some of the most useful commands for the module system. In the list below, MODULE is used as a stand-in for any software module.

  • See which modules exists: module spider or ml spider
  • See which versions exist of a specific module: module spider MODULE or ml spider MODULE
    • This way is only recommended at HPC2N, LUNARC, C3SE, and PDC
  • See prerequisites and how to load a specfic version of a module: module spider MODULE/VERSION or ml spider MODULE/VERSION
  • List modules depending only on what is currently loaded: module avail or ml av
    • At UPPMAX and NSC this will list all available modules!
  • See which modules are currently loaded: module list or ml
  • Loading a module: module load MODULE or ml MODULE
  • Loading a specific version of a module: module load MODULE/VERSION or ml MODULE/VERSION
  • Unload a module: module unload MODULE or ml -MODULE
  • Get more information about the paths etc. of a module: ml show MODULE or module show MODULE
  • Get information about what is in a module: module help MODULE or ml help MODULE
  • Unload all modules except the ‘sticky’ modules: module purge or ml purge
  • Module collections to load/unload a bunch of modules: module save <collection> and module restore <collection>

Finding existing modules

Warning

This differs somewhat between centres. Some centres recommend using module avail while at others it is better to use module spider!

This is mainly to do with whether or not modules in general have prerequisite modules that needs loading before, or not.

  • module spider: HPC2N, LUNARC, C3SE, PDC
  • module avail: UPPMAX, NSC

With module spider

This is the recommended way to find existing software modules at HPC2N, LUNARC, C3SE, and PDC.

Hint

module spider can be written in short form as ml spider

Example, HPC2N 
b-an01 [~]$ module spider

--------------------------------------------------------------------------------------------------------------
The following is a list of the modules and extensions currently available:
--------------------------------------------------------------------------------------------------------------
  :  (E)

  ABRicate: ABRicate/1.0.0
    Mass screening of contigs for antimicrobial and virulence genes

  ABySS: ABySS/2.2.5
    Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

  ACTC: ACTC/1.1
    ACTC converts independent triangles into triangle strips or fans.

  ADGofTest: ADGofTest/0.3 (E)

  AICcmodavg: AICcmodavg/2.3-0 (E), AICcmodavg/2.3-1 (E), ...

  ALDEx2: ALDEx2/1.20.0 (E), ALDEx2/1.26.0 (E), ALDEx2/1.28.1 (E), ...

  ALL: ALL/1.30.0 (E), ALL/1.36.0 (E), ALL/1.38.0 (E), ...

  AMAPVox: AMAPVox/0.12.0 (E), AMAPVox/1.0.0 (E), AMAPVox/1.0.1 (E), ...

  AMGX: AMGX/2.2.0-CUDA-11.3.1
    Distributed multigrid linear solver library on GPU

  AMOS: AMOS/3.1.0
    The AMOS consortium is committed to the development of open-source whole genome assembly software

  AMPtorch: AMPtorch/0.1
    AMPtorch is a PyTorch implementation of the Atomistic Machine-learning Package (AMP) code that seeks to provide users with improved performance and flexibility as compared to the original code. The implementation does so by benefiting from state-of-the-art machine learning methods and techniques to be optimized in conjunction with high-throughput supercomputers.

  ANCOMBC: ANCOMBC/1.6.4 (E), ANCOMBC/2.4.0 (E), ANCOMBC/2.6.0 (E)

...

Hint

You can check if a specific software module is installed by trying module spider <SOFTWARE>

Example, GROMACS at HPC2N (it works the same at LUNARC, C3SE, and PDC): 

b-an01 [~]$ module spider GROMACS

--------------------------------------------------------------------------------------------------------------------
  GROMACS:
--------------------------------------------------------------------------------------------------------------------
    Description:
      GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

     Versions:
        GROMACS/3.3.3-cphmd-1.3
        GROMACS/3.3.3-cphmd-1.3-1lpernode
        GROMACS/3.3.3-cphmd-1.4
        GROMACS/4.0.7-ionstr
        GROMACS/5.1.4
        GROMACS/2016.x-drude-20180214-g3f7439a
        GROMACS/2016.x-drude-20220117-g78fe3d1e
        GROMACS/2016.x-drude-20220120-ge35ae4e2
        GROMACS/2016.4
        GROMACS/2018.8
        GROMACS/2019
        GROMACS/2019.4-PLUMED-2.5.4
        GROMACS/2021
        GROMACS/2022.4
        GROMACS/2023.1-CUDA-11.7.0
        GROMACS/2023.1
        GROMACS/2023.3-CUDA-12.1.1-PLUMED-2.9.0
        GROMACS/2024.1
        GROMACS/2024.3-CUDA-12.4.0
     Other possible modules matches:
        GROMACS-LS

--------------------------------------------------------------------------------------------------------------------
  To find other possible module matches execute:

      $ module -r spider '.*GROMACS.*'

--------------------------------------------------------------------------------------------------------------------
  For detailed information about a specific "GROMACS" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider GROMACS/2024.3-CUDA-12.4.0
--------------------------------------------------------------------------------------------------------------------

NOTE: Beware that you may have to try with different capitalization to find the software!

With module avail

This is the recommended way to find existing software modules at UPPMAX and NSC.

Hint

module avail can be written in short form as ml av

Example, UPPMAX (NSC works the same) 
[bbrydsoe@rackham1 ~]$ module avail

--------------------------------- /sw/mf/rackham/applications ----------------------------------
  ABINIT/8.10.3                          comsol/6.1
  ALPS/2.3.0                             comsol/6.2                       (D)
  Amber/20                               comsol/6.3
  Ansys/19.1                             conda/latest
  Ansys/19.5                             coreutils/8.27
  Ansys/2020R1                    (D)    coreutils/9.1                    (D)
  BLAKE2/20230212-ed1974e                cowsay/3.03
  CDO/1.9.5                              cp2k/4.1-gcc
  CDO/1.9.7.1-intel18.3                  cp2k/6.1-gcc
  CDO/1.9.7.1                     (D)    cp2k/8.1-gcc                     (D)
  COIN-OR-OptimizationSuite/1.8.0        darsync/20240208-7ff09d9
  CPLEXOptimizationStudio/12.9.0         desmond/2022-2
  CPLEXOptimizationStudio/20.10   (D)    doxygen/1.8.11
  CST_Studio/2023.0                      doxygen/1.9.6                    (D)
  Cromwell/71                            eLSA/20160907-febe2d7a57c8
  Cromwell/86                     (D)    emacs/25.2
  DBdeployer/latest                      emacs/27.2
  DOCK/3.7                               emacs/28.2                       (D)
  FFmpeg/4.4                             freesurfer/6.0.0
  FFmpeg/5.1.2                    (D)    freesurfer/7.4.1                 (D)
  GDAL/2.1.0                             gamess/20170930
  GDAL/3.1.0                             gaussian/g09.d01
  GDAL/3.6.2                             gaussview/5.0.8
  GDAL/3.7.2                      (D)    gawk/4.1.4
  GOTM/5.3-221-gac7ec88d                 gdl/1.0.0-rc.1
  GhostPDL/9.53.3                        gnuplot/system
  GoogleCloudSDK/217.0.0                 gnuplot/5.0.7
  GoogleCloudSDK/447.0.0                 gnuplot/5.2.7                    (D)
...

Hint

You can check if a specific software module is installed by trying module avail <SOFTWARE>

Example, GROMACS at NSC: 

[x_birbr@tetralith3 ~]$ module avail GROMACS

--------------------- /software/sse2/tetralith_el9/modules ---------------------
   GROMACS/recommendation                    (D)
   GROMACS/2021.3-PLUMED-nsc1-gcc-9.3.0-bare
   GROMACS/2022.2-nsc1-gcc-9.3.0-bare
   GROMACS/2023.4-gpu-hpc1-g9
   GROMACS/2023.4-mpi+omp-hpc1-g9
   GROMACS/2024.2-mpi+omp-hpc1-g11
   GROMACS/2024.4-mpi+omp+double-cp2k-g11

  Where:
   D:  Default Module

Warning

If you do module avail at one of the centres that recommend module spider you will not get a full list of software, only those are available to load with no other prerequisites than are currently loaded. This is however, a good way to find compiler toolchains (more about that later).

Example, HPC2N

Here you only get what is available without loading anything else. Most modules have prerequisistes so this is not the way to find all modules! 

b-an01 [~]$ module avail

------------------------------------------- /hpc2n/eb/modules/all/Core -------------------------------------------
  ATSAS/3.2.1-1_amd64                                binutils/2.34
  Advisor/2023.2.0                                   binutils/2.35
  BLAST/2.11.0-Linux_x86_64                          binutils/2.36.1
  Bison/3.0.4                                        binutils/2.37
  Bison/3.0.5                                        binutils/2.38
  Bison/3.3.2                                        binutils/2.39
  Bison/3.5.3                                        binutils/2.40
  Bison/3.7.1                                        binutils/2.42                  (D)
  Bison/3.7.6                                        biosoup/0.11.0
  Bison/3.8.2                              (D)       code-server/4.97.2
  CMake/3.18.4                                       cuDNN/8.0.4.30-CUDA-11.1.1
  COMSOL/5.4.0.225                                   cuDNN/8.2.1.32-CUDA-11.3.1
  COMSOL/5.6.0.401                                   cuDNN/8.2.2.26-CUDA-11.4.1
  COMSOL/6.0.0.354                         (D)       cuDNN/8.4.1.50-CUDA-11.7.0
  CUDA/8.0.61                                        cuDNN/8.9.2.26-CUDA-12.1.1
  CUDA/10.1.105                                      cuDNN/9.1.1.17-CUDA-12.4.0
  CUDA/10.1.243                                      cuDNN/9.2.0.82-CUDA-12.4.0
  CUDA/11.3.1                                        cuDNN/9.5.0.50-CUDA-12.6.0     (D)
  CUDA/11.4.1                                        cuSPARSELt/0.6.0.6-CUDA-12.1.1
  CUDA/11.5.0                                        cuTENSOR/1.2.2.5-CUDA-11.1.1
  CUDA/11.6.0                                        cuTENSOR/2.0.1.2-CUDA-12.1.1   (D)
  CUDA/11.7.0                                        ffnvcodec/11.1.5.2
  CUDA/12.0.0                                        ffnvcodec/12.0.16.0
  CUDA/12.1.1                                        ffnvcodec/12.1.14.0
  CUDA/12.4.0                                        ffnvcodec/12.2.72.0            (D)
  CUDA/12.5.0                                        flex/2.6.3
  CUDA/12.6.0                              (D)       flex/2.6.4                     (D)
  CUDAcore/11.0.2                                    foss/2019a
  CUDAcore/11.1.1                          (D)       foss/2019b
  Catch2/2.13.9                                      foss/2020a
  Cereal/1.3.2                                       foss/2020b
  CheckM-Database/2015_01_16                         foss/2021a
  ChimeraX/1.1                                       foss/2021b
...

Exercise

  1. Try listing the available modules. Use either module spider or module avail, depending on your centre.
  2. Try checking for a specific software module to see if it is installed:
    • GROMACS
    • Python
    • VASP
    • R
  3. What happens if you change the capitalization when you search for a module? Do you still find it? (Centre-dependent!)

Summary

Note

  • We learned about some of the most useful commands
  • We saw how to find which modules are available at a centre
    • Using module spider
    • Using module avail