Environment Modules
Access to many applications and libraries is controlled by the modules utility. The module command allows you to easily manipulate your Linux environment to use various applications and programming libraries, sometimes including older or newer versions than the default. When you need to change your environment you simply add or rm modules. Here are some of the commands you’ll need.
List Available Software
[username@bisonnet-hpc ~]$ module avail
-------------------------------------- /software/etc/modulefiles ---------------------------------------
admixture/1.3.0 gurobi-optimizer/12.0.1 python/3.11-genome
alignment/2025.03.26 insectOR/2024.05.09 python/3.12-bio
annontation/2025.03.27 jdftx/1.7.0 python/3.12-deeplearn
assembly/2025.03.27 kraken2/2.1.4 python/3.12-gpu
assembly_assessment/2025.03.26 lammps/2024.08.29 python/3.12-jdreese-test
avogadro2/1.100 mathematica/14.2.1 python/3.12-minimal
bcftools/1.21 matlab/R2024b python/3.12-omnic
blast/2.2.26 molecular_evolution/2025.03.26 python/3.12-seff
braker3/3.0.8 ncbi-blast/2.16.0+ qc/2025.03.28
comsol/6.3 octave/9.4.0 R/4.4.3
CPLEX/22.1.2 Omni-C/2025.03.25 radseq/2025.03.25
cuda/12.4.1 opencv/4.11.0 RELION/5.0
cudnn/9.8.0 openmpi/4.1.8 repeats/2025.04.11
dfam-tetools/2025.03.26 openmpi/5.0.7 seq_tools/2025.03.27
emacs/30.1 orca/6.0.1 SIMULIA/2025
exonerate/2.4.0 perl/5.40.1 stacks/2.68
fastp/0.24 pfamscan/1.6 structure/2.3.4
ffmpeg/7.1 phylogeny/2025.03.28 transdecoder/5.7.1
gaussian/16.B.01 plink/1.9 Trinity/2.15.2
genome/2025.03.26 python/3.10-ahf009 vscode/1.100.3
glimmer/3.02 python/3.10-misc xcrysden/1.6.2
GT-POWER/2025.1.0001 python/3.11-curation xmgrace/5.1.25
------------------------------------ /usr/share/Modules/modulefiles ------------------------------------
dot module-git module-info modules null use.own
Key:
modulepath default-version
List Software In Your Environment
[username@bisonnet-hpc ~]$ module list
Currently Loaded Modulefiles:
1) python/3.12-minimal
Key:
default-version
Add Software to Your Environment
[username@bisonnet-hpc ~]$ module load python/3.12-minimal
You can also load the default version of a software package by dropping the version:
[username@bisonnet-hpc ~]$ module load python
Remove Software from Your Environment
[username@bisonnet-hpc ~]$ module unload python/3.12-minimal
Module Conflicts
Modules will prevent you from adding conflicting packages. For example, you’ll receive an error if you try to add two versions of Python to your environment. To change to a new version, either unload one version and load another or use the switch command:
[username@bisonnet-hpc ~]$ module list
Currently Loaded Modulefiles:
1) python/3.12-minimal
Key:
default-version
[username@bisonnet-hpc ~]$ module switch python/3.12-deeplearn
Switching from python/3.12-minimal to python/3.12-deeplearn
Loading requirement: cuda/12.4.1 cudnn/9.8.0Add Modules at Login
To add modules to your Linux environment that will load every time you login, use:
(NOTE: only run the echo command once; then just use initadd to add additional modules):
[username@bisonnet-hpc ~]$ echo "module add null" >> ~/.bashrc
[username@bisonnet-hpc ~]$ module initadd python/3.12-minimalLikewise, you can remove commands from your initial environment using:
[username@bisonnet-hpc ~]$ module initrm python/3.12-minimalAdditional Help
[username@bisonnet-hpc ~]$ module help