The cluster uses environment modules v3.2 to control what software is loaded in your environment. Certain software will be loaded by default, but there are other versions available to keep analyses consistent across a study or additional software that you may wish to load.

- “module list” will show you what is currently loaded

[cmp12@blade08 ~]$ module list
Currently Loaded Modulefiles:
  1) fsl/6.0.3           2) freesurfer/7.1.1    3) afni/21.1.04        4) ants/2.3.4          
  5) mrtrix3/3.0.2       6) singularity/3.6.3   7) matlab/R2019b

- “module avail” will show you what additional software or alternative are available

[cmp12@blade08 ~]$ module avail

------------------------------------------ /etc/modulefiles -----------------------------------------------
afni/18.2.15                dtk/0.6.4.1                 fsl/5.0.10                  laynii/2.0.0                miniconda                   singularity/2.5.2
afni/21.1.04                ffmpeg/4.1                  fsl/5.0.6                   mango/4.0.1                 mpi/mpich-3.0-x86_64        singularity/3.6.3
ansysEM/19.0                fidl/2.66                   fsl/5.0.9                   mango/4.1                   mpi/mpich-x86_64            slicer/4.6.2
ansysEM/19.5                freesurfer/0_dev            fsl/6.0.0                   matlab/R2014a               mpi/openmpi-x86_64(default) trackvis/0.6.1
ants/2.3.4                  freesurfer/5.3.0            fsl/6.0.3                   matlab/R2017a               mricron                     weka/3.8.4
c3d/1.1.0                   freesurfer/6.0.0            hcp_pipelines/3.27.0        matlab/R2018a               mrtrix3/3.0.2(default)
camino/2.1                  freesurfer/6.0.1            hcp_workbench/1.4.0         matlab/R2019b(default)      mrtrix3/mact
dcm2niix                    freesurfer/7.1.1            hcp_workbench/1.4.2         matlab/R2021a               mrtrix3/tissue
dramms/1.5.1                fscan                       hcp_workbench/1.5.0         medinria/2.2.3(default)     rar/5.70
dtiprep/1.2.4               fsl/5.0.1                   laynii/1.5.6                medinria/4.0.0              simnibs/2.0.1

- to load additional software use “module load modulename(s)”

[cmp12@blade08 ~]$ module load laynii dcm2niix fscan

[cmp12@blade08 ~]$ module list
Currently Loaded Modulefiles:
  1) fsl/6.0.3           3) afni/21.1.04        5) mrtrix3/3.0.2       7) matlab/R2019b       9) dcm2niix
  2) freesurfer/7.1.1    4) ants/2.3.4          6) singularity/3.6.3   8) laynii/2.0.0       10) fscan

- to switch to an alternative version of a loaded software use “module switch modulename/version”

[cmp12@blade08 ~]$ which feat
/usr/local/packages/fsl-6.0.3/bin/feat

[cmp12@blade08 ~]$ module switch fsl/5.0.10

[cmp12@blade08 ~]$ module list
Currently Loaded Modulefiles:
  1) **fsl/5.0.10**      3) afni/21.1.04        5) mrtrix3/3.0.2       7) matlab/R2019b       9) dcm2niix
  2) freesurfer/7.1.1    4) ants/2.3.4          6) singularity/3.6.3   8) laynii/2.0.0       10) fscan

[cmp12@blade08 ~]$ which feat
/usr/local/packages/fsl-5.0.10/bin/feat

- to remove a loaded package “module rm modulename” - to unload everything “module purge”

[cmp12@blade08 ~]$ module rm fsl

[cmp12@blade08 ~]$ module list
Currently Loaded Modulefiles:
  1) freesurfer/7.1.1    3) ants/2.3.4          5) singularity/3.6.3   7) laynii/2.0.0        9) fscan
  2) afni/21.1.04        4) mrtrix3/3.0.2       6) matlab/R2019b       8) dcm2niix

[cmp12@blade08 ~]$ module purge

[cmp12@blade08 ~]$ module list
No Modulefiles Currently Loaded.

You can add module calls to your submission scripts to keep the environment consistent for your jobs or you can add module calls to your ~/.bashrc initialization file to have a specific set of modules across all of your cluster jobs or interactive sessions.

[cmp12@blade01 ~]$ tail -n 10 ~/.bashrc 

module purge
module load fsl/6.0.0 freesurfer/6.0.1 matlab/R2018a


[cmp12@blade01 ~]$ module list
Currently Loaded Modulefiles:
  1) fsl/6.0.0          2) freesurfer/6.0.1   3) matlab/R2018a