Access to Software

Accessing Scientific Software (quarantine aka modules)

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Scientific software is deployed across all computers in the platform via shared network drive, ensuring the same version of software is run on all machines during any kind of cluster processing. To make multiple versions of software available, software is isolated in separate installation directories and access is managed via the module system. The module system allows for multiple versions to live side-by-side, for dependencies between software to be specified, and for conflicting versions to be specified.

On which machines is the quarantine available?

The software quarantine (aka modules) is available on workstation systems (cicwsNN) and the compute nodes (ciccsNN).

It is not available on the login or storage servers as scientific processing should not take place there.

The obtain a list of available software, run module avail, below is an example generated on 2022-11-01, the format of the naming below is <modulename>/<moduleversion>:

--------------------------------- /opt/quarantine/modulefiles/Linux ---------------------------------
AFNI/20220609                      R/4.1.3                       itksnap/4.0.0-20220623-nightly
ANTs/2.4.0                  (D)    RMINC/v1.5.3.0                julia/1.8.2
ANTs/20220513                      SDM/6.22                      mango/4.1
CAT12/r2043                        SPM12/r7771                   minc-stuffs/v0.1.25
CIVET/2.1.1                        anaconda/2022.05              minc-toolkit-extras/1.0
FID-A/1.2                          bart/0.7.00                   minc-toolkit-v2/
FSL/                        bpipe/0.9.11                  mrtrix3/3.0.3
GlobusConnectPersonal/3.1.6        brkraw/0.3.5           (D)    mrtrix3tissue/5.2.9
INSPECTOR/20201115                 brkraw/20220210               plink/1.07
MATLAB/R2021a                      dcm2niix/v1.0.20211006        pydpiper/v2.0.16
MATLAB/R2022a               (D)    fiji/20220414-1745            pyminc/v0.56
MRIcroGL/v1.2.20211007             fmriprep/20.2.7               qbatch/2.3
MRIcron/v1.2.20211006              fmriprep/22.0.0        (D)    remotemesa/1.0
MVGC/1.3                           freesurfer/7.2.0              rstudio/2022.02.3+492
PLS/6.15.1                         gift/                  tapas/6.0.1
PyQC/3.0                           imagej/20220414-1745

To load a module, use the load command, module load <modulename> which will load the default version (D) if it is specified in the module system, otherwise it will load the latest version. To load a specific version of a module, specify the version during loading, module load <modulename>/<moduleversion>.

Module Dependencies

If you try to load a module which has dependencies you have not yet satisfied, you will receive an error that will specify the dependencies and modules available that would satisfy it, each missing dependency stops the module loading so this may occur several times as you load all dependencies:

$ module load pyminc
Lmod has detected the following error:  Cannot load module "pyminc/v0.56" without these module(s) loaded:

While processing the following module(s):
Module fullname  Module Filename
---------------  ---------------
pyminc/v0.56     /opt/quarantine/modulefiles/Linux/pyminc/v0.56.lua