Access to Software
Accessing Scientific Software (quarantine aka modules)
All computer systems have installed a standard suite of desktop productivity software (office, image manipulation, web browser, etc.). If a readily available productivity software package is not installed and you wish to use it, please contact us at support@douglasneuroinformatics.ca to request installation.
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-v2/1.9.18.2
FSL/6.0.5.1 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/4.0.3.0 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:
minc-toolkit-v2
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
pyminc/v0.56 /opt/quarantine/modulefiles/Linux/pyminc/v0.56.lua