Environment Modules are a means of changing your environment to run specfic versions of installed sotware. This section provides information on how they are used on Katana.
How do I discover what software is available?
z1234567@katana3:~ $ module avail
----------------------------------------- /apps/Modules/linux-rocky8-ivybridge -----------------------------------------
adios2/2.8.3 icu4c/67.1 openfoam-org/9_20240202
alsa-lib/1.2.3.2 icu4c/73.2 openfoam-org/10_20240227
amber/22 idba/1.1.1 openfoam-org/11
amber/22-gcc-8.5.0-cuda idba/1.1.3 openfoam/2206
ansys/2021R1 igv/2.12.3 openfoam/2206-hdf4
ansys/2021R2 imagemagick/7.0.8-7 openfoam/2312
ansys/2022R2 infernal/1.1.4 openfoam/2406
ansys/2023R1 inputproto/2.3.2 openfoam/2506
ansys/2023R2 intel-compilers/2022.2.1 openjpeg/1.5.1
ansys/2024R2 intel-mkl/2022.2.1 openjpeg/1.5.2
ansys/2025R1 intel-mpi/2021.7.1 openjpeg/2.3.1
etc..
Environment Modules allow you to modify your environment so you can run specific software versions on Katana.
Discovering Available Software
Run:
module avail
Loading a Software Version
module add adios2/2.8.3
# or
module load adios2/2.8.3
Viewing Loaded Modules
module list
Would return:
Currently Loaded Modulefiles:
1) adios2/2.8.3
Removing Software
module rm adios2/2.8.3
# or
module unload adios2/2.8.3
Removing All Modules
module purge
Module Help
module help mrbayes
Switching Versions
module switch ansys/2021R1 ansys/2021R2
Would return:
Switching from ansys/2021R1 to ansys/2021R2
Unloading useless requirement: krb5/1.19.3
Loading requirement: krb5/1.19.3
Viewing Modifications a Module Makes
module show mothur/1.42.3
Why Modules Reset
Modules only apply to the current session.
They must be loaded again in new SSH sessions or inside job scripts.
Using Modules in a Job Script
#!/bin/bash
#PBS -l select=1:ncpus=1:mem=4gb
#PBS -j oe
module purge
module add intel/18.0.1.163 #(add these two lines to the script as needed)
cd ${PBS_O_WORKDIR}
./myprog
What if the software that I want is not on the list?
If you require additional software installed on Katana then please email the details to restech.support@unsw.edu.au including URLs and the version number that you wish installed.
How do I find out more about a particular piece of software?
You can find out more about a piece of software by using the module help command. For example:
[z1234567@katana1 ~]$ module help ansys/2021R2
----------- Module Specific Help for 'mrbayes/3.2.2' --------------
MrBayes 3.2.2 is installed in /apps/mrbayes/3.2.2
This module was complied against beagle/2.1.2 and openmpi/1.6.4 with MPI support.
More information about the commands made available by this module is available
at http://mrbayes.sourceforge.net
How can I find out what paths and other environment variables a module uses?
[z1234567@katana1 ~]$ module show mothur/1.42.3
-------------------------------------------------------------------
/apps/modules/bio/mothur/1.42.3:
module-whatis Mothur 1.42.3
conflict mothur
setenv MOTHUR_ROOT /apps/mothur/1.42.3
prepend-path PATH /apps/mothur/1.42.3/bin
setenv LAST_MODULE_TYPE bio
setenv LAST_MODULE_NAME mothur/1.42.3
setenv LAST_MODULE_VERSION 1.42.3
-------------------------------------------------------------------
Why does the cluster forget my choice of modules?
Environment modules are desined to make a temporary change to your evironment and only affect the session in which they are loaded. Loading a module in one SSH session will not affect any other SSH session or any jobs submitted from that session. Modules must be loaded in every session where they will be used.
How do module files interact with Perl, Python and R?
Perl, Python and R all have their own library/module systems: CPAN, PyPI and CRAN. Information on installing a library or module for yourself can be found on the help pages for Perl, Python and R. If you are having difficulty installing the library or module then can help you. Please email such requests to restech.support@unsw.edu.au.