Environment Modules
Environment Modules offer a simple means of customising your environment to access the required versions of installed software and this section provides information on how they are used on Katana.
When we use modules, we are changing our "environment", hence the name.
How do I discover what software is available?¶
[z1234567@katana ~]$ module avail
-------------------------- /share/apps/modules/intel ---------------------------
intel/11.1.080(default) intel/12.1.7.367 intel/13.0.1.117 intel/13.1.0.146
--------------------------- /share/apps/modules/pgi ----------------------------
pgi/13.7
-------------------------- /share/apps/modules/matlab --------------------------
matlab/2007b matlab/2010b matlab/2012a(default)
matlab/2008b matlab/2011a matlab/2012b
matlab/2009b matlab/2011b matlab/2013a
What if the software that I want is not on the list?¶
If you require software installed on Katana then please email the details to restech.support@unsw.edu.au including URLs and desired version numbers.
How do I add a particular version of software to my environment?¶
[z1234567@katana1 ~]$ module add matlab/2018b
[z1234567@katana1 ~]$ module load matlab/2018b
How do I remove a particular version of software from my environment?¶
[z1234567@katana1 ~]$ module rm matlab/2018b
or
[z1234567@katana1 ~]$ module unload matlab/2018b
How do I remove all modules from my environment?¶
[z1234567@katana1 ~]$ module purge
Which versions of software am I currently using?¶
[z1234567@katana1 ~]$ module list
Currently Loaded Modulefiles:
1) intel/18.0.1.163 2) matlab/2018b
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 mrbayes
----------- 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 do I switch between particular versions of software?¶
[z1234567@katana1 ~]$ module switch matlab/2018b matlab/2017b
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 only affect the particular session in which they are loaded. Loading a module in one SSH session will not affect any other SSH session or even any jobs submitted from that session. Modules must be loaded in every session where they will be used.
How can I invoke my module commands automatically?¶
Add environment module commands to your job script. This approach is useful for preserving the required environment for each job. For example:
#!/bin/bash
#PBS -l select=1:ncpus=1:mem=4gb
#PBS -j oe
module purge
module add intel/18.0.1.163
cd ${PBS_O_WORKDIR}
./myprog
Perl, Python and R all have their own library/module systems: CPAN, PyPI and CRAN. If you need a library or module from one of these sources, and there is significant demand, then we will install it. Please email such requests to restech.support@unsw.edu.au.