HII-HPC Cluster

Modules

Custom software built by USF Research Computing available via the Modules system.

Modules gives the user fine-grained control to select a set of applications as well as the specific versions they wish to use without manually configuring and cleaning up necessary environmental variables such as PATH and LD_LIBRARY_PATH.

Load a Module

This loads a module into the current environment by modifying environment variables such as PATH, MANPATH and LD_LIBRARY_PATH to include locations that are necessary for running a particular application. Note these changes are lost on subsequent logins.

hii$ module add apps/R/3.2.3

hii$ which R
/apps/R/3.2.3/bin/R

List Modules

To list all applications available via the module command (we add the -t option to display as a single column):

hii$ module avail -t
/etc/modulefiles:
admin/genders
admin/module-cvs
admin/module-info
admin/pdsh
admin/rsge
admin/stress-ng
admin/tools
apps/R/3.2.3
... etc.

The module avail command outputs to STDERR rather than STDOUT so any program you send the output to will not capture it unless you use shell redirection (2>&1). For example to pipe the output of module avail into the pager less (press up-arrow / down-arrow to page up and down and q to quit):

hii$ module avail -t 2>&1 | less

You may also search for an application using grep with shell redirection, for example:

hii$ module avail -t 2>&1 | grep R
apps/R/2.11.1
apps/R/2.15.3
apps/R/3.0.3-pbdR
apps/R/3.1.2
apps/R/3.2.3

List Loaded Modules

To list the modules you currently have loaded:

hii$ module list
Currently Loaded Modulefiles:
  1) compilers/intel/2015_cluster_xe   3) apps/jdk/1.6.0_22.x86_64
  2) apps/openbugs/3.2.2               4) apps/R/3.2.3

Remove a Module

Sometimes you need to remove support for an application from the current environment.

hii$ module rm apps/R/3.2.3

hii$ which R
/usr/bin/which: no R in (/usr/bin:/usr/local/bin)

Purge all Modules

To unload all modules, issue the following command:

hii$ module purge