The lmod modules system on Rivanna enables users to easily set their environments for selected software and to choose versions if appropriate.
The lmod system is hierarchical; not every module is available in every environment. We provide a core environment which contains most of the software installed by Research Computing staff, but software that requires a compiler or MPI is not in that environment and a compiler must first be loaded.
List all available software in the core environment:
Use "module spider" to find all possible modules.
module spider hdf5
If a version is specified to
spider, it will indicate how to load that version.
module spider openmpi/2.1.1
spider will sometimes show modules whose version numbers begin with a period, e.g.
icc/.17.0. Any such module is “hidden” and users should not be required to load them explicitly.
key to list all modules in a particular category. The current choices are
base, bio, cae, chem, compiler, data, debugger, devel, geo, ide, lang, lib, math, mpi, numlib, perf, phys, system, toolchain, tools, vis, licensed
module key bio
Load the environment for a particular package:
module load thepackage
If you do not specify a version, the system default is loaded. For example, to load the default version of R, run
module load R
If you do not wish to use the default version chosen by the modules environment, you may specify a path to the module script. For example, to select the older version of R
module load R/3.3.0
Note that the 'default' version of a module may change, so if you are developing applications yourself we highly recommend that you load explicit versions of modules; that is, do not invoke the default X, but specify a version. If the package is upgraded, loading that module will fail, however.
Delete a module:
module unload thepackage
List all modules you have loaded in the current shell:
To change from one version to another, use
For example, if you have loaded
gcc/7.1.0 and you wish to switch to
module swap gcc/7.1.0 intel/17.0
This will unload the
gcc/7.1.0 environment entirely, and load the
To clear all modules you have loaded and return to the default state:
More about these commands can be found in the documentation.
Modules in Job Scripts
After the definition of job variables, and before the command line to run the program, add module load X lines for every application that you want included in your run environment. For example, to run R version 3.3.0 your job script should resemble the following:
#!/bin/bash #SBATCH -p standard #SBATCH -A MyAcct #SBATCH -n 1 #SBATCH --time=00:10:00 #SBATCH --mem-per-cpu=4000 module load R/3.3.0 Rscript myScript.R
Please contact us if you encounter any problems using these applications in your job scripts.