Modules Software Environment Manager on Quest

Quest uses Environment Modules to give users access to the software installed on Quest.

Modules are used to manage:

• multiple versions of applications, tools and libraries

• software where complex changes to the environment are necessary

• software where name conflicts with other software would cause problems

Loading a module for a particular piece of software often adds the path to the executable to $PATH, the path to the library to $LD_LIBRARY_PATH, and so on. Loading a module, then, relieves the user of having to remember or look up and type long path names.

Available Modules

Use the command

module avail

to list all modules available on Quest.

A listing of key software packages can also be found on the Quest Software page.

Loading a Module

To access almost every software application on Quest, you must first load the appropriate module:

module load <modulename>

Then you can reference software commands by name.

Examples of Loading Popular Software via Modules

There may be other ways to run these programs as well. These commands are only provided as a convenient reference.

Python

module load python-anaconda3
python myscript.py

There are multiple versions of Python available on Quest. module load python-anaconda3 will load Python 3.7. For other versions of Python, use the appropriate Anaconda Python module. See Using Python on Quest for more information and examples.

R

module load R/4.1.1
Rscript mycode.R

See Using R on Quest for more information and examples.

MATLAB

module load matlab/r2018a
matlab -nosplash -nodesktop -singleCompThread -r 'commands;exit'

or

module load matlab/r2018a
matlab -nosplash -nodesktop -singleCompThread -r myscript

Where myscript is a .m file. Note that there are multiple versions of MATLAB. You should specify the version you want, as the default may change over time. Seeing Using MATLAB on Quest for more information and examples.

Stata

module load stata/14
stata-mp < myprog.do > myprog.log

or

module load stata/14
stata-mp -b do myprog

Stata will read its commands from myprog.do and write its output to myprog.log in the working directory.

Note that Stata-MP is licensed for 4 cores, so please request exactly 4 cores per job in your job submission script. If you request more, you'll be wasting resources; if you request less and do not set the corresponding options appropriately in your script, Stata may use more cores than you've been assigned, resulting in your job being terminated. If you don't need Stata-MP's parallelization capabilities, you can run Stata SE with stata instead.

SAS

module load sas
sas myprog.sas

SAS can write very large temporary files. You can redirect such files to your project space with the -work option when you start-up SAS.

Mathematica

module load mathematica
math -script input.txt > output.txt

Module Versions

There are multiple versions of many software programs on Quest. Modules are named with the format softwarename/version. For example, if you look at the modules available for Python, you'll see several versions:

module avail python

---------------------------------------- /software/Modules/3.2.9/modulefiles -----------------------------------------
python/2.7.13            python/ActivePython-3.2  python/anaconda(default) python/anaconda3.6
python/ActivePython-2.7  python/Canopy            python/anaconda3         python/epd-7.3-2

(default) indicates which module will be loaded if you don't specify the version (e.g. module load python). Defaults can change over time, however, so it is strongly recommended that you always specify the module version even if you are using the default version. For example,

module load python-anaconda3

Useful Module Commands

Command	Action
module avail	Shows the available software packages
module avail <search>	Shows all modules that have <search> in the main part of the name (not in the version, which comes after the /). <search> is case sensitive. This is useful for viewing the versions available for a particular program instead of having to sort through the long list of all modules.
module -r spider '^p' module -r spider mpi module -r spider 'mpi$	Finds all the modules that start with `p' or `P' Finds all modules that have "mpi" in their name. Finds all modules that end with "mpi" in their name.
module list	Shows which modules are currently loaded
module load <module>	Loads a software package’s path information into your local environment so your session can find the software to run it
module purge <module>	Takes the software package’s information out of your local environment; this is generally more reliable than module unload
module purge all	Unloads all of the module packages currently in your local environment
module display <foo>	Displays the changes that are made to the environment by loading module <foo> without actually loading it

See Also:

• Quest Quick Start Guide
• Software on Quest