Accessing software via Modules

Last updated on 2026-07-07 | Edit this page

Estimated time: 45 minutes

Overview

Questions

How do we load and unload software packages?

Objectives

Load and use a software package.
Explain how the shell environment changes when the module mechanism loads or unloads packages.

On a high-performance computing system, it is seldom the case that the software we want to use is available when we log in. It is installed, but we will need to “load” it before it can run.

Before we start using individual software packages, however, we should understand the reasoning behind this approach. The three biggest factors are:

software incompatibilities
versioning
dependencies

Software incompatibility is a major headache for programmers. Sometimes the presence (or absence) of a software package will break others that depend on it. Two well known examples are Python and C compiler versions. Python 3 famously provides a python command that conflicts with that provided by Python 2. Software compiled against a newer version of the C libraries and then run on a machine that has older C libraries installed will result in an opaque 'GLIBCXX_3.4.20' not found error.

Software versioning is another common issue. A team might depend on a certain package version for their research project – if the software version was to change (for instance, if a package was updated), it might affect their results. Having access to multiple software versions allows a set of researchers to prevent software versioning issues from affecting their results.

Dependencies are where a particular software package (or even a particular version) depends on having access to another software package (or even a particular version of another software package). For example, the VASP materials science software may require a particular version of the FFTW (Fastest Fourier Transform in the West) software library available for it to work.

Environment Modules

Environment modules are the solution to these problems. A module is a self-contained description of a software package – it contains the settings required to run a software package and, usually, encodes required dependencies on other software packages.

There are a number of different environment module implementations commonly used on HPC systems: the two most common are TCL modules and Lmod. Both of these use similar syntax and the concepts are the same so learning to use one will allow you to use whichever is installed on the system you are using. In both implementations the module command is used to interact with environment modules. An additional subcommand is usually added to the command to specify what you want to do. For a list of subcommands you can use module -h or module help. As for all commands, you can access the full help on the man pages with man module.

On login you may start out with a default set of modules loaded or you may start out with an empty environment; this depends on the setup of the system you are using.

Listing Available Modules

To see available software modules, use module avail:

BASH

[yourUsername@login1 ~]$ module avail | less

OUTPUT

~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a

[removed most of the output here for clarity]

  Where:
   L:        Module is loaded
   D:        Default Module
   Aliases exist: foo/1.2.3 (1.2) means that
             "module load foo/1.2" will load foo/1.2.3

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching
any of the "keys".

Note that piping the output through less allows us to search within the output using the / key.

Listing Currently Loaded Modules

You can use the module list command to see which modules you currently have loaded in your environment. If you have no modules loaded, you will see a message telling you so.

BASH

[yourUsername@login1 ~]$ module list

OUTPUT

No modules loaded

Loading and Unloading Software

To load a software module, use module load.

In this example we will use “Python 3”. Initially, it is not loaded. We can test this by using the which command. which searches for executables using directories listed in $PATH, similar to how Bash locates commands.

BASH

[yourUsername@login1 ~]$ which python3

If the python3 command is available, which shows the path to the executable:

OUTPUT

/usr/bin/python3

The shell finds executables by searching through the directories listed in the $PATH environment variable.

If we accidentally make a typo for example:

BASH

[yourUsername@login1 ~]$ which pyython3

we instead see something like:

OUTPUT

/usr/bin/which: no pyython3 in (/yourUsername/.local/bin:/yourUsername/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)

This wall of text is actually a list of directories separated by the : character. The output tells us that the shell searched the following directories for pyython3, but could not find it:

OUTPUT

/yourUsername/.local/bin
/yourUsername/bin
/usr/local/bin
/usr/bin
/usr/local/sbin
/usr/sbin

The Python installation located in /usr/bin is the system-provided version. On HPC systems, we often need a different Python build that is compiled with specific compiler toolchains, libraries, or scientific software stacks. Environment Modules allow us to dynamically switch to these alternative software environments.

We can load a different Python environment using module load:

BASH

[yourUsername@login1 ~]$ module load Python
[yourUsername@login1 ~]$ which python3

OUTPUT

/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3

So, what just happened?

To understand the output, first we need to understand the nature of the $PATH environment variable. $PATH is a special environment variable that controls where a shell looks for executables. Specifically, $PATH is a list of directories (separated by :) that the shell searches through for a command before reporting that the command could not be found. As with all environment variables, we can print it out using echo.

BASH

[yourUsername@login1 ~]$ echo $PATH

OUTPUT

/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/SQLite/3.31.1-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Tcl/8.6.10-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/GCCcore/x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/user01/.local/bin:/home/user01/bin

You’ll notice a similarity to the output of the which command. In this case, there is one important difference: an additional directory appears at the beginning. When we ran the module load command, it added a directory to the front of our $PATH – or “prepended to PATH”. Because this directory appears before /usr/bin in $PATH, the shell now finds the module-provided python3 executable before the system version. Let’s examine what’s located there:

BASH

[yourUsername@login1 ~]$ ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin

OUTPUT

idle3     pip   pip3.13  pydoc3.13  python3     python3.13-config  python-config
idle3.13  pip3  pydoc3   python     python3.13  python3-config     wheel

Note that the exact output may vary from cluster to cluster.

Taking this to its conclusion, module load adds software locations to your $PATH. It effectively “loads” software into the current shell environment. A special note on this: depending on the module system configuration at your site, module load may also automatically load additional software dependencies required by the application.

To demonstrate, let’s use module list. module list shows all loaded software modules.

BASH

[yourUsername@login1 ~]$ module list

OUTPUT

Currently Loaded Modules:
  1) GCCcore/x.y.z                 4) GMP/6.2.0-GCCcore-x.y.z
  2) Tcl/8.6.10-GCCcore-x.y.z      5) libffi/3.3-GCCcore-x.y.z
  3) SQLite/3.31.1-GCCcore-x.y.z   6) Python/3.x.y-GCCcore-x.y.z

BASH

[yourUsername@login1 ~]$ module load GROMACS
[yourUsername@login1 ~]$ module list

OUTPUT

Currently Loaded Modules:
  1) GCCcore/x.y.z                    14) libfabric/1.11.0-GCCcore-x.y.z
  2) Tcl/8.6.10-GCCcore-x.y.z         15) PMIx/3.1.5-GCCcore-x.y.z
  3) SQLite/3.31.1-GCCcore-x.y.z      16) OpenMPI/4.0.3-GCC-x.y.z
  4) GMP/6.2.0-GCCcore-x.y.z          17) OpenBLAS/0.3.9-GCC-x.y.z
  5) libffi/3.3-GCCcore-x.y.z         18) gompi/2020a
  6) Python/3.x.y-GCCcore-x.y.z       19) FFTW/3.3.8-gompi-2020a
  7) GCC/x.y.z                        20) ScaLAPACK/2.1.0-gompi-2020a
  8) numactl/2.0.13-GCCcore-x.y.z     21) foss/2020a
  9) libxml2/2.9.10-GCCcore-x.y.z     22) pybind11/2.4.3-GCCcore-x.y.z-Pytho...
 10) libpciaccess/0.16-GCCcore-x.y.z  23) SciPy-bundle/2020.03-foss-2020a-Py...
 11) hwloc/2.2.0-GCCcore-x.y.z        24) networkx/2.4-foss-2020a-Python-3.8...
 12) libevent/2.1.11-GCCcore-x.y.z    25) GROMACS/2020.1-foss-2020a-Python-3...
 13) UCX/1.8.0-GCCcore-x.y.z

So in this case, loading the GROMACS module (a bioinformatics software package), also loaded GMP/6.2.0-GCCcore-x.y.z and SciPy-bundle/2020.03-foss-2020a-Python-3.x.y as well. Let’s try unloading the GROMACS package.

BASH

[yourUsername@login1 ~]$ module unload GROMACS
[yourUsername@login1 ~]$ module list

OUTPUT

Currently Loaded Modules:
  1) GCCcore/x.y.z                    13) UCX/1.8.0-GCCcore-x.y.z
  2) Tcl/8.6.10-GCCcore-x.y.z         14) libfabric/1.11.0-GCCcore-x.y.z
  3) SQLite/3.31.1-GCCcore-x.y.z      15) PMIx/3.1.5-GCCcore-x.y.z
  4) GMP/6.2.0-GCCcore-x.y.z          16) OpenMPI/4.0.3-GCC-x.y.z
  5) libffi/3.3-GCCcore-x.y.z         17) OpenBLAS/0.3.9-GCC-x.y.z
  6) Python/3.x.y-GCCcore-x.y.z       18) gompi/2020a
  7) GCC/x.y.z                        19) FFTW/3.3.8-gompi-2020a
  8) numactl/2.0.13-GCCcore-x.y.z     20) ScaLAPACK/2.1.0-gompi-2020a
  9) libxml2/2.9.10-GCCcore-x.y.z     21) foss/2020a
 10) libpciaccess/0.16-GCCcore-x.y.z  22) pybind11/2.4.3-GCCcore-x.y.z-Pytho...
 11) hwloc/2.2.0-GCCcore-x.y.z        23) SciPy-bundle/2020.03-foss-2020a-Py...
 12) libevent/2.1.11-GCCcore-x.y.z    24) networkx/2.4-foss-2020a-Python-3.x.y

So using module unload “un-loads” a module, and depending on how a site is configured it may also unload all of the dependencies (in our case it does not). If we wanted to unload everything at once, we could run module purge (unloads everything).

BASH

[yourUsername@login1 ~]$ module purge
[yourUsername@login1 ~]$ module list

OUTPUT

No modules loaded

Note that module purge is informative. It will also let us know if a default set of “sticky” packages cannot be unloaded (and how to actually unload these if we truly so desired).

Note that this module loading process happens primarily through the manipulation of environment variables like $PATH. There is usually little or no data transfer involved.

The module system modifies other environment variables as well, including variables that influence where the shell and runtime linker look for software libraries. Examples include variables such as:

OUTPUT

LD_LIBRARY_PATH
LIBRARY_PATH
CPATH
MANPATH
PKG_CONFIG_PATH

On some systems, modules may also configure environment variables that tell commercial software packages where to locate license servers. The module command restores these shell environment variables to their previous state when a module is unloaded. This allows users to switch between different software environments cleanly and reproducibly.

Software Versioning

So far, we’ve learned how to load and unload software packages. This is very useful. However, we have not yet addressed the issue of software versioning. At some point or other, you will run into issues where only one particular version of some software will be suitable. Perhaps a key bugfix only happened in a certain version, or version X broke compatibility with a file format you use. In either of these example cases, it helps to be very specific about what software is loaded.

Let’s examine the output of module avail more closely, using the pager since there may be reams of output:

BASH

[yourUsername@login1 ~]$ module avail | less

OUTPUT

~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a

[removed most of the output here for clarity]

  Where:
   L:        Module is loaded
   D:        Default Module
   Aliases exist: foo/1.2.3 (1.2) means that
             "module load foo/1.2" will load foo/1.2.3

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching
any of the "keys".

If the software your Slurm script runs requires on a specific version of a dependency, make sure you use the full name of the module, rather than the default loaded when you give only its name (up to the first slash).

Challenge

Using Software Modules in Scripts

Create a job that is able to run python3 --version. Remember, no software is loaded by default! Running a job is just like logging on to the system (you should not assume a module loaded on the login node is loaded on a compute node).

Show me the solution

BASH

[yourUsername@login1 ~]$ nano python-module.sh
[yourUsername@login1 ~]$ cat python-module.sh

OUTPUT

#!/bin/bash
#SBATCH

#SBATCH --time 00:00:30

module load Python

python3 --version

BASH

[yourUsername@login1 ~]$ sbatch  python-module.sh

Key Points

Load software with module load softwareName.
Unload software with module unload
The module system handles software versioning and package conflicts for you automatically.