Accessing software via Modules
Last updated on 2025-06-24 | Edit this page
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against a newer version of the C libraries and then run on a machine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 a nasty
'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 depend on having 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:
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
Aliases: Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
will load foo/1.2.3
D: Default Module
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".Loading and Unloading Software
To load a software module, use module load. In this
example we will use Python 3.
Initially, Python 3 is not loaded. We can test this by using the
which command. which looks for programs the
same way that Bash does, so we can use it to tell us where a particular
piece of software is stored.
If the python3 command was unavailable, we would see
output like
OUTPUT
/usr/bin/which: no python3 in (/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/{{site.remote.user}}/.local/bin:/home/{{site.remote.user}}/bin)Note that this wall of text is really a list, with values separated
by the : character. The output is telling us that the
which command searched the following directories for
python3, without success:
OUTPUT
/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/{{site.remote.user}}/.local/bin
/home/{{site.remote.user}}/binHowever, in our case we do have an existing python3
available so we see
OUTPUT
/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin/python3We need a different Python than the system provided one though, so let us load a module to access it.
We can load the python3 command with
module load:
BASH
{{ site.remote.prompt }} module load {{ site.remote.module_python3 }}
{{ site.remote.prompt }} which python3OUTPUT
/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3So, 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 UNIX system looks for
software. Specifically $PATH is a list of directories
(separated by :) that the OS searches through for a command
before giving up and telling us it can’t find it. As with all
environment variables we can print it out using echo.
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/binYou’ll notice a similarity to the output of the which
command. In this case, there’s only one difference: the different
directory at the beginning. When we ran the module load
command, it added a directory to the beginning of our
$PATH. Let’s examine what’s there:
BASH
{{ site.remote.prompt }} ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/binOUTPUT
2to3 nosetests-3.8 python rst2s5.py
2to3-3.8 pasteurize python3 rst2xetex.py
chardetect pbr python3.8 rst2xml.py
cygdb pip python3.8-config rstpep2html.py
cython pip3 python3-config runxlrd.py
cythonize pip3.8 rst2html4.py sphinx-apidoc
easy_install pybabel rst2html5.py sphinx-autogen
easy_install-3.8 __pycache__ rst2html.py sphinx-build
futurize pydoc3 rst2latex.py sphinx-quickstart
idle3 pydoc3.8 rst2man.py tabulate
idle3.8 pygmentize rst2odt_prepstyles.py virtualenv
netaddr pytest rst2odt.py wheel
nosetests py.test rst2pseudoxml.pyTaking this to its conclusion, module load will add
software to your $PATH. It “loads” software. A special note
on this - depending on which version of the module program
that is installed at your site, module load will also load
required software dependencies.
To demonstrate, let’s use module list.
module list shows all loaded software modules.
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.zOUTPUT
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.zSo 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.
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.ySo 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).
OUTPUT
No modules loadedNote 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 principally through the
manipulation of environment variables like $PATH. There is
usually little or no data transfer involved.
The module loading process manipulates other special environment variables as well, including variables that influence where the system looks for software libraries, and sometimes variables which tell commercial software packages where to find license servers.
The module command also restores these shell environment variables to their previous state when a module is unloaded.
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.
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
Aliases: Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
will load foo/1.2.3
D: Default Module
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".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).
OUTPUT
{{ site.remote.bash_shebang }}
{{ site.sched.comment }} {{ site.sched.flag.partition }}{% if site.sched.flag.qos %}
{{ site.sched.comment }} {{ site.sched.flag.qos }}
{% endif %}{{ site.sched.comment }} {{ site.sched.flag.time }} 00:00:30
module load {{ site.remote.module_python3 }}
python3 --versionKey Points
- Load software with
module load softwareName. - Unload software with
module unload - The module system handles software versioning and package conflicts for you automatically.