Accessing software via Modules
Last updated on 2025-03-05 | Edit this page
Overview
Questions
- How do we load and unload software packages?
Objectives
- Understand how to load and use a software package.
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 of the most famous examples are Python 2
and 3 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 Software compiled against a newer version of the C libraries and then
used when they are not present will result in a nasty
'GLIBCXX_3.4.20' not found error, for instance.
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 allow 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
------------------------------------------- /mnt/storage/apps/at11.0/share/modules --------------------------------------------
modulefiles/at11.0-powerpc64le-linux-gnu
---------------------------------------------- /mnt/storage/apps/eb/modules/all -----------------------------------------------
ABINIT/8.2.2-intel-2017.03-GCC-6.3
ABINIT/8.4.4-foss-2017b
ABINIT/8.4.4-intel-2017.03-GCC-6.3
ABINIT/8.10.1-intel-2018b
ABINIT/9.4.2-foss-2021b (D)
ABRicate/1.0.0-gompi-2021a
AFNI/20160329-intel-2017.03-GCC-6.3-Python-2.7.12
ALE/1.0.0-foss-2021a
ANSYS/17.0
ANSYS/18.1
ANSYS/19.4
ANSYS/2020-R2
ANSYS/2021
ANSYS/2022-R1
ANSYS/2024R1 (D)
ANTLR/2.7.7-GCCcore-11.2.0-Java-11.0.2
ANTLR/2.7.7-GCCcore-11.3.0-Java-11.0.2 (D)
ANTs/2.3.1-foss-2018b-Python-3.6.6
ANTs/2.3.2-foss-2019b-Python-3.7.4
ANTs/2.3.5-foss-2021a (D)
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 (/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/mnt/nfs/home/userid/bin/:/opt/ibutils/bin:/mnt/nfs/home/userid/bin/:/mnt/nfs/home/userid/.local/bin:/mnt/nfs/home/userid/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:
BASH
usr/local/bin
/usr/bin
/usr/local/sbin
/usr/sbin
/mnt/nfs/home/userid/bin/
/opt/ibutils/bin
/mnt/nfs/home/userid/bin/
/mnt/nfs/home/userid/.local/bin
/mnt/nfs/home/userid/binWe can load the python3 command with
module load:
OUTPUT
/mnt/storage/apps/eb/software/Python/3.7.0-foss-2018b/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
/mnt/storage/apps/eb/software/Python/3.7.0-foss-2018b/bin:/mnt/storage/apps/eb/software/OpenSSL/1.1.0h-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/SQLite/3.24.0-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/Tcl/8.6.8-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/libreadline/7.0-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/ncurses/6.1-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/bzip2/1.0.6-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/FFTW/3.3.8-gompi-2018b/bin:/mnt/storage/apps/eb/software/OpenMPI/3.1.1-GCC-7.3.0-2.30/bin:/mnt/storage/apps/eb/software/hwloc/1.11.10-GCCcore-7.3.0/sbin:/mnt/storage/apps/eb/software/hwloc/1.11.10-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/libxml2/2.9.8-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/XZ/5.2.4-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/numactl/2.0.11-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/binutils/2.30-GCCcore-7.3.0/bin:/mnt/storage/apps/eb/software/GCCcore/7.3.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/mnt/nfs/home/userid/bin:/opt/ibutils/bin:/mnt/nfs/home/userid/.local/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:
OUTPUT
2to3 cython f2py nosetests pip3 python python3.7m pyvenv-3.7
2to3-3.7 cythonize idle3 nosetests-3.7 pip3.7 python3 python3.7m-config runxlrd.py
chardetect easy_install idle3.7 pbr pydoc3 python3.7 python3-config tabulate
cygdb easy_install-3.7 netaddr pip pydoc3.7 python3.7-config pyvenv virtualenvTaking this to its conclusion, module load will add
software to your $PATH. It “loads” software. A special note
on this - depending on which version of the module program
that is installed at your site, module load will also load
required software dependencies.
To demonstrate, let’s use module list.
module list shows all loaded software modules.
OUTPUT
Currently Loaded Modules:
1) GCCcore/7.3.0 9) hwloc/1.11.10-GCCcore-7.3.0 17) ncurses/6.1-GCCcore-7.3.0
2) zlib/1.2.11-GCCcore-7.3.0 10) OpenMPI/3.1.1-GCC-7.3.0-2.30 18) libreadline/7.0-GCCcore-7.3.0
3) binutils/2.30-GCCcore-7.3.0 11) OpenBLAS/0.3.1-GCC-7.3.0-2.30 19) Tcl/8.6.8-GCCcore-7.3.0
4) GCC/7.3.0-2.30 12) gompi/2018b 20) SQLite/3.24.0-GCCcore-7.3.0
5) numactl/2.0.11-GCCcore-7.3.0 13) FFTW/3.3.8-gompi-2018b 21) GMP/6.1.2-GCCcore-7.3.0
6) XZ/5.2.4-GCCcore-7.3.0 14) ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1 22) libffi/3.2.1-GCCcore-7.3.0
7) libxml2/2.9.8-GCCcore-7.3.0 15) foss/2018b 23) OpenSSL/1.1.0h-GCCcore-7.3.0
8) libpciaccess/0.14-GCCcore-7.3.0 16) bzip2/1.0.6-GCCcore-7.3.0 24) Python/3.7.0-foss-2018bLet’s try unloading the Python module:
OUTPUT
[userid@login01 ~]$ module list
Currently Loaded Modules:
1) GCCcore/7.3.0 9) hwloc/1.11.10-GCCcore-7.3.0 17) ncurses/6.1-GCCcore-7.3.0
2) zlib/1.2.11-GCCcore-7.3.0 10) OpenMPI/3.1.1-GCC-7.3.0-2.30 18) libreadline/7.0-GCCcore-7.3.0
3) binutils/2.30-GCCcore-7.3.0 11) OpenBLAS/0.3.1-GCC-7.3.0-2.30 19) Tcl/8.6.8-GCCcore-7.3.0
4) GCC/7.3.0-2.30 12) gompi/2018b 20) SQLite/3.24.0-GCCcore-7.3.0
5) numactl/2.0.11-GCCcore-7.3.0 13) FFTW/3.3.8-gompi-2018b 21) GMP/6.1.2-GCCcore-7.3.0
6) XZ/5.2.4-GCCcore-7.3.0 14) ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1 22) libffi/3.2.1-GCCcore-7.3.0
7) libxml2/2.9.8-GCCcore-7.3.0 15) foss/2018b 23) OpenSSL/1.1.0h-GCCcore-7.3.0
8) libpciaccess/0.14-GCCcore-7.3.0 16) bzip2/1.0.6-GCCcore-7.3.0So 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 loadedMore on modules
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 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 look specifically for Python in module avail:
Because so many modules match Python we’ve cheated a little
and added /3 focus down on Python 3 modules
OUTPUT
----------------------- /mnt/storage/apps/eb/modules/all -----------------------
GitPython/3.1.24-GCCcore-11.2.0
Python/3.6.1-goolf-2017a
Python/3.6.1-intel-2017.03-GCC-6.3
Python/3.6.3-foss-2017b
Python/3.6.6-foss-2018b
Python/3.6.6-intel-2018b
Python/3.7.0-foss-2018b (D)
Python/3.7.0-intel-2018b
Python/3.7.2-GCCcore-8.2.0
Python/3.7.4-GCCcore-8.3.0
Python/3.7.5-GCCcore-8.3.0
Python/3.8.2-GCCcore-9.3.0
Python/3.8.6-GCCcore-10.2.0
Python/3.9.5-GCCcore-10.3.0-bare
Python/3.9.5-GCCcore-10.3.0
Python/3.9.6-GCCcore-11.2.0-bare
Python/3.9.6-GCCcore-11.2.0
Python/3.10.4-GCCcore-11.3.0-bare
Python/3.10.4-GCCcore-11.3.0
Python/3.10.8-GCCcore-12.2.0-bare
Python/3.10.8-GCCcore-12.2.0
Python/3.11.3-GCCcore-12.3.0
protobuf-python/3.3.0-intel-2017.03-GCC-6.3-Python-2.7.13
protobuf-python/3.3.0-intel-2017.03-GCC-6.3-Python-3.6.1
protobuf-python/3.13.0-foss-2020a-Python-3.8.2
protobuf-python/3.14.0-GCCcore-10.2.0
protobuf-python/3.17.3-GCCcore-10.3.0 (D)
Where:
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".Note that we have several different versions of Python3.
In this case, Python/3.7.0-foss-2018b has a
(D) next to it. This indicates that it is the default - if
we type module load Python, this is the copy that will be
loaded.
Using Software Modules in Scripts
Create a job to report what version of python is running, uisng the
command python3 --version. 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).
Default Versions and Module Swap
Let’s take a closer look at the gcc module. GCC is an
extremely widely used C/C++/Fortran compiler. Lots of software is
dependent on the GCC version, and might not compile or run if the wrong
version is loaded. In this case, there are 18 different versions, named
like GCC/12.2.0. How do we load each copy and which copy is
the default?
OUTPUT
---------------------------------------------------------------------------- /mnt/storage/apps/eb/modules/all -----------------------------------------------------------------------------
GCC/4.8.2 GCC/4.9.3-2.25 GCC/5.4.0-2.26 GCC/6.3.0-2.27 GCC/7.3.0-2.30 GCC/8.3.0 GCC/10.2.0 GCC/11.2.0 GCC/12.2.0
GCC/4.9.3-binutils-2.25 GCC/5.2.0 GCC/6.1.0-2.27 GCC/6.4.0-2.28 GCC/8.2.0-2.31.1 GCC/9.3.0 GCC/10.3.0 GCC/11.3.0 GCC/12.3.0 (D)
Where:
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".In this case, GCC/12.3.0 has a (D) next to
it. This indicates that it is the default - if we type
module load GCC, this is the copy that will be loaded.
Let’s check this:
BASH
[userid@login01 ~]$ module purge
[userid@login01 ~]$ module load GCC
[userid@login01 ~]$ module listOUTPUT
Currently Loaded Modules:
1) GCCcore/12.3.0 2) zlib/1.2.13-GCCcore-12.3.0 3) binutils/2.40-GCCcore-12.3.0 4) GCC/12.3.0OUTPUT
gcc (GCC) 12.3.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.So how do we load the non-default copy of a software package? In this case, the only change we need to make is be more specific about the module we are loading. To load a non-default module, we need to make add the version number after the / in our module load command:
OUTPUT
The following have been reloaded with a version change:
1) GCC/12.3.0 => GCC/11.2.0 3) binutils/2.40-GCCcore-12.3.0 => binutils/2.37-GCCcore-11.2.0
2) GCCcore/12.3.0 => GCCcore/11.2.0 4) zlib/1.2.13-GCCcore-12.3.0 => zlib/1.2.11-GCCcore-11.2.0What happened? The module command is teling us that it swapped out
GCC/12.3.0 and replaced it with GCC/11.2.0
OUTPUT
gcc (GCC) 11.2.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.can’t load a new module version?
Sometimes the module command gives a warning requiring you to unload
the current version of a module before loading the new version. As
switching between different versions of the same module is often used
you can use module swap rather than unloading one version
before loading another. The equivalent of the steps above would be:
BASH
[userid@login01 ~]$ module purge
[userid@login01 ~]$ module load GCC
[userid@login01 ~]$ module swap GCC GCC/11.2.0OUTPUT
The following have been reloaded with a version change:
1) GCC/12.3.0 => GCC/11.2.0 3) binutils/2.40-GCCcore-12.3.0 => binutils/2.37-GCCcore-11.2.0
2) GCCcore/12.3.0 => GCCcore/11.2.0 4) zlib/1.2.13-GCCcore-12.3.0 => zlib/1.2.11-GCCcore-11.2.0And what happens when we load python again?
OUTPUT
The following have been reloaded with a version change:
1) GCC/11.2.0 => GCC/7.3.0-2.30 3) binutils/2.37-GCCcore-11.2.0 => binutils/2.30-GCCcore-7.3.0
2) GCCcore/11.2.0 => GCCcore/7.3.0 4) zlib/1.2.11-GCCcore-11.2.0 => zlib/1.2.11-GCCcore-7.3.0Because the version of python isn’t compatible with the currently loaded version of gcc, module has done a swap for us.
system python
Watch out for system provided python, it may not be the version you
need. It’s best to always specify your python version. On Rocket, the
default version of Python is Python2. To confirm the version type
python --version which, on Rocket, will return
Python 2.7.5.
Key Points
- “Load software with
module load softwareName.” - “Unload software with
module unloadormodule purge” - “The module system handles software versioning and package conflicts for you automatically.”