Accessing software via Modules
Overview
Teaching: 30 min
Exercises: 15 minQuestions
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 Software compiled against a newer version of the C libraries and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:
[netid@dev-amd20 ~]$ module avail
------------ /opt/modules/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.2 ------------
ABySS/2.0.2
ABySS/2.1.1
ABySS/2.1.5 (D)
ANTs/2.3.2
ATK/2.28.1
Armadillo/8.400.0
BBMap/37.93
BCFtools/1.9
BLAST+/2.7.1 (D)
BUSCO/3.1.0-Python-3.6.4
BWA/0.7.17
BamTools/2.5.1
BioPerl/1.7.2-Perl-5.26.1
Boost.Python/1.66.0-Python-3.6.4
[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".
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
[netid@dev-amd20 ~]$ module list
Currently Loaded Modules:
1) GCCcore/6.4.0 6) OpenMPI/2.1.2 11) ScaLAPACK/2.0.2-OpenBLAS-0.2.20 16) ncurses/6.0 21) libffi/3.2.1
2) binutils/2.28 7) tbb/2018_U3 12) bzip2/1.0.6 17) libreadline/7.0 22) Python/3.6.4
3) GNU/6.4.0-2.28 8) imkl/2018.1.163 13) zlib/1.2.11 18) Tcl/8.6.8 23) Java/1.8.0_152
4) numactl/2.0.11 9) OpenBLAS/0.2.20 14) Boost/1.67.0 19) SQLite/3.21.0 24) MATLAB/2018a
5) hwloc/1.11.8 10) FFTW/3.3.7 15) CMake/3.11.1 20) GMP/6.1.2 25) powertools/1.2
You should generally find and select modules based on your needs rather than using the defaults. We alway recommend clearing out all modules before you try loading new ones to help avoid conflicts. To do this, use the module purge command:
[netid@dev-amd20 ~]$ module purge
[netid@dev-amd20 ~]$ module list
No modules loaded
Loading and Unloading Software
To load a software module, use module load. In this example we will use
Python 3.
Initially, there is only one version of Python 3 that is available. 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.
[netid@dev-amd20 ~]$ which python3
If python3 did not exist we would see output like
which: no python3 in (
/opt/software/core/lua/lua/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:
/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/hpcc/bin:/usr/lpp/mmfs/bin:
/opt/ibutils/bin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin)
However, in our case we do have an existing python3 available so we see
/usr/bin/python3
We 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:
[netid@dev-amd20 ~]$ module load GCC/10.2.0 OpenMPI/4.0.5 Python/3.8.6
[netid@dev-amd20 ~]$ which python3
/opt/software/Python/3.8.6-GCCcore-10.2.0-new/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 UNIX system looks for software. Specifically $PATH is a list of
directories (separated by :) that the OS searches through for a command
before giving up and telling us it can’t find it. As with all environment
variables we can print it out using echo.
[netid@dev-amd20 ~]$ echo $PATH
/opt/software/Python/3.8.6-GCCcore-10.2.0-new/bin:/opt/software/SQLite/3.33.0-GCCcore-10.2.0/bin:/opt/software/Tcl/8.6.10-GCCcore-10.2.0/bin:/opt/software/ncurses/6.2-GCCcore-10.2.0/bin:/opt/software/bzip2/1.0.8-GCCcore-10.2.0/bin:/opt/software/OpenMPI/4.0.5-GCC-10.2.0/bin:/opt/software/libfabric/1.11.0-GCCcore-10.2.0/bin:/opt/software/UCX/1.9.0-GCCcore-10.2.0/bin:/opt/software/hwloc/2.2.0-GCCcore-10.2.0/sbin:/opt/software/hwloc/2.2.0-GCCcore-10.2.0/bin:/opt/software/libxml2/2.9.10-GCCcore-10.2.0/bin:/opt/software/XZ/5.2.5-GCCcore-10.2.0/bin:/opt/software/numactl/2.0.13-GCCcore-10.2.0/bin:/opt/software/binutils/2.35-GCCcore-10.2.0/bin:/opt/software/GCCcore/10.2.0/bin:/opt/software/powertools/bin:/opt/software/core/lua/lua/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/hpcc/bin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin
You’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
$PATH. Let’s examine what’s there:
[netid@dev-amd20 ~]$ ls /opt/software/Python/3.8.6-GCCcore-10.2.0-new/bin
2to3 netaddr pytest rst2s5.py
2to3-3.8 nosetests py.test rst2xetex.py
chardetect nosetests-3.8 python rst2xml.py
cygdb pasteurize python3 rstpep2html.py
cython pbr python3.8 runxlrd.py
cythonize pip python3.8-config sphinx-apidoc
doesitcache pip3 python3-config sphinx-autogen
easy_install pip3.8 rst2html4.py sphinx-build
easy_install-3.8 pkginfo rst2html5.py sphinx-quickstart
flit poetry rst2html.py tabulate
futurize pybabel rst2latex.py virtualenv
idle3 __pycache__ rst2man.py wheel
idle3.8 pydoc3 rst2odt_prepstyles.py
jsonschema pydoc3.8 rst2odt.py
keyring pygmentize rst2pseudoxml.py
Taking this to its conclusion, module load will add software to your $PATH.
It “loads” software. A special note on this - depending on which version of the
module program that is installed at your site, module load will also load
required software dependencies.
To demonstrate, let’s use module list. module list shows all loaded
software modules.
[netid@dev-amd20 ~]$ module list
Currently Loaded Modules:
1) powertools/1.2 8) libxml2/2.9.10 15) ncurses/6.2
2) GCCcore/10.2.0 9) libpciaccess/0.16 16) libreadline/8.0
3) zlib/1.2.11 10) hwloc/2.2.0 17) Tcl/8.6.10
4) binutils/2.35 11) UCX/1.9.0 18) SQLite/3.33.0
5) GCC/10.2.0 12) libfabric/1.11.0 19) GMP/6.2.0
6) numactl/2.0.13 13) OpenMPI/4.0.5 20) libffi/3.3
7) XZ/5.2.5 14) bzip2/1.0.8 21) Python/3.8.6
[netid@dev-amd20 ~]$ module load GROMACS
[netid@dev-amd20 ~]$ module list
Currently Loaded Modules:
Currently Loaded Modules:
1) powertools/1.2 11) UCX/1.9.0 21) Python/3.8.6
2) GCCcore/10.2.0 12) libfabric/1.11.0 22) OpenBLAS/0.3.13
3) zlib/1.2.11 13) OpenMPI/4.0.5 23) FFTW/3.3.8
4) binutils/2.35 14) bzip2/1.0.8 24) ScaLAPACK/2.1.0
5) GCC/10.2.0 15) ncurses/6.2 25) pybind11/2.6.0
6) numactl/2.0.13 16) libreadline/8.0 26) SciPy-bundle/2020.11
7) XZ/5.2.5 17) Tcl/8.6.10 27) networkx/2.5
8) libxml2/2.9.10 18) SQLite/3.33.0 28) GROMACS/2021
9) libpciaccess/0.16 19) GMP/6.2.0
10) hwloc/2.2.0 20) libffi/3.3
So in this case, loading the GROMACS module (a bioinformatics software
package), also loaded GMP/6.2.0 and
SciPy-bundle/2020.11 as well. Let’s try unloading the
GROMACS package.
[netid@dev-amd20 ~]$ module unload GROMACS
[netid@dev-amd20 ~]$ module list
Currently Loaded Modules:
1) powertools/1.2 8) libxml2/2.9.10 15) ncurses/6.2
2) GCCcore/10.2.0 9) libpciaccess/0.16 16) libreadline/8.0
3) zlib/1.2.11 10) hwloc/2.2.0 17) Tcl/8.6.10
4) binutils/2.35 11) UCX/1.9.0 18) SQLite/3.33.0
5) GCC/10.2.0 12) libfabric/1.11.0 19) GMP/6.2.0
6) numactl/2.0.13 13) OpenMPI/4.0.5 20) libffi/3.3
7) XZ/5.2.5 14) bzip2/1.0.8 21) Python/3.8.6
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).
If we wanted to unload everything at once, we could run module purge
(unloads everything).
[netid@dev-amd20 ~]$ module purge
[netid@dev-amd20 ~]$ module list
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 principally through
the manipulation of environment variables like $PATH. There
is usually little or no data transfer involved.
The module loading process manipulates other special environment variables as well, including variables that influence where the system looks for software libraries, and sometimes variables which tell commercial software packages where to find license servers.
The module command also restores these shell environment variables to their previous state when a module is unloaded.
Using Software Modules in Scripts
Create a job that is able to run
python3 --version. Remember, no software is loaded by default! Running a job is just like logging on to the system (you should not assume a module loaded on the login node is loaded on a compute node).Solution
[netid@dev-amd20 ~]$ nano python-module.sh [netid@dev-amd20 ~]$ cat python-module.sh#!/usr/bin/env bash #SBATCH #SBATCH -t 00:00:30 module purge module load GCC/10.2.0 OpenMPI/4.0.5 Python/3.8.6 python3 --version[netid@dev-amd20 ~]$ sbatch python-module.sh
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 use Python 3 as an example and try to load another version. We can see what versions are available using the module spider command:
[netid@dev-amd20 ~]$ module spider Python
----------------------------------------------------------------------------
Python:
----------------------------------------------------------------------------
Description:
Python is a programming language that lets you work more quickly and
integrate your systems more effectively.
Versions:
Python/2.7.9
Python/2.7.10
Python/2.7.11
...skipping...
Python/3.10.8-bare
Python/3.10.8
Python/3.11.3
Other possible modules matches:
Biopython Boost.Python GitPython IPython ScientificPython ...
----------------------------------------------------------------------------
To find other possible module matches execute:
$ module -r spider '.*Python.*'
----------------------------------------------------------------------------
For detailed information about a specific "Python" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider Python/3.11.3
----------------------------------------------------------------------------
To find out what command to use to load a specific version, we can use module spider with that version:
module spider Python/3.11.3
----------------------------------------------------------------------------
Python: Python/3.11.3
----------------------------------------------------------------------------
Description:
Python is a programming language that lets you work more quickly and
integrate your systems more effectively.
You will need to load all module(s) on any one of the lines below before the "Python/3.11.3" module is available to load.
GCCcore/12.3.0
Help:
Description
===========
Python is a programming language that lets you work more quickly and integrate your systems
more effectively.
More information
================
- Homepage: https://python.org/
Included extensions
===================
flit_core-3.9.0, pip-23.1.2, setuptools-67.7.2, wheel-0.40.0
In this case, we need to load the GCCcore/12.3.0 module first first, since Python/3.11.3 needs it to be able to run
[netid@dev-amd20 ~]$ module load GCCcore/12.3.0 Python/3.11.3
Dependency consistency
If you need to load multiple pieces of software at the same time, you need to make sure they use the same versions of any common dependencies. There is unfortunately not a good solution to this yet! The best way is to use
module spideron different versions to try to find a match.
Key Points
Load software with
module load softwareName.Unload software with
module unloadClean out all loaded modules with
module purgeto avoid conflictsMultiple pieces of software need to use compatible dependencies