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 Software compiled against a newer version of the C libraries and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:
[SUNetID@rice-02:~]$ module avail
------------------ /software/modules/linux-ubuntu22.04-x86_64/Core -------------------
apptainer/1.1.9 libjpeg-turbo/2.1.5.1
blast-plus/2.14.1 libpng/1.5.30
boost/1.85.0 llvm/18.1.3
bowtie2/2.5.2 micromamba/1.4.2
cuda/11.4.4 mpich/4.2.1
[removed most of the output here for clarity]
Where:
D: Default Module
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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
[SUNetID@rice-02:~]$ 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, 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.
[SUNetID@rice-02:~]$ which python3
If the python3 command was unavailable, we would see output like
/usr/bin/which: no python3 in (/home/users/SUNetID/bin:/home/users/SUNetID/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/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:
/home/users/SUNetID/bin
/home/users/SUNetID/.local/bin
/usr/local/sbin
/usr/local/bin
/usr/sbin
/usr/bin
/sbin
/bin
/usr/games
/usr/local/games
/snap/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:
[SUNetID@rice-02:~]$ module load python
[SUNetID@rice-02:~]$ which python3
/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/python-3.11.7-pph34wf44o63tsszsra7m7ihjrmcniaj/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 $PATH is a list of
directories (separated by :) that the OS searches through for a command
before giving up and telling us it can’t find it. As with all environment
variables we can print it out using echo.
[SUNetID@rice-02:~]$ echo $PATH
/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/python-3.11.7-pph34wf44o63tsszsra7m7ihjrmcniaj/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/util-linux-uuid-2.38.1-zaohlkc7x4n5d3fbxpfb672inndarvau/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/sqlite-3.43.2-4hpmcprlw5equdicrtcmacl5psvhhmxf/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/openssl-3.3.0-4gl4yy3vwevsukqvlffjeeyofzrqrsxy/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/gettext-0.22.5-yrjlrvvghvrkmemdgnymjytmqnjydwnf/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/tar-1.34-ddpzee5n4ckjguinf6mvzwdnmhjezjln/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/zstd-1.5.6-77bmnajavm5hebchfmfxhjq3xgp45w7r/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/pigz-2.8-gvcpolzhshratajggf3jptqfnqsufhhn/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/libxml2-2.10.3-pwcbmqyzxybnsdc65wpvi4szbxgs5ywx/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/xz-5.4.6-x7ef77ycuvfkealpqz7efodaehjj2xbm/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/libiconv-1.17-agtuexjs5f4hbr34gniwqgcza6wlsdh5/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/gdbm-1.23-rtgm7swq4xhs6uosx7kd2zbx2lgn4rsy/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/readline-8.2-yy655utp5k7pzjkxjpadu7lnbg2vq3bl/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/ncurses-6.5-l7iqip2kzaxff54gqpuxtqwse222qvea/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/expat-2.6.2-gugyyi4jfqm36v2pvpmz2ij34e77cokg/bin:/software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/bzip2-1.0.8-4z7zft5br5b6o2m7zr5oiqoxxsgv3gxf/bin:/home/users/SUNetID/bin:/home/users/SUNetID/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/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
$PATH. Let’s examine what’s there:
[SUNetID@rice-02:~]$ ls /software/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-13.2.0/python-3.11.7-pph34wf44o63tsszsra7m7ihjrmcniaj/bin
2to3 idle3.11 python python3-config python3.11-gdb.py
2to3-3.11 pydoc3 python-config python3.11
idle3 pydoc3.11 python3 python3.11-config
Taking this to its conclusion, module load will add software to your $PATH.
It “loads” software. A special note on this - depending on which version of the
module program that is installed at your site, module load will also load
required software dependencies.
To demonstrate, let’s use module list. module list shows all loaded
software modules.
[SUNetID@rice-02:~]$ module list
Currently Loaded Modules:
1) glibc/2.35-hwm6jll 13) libxml2/2.10.3-pwcbmqy
2) gcc-runtime/13.2.0-4b46r64 14) pigz/2.8-gvcpolz
3) bzip2/1.0.8-4z7zft5 15) zstd/1.5.6-77bmnaj
4) libmd/1.0.4-zgn4nm3 16) tar/1.34-ddpzee5
5) libbsd/0.12.1-i7vok2f 17) gettext/0.22.5-yrjlrvv
6) expat/2.6.2-gugyyi4 18) libffi/3.4.6-3p64pum
7) ncurses/6.5-l7iqip2 19) libxcrypt/4.4.35-3ofajra
8) readline/8.2-yy655ut 20) openssl/3.3.0-4gl4yy3
9) gdbm/1.23-rtgm7sw 21) sqlite/3.43.2-4hpmcpr
10) libiconv/1.17-agtuexj 22) util-linux-uuid/2.38.1-zaohlkc
11) xz/5.4.6-x7ef77y 23) python/3.11.7
12) zlib-ng/2.1.6-4xk6kiq
[SUNetID@rice-02:~]$ module load julia
[SUNetID@rice-02:~]$ module list
Currently Loaded Modules:
1) glibc/2.35-hwm6jll 27) curl/8.7.1-dilktws
2) gcc-runtime/13.2.0-4b46r64 28) dsfmt/2.2.5-yrb7poa
3) bzip2/1.0.8-4z7zft5 29) gmp/6.2.1-brxkiho
4) libmd/1.0.4-zgn4nm3 30) libblastrampoline/5.8.0-pajuz6u
5) libbsd/0.12.1-i7vok2f 31) pcre/8.45-bsep6cd
6) expat/2.6.2-gugyyi4 32) libgit2/1.6.4-6n6p7pm
7) ncurses/6.5-l7iqip2 33) libunwind/1.6.2-bzhjldn
8) readline/8.2-yy655ut 34) libuv-julia/1.44.3-mpcmz2j
9) gdbm/1.23-rtgm7sw 35) binutils/2.42-pyz2his
10) libiconv/1.17-agtuexj 36) pkgconf/2.2.0-euy2z2u
11) xz/5.4.6-x7ef77y 37) elfutils/0.190-r6vhdnt
12) zlib-ng/2.1.6-4xk6kiq 38) libpciaccess/0.17-pfgymna
13) libxml2/2.10.3-pwcbmqy 39) hwloc/2.9.1-smlej6r
14) pigz/2.8-gvcpolz 40) libedit/3.1-20230828-ls2cusj
15) zstd/1.5.6-77bmnaj 41) unzip/6.0-w3hyu2g
16) tar/1.34-ddpzee5 42) lua/5.3.6-bshf2me
17) gettext/0.22.5-yrjlrvv 43) swig/4.0.2-fortran-irv7aqc
18) libffi/3.4.6-3p64pum 44) llvm/15.0.7-aibkinw
19) libxcrypt/4.4.35-3ofajra 45) mpfr/4.2.1-bpff5zj
20) openssl/3.3.0-4gl4yy3 46) openlibm/0.8.1-vk6saea
21) sqlite/3.43.2-4hpmcpr 47) p7zip/17.05-gtsuz3k
22) util-linux-uuid/2.38.1-zaohlkc 48) pcre2/10.43-lfijy3h
23) python/3.11.7 49) metis/5.1.0-jfogols
24) mbedtls/2.28.2-7husfdf 50) suite-sparse/7.2.1-ybtegdu
25) libssh2/1.11.0-z7hjcm2 51) utf8proc/2.8.0-ib2ggng
26) nghttp2/1.52.0-zz56qrn 52) julia/1.10.2
So in this case, loading the julia module (a high-level, high-performance
dynamic programming language for numerical computing), also loaded many other
dependencies as well. Let’s try unloading the julia package.
[SUNetID@rice-02:~]$ module unload julia
[SUNetID@rice-02:~]$ module list
Currently Loaded Modules:
1) glibc/2.35-hwm6jll 13) libxml2/2.10.3-pwcbmqy
2) gcc-runtime/13.2.0-4b46r64 14) pigz/2.8-gvcpolz
3) bzip2/1.0.8-4z7zft5 15) zstd/1.5.6-77bmnaj
4) libmd/1.0.4-zgn4nm3 16) tar/1.34-ddpzee5
5) libbsd/0.12.1-i7vok2f 17) gettext/0.22.5-yrjlrvv
6) expat/2.6.2-gugyyi4 18) libffi/3.4.6-3p64pum
7) ncurses/6.5-l7iqip2 19) libxcrypt/4.4.35-3ofajra
8) readline/8.2-yy655ut 20) openssl/3.3.0-4gl4yy3
9) gdbm/1.23-rtgm7sw 21) sqlite/3.43.2-4hpmcpr
10) libiconv/1.17-agtuexj 22) util-linux-uuid/2.38.1-zaohlkc
11) xz/5.4.6-x7ef77y 23) python/3.11.7
12) zlib-ng/2.1.6-4xk6kiq
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).
[SUNetID@rice-02:~]$ module purge
[SUNetID@rice-02:~]$ 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 $PATH. There
is usually little or no data transfer involved.
The module loading process manipulates other special environment variables as well, including variables that influence where the system looks for software libraries, and sometimes variables which tell commercial software packages where to find license servers.
The module command also restores these shell environment variables to their previous state when a module is unloaded.
Software Versioning
So far, we’ve learned how to load and unload software packages. This is very useful. However, we have not yet addressed the issue of software versioning. At some point or other, you will run into issues where only one particular version of some software will be suitable. Perhaps a key bugfix only happened in a certain version, or version X broke compatibility with a file format you use. In either of these example cases, it helps to be very specific about what software is loaded.
Let’s examine the output of module avail more closely.
[SUNetID@rice-02:~]$ module avail
------------------ /software/modules/linux-ubuntu22.04-x86_64/Core -------------------
apptainer/1.1.9 libjpeg-turbo/2.1.5.1
blast-plus/2.14.1 libpng/1.5.30
boost/1.85.0 llvm/18.1.3
bowtie2/2.5.2 micromamba/1.4.2
cuda/11.4.4 mpich/4.2.1
[removed most of the output here for clarity]
Where:
D: Default Module
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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).Solution
[SUNetID@rice-02:~]$ nano python-module.sh [SUNetID@rice-02:~]$ cat python-module.sh#!/bin/bash #SBATCH #SBATCH -t 00:00:30 module load python python3 --version[SUNetID@rice-02:~]$ sbatch python-module.sh
Key Points
Load software with
module load softwareName.Unload software with
module unloadThe module system handles software versioning and package conflicts for you automatically.