| title | teaching | exercises | questions | objectives | keypoints | |||||
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Accessing software via Modules |
30 |
15 |
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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 Software compiled against a newer version of the C libraries and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 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.
To see available software modules, use module avail:
{{ site.remote.prompt }} module avail
{: .language-bash}
{% include {{ site.snippets }}/modules/available-modules.snip %}
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
{{ site.remote.prompt }} module list
{: .language-bash}
No Modulefiles Currently Loaded.
{: .output}
To load a software module, use module load. In this example we will use
Python.
The Python installed on the system may differ from the head node to the compute nodes and may not be the version you need. We can test this by using the which command and the 'version' option of the python 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. Using the '--version' option will tell us what version is the default.
{: .language-bash}
{{ site.remote.prompt }} which python3
{% include {{ site.snippets }}/modules/missing-python.snip %}
{: .language-bash}
{{ site.remote.prompt }} python3 --version
{% include {{ site.snippets }}/modules/python-version.snip %}
We can see which versions of python are available to use with module avail:
{{ site.remote.prompt }} module avail python
{: .language-bash}
{% include {{ site.snippets }}/modules/module-avail-python.snip %}
If we need an older version of python we can load it with module load:
{% include {{ site.snippets }}/modules/module-load-python.snip %}
{% include {{ site.snippets }}/modules/python-executable-dir.snip %}
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.
{{ site.remote.prompt }} echo $PATH
{: .language-bash}
{% include {{ site.snippets }}/modules/python-module-path.snip %}
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:
{% include {{ site.snippets }}/modules/python-ls-dir-command.snip %}
{% include {{ site.snippets }}/modules/python-ls-dir-output.snip %}
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.
{% include {{ site.snippets }}/modules/software-dependencies.snip %}
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.
{: .language-bash}
{{ site.remote.prompt }} module avail
{: .language-bash}
{% include {{ site.snippets }}/modules/available-modules.snip %}
{% include {{ site.snippets }}/modules/wrong-gcc-version.snip %}
Create a job that is able to run a version of Anaconda Python36 and output
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).{{ site.remote.prompt }} nano python-module.sh {{ site.remote.prompt }} cat python-module.sh{: .language-bash}
{{ site.remote.bash_shebang }} module load python/py36-anaconda-5.2.0 python3 --version{: .output}
{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}python-module.sh{: .language-bash} {: .solution} {: .challenge}
{% include links.md %}