Applications

Videos

Videos of this topic may be available from one of our kickstart course playlists: 2024, 2023, 2022 Summer, 2022 February, 2021 Summer, 2021 February.

In this tutorial, we talk about the overall process of finding, building, and compiling software. These days, installing and managing scientific software is taking more and more time, thus we need to specifically talk about it.

Clusters, being shared systems, have more complicated software requirements. In this tutorial, you will learn how to use existing software. Be aware that installing your own is possible (and people do it all the time), but does require some attention to details. Either way, you will need to know the basics of software on Linux.

Abstract

• There are many ways to get software on Triton:

  • Usually, you can’t install software the normal operating system way.

  • The cluster admins install many things for you, and they are loadable with Modules.

  • Sometimes, you need to install some stuff on top of that (your own libraries or environments)

  • You can actually install your own applications, but you need to modify instructions to work in your own directories.

• Singularity containers allow you to run other hard-to-install software.

• Ask us to install software if you need it. Ask for help if you try it yourself and it seems to be taking too long.

See also

Main article: Applications: General info

Local differences

Almost every site will use modules. The exact module names, and anything beyond that, will be different. Containers are becoming more common, but they are less standardized.

There are four main ways of getting software:

• It’s installed through the operating system some relatively “normal” way.

• Someone (a cluster admin) has already installed it for you. Or you ask someone to install what you need.

• Someone has installed the base of what you need. You do some extra.

• Install it yourself in a storage place you have access to. (Maybe you share it with others?)

Installed through operating system

People sometimes expect the cluster to work just like your laptop: install something through a package manager or app store. This doesn’t really work when you have hundreds of users on the same system: if you upgrade X, how many other people’s work suddenly breaks?

Thus, this isn’t really done, except for very basic, standalone applications. If it is done, this stuff isn’t upgraded and often old: instead, we install through modules (the next point) so that people can choose the version they want.

One unfortunate side-effect is that almost all software installation instructions you find online don’t work on the cluster. Often times, it can be installed, but people don’t think to mention it in the documentation. This often requires some thought to figure out: if you can’t figure it out, ask for help!

Cluster admin has installed it for you

The good thing about the cluster is that a few people can install software and make it usable by a lot of people. This can save you a lot of time. Your friendly admins can install things through the Software modules (an upcoming lesson), so that you can module load it with very little work. You can even choose your exact version, so that it keeps working the same even if someone else needs a newer version.

Some clusters are very active in this, some expect the users to do more. Some things are so obscure, or so dependent on local needs, that it only makes sense to help people install it themselves. To look for what is available:

• Check out the page Applications: General info and its sub-pages.

• Search the issue tracker to see if someone has already requested it and documented there.

• Ask us: Our issue tracker, Zulip chat or our support garage.

• Modules (Software modules - next lesson) are the usual way of making this available. The command module spider NAME will search for anything of that name.

If you need something installed, contact us. The issue tracker is usually the best way to do this.

Some of the most common stuff that is available:

• Python: module load scicomp-python-env for the an Aalto Scientific Computing managed Python environment with common packages. More info.

  • module load mamba for mamba/conda for making your own environments (see below)

• R: module load r for a basic R package. More info.

  • module load scicomp-r-env for an R module with various packages pre-installed

• Matlab: module load matlab for the latest Matlab version. More info.

Important

This is Aalto-specific. Some of these will work if you module load fgci-common at other Finnish sites (but not CSC). This is introduced in the next lesson.

Already installed, you add extra modules you need

Even if a cluster admin installs some software, often you might need to improve it some. One classic example is Python: we provide Python installations, but you need your own modules there. So, you can use our base Python installation to create your own environments - self-contained systems where you can install whatever you need. Different languages have different ways of doing this:

• Python: Conda environments, virtual environments. See Python Environments with Conda.

Environments have an advantage that you can do multiple projects at once, and move between computers more easily.

Install it yourself

Sometimes, you need to install software yourself - which you can do if you can tell it to install just into your home directory. Usually, the software’s instructions don’t talk about how to do this (and might not even mention things like the environments in the previous point).

One common way of doing this is containers (for example, Docker or Apptainer/Singularity). These basically allow you to put an entire operating system in one file, so that your software works everywhere. Very nice when software is difficult to install or needs to be moved from computer to computer, but can take some work to set up. See Singularity Containers or the longer lesson on containers on HPC for more information.

We can’t go into this more right now - ask us for help if needed. If you make a “we need X installed” request, we’ll tell you how to do it if self-installation is the easiest way.

What you should do

• Check if you can find what you need already: issue tracker and searching this site.

• Ask for help if you can’t find it.

• Once you get there, make your software nice and reusable, so that others won’t have the same problems you did: make it easy to install and reusable. Contact the Research Software Engineers for help!

Exercises

These are more for thinking than anything.

Applications-1: Check your needs

Find the Applications page link above, the issue tracker, etc., and if we already have your software installed. See if we have what you need, using any of the strategies on that list.

(optional) Applications-2: Your group’s needs

Discuss among your group what software you need, if it’s available, and how you might get it. Can they tell you how to get started?

What’s next?

The next tutorial covers software modules in more detail.