Applications

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 some.

See also

Main article: Applications: General info

Available softwares

You can find what softwares we have available in different ways:

  • First, you should check our Applications page and see if the software you need is already available and has instructions.
  • If you find the software you need available, you can usually load it via a module. The next tutorial, Software modules explains what modules are and how to work with them.
  • You can also search this tutorial to see what you can find (though note that not everything is in the Triton section here - some applies to Aalto workstations or own computers).
  • It’s always a good idea to search the issue tracker to see if there are previous issues about it - not everything is always updated.

Modules

You can learn about modules on the Software modules tutorial. But generally, module is a command that allows you to get and remove access to other software - because not everything can be available at once. The Software modules tutorial teaches how to load modules using the command module load $NAME, etc.

Not all of the software we have available is documented. You can module spider $NAME to try to see if you can find a module that way. Note that this is partially case sensitive so it can be hard to find things - you might need to look through module avail too, to find all the available modules.

Common applications

Important

This is Aalto-specific. Some of these will work if you module load fgci-common at other Finnish sites. This is introduced in the next lesson.

For reference, here are the most common softwares:

  • Python: module load anaconda for the Anaconda distribution of Python 3, including a lot of useful packages. More info.
  • R: module load r for a basic R package. More info.
  • Matlab: module load matlab for the latest Matlab version. More info.

If one of these module load commands does not work at your site, try module spider $NAME and see if you can find it. This is actually covered under the upcoming modules tutorial.

Singularity containers

See also

Main article: Singularity Containers

Some softwares have become so complicated that they just can’t be installed, and for that we use containers. A software container is basically a complete self-contained operating system environment. Another advantage of containers is that they make it easy to move installed software from system to system, so that you can have the same environment everywhere.

You can read about singularity containers here. If you load a module that uses singularity, nothing will happen at first. You execute your software using singularity_wrapper exec, or use singularity_wrapper shell to get a shell in there.

We also provide some containers built by NVIDIA. These containers are from NVIDIA’s NGC-repository and meant for GPU computations.

Requesting new software

We aim to install a good base of software for our users - but it’s not possible to keep up with all requests. If you need something, submit a request to our issue tracker, but be aware that despite best efforts, we can’t do everything. See the main Applications page for more information.

A plea: make your software reusable!

Five years from now, when you are releasing your own software that you want others to use, make it easy to install and reusable.

Exercises

If you are not at Aalto, you need to module load fgci-common before you can do these.

  1. Figure out how to use tensorflow (this is not a software problem, but a searching the documentation problem). Make it work enough to do python and import tensorflow – though you will get an error which you will learn to solve in a later lesson.
  2. Figure out how to load the module for NVIDIA’s tensorflow container. Using singularity_wrapper, run python -V and obtain python version. Compare that to the python version on the login node. Try singularity_wrapper shell too and use cat to check the operating system version stored in /etc/issue: cat /etc/issue. Verify that this is different from what is outside the container.
  3. Find the Applications page link above, and check the list for ways to find out if we already have your software installed. See if we have what you need, using any of the strategies on that list.
  4. (optional) From the Applications page, find the Spack package list (warning: it’s a very long page and takes a while to load). Does it have anything useful to you?
  5. (optional) Discuss among your group what software you need, if it’s available, and how you might get it.

What’s next?

The next tutorial covers software modules in more detail.