Hábrók upgrade from Alma Linux 8 to 9

This page covers a general overview of Hábrók's move to Alma Linux 9 and what it means for your software. Make sure you also check the following related pages:

• Migration plan — the three-step rollout (testing → mixed environment → completion), the Alma 9 test reservation, and how to target Alma 8 or Alma 9 explicitly with sbatch
• FAQ — answers to common questions about the migration

Hábrók's OS is currently Alma Linux 8.10 and we will start a migration to Alma Linux 9.8 on a date to be announced soon. This migration will be gradual and we will first set up a test environment for our users. After the initial test period we will gradually migrate login, interactive and compute nodes from Alma Linux 8 to 9. This means there will be a mixed environment for a while, see here for details, including on how to access a particular Alma Linux version.

The upgrade to Alma Linux 9 will not change the way the cluster works, but there are a few important details about your software that you should be aware of.

The current applications are expected to work. In the near future you need to load a module to access the EESSI software stack, which will become the default on Alma Linux 9 nodes. You will still be able the existing software but you will need to explicitly load the module 2023.01. This change will be announced to the users before it is being made.

The node names of the compute nodes will change after the migration to Alma Linux 9.

All further changes will be announced in the login messages, and a change log is kept on the wiki at: Hábrók Changelog

We have compiled an FAQ page about the migration.

The current OS used on Hábrók, Alma Linux 8 (which is based on RedHat Enterprise Linux 8), originates in 2019, with the final version 8.10 released in 2024. The OS still gets security updates for several more years, but may no longer support new hardware. Furthermore the versions of the software inside it are getting outdated.

The latter means that it is becoming necessary to move to a newer release of Alma Linux to make sure newer applications are supported. Since Alma Linux version 10 was just released last year, we will migrate to the proven stable Alma Linux 9.

This page documents the impact that this may have for you as a Hábrók user. The migration will have an effect on the application side and there will be a mixed environment for a certain period. These parts will be described in the Software support section below and on the Migration plan page.

The main impact for users will be at the application side. We do expect the cluster to run in the same way it did before, since we will not change the scheduler or storage platform. On the cluster we can distinguish several software categories, each of which will be described in a subsection.

Many applications are available by loading these through our “module” system. By default these modules are taken from the current 2023.01 software stack. All these applications have been built by us on a RedHat Enterprise Linux 8 derivative with optimizations for most of the CPU architectures that we have available in Hábrók.

We have tested several of these applications on an Alma Linux 9 system and have not encountered issues. We have not been able to test the hundreds of applications that are installed, but since all applications that we tested work properly, including R and Python, we expect the current stack to still work in Alma Linux 9.

Although the current software stack still works, we cannot continue building new applications on Alma Linux 8 and we therefore need to move to a new software stack for the future. This stack will be based on EESSI and is described in a later section.

New applications will be built on top of the EESSI software stack. EESSI is a collaborative project, where applications are provided centrally. See https://www.eessi.io/ for more information. These applications are built on top of a so called “compatibility layer”, which means they can run on many Linux distributions. The main advantages of EESSI are:

1. The software is provided centrally from a collaborative organization. This saves us a lot of work in building the applications locally.
2. The software is built for many CPU architectures, not only including Intel/AMD x86_64 based, but also Arm and RISC-V. This gives us more flexibility in the types of hardware we can support in the cluster.
3. The software stack will also be available at compute clusters at other universities and you can even mount and use it on local systems like your laptop
4. The software supports many Linux distributions and has a limited dependency on the host operating system, which means that upgrading the host OS does not impact the application stack.

You can switch to the new software stack using:

module load EESSI/2025.06

This will load the latest release of EESSI, which is the 2025.06 release. Currently there is also a 2023.06 release available. New applications will be installed on top of the 2025.06 release, and the 2023.06 release will be deprecated in the future. An overview of the software that is available in EESSI can be found at https://www.eessi.io/docs/available_software/.

There are two ways to add software to EESSI. The first is to have the software added to the centrally managed repository. This can be done if a working build recipe is available in the Easybuild Easyconfig repository. See https://easybuild.io/ for more information on EasyBuild. The recipe has to be supported on the CPU architectures supported by EESSI.

The second way is by building the software on top of the EESSI software stack, but to host it locally at the university. This is the mechanism we will use for applications that are needed at the University of Groningen, which can currently not be supported by EESSI centrally.

We have tested the applications in the Open OnDemand web portal. The current versions work properly and will be supported for the near future. All new applications, or updated versions, will be built on top of the EESSI software stack.

Binary applications, compiled on Alma Linux 8, may still work on Alma Linux 9. We strongly encourage you to recompile these applications. Applications built with the OS compilers can be recompiled on Alma Linux 9 directly. Applications that have been built using compiler modules from the 2023.01 software stack should be recompiled using a compiler from EESSI/2025.06.

Most Python libraries are distributed as binary wheels. These binary wheels are expected to work on Alma Linux 9. Some wheels that no longer supported Alma Linux 8, may even work again on Alma Linux 9.

We do advise you to reinstall your virtual environments with a Python version from the EESSI/2025.06 software stack, as the 2023.01 software stack will be deprecated in the future. See here for more details on EESSI).

If needed you can still use the R versions that are available in the 2023.01 software stack. The libraries that you compiled are still expected to work.

We do advise you to start using the latest version of R from the EESSI/2025.06 software stack. After switching you can reinstall your R libraries with the compiler underpinning the R version in EESSI/2025.06.