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habrok:migration:alma9:start [2026/06/09 09:26] – created vladahabrok:migration:alma9:start [2026/06/10 11:55] (current) – [TLDR] pedro
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 ====== Hábrók upgrade from Alma Linux 8 to 9 ====== ====== Hábrók upgrade from Alma Linux 8 to 9 ======
  
-**This guide spans three pages:**+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:
  
-  * **Overview** (you are here) — Hábrók's move to Alma Linux 9 and what it means for your software 
   * [[habrok:migration:alma9:plan|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''   * [[habrok:migration:alma9:plan|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''
   * [[habrok:migration:alma9:faq|FAQ]] — answers to common questions about the migration   * [[habrok:migration:alma9:faq|FAQ]] — answers to common questions about the migration
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 ---- ----
  
-===== 1. TLDR =====+===== TLDR =====
  
-Hábrók's OS is currently Alma Linux 8.10 and we will start a migration to Alma Linux 9.8 on **DATE**. 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 [[habrok:migration:alma9:plan|here]] for details, including on how to access a particular Alma Linux version.+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 [[habrok:migration:alma9:plan|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 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 [[habrok:software_environment:eessi|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 current applications are expected to work. In the near future you need to load a module to access the [[habrok:software_environment:eessi|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. The node names of the compute nodes will change after the migration to Alma Linux 9.
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 We have compiled an [[habrok:migration:alma9:faq|FAQ page]] about the migration. We have compiled an [[habrok:migration:alma9:faq|FAQ page]] about the migration.
  
-===== 2. Introduction =====+===== Introduction =====
  
 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 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.
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 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 [[#3_software_support|Software support]] section below and on the [[habrok:migration:alma9:plan|Migration plan]] page. 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 [[#3_software_support|Software support]] section below and on the [[habrok:migration:alma9:plan|Migration plan]] page.
  
-===== 3. Software support =====+===== Software support =====
  
 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. 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.
  
-==== 3.1 Software modules ====+==== Software modules ====
  
-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.+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. 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.
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 **Consult [[#3.4_self-compiled_applications|this section]] if you install or compile applications by yourself.** **Consult [[#3.4_self-compiled_applications|this section]] if you install or compile applications by yourself.**
  
-You might have software you installed yourself on your personal directories. This might be, for example, code you self-compile, or Python or R packages that you install to personal environments. In that case, it is very important that you consult the relevant sections as you likely need to reinstall your personal software environment and recompile your code. See [[#3.4_self-compiled_applications|3.4 Self-compiled applications]] for self-compiled code and [[#3.5_personal_python_and_r_libraries|3.5 Personal Python and R libraries]] for R and Python packages.+You might have software you installed yourself on your personal directories. This might be, for example, code you self-compile, or Python or R packages that you install to personal environments. In that case, it is very important that you consult the relevant sections as you likely need to reinstall your personal software environment and recompile your code. See [[#self-compiled_applications| Self-compiled applications]] for self-compiled code and [[#personal_python_and_r_libraries| Personal Python and R libraries]] for R and Python packages.
 </WRAP> </WRAP>
  
-==== 3.2 Migration to EESSI modules based software stack ====+==== Migration to EESSI modules based software stack ====
  
 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/|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: 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/|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:
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 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/|https://www.eessi.io/docs/available_software/]]. 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/|https://www.eessi.io/docs/available_software/]].
  
-=== 3.2.1 Support for new applications ===+=== Support for new applications ===
  
 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/|https://easybuild.io/]] for more information on EasyBuild. The recipe has to be supported on the CPU architectures supported by EESSI. 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/|https://easybuild.io/]] for more information on EasyBuild. The recipe has to be supported on the CPU architectures supported by EESSI.
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 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. 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.
  
-==== 3.3 Portal applications ====+==== Portal applications ====
  
 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. 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.
  
-==== 3.4 Self-compiled applications ====+==== Self-compiled applications ====
  
 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''. 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''.
  
-==== 3.5 Personal Python and R libraries ====+==== Personal Python and R libraries ====
  
 === Python libraries === === Python libraries ===