CIT Research Documentation

Migration plan - Fix reservation command

pedro (pedro@undisclosed.example.com) — 2026-07-01T18:04:20+00:00

Migration plan We will migrate Hábrók to Alma Linux 9 in a three step procedure. The first step consists of a testing phase, in which some nodes will be made available to the users for testing their workloads on Alma Linux 9. This is followed by a migration phase, in which compute and user interface nodes will be gradually moved over from Alma Linux 8 to 9. The final phase is when all nodes have been migrated, including the last user interface nodes.

Storage areas - [/scratch]

pedro (pedro@undisclosed.example.com) — 2026-06-29T12:47:44+00:00

Storage areas This page describes the directories / file systems that are available to each user for storing files and data sets. To see how much space you have available at the different file systems, the hbquota tool can be used. Please refer to the

Running jobs on GPUs - [Running interactive jobs]

pedro (pedro@undisclosed.example.com) — 2026-06-29T12:46:27+00:00

Running jobs on GPUs If you want your job to make use of a special resource like a GPU, you will have to request these. This can be done using the new Slurm option: #SBATCH --gpus-per-node=n Where n is the number of GPUs you want to use per node.

Apptainer Containers - [Using a GPU in your container]

pedro (pedro@undisclosed.example.com) — 2026-06-29T12:45:36+00:00

Apptainer Containers What is a container? A container is an isolated runtime environment that is often used to run a packaged version of some software (and its dependencies). A container is based on an image that defines the software environment, and can be run on any machine that supports your container technology. This allows you to run your application inside this container environment, which is always the same, regardless of the (operating) system you are running on. The container image us…

Resource allocation: Jobs and jobscripts - [Resource allocation: Jobs and jobscripts]

pedro (pedro@undisclosed.example.com) — 2026-06-29T12:40:11+00:00

Resource allocation: Jobs and jobscripts On the cluster users can execute sets of tasks, which are called jobs. These jobs are a combination of a set of requirements and a list of tasks that need to be run. A scheduling system will take these jobs and run them on the available resources.

Hábrók Changelog - [2026-06-24]

pedro (pedro@undisclosed.example.com) — 2026-06-25T08:35:59+00:00

Hábrók Changelog This page records major changes to Hábrók, which are mostly carried out during scheduled maintenance periods. This changelog is kept since August 13th 2025, although changes have been made during past scheduled maintenance periods and on-demand as necessary.

Permissions and Inheritance - Removed reference to permissions being different in the GUI

giulio (giulio@undisclosed.example.com) — 2026-06-24T08:10:05+00:00

Permissions and Inheritance With the current version of iRODS, ten levels of permissions on data and metadata are available to the user. These permissions are either automatically assigned when a file or folder enters the RDMS, or they can be defined by the user(s). In an order of ascending privileges, these permissions are 'Null', 'Read_Metadata', 'Read_Object', 'Create_Metadata', 'Modify_Metadata', 'Delete_Metadata', 'Create_Object', 'Modify_Object', 'Delete_Object', and 'Own'. You can set th…

Migration to Hábrók

pedro (pedro@undisclosed.example.com) — 2026-06-23T14:23:12+00:00

Migration to Hábrók You can find the slides for the presentation on March 27th [ here ]. Accounts and groups Account types Because of increased security requirements we will only allow RUG accounts on Hábrók. Since most people are already using their p- or s-number to login this should not cause issues. Existing f-accounts can also still be used, but note that the RUG is working on reducing the number of f-accounts, and external collaborators may need a p-number in the future. Given the lack…

hpc-iaas-user-guides.jpg - created

admin (admin@undisclosed.example.com) — 2026-06-18T13:52:51+00:00

de-identification_matrix2.png

marlon (marlon@undisclosed.example.com) — 2026-06-18T11:14:03+00:00

de-identification_matrix.pdf - created

marlon (marlon@undisclosed.example.com) — 2026-06-18T11:01:59+00:00

metadata_de-identification.png - created

marlon (marlon@undisclosed.example.com) — 2026-06-01T12:36:15+00:00

confidential_bin.png - created

marlon (marlon@undisclosed.example.com) — 2026-05-12T10:31:04+00:00

de-identification_matrix.png - created

marlon (marlon@undisclosed.example.com) — 2026-04-30T10:00:21+00:00

pseudmatrix.png - created

marlon (marlon@undisclosed.example.com) — 2026-04-28T12:24:19+00:00

datamin1.png

alba (alba@undisclosed.example.com) — 2026-04-13T12:05:25+00:00

human_subject_data.png

alba (alba@undisclosed.example.com) — 2026-04-13T11:09:07+00:00

whisper1.png - created

marguerite (marguerite@undisclosed.example.com) — 2026-04-08T15:14:51+00:00

whisper2.png - created

marguerite (marguerite@undisclosed.example.com) — 2026-04-08T15:13:20+00:00

data_minimization.png - created

alba (alba@undisclosed.example.com) — 2026-04-08T13:37:53+00:00