CIT Research Documentation - habrok:examples

AlphaFold

Anonymous (anonymous@undisclosed.example.com) — 2024-11-22T14:41:41+00:00

AlphaFold AlphaFold 3 AlphaFold 3 is not available as module yet, and due to the complex installation this may still take a while. Meanwhile, it should be possible to run AlphaFold 3 with an Apptainer container. You can either try to build your own container using the instructions at

Apptainer Containers

Anonymous (anonymous@undisclosed.example.com) — 2024-05-03T18:51:12+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…

DIRAC

Anonymous (anonymous@undisclosed.example.com) — 2025-07-22T07:43:04+00:00

DIRAC Warning for DIRAC users Users running the DIRAC RELCCSD module should be aware that they must use the following configuration in their inputs: **RELCC .INTERFACE DIRAC6 If they also use the MOLTRA module in their CCSD (or CCSD(T) or FSCC) calculations, they

Gaussian

Anonymous (anonymous@undisclosed.example.com) — 2026-03-29T22:07:57+00:00

Gaussian Please be aware that we don't have a site license for Gaussian. People should contact the owner of the license to check if they are allowed to the software under the group license. You can find the name of the person by trying to load the module:

Jupyter notebooks

Anonymous (anonymous@undisclosed.example.com) — 2026-04-07T15:43:45+00:00

Jupyter notebooks Jupyter notebooks are used quite heavily in data science applications, and it can be useful to be able to run them on the cluster. The main issue that you'll encounter is that running them in a batch scheduled system has the disadvantage that the notebook server may not start immediately. You can also run a notebook server on the interactive or GPU frontend node, but you should only use these for a limited time.

Running LLMs

Anonymous (anonymous@undisclosed.example.com) — 2026-02-26T13:23:37+00:00

Running LLMs If you want to run a Large Language Model (LLM) on Habrok, here's one possible and relatively easy way to do it. Note that the versions are recent as of 26 February 2026. Installation 1. Login with your account on Habrok on an interactive node for the installation procedure.

Mamba installation

Anonymous (anonymous@undisclosed.example.com) — 2026-03-23T13:04:21+00:00

Mamba installation Mamba () is an alternative to Anaconda, which is released under an open source license. In order to use it on Hábrók you can install it into your home directory. This can be done following the instructions on their website. Caveat

Mathematica

Anonymous (anonymous@undisclosed.example.com) — 2025-06-11T12:09:36+00:00

Mathematica Submitting a single-core Mathematica job The following example can be used as a template for Mathematica jobs: #!/bin/bash #SBATCH --job-name=Mathematica #SBATCH --partition=regular #SBATCH --nodes=1 #SBATCH --cpus-per-task=1 #SBATCH --time=00:05:00 module purge module load Mathematica/13.1.0 math -script myscript.m

MATLAB

Anonymous (anonymous@undisclosed.example.com) — 2026-02-18T15:51:42+00:00

MATLAB MATLAB Parallel Computing The university now has a campus license for MATLAB, which makes it possible to submit jobs from MATLAB to the cluster, and run jobs on multiple nodes. For all details, see [the attached manual]. Note that the functionality currently only works with MATLAB 2020b; if you want to submit jobs from your own workstation, make sure to use the same MATLAB version and install the set of scripts as described in the manual.

MPI

Anonymous (anonymous@undisclosed.example.com) — 2025-08-21T11:36:12+00:00

MPI Software with MPI support can run on multiple nodes, and in this case the software is launched with one or more tasks (instances) per node. All these tasks use the network for inter-node communication. The following is an example of a jobscript that can be used for MPI applications:

Ollama on Hábrók

Anonymous (anonymous@undisclosed.example.com) — 2025-10-15T11:42:07+00:00

Ollama on Hábrók You can run an LLM on Hábrók with Ollama in a Jupyter environment by using the Ollama (Jupyter) Interactive App on the Web Portal. Setting up the virtual environment To be able to use the app, you first need to set up a Python virtual environment. The version of Ollama installed on Hábrók is

ORCA

Anonymous (anonymous@undisclosed.example.com) — 2026-01-08T13:40:36+00:00

ORCA Accessing ORCA ORCA is available for free on Hábrók, but the developers require that users agree to the End User License Agreement (EULA) for the ORCA software. Without doing so, attempting to load the ORCA modules will result in a error. To confirm your agreement, please open a ticket with us at

ParaView

Anonymous (anonymous@undisclosed.example.com) — 2023-03-22T13:27:37+00:00

ParaView ParaView () is a data analysis and visualization application. ParaView is available on the cluster and can be run in a server client model, where the server runs on the cluster and the client on your local machine. In this document we'll describe how to connect to the ParaView server running on one of the cluster nodes.

Perl

Anonymous (anonymous@undisclosed.example.com) — 2023-03-21T13:18:06+00:00

Perl Installing additional libraries The Perl modules available from the module system already contain a lot of built-in libraries, but if you need to install additional libraries, you can do this in your home directory. In order to install Perl libraries to a custom location (in the following example we use

Python

Anonymous (anonymous@undisclosed.example.com) — 2024-01-29T10:16:31+00:00

Python This page describes the recommended way to use Python on the cluster. This is a long page, so please check the table of contents menu on the right to find the information most relevant for you. The main take home message for Python is to load the Python module for the version you want to start with, possibly by loading

R

Anonymous (anonymous@undisclosed.example.com) — 2025-06-11T12:15:42+00:00

R Submitting a single job Single CPU In order to run a simple R script on one core, two files should be constructed. The first file is the R script (with the .R extension), here it is called R_example1.R and it holds the following textual contents:

Spyder

Anonymous (anonymous@undisclosed.example.com) — 2024-12-06T15:54:47+00:00

Spyder Spyder () is a Python IDE and tool to run interactive Python applications in a GUI. Unfortunately we don't have a recipe for integration into the web portal. It can be installed by cluster users, however, and run from an interactive desktop session. Here are some instructions for how to set up Spyder.

Examples

Anonymous (anonymous@undisclosed.example.com) — 2020-08-27T09:31:33+00:00

Examples examples index

Stata

Anonymous (anonymous@undisclosed.example.com) — 2023-03-22T13:29:22+00:00

Stata The following example can be used as a job script for running Stata jobs: #!/bin/bash #SBATCH --job-name=my_stata_job #SBATCH --time=0-01:00:00 #SBATCH --partition=regular #SBATCH --ntasks=1 #SBATCH --mem=2gb module add StataSE/17 stata-se -b do my_stata_file.do

Using Python modules in VScode

Anonymous (anonymous@undisclosed.example.com) — 2026-04-08T21:49:06+00:00

Using Python modules in VScode VScode is available on the cluster in the Web portal or through an ssh connection from your local VScode software. See Advanced: Connecting to Hábrók with Visual Studio Code for details on the connection methods. When using VScode to develop your software on the cluster it is best to make use of virtual environments. These virtual environments work in the same way as other virtual environments outside of VScode. The best way to handle these is to create the virtu…