Category: Interactive HPC

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Application Interactive HPC Supercomputing UCloud

OMERO Now Available on UCloud

A Powerful Tool for Biological and Health Science Image Data Management

The DeiC Interactive HPC – UCloud Consortium introduces OMERO on UCloud. OMERO is a robust open-source image data management system tailored for biological research and health science. Designed to handle vast volumes of microscopy images and their associated metadata, OMERO empowers researchers to store, organize, visualize, and analyze imaging data with precision and ease. 

What is OMERO? 

OMERO (Open Microscopy Environment Remote Objects) is a comprehensive solution for managing biological and health science imaging data. Whether you’re working in digital pathology, cellular biology, or any other imaging-intensive field, OMERO provides a secure repository to support your research workflows. 

“The microscopic images that biologist and health scientists typically work with have a lot of pixels and can be extremely heavy. With Omero on UCloud, you not only have the possibility of storing your images on UCloud, but you can also create storage groups and give different permissions. This is extremely helpful for large projects where the PI can divide images into smaller groups or projects and see statistics of how each project is progressing,” says Dr. Federica Lo Verso, Computational Scientist at the SDU eScience Center’s research support team. Federica has been the developer in charge of implementing the OMERO app on UCloud.     

Key Features of OMERO 

  • Image Management 
    OMERO serves as a secure repository for diverse imaging datasets, ensuring that your data is organised and accessible from anywhere. 
  • Multi-Format Support 
    Powered by Bio-Formats, OMERO supports over 150 proprietary and open-source image formats, making it a versatile choice for labs with varied imaging technologies. 
  • Secure Collaboration 
    OMERO includes robust permission controls, enabling safe sharing and collaboration across teams and institutions. 
  • Data Visualisation and Analysis 
    Built-in tools allow users to display, annotate, and explore image data interactively, enhancing interpretation and insight. 
  • Publication Tools 
    OMERO.figure simplifies the creation of high-quality figures for presentations and publications, directly from your image datasets. 
Image source

Why Use OMERO on UCloud? 

Deploying OMERO on UCloud offers significant advantages: 

  • Scalable Storage Resources 
    UCloud provides access to vast and flexible storage, ideal for handling the large datasets typical in biological imaging. 
  • Suitable for Sensitive Data 
    UCloud’s secure architecture makes it well-suited for handling sensitive or confidential research data, ensuring compliance with data protection regulations. 
  • Integrated Research Environment 
    OMERO on UCloud integrates seamlessly with other tools and services, supporting collaborative and reproducible research. 
  • Accessibility and Performance 
    With UCloud’s high-performance infrastructure, researchers can access and process their data efficiently from anywhere. 

Whether you’re managing terabytes of microscopy images or preparing figures for your next publication, OMERO on UCloud is a game-changer for biological research. Start exploring its capabilities today and elevate your data management workflow. 

Categories
Interactive HPC Supercomputing UCloud

UCloud 2025.4.0 Release

Command palette, integrated editor & terminal, faster file search and a simpler Syncthing UI. Today we’re releasing UCloud 2025.4.0! This update introduces a keyboard-driven command palette, a built-in text editor, an integrated terminal, a fully revamped file search, and a simplified Syncthing experience.

While these new tools will be the most visible changes for users, they are also part of a broader, long-term effort to refine UCloud’s foundations.

“Software development on UCloud started back in 2017. Since then, we have make many architectural and design changes. This progress inevitably caused a build-up of inconsistensies and inefficiencies. With our understanding of the goal now being a lot clearer than in 2017, the aim is to simplify the internal code structure and get rid of old legacy code to ensure stability, performance and faster development of the service.”

Dan Sebastian Thrane, Senior Software Architect for Research Infrastructure

With that context in mind, here’s a closer look at what’s new in UCloud 2025.4.0.

Navigation and shortcuts

We have added a fast way to move around UCloud without leaving the keyboard.

  • Keyboard-first workflow: Use it to access shortcuts to common actions, jump to your favorite applications, or quickly switch projects.
  • Command palette: Open the palette with Ctrl+P on Windows/Linux or Cmd+P on macOS.

Files and search

Finding things is now much quicker and more reliable and edit text files directly in UCloud without needing to start a job.

  • Revamped file search: File search has been completely rebuilt and is now significantly faster. This requires your files to be indexed. Indexing of files may take up to 24 hours after the file has been created.
  • Edit-in-place: Double-click any text file in the file browser to open it in the new integrated editor.
  • Syntax highlighting: The editor supports basic syntax highlighting.
  • Tabs & file tree: Work across multiple tabs and use the sidebar to navigate your project’s file tree quickly.

Integrated terminal

A lightweight terminal is now available across Kubernetes-based service providers.

  • Auto-shutdown: Sessions shut down automatically when inactive. (Do not use it for long-running or background tasks.)
  • Availability: The integrated terminal is now available on the SDU/K8s provider. It works similar to the terminal released last year for the SDU/Hippo provider. You can open a terminal in any folder via “Open terminal” button.
  • For small tasks: Ideal for quick edits and running common utilities.
  • Resource limits: The terminal has low CPU and memory and (is not intended for running jobs).

Jobs and Syncthing

New real-time metrics have been added to jobs and the Syncthing has been made easier to understand and operate.

  • Simplified interface: A cleaner, more approachable Syncthing UI for managing synchronization.
  • Real-time job metrics: You can now monitor real time metrics about CPU, memory and GPU utilization from the job view.

Improved data transfer

The integration module has received a large upgrade to the upload protocol.

  • This protocol is used both by end-users and between service providers.
  • Data transfer between the SDU and AAU provider is now much easier and faster.
  • The upload protocol is smart and attempts to avoid sending files which are already present. It also utilizes multiple TCP streams and threads to maximize performance.

As always, you can visit UCloud’s documentation at https://docs.cloud.sdu.dk for more information.

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Interactive HPC Teaching Tutorial Webinars & Tutorials - video

Webinar Recording: Transcribing and editing audio transcriptions with Transcriber and Speech Analyzer apps

In this video we will guide you through the complete pipeline of transcribing audio files from speech to text and editing and classifying transcription segments.

In this session, you’ll learn how to:

  • Use Transcriber for transcribing audio/video files. Transcriber is based on Open AI’s Whisper language model. The app can transcribe speech audio to text in various formats and uses the WhisperX package to perform speaker recognition.
  • Navigate the new, simple, drag and drop Transcriber user interface to make it easier for you to use AI to transcribe audio files.
  • Edit and classify the transcriptions with Speech Analyzer. Speech Analyzer is an application built on top of Label Studio, specifically optimized for dialogue analysis. It enables you to label, edit, and annotate transcriptions generated using Transcriber.
  • Perform a comprehensive dialogue analysis on UCloud involving transcribing audio files using Transcriber, followed by transcription analysis with Speech Analyzer.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Researchers across all Departments, particularly Digital Humanities and Social Science, Students, AI interested.

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Interactive HPC Supercomputing Tutorial UCloud Webinars & Tutorials - video Workshop

Webinar recording: Fine-Tuning and Deploying  Large Language Models

In this video we will guide you through the complete pipeline of fine-tuning large language models (LLMs) for specialised tasks such as medical question-answering using NeMo Framework and Triton Inference Server.

  • Prepare and preprocess open-source datasets for fine-tuning.
  • Apply Parameter-Efficient Fine-Tuning (PEFT) using LoRA with NVIDIA NeMo Framework.
  • Deploy optimised LLMs using NVIDIA Triton Inference Server and TensorRT-LLM.
  • Generate a synthetic Q&A dataset using Label Studio connected to a live inference backend.
  • Fine-tune and evaluate your customised LLM for domain-specific applications.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Machine learning practitioners, researchers, and engineers interested in LLM customisation, domain adaptation, or scalable model deployment.

Technical Level: Intermediate to Advanced.

Notebooks: https://github.com/emolinaro/ucloud-workshop-28-05-2025

Categories
Application Interactive HPC Supercomputing Teaching Tutorial Webinars & Tutorials - video

Webinar recording: UCloud courses hands-on

In this video we will go through the process of developing a course on UCloud, using UCloud Courses – a tool for hosting and managing university courses on UCloud. Want to know more about this new feature, check out our webinar recording introducing UCloud Courses.

Introduction

00:00 – Outline of the workshop agenda
03:10 – Introduction to the UCloud Courses concept
04:23 – Advantages of using UCloud Courses
05:56 – Outline of the steps involved in developing a UCloud Course
09:54 – Requesting and planning a UCloud Course
10:20 – Example of the planning and structuring of an existing UCloud Course

Developing a UCloud Course step by step

Setting up the environment
15:53 – Preliminary remarks
17:15 – Showing the existing UCloud Course that will be re-developed in the workshop
18:02 – Showing the UCloud-Courses GitHub repository
18:40 – Software requirements and -recommendations
20:22 – Short introduction to Git and GitHub
24:27 – Cloning the repository
25:15 – Creating a working branch
26:12 – What should go in the UCloud-Courses repository and what shouldn’t
27:24 – Installing the required dependencies

Creating a new UCloud Course and modifying the templates
28:00 – Creating a UCloud Course using a prepared script
30:31 – Walk-through of the different auto-generated files/folders in the course folder
33:35 – Short introduction to Docker
38:15 – Modifying the Dockerfile
42:32 – What should go in the UCloud-Courses repository and what shouldn’t
45:28 – Building the Docker image locally using a prepared script
47:54 – Modifying the starting script
01:00:50 – What can, shouldn’t, and mustn’t be changed while the course is running

Building and testing the course locally
01:05:00 – Re-building the Docker image locally using a prepared script
01:05:25 – Running a Docker container locally using a prepared script
01:10:58 – Opening the JupyterLab interface on localhost

Finalising the course app
01:12:48 – Opening a pull request and requesting code review
01:19:44 – Testing the course app on UCloud before it’s deployed

Closing remarks

01:25:44 – Reusing/updating an existing UCloud course
01:28:19 – The financial model in brief
01:29:38 – Useful links and resources

UCloud-Courses GitHub repository:
https://github.com/SDU-eScience/UCloud-Courses

README in the UCloud-Courses GitHub repository:
https://github.com/SDU-eScience/UCloud-Courses/blob/main/README.md

Wiki page in the UCloud-Courses GitHub repository:
https://github.com/SDU-eScience/UCloud-Courses/wiki

The UCloud course app redeveloped in the workshop (UCloud login required):
https://cloud.sdu.dk/app/jobs/create?app=nlp-demo-course_147222U005

eScience Servicedesk (point of first contact):
https://support.escience.sdu.dk/

Categories
Application Interactive HPC

New App: AlphaFold 3 – a game-changing tool for predicting protein structure

AlphaFold 3, the new AI model developed by Google DeepMind and Isomorphic Labs, can predict the structures of complexes formed by different biomolecules, including protein-DNA, protein-RNA, and protein-ligand interactions. 

AlphaFold 3 deployment on Interactive HPC – UCloud is optimized for use with GPUs, and includes the necessary multiple genetic (sequence) protein and RNA databases to run.

Beside the Batch Mode, additional app flavors (Lab Mode and Visualization Mode) allow respectively to use the software in a JupyterLab environment and to visualize protein structures obtained by running AlphaFold 3.

AlphaFold 3 has been implemented on Interactive HPC – UCloud to support specific type of work, e.g., accurate structure prediction and modelling, and is ready for use by all Interactive HPC – UCloud users.

For more details, visit the UCloud documentation for the app.

Categories
Call Interactive HPC Supercomputing

Reduced Resources in Upcoming national HPC Call

The position of Chair of the DeiC Board is currently vacant, leading to delays in decision-making processes and affecting upcoming national HPC calls.

John Renner Hansen has stepped down as Chair of the DeiC Board. As a result, the DeiC Board is currently unable to make financial decisions, which impacts several ongoing and upcoming HPC activities.

A new Chair is expected to be appointed by the Rectors’ Conference of Danish Universities in early August 2025.

Fewer Resources in Upcoming National HPC Call

The next national HPC call will open on 15 July 2025 and covers the compute period from 1 January to 31 December 2026. DeiC’s current contracts with DeiC Interactive HPC will expire on 31 December 2025, and work is underway to establish a new agreement. However, as the Board is not currently quorate, there is no guarantee that new agreements will be in place before the call opens. Therefore, the upcoming national call will only include national compute time on LUMI.

For more information, please contact your local Front Office.

This is an adaption of the story published by DeiC https://deic.dk/en/news/2025-6-20/delayed-quantum-calls-and

Categories
Application Interactive HPC Supercomputing

New App: Apache Kafka 

Users of DeiC Interactive HPC – UCloud can now access Apache Kafka, a high-performance event streaming platform designed for managing real-time data at scale. 

Kafka deployments on UCloud support multi-node configurations, enabling production-grade distributed logging, stream processing, data integration, and publish/subscribe messaging systems. 

Students and researchers can use Apache Kafka to collect, process, and analyse large volumes of real-time data – for example, streaming data from lab sensors, social media, or web clickstreams. It’s especially useful for building data pipelines in projects involving machine learning, IoT, or real-time analytics, enabling reproducible and scalable research workflows. 

For more details on the Apache Kafka application, visit UCloud docs for the full documentation.



Categories
Interactive HPC Supercomputing UCloud Workshop

Workshops on AI applications

Join us for three new and free online workshops to explore how these tools can transform your work. Discover AI Applications on DeiC Interactive HPC – UCloud

Workshop 1:

Transcribing and editing audio transcriptions with Transcriber and Speech Analyzer apps

Date: 22 May 2025

Time: 13:00 – 15:00 (CET)

Location: Online, via Zoom (link TBA)

Join us for a hands-on workshop where we guide you through the complete pipeline of transcribing audio files from speech to text and editing and classifying transcription segments.

In this session, you’ll learn how to:

  • Use Transcriber for transcribing audio/video files. Transcriber is based on Open AI’s Whisper language model. The app can transcribe speech audio to text in various formats and uses the WhisperX package to perform speaker recognition.
  • Navigate the new, simple, drag and drop Transcriber user interface to make it easier for you to use AI to transcribe audio files.
  • Edit and classify the transcriptions with Speech Analyzer. Speech Analyzer is an application built on top of Label Studio, specifically optimized for dialogue analysis. It enables you to label, edit, and annotate transcriptions generated using Transcriber.
  • Perform a comprehensive dialogue analysis on UCloud involving transcribing audio files using Transcriber, followed by transcription analysis with Speech Analyzer.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Researchers across all Departments, particularly Digital Humanities and Social Science, Students, AI interested.

Technical Level: Basic to Intermediate.

Sign up for this workshop

Workshop 2:

ChatUI and CVAT pipelines

Date: 27 May 2025

Time: 13:00 – 15:00 (CET)

Location: Online, via Zoom (link TBA)

Join us for a hands-on workshop where we guide you through two different AI based workflows, involving ChatUI and CVAT apps.

In this session, you’ll learn how to:

  • Use Chat UI as a flexible interface for hosting of various LLM models, and interact via a chat or API environment.
  • Use ChatUI for semantic search in a knowledge base.
  • Use CVAT as a powerful annotation tool, including image classification, object detection, semantic and instance segmentation, and video / 3D annotations.
  • Use advanced CVAT features including auto-annotation, algorithmic assistance, management and analytics.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Researchers across all fields, particularly transport, robotics, digital humanities, social sciences, machine learning and students.

Technical Level: Basic to Intermediate.

Sign up for this workshop

Workshop 3:

Fine-Tuning and Deploying  Large Language Models with NeMo Framework and Triton Inference Server

Date: 28 May 2025

Time: 13:00 – 15:00 (CET)

Location: Online, via Zoom (link TBA)

Join us for a hands-on workshop where we guide you through the complete pipeline of fine-tuning large language models (LLMs) for specialized tasks such as medical question-answering!

In this session, you’ll learn how to:

  • Prepare and preprocess open-source datasets for fine-tuning.
  • Apply Parameter-Efficient Fine-Tuning (PEFT) using LoRA with NVIDIA NeMo Framework.
  • Deploy optimized LLMs using NVIDIA Triton Inference Server and TensorRT-LLM.
  • Generate a synthetic Q&A dataset using Label Studio connected to a live inference backend.
  • Fine-tune and evaluate your customized LLM for domain-specific applications.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Machine learning practitioners, researchers, and engineers interested in LLM customization, domain adaptation, or scalable model deployment.

Technical Level: Intermediate to Advanced.

Sign up for this workshop

DeiC Interactive HPC provides researchers at Danish universities with access to a variety of AI applications on UCloud that enable them to accelerate their research through powerful and secure computational tools.

Through online workshops the DeiC Interactive HPC Consortium will introduce both new and experienced users to DeiC Interactive HPC/UCloud’s AI app portfolio.

The sessions are designed to equip researchers and students with the knowledge and skills needed to effectively harness DeiC Interactive HPC/UCloud’s AI tools for their research.

Feel free to share with colleagues and peers who might benefit. See you there!

Categories
Interactive HPC Supercomputing UCloud

DeiC Interactive HPC now has 15,000 Users

The DeiC Interactive HPC consortium is thrilled to announce that the service, powered by the UCloud software, has reached another significant milestone: 15,000 users. This achievement underscores the service’s growing popularity and its pivotal role in advancing digital research through user-friendly supercomputing access.

Since its inception, DeiC Interactive HPC has been dedicated to providing researchers with seamless access to high-performance computing (HPC) resources. The service’s intuitive interface and capabilities have revolutionized the way researchers approach complex computational tasks, making HPC accessible to a broader audience.

DeiC Interactive HPC’s success is a testament to the collaborative efforts of the consortium that operates the service. Together, we have created an environment where researchers from diverse fields can leverage cutting-edge technology to drive innovation and discovery.

As DeiC Interactive HPC and UCloud continues to grow, we remain committed to enhancing the service’s features and expanding its reach. The goal is to empower even more researchers with the tools they need to tackle some of the most pressing scientific challenges of our time.