7th de.NBI Cloud User Meeting

2 Dec 2024, 09:00 → 6 Dec 2024, 21:00 Europe/Berlin

For more than 6 years, the de.NBI Cloud has provided free of charge computing resources to the life sciences community in Germany. Scientists involved in various research topics, such as metagenomics, medical imaging, epigenetics, and plant biology benefit from the opportunities provided by the de.NBI Cloud.

With our annual user meeting, we would like to highlight topics of interest to our user community.

This year we are focusing exclusively on experienced users. We will give our current users the opportunity to deepen their understanding of best practices in cloud computing. There will be workshops on advanced topics such as container orchestration with Kubernetes or handling cloud-based clusters with BiBiGrid.

The de.NBI Cloud User Meeting supports the interaction with our growing community. Thus, we would like to hear from you about the specific needs of the scientific life sciences community, allowing us to shape the future of the de.NBI Cloud according to sophisticated and specialized use cases.

This year, we are organizing the de.NBI Cloud User Meeting as an online event via zoom in December from 02.12 to 06.12.

The scope of this meeting includes advanced workshops tailored for experienced users and opportunities to engage with experts on diverse cloud computing topics

We look forward to welcoming experienced researchers from many different bioinformatics and life-science research areas to delve deeper into cloud computing and the de.NBI Cloud.

 

Registration Deadline: 27.11

data_protection_CLUM_2024.pdf

Monday 2 December

09:00 → 10:00 Welcome & Introduction

10:00 → 13:00 OpenStack

OpenStack is the underlying infrastructure of the de.NBI Cloud. Participants of this workshop will learn how to start one or multiple virtual machines by using a graphical interface or via an API and get familiar with basic principles how-to use OpenStack for their projects e.g. assign floating IPs, mount volumes, setup security groups, etc.

Requirements: basic termial knowledge, Linux/OSX Terminal or Windows 10 PowerShell, Browser

14:00 → 18:00 Advanced Kubernetes (Part 1)

The Kubernetes workshop covers essential topics for mastering scientific workflows in a cloud-native environment. Participants will learn how to schedule scientific workflows using Nextflow and Snakemake, as well as cloud-native workflow engines such as Argo Workflows on Kubernetes. The workshop will also dive into Kubernetes-based DevOps practices, explore GitOps principles for automating deployments via CI/CD pipelines, and gain hands-on experience deploying and scaling production workloads in Kubernetes. In addition, the workshop will cover the latest updates to Kubernetes, with a particular focus on use of new networking techniques such as the Gateway API, TCP/UDP services, and load balancing.

By the end of the workshop, attendees will have a deep understanding of how to streamline scientific use cases with K8s, including workflows, automating deployments, and using Kubernetes environments for production operations.

Requirements: Have an understanding of the basics of Kubernetes

Tuesday 3 December

09:00 → 12:00 BiBiGrid

BiBiGrid is an open-source tool hosted on GitHub that facilitates easy cluster setups in openstack cloud environments. It provides an HPC like environment, providing a shared filesystem (NFS) between all nodes, a job scheduler (Slurm) and a monitoring system (Zabbix) on top of Ubuntu LTS or Debian. In this hands-on session we will learn how to setup a cluster in the cloud using BiBiGrid and execute a simple workflow (nextflow) on it. We will then briefly explore how to tailor the cluster to your specific needs using self-written Ansible tasks.

Requirements: basic terminal knowledge, Python3 and ssh/ssh-keygen locally installed, Linux/OSX Terminal or Linux for Windows (WSL2) , Browser No previous knowledge in NFS, Slurm, Zabbix, nextflow or Ansible is required.

13:00 → 16:00 Security Considerations and Best Practices for OpenStack projects

This OpenStack Security course emphasizes the importance of IT security in the cloud to prevent attacks and data loss. Common threats include cryptomining, botnets, and ransomware, often resulting from unprotected services on public ports. To counter these threats, it's essential to implement secure access via VPN or SSHuttle, encryption (HTTPS) with domain name and certificate authority validation, and use a reverse proxy for additional security layers. Additionally, best practices include verifying Dockerfile and updating packages regularly, using trusted sources, changing default credentials, and seeking help from local admins when needed. By following these guidelines, project owners can ensure the security of their VMs and prevent potential threats.

Requirements: Have an understanding of the basics of OpenStack

Wednesday 4 December

09:00 → 17:00 Advanced Kubernetes (Part 2)

The Kubernetes workshop covers essential topics for mastering scientific workflows in a cloud-native environment. Participants will learn how to schedule scientific workflows using Nextflow and Snakemake, as well as cloud-native workflow engines such as Argo Workflows on Kubernetes. The workshop will also dive into Kubernetes-based DevOps practices, explore GitOps principles for automating deployments via CI/CD pipelines, and gain hands-on experience deploying and scaling production workloads in Kubernetes. In addition, the workshop will cover the latest updates to Kubernetes, with a particular focus on use of new networking techniques such as the Gateway API, TCP/UDP services, and load balancing.

By the end of the workshop, attendees will have a deep understanding of how to streamline scientific use cases with K8s, including workflows, automating deployments, and using Kubernetes environments for production operations.

Requirements: Have an understanding of the basics of Kubernetes

Friday 6 December

09:00 → 12:00 Advanced Kubernetes (Part 3)

The Kubernetes workshop covers essential topics for mastering scientific workflows in a cloud-native environment. Participants will learn how to schedule scientific workflows using Nextflow and Snakemake, as well as cloud-native workflow engines such as Argo Workflows on Kubernetes. The workshop will also dive into Kubernetes-based DevOps practices, explore GitOps principles for automating deployments via CI/CD pipelines, and gain hands-on experience deploying and scaling production workloads in Kubernetes. In addition, the workshop will cover the latest updates to Kubernetes, with a particular focus on use of new networking techniques such as the Gateway API, TCP/UDP services, and load balancing.

By the end of the workshop, attendees will have a deep understanding of how to streamline scientific use cases with K8s, including workflows, automating deployments, and using Kubernetes environments for production operations.

Requirements: Have an understanding of the basics of Kubernetes

12:30 → 15:00 Discussion Round or One-on-One Consultation: Consult with Admin and/or de.NBI Cloud Governance

Is there a topic you’d like to discuss in a one-on-one Zoom call with an admin or a member of the de.NBI Cloud Governance? If so, please specify. If the same topic is mentioned multiple times, it will be part of the discussion round.