High Performance Computing, Deliver a Hybrid HPC & Kubernetes Scheduling Proof of Concept
Background/Impact of this placement
UK Health Security Agency (UKHSA) is seeking to commission an academic PhD student/or equivalent experience to support the High-Performance Computing (HPC) team and the Bioinformatics team to deliver a Hybrid HPC & Kubernetes Scheduling Proof of Concept.
The UK Health Security Agency (UKHSA) is responsible for protecting every member of every community from the impact of infectious diseases, chemical, biological, radiological and nuclear incidents and other health threats. The project outlined supports UKHSA’s remit to improve public health security through robust, secure, and scalable computational infrastructure for pathogen genomics, outbreak preparedness, and prevention.
Placement Details
Modern genomics and outbreak response workloads often require flexible, scalable computing infrastructure. Traditionally, HPC clusters use job schedulers like Slurm, but these can be complemented by Kubernetes to provide cloud-native autoscaling. Slinky.ai enables Slurm to integrate with Kubernetes, allowing workloads to benefit from dynamic scaling to meet unpredictable demands (a key advantage during large-scale outbreak scenarios).
Objectives:
- Set up a proof of concept integrating Slurm with Kubernetes using Slinky.ai.
- Test dynamic scaling of compute resources using Kubernetes’ Horizontal Pod Autoscaler (HPA).
- Synthetic benchmark the system’s ability to handle pathogen genomics workloads under variable loads.
Methods & Tasks:
- Deploy Slurm on a OpenShift/Kubernetes clusters (using Slinky.ai) in a testbed.
- Install and configure Slinky.ai to bridge Slurm and Kubernetes.
- Design representative test workloads that simulate bioinformatics jobs.
- Monitor scaling behaviour, resource allocation, and scheduling efficiency.
- Evaluate feasibility, potential cost savings, and recommendations for production use.
Expected Deliverables
- Demonstrated framework for resource optimisation in a hybrid HPC/Kubernetes environment.
- Increased agility and resilience of computational resources.
- Practical guidelines for scaling outbreak preparedness computing environments.
Timescales
It is expected the academic student would support the HPC team for a 3-month placement starting between December 2026 and February 2027. It is preferred that the academic support the team full-time, however part-time and flexible working arrangements can be discussed, if required.
Costs
The placement student will be reimbursed £12,000 for their time on this project. UKHSA will also cover any travel and subsistence costs associated with the placement such as travel to the office for meetings or away days.
Working pattern and location of the placement:
Placements will be remote with the occasional office/event attendance, but this is at the successful candidate’s discretion. Our head office is in Canary Wharf, we also have offices in Liverpool, Bristol and Birmingham, if you would like to attend one of the offices more regularly, we can look at getting you a government pass.
Full-time is preferred so you can fully immerse yourself in the team and project, but we will work flexibly if part-time hours are required. We do however need the placement to be undertaken in one continuous block due to IT and data access/security requirements.
The Ideal Candidate
Essential
- Basic experience with Linux system administration and shell scripting.
- Working knowledge of HPC job scheduling (e.g., Slurm basics).
- Understanding of Kubernetes fundamentals (pods, nodes, autoscaling).
- Familiarity with version control (e.g., Git) and CI/CD concepts.
- Interest in cloud-native technologies and resource orchestration.
Desirable
- Experience with OpenShift.
- Exposure to HPC cluster environments.
- Experience configuring or running Slurm clusters.
- Familiarity with Kubernetes autoscaling tools (HPA, Cluster Autoscaler).
- Exposure to hybrid or cloud HPC architectures.
- Basic scripting (Python, Bash) for automation and benchmarking.
- Understanding of container technologies (e.g., Docker, Podman, Singularity).
Support for Postgraduate Researcher:
UKHSA is an excellent placement opportunity as we have a developed culture of learning and development, fostered in an inclusive environment. To ensure that the student has opportunities to expand their skillsets and to develop professionally, we can provide some training in analysis, where required, but we also encourage the student to engage with subject matter experts and other early career researchers (ECR) across the UKHSA. At UKHSA, we have a thriving Early Career Research (ECR) network led by our CDO Partnerships team. The student will have the opportunity to join and be supported by the ECR network within the UKHSA, and by other ECRs and team members within the host team.
After your placement you will also join our Alumni ECR Network, where you will receive exclusive insights, future opportunities and development from CDO. So, invest in your future and apply, if you think you fit the skills criteria below, we’d love to hear from you!
How to apply:
Closing date for applications: Friday 30th October 2026 by 12pm
Application format: CV and a 500-word cover letter to evidence how you fit the project requirements, skills and what you can bring to this role.
How to submit an application:
Send your CV and a cover letter (max 500 words) to the CDO Partnerships Team, UKHSA, CDOPartnerships@ukhsa.gov.uk with the subject line “REF30 HPC placement application”.
Please note if we find the successful candidate prior to the closing date we will not accept any more applications and notify you of this.
If you have any queries or questions, please do get in touch with us at CDOPartnerships@ukhsa.gov.uk.