HPC Symposium 2023
Wednesday 6th September
10am – 4pm
Applied Science 3 Building, Floor 1,
West Lecture Theatre

We are excited to announce that we will be holding a HPC Symposium on Wednesday September 6th where there will be the opportunity for us to share and celebrate the range of research that benefits from HPC at the University of Hull.

There will be talks from a range of Viper users, talking about the research they carry out on Viper, along with poster sessions over the provided lunch.

There will also be an update on the exciting future of High Performance Computing at the University of Hull.

Provisional Agenda:

10:00Session 1
Prof Brad Gibson – Welcome
Graeme Murphy / Chris Collins- Viper Review and future of HPC update
Dr David Benoit – Viper Powered Science!
11:30 – 11:50Coffee
11:50Session 2
Eamon Faulkner (Health Science) – Endothelial cells in chronic disease
Merideth Freiheit (EvoHull and HYMS) –Microbiome Metagenomics & Viper
12:30 – 13:30Lunch
13:30Session 3
Dr Claire Cashmore – E.A. Milne Centre for Astrophysics
Dr Amangeldi Kenjegaliev (Economics) – The spatio-industrial ESG spillovers on the external returns to scale in the United States
Dr Charlie Lloyd (EEI) – HPC for Fluid Dynamics; boundary layers, shark scales, and mixing
14:30 – 14:50Coffee
14:50Session 4
Lydia Bryan-Smith (Computer Science) – Using multimodal data to dynamically map flood risk
Dr Tim Bellerby (Environmental Sciences) – The PM Programming Language – implementing numerical models on distributed hardware

Please use the link https://forms.office.com/e/GXMBJXRqNh to register for the event so we know numbers for refreshments and lunch!

(The linked Office Form is for University of Hull accounts only, if the form does not work to register, please email viper@hull.ac.uk with your details)

Speakers Include:

Dr David Benoit – Senior Lecturer in Molecular Physics and Astrochemistry

Dr Benoit was part of the HPC Steering Group who helped bring Viper to the University of Hull.

Since then David has been one of Viper’s main users. As well as research in the fields of Chemistry and Astrophysics, David has used Viper for work published in journals covering Chemical Ecology, Climate Change, Cardiology, Materials Science and Physiology.

David will talk about his use of Viper and the variety of his research.

Dr Aman Kenjegaliev – Lecturer in Economics

Dr Aman Kenjegaliev is a member of the HPC Steering Group. His main research is in Economics and Finance. Some of his research depends on the Viper. For example, he is currently conducting a study on the ESG spillovers where he uses HPC to run a translog model to obtain highest posterior density of the unknown variance. It is still in progress.

He will talk about his recent paper, co-authored with researchers from Bath, Leicester and Nottingham.

Lydia Bryan-Smith – PhD Student, Big Data Analytics research group, Computer Science

Lydia is a Computer Science PhD Student in the Energy and Environment Institute, and a member of Nina Dethlef’s Big Data Analytics research group.

Lydia’s primary focus is predicting and assessing the severity of floods using artificial intelligence (AI). Lydia uses Viper to train models to understand complex datasets, consisting of sensor data (rainfall radar data), natural language data (social media posts), and more.

Lydia will present on her work predicting and increasing the situational awareness of floods, and how she uses Viper to accelerate the training of her AI models.

Eamon Faulkner – PhD Student, The Endothelial Cell Biology in Health and Chronic Disease Research Group

Eamon is a PhD student at the Hull York Medical School and a member of the Endothelial cell biology in health and chronic disease research group led by Dr Leonid Nikitenko. 

Eamon’s primary research focus is on the contribution of blood vessel endothelial cells to lung fibrosis. Eamon has used Viper to discover disease-associated changes in heterogeneity of blood vessel endothelial cells by analysing single cell RNA sequencing datasets of lung tissues from older donors and age-matched patients with idiopathic pulmonary fibrosis.

Eamon will present on how PhD students from Endothelial cell biology in health and chronic disease research group (himself and Dimitrios Manolis) utilise Viper for cutting edge health science research including studies of human cells and clinical samples using single cell RNA sequencing and label free quantitative proteomics.

Merideth Freiheit – PhD Student, Bioinformatics of the Human Microbiome

I am a third year PhD student studying the computer science of genetic information taken from human microbiome samples. I am a member of the EvoHull lab group at the University of Hull and the Wound Healing and Respiratory research group at Hull York Medical School led by Dr. Matthew Hardman.

My research focuses on developing workflows and utilizing novel technology to efficiently and effectively analyse the genetic information of microbes found on skin and in wounds. Ultimately, the goal is to use this knowledge to help medical researchers and health care providers gain a more accurate understanding of the human microbiome and apply this understanding to health care interventions.

I use Viper to develop a variety of workflows, perform the heavy lifting required by some software, and manage and analyse the massive amounts of data produced by DNA sequencing. I am going to give a presentation that covers an overview of the microbiome metagenomic research I have conducted and how Viper has made it possible.

Dr Tim Bellerby. Senior Lecturer in the School of Environmental Sciences

Dr Tim Bellerby’s main research is in hydrometeorology. However, over the last 10 years he has also been developing a new programming language, PM (Parallel Models), targeting numerical model development on distributed HPC hardware such as VIPER.

Most HPC software is created using combinations of languages and libraries: FORTRAN, C, MPI, OpenMP, OpenACC, CUDA, etc.. These combinations can be both difficult to program and specific to a given hardware configuration. The PM language has been developed to enable a programmer to concentrate on developing a model, rather than on making that model run on a particular system. A PM program will naturally scale from laptop to large cluster, taking full advantage of the hardware on each platform.

At the same time, it is possible to take direct control of distributed hardware when necessary. The aim is to allow a seamless transition from experimental code developed at the start of a research project all the way through to routine large runs on a supercomputer without extensive rewriting or restructuring. This talk will describe Version 0.4 of the PM language (available at www.pm-lang.org ), which includes both a PM interpreter and a PM to FORTRAN/MPI cross-compiler. A PM to FORTRAN/MPI/OpenMP/OpenACC cross-compiler is planned for a future release.

Graeme Murphy and Chris Collins – IT Services

Graeme Murphy (Director of ICT Operations, IT Services) and Chris Collins (Research Systems Manager, IT Services) will look at the journey of High Performance Computing at the University of Hull, with a view back at the impact Viper has had on research and a view of what the future holds for HPC at Hull.

More speakers being confirmed all the time…


If you would like to attend or submit a poster please register your interest via https://forms.office.com/e/GXMBJXRqNh