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UCL attends SuperComputing 24

By dorothy.chung, on 29 January 2025

In November, UCL Advanced Research Computing (ARC) provided funding for select UCL staff to attend SC24, the 2024 running of the annual SuperComputing (SC) conference, hosted in Atlanta, Georgia, USA. UCL was one of 494 exhibitors, with a stand showcasing several novel High-Performance Computing (HPC) research initiatives taking place at UCL through posters and talks. Representatives from multiple departments beyond ARC attended, including Computer Science, Information Services Division, Chemistry, Biology, and the Bartlett, putting the diverse range of achievements of UCL’s interdisciplinary HPC community on display. 

Conference background 

SC is a preeminent conference for HPC, networking, storage, and analysis, held each November at a series of US conference centres. The event includes exhibits of emerging hardware and software technology, with exhibitors including government agencies, universities, and private companies. The participants range from students to senior-level researchers and HPC industry executives, and numerous awards are given for achievements in HPC innovation, research excellence and student projects. The 2024 running was the largest yet given the growing prominence of Artificial Intelligence and the associated enabling technologies. 

Photo of UCL stand at SC24

Photo of UCL stand at SC24

UCL was represented at the conference in 2024, with ARC as the sponsor of attendance. This allowed UCL’s HPC community to connect with a vast and international base of likeminded individuals as well as disseminating UCL’s research interests. The UCL stand was well attended and featured numerous talks at the booth over three days, as well as the presentation of research posters and a live model of a digital twin. 

UCL’s attendance and experience 

Given the variety of backgrounds represented amongst UCL’s attendees, the subjects shared covered numerous different topics from across the HPC spectrum. These aimed to highlight both UCL’s relevant programs and scientific computing research, promoting UCL and its staff’s standing in the field. ARC staff in particular shared seven posters and the majority of the booth talks, but also shared the display space with other departments’ presentations covering molecular simulation using supercomputers from UCL’s Physical Chemistry research and industry partners NVIDA, Quantum and DataVita.

Poster presentation at the UCL stand

Poster presentation at the UCL stand

UCL was one of few universities attending from outside of the US and thus stood out due to the larger scale of the booth in comparison to other non-US institutions. The booth drew questions from many attendees intrigued with how HPC is applied in academia and engaging with the research presented.  

Conference presentation

Conference presentation

Outlook

Following a successful showing at SC24, sights are set on improving the showing for SC25. Given the wealth of HPC research taking place all throughout UCL’s STEM departments and the great capacity for collaboration in academia, ARC hopes to showcase even more of UCL’s HPC research as well as potentially bringing in academics from other UK universities to improve the presence of institutions from abroad. UCL staff interested in HPC are encouraged to stay tuned for information on applications for attending next year’s conference. 

Workshop on Open-Source Software for Surgical Technologies

By m.xochicale, on 20 December 2024

To champion the creation of sustainable, robust, and equitable digital healthcare systems that prevent the perpetuation of healthcare inequalities, ARC researchers took the lead in organising the second workshop on Open-Source Software for Surgical Technologies at the Hamlyn Symposium on Medical Robotics on June 28th, 2024.

The workshop focused on a key question: how can we transform open-source software libraries into sustainable, long-term supported tools that are translatable to clinical practice? To address this, the event brought together engineers, researchers, and clinicians from academia and industry to present their work, discuss current progress, challenges, and trends, and lay the foundation for building a collaborative community around Open-Source Software Innovations in Surgical, Medical and AI Technologies.

In this post, we are excited to share recordings of our exceptional lineup of speakers and celebrate the poster awardees from the workshop, along with Zenodo links to other posters. The talks and posters spanned a variety of topics, including certification, commercialisation, and case studies of open-source software in research and industry scenarios. This workshop highlighted the profound impact of open-source software in advancing surgical technologies and medical innovation.

Speakers

Watch all the recorded talks on this YouTube Playlist.

️Poster awardees
Congratulations to all the awardees for their outstanding contributions to advancing innovation in surgical technologies!

Best Poster Award
Martin Huber et al. from King’s College London “LBR-Stack: ROS 2 and Python Integration of KUKA FRI for Med and IIWA Robots”
GitHub: https://github.com/lbr-stack/lbr_fri_ros2_stack/
arXiv: https://arxiv.org/abs/2311.12709

Runner-Up Awards (Three-Way Tie)

  • Keisuke Ueda et al. from Medical DATAWAY “Automated Surgical Report Generation Using In-context Learning with Scene Labels from Surgical Videos” Poster in Zenodo https://zenodo.org/records/12518729
  • Mikel De Iturrate Reyzabal et al. from King’s College London “PyModalSurgical. An image-space modal analysis library for surgical videos: generating haptic and visual feedback” Poster in Zenodo: https://zenodo.org/records/12204075​
  • Ewald Ury et al. from KU LEUVEN “Markerless Augmented Reality Guidance System for Maxillofacial Surgery”

See other posters Peter Kazanzides et al., dVRK-Si: The Next Generation da Vinci Research Kit, Reza Haqshenas et al., OptimUS: an open-source fast full-wave solver for calculating acoustic wave propagation with applications in biomedical ultrasound.

Get in touch

We can’t wait to see you again next year!
Warm regards, Eva, Stephen, & Miguel

 

 

 

#HSMR24 #HamlynSymposium2024 #Healthcare #OpenSource #ArtificialIntelligence #SurgTech #MedTech #AITech

Team (u)CLI finish 3rd!

By Samantha Ahern, on 9 December 2024

Team (u)CLI finish 3rd in the national Computing Insights UK student Cluster Challenge!

(u)CLI team members:Zak Morgan, Dept of Computer Science
Rozenn Raffaut, Dept of Med Phys & Biomedical Eng
Qi Li,  Dept of Med Phys & Biomedical Eng
Yuliang Huang, Dept of Med Phys & Biomedical Eng
Tom Bickley, Dept of Chemistry

Team (u)CLI

Team members from left to right:

  • Zak Morgan, Dept of Computer Science
  • Rozenn Raffaut, Dept of Med Phys & Biomedical Eng
  • Tom Bickley, Dept of Chemistry
  • Yuliang Huang, Dept of Med Phys & Biomedical Eng
  • Qi Li,  Dept of Med Phys & Biomedical Eng

 

 

 

 

The CIUK Cluster Challenge is a national inter-collegiate competition. This year there were 16 student teams taking part from across the UK.

The competition was formed of three challenges during October and November, before culminating in an additional three challenges at Computing Insights UK (CIUK) in Manchester in December.

The team performed well in the initial pre-conference challenges, and were at the top of the leaderboard heading into the onsite challenges.

They were supported throughout by the team mascot, Archie ‘ARC’vark.

Archie 'ARC'vark at CIUK

Team mascot: Archie ‘ARC’vark

Competition was fierce and overall team (u)CLI finished 3rd out of 15 teams who completed all challenges. Narrowly missing out on 2nd place by 2 points. Full results are available on the CIUK Cluster Challenge website.

Overall the team performed very well and received some very positive feedback from some of the challenge setters.

We look forward to supporting future teams in new challenges, and building a community of students who want to participate through our termly Cluster Club sessions.

 

 

 

UCL ARC at the 2024 International RSE Conference

By Jonathan Cooper, on 18 November 2024

This year’s RSE conference took place from 3rd – 5th September in Newcastle. Around 20 ARC staff attended in person, with several others joining in the hybrid experience remotely. The latter has been steadily improving year on year, at least for contributing to the formal parts of the conference programme. The informal conversations are still much better in person, and this aspect was particularly appreciated by our newer RSEs. This blog post summarises our joint impressions of the conference, based on a debriefing discussion we had in our weekly “Collaboration Hour” later in September, and edited by Jonathan Cooper. We have raced against the conference committee to get this blog post out before the conference materials are published!

The programme had a mix of technical topics and sessions devoted to how we work as RSEs, and indeed wider “Research Technology Professionals” (RTPs) as well. RTP is a newly coined phrase used by UKRI among others to refer to the wide range of specialist roles that exist alongside traditional researchers, encompassing all the ARC professions and more. Several initiatives are aiming to leverage the success of the RSE movement to advance other professions in a similar way, some of which we are involved in or proposed at the conference, notably in the RSE leaders and aspiring leaders satellite event on the Monday. This has grown massively since its inception as a safe space for those struggling to create RSE groups to share the pain and learn from each other! Now there are many kinds of RSE group, many individuals in different RTP leadership roles, and much more wide-ranging discussions as a result. I particularly appreciated the session on the skills that leaders need in this environment – what people have found helpful and how we should be growing the next generation.

A similar topic was covered in the RSE Competencies workshop, although this covered all areas of RSE skills and tried to categorise these. We ended up with more non-technical skills than those focused on specific technologies. The work is ongoing with monthly community meetings, aiming to build a toolkit that will help people advance their careers: identify skills they need and avenues for training and professional development.

Several sessions focused on project management and Agile approaches. We heard from Manchester how they are adapting Scrum for their research projects, notably the categorisation of projects that they have according to how large they are and how engaged the researchers are, and therefore the different sort of tweaks they’re made to Scrum in each case. These seem to be fairly similar to how we operate in ARC, but in a more formalised structure. We contributed to the discussion session they ran on the following day (led by Sarah Jaffa, formerly of ARC!) with Monika and I doing a double act presenting a high level view of our approach and a summary of Kanban. An important theme of that session was that project management is as much about self-care as it is delivering on the goals of the project, and these aspects need to be well balanced or both suffer. A special interest group (SIG) is being set up dedicated to project management, and we have continued discussions within ARC too, with a recent blog post on adapting the agile values and principles to a research context.

Others in the group focused more on the technical programme. Mutation testing was one highlight – described as sort of like test coverage, but your code is randomly changed to see what breaks. If no tests fail then you may have revealed an untested code path that needs to be tested and fixed. It’s good for catching edge cases that haven’t been thought of but does take time to run. We noted that this is good as part of a wider array of testing approaches that can be used, for example hypothesis testing (randomising code inputs rather than the code itself).

Best practices for setting up development environments were covered in a couple of talks, and how this is perhaps one aspect that distinguishes an RSE from a CS researcher. These range from use of pip and pipenv in Python to things like dev containers and Nix. These are important for reproducibility. The Netherlands eScience Centre python project template had a nice feature that allows updating projects created using a template when updates to the template itself are made.

Several talks looked at performant Python. We were surprised (perhaps unfairly) at how much impact simply upgrading to the latest Python version can have. Tools like numba and approaches such as vectorisation were well known, but tips for using list comprehensions, sometimes in preference even to Pandas apply operations, were appreciated and will be useful for several of our projects.

As you might expect from ARC we had significant involvement in the high-performance computing sessions, including Tuomas running a “birds of a feather” (BOF) event for the HPC RSE community and giving several talks. Talks not by us covered a range of topics, including the age-old comparison of the merits of different languages and porting between them, the newer frameworks aiming to ease GPU programming, portability between different hardware, and debugging parallel programs. We enjoyed trying out the Grace Hopper chips in IsambardAI, and discussing how to utilise HPC in the most environmentally sustainable way. The conclusion from Archer2 is that given the CO2 released by manufacturing HPC systems, the best option is to run them as intensively as possible since this maximises the research done for a given carbon cost – and indeed that personal lifestyle changes may be a better option for minimising your impact!

Green RSE was the focus for another BOF which some ARC staff attended. A SIG is being set up for this, trying to raise awareness of what RSEs can do and consider what training might be helpful. This is something we want to get involved with more at ARC, starting with an inventory of our current state in conjunction with the department’s Green Team.

The Fortran satellite event was very well run. It revealed that many people want similar improvements to the Fortran ecosystem to support automated testing and the like. We have recently started an initiative along those lines at ARC so will be trying to work with the wider community on this and avoid duplication of effort, having now met some relevant people.

Some talks focused more on particular research domains. Given ARC’s current efforts developing Trusted Research Environments (TREs) we were interested by the Turing’s approach. They worry less about packages coming into the secure environment, and advocated for just proxying CRAN, PyPI and the like, while making sure that your infrastructure is set up securely enough that things can’t get out unless you want them to. So if something does get in and cause havoc, it shouldn’t be able to egress any data and it should only affect a single study or project. This is also the approach we take in ARC’s TRE.

The unconference session was a highlight for some, particularly discussion of developing software as a medical device. This covered trying to work with people in the institution to come up with processes, but also trying to figure out what the role of RSEs and the Society of RSE should be in that process. Are we just followers or the ones coming up with the process? How much of the regulatory side is our responsibility and who else we need to work with? No firm answers from that, but lots of questions! A prototype tool we developed for one project may be useful here if we can get funding and/or collaborators to continue the work.

All found the keynote talks inspiring, especially the one from Anne-Marie Imafidon. The test driven development workshop got a mention as being really clearly presented with great materials, as did an interesting C++ graphics library called Morphologica.

We are all looking forward to next year’s conference in Warwick. On a personal level, I’m especially pleased that it is likely not to conflict with INSET days and I’ll be able to be there in person again.

Team (u)CLI are Go!

By Samantha Ahern, on 22 October 2024

ARC are excited to announce this year’s team for the CIUK Cluster Challenge – (u)CLI!

Group photo of team members of (u)CLI

Team (u)CLI

  • Zak Morgan, Dept of Computer Science
  • Rozenn Raffaut, Dept of Med Phys & Biomedical Eng
  • Qi Li,  Dept of Med Phys & Biomedical Eng
  • Yuliang Huang, Dept of Med Phys & Biomedical Eng
  • Tom Bickley, Dept of Chemistry
  • Shahid Khalid, Neonatology

 

 

The CIUK Cluster Challenge is a national inter-collegiate competition. This year there are 16 student teams taking part from across the UK.

The competition is formed of four challenges during October and November, before culminating in an additional four challenges at Computing Insights UK (CIUK) in Manchester in December.

The competition is an opportunity for students to develop technical skills in high performance compute, network with compute professionals and develop a range of employability skills.

Last week, the team competed in the 1st challenge, set by Alces Flight, and finished 2nd. Well done team (u)CLI!

We wish them well for their future challenges and supporting them at CIUK in Manchester.

Could you be a future Cluster Challenge team member? Start your HPC journey by joining the Cluster Club.