The newest pre-exascale machines have come online and the codes are ready to run on those. In particular, there have been significant efforts to make GROMACS perform well on LUMI. This has been a challenge, not so much because of the new architecture of the AMD GPUs, but rather because of the software stack, which has had some stability issues. By now, GROMACS achieves good performance on LUMI and we have scaling benchmarks to back this up. Notably, while BioExcel as a whole was designed for track 2 of the CoE mechanism since most users have a strong need for ensemble parallelism, GROMACS in particular achieves outstanding scalability, performance and portability to all major GPU hardware. Scaling benchmarks have been run for both GROMACS and HADDOCK on different HPC machines, including LUMI. They show scaling up to 128 GPUs or 2048 CPU cores. In BioExcel-3 we have moved to systematic user driven development. We have sent out and analysed questionnaires with similar structure for all the codes. Work on new features is prioritised based on the outcomes.
Usability and reproducibility are being improved in HPC supercomputers, with the work on a new set of BioBB and PyCOMPSs Spack packages, easing the installation of our workflows in the new EuroHPC machines. The combination of AI-based workflows with EuroHPC supercomputers and HPC-focused workflow managers will enable real science with automation and efficient use of resources, reducing the time-to-result, similarly to what was achieved in BioExcel-2 with our Pre-exascale HPC approaches for molecular dynamics simulations on the Covid-19 research.
By conducting user surveys and analysing the results of those, we have demonstrated our commitment of understanding and integrating user needs into the software development process. The surveys collected for the core BioExcel codes have helped shape the roadmap and training plans, reflecting a user-driven approach to software enhancement. The newly started Ambassador Program and community-driven activities play a strategic role in engaging the user community and understanding and addressing specific requirements of different user groups. In the first year of the project, we successfully built an ambassador community of 21 country representatives. This program has already successfully expanded our community engagement through workshops and activities. A first outcome of this programme, the “Carpathian edition” was a GROMACS/HADDOCK training workshop organised in Bratislava in October 2023, organized jointly with NCCs of Slovakia, Czech Republic, Austria and Hungary. Our Ambassador Program has already facilitated direct interactions with users with more activities already planned.
The 8th edition of our Flagship training event “BioExcel Summer school” was organised in Sardinia in September 2023 for 30 students containing lectures and hands-on sessions of the core tools. The three best posters were selected by vote and their authors were given an opportunity to present their research in an additional BioExcel webinar in late 2023. The Summer school average of feedback from participants was excellent 9,5/10. Two other on-site training events were organised: A fully on-site event, the Spring School on Computational Chemistry, was organised in Finland already in April. In October, a hybrid meeting for the new ambassadors linked with a training workshop, was organised in Bratislava, together with the BioExcel all hands meeting. The successful BioExcel webinar series was relaunched in April 2023. A total of eight new webinars were organised during the reporting period, see
https://bioexcel.eu/category/webinar/(odnośnik otworzy się w nowym oknie). Additionally, BioExcel partners participated in numerous other events promoting the core software and by direct support via the Ask BioExcel forum.
A high level of dissemination of BioExcel events, news, job postings and related activities has happened mainly through the three key social media platforms (X/Twitter, LinkedIn, YouTube) as well as through the bi-monthly BioExcel newsletter. This is reflected in the increased numbers of users, followers and subscribers for each of the channels. BioExcel has over 3,500 followers on X/Twitter (7% increase in 2023), over 2,100 followers on LinkedIn (45% increase in 2023) and over 3,700 subscribers of the YouTube channel (26% increase in 2023) with more than 191,000 total views of overall content. In addition, the BioExcel mailing list which is used to distribute the bi-monthly newsletter had approximately 2,800 subscribers at the end of 2023 (19% increase).
