BioExcel-2 D1.3 – Updated Software Roadmap
Creators: name: Hess, Berk
name: Bauer, Paul
name: Lindahl, Erik
name: Honorato, Rodrigo
name: Bonvin, Alexandre
name: Jimenez-Garcia, Brian
name: Proeme, Arno
name: Morozov, Dmitry
name: Groenhof, Gerrit
name: De Groot, Bert L.
name: Gapsys, Vytautas
Publisher: name: Zenodo
Year: 2020
Subjects: Software development
Roadmap
exascale computing
modularization
workflows

description: This deliverable reports on the present state of the BioExcel-2 core application roadmaps, how user and infrastructure needs have been prioritized, the specific tasks this corresponds to in the codes, and what the long-term directions of the codes are – even beyond the present BioExcel funding period. As part of BioExcel2, the software roadmaps have been updated to balance development driven by user requests for features as well as strategic efforts targeting EuroHPC and preparing for next-generation processor and accelerator hardware. The <strong>GROMACS </strong>development will focus on a number of key user-requested features, in particular adding multiple time stepping, driving simulations with external data, facilitating generation of input data, and better free energy tools. The development of performance optimization for additional new platforms will also continue together with efforts targeting significantly improved scaling by using ensemble parallelism, as well as co-design projects to port the code to new accelerator platforms. The development of the <strong>PMX </strong>package will follow two main directions. Firstly, the core code will be updated with the changes necessary for the successful future usability of the software. In particular, with the end of Python2 lifetime, pmx will be fully rewritten in Python3. The continuous support of the main pmx functionalities will be ensured. The second major development direction comprises the incorporation of features frequently requested by users, the addition of new mutation libraries and creation of workflows for free energy calculation setup and analysis. <strong>HADDOCK</strong>’s development focuses on the continuous improvement of the web server, which functions as the main user’s interface, the implementation of relevant features and the design of a new modular version, HADDOCK3. The web server is being co-developed alongside the local HADDOCK version, so that new features (coarse-grained and shape docking, etc.) are readily available in an intuitive and responsive user-friendly interface. A major rework of the current code is in place, for what will become HADDOCK3, with this modular design we aim to provide flexibility for workflow creation and a straightforward framework to integrate new tools. This new modular architecture will also enable more efficient execution on HPC resources. To provide users with access to chemical reactivity in biomolecular simulations, we will develop an interface between GROMACS and CP2K, a highly parallelized density functional theory (DFT) computer program. With the new interface, users can perform multi-scale simulations, in which one part of the system is modelled with DFT, while the remainder is described with a molecular mechanics force field (i.e. QM/MM). Our developments focus on providing the community with an accurate, scalable and user-friendly QM/MM solution. Compared to the previous BioExcel software roadmap, which focused on CPMD for DFT functionality in QM/MM simulations, this updated roadmap reflects the project’s transition to CP2K, which has more wide-spread availability and uptake in the community.