Establishing the Accessible Computational Regimes for Biomolecular Simulations at Exascale
Lead Research Organisation:
University of Sheffield
Department Name: Physics and Astronomy
Abstract
The ExaBioSim research team is a community of experts in biomolecular simulation that use High Performance Computing (HPC) with the ambition to build a strong and inclusive community, and to push the frontiers of biomolecular simulations into the Exascale era. We collectively represent the diverse range of computations employed to understand molecular biology, from quantum chemistry of enzyme catalysis up to the dynamics of sub-cellular ultra-structures, such as cell walls and organelles. Biomolecular simulations have important applications in the healthcare and pharmaceutical industries, for example in computer aided drug design, and can enhance the data we extract from experiments, such as for cryo-electron microscopy. Currently, the computational expense of biomolecular simulations can limit their predictive power, so here we explore the potential of Exascale to overcome these limitations.
Related Projects
| Project Reference | Relationship | Related To | Start | End | Award Value |
|---|---|---|---|---|---|
| EP/Y008693/1 | 31/05/2023 | 31/01/2024 | £471,209 | ||
| EP/Y008693/2 | Transfer | EP/Y008693/1 | 01/02/2024 | 30/03/2025 | £321,666 |
| Description | We have established the performance of biomolecular simulation software on UK HPC architectures and made recommendations for how HPC should be set up to benefit users. |
| Exploitation Route | We will made recommendations to the UK HPC community for supporting biomolecular simulations. |
| Sectors | Digital/Communication/Information Technologies (including Software) Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Title | ExaBioSim Benchmark Results |
| Description | This is the output data for the biomolecular simulation, Quantum Chemistry and Cryo-Electron microscopy benchmarks. It contains systems of several biological systems ranging in size and biology for the codes; amber, gromacs, namd, lammps, openmm, psi4 and relion. The results in this repository include performance data across several UK and EU HPC machines. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The benchmark data contained in this set of files will form key recommendations to UKRI about future HPC requirements of the field, they are used to extend the HECBioSim resource calculator and also have been incorporated into other benchmarking initiatives of note is an initiative to create a set of automated and reproducible benchmarks for future HPC procurement by UKRI. |
| URL | https://github.com/HECBioSim/benchmark-results |
| Title | ExaBioSim Benchmark set |
| Description | This is the input files for the biomolecular simulation, Quantum Chemistry and Cryo-Electron microscopy benchmarks. It contains systems of several biological systems ranging in size and biology for the codes; amber, gromacs, namd, lammps, openmm, psi4 and relion. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | The benchmarks derived from this set of files will form key recommendations to UKRI about future HPC requirements of the field, they are used to extend the HECBioSim resource calculator and also have been incorporated into other benchmarking initiatives of note is an initiative to create a set of automated and reproducible benchmarks for future HPC procurement by UKRI. |
| URL | https://github.com/HECBioSim/benchmarks |
| Title | HECBioSim HPC calculator |
| Description | This web application is used by the biomolecular simulation community both as a resource estimator for their HPC grant applications but also for the research specialists on the ground to optimise their use of HPC facilities. This extension of it is related to incorporation of the ExaBioSim benchmarks and data to improve the models and machines available. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | This calculator improves community understanding of resource requirements of their calculations, reducing wasted cycles on HPC facilities and thus helps to protect UKRI investment into HPC. |
| URL | https://github.com/HECBioSim/com_hecbiosim_calculator |
| Title | hpcbench |
| Description | A set of benchmarking utilities for biomolecular simulation tools. This package creates an automated set of tools for reproducing the benchmarking study performed within the ExaBioSim initiative. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | This tool made it very simple to benchmark any machine by rapidly creating the necessary steps to setup and perform the benchmark suite. Benchmarks contained in this tool are now being incorporated into a standard set of benchmarks across UKRI domains to support future UKRI HPC procurement decisions and tests. |
| URL | https://github.com/HECBioSim/hpcbench |
| Description | Biomolecular Simulation at the Exascale (is not enough) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Close to final talk, mostly focused on communicating key results, at excalibur sunset meeting |
| Year(s) Of Engagement Activity | 2024 |
| Description | Yet Another HPC Benchmarking Project |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | HPCBench talk including preliminary results and feedback gathering for methods |
| Year(s) Of Engagement Activity | 2024 |