BioExcel Webinar #66: Efficient (GROMACS+)CP2K compute resource usage for biomolecular QM/MM
Channel: BioExcel CoE
Date: 2022-05-26

Efficient (GROMACS+)CP2K compute resource usage for QM/MM simulation of biomolecular systems
Slides: https://doi.org/10.5281/zenodo.6606885

BioExcel QM/MM Benchmark Suite: 
https://github.com/bioexcel/qmmm_benchmark_suite

Report with larger set of parallel scaling figures and performance profiles including for different threading options for BioExcel QM/MM benchmarks and HPC machines described in this webinar:
https://doi.org/10.5281/zenodo.6591574

Raw CP2K output data used to generate figures in above report: 
https://github.com/bioexcel/qmmm_benchmark_results

Script used to generate performance figures in above report from raw CP2K output data:
https://github.com/bioexcel/qmmm_benchmark_script

BioExcel Best Practice Guide: GROMACS+CP2K for QM/MM simulation of biomolecular systems: 
https://docs.bioexcel.eu/qmmm_bpg/



Presenting: Arno Proeme and Holly Judge

Webinar abstract:
Hybrid quantum/classical (QM/MM) simulation of biomolecular systems has grown in popularity in recent years, facilitated in part by the availability of software such as the GROMACS-CP2K and GROMACS-CPMD interfaces developed within BioExcel, which couple GROMACS with the CP2K and CPMD quantum chemistry / electronic structure codes.

Performing productive QM/MM simulation of biomolecular systems requires researchers to not only carefully choose suitable QM and QM-MM coupling treatments – a topic covered in depth in our workshop on Best Practices in QM/MM simulation of Biomolecular Systems – but also to consider how best to make use of available computational resources, which are needed mainly for costly QM calculations. Available computational resources may constrain the choice of treatment that is feasible and hence the quality of results obtained, which may amount not merely to a quantitative difference in accuracy but even to qualitatively different conclusions regarding structure or function.

Understanding how the QM/MM simulation software employed can best make use of available hardware including processors (CPUs) and accelerators (GPUs) has the potential to not only improve efficient utilisation of these resources but also to significantly accelerate research and individual researcher productivity. Moreover, knowing what computational resources would be needed to pursue a given treatment helps justify and obtain access to high-performance computing (HPC) resources at an institutional, regional, or national level, including the largest facilities available to researchers in the form of – in the EU – supercomputing infrastructure provided through PRACE and EuroHPC.

With that in mind and in order to assist researchers using or considering using CP2K – with GROMACS or as a standalone application – for QM/MM simulation of biomolecular systems, we provide in this webinar a brief overview of the parallel performance of CP2K on hardware commonly found on modern HPC machines for a range of biomolecular systems and QM treatments that together make up the BioExcel QM/MM Benchmark Suite. This overview is intended to function as a rough reference and a useful starting point to guide researchers towards obtaining good performance on available hardware for their system of interest, and/or to help plan future work that includes access to and increased usage of HPC resources.