arXiv subjects

Rafael Ravedutti Lucio Machado

Publications and source records attributed to Rafael Ravedutti Lucio Machado.

3 recordsLinked to original sources

arXiv2025

On the Challenges of Energy-Efficiency Analysis in HPC Systems: Evaluating Synthetic Benchmarks and Gromacs

This paper discusses the challenges encountered when analyzing the energy efficiency of synthetic benchmarks and the Gromacs package on the Fritz and Alex HPC clusters. Experiments were conducted using MPI parallelism on full sockets of Intel Ice Lake and Sapphire Rapids CPUs, as well as Nvidia A40 and A100 GPUs. The metrics and measurements obtained with the Likwid and Nvidia profiling tools are presented, along with the results. The challenges and pitfalls encountered during experimentation and analysis are revealed and discussed. Best practices for future energy efficiency analysis studies are suggested.

cs.DC↗

arXiv2023

MD-Bench: Engineering the in-core performance of short-range molecular dynamics kernels from state-of-the-art simulation packages

Molecular dynamics (MD) simulations provide considerable benefits for the investigation and experimentation of systems at atomic level. Their usage is widespread into several research fields, but their system size and timescale are also crucially limited by the computing power they can make use of. Performance engineering of MD kernels is therefore important to understand their bottlenecks and point out possible improvements. For that reason, we developed MD-Bench, a proxy-app for short-range MD kernels that implements state-of-the-art algorithms from multiple production applications such as LAMMPS and GROMACS. MD-Bench is intended to have simpler, understandable and extensible source code, as well as to be transparent and suitable for teaching, benchmarking and researching MD algorithms. In this paper we introduce MD-Bench, describe its design and structure and implemented algorithms. Finally, we show five usage examples of MD-Bench and describe how these are useful to have a deeper understanding of MD kernels from a performance point of view, also exposing some interesting performance insights.

physics.chem-ph↗

arXiv2022

MD-Bench: A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms

Proxy-apps, or mini-apps, are simple self-contained benchmark codes with performance-relevant kernels extracted from real applications. Initially used to facilitate software-hardware co-design, they are a crucial ingredient for serious performance engineering, especially when dealing with large-scale production codes. MD-Bench is a new proxy-app in the area of classical short-range molecular dynamics. In contrast to existing proxy-apps in MD (e.g. miniMD and coMD) it does not resemble a single application code, but implements state-of-the art algorithms from multiple applications (currently LAMMPS and GROMACS). The MD-Bench source code is understandable, extensible and suited for teaching, benchmarking and researching MD algorithms. Primary design goals are transparency and simplicity, a developer is able to tinker with the source code down to the assembly level. This paper introduces MD-Bench, explains its design and structure, covers implemented optimization variants, and illustrates its usage on three examples.

physics.comp-ph↗