arXiv subjects

Lorién López-Villellas

Publications and source records attributed to Lorién López-Villellas.

4 recordsLinked to original sources

arXiv2026

REPTILES: Repeated Tiles of Sargantana, a RISC-V multicore based on OpenPiton

Chip industry continues advancing and expanding modern computing systems, resulting in more complex multi-core processors. Conversely, academic projects face scalability challenges due to limited resources, highlighting the need for open-source frameworks that enable innovation and knowledge sharing. Recently, several open-source proposals have emerged, offering flexible and scalable designs, but fail to meet the performance demands of modern High-Performance Computing (HPC) applications. In this project, we present REPTILES, an open-source RISC-V multicore framework based on OpenPiton\thanks. REPTILES interconnects multiple Sargantana cores with the memory hierarchy of OpenPiton. Moreover, we present the new features incorporated in Sargantana and OpenPiton designs to improve the performance of HPC applications. We demonstrate that REPTILES presents suitable scalability, achieving a speedup of 3.1x on average with 4 cores. Additionally, we show that Sargantana's new features increase the performance of vector addition benchmark in a 9.3x.

cs.AR↗

arXiv2025

ILVES: Accurate and efficient bond length and angle constraints in molecular dynamics

All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation timescales increase, so does the associated computational cost. To extend simulated time using the same resources, a common strategy is to constrain the fastest degrees of freedom, such as bond lengths, allowing for larger integration time steps without compromising accuracy. The de facto state-of-the-art algorithms for this purpose (SHAKE, LINCS, and P-LINCS) are integrated into most molecular dynamics packages and widely adopted across the field. Despite their impact, these methods exhibit limitations: all converge slowly when high numerical accuracy is required, and the LINCS and P-LINCS algorithms cannot handle general angular constraints, limiting further increases in time step. In this article, we introduce ILVES, a family of parallel algorithms that converge so rapidly that it is now practical to solve bond length and associated angular constraint equations as accurately as the hardware will allow. We have integrated ILVES into Gromacs and our analysis demonstrates that it is superior to the state-of-the-art when constraining bond lengths. Due to its better convergence properties, we also show that if the time step is increased up to 3.5 fs by enforcing angular constraints, ILVES enables a 1.65x increase in simulated time using the same computational resources and wall-clock time, an outcome unattainable with current methods. This advance can significantly reduce the computational cost of most all-atom molecular dynamics simulations while improving their accuracy and extending access to larger systems and longer timescales.

physics.chem-ph↗

arXiv2024

The need for accuracy and smoothness in numerical simulations

We consider the problem of estimating the error when solving a system of differential algebraic equations. Richardson extrapolation is a classical technique that can be used to judge when computational errors are irrelevant and estimate the discretization error. We have simulated molecular dynamics with constraints using the GROMACS library and found that the output is not always amenable to Richardson extrapolation. We derive and illustrate Richardson extrapolation using a variety of numerical experiments. We identify two necessary conditions that are not always satisfied by the GROMACS library.

math.NA↗

arXiv2023

How accurate does Newton have to be?

We analyze the convergence of quasi-Newton methods in exact and finite precision arithmetic. In particular, we derive an upper bound for the stagnation level and we show that any sufficiently exact quasi-Newton method will converge quadratically until stagnation. In the absence of sufficient accuracy, we are likely to retain rapid linear convergence. We confirm our analysis by computing square roots and solving bond constraint equations in the context of molecular dynamics. We briefly discuss implications for parallel solvers.

math.NA↗