Electronic Structure Theory Calculations Using Modern Architectures: KNL vs Haswell.

J Chem Theory Comput

Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States.

Published: November 2021

The time to solution and parallel efficiency of several commonly used electronic structure methods (Hartree-Fock, density functional theory, second order perturbation theory, resolution of the identity second order perturbation theory, coupled cluster) are evaluated on both the Intel Xeon Haswell and the Intel Xeon Phi Knights Landing (KNL) architectures. The Haswell completes the benchmark calculations with a faster time to solution than the KNL for all molecules and methods tested. While the Haswell exhibits an average speedup of at least 3.5 relative to the KNL for all nonthreaded computations, the KNL has a better parallel efficiency than the Haswell with increasing core counts. The architectures are further tested using a more computationally costly coupled cluster method on a transition state reaction. The Haswell appears to be the best choice to minimize the time to solution, though for very large systems and high levels of theory that require memory intensive processes the superior memory hierarchy and larger on node memory of the KNL can make it a better choice. These results are used to showcase aspects of novel architectures that will increase efficiency for quantum chemistry applications.

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jctc.1c00705DOI Listing

Publication Analysis

Top Keywords

time solution
12
electronic structure
8
parallel efficiency
8
second order
8
order perturbation
8
perturbation theory
8
coupled cluster
8
intel xeon
8
knl better
8
knl
6

Similar Publications

Using genetic data to infer evolutionary distances between molecular sequence pairs based on a Markov substitution model is a common procedure in phylogenetics, in particular for selecting a good starting tree to improve upon. Many evolutionary patterns can be accurately modelled using substitution models that are available in closed form, including the popular general time reversible model (GTR) for DNA data. For more complex biological phenomena, such as variations in lineage-specific evolutionary rates over time (heterotachy), other approaches such as the GTR with rate variation (GTR ) are required, but do not admit analytical solutions and do not automatically allow for likelihood calculations crucial for Bayesian analysis.

View Article and Find Full Text PDF

Background: The effects of ionizing radiation (IR) involve a highly orchestrated series of events in cells, including DNA damage and repair, cell death, and changes in the level of proliferation associated with the stage of the cell cycle. A large number of existing studies in literature have examined the activity of genes and their regulators in mammalian cells in response to high doses of ionizing radiation. Although there are many studies, the research in effect of low doses of ionizing radiation remains limited.

View Article and Find Full Text PDF

Diabetic wounds with chronic infections present a significant challenge, exacerbated by the growing issue of antimicrobial resistance, which often leads to delayed healing and increased morbidity. This study introduces a novel silver-zinc oxide-eugenol (Ag+ZnO+EU) nanocomposite, specifically designed to enhance antimicrobial activity and promote wound healing. The nanocomposite was thoroughly characterized using advanced analytical techniques, confirming its nanoscale structure, stability and chemical composition.

View Article and Find Full Text PDF

Catechins in tea, as promoters of human health, have attracted widespread attention. Herein, a dual-signal mode (colorimetric and fluorescence) sensor array for catechin species fingerprinting was built based on PtNi bunched nanoparticle (PtNi-BNP)--phenylenediamine (OPD)-HO system. PtNi-BNPs catalyze the reaction between OPD and HO to produce oxidized OPD (oxOPD) with both colorimetric (yellow) and fluorescent properties.

View Article and Find Full Text PDF

Miniaturization of next-generation active neural implants requires novel micro-packaging solutions that can maintain their long-term coating performance in the body. This work presents two thin-film coatings and evaluates their biostability and in vivo performance over a 7-month animal study. To evaluate the coatings on representative surfaces, two silicon microchips with different surface microtopography are used.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!