Literature DB >> 25345784

Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units.

Raymundo Hernández-Esparza1, Sol-Milena Mejía-Chica, Andy D Zapata-Escobar, Alfredo Guevara-García, Apolinar Martínez-Melchor, Julio-M Hernández-Pérez, Rubicelia Vargas, Jorge Garza.   

Abstract

Using a grid-based method to search the critical points in electron density, we show how to accelerate such a method with graphics processing units (GPUs). When the GPU implementation is contrasted with that used on central processing units (CPUs), we found a large difference between the time elapsed by both implementations: the smallest time is observed when GPUs are used. We tested two GPUs, one related with video games and other used for high-performance computing (HPC). By the side of the CPUs, two processors were tested, one used in common personal computers and other used for HPC, both of last generation. Although our parallel algorithm scales quite well on CPUs, the same implementation on GPUs runs around 10× faster than 16 CPUs, with any of the tested GPUs and CPUs. We have found what one GPU dedicated for video games can be used without any problem for our application, delivering a remarkable performance, in fact; this GPU competes against one HPC GPU, in particular when single-precision is used.
© 2014 Wiley Periodicals, Inc.

Entities:  

Keywords:  atoms in molecules; electron density; graphics processing units; parallel computing

Year:  2014        PMID: 25345784     DOI: 10.1002/jcc.23752

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  5 in total

1.  Analyzing ZnO clusters through the density-functional theory.

Authors:  Irineo-Pedro Zaragoza; Luis-Antonio Soriano-Agueda; Raymundo Hernández-Esparza; Rubicelia Vargas; Jorge Garza
Journal:  J Mol Model       Date:  2018-06-16       Impact factor: 1.810

2.  Coordination numbers in hydrated Cu(II) ions.

Authors:  Alejandra Monjaraz-Rodríguez; Mariano Rodriguez-Bautista; Jorge Garza; Rafael A Zubillaga; Rubicelia Vargas
Journal:  J Mol Model       Date:  2018-07-02       Impact factor: 1.810

3.  Confined toluene within InOF-1: CO2 capture enhancement.

Authors:  L Pamela Garrido-Olvera; Jonathan E Sanchez-Bautista; Daniel Alvarado-Alvarado; Bruno Landeros-Rivera; J Raziel Álvarez; Rubicelia Vargas; Eduardo González-Zamora; Jorge Balmaseda; Hugo A Lara-García; Ana Martínez; Ilich A Ibarra
Journal:  RSC Adv       Date:  2019-10-15       Impact factor: 4.036

4.  SBA15-Fluconazole as a Protective Approach Against Mild Steel Corrosion: Synthesis, Characterization, and Computational Studies.

Authors:  Victoria Bustos-Terrones; Iris N Serratos; Rubicelia Vargas; Bruno C Landeros-Rivera; Yaneth A Bustos-Terrones; Ana M Soto Estrada; Jonathan O Vicente Escobar; Mario A Romero Romo; Jorge Uruchurtu; Carmina Menchaca; Juan M Esparza Schulz; Armando Domínguez
Journal:  ChemistryOpen       Date:  2018-11-28       Impact factor: 2.911

5.  Non-covalent interactions between sertraline stereoisomers and 2-hydroxypropyl-β-cyclodextrin: a quantum chemistry analysis.

Authors:  Joanatan-Michael Bautista-Renedo; Erick Cuevas-Yañez; Horacio Reyes-Pérez; Rubicelia Vargas; Jorge Garza; Nelly González-Rivas
Journal:  RSC Adv       Date:  2020-05-27       Impact factor: 3.361

  5 in total

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