Article
Computer Science, Information Systems
Chanyoung Oh, Saehanseul Yi, Jongkyu Seok, Hyeonjin Jung, Illo Yoon, Youngmin Yi
Summary: This paper proposes a CPU-GPU hybrid scheduling algorithm in Hadoop that fully utilizes the CPU and GPU in a node in an adaptive manner, with the help of a GPU monitor to adjust the Container number. Experimental results show that the proposed scheduling algorithm achieves an average speedup of 3.87x compared to a CPU-only Hadoop.
CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS
(2023)
Article
Chemistry, Physical
Ji Qi, Yingfeng Zhang, Minghui Yang
Summary: The calculation of two-electron repulsion integrals (ERIs) is crucial in Hartree-Fock calculations. A hybrid CPU/GPU method has been proposed to accelerate the computation and improve efficiency, especially for ERIs with varying angular momentum.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Computer Science, Information Systems
Fei Yin, Feng Shi
Summary: This paper integrates the Kriging proxy model and energy efficiency modeling method into a cluster optimization algorithm of CPU and GPU hybrid architecture, proposing a parallel computing model for large-scale CPU/GPU heterogeneous high-performance computing systems and providing algorithm optimization for CPU/GPU heterogeneous clusters. The experimental results show significant speedup ratios for constructing the Kriging proxy model and the search algorithm, demonstrating the high feasibility of this heterogeneous cluster optimization algorithm.
CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS
(2022)
Article
Computer Science, Hardware & Architecture
R. Acosta-Quinonez, D. Torres-Roman, R. Rodriguez-Avila
Summary: Efficient prototyping tools can reduce design and validation efforts for enterprises and research centers, leading to shorter time-to-market and increased competitiveness. By implementing high-performance software libraries in a modular way, it is possible to quickly compare prototype designs under different criteria and improve throughput and reusability.
JOURNAL OF SYSTEMS ARCHITECTURE
(2021)
Article
Computer Science, Artificial Intelligence
Jose J. Calvino, Elena Fernandez, Miguel Lopez-Haro, Juan M. Munoz-Ocana, Antonio M. Rodriguez-Chia
Summary: This paper introduces an l(1)-norm model based on Total Variation Minimization for tomographic reconstruction. The reconstructions produced by this model are more accurate than classical reconstruction models based on the l(2)-norm. The model can be linearized and solved using linear programming, and the dimension of the formulation can be further reduced by exploiting complementary slackness conditions.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Computer Science, Interdisciplinary Applications
Jakub Skrzypczak, Pawel Czarnul
Summary: In this paper, we introduce a modern and efficient parallel OpenMP+CUDA implementation for hybrid CPU+GPU systems, and demonstrate its superior performance compared to CPU-only and GPU-only implementations for various problem sizes. We investigate the impact of tile sizes and CPU-GPU load balancing settings on performance, and analyze the execution time based on the number of agents and CUDA streams used. The design and implementation of the algorithm, including CPU computational threads, GPU management threads, task assignment, and memory utilization, are discussed for maximizing performance.
SIMULATION MODELLING PRACTICE AND THEORY
(2023)
Article
Mathematics, Applied
Remy Dubois, Eric Goncalves da Silva, Philippe Parnaudeau
Summary: SCB is an efficient fluid solver developed for computing two-phase compressible flows involving strong shocks and expansion waves. It solves a four-equation diffuse-interface model using explicit time stepping. The solver uses a fully parallel environment via MPI and presents a hybrid parallelization strategy based on MPI library and OpenACC.
COMPUTERS & MATHEMATICS WITH APPLICATIONS
(2021)
Article
Computer Science, Software Engineering
Vasyl Skorych, Maksym Dosta
Summary: The efficiency of simulations using the discrete element method (DEM) has been significantly improved with a novel computational strategy that focuses on parallel execution on both CPU and GPU, resulting in decreased computational time and more efficient utilization of available resources. Furthermore, the overall energy requirement for this strategy does not exceed that of conventional sequential CPU-GPU computations.
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2022)
Article
Engineering, Multidisciplinary
Sophia B. Coban, William R. B. Lionheart, Philip J. Withers
Summary: The paper discusses the performance assessment of CT reconstruction algorithms and introduces a evaluation technique called physical quantification, which measures the features of the test object to assess the reconstruction efficacy. The study highlights the importance of choosing the optimal reconstruction strategy based on the features extracted from the scan.
MEASUREMENT SCIENCE AND TECHNOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
Sambit Das, Phani Motamarri, Vishal Subramanian, David M. Rogers, Vikram Gavini
Summary: DFT-FE 1.0 is an improved version of DFT-FE 0.6, which allows for fast and accurate large-scale DFT calculations on various computing architectures. The improvements include enhanced treatment of electrostatic interactions and GPU acceleration. The method has been shown to be accurate and efficient in benchmark systems.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Gaogao Liu, Wenbo Yang, Peng Li, Guodong Qin, Jingjing Cai, Youming Wang, Shuai Wang, Ning Yue, Dongjie Huang
Summary: This paper focuses on the time division signal processing flow for MIMO radar and proposes an improved algorithm to enhance its processing speed. A parallel simulation system based on CPU/GPU architecture is introduced, which performs significantly faster than serial computing equipment and achieves satisfactory acceleration effects.
Article
Computer Science, Interdisciplinary Applications
Andrey Gorobets, Pavel Bakhvalov
Summary: This paper presents a heterogeneous parallel algorithm and its software implementation for simulating compressible turbulent flows. The algorithm is based on a family of higher accuracy edge-based reconstruction schemes on unstructured mixed-element meshes. The parallel solution can utilize a large number of computing devices on various computing architectures, including manycore CPUs and GPUs. The paper provides a detailed description of the parallel algorithm and its efficient implementation, as well as demonstrations of parallel performance on different supercomputers.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Computer Science, Information Systems
Juan Fang, Kuan Zhou, Mengyuan Zhang, Wei Xiang
Summary: This paper focuses on the utilization and efficiency of heterogeneous cores in heterogeneous systems and designs reasonable resource scheduling strategies. The combination strategy and the multi-task scheduling strategy proposed in this study improve system performance and resource utilization.
CMC-COMPUTERS MATERIALS & CONTINUA
(2022)
Article
Computer Science, Interdisciplinary Applications
W. Trojak, F. D. Witherden
Summary: A novel inline data compression method for single-precision vectors in three dimensions is presented, achieving a fixed compression ratio of 1.5. Numerical evaluation within the context of high-order computational fluid dynamics shows results comparable to those without compression. Performance evaluation on an NVIDIA Titan V GPU demonstrates a 1.5x speedup can be achieved.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Engineering, Multidisciplinary
Shengquan Wang, Yujie Wang, Shuai Zhang, Yong Cai, Guangyao Li, Hao Zheng
Summary: A heterogeneous parallel computing method for solving 3D transient nonlinear thermomechanical problems is proposed based on CPU-GPU platforms. The method utilizes the stable node-based smoothed finite element method (SNS-FEM) and element-by-element (EBE) strategy, and incorporates a series of parallel computing strategies to improve computational efficiency, achieving accurate and efficient computation.
ENGINEERING ANALYSIS WITH BOUNDARY ELEMENTS
(2023)
Article
Plant Sciences
Francisco Marquez-Garcia, David Garcia-Alonso, Maria Josefa Guerra-Barrena, Francisco Maria Vazquez-Pardo
Summary: The HSS herbarium database contains a vast number of vascular plant classification records, covering the majority of specimens, with a concentration in the southwest quadrant of the Iberian Peninsula. Nearly all of these records have been georeferenced.
Article
Biodiversity Conservation
Lucia D. Moreyra, Francisco Marquez, Alfonso Susanna, Nuria Garcia-Jacas, Francisco Maria Vazquez, Jordi Lopez-Pujol
Summary: Within the genus Centaurea L., polyploidy is common and believed to play a key role in diversification and evolution. In this study, molecular markers and environmental niche modeling were used to suggest that Centaurea tentudaica likely originated from Centaurea amblensis. The analysis supports the hypothesis of autopolyploidy, showing a close relationship between the two species.
Article
Biochemistry & Molecular Biology
Gines Avila-Perez, Maria Teresa Rejas, Francisco Javier Chichon, Milagros Guerra, Jose Jesus Fernandez, Dolores Rodriguez
Summary: This study used electron tomography to characterize the replication organelles of toroviruses, revealing the formation of a reticulovesicular network in BEV-infected cells. The outer membranes of DMVs were found to be interconnected with each other and with the ER, with paired ER membranes likely representing early structures that evolve into DMVs. Late-stage paired membranes forming small spherule-like invaginations were also observed, showing similarities but also differences with true spherules described for coronaviruses.
MOLECULAR MICROBIOLOGY
(2022)
Article
Computer Science, Interdisciplinary Applications
V. Gonzalez-Ruiz, J. P. Garcia-Ortiz, M. R. Fernandez-Fernandez, J. J. Fernandez
Summary: In this study, an Optical Flow (OF)-driven interpolation strategy was developed to address the significant changes between consecutive images in FIB-SEM stacks. The approach compensated for variations by aligning the spatial regions of the biological structures using OF, resulting in sharp interpolated images. The OF-driven interpolation outperformed classical interpolation methods and produced isotropic resolution in anisotropic data.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Computer Science, Interdisciplinary Applications
Jose -Jesus Fernandez, A. Martinez-Sanchez
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Plant Sciences
Carlos Vila-Vicosa, Jorge Capelo, Paulo Alves, Rubim Almeida, Francisco Maria Vazquez
Summary: We conducted a thorough taxonomical and nomenclatural review of Portuguese oaks, utilizing various data sources such as biogeographical information, historical records, bibliographic sources, field surveys, and herbarium collections. Our study resulted in a new annotated checklist of Quercus taxa and nothotaxa found in Portugal, as well as an understanding of their broader biogeographical context in the Western Mediterranean subregion. We discovered 11 native oaks, one subspecies, and 23 additional nothotaxa, and designated lectotypes for 27 names. Furthermore, we proposed the recognition of Q. pseudococcifera and Q. airensis as native oaks in the Western Mediterranean subregion, provided updates on Q. faginea, and introduced new subsections within Section Quercus.
MEDITERRANEAN BOTANY
(2023)
Article
Microscopy
V. Gonzalez-Ruiz, M. R. Fernandez-Fernandez, J. J. Fernandez
Summary: FIB-SEM is an imaging technique that allows 3D ultra-structural analysis of cells and tissues at the nanoscale. Our study developed a new approach to structure-preserving noise reduction, which combines the simplicity of Gaussian filtering with the adaptability to biological structures. The results showed that our denoising approach outperforms standard Gaussian filtering and is competitive with state-of-the-art methods in terms of noise reduction and preservation of structure sharpness.
Article
Computer Science, Theory & Methods
F. Orts, A. M. Puertas, G. Ortega, E. M. Garzon
Summary: This paper introduces quantum computing and focuses on adiabatic quantum computing as a quantum programming model. It has been successfully applied in solving problems like graph partitioning, traffic routing, and task scheduling. Specifically, the paper discusses the scheduling of unrelated parallel machines and extends the model to consider task priorities and delays. The proposed quantum nonlinear programming framework solves the Quadratic Unconstrained Binary Optimization problem on the D-Wave platform. It also utilizes compact models to handle larger scheduling problems and estimates the required qubits based on scheduling parameters.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2023)
Article
Chemistry, Physical
F. Orts, M. Maier, M. Fuchs, G. Ortega, E. M. Garzon, A. M. Puertas
Summary: The dynamics of a tracer particle in a bath of quasi-hard colloidal spheres is investigated using Langevin dynamics simulations and mode coupling theory. The study reveals that the size of the tracer particle has a significant impact on its motion, as well as on the dynamics of the bath particles.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Computer Science, Software Engineering
Vicente Gonzalez-Ruiz, Jose-Jesus Fernandez
Summary: FlowDenoising is a software tool that utilizes an adaptive Gaussian denoising filter to preserve visually appreciable structures in 3D electron microscopy volumes. It achieves this by nonrigidly aligning 2D slices in each dimension using an optical flow estimator, followed by applying a standard separable Gaussian filter. Developed in Python, FlowDenoising makes use of well-known public domain libraries like OpenCV and NumPy. It also utilizes data-level parallelism to greatly reduce processing times, allowing for efficient denoising of large volumes on standard multicore computers. It proves to be a valuable tool in 3DEM for exploring the interior of cells and tissues at the nanoscale.
Article
Optics
F. Orts, E. Filatovas, G. Ortega, J. F. SanJuan-Estrada, E. M. Garzon
Summary: This paper presents a circuit design for multiplication of two integers, using only Clifford +T gates for compatibility with error detection and correction codes. The circuit outperforms the state-of-the-art circuits in terms of T count and T depth.
Article
Computer Science, Information Systems
Luis O. Lopez, Gloria Ortega, Francisco Aguera-Vega, Fernando Carvajal-Ramirez, Patricio Martinez-Carricondo, Ester M. Garzon
Summary: A new methodology for improving herbicide assessment efficiency is presented, which involves an automatic tool to quantify the percentage of weeds and sunflowers in a given area. Images captured by the Sequoia camera are used, and the quality of each band's images is enhanced. The resulting multispectral images are then classified into soil, sunflower, and weed categories using a novel algorithm implemented in e-Cognition software. The classification results are compared with two deep learning-based segmentation methods (U-Net and FPN).
Proceedings Paper
Computer Science, Interdisciplinary Applications
Savins Puertas-Martin, Juana L. Redondo, Ester M. Garzon, Horacio Perez-Sanchez, Pilar M. Ortigosa
Summary: OptiPharm is a new software that optimizes the similarity of molecules and competes well with other algorithms. However, all methods, including OptiPharm, assuming proteins as rigid can lead to inaccurate predictions. This study extends OptiPharm's functionality by considering molecular flexibility, introducing improvements that enhance prediction accuracy.
BIOINFORMATICS AND BIOMEDICAL ENGINEERING, PT II
(2022)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Francisco Orts, Gloria Ortega, Ester M. Garzon
Summary: This paper analyses the known techniques for constructing multi-qubit Toffoli gates and the latest designs for the 2-qubit version. It focuses on the construction of a temporary logical-AND gate with more than two control qubits. The results are presented in comparative tables to facilitate researchers and interested individuals in choosing the design that suits their needs.
COMPUTATIONAL SCIENCE, ICCS 2022, PT IV
(2022)
Article
Plant Sciences
Carlos Vila-Vicosa, Cristiana Vieira, Francisco Marquez, Rubim Almeida, Francisco Maria Vazquez
Summary: This study assessed the naming of three western Mediterranean oak species through a comprehensive examination of specimens and analysis of original descriptions. The results highlight the importance of conducting extensive natural history and classic herbaria surveys to further discuss and understand species delimitation and biogeographic awareness.
MEDITERRANEAN BOTANY
(2022)
Article
Microscopy
C. Gao, C. Hofer, T. J. Pennycook
Summary: Ptychography provides high dose efficiency images that can reveal light elements next to heavy atoms. However, contrast reversals can occur when the projected potential becomes strong. Recent research has shown that these reversals can be counteracted by adapting the focus. This study explains why the best contrast is often found with the probe focused to the middle of the sample and highlights the importance of convergence angle in thin samples to remove contrast reversals.
Article
Microscopy
J. Lindner, U. Ross, T. Meyer, V. Boureau, M. Seibt, Ch. Jooss
Summary: Phase-shifting electron holography is an excellent method with high phase sensitivity to reveal electron wave phase information. An advanced drift correction scheme is proposed in this study, which exploits the interface of the TEM specimen and the vacuum area in the hologram. This method allows for obtaining reliable phase information.
Article
Microscopy
Ali Jaberi, Nicolas Brodusch, Jun Song, Raynald Gauvin
Summary: This study investigates knock-on damage in lithium-ion batteries (LIBs) by computing threshold displacement energies (TDEs) and performing Monte Carlo simulation. The results indicate that Li is most sensitive to knock-on damage at moderate electron energies, and TDE is the principal parameter for assessing Li sensitivity to knock-on damage across similar structures.
Article
Microscopy
Alexander Schroeder, Christopher Rathje, Leon van Velzen, Maurits Kelder, Sascha Schaefer
Summary: This study utilizes novel event-based electron detector platforms to extend the temporal resolution of electron microscopy. By training a neural network to predict electron arrival time, the researchers were able to improve the timing accuracy and achieve a promising solution for enhancing electron timing precision in various electron microscopy applications.
Article
Microscopy
Avi Auslender, Nivedita Pandey, Amit Kohn, Oswaldo Dieguez
Summary: This article describes a faster implementation based on DFT for computing the mean inner potential of crystals, providing quantum-mechanical calculations beyond the independent-atom approximation. The study also reveals the dependence of the mean inner potential on sample boundary conditions, mass density, and magnetic susceptibility, highlighting its correlation with various material properties.
Article
Microscopy
Zhidong Yang, Dawei Zang, Hongjia Li, Zhao Zhang, Fa Zhang, Renmin Han
Summary: In this work, we propose a self-supervised deep learning model for cryo-ET volumetric image denoising based on noise modeling and sparsity guidance. Experimental results demonstrate that our method can achieve reliable denoising by training on single noisy volume and outperform existing methods.
Article
Microscopy
J. Kuttruff, J. Holder, Y. Meng, P. Baum
Summary: In this study, a robust clustering algorithm is proposed that can find clusters in a continuous stream of raw data in real time. This algorithm converts pixel hits measured by hybrid pixel detectors to real single-electron events. By continuously comparing with previous hits, the algorithm efficiently identifies the merging of new and old events.
Article
Microscopy
D. G. Senturk, C. P. Yu, A. De Backer, S. Van Aert
Summary: This article presents a statistics-based method for accurately counting the number of atoms in nanostructures, especially for images acquired with low electron doses and multiple element structures.
Article
Microscopy
Mauricio J. Prieto, Lucas de Souza Caldas, Liviu C. Tanase, Thomas Schmidt, Oscar Rodriguez de la Fuente
Summary: This study presents a synchrotron-based investigation of the synthesis process of a magnetite/hematite bilayer. Ion bombardment gradually transforms hematite into magnetite, and the growth of magnetite leads to the formation of stable boundaries. These findings are significant for understanding novel oxide heterostructures.
Article
Microscopy
Emre Yoruk, Holger Klein, Stephanie Kodjikian
Summary: Beam sensitive nanomaterials pose challenges for crystallographic structure determination. A dose symmetric electron diffraction tomography (DS-EDT) method is developed to reduce beam damage and obtain complete data sets by merging individual datasets from multiple crystals.
Article
Microscopy
A. Pofelski, Y. Zhu, G. A. Botton
Summary: The precision and sensitivity of the GPA method for strain characterization is a widely discussed topic. This study introduces the concept of phase noise and analyzes the parameter of sampling to improve the precision of GPA. Experimental and theoretical results demonstrate that using a larger pixel spacing in STEM can enhance the precision and sensitivity of the GPA method.
Article
Microscopy
Sangjun Kang, Di Wang, Christian Kuebel, Xiaoke Mu
Summary: Transmission electron microscopy is a valuable tool for assessing strain fields within materials. However, using thin specimens in TEM analysis can affect atomic configuration and deformation structure.
