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Design and Implementation of an Extended Collectives Library for Unified Parallel C

journal of Computer Science & Technology 2013年第1期28卷 72-89页

作者： Carlos Teijeiro Guillermo L.Taboada juan Tourio Ramón Doallo jos C.Mourio Damivn A.Mallón Brian Wibecan Computer Architecture Group University of A Corua Galicia supercomputing center jlich supercomputing Centre Institute for Advanced SimulationForschungszentrum Jlich Industry Standard Servers Group Hewlett-Packard Company

Unified Parallel C （UPC） is a parallel extension of ANSI C based on the Partitioned Global Address Space （PGAS） programming model, which provides a shared memory view that simplifies code development while it can take advantage of the scalability of distributed memory architectures. Therefore, UPC allows programmers to write parallel applications on hybrid shared/distributed memory architectures, such as multi-core clusters, in a more productive way, accessing remote memory by means of different high-level language constructs, such as assignments to shared variables or collective primitives. However, the standard UPC collectives library includes a reduced set of eight basic primitives with quite limited functionality. This work presents the design and implementation of extended UPC collective functions that overcome the limitations of the standard collectives library, allowing, for example, the use of a specific source and destination thread or defining the amount of data transferred by each particular thread. This library fulfills the demands made by the UPC developers community and implements portable algorithms, independent of the specific UPC compiler/runtime being used. The use of a representative set of these extended collectives has been evaluated using two applications and four kernels as case studies. The results obtained confirm the suitability of the new library to provide easier programming without trading off performance, thus achieving high productivity in parallel programming to harness the performance of hybrid shared/distributed memory architectures in high performance computing.

关键词： Unified Parallel C collective operation programmability partitioned global address space high performance computing

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Trends in the hyperfine interactions of magnetic adatoms on thin insulating layers

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npj Computational Materials 2021年第1期7卷 787-796页

作者： Sufyan Shehada Manuel dos Santos Dias Filipe Souza Mendes Guimarães Muayad Abusaa Samir Lounis Peter Grünberg Institut and Institute for Advanced Simulation Forschungszentrum Jülich&JARAJülichGermany Department of Physics RWTH Aachen UniversityAachenGermany jülich supercomputing center Forschungszentrum Jülich&JARAJülichGermany Department of Physics Arab American UniversityJeninPalestine Faculty of Physics University of Duisburg-Essen&CENIDEDuisburgGermany

Nuclear spins are among the potential candidates prospected for quantum information technology.A recent breakthrough enabled to atomically resolve their interaction with the electron spin,the so-called hyperfine interaction,within individual atoms utilizing scanning tunneling microscopy(STM).Intriguingly,this was only realized for a few species put on a two-layers thick ***,we systematically quantify from first-principles the hyperfine interactions of the whole series of 3d transition adatoms deposited on various thicknesses of MgO,NaF,NaCl,h–BN,and Cu2N *** identify the adatom-substrate complexes with the largest hyperfine interactions and unveil the main trends and *** reveal the core mechanisms at play,such as the interplay of the local bonding geometry and the chemical nature of the thin films,which trigger transitions between high-and low-spin states accompanied with subtle internal rearrangements of the magnetic *** providing a general map of hyperfine interactions,our work has immediate implications in future STM investigations aiming at detecting and realizing quantum concepts hinging on nuclear spins.

关键词： quantum utilizing breakthrough

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The AiiDA-KKR plugin and its application to highthroughput impurity embedding into a topological insulator

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npj Computational Materials 2021年第1期7卷 108-116页

作者： Philipp Rüßmann Fabian Bertoldoand Stefan Blügel Peter Grünberg Institut and Institute for Advanced Simulation Forschungszentrum Jülich and JARAD-52425 JülichGermany

The ever increasing availability of supercomputing resources led computer-based materials science into a new era of highthroughput ***,Pizzi et *** the AiiDA framework that provides a way to automate calculations while allowing to store the full provenance of complex workflows in a *** present the development of the AiiDA-KKR plugin that allows to perform a large number of ab initio impurity embedding calculations based on the relativistic full-potential Korringa-Kohn-Rostoker Green function *** capabilities of the AiiDA-KKR plugin are demonstrated with the calculation of several thousand impurities embedded into the prototypical topological insulator *** results are collected in the juDiT database which we use to investigate chemical trends as well as Fermi level and layer dependence of physical properties of *** includes the study of spin moments,the impurity’s tendency to form in-gap states or its effect on the charge doping of the *** properties depend on the detailed electronic structure of the impurity embedded into the host crystal which highlights the need for ab initio calculations in order to get accurate predictions.

关键词： method topological embedding

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On the friction and adhesion hysteresis between polymer brushes attached to curved surfaces: Rate and solvation effects

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Friction 2015年第2期3卷 148-160页

作者： Sissi de BEER G.DjuidjéKENMOÉ Martin H.MÜSER Materials Science and Technology of Polymers MESA+Institute for NanotechnologyUniversity of TwenteP.O.Box 2177500 AE Enschedethe Netherlands jülich supercomputing Centre Institute for Advanced Simulation FZ jülich 52425 JülichGermany Department of Physics Laboratory of Mechanics Faculty of ScienceUniversity of YaoundéP.O.Box 812YaoundéCameroon

Computer simulations of friction between polymer brushes are usually simplified compared to real systems in terms of solvents and *** most simulations,the solvent is only implicit with infinite compressibility and zero *** addition,the model geometries are parallel walls rather than curved or rough as in *** this work,we study the effects of these approximations and more generally the relevance of solvation on dissipation in polymer-brush systems by comparing simulations based on different solvation *** find that the rate dependence of the energy loss during the collision of brush-bearing asperities can be different for explicit and implicit ***,the non-Newtonian rate dependences differ noticeably between normal and transverse motion,i.e.,between head-on and off-center asperity ***,when the two opposing brushes are made immiscible,the friction is dramatically reduced compared to an undersaturated miscible polymer-brush system,irrespective of the sliding direction.

关键词： polymer brushes biomimetic materials molecular dynamics simulation

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Three-dimensional Numerical Simulation of Viscoelastic Phase Separation under Shear: the Roles of Bulk and Shear Relaxation Moduli

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Chinese journal of Polymer Science 2015年第11期33卷 1562-1573页

作者： jing-yi Chen Zhong jin 杨科大 School of Materials Science and Engineering Beihang University supercomputing center Computer Network Information Center Chinese Academy of Sciences

The morphological, dynamic and rheological characteristics in the viscoelastic phase separation（VPS） of sheared polymer solutions are investigated by three-dimensional（3D） numerical simulations of viscoelastic model. The simulations are accelerated by graphic process unit（GPU） to break through the limitation of computation power. Firstly, the morphological and dynamic characteristics of VPS under shear are presented by comparing with those in classic phase separation（CPS）. The results show that the phase inversion and phase shrink take place in VPS under shear. Then, the roles of bulk and shear relaxation moduli in VPS are investigated in details. The bulk relaxation modulus slows down the phase separation process under shear, but not affects the dynamic path of VPS. The dynamic path can be divided into three stages： freezing stage, growth stage and stable stage. The second overshoot phenomenon in the shear stress is observed, and explained by the breakdown and reform of string structures. The shear modulus affects morphology evolution in the late stage of VPS under shear.

关键词： Viscoelastic model Phase separation Polymer solution Shear

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Parallel computing approach for efficient 3-D X-ray-simulated image reconstruction

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Nuclear Science and Techniques 2023年第7期34卷 122-136页

作者： Ou-Yi Li Yang Wang Qiong Zhang Yong-Hui Li University of Electronic Science and Technology of China Chengdu 610000China National supercomputing center in Chengdu Chengdu 610041China

Accurate 3-dimensional(3-D)reconstruction technology for nondestructive testing based on digital radiography(DR)is of great importance for alleviating the drawbacks of the existing computed tomography(CT)-based *** commonly used Monte Carlo simulation method ensures well-performing imaging results for ***,for 3-D reconstruction,it is limited by its high time *** solve this problem,this study proposes a parallel computing method to accelerate Monte Carlo simulation for projection images with a parallel interface and a specific DR *** images are utilized for 3-D reconstruction of the test *** verify the accuracy of parallel computing for DR and evaluate the performance of two parallel computing modes-multithreaded applications(G4-MT)and message-passing interfaces(G4-MPI)-by assessing parallel speedup and *** study explores the scalability of the hybrid G4-MPI and G4-MT *** results show that the two parallel computing modes can significantly reduce the Monte Carlo simulation time because the parallel speedup increment of Monte Carlo simulations can be considered linear growth,and the parallel efficiency is maintained at a high *** hybrid mode has strong scalability,as the overall run time of the 180 simulations using 320 threads is 15.35 h with 10 billion particles emitted,and the parallel speedup can be up to *** 3-D reconstruction of the model is achieved based on the filtered back projection(FBP)algorithm using 180 projection images obtained with the hybrid G4-MPI and *** quality of the reconstructed sliced images is satisfactory because the images can reflect the internal structure of the test *** method is applied to a complex model,and the quality of the reconstructed images is evaluated.

关键词： Parallel computing Monte Carlo Digital radiography 3-D reconstruction

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Comparisons of three data storage models in parametric temporal databases

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journal of Central South University 2013年第7期20卷 1919-1927页

作者： Seo-Young NOH Shashi K. GADIA Haengjin jANG supercomputing center Korea Institute of Science and Technology Information Department of Computer Science Iowa State University

The parametric temporal data model captures a real world entity in a single tuple, which reduces query language complexity. Such a data model, however, is difficult to be implemented on top of conventional databases because of its unfixed attribute sizes. XML is a matured technology and can be an elegant solution for such challenge. Representing data in XML trigger a question about storage efficiency. The goal of this work is to provide a straightforward answer to such a question. To this end, we compare three different storage models for the parametric temporal data model and show that XML is not worse than any other approaches. Furthermore, XML outperforms the other storages under certain conditions. Therefore, our simulation results provide a positive indication that the myth about XML is not true in the parametric temporal data model.

关键词： data representation parametric data model XML-based representation

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AINV AND BILUM PRECONDITIONING TECHNIQUES

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Applied Mathematics and Mechanics(English Edition) 2004年第9期25卷 1012-1021页

作者：谷同祥迟学斌刘兴平 Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics supercomputing center of Computer Network Information center Chinese Academy of Science

It was proposed that a robust and efficient parallelizable preconditioner for solving general sparse linear systems of equations, in which the use of sparse approximate inverse (AINV) techniques in a multi-level block ILU (BILUM) preconditioner were investigated. The resulting preconditioner retains robustness of BILUM preconditioner and has two advantages over the standard BILUM preconditioner: the ability to control sparsity and increased parallelism. Numerical experiments are used to show the effectiveness and efficiency of the new preconditioner.

关键词： sparse matrix preconditioning technique BILUM AINV Krylov subspace method

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Multi-hybrid method for investigation of EM scattering from inhomogeneous object above a dielectric rough surface

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Science China(Physics,Mechanics & Astronomy) 2012年第10期55卷 1781-1790页

作者： LI jie GUO LiXin HE Qiong WEI Bing School of Science Xidian UniversityXi'an 710071China National supercomputing center in Shenzhen Shenzhen 518055China

An iterative strategy combining Kirchhoff approximation （KA） method is presented in this paper to study the interactions between KA is applied to study scattering from underlying rough surfaces with the hybrid finite element-boundary integral （FE-BI） the inhomogeneous object and the underlying rough surface. whereas FE-BI deals with scattering from the above target. Both two methods use updated excitation sources. Huygens equivalence principle and an iterative strategy are employed to consider the multi-scattering effects. This hybrid FE-BI-KA scheme is an improved and generalized version of previous hybrid Kirchhoff approximation-method of moments （KA-MoM）. This newly presented hybrid method has the following advantages：（1） the feasibility of modeling multi-scale scattering problems （large scale underlying surface and small scale target）; （2） low memory requirement as in hybrid KA-MoM; （3） the ability to deal with scattering from inhomogeneous （including coated or layered） scatterers above rough surfaces. The numerical results are given to evaluate the accuracy of the multi-hybrid technique; the computing time and memory requirements consumed in specific numerical simulation of FE-BI-KA are compared with those of MoM. The convergence performance is analyzed by studying the iteration number variation caused by related parameters. Then bistatic scattering from inhomogeneous object of different configurations above dielectric Gaussian rough surface is calculated and the influences of dielectric compositions and surface roughness on the scattering pattern are discussed.

关键词： electromagnetic scattering hybrid method rough surface inhomogeneous target

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Counterfactual Definiteness and Bell’s Inequality

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journal of Modern Physics 2016年第13期7卷 1651-1660页

作者： Karl Hess Hans De Raedt Kristel Michielsen center for Advanced Study University of Illinois Urbana IL USA Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands Institute for Advanced Simulation Jülich Supercomputing Centre Jülich Germany RWTH Aachen University Aachen Germany

Counterfactual definiteness must be used as at least one of the postulates or axioms that are necessary to derive Bell-type inequalities. It is considered by many to be a postulate that not only is commensurate with classical physics (as for example Einstein’s special relativity), but also separates and distinguishes classical physics from quantum mechanics. It is the purpose of this paper to show that Bell’s choice of mathematical functions and independent variables implicitly includes counterfactual definiteness. However, his particular choice of variables reduces the generality of his theory, as well as the physics of all Bell-type theories, so significantly that no meaningful comparison of these theories with actual Einstein-Podolsky-Rosen experiments can be made.

关键词： Foundations of Quantum Mechanics Foundations of Probability Bell Inequality

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