共查询到20条相似文献,搜索用时 15 毫秒
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Omar Awile Ferit Büyükkeçeci Sylvain Reboux Ivo F. Sbalzarini 《Computer Physics Communications》2012,183(5):1073-1081
Particle methods provide a simple yet powerful framework for simulating both discrete and continuous systems either deterministically or stochastically. The inherent adaptivity of particle methods is particularly appealing when simulating multiscale models or systems that develop a wide spectrum of length scales. Evaluating particle–particle interactions using neighbor-finding algorithms such as cell lists or Verlet lists, however, quickly becomes inefficient in adaptive-resolution simulations where the interaction cutoff radius is a function of space. We present a novel adaptive-resolution cell list algorithm and the associated data structures that provide efficient access to the interaction partners of a particle, independent of the (potentially continuous) spectrum of cutoff radii present in a simulation. We characterize the computational cost of the proposed algorithm for a wide range of resolution spans and particle numbers, showing that the present algorithm outperforms conventional uniform-resolution cell lists in most adaptive-resolution settings. 相似文献
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Yousuke Ohno Rio Yokota Hiroshi Koyama Gentaro Morimoto Aki Hasegawa Gen Masumoto Noriaki Okimoto Yoshinori Hirano Huda Ibeid Tetsu Narumi Makoto Taiji 《Computer Physics Communications》2014
In this paper, we report all-atom simulations of molecular crowding — a result from the full node simulation on the “K computer”, which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are “crowded” because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the “K computer”, we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the “K computer”, as well as comparisons with Ewald summation methods. 相似文献
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Jon A. Solworth 《The Journal of supercomputing》1988,2(3):331-347
A data structure called strips is described for representing linked lists, which enables unit time access of random list elements. Running parallel prefix on strips effectively converts a list into an array. When combined with nondeterministic statement sequencing and data operations, loops for performing iterations over lists, and insertions and deletions on lists can be parallelized yielding very efficient algorithms. The strips-based representation also allows efficient serial operations on lists, which is important both when loops cannot be parallelized or when there is more parallelism than processors.This work was supported in part under ONR Grant N00014-86-K-0215 and under NSF Grant DCR-8503610. 相似文献
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D.C. Rapaport 《Computer Physics Communications》2006,174(7):521-529
Progress in adapting molecular dynamics algorithms for systems with short-range interactions to utilize the features of modern supercomputers is described. Efficient utilization of the latest generation of processor architectures requires algorithms that can be both vectorized and parallelized. The approach adopted for vectorization involves combining the layer and neighbor-list methods, while parallelization employs spatial subdivision with explicit communication. The techniques presented here have been used in performance tests on the Cray X1 vector-parallel supercomputer with systems containing over 12 billion atoms. 相似文献
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Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters 总被引:4,自引:0,他引:4
Liu Peng Manaschai Kunaseth Hikmet Dursun Ken-ichi Nomura Weiqiang Wang Rajiv K. Kalia Aiichiro Nakano Priya Vashishta 《The Journal of supercomputing》2011,58(1):20-33
Many computer vision applications, such as object recognition and content-based image retrieval could function more reliably
and effectively if regions of interest were isolated from their background. A new method for regions of interest extraction
from color image based on visual saliency in HSV color space is proposed in this paper. Color saliency is calculated by a
two-dimensional sigmoid function using the saturation component and brightness component, and we can identify regions with
vivid color. Discrete Moment Transform (DMT)-based saliency can determine large areas of interest. A visual saliency map is
obtained by combining color saliency and DMT-based saliency, which is denoted the S image. A criterion for the local homogeneity called the E image is calculated in the image. Based on S image and E image, the high visual saliency object seed points set and low visual saliency object seed points set are determined. The
seeded regions growing and merging are used to extract regions of interest. Experimental results demonstrate the effectiveness
and efficiency of the method for the natural color images. 相似文献
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Modern computers provide excellent opportunities for performing fast computations. They are equipped with powerful microprocessors and large memories. However, programs are not necessarily able to exploit those computer resources effectively. In this paper, we present the way in which we have implemented a nearest neighbor classification. We show how performance can be improved by exploiting the ability of superscalar processors to issue multiple instructions per cycle and by using the memory hierarchy adequately. This is accomplished by the use of floating-point arithmetic which usually outperforms integer arithmetic, and block (tiled) algorithms which exploit the data locality of programs allowing for an efficient use of the data stored in the cache memory. Our results are validated with both an analytical model and empirical results. We show that regular codes could be performed faster than more complex irregular codes using standard data sets. 相似文献
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Establishing the neighbor list to efficiently calculate the inter-atomic forces consumes the majority of computation time in molecular dynamics (MD) simulation. Several algorithms have been proposed to improve the computation efficiency for short-range interaction in recent years, although an optimized numerical algorithm has not been provided. Based on a rigorous definition of Verlet radius with respect to temperature and list-updating interval in MD simulation, this paper has successfully developed an estimation formula of the computation time for each MD algorithm calculation so as to find an optimized performance for each algorithm. With the formula proposed here, the best algorithm can be chosen based on different total number of atoms, system average density and system average temperature for the MD simulation. It has been shown that the Verlet Cell-linked List (VCL) algorithm is better than other algorithms for a system with a large number of atoms. Furthermore, a generalized VCL algorithm optimized with a list-updating interval and cell-dividing number is analyzed and has been verified to reduce the computation time by 30∼60% in a MD simulation for a two-dimensional lattice system. Due to similarity, the analysis in this study can be extended to other many-particle systems. 相似文献
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A linear-scaling algorithm has been developed to perform large-scale molecular-dynamics (MD) simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory. A divide-and-conquer algorithm is used to compute the electronic structure, where non-additive contribution to the kinetic energy is included with an embedded cluster scheme. Electronic wave functions are represented on a real-space grid, which is augmented with coarse multigrids to accelerate the convergence of iterative solutions and adaptive fine grids around atoms to accurately calculate ionic pseudopotentials. Spatial decomposition is employed to implement the hierarchical-grid algorithm on massively parallel computers. A converged solution to the electronic-structure problem is obtained for a 32,768-atom amorphous CdSe system on 512 IBM POWER4 processors. The total energy is well conserved during MD simulations of liquid Rb, showing the applicability of this algorithm to first principles MD simulations. The parallel efficiency is 0.985 on 128 Intel Xeon processors for a 65,536-atom CdSe system. 相似文献
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A parallel molecular dynamics simulation method, designed for large-scale problems, employing dynamic spatial domain decomposition for short-ranged molecular interactions is proposed. In this parallel cellular molecular dynamics (PCMD) simulation method, the link-cell data structure is used to reduce the searching time required for forming the cut-off neighbor list as well as for domain decomposition, which utilizes the multi-level graph-partitioning technique. A simple threshold scheme (STS), in which workload imbalance is monitored and compared with some threshold value during the runtime, is proposed to decide the proper time for repartitioning the domain. The simulation code is implemented and tested on the memory-distributed parallel machine, e.g., PC-cluster system. Parallel performance is studied using approximately one million L-J atoms in the condensed, vaporized and supercritical states. Results show that fairly good parallel efficiency at 49 processors can be obtained for the condensed and supercritical states (∼60%), while it is comparably lower for the vaporized state (∼40%). 相似文献
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Paolo Barletta 《Computer Physics Communications》2011,(2):388-399
COOL is a program to simulate evaporative and sympathetic cooling for a mixture of two gases co-trapped in a harmonic potential. The collisions involved are assumed to be exclusively elastic, and losses are due to evaporation from the trap. Each particle is followed individually in its trajectory, consequently properties such as spatial densities or energy distributions can be readily evaluated. The code can be used sequentially, by employing one output as input for another run. The code can be easily generalised to describe more complicated processes, such as the inclusion of inelastic collisions, or the possible presence of more than two species in the trap.
Program summary
Program title: COOLCatalogue identifier: AEHJ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHJ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 1 111 674No. of bytes in distributed program, including test data, etc.: 18 618 045Distribution format: tar.gzProgramming language: C++Computer: DesktopOperating system: LinuxRAM: 500 MbytesClassification: 16.7, 23Nature of problem: Simulation of the sympathetic process occurring for two molecular gases co-trapped in a deep optical trap.Solution method: The Direct Simulation Monte Carlo method exploits the decoupling, over a short time period, of the inter-particle interaction from the trapping potential. The particle dynamics is thus exclusively driven by the external optical field. The rare interparticle collisions are considered with an acceptance/rejection mechanism, that is by comparing a random number to the collisional probability defined in terms of the inter-particle cross section and centre-of-mass energy. All particles in the trap are individually simulated so that at each time step a number of useful quantities, such as the spatial densities or the energy distributions, can be readily evaluated.Restrictions: The in-trap motion of the particles is treated classically.Running time: The running time is relatively short, 1–2 hours. However it is convenient to replicate each simulation several times with different initialisations of the random sequence. 相似文献12.
Lupo JA Wang Z McKenney AM Pachter R Mattson W 《Journal of molecular graphics & modelling》2002,21(2):89-99
We present the performance of the fast classical molecular dynamics (MD) code, fast molecular dynamics (FMD), designed for efficient, object-oriented, and scalable large scale simulations, and summarize its application to a liquid crystalline cluster. FMD uses an implementation of the three-dimensional fast multipole method, developed in our group. The fast multipole method offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus, enabling more realistic simulations of large molecular systems. Performance testing was carried out on IBM SP2, SGI Origin 2000, and CRAY T3E massively parallel systems using the MPI massage passing library. The electrostatic forces were tested on models of up to 100,000 randomly placed charges, and on protein and liquid crystalline molecular systems of over 99,000 atoms. Tests on the stability of the method are presented, along with comparisons with direct calculations, the NAMD2 code, and the physical multipole-based cell-multipole method. 相似文献
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Yang Qifen Li Ziyang Han Gang Gao Wanyi Zhu Shuhua Wu Xiaotian Deng Yuhui 《The Journal of supercomputing》2022,78(12):14597-14625
The Journal of Supercomputing - Spectral clustering algorithm has become more popular in data clustering problems in recent years, due to the idea of optimally dividing the graph to solve the data... 相似文献
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The k nearest neighbor is a lazy learning algorithm that is inefficient in the classification phase because it needs to compare the query sample with all training samples. A template reduction method is recently proposed that uses only samples near the decision boundary for classification and removes those far from the decision boundary. However, when class distributions overlap, more border samples are retrained and it leads to inefficient performance in the classification phase. Because the number of reduced samples are limited, using an appropriate feature reduction method seems a logical choice to improve classification time. This paper proposes a new prototype reduction method for the k nearest neighbor algorithm, and it is based on template reduction and ViSOM. The potential property of ViSOM is displaying the topology of data on a two-dimensional feature map, it provides an intuitive way for users to observe and analyze data. An efficient classification framework is then presented, which combines the feature reduction method and the prototype selection algorithm. It needs a very small data size for classification while keeping recognition rate. In the experiments, both of synthetic and real datasets are used to evaluate the performance. Experimental results demonstrate that the proposed method obtains above 70 % speedup ratio and 90 % compression ratio while maintaining similar performance to kNN. 相似文献
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A domain decomposition algorithm for molecular dynamics simulation of atomic and molecular systems with arbitrary shape and non-periodic boundary conditions is described. The molecular dynamics program uses cell multipole method for efficient calculation of long range electrostatic interactions and a multiple time step method to facilitate bigger time steps. The system is enclosed in a cube and the cube is divided into a hierarchy of cells. The deepest level cells are assigned to processors such that each processor has contiguous cells and static load balancing is achieved by redistributing the cells so that each processor has approximately same number of atoms. The resulting domains have irregular shape and may have more than 26 neighbors. Atoms constituting bond angles and torsion angles may straddle more than two processors. An efficient strategy is devised for initial assignment and subsequent reassignment of such multiple-atom potentials to processors. At each step, computation is overlapped with communication greatly reducing the effect of communication overhead on parallel performance. The algorithm is tested on a spherical cluster of water molecules, a hexasaccharide and an enzyme both solvated by a spherical cluster of water molecules. In each case a spherical boundary containing oxygen atoms with only repulsive interactions is used to prevent evaporation of water molecules. The algorithm shows excellent parallel efficiency even for small number of cells/atoms per processor. 相似文献
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We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. 相似文献
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Single walled carbon nanotubes as all-carbon molecules of tubular form exemplify modern nanometre scale material structures, where the number of atoms range from less than a million up to few millions. Such system are quite ideal for computational studies like Molecular Dynamics simulations because the studies can be done at the realistic limit, rendering them in a way predictive. This point of view we try to explore through simulations of novel ring-like carbon nanotubes, observed experimentally. Whether these structures are toroidal or coiled is under debate. To this question we seek insight by studying the structure, the minimum energy configuration, and the thermal stability of large toroidal nanotubes of (n,n)- and (n,0)-helicity using large scale Molecular Dynamics simulations based on the interaction potential by Brenner. The system sizes of the studied tori range one and half orders of magnitude, in diameter from about 22 nm up to 700 nm, where the latter corresponds to the sizes of experimentally observed ring-like structures. Our simulations indicate that the toroidal form influences strongly the structure of the tubes for small tori while for the larger tori the structural changes are extremely small. We also find that there exists a critical tube radius dependent buckling radius at which the torus buckles. This was also found to be helicity dependent. 相似文献
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To get an insight into the effects of molecular architecture in the behaviour of thin lubricant films we have devised an algorithm for simulation of branched molecules. We have used this algorithm successfully to simulate branched isomers of C30. However the algorithm is flexible enough to be used for the simulation of more complex branched molecules. The resulting algorithm can be used in molecular dynamics simulation of branched molecules and could be helpful in designing new materials at the molecular level. 相似文献
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具有良好的低温流动性是生物柴油的重要特性之一,而这一性质与系统的凝点相关联.本文以硬脂酸甲酯、油酸甲酯等7种常见生物柴油组成分子为研究对象,通过建模构建了7种单组份生物柴油分子的模拟液态模型.利用分子动力学方法对7种液态模型系统的凝固过程进行了研究.采用PCFF力场,在一定的模拟条件下,对系统进行逐次降温分子动力学模拟.根据分子动力学轨迹,计算了不同温度下系统的热容、碳原子自扩散系数以及分子链的头尾距.模拟计算得到的液态热容合理.利用“热容法”和“扩散系数法”对不同系统的凝点进行判断,发现凝点区间基本一致,且与实际凝点基本相吻合.而采用2种区间交集的方法得到的凝点区间则与实际凝点十分相近.以油酸甲酯为例,模拟观察到,随着温度降低,分子链总体呈伸展趋势,符合热力学基本原理.在油酸甲酯的凝点前后,链长及链的微观结构存在明显差异.模拟结果表明,本实验方法对研究生物柴油分子系统确实有效. 相似文献