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1.
The family of expectation--maximization (EM) algorithms provides a general approach to fitting flexible models for large and complex data. The expectation (E) step of EM-type algorithms is time-consuming in massive data applications because it requires multiple passes through the full data. We address this problem by proposing an asynchronous and distributed generalization of the EM called the distributed EM (DEM). Using DEM, existing EM-type algorithms are easily extended to massive data settings by exploiting the divide-and-conquer technique and widely available computing power, such as grid computing. The DEM algorithm reserves two groups of computing processes called workers and managers for performing the E step and the maximization step (M step), respectively. The samples are randomly partitioned into a large number of disjoint subsets and are stored on the worker processes. The E step of DEM algorithm is performed in parallel on all the workers, and every worker communicates its results to the managers at the end of local E step. The managers perform the M step after they have received results from a γ-fraction of the workers, where γ is a fixed constant in (0, 1]. The sequence of parameter estimates generated by the DEM algorithm retains the attractive properties of EM: convergence of the sequence of parameter estimates to a local mode and linear global rate of convergence. Across diverse simulations focused on linear mixed-effects models, the DEM algorithm is significantly faster than competing EM-type algorithms while having a similar accuracy. The DEM algorithm maintains its superior empirical performance on a movie ratings database consisting of 10 million ratings. Supplementary material for this article is available online.  相似文献   
2.
The paper focuses on the development of a numerical code for the computation of basins of attraction by using the parallel programming. Two different approaches based on the massage passing interface (MPI) standard are presented; the performance analysis presented encourages us to use a massive communication between nodes only for a few-cores architecture. The critical issues arising from the study of a generic dynamical system are discussed while the computation of basins is performed on a benchmark system described by Duffing׳s equation. We paid attention at the optimization of the computing time as well as the work time load on each node in order to develop a performing and portable code. For the presented codes, both the scalability with an implementation on a professional cluster and the capabilities of the parallelism in the elaborations of basins with a large set of initial conditions have been tested.  相似文献   
3.
A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster‐type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re‐docking of X‐ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 Å. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. © 2013 Wiley Periodicals, Inc.  相似文献   
4.
针对ADS颗粒靶概念的研究和设计,中国科学院近代物理研究所自主研发了蒙特卡罗模拟软件GMT。为了提高GMT程序的计算效率,研究了MPI在GMT中的应用和发展,实现了大规模随机数在进程中的随机分配,并采用快速读写文件的方式替代了MPI相关数据通信函数,极大地提高了计算效率。并研究了不同规模计算实例进程数、加速比、效率之间的关系,确定了最大加速进程数及并行效率最高时的进程数,为科研工作者在计算资源和计算效率之间选择最优计算方案提供了科学依据。MPI在GMT中的成功应用使计算资源得到了充分、高效的利用,极大地提高了计算效率,解决了蒙特卡罗方法中大规模事件模拟计算时间长、计算不稳定等问题,在散裂靶大规模扫描计算中发挥了重要的作用。For the research and design of the ADS granular-flow target concept, the Institute of Modern Physics, CAS has developed a Monte Carlo simulation software (GPU-accelerated Monte Carlo Transport program, GMT). In order to improve the computational efficiency of the GMT program, development and application of MPI in GMT were studied, to realize random distribution of the large-scale random number in the sub processes. Rapid reading and writing files were employed instead of the MPI data communication function, which greatly improves the computational efficiency. Different scale calculations were performed to study the relationship of process instance number, speedup to find the maximum acceleration process number and the number of processes when parallel efficiency is highest, which provides a scientific basis for researchers to optimize the computational program between computational resources and computation efficiency. The successful application of MPI in GMT, utilizes the computing resources fully and efficiently, improves the computational efficiency, solve the long time cost and unstable problem of Monte Carlo method in large-scale event simulations, plays an important role in the large-scale scanning calculation of the spallation target.  相似文献   
5.
Nowadays, high performance computing (HPC) systems experience a disruptive moment with a variety of novel architectures and frameworks, without any clarity of which one is going to prevail. In this context, the portability of codes across different architectures is of major importance. This paper presents a portable implementation model based on an algebraic operational approach for direct numerical simulation (DNS) and large eddy simulation (LES) of incompressible turbulent flows using unstructured hybrid meshes. The strategy proposed consists in representing the whole time-integration algorithm using only three basic algebraic operations: sparse matrix–vector product, a linear combination of vectors and dot product. The main idea is based on decomposing the nonlinear operators into a concatenation of two SpMV operations. This provides high modularity and portability. An exhaustive analysis of the proposed implementation for hybrid CPU/GPU supercomputers has been conducted with tests using up to 128 GPUs. The main objective consists in understanding the challenges of implementing CFD codes on new architectures.  相似文献   
6.
三维爆炸与冲击问题的大规模高性能计算研究   总被引:1,自引:1,他引:0  
爆炸与冲击问题常常涉及到材料的大变形、多种物质交界面处理及各种强间断的处理,对此类问题采用Euler方法具有显著的优势.对于Euler方法的并行计算,由于在扰动未到达之前某些网格的物理量是不发生变化的,采用固定分区方法并行策略容易出现负载不均衡,且计算效率不高.为解决这一问题,采用动态并行策略,即计算域随着扰动传播而扩充,并采用国际上通用的MPI并行模式设计出相应的动态并行程序.从程序测试结果来看,动态并行程序结果与原有并行程序结果一致,且与实际情况也是一致的.  相似文献   
7.
分布式系统上并行矩阵乘法   总被引:9,自引:0,他引:9  
1.引言矩阵乘法是最简单的数学问题,同时由于其计算量大而通常被用来对计算机的浮点运算速度进行测试,尤其是对于并行计算机,其并行效率的好坏可通过这个简单的问题反应出来,如果在这个问题上都不能取得很好的效果,对于其它问题就更不可能.此外,为了提高计算性能,对求解数值代数中的问题最终会归结到有矩阵乘法的计算,如LAPACK,ScaLAPACK等,因此有效地并行计算矩阵乘法在实际应用中是非常重要的.矩阵乘法是做C=A×B,其中A是m×k阵,B是k×n阵,C是m×n阵.设矩阵A,B可以分成p×p块矩阵,即A=(Ai,j)p×p,B=(B…  相似文献   
8.
基于混合网格Navier-Stokes方程的并行隐式计算方法研究   总被引:2,自引:0,他引:2  
针对结构网格很难处理复杂外形和非结构网格无法计算具有边界层的粘性流动的缺点,发展了基于混合网格格点的隐式算法,成功地解决了在工程应用中难于处理的复杂外形粘性流场计算和效率问题。同时针对大规模的工程问题,发展了基于MPI通信技术的染色分层通讯并行计算方法。其中空间离散采用基于Roe格式发展的三阶迎风HLLEW(Harten-Lax-Van Leer-Einfeldt-Wada)或AUSM格式,湍流模型采用k??两方程湍流模型,时间推进考虑到LU-SGS并行等效较困难则采用基于DP-LUR(Data-Parallel Lower-Upper Relaxation)格式的隐式算法,计算CFL数可取到105量级,从2个到128个CPU的并行加速效率都保持在90%以上,大大提高了计算效率。算例对标模M6机翼模型流场进行计算,验证了方法的可靠性;然后对标模DLR-F6翼身组合体进行混合网格粘性与无粘计算结果进行比较,进一步验证混合网格方法;最后计算了DLR-WBNP外挂发动机翼身组合体模型,准确模拟了外挂和超临界机翼的相互干扰流动问题,采用4 CPU 16 CORE到24 CPU 96 CORE,2000步计算时间都不超...  相似文献   
9.
Events with a large transverse momentum (>1 GeV/c) pion or nucleon have been selected from the data of a high-statistics pp bubble chamber experiment (√s=6.84 GeV). Only events in which all secondary particles could be identified were used. One finds that fewer pions are produced in the azimuthal hemisphere containing the large transverse momentum particle than in the opposite hemisphere. An indication for coplanarity is found. Most pions associated with a large transverse momentum pion are emitted with small absolute c.m. rapidities, whereas those associated with large transverse momentum nucleons show some back-to-back structure. Various results of this investigation are similar to those obtained at the ISR. Most of the findings are compatible with predictions from an independent emission model.  相似文献   
10.
In this paper the methods of wave theory based prestack depth migration and their implementation are studied. Using the splitting of wave operator, the wavefield extrapolation equations are deduced and the numerical schemes are presented. The numerical tests for SEG/EAEG model with MPI are performed on the PC-cluster. The numerical re-  相似文献   
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