Parallel Smoothed Aggregation Multilevel Schwarz Preconditioned Newton-Krylov Algorithms for Poisson-Boltzmann Problems

We study a multilevel Schwarz preconditioned Newton-Krylov algorithm to solve the Poisson-Boltzmann equation with applications in multi-particle colloidal simulation. The smoothed aggregation-type coarse mesh space is introduced in collaboration with the one-level Schwarz method as a composite preconditioner for accelerating the convergence of a Krylov subspace method for solving the Jacobian system at each Newton step. The important feature of the proposed solution algorithm is that the geometric mesh information needed for constructing the multilevel preconditioner is the same as the one-level Schwarz method on the fine mesh. Other components, such as the definition of the coarse mesh, all the mesh transfer operators, and the coarse mesh problem, are taken care of by the Trillinos/ML packages of the Sandia National Laboratories in the United States. After algorithmic parameter tuning, we show that the proposed smoothed aggregation multilevel Newton-Krylov-Schwarz (NKS) algorithm numerically outperforms than smoothed aggregation multigrid method and one-level version of the NKS algorithm with satisfactory parallel performances up to a few thousand cores. Besides, we investigate how the electrostatic forces between particles for the separation distance depend on the radius of spherical colloidal particles and valence ratios of cation and anion in a cubic system.     

A conservative parallel difference method for 2-dimension diffusion equation

In this paper, a conservative parallel difference scheme, which is based on domain decomposition method, for 2-dimension diffusion equation is proposed. In the construction of this scheme, we use the numerical solution on the previous time step to give a weighted approximation of the numerical flux. Then the sub-problems with Neumann boundary are computed by fully implicit scheme. What is more, only local message communication is needed in the program. We use the method of discrete functional analysis to give the proof of the unconditional stability and second-order convergence accuracy. Some numerical tests are given to verify the theory results.     

A parallel multiple reference point approach for multi-objective optimization

This paper presents a multiple reference point approach for multi-objective optimization problems of discrete and combinatorial nature. When approximating the Pareto Frontier, multiple reference points can be used instead of traditional techniques. These multiple reference points can easily be implemented in a parallel algorithmic framework. The reference points can be uniformly distributed within a region that covers the Pareto Frontier. An evolutionary algorithm is based on an achievement scalarizing function that does not impose any restrictions with respect to the location of the reference points in the objective space. Computational experiments are performed on a bi-objective flow-shop scheduling problem. Results, quality measures as well as a statistical analysis are reported in the paper.     

A minimum distance estimator in an imprecise probability model - Computational aspects and applications

The article considers estimating a parameter θ in an imprecise probability model which consists of coherent upper previsions . After the definition of a minimum distance estimator in this setup and a summarization of its main properties, the focus lies on applications. It is shown that approximate minimum distances on the discretized sample space can be calculated by linear programming. After a discussion of some computational aspects, the estimator is applied in a simulation study consisting of two different models. Finally, the estimator is applied on a real data set in a linear regression model.     

陀螺特征值问题的并行子空间迭代法

<正>1引言陀螺系统特征值问题是转子动力学中的基本问题,是一类特殊的二次特征值问题.假设M和K是n阶对称矩阵,C是n阶反对称矩阵,则二次特征值问题(λ~2M+λC+K)x=0(1)     

An inexact parallel splitting augmented Lagrangian method for large system of linear equations

Parallel iterative methods are powerful in solving large systems of linear equations (LEs). The existing parallel computing research results focus mainly on sparse systems or others with particular structure. Most are based on parallel implementation of the classical relaxation methods such as Gauss-Seidel, SOR, and AOR methods which can be efficiently carried out on multiprocessor system. In this paper, we propose a novel parallel splitting operator method in which we divide the coefficient matrix into two or three parts. Then we convert the original problem (LEs) into a monotone (linear) variational inequality problem (VI) with separable structure. Finally, an inexact parallel splitting augmented Lagrangian method is proposed to solve the variational inequality problem (VI). To avoid dealing with the matrix inverse operator, we introduce proper inexact terms in subproblems such that the complexity of each iteration of the proposed method is O(n²). In addition, the proposed method does not require any special structure of system of LEs under consideration. Convergence of the proposed methods in dealing with two and three separable operators respectively, is proved. Numerical computations are provided to show the applicability and robustness of the proposed methods.     

组合几何蒙特卡罗粒子输运支撑软件框架JCOGIN介绍

介绍了JCOGIN支撑软件框架层次式、模块化的体系结构及其核心数据结构。这些使得JCOGIN软件框架能够支撑大规模复杂几何的蒙特卡罗（MC）粒子输运并行计算。同时介绍了在JCOGIN支撑软件框架下研发的JMCT程序,并进行了性能测试,在2万处理器核上模拟20亿粒子,并行效率达到70%。     

Simulation of electronic structure Hamiltonians using quantum computers

Over the last century, a large number of physical and mathematical developments paired with rapidly advancing technology have allowed the field of quantum chemistry to advance dramatically. However, the lack of computationally efficient methods for the exact simulation of quantum systems on classical computers presents a limitation of current computational approaches. We report, in detail, how a set of pre-computed molecular integrals can be used to explicitly create a quantum circuit, i.e. a sequence of elementary quantum operations, that, when run on a quantum computer, obtains the energy of a molecular system with fixed nuclear geometry using the quantum phase estimation algorithm. We extend several known results related to this idea and discuss the adiabatic state preparation procedure for preparing the input states used in the algorithm. With current and near future quantum devices in mind, we provide a complete example using the hydrogen molecule of how a chemical Hamiltonian can be simulated using a quantum computer.     

Users,Programmers, and Statistical Software

Abstract

Statistical software provides essential support for statisticians and others who are analyzing data or doing research on new statistical techniques. Those supported typically regard themselves as “users” of the software, but as soon as they need to express their own ideas computationally, they in fact become “programmers.” Nothing is more important for the success of statistical software than enabling this transition from user to programmer, and on to gradually more ambitious software design. What does the user need? How can the design of statistical software help? This article presents a number of suggestions based on past experience and current research. The evolution of the S system reflects some of these opinions. Work on the Omegahat software provides a promising direction for future systems that reflect similar motivations.     

Parallel Markov chain Monte Carlo Simulation by Pre-Fetching

In recent years, parallel processing has become widely available to researchers. It can be applied in an obvious way in the context of Monte Carlo simulation, but techniques for “parallelizing” Markov chain Monte Carlo (MCMC) algorithms are not so obvious, apart from the natural approach of generating multiple chains in parallel. Although generation of parallel chains is generally the easiest approach, in cases where burn-in is a serious problem, it is often desirable to use parallelization to speed up generation of a single chain. This article briefly discusses some existing methods for parallelization of MCMC algorithms, and proposes a new “pre-fetching” algorithm to parallelize generation of a single chain.