Study of preconditioners based on Markov Chain Monte Carlo methods

Nowadays, analysis and design of novel scalable methods and algorithms for fundamental linear algebra problems such as solving Systems of Linear Algebraic Equations with focus on large scale systems is a subject of study. This research focuses on the study of novel mathematical methods and scalable algorithms for computationally intensive problems such as Monte Carlo and Hybrid Methods and Algorithms

Enhanced goal-oriented error assessment and computational strategies in adaptive reduced basis solver for stochastic problems

This work focuses on providing accurate low-cost approximations of stochastic ¿nite elements simulations in the framework of linear elasticity. In a previous work, an adaptive strategy was introduced as an improved Monte-Carlo method for multi-dimensional large stochastic problems. We provide here a complete analysis of the method including a new enhanced goal-oriented error estimator and estimates of CPU (computational processing unit) cost gain. Technical insights of these two topics are presented in details, and numerical examples show the interest of these new developments.Postprint (author's final draft

On the impact of three dimensional radiative transfer on cloud evolution

The goal of this study is to gain insight into cloud-radiative feedback mechanisms and what role three-dimensional radiative transfer effects play in the evolution of convective clouds. The usually employed one-dimensional radiative transfer solvers neglect any horizontal energy transfer and thereby introduce considerable errors in surface and atmospheric heating rates. While fully three-dimensional radiative transfer solvers exist, they are several orders of magnitude too slow. In conclusion, so far, there is no straightforward solution that would solve the task at hand — namely, compute accurate three-dimensional radiative heating rates in the atmosphere — fast enough to be coupled interactively to a cloud resolving model. This thesis presents a new method — the TenStream solver — that provides a fast yet accurate approximation for three-dimensional heating rates. The TenStream is furthermore integrated into the University of California, Los Angeles large-eddy simulation (UCLA-LES) cloud-resolving model. This setup allows to study the effects of three-dimensional radiative heating on the evolution of clouds. The TenStream method extends the well-known one-dimensional two-stream theory to 10 streams. The new solver significantly reduces the root mean square error for atmospheric heating and surface heating rates when compared to traditionally employed one-dimensional solvers. In the case of a cumulus cloud field and the solar zenith angle being 60 ◦ , the error is reduced from 178 % to 31 %. Parallel scalability was a primary concern developing the TenStream solver. This thesis documents the overall performance of the solver as well as the technical challenges of migrating from 1-D schemes to 3-D schemes. To understand the performance characteristics of the TenStream solver, weak as well as strong-scaling experiments are conducted. In this context, two matrix preconditioner are investigated: geometric algebraic multigrid preconditioning (GAMG) and block Jacobi incomplete LU (ILU) factorization and it is found that algebraic multigrid preconditioning performs well for complex scenes and highly parallelized simulations. The TenStream solver is tested on several state of the art super-computers for up to 4096 cores and shows a parallel scaling efficiency of 80 % to 90 %. The central part of this thesis examines the influence of three-dimensional radiative transfer effects on the development of convective cumulus clouds. The influence is tested on short time scales of a single convective warm-bubble and over a longer period of time and a reasonably large domain for shallow cumulus clouds. The directionality of the direct solar beam introduces an asymmetry in the atmospheric heating of the convective motion and tilts the updraft. While a cloud’s shadow is always directly beneath itself in a one-dimensional radiative transfer solver. In contrast, the TenStream solver correctly displaces the shadowy region according to the sun’s zenith angle. The constant supply of warm and moist air due to the local heating in the updraft region beneath the cloud, prolongs the cloud’s lifetime by a factor of two and generally increases cloud development. The influence of three-dimensional heating on the evolution of clouds shows to be persistent even in the presence of a horizontal wind. The results presented here motivate further research in the field of cloud- radiative feedbacks and their role in weather and climate prediction simulations

Parallel Selected Inversion for Space-Time Gaussian Markov Random Fields

Performing a Bayesian inference on large spatio-temporal models requires extracting inverse elements of large sparse precision matrices for marginal variances. Although direct matrix factorizations can be used for the inversion, such methods fail to scale well for distributed problems when run on large computing clusters. On the contrary, Krylov subspace methods for the selected inversion have been gaining traction. We propose a parallel hybrid approach based on domain decomposition, which extends the Rao-Blackwellized Monte Carlo estimator for distributed precision matrices. Our approach exploits the strength of Krylov subspace methods as global solvers and efficiency of direct factorizations as base case solvers to compute the marginal variances using a divide-and-conquer strategy. By introducing subdomain overlaps, one can achieve a greater accuracy at an increased computational effort with little to no additional communication. We demonstrate the speed improvements on both simulated models and a massive US daily temperature data.Comment: 17 pages, 7 figure

Compressive sensing Petrov-Galerkin approximation of high-dimensional parametric operator equations

We analyze the convergence of compressive sensing based sampling techniques for the efficient evaluation of functionals of solutions for a class of high-dimensional, affine-parametric, linear operator equations which depend on possibly infinitely many parameters. The proposed algorithms are based on so-called "non-intrusive" sampling of the high-dimensional parameter space, reminiscent of Monte-Carlo sampling. In contrast to Monte-Carlo, however, a functional of the parametric solution is then computed via compressive sensing methods from samples of functionals of the solution. A key ingredient in our analysis of independent interest consists in a generalization of recent results on the approximate sparsity of generalized polynomial chaos representations (gpc) of the parametric solution families, in terms of the gpc series with respect to tensorized Chebyshev polynomials. In particular, we establish sufficient conditions on the parametric inputs to the parametric operator equation such that the Chebyshev coefficients of the gpc expansion are contained in certain weighted $\ell_p$-spaces for $0<p\leq 1$. Based on this we show that reconstructions of the parametric solutions computed from the sampled problems converge, with high probability, at the $L_2$, resp. $L_\infty$ convergence rates afforded by best $s$-term approximations of the parametric solution up to logarithmic factors.Comment: revised version, 27 page

Problems in Lattice Gauge Fixing

We review many topics and results about numeric gauge fixing in lattice QCD.Comment: 47 pages, 16 eps figures. Review article sent to IJMP

큰 그래프 상에서의 개인화된 페이지 랭크에 대한 빠른 계산 기법

학위논문 (박사) -- 서울대학교 대학원 : 공과대학 전기·컴퓨터공학부, 2020. 8. 이상구.Computation of Personalized PageRank (PPR) in graphs is an important function that is widely utilized in myriad application domains such as search, recommendation, and knowledge discovery. Because the computation of PPR is an expensive process, a good number of innovative and efficient algorithms for computing PPR have been developed. However, efficient computation of PPR within very large graphs with over millions of nodes is still an open problem. Moreover, previously proposed algorithms cannot handle updates efficiently, thus, severely limiting their capability of handling dynamic graphs. In this paper, we present a fast converging algorithm that guarantees high and controlled precision. We improve the convergence rate of traditional Power Iteration method by adopting successive over-relaxation, and initial guess revision, a vector reuse strategy. The proposed method vastly improves on the traditional Power Iteration in terms of convergence rate and computation time, while retaining its simplicity and strictness. Since it can reuse the previously computed vectors for refreshing PPR vectors, its update performance is also greatly enhanced. Also, since the algorithm halts as soon as it reaches a given error threshold, we can flexibly control the trade-off between accuracy and time, a feature lacking in both sampling-based approximation methods and fully exact methods. Experiments show that the proposed algorithm is at least 20 times faster than the Power Iteration and outperforms other state-of-the-art algorithms.그래프 내에서 개인화된 페이지랭크 (P ersonalized P age R ank, PPR 를 계산하는 것은 검색 , 추천 , 지식발견 등 여러 분야에서 광범위하게 활용되는 중요한 작업 이다 . 개인화된 페이지랭크를 계산하는 것은 고비용의 과정이 필요하므로 , 개인화된 페이지랭크를 계산하는 효율적이고 혁신적인 방법들이 다수 개발되어왔다 . 그러나 수백만 이상의 노드를 가진 대용량 그래프에 대한 효율적인 계산은 여전히 해결되지 않은 문제이다 . 그에 더하여 , 기존 제시된 알고리듬들은 그래프 갱신을 효율적으로 다루지 못하여 동적으로 변화하는 그래프를 다루는 데에 한계점이 크다 . 본 연구에서는 높은 정밀도를 보장하고 정밀도를 통제 가능한 , 빠르게 수렴하는 개인화된 페이지랭크 계산 알고리듬을 제시한다 . 전통적인 거듭제곱법 (Power 에 축차가속완화법 (Successive Over Relaxation) 과 초기 추측 값 보정법 (Initial Guess 을 활용한 벡터 재사용 전략을 적용하여 수렴 속도를 개선하였다 . 제시된 방법은 기존 거듭제곱법의 장점인 단순성과 엄밀성을 유지 하면서 도 수렴율과 계산속도를 크게 개선 한다 . 또한 개인화된 페이지랭크 벡터의 갱신을 위하여 이전에 계산 되어 저장된 벡터를 재사용하 여 , 갱신 에 드는 시간이 크게 단축된다 . 본 방법은 주어진 오차 한계에 도달하는 즉시 결과값을 산출하므로 정확도와 계산시간을 유연하게 조절할 수 있으며 이는 표본 기반 추정방법이나 정확한 값을 산출하는 역행렬 기반 방법 이 가지지 못한 특성이다 . 실험 결과 , 본 방법은 거듭제곱법에 비하여 20 배 이상 빠르게 수렴한다는 것이 확인되었으며 , 기 제시된 최고 성능 의 알고리 듬 보다 우수한 성능을 보이는 것 또한 확인되었다1 Introduction 1 2 Preliminaries: Personalized PageRank 4 2.1 Random Walk, PageRank, and Personalized PageRank. 5 2.1.1 Basics on Random Walk 5 2.1.2 PageRank. 6 2.1.3 Personalized PageRank 8 2.2 Characteristics of Personalized PageRank. 9 2.3 Applications of Personalized PageRank. 12 2.4 Previous Work on Personalized PageRank Computation. 17 2.4.1 Basic Algorithms 17 2.4.2 Enhanced Power Iteration 18 2.4.3 Bookmark Coloring Algorithm. 20 2.4.4 Dynamic Programming 21 2.4.5 Monte-Carlo Sampling. 22 2.4.6 Enhanced Direct Solving 24 2.5 Summary 26 3 Personalized PageRank Computation with Initial Guess Revision 30 3.1 Initial Guess Revision and Relaxation 30 3.2 Finding Optimal Weight of Successive Over Relaxation for PPR. 34 3.3 Initial Guess Construction Algorithm for Personalized PageRank. 36 4 Fully Personalized PageRank Algorithm with Initial Guess Revision 42 4.1 FPPR with IGR. 42 4.2 Optimization. 49 4.3 Experiments. 52 5 Personalized PageRank Query Processing with Initial Guess Revision 56 5.1 PPR Query Processing with IGR 56 5.2 Optimization. 64 5.3 Experiments. 67 6 Conclusion 74 Bibliography 77 Appendix 88 Abstract (In Korean) 90Docto

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie