Large scale petroleum reservoir simulation and parallel preconditioning algorithms research

Solving large scale linear systems efficiently plays an important role in a petroleum reservoir simulator, and the key part is how to choose an effective parallel preconditioner. Properly choosing a good preconditioner has been beyond the pure algebraic field. An integrated preconditioner should include such components as physical background, characteristics of PDE mathematical model, nonlinear solving method, linear     

清华物理系量子信息研究的新进展

在清华大学物理系成立60周年之际,我们对近年来清华大学物理系量子信息研究的主要进展情况作一介绍,包括量子搜索算法研究,核磁共振量子计算的实验研究,量子通讯的理论与实验研究.在量子搜索算法研究方面,我们提出了量子搜索算法的相位匹配,纠正了当时的一种错误观点,并且提出了一种成功率为100%的量子搜索算法,改进了Grover算法;在核磁共振量子计算实验方面,我们实现了2到7个量子比特的多种量子算法的实验演示;在量子通讯方面,我们提出了分布式传输的量子通讯的思想,应用于量子密钥分配、量子秘密共享、量子直接安全通讯等方面,构造了多个量子通讯的理论方案.在实验室,我们实现了2米距离的空间量子密码通讯的演示实验.     

A two-stage parallel branch and bound algorithm for mixed integer programs

Mixed integer programming (MIP) models are extensively usedto aid strategic and tactical decision making in many businesssectors. Solving MIP models is a computationally intensive processand there is a need to develop solution approaches that enablelarger models to be solved within acceptable timeframes. Inthis paper, we describe the implementation of a two-stage parallelbranch and bound (PB & B) algorithm for MIP. In stage 1of the algorithm, a multiple heuristic search is implementedin which a number of alternative search trees are investigatedusing a forest search in the hope of finding a good solutionquickly. In stage 2, the search is reorganized so that the branchesof a chosen tree are investigated in parallel. A new heuristicis introduced, based on a best projection criterion, which evaluatesalternative B & B trees in order to choose one for investigationin stage 2 of the algorithm. The heuristic also serves as away of implementing a quality load balancing scheme for stage2 of the algorithm. The results of experimental investigationsare reported for a range of models taken from the MIPLIB libraryof benchmark problems.     

A comparison of two algorithms for the assignment problem

State-of-the-art computational results have shown that the shortest augmenting path (SAP) methods are more efficient than other primal-dual and primal-simplex based methods for solving the linear assignment problem on uniprocessor computers. There is, however, some controversy concerning their merits when compared with Bertsekas' auction algorithm on multiprocessor computers. In this study we investigate the performance of these competing methods on the Alliant FX/8. For each method, theoretical motivation, sources of parallelism and computational results are presented.     

Solving large-scale semidefinite programs in parallel

We describe an approach to the parallel and distributed solution of large-scale, block structured semidefinite programs using the spectral bundle method. Various elements of this approach (such as data distribution, an implicitly restarted Lanczos method tailored to handle block diagonal structure, a mixed polyhedral-semidefinite subdifferential model, and other aspects related to parallelism) are combined in an implementation called LAMBDA, which delivers faster solution times than previously possible, and acceptable parallel scalability on sufficiently large problems. This work was supported in part by NSF grants DMS-0215373 and DMS-0238008.     

论浮力的计算

通过讨论物体下表面不与液体接触时浮力的计算,总结浮力计算的一般方法.     

Computing Aviation Sparing Policies: Solving a Large Nonlinear Integer Program

Deployed US Navy aircraft carriers must stock a large number of spare parts to support the various types of aircraft embarked on the ship. The sparing policy determines the spares that will be stocked on the ship to keep the embarked aircraft ready to fly. Given a fleet of ten or more aircraft carriers and a cost of approximately 50 million dollars per carrier plus the cost of spares maintained in warehouses in the United States, the sparing problem constitutes a significant portion of the Navy’s resources. The objective of this work is to find a minimum-cost sparing policy that meets the readiness requirements of the embarked aircraft. This is a very large, nonlinear, integer optimization problem. The cost function is piecewise linear and convex while the constraint mapping is highly nonlinear. The distinguishing characteristics of this problem from an optimization viewpoint are that a large number of decision variables are required to be integer and that the nonlinear constraint functions are essentially “black box” functions; that is, they are very difficult (and expensive) to evaluate and their derivatives are not available. Moreover, they are not convex. Integer programming problems with a large number of variables are difficult to solve in general and most successful approaches to solving nonlinear integer problems have involved linear approximation and relaxation techniques that, because of the complexity of the constraint functions, are inappropriate for attacking this problem. We instead employ a pattern search method to each iteration of an interior point-type algorithm to solve the relaxed version of the problem. From the solution found by the pattern search on each interior point iteration, we begin another pattern search on the integer lattice to find a good integer solution. The best integer solution found across all interations is returned as the optimal solution. The pattern searches are distributed across a local area network of non-dedicated, heterogeneous computers in an office environment, thus, drastically reducing the time required to find the solution.     

Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.