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MOLLER-PLESSET (MP2) PERTURBATION-THEORY FOR LARGE MOLECULES

THEORETICA CHIMICA ACTA 1993年第1-2期87卷 147-173页

作者： HASER, M Institut für Physikalische Chemie Lehrstuhl für Theoretische Chemie Universität Karlsruhe Karlsruhe Germany

A novel formulation of MP2 theory is presented which starts from the Laplace transform MP2 ansatz, and subsequently moves from a molecular orbital (MO) representation to an atomic orbital (AO) representation. Consequently, the new formulation is denoted AO-MP2. As in traditional MP2 approaches electron repulsion integrals still need to be transformed. Strict bounds on the individual MP2 energy contribution of each intermediate four-index quantity allow to screen off numerically insignificant integrals with a single threshold parameter. Implicit in our formulation is a bound to two-particle density matrix elements. For small molecules the computational cost for AO-MP2 calculations is about a factor of 100 higher than for traditional MO-based approaches, but due to screening the computational effort in larger systems will only grow with the fourth power of the size of the system (or less) as is demonstrated both in theory and in application. MP2 calculations on (non-metallic) crystalline systems seem to be a feasible extension of the Laplace transform approach. In large molecules the AO-MP2 ansatz allows massively parallel MP2 calculations without input/output of four-index quantities provided that each processor has in-core memory for a limited number of two-index quantities. Energy gradient formulas for the AO-MP2 approach are derived.

关键词： CORRELATION MP2 AO LAPLACE TRANSFORM BOUNDS parallel computer GRADIENT CRYSTAL SOLID

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PERFORMANCE EVALUATION OF SUPRENUM FOR THE LINPACK BENCHMARK

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parallel COMPUTING 1992年第2期18卷 231-238页

作者： KOHLHOFF, S KRONE, J SUPRENUM GMBH W-5300 BONN 1GERMANY

We report on some performance measurements obtained on the SUPRENUM parallel supercomputer for the LINPACK benchmark. We shortly describe some features of our implementation of the LINPACK routines suitable for the SUPRENUM architecture. Performance measurements are presented for various numbers of processors and different matrix sizes. For the 1000 by 1000 problem we obtain over 100 Mflops on 1 cluster which contains 16 processors.

关键词： parallel computer SUPRENUM LINPACK BENCHMARK LU FACTORIZATION PERFORMANCE RESULTS

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Spatially resolved in vitro molecular ecology

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BIOPHYSICAL CHEMISTRY 1997年第2-3期66卷 145-158页

作者： McCaskill, JS Inst. für Molec. Biotechnologie Dept. of Molec. Info. Processing Beutenbergstr. 11 D-07745 Jena Germany Inst. Molekulare Biotechnologie Dept. Molecular Inform. Processing Beutenbergstr. 11 D-07745 Jena Germany

Sensitive CCD-based fluorescence detection has made spatially resolved studies of evolving cell-free molecular systems possible. In recent years our attention has focussed on making the transition to open and interacting spatially-resolved amplification systems using silicon microreactor technology and on providing a hardware platform for individual based simulation of such systems. Significant progress has been achieved in this direction. Open microflow reactors have been realized in zero (well-mixed), one and two dimensions with volumes small enough to allow long-time studies with limited biochemical materials. The primer directed 3SR reaction (amplifying DNA and RNA) has been used as a basis for constructing interacting model systems with both predator-prey and cooperative amplification character. Theoretical work has demonstrated the need for individual based modeling of such systems: a significant fraction of the population consists of distinct sequence polymers in any case. A massively parallel processor-configurable computer NGEN has been designed and constructed which allows the high speed simulation in hardware of relatively large populations of locally interacting individual strings of chosen length (e.g. up to 2000*2000 for 64 bases), in addition to its application as an evolvable hardware machine. Simulations show self-replicating spots to stabilize the cooperative amplification in evolving systems (a mechanism proposed by the author in 1994). Both oscillatory kinetics and pattern formation are expected in the experimental model systems under investigation which profoundly affect the course of evolution. Such in vitro model systems serve both to test current theories of cooperative evolution and provide clues for optimisation strategies in molecular biotechnology. (C) 1997 Published by Elsevier Science B.V.

关键词： in vitro amplification molecular ecology reaction-diffusion evolutionary biotechnology evolvable hardware parallel computer fluorescence detection DNA RNA FPGA

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OPTIMALITY OF A 2-PHASE STRATEGY FOR ROUTING IN INTERCONNECTION NETWORKS

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IEEE TRANSACTIONS ON computerS 1983年第9期32卷 861-863页

作者： VALIANT, LG Aiken Computation Laboratory Harvard University Abstract Authors References Cited By Keywords Metrics Similar Download Citation Email Print Request Permissions

It is shown that for d-way shuffle graphs all oblivious algorithms for realizing permutations in logarithmic time send packets along routes twice as long as the diameter of the graph. This confirms the optimality of the strategy that sends packets to random nodes in a first phase and to the correct destinations in the second. For the shuffle-exchange graph the corresponding route length is shown to be strictly longer than for the 2-way shuffle.

关键词： Complexity interconnection network parallel computer routing shuffle graph

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COMPUTING EIGENVALUES OF BANDED SYMMETRICAL TOEPLITZ MATRICES

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SIAM JOURNAL ON SCIENTIFIC AND STATISTICAL COMPUTING 1991年第4期12卷 743-754页

作者： ARBENZ, P

A recently proposed algorithm for the computation of the eigenvalues of symmetric banded Toeplitz matrices is investigated. The basic idea of the algorithm is to embed the Toeplitz matrix in a symmetric circulant matrix of higher order. After having computed the spectral decomposition of the circulant matrix-which is trivial since the eigenvectors of circulants are known a priori and the eigenvalues can be obtained by Fourier transform-the Toeplitz eigenvalue problem is treated as a restricted eigenvalue problem. In doing this, use can be made of the theory for intermediate problems of Weinstein and Aronszajn and its recent refinements. Since the main part of the proposed algorithm consists of independent searches for zeros in disjoint real intervals, the algorithm is well suited for parallel computers. Implementations of the algorithm are discussed and some numerical results are given. The (sequential) complexity of the computation of s eigenvalues of the Toeplitz matrix T is O(sr(n + r2)), where n is the order and r the bandwidth of T.

关键词： TOEPLITZ MATRIX CIRCULANT MATRIX RESTRICTED EIGENVALUE PROBLEM parallel computer

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DETERMINATION OF MONOPOLE CURRENT CLUSTERS IN 4-DIMENSIONAL QUANTUM ELECTRODYNAMICS

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INTERNATIONAL JOURNAL OF MODERN PHYSICS C-PHYSICS AND computerS 1993年第6期4卷 1205-1219页

作者： BODE, A LIPPERT, T SCHILLING, K UEBERHOLZ, P Bergische Universität — Gesamthochschule Wuppertal 42097 Wuppertal Germany Talk presented by Th. Lippert

Magnetic monopole currents are believed to have a strong impact on the Monte Carlo dynamics of compact quantum electrodynamics near the phase transition. We have indications that updating algorithms have to form and to break up monopole current clusters in order to force the tunneling of the system between the coexisting phases, the confined phase and the Coulomb phase. This might be responsible for long lived metastabilities in the time series. We present parallel numerical algorithms which allow the fast identification of clusters of monopole loops, the determination of their topological properties as well as their visualization in the course of a Monte Carlo simulation. The algorithms are implemented on the Connection Machine CM-5. We compare the data parallel programming style with a message passing approach. Complexity and performance are discussed.

关键词： LATTICE QED MAGNETIC MONOPOLES CLUSTER DETERMINATION parallel computer

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A multiprocessor system architecture suited for power system transient calculation

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ELECTRICAL ENGINEERING IN JAPAN 1999年第1期128卷 26-36页

作者： Yamamoto, M Nakata, T Kurita, Y Tokyo Elect Power Co Ltd Tokyo Japan NEC Corp Ltd Kawasaki Kanagawa 213 Japan

In the field of power system calculation, much research has been devoted to using parallel computers to increase computation speed. However, unlike examples in other application areas, such as circuit simulation or computational fluid dynamics, the performance gain is small. Also, the performance gain begins to saturate after a small number of processors are utilized. This is due to the essential features of power system calculation: mainly, (1) the size of the problem is usually much smaller than in other application fields and (2) the sparsity of the problem is high. These two features amplify the effect of interprocessor communication overhead. In this study, the authors sought the most suitable parallel architecture for power system calculation, restricting the number of processors to about 16. The architectural features of interest are the memory architecture and the interprocessor connection method. The candidates chosen are: (1) distributed memory architecture connected by an interprocessor communication network, (2) distributed memory architecture connected by a bus, (3) shared memory architecture connected by a bus, and (4) composite distributed/shared memory architecture connected by a bus. We evaluate each architecture in terms of the data for transient stability analysis from a single PE execution, with consideration of memory operations, necessary interprocessor communication, and computations. The results show that although little increase in speed is gained by using a distributed shared memory architecture connected by an interconnection network, it is possible to attain a speedup by a factor of 6.5 by using 16 PEs on a composite distributed/shared memory architecture connected by a bus. (C) 1999 Scripta Technica.

关键词： parallel computer architecture distributed memory shared memory power system analysis transient stability analysis

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The fast multipole method on parallel clusters, multicore processors, and graphics processing units

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COMPTES RENDUS MECANIQUE 2011年第2-3期339卷 185-193页

作者： Darve, Eric Cecka, Cris Takahashi, Toru Stanford Univ Dept Mech Engn Inst Computat & Math Engn Stanford CA 94305 USA Nagoya Univ Dept Mech Sci & Engn Nagoya Aichi 4648601 Japan

In this article, we discuss how the fast multipole method (FMM) can be implemented on modern parallel computers, ranging from computer clusters to multicore processors and graphics cards (CPU). The FMM is a somewhat difficult application for parallel computing because of its tree structure and the fact that it requires many complex operations which are not regularly structured. Computational linear algebra with dense matrices for example allows many optimizations that leverage the regular computation pattern. FMM can be similarly optimized but we will see that the complexity of the optimization steps is greater. The discussion will start with a general presentation of FMMs. We briefly discuss parallel methods for the FMM, such as building the FMM tree in parallel, and reducing communication during the FMM procedure. Finally, we will focus on porting and optimizing the FMM on CPUs. (C) 2011 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

关键词： computer science Fast multipole method parallel computer

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Analysis of crossovers and selections in a coarse-grained parallel genetic algorithm

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MATHEMATICAL AND computer MODELLING 2003年第11-13期38卷 1275-1282页

作者： Katayama, K Hirabayashi, H Narihisa, H Okayama Univ Sci Dept Informat & Comp Engn Okayama 7000005 Japan Matsushita Syst & Technol Co Ltd Kyoto 6178520 Japan

The parallel genetic algorithms (PGA) have been developed for combinatorial optimization problems, and its parallel efficiencies have been investigated on a specific problem. These investigations were. concerned with how to design a topology and the determination of the optimum setting for parameters (for example, size of subpopulations, migration interval, and so on) rather than the effectiveness of genetic operators. This paper investigates a relation between the parallel efficiency of the coarse-grained PGA and genetic (crossover and selection) operators for the traveling salesman problem on an MIMD parallel computer. The following genetic operators are considered: improved edge recombination (IERX), distance preserving (DPX), and complete subtour exchange (CSEX) crossovers, and two selection operators, which have relatively high selection pressures. Computational results indicate that the parallel efficiency is significantly affected by the difference of crossovers rather than the selections, and the PGA with CSEX gives better properties. (C) 2003 Elsevier Ltd. All rights reserved.

关键词： parallel genetic algorithm parameter determination traveling salesman problem parallel computer genetic operators

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CLASS-CONGRUENCE PROPERTY AND 2-PHASE ROUTING OF BOREL CAYLEY-GRAPHS

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IEEE TRANSACTIONS ON computerS 1995年第12期44卷 1462-1468页

作者： TANG, KW ARDEN, BW UNIV ROCHESTER DEPT ELECT ENGNROCHESTERNY 14627

Dense, symmetric graphs are useful interconnection models for multicomputer systems. Borel Cayley graphs, the densest degree-4 graphs for a range of diameters [1], are attractive candidates, However, the group-theoretic representation of these graphs makes the development of efficient routing algorithms difficult. In earlier reports, we showed that all degree-4 Borel Cayley graphs have generalized chordal ring (GCR) and chordal ring (CR) representations [2], [3]. In this paper, we present the class-congruence property and use this property to develop the two-phase routing algorithm for Borel Cayley graphs in a special GCR representation. The algorithm requires a small space complexity of O(p + k) for n = p x k nodes. Although suboptimal, the algorithm finds paths with length bounded by 2D, where D is the diameter. Furthermore, our computer implementation of the algorithm on networks with 1,081 and 15,657 nodes shows that the average path length is on the order of the diameter. The performance of the algorithm is compared with that of existing optimal and suboptimal algorithms.

关键词： GENERALIZED CHORDAL RING INTERCONNECTION NETWORK parallel computer

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