Analysis and performance of a UPC implementation of a parallel longest common subsequence algorithm

An important problem in computational biology is finding the longest common subsequence (LCS) of two nucleotide sequences. This paper examines the correctness and performance of a recently proposed parallel LCS algorithm that uses successor tables and pruning rules to construct a list of sets from which an LCS can be easily reconstructed. Counterexamples are given for two pruning rules that were given with the original algorithm. Because of these errors, performance measurements originally reported cannot be validated. The work presented here shows that speedup can be reliably achieved by an implementation in Unified Parallel C that runs on an Infiniband cluster. This performance is partly facilitated by exploiting the software cache of the MuPC runtime system. In addition, this implementation achieved speedup without bulk memory copy operations and the associated programming complexity of message passing.

Parallel algorithm for solving integer linear programs

Linear programs, or LPs, are often used in optimization problems, such as improving manufacturing efficiency of maximizing the yield from limited resources. The most common method for solving LPs is the Simplex Method, which will yield a solution, if one exists, but over the real numbers. From a purely numerical standpoint, it will be an optimal solution, but quite often we desire an optimal integer solution. A linear program in which the variables are also constrained to be integers is called an integer linear program or ILP. It is the focus of this report to present a parallel algorithm for solving ILPs. We discuss a serial algorithm using a breadth-first branch-and-bound search to check the feasible solution space, and then extend it into a parallel algorithm using a client-server model. In the parallel mode, the search may not be truly breadth-first, depending on the solution time for each node in the solution tree. Our search takes advantage of pruning, often resulting in super-linear improvements in solution time. Finally, we present results from sample ILPs, describe a few modifications to enhance the algorithm and improve solution time, and offer suggestions for future work.

Numerical solutions of elliptic inverse problems via the equation error method

To estimate a parameter in an elliptic boundary value problem, the method of equation error chooses the value that minimizes the error in the PDE and boundary condition (the solution of the BVP having been replaced by a measurement). The estimated parameter converges to the exact value as the measured data converge to the exact value, provided Tikhonov regularization is used to control the instability inherent in the problem. The error in the estimated solution can be bounded in an appropriate quotient norm; estimates can be derived for both the underlying (infinite-dimensional) problem and a finite-element discretization that can be implemented in a practical algorithm. Numerical experiments demonstrate the efficacy and limitations of the method.

Control design and genetic algorithm optimization for electrostatic MEMS

This dissertation discusses structural-electrostatic modeling techniques, genetic algorithm based optimization and control design for electrostatic micro devices. First, an alternative modeling technique, the interpolated force model, for electrostatic micro devices is discussed. The method provides improved computational efficiency relative to a benchmark model, as well as improved accuracy for irregular electrode configurations relative to a common approximate model, the parallel plate approximation model. For the configuration most similar to two parallel plates, expected to be the best case scenario for the approximate model, both the parallel plate approximation model and the interpolated force model maintained less than 2.2% error in static deflection compared to the benchmark model. For the configuration expected to be the worst case scenario for the parallel plate approximation model, the interpolated force model maintained less than 2.9% error in static deflection while the parallel plate approximation model is incapable of handling the configuration. Second, genetic algorithm based optimization is shown to improve the design of an electrostatic micro sensor. The design space is enlarged from published design spaces to include the configuration of both sensing and actuation electrodes, material distribution, actuation voltage and other geometric dimensions. For a small population, the design was improved by approximately a factor of 6 over 15 generations to a fitness value of 3.2 fF. For a larger population seeded with the best configurations of the previous optimization, the design was improved by another 7% in 5 generations to a fitness value of 3.0 fF. Third, a learning control algorithm is presented that reduces the closing time of a radiofrequency microelectromechanical systems switch by minimizing bounce while maintaining robustness to fabrication variability. Electrostatic actuation of the plate causes pull-in with high impact velocities, which are difficult to control due to parameter variations from part to part. A single degree-of-freedom model was utilized to design a learning control algorithm that shapes the actuation voltage based on the open/closed state of the switch. Experiments on 3 test switches show that after 5-10 iterations, the learning algorithm lands the switch with an impact velocity not exceeding 0.2 m/s, eliminating bounce.

Effect of high order interpolation in the stability and efficiency of the time-integration process in vorticity-velocity CFD algorithms

The numerical solution of the incompressible Navier-Stokes Equations offers an effective alternative to the experimental analysis of Fluid-Structure interaction i.e. dynamical coupling between a fluid and a solid which otherwise is very complex, time consuming and very expensive. To have a method which can accurately model these types of mechanical systems by numerical solutions becomes a great option, since these advantages are even more obvious when considering huge structures like bridges, high rise buildings, or even wind turbine blades with diameters as large as 200 meters. The modeling of such processes, however, involves complex multiphysics problems along with complex geometries. This thesis focuses on a novel vorticity-velocity formulation called the KLE to solve the incompressible Navier-stokes equations for such FSI problems. This scheme allows for the implementation of robust adaptive ODE time integration schemes and thus allows us to tackle the various multiphysics problems as separate modules. The current algorithm for KLE employs a structured or unstructured mesh for spatial discretization and it allows the use of a self-adaptive or fixed time step ODE solver while dealing with unsteady problems. This research deals with the analysis of the effects of the Courant-Friedrichs-Lewy (CFL) condition for KLE when applied to unsteady Stoke’s problem. The objective is to conduct a numerical analysis for stability and, hence, for convergence. Our results confirmthat the time step ∆t is constrained by the CFL-like condition ∆t ≤ const. hα, where h denotes the variable that represents spatial discretization.

Problems in the classical calculus of variations

This dissertation concerns convergence analysis for nonparametric problems in the calculus of variations and sufficient conditions for weak local minimizer of a functional for both nonparametric and parametric problems. Newton's method in infinite-dimensional space is proved to be well-defined and converges quadratically to a weak local minimizer of a functional subject to certain boundary conditions. Sufficient conditions for global converges are proposed and a well-defined algorithm based on those conditions is presented and proved to converge. Finite element discretization is employed to achieve an implementable line-search-based quasi-Newton algorithm and a proof of convergence of the discretization of the algorithm is included. This work also proposes sufficient conditions for weak local minimizer without using the language of conjugate points. The form of new conditions is consistent with the ones in finite-dimensional case. It is believed that the new form of sufficient conditions will lead to simpler approaches to verify an extremal as local minimizer for well-known problems in calculus of variations.

Transformer modeling ATP : internal faults & high-frequency discretization

Power transformers are key components of the power grid and are also one of the most subjected to a variety of power system transients. The failure of a large transformer can cause severe monetary losses to a utility, thus adequate protection schemes are of great importance to avoid transformer damage and maximize the continuity of service. Computer modeling can be used as an efficient tool to improve the reliability of a transformer protective relay application. Unfortunately, transformer models presently available in commercial software lack completeness in the representation of several aspects such as internal winding faults, which is a common cause of transformer failure. It is also important to adequately represent the transformer at frequencies higher than the power frequency for a more accurate simulation of switching transients since these are a well known cause for the unwanted tripping of protective relays. This work develops new capabilities for the Hybrid Transformer Model (XFMR) implemented in ATPDraw to allow the representation of internal winding faults and slow-front transients up to 10 kHz. The new model can be developed using any of two sources of information: 1) test report data and 2) design data. When only test-report data is available, a higher-order leakage inductance matrix is created from standard measurements. If design information is available, a Finite Element Model is created to calculate the leakage parameters for the higher-order model. An analytical model is also implemented as an alternative to FEM modeling. Measurements on 15-kVA 240?/208Y V and 500-kVA 11430Y/235Y V distribution transformers were performed to validate the model. A transformer model that is valid for simulations for frequencies above the power frequency was developed after continuing the division of windings into multiple sections and including a higher-order capacitance matrix. Frequency-scan laboratory measurements were used to benchmark the simulations. Finally, a stability analysis of the higher-order model was made by analyzing the trapezoidal rule for numerical integration as used in ATP. Numerical damping was also added to suppress oscillations locally when discontinuities occurred in the solution. A maximum error magnitude of 7.84% was encountered in the simulated currents for different turn-to-ground and turn-to-turn faults. The FEM approach provided the most accurate means to determine the leakage parameters for the ATP model. The higher-order model was found to reproduce the short-circuit impedance acceptably up to about 10 kHz and the behavior at the first anti-resonant frequency was better matched with the measurements.

Variations of the FEAST Eigenvalue Algorithm

FEAST is a recently developed eigenvalue algorithm which computes selected interior eigenvalues of real symmetric matrices. It uses contour integral resolvent based projections. A weakness is that the existing algorithm relies on accurate reasoned estimates of the number of eigenvalues within the contour. Examining the singular values of the projections on moderately-sized, randomly-generated test problems motivates orthogonalization-based improvements to the algorithm. The singular value distributions provide experimentally robust estimates of the number of eigenvalues within the contour. The algorithm is modified to handle both Hermitian and general complex matrices. The original algorithm (based on circular contours and Gauss-Legendre quadrature) is extended to contours and quadrature schemes that are recursively subdividable. A general complex recursive algorithm is implemented on rectangular and diamond contours. The accuracy of different quadrature schemes for various contours is investigated.