Computation Time Usage Research Articles

Fast Computation by MLFMM-FFT with NURBS in Large Volumetric Dielectric Structures

A refinement for the computation of the rigorous part of the multi-level fast multipole method (MLFMM) of analyzing volumetric objects is presented. A scheme based on the fast Fourier technique (FFT) is proposed with the objective of reducing the computational resources required to accurately analyze large homogeneous and non-homogeneous dielectric volumes. In order to reduce the memory requirements, the storage of the near-field terms of the method of moments (MoM) matrix is performed only for the positions corresponding to a parallelepiped with the size of the level 1 block of the MLFMM, computed with the vacuum permittivity, taking advantage of the Toeplitz symmetry present in regular hexahedral meshes. The FFT avoids applying the near-field MoM matrix in the iterative solution process. The application of this approach results in huge improvements in terms of memory usage, but also a speeds up the iterative solution process because the use of three-dimensional (3D) FFTs is very efficient for computing convolutions when the number of unknowns of the problems becomes very large as happens in volumetric problems. We also propose a new approach for the numerical treatment of the transition of the dielectric permittivity between different dielectrics or between a dielectric and a free space. To validate the computation technique, the radar cross section (RCS) of several dielectric bodies is computed using the classical MLFMM approach and it is compared with the presented FFT-based-MLFMM solution. The results demonstrate that the efficient memory and computation time usage of the proposed approach.

Experimental and numerical investigation on penetration of clay masonry by small high-speed projectile

This study investigates a kind of masonry consisting of clay-fired brick (fc = 10 MPa; ρ=1.38g/cm3) and mortar (fc = 10 MPa; ρ=1.8g/cm3). Clay-fired brick masonry connotes a traditional construction material of old architecture and public buildings. We carried out penetration experiments in which four clay-fired brick walls employing two different patterns were subjected to impact from small high-speed projectile, i.e. 12.7 mm armor-piercing explosive incendiary projectile and material tests in which the static and dynamic compressive strengths of clay-fired brick and mortar were determined by quasi-static and SHPB (Split Hopkinson Pressure Bar) tests. The experimental data include hit and exit velocities, damage configuration of clay brick masonry and mechanical properties of material at low and high strain rates, though which influence of thickness and bonding patterns of wall on kinetic loss of bullet, the damage patterns of masonry observed experimentally and dynamic increase of material strengths are analyzed. To keep minimum boundary inconsistency with reality, full 3D detailed finite element model consisting of two different material is established. Sharing common nodes and employing automatic tiebreak contact are combined to reduce computational time usage of large-scale model. For description of clay-fired brick and mortar Riedel–Hiermaier–Thoma (RHT) material model is employed. Material parameter set is derived based on experimental data, available literature and engineering assumptions. The numerical simulations study the mesh resolution dependency of material model, reproduce the crucial phenomena of masonry in experiment acceptably and offer more time-resolved insight into motion of bullet in the process of penetration. The feasibility of means of constructing finite element model and applying RHT model to the masonry herein and analogous constructions is explored through numerical investigation.

A COMPARISON OF PARALLEL BRANCH AND BOUND ALGORITHMS FOR LOCATION-TRANSPORTATION PROBLEMS IN HUMANITARIAN RELIEF

This paper studies the effect of branching rules (BR) and heuristic algorithms (HA) to findfeasible solutions for a branch and bound (BB) algorithm used to solve sub-problems in a parallel two-phasebranch and bound (PTBB) approach. The nine PTBB algorithms, which are developed by varying 32combinations of BR and HA strategies, are tested on the facility location-transportation problem for disasterresponse (FLTDR). The mathematical model for the problem determines the number and location ofdistribution centres in a relief network, the amount of relief supplies to be stocked at each distribution centreand the vehicles to take the supplies in order to maximize the percentage of needs coverage of disaster victimsunder capacity restriction, transportation and budgetary constraints. To examine the performance of thealgorithms, computational experiments are conducted on the various sizes of generated problems. Threestrategies of BR and HA provided in the “intlinprog” function of MATLAB were applied for these problems.The objective function values and the computational times of all algorithms were collected and analyzed. Theresults showed that all PTBB algorithms can solve problem sizes of four candidate locations with fifteendemand points without premature termination by time. The PTBB algorithm using “maxfun” branching rulesand “rss” heuristic to find a feasible solution is recommended for FLTDR because of the least computationaltime usage.

IDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems

RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA) to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of iDoRNA can be downloaded from the site http://synbio.sbi.kmutt.ac.th.

Applications of Parallel Computing for Facility Location-Transportation Problems for Disaster Response

This study extends the capability and increases the performance of a traditional Branch and Bound (BB) algorithm to solve Facility Location-Transportation problems for Disaster Response (FLTDR) using parallel computing. A Two-Stage Branch and Bound (TBB) algorithm was developed to support two parallel computing approaches. This algorithm divides problems into two small sub-problems, which are a facility location sub-problem and a transportation sub-problem. All possible numbers of distribution centers are determined. All possible locations relating to any number of distribution centers are explicitly explored. The transportation sub-problem corresponding to any selected location is then solved. Two parallel approaches for the TBB algorithm (PTBB) differ in partitioning the list of sub-problems. The first approach (PTBB1) solves both sub-problems in parallel. The other (PTBB2) explores the locations in sequence and solves only the transportation sub-problems in parallel. The numerical experiments were conducted on various sizes of generated problems. The quality of the solution and the computing time of both approaches were compared with a BB algorithm with premature termination by time. The experimental experiences showed that both PTBB1 and PTBB2 are more efficient and effective than a BB algorithm. However, the PTBB1 should be suggested for the FLTDR because of the least computational time usage.

An Out-of-Core Dataflow Middleware Applied to Spare Linear Algebra

Many applications in scientific computing require a tremendous amount of data, running on thousands of computing nodes so as to ensure all the data fits in the main memory of the distributed machine. However, for some irregular applications, like sparse linear solvers, running on thousands of nodes typically do not achieve high efficiency, leading to a significant waste of computing time. Out-ofcore computing allows using hard drives to store the state of the application. In this paper, we propose to build a task-based out-of-core programming model based on the filter stream programming model. Coupling a distributed storage system with a data-aware scheduler allows achieving communication and computation overlapping as well as a reutilization. Experiments on an in-house cluster equipped with regular hard drive indicates that using a single SSD drive per node should be enough to reach equivalent computation time usage between in-core and out-of-core computations, while a RAID SSD configuration will achieve higher efficiency in out-of-core mode.

Simulation algorithms for the random-cluster model

We compare the performance of Monte Carlo algorithms for the simulation of the random-cluster representation of the q-state Potts model for continuous values of q. In particular we consider a local bond update method, a statistical reweighting method of percolation configurations, and a cluster algorithm, all of which generate Boltzmann statistics. The dynamic exponent z of the cluster algorithm appears to be quite small, and to assume the values of the Swendsen-Wang algorithm for q = 2 and 3. The cluster algorithm appears to be much more efficient than our versions of the other two methods for the simulation of the random-cluster model. The higher efficiency of the cluster method with respect to the local method is primarily due to the fact that the computer time usage of the local method increases more rapidly with system size; the difference between the dynamic exponents is less important.

Transient Aquifer Flows by Characteristics Methods

A numerical model is presented to analyze nonsteady radial flow in a finite or infinite leaky aquifer system. An equation of motion alteration, which involves the introduction of an inertia multiplier, converts the standard equations of transient ground-water flow to a form suitable for efficient solution by the method of characteristics. The result is a numerical method that should be attractively competitive in computer time usage with other numerical procedures currently in use. The equations are presented and the procedure developed for axisymmetrical flow. Several examples are used to expose the influence of the size of the distance intervals and the size of the inertia multiplier on the accuracy of the numerical process. Either constant or time-variable discharge or drawdown rates may be used as boundary conditions in infinite or bounded radial aquifer systems. Radially varying aquifer properties and leakage may also be treated.