A new parallel algorithm for parsing arithmetic infix expressions

A new parallel algorithm for transforming an arithmetic infix expression into a par se tree is presented. The technique is based on a result due to Fischer (1980) which enables the construction of the parse tree, by appropriately scanning the vector of precedence values associated with the elements of the expression. The algorithm presented here is suitable for execution on a shared memory model of an SIMD machine with no read/write conflicts permitted. It uses O(n) processors and has a time complexity of O(log2n) where n is the expression length. Parallel algorithms for generating code for an SIMD machine are also presented.

An optimal parallel algorithm for sparse matrix bandwidth reduction on a linear array

A simple and efficient algorithm for the bandwidth reduction of sparse symmetric matrices is proposed. It involves column-row permutations and is well-suited to map onto the linear array topology of the SIMD architectures. The efficiency of the algorithm is compared with the other existing algorithms. The interconnectivity and the memory requirement of the linear array are discussed and the complexity of its layout area is derived. The parallel version of the algorithm mapped onto the linear array is then introduced and is explained with the help of an example. The optimality of the parallel algorithm is proved by deriving the time complexities of the algorithm on a single processor and the linear array.

A Hybrid Parallel Algorithm for Computing and Tracking Level Set Topology

The contour tree is a topological abstraction of a scalar field that captures evolution in level set connectivity. It is an effective representation for visual exploration and analysis of scientific data. We describe a work-efficient, output sensitive, and scalable parallel algorithm for computing the contour tree of a scalar field defined on a domain that is represented using either an unstructured mesh or a structured grid. A hybrid implementation of the algorithm using the GPU and multi-core CPU can compute the contour tree of an input containing 16 million vertices in less than ten seconds with a speedup factor of upto 13. Experiments based on an implementation in a multi-core CPU environment show near-linear speedup for large data sets.

PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites

Knowledge of protein-ligand interactions is essential to understand several biological processes and important for applications ranging from understanding protein function to drug discovery and protein engineering. Here, we describe an algorithm for the comparison of three-dimensional ligand-binding sites in protein structures. A previously described algorithm, PocketMatch (version 1.0) is optimised, expanded, and MPI-enabled for parallel execution. PocketMatch (version 2.0) rapidly quantifies binding-site similarity based on structural descriptors such as residue nature and interatomic distances. Atomic-scale alignments may also be obtained from amino acid residue pairings generated. It allows an end-user to compute database-wide, all-to-all comparisons in a matter of hours. The use of our algorithm on a sample dataset, performance-analysis, and annotated source code is also included.

Optimization Of Groundwater Remediation With New Efficient Parallel Algorithm For Global Optimization

Application of optimization algorithm to PDE modeling groundwater remediation can greatly reduce remediation cost. However, groundwater remediation analysis requires a computational expensive simulation, therefore, effective parallel optimization could potentially greatly reduce computational expense. The optimization algorithm used in this research is Parallel Stochastic radial basis function. This is designed for global optimization of computationally expensive functions with multiple local optima and it does not require derivatives. In each iteration of the algorithm, an RBF is updated based on all the evaluated points in order to approximate expensive function. Then the new RBF surface is used to generate the next set of points, which will be distributed to multiple processors for evaluation. The criteria of selection of next function evaluation points are estimated function value and distance from all the points known. Algorithms created for serial computing are not necessarily efficient in parallel so Parallel Stochastic RBF is different algorithm from its serial ancestor. The application for two Groundwater Superfund Remediation sites, Umatilla Chemical Depot, and Former Blaine Naval Ammunition Depot. In the study, the formulation adopted treats pumping rates as decision variables in order to remove plume of contaminated groundwater. Groundwater flow and contamination transport is simulated with MODFLOW-MT3DMS. For both problems, computation takes a large amount of CPU time, especially for Blaine problem, which requires nearly fifty minutes for a simulation for a single set of decision variables. Thus, efficient algorithm and powerful computing resource are essential in both cases. The results are discussed in terms of parallel computing metrics i.e. speedup and efficiency. We find that with use of up to 24 parallel processors, the results of the parallel Stochastic RBF algorithm are excellent with speed up efficiencies close to or exceeding 100%.

An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Performance evaluation of a parallel algorithm for simultaneous untangling and smoothing of tetrahedral meshes

[EN]A new parallel algorithm for simultaneous untangling and smoothing of tetrahedral meshes is proposed in this paper. We provide a detailed analysis of its performance on shared-memory many-core computer architectures. This performance analysis includes the evaluation of execution time, parallel scalability, load balancing, and parallelism bottlenecks. Additionally, we compare the impact of three previously published graph coloring procedures on the performance of our parallel algorithm. We use six benchmark meshes with a wide range of sizes. Using these experimental data sets, we describe the behavior of the parallel algorithm for different data sizes. We demonstrate that this algorithm is highly scalable when it runs on two different high-performance many-core computers with up to 128 processors...

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.

An hybrid parallel algorithm for solving tridiagonal linear systems versus the Wang’s method in a Cray T3D BSP computer

In this paper we describe an hybrid algorithm for an even number of processors based on an algorithm for two processors and the Overlapping Partition Method for tridiagonal systems. Moreover, we compare this hybrid method with the Partition Wang’s method in a BSP computer. Finally, we compare the theoretical computation cost of both methods for a Cray T3D computer, using the cost model that BSP model provides.

Delimited Massively Parallel Algorithm Based on Rules Elimination for Application of Active Rules in Transition P Systems

In the field of Transition P systems implementation, it has been determined that it is very important to determine in advance how long takes evolution rules application in membranes. Moreover, to have time estimations of rules application in membranes makes possible to take important decisions related to hardware / software architectures design. The work presented here introduces an algorithm for applying active evolution rules in Transition P systems, which is based on active rules elimination. The algorithm complies the requisites of being nondeterministic, massively parallel, and what is more important, it is time delimited because it is only dependant on the number of membrane evolution rules.

Parallel Algorithm for the Local Variations Method

Димитър С. Илиев, Станимир Д. Илиев - Актуално е изследването на поведението на течен менискус в околността на хетерогенна стена. До сега няма получено числено решение за формата на менискуса около стена, която е с хаотична хетерогенност. В настоящата статия е разработен алгоритъм за метода на локалните вариации, който може да се използва на многопроцесорни системи. С този метод е получен за първи път профила на равновесен течен менискус около вертикална стена с хаотична хетерогенност.