Parallel Computation Approach Research Articles

A Heterogeneous Parallel Computing Approach Optimizing SpTTM on CPU-GPU via GCN

Sparse Tensor-Times-Matrix (SpTTM) is the core calculation in tensor analysis. The sparse distributions of different tensors vary greatly, which poses a big challenge to designing efficient and general SpTTM. In this paper, we describe SpTTM on CPU-GPU heterogeneous hybrid systems and give a parallel execution strategy for SpTTM in different sparse formats. We analyze the theoretical computer powers and estimate the number of tasks to achieve the load balancing between the CPU and the GPU of the heterogeneous systems. We discuss a method to describe tensor sparse structure by graph structure and design a new graph neural network SPT-GCN to select a suitable tensor sparse format. Furthermore, we perform extensive experiments using real datasets to demonstrate the advantages and efficiency of our proposed input-aware slice-wise SpTTM. The experimental results show that our input-aware slice-wise SpTTM can achieve an average speedup of 1.310 × compared to ParTI! library on a CPU-GPU heterogeneous system.

A Parallel Computing Approach to Gene Expression and Phenotype Correlation for Identifying Retinitis Pigmentosa Modifiers in Drosophila

As a genetic eye disorder, retinitis pigmentosa (RP) has been a focus of researchers to find a diagnosis through either genome-wide association (GWA) or RNAseq analysis. In fact, GWA and RNAseq are considered two complementary approaches to gaining a more comprehensive understanding of the genetics of different diseases. However, RNAseq analysis can provide information about the specific mechanisms underlying the disease and the potential targets for therapy. This research proposes a new approach to differential gene expression (DGE) analysis, which is the heart of the core-analysis phase in any RNAseq study. Based on the Drosophila Genetic Reference Panel (DGRP), the gene expression dataset is computationally analyzed in light of eye-size phenotypes. We utilized the foreach and the doParallel R packages to run the code on a multicore machine to reduce the running time of the original algorithm, which exhibited an exponential time complexity. Experimental results showed an outstanding performance, reducing the running time by 95% while using 32 processes. In addition, more candidate modifier genes for RP were identified by increasing the scope of the analysis and considering more datasets that represent different phenotype models.

A Parallel Implementation of the Differential Evolution Method

Global optimization is a widely used technique that finds application in many sciences such as physics, economics, medicine, etc., and with many extensions, for example, in the area of machine learning. However, in many cases, global minimization techniques require a high computational time and, for this reason, parallel computational approaches should be used. In this paper, a new parallel global optimization technique based on the differential evolutionary method is proposed. This new technique uses a series of independent parallel computing units that periodically exchange the best solutions they have found. Additionally, a new termination rule is proposed here that exploits parallelism to accelerate process termination in a timely and valid manner. The new method is applied to a number of problems in the established literature and the results are quite promising.

Solving the 3‐Satisfiability Problem Using Network‐Based Biocomputation

The 3‐satisfiability Problem (3‐SAT) is a demanding combinatorial problem that is of central importance among the nondeterministic polynomial (NP) complete problems, with applications in circuit design, artificial intelligence, and logistics. Even with optimized algorithms, the solution space that needs to be explored grows exponentially with the increasing size of 3‐SAT instances. Thus, large 3‐SAT instances require excessive amounts of energy to solve with serial electronic computers. Network‐based biocomputation (NBC) is a parallel computation approach with drastically reduced energy consumption. NBC uses biomolecular motors to propel cytoskeletal filaments through nanofabricated networks that encode mathematical problems. By stochastically exploring possible paths through the networks, the cytoskeletal filaments find possible solutions. However, to date, no NBC algorithm for 3‐SAT has been available. Herein, an algorithm that converts 3‐SAT into an NBC‐compatible network format is reported and four small 3‐SAT instances (with up to three variables and five clauses) using the actin–myosin biomolecular motor system are experimentally solved. Because practical polynomial conversions to 3‐SAT exist for many important NP complete problems, the result opens the door to enable NBC to solve small instances of a wide range of problems.

An Accelerated and Flexible SIFT Parallel-Computing Approach Based on the General Multi-Core Platform

Visual retrieval has been a significant technology in the computer vision task. Visual feature descriptors are the key to the visual retrieval. The famous local feature descriptor is called the Scale Invariant Feature Transform (SIFT), which can keep invariant mapping for the scale, rotate and simulate images. To utilize effectively the SIFT feature descriptor for visual matching on different hardware platforms, this paper proposes an accelerated SIFT algorithm based on the SIFT feature computing principle of the general multi-core platform. First, our multi-core task allocation method introduces the WFM theory into task assignment for each core to improve the core computing resource utilization for high-efficient parallel computing. Then, to improve the efficiency of picture matching, we introduce global geometric constraints condition to optimal picture matching for the multi-core parallelization approach. Experimental results show that the proposed approach can save on average 87.31% on the Intel X86 platform, compared to the single-core time. Also, our approach can save on average 33.79% on the Raspberry Pi platform, compared to the single-core time.

In-Memory Interval Joins

The interval join is a popular operation in temporal, spatial, and uncertain databases. The majority of interval join algorithms assume that input data reside on disk and so, their focus is to minimize the I/O accesses. Recently, an in-memory approach based on plane sweep (PS) for modern hardware was proposed which greatly outperforms previous work. However, this approach relies on a complex data structure and its parallelization has not been adequately studied. In this article, we investigate in-memory interval joins in two directions. First, we explore the applicability of a largely ignored forward scan (FS)-based plane sweep algorithm, for single-threaded join evaluation. We propose four optimizations for FS that greatly reduce its cost, making it competitive or even faster than the state-of-the-art. Second, we study in depth the parallel computation of interval joins. We design a non-partitioning-based approach that determines independent tasks of the join algorithm to run in parallel. Then, we address the drawbacks of the previously proposed hash-based partitioning and suggest a domain-based partitioning approach that does not produce duplicate results. Within our approach, we propose a novel breakdown of the partition-joins into mini-joins to be scheduled in the available CPU threads and propose an adaptive domain partitioning, aiming at load balancing. We also investigate how the partitioning phase can benefit from modern parallel hardware. Our thorough experimental analysis demonstrates the advantage of our novel partitioning-based approach for parallel computation.

A Parallel Computing Approach to Spatial Neighboring Analysis of Large Amounts of Terrain Data Using Spark.

Spatial neighboring analysis is an indispensable part of geo-raster spatial analysis. In the big data era, high-resolution raster data offer us abundant and valuable information, and also bring enormous computational challenges to the existing focal statistics algorithms. Simply employing the in-memory computing framework Spark to serve such applications might incur performance issues due to its lack of native support for spatial data. In this article, we present a Spark-based parallel computing approach for the focal algorithms of neighboring analysis. This approach implements efficient manipulation of large amounts of terrain data through three steps: (1) partitioning a raster digital elevation model (DEM) file into multiple square tile files by adopting a tile-based multifile storing strategy suitable for the Hadoop Distributed File System (HDFS), (2) performing the quintessential slope algorithm on these tile files using a dynamic calculation window (DCW) computing strategy, and (3) writing back and merging the calculation results into a whole raster file. Experiments with the digital elevation data of Australia show that the proposed computing approach can effectively improve the parallel performance of focal statistics algorithms. The results also show that the approach has almost the same calculation accuracy as that of ArcGIS. The proposed approach also exhibits good scalability when the number of Spark executors in clusters is increased.

A Seamless, Reconfigurable, and Highly Parallel In-Memory Stochastic Computing Approach With Resistive Random Access Memory Array

A seamless, reconfigurable, and highly parallel in-memory stochastic computing (SC) approach is proposed and experimentally demonstrated in resistive random access memory (RRAM) array. By utilizing the probabilistic switching behavior of RRAM and parallel writing, stochastic bit streams (SBS) are generated in parallel. By employing in-memory stateful logic, parallel stochastic logic is directly performed within the same memory array. This in-memory SC approach has three merits: 1) true stochastic number generator (SNG) can be obtained with low cost, 2) the signal conversion overhead between SNG and stochastic logic is eliminated, 3) it is highly parallel and the stochastic logic is reconfigurable. This work provides an efficient and low-cost alternative approach to achieve SC.

A comparison study on nonlinear dimension reduction methods with kernel variations: Visualization, optimization and classification

Because of high dimensionality, correlation among covariates, and noise contained in data, dimension reduction (DR) techniques are often employed to the application of machine learning algorithms. Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA), and their kernel variants (KPCA, KLDA) are among the most popular DR methods. Recently, Supervised Kernel Principal Component Analysis (SKPCA) has been shown as another successful alternative. In this paper, brief reviews of these popular techniques are presented first. We then conduct a comparative performance study based on three simulated datasets, after which the performance of the techniques are evaluated through application to a pattern recognition problem in face image analysis. The gender classification problem is considered on MORPH-II and FG-NET, two popular longitudinal face aging databases. Several feature extraction methods are used, including biologically-inspired features (BIF), local binary patterns (LBP), histogram of oriented gradients (HOG), and the Active Appearance Model (AAM). After applications of DR methods, a linear support vector machine (SVM) is deployed with gender classification accuracy rates exceeding 95% on MORPH-II, competitive with benchmark results. A parallel computational approach is also proposed, attaining faster processing speeds and similar recognition rates on MORPH-II. Our computational approach can be applied to practical gender classification systems and generalized to other face analysis tasks, such as race classification and age prediction.

EM-Centric Multiphysics Optimization of Microwave Components Using Parallel Computational Approach

For the high-performance microwave component and system design, besides electromagnetic (EM) physics domain, we also need to consider the operation of the real-world multiphysics (MP) environment that contains the effects of other physics domains. EM-centric MP analysis and design optimization become very important. In this article, for the first time, we develop a novel parallel EM-centric multiphysics optimization (MPO) technique. In our proposed technique, the pole/residue-based transfer function is exploited to build an effective and robust surrogate model. A group of modified quadratic mapping functions is formulated to map the relationships between pole/residues of the transfer function and the design variables. Multiple EM-centric MP evaluations are performed in parallel to generate the training samples for establishing the surrogate model. Using our proposed technique, the surrogate model can be valid in a relatively large neighborhood, which makes an effective and large optimization update in each optimization iteration. The trust region algorithm is performed to guarantee the convergence of the proposed MPO algorithm. Our proposed MPO technique takes a small number of iterations to obtain the optimal EM-centric MP response. Two microwave filter examples are used to demonstrate the validity of the proposed technique.

Accelerating phase-field modeling of solidification with a parallel adaptive computational domain approach

We developed a parallel adaptive computational domain method for accelerating the simulation of solidification in two dimensions using the phase-field model. The algorithm is paralled with the MPI library based on the domain decomposition approach. We discuss the implementation details of the parallel adaptive computational domain method and the domain decomposition based strongly implicit linear solver. We examined the performance of our algorithm by comparing with the algorithm based on the fixed computational domain and show that it greatly reduces the computational cost of solving the phase-field model. We also simulate the competitive growth process of the second and ternary dendritic arms successfully.

Parallel evolutionary computation for multiobjective gene interaction analysis

Multiple studies provide evidence on the impact of certain gene interactions in the occurrence of diseases. Due to the complexity of genotype–phenotype relationships, it is required the development of highly efficient algorithmic strategies that successfully identify high-order interactions attending to different evaluation criteria. This work investigates parallel evolutionary computation approaches for multiobjective gene interaction analysis. A multiobjective genetic algorithm, with novel optimized design features, is developed and parallelized under problem-independent and problem-dependent schemes. Experimental results show the relevant performance of the method for complex interaction orders, significantly accelerating execution time (up to 296×) with regard to other state-of-the-art multiobjective tools.

BUILDING EFFICIENT COMPUTATIONAL CELLULAR AUTOMATA MODELS OF COMPLEX SYSTEMS: BACKGROUND, APPLICATIONS, RESULTS, SOFTWARE, AND PATHOLOGIES

Cellular automaton models of complex systems (CSs) are gaining greater popularity; simultaneously, they have proven the capability to solve real scientific and engineering applications. To enable everybody a quick penetration into the core of this type of modeling, three real applications of cellular automaton models, including selected open source software codes, are studied: laser dynamics, dynamic recrystallization (DRX) and surface catalytic reactions.The paper is written in a way that it enables any researcher to reach the cutting edge knowledge of the design principles of cellular automata (CA) models of the observed phenomena in any scientific field. The whole sequence of design steps is demonstrated: definition of the model using topology and local (transition) rule of a cellular automaton, achieved results, comparison to real experiments, calibration, pathological observations, flow diagrams, software, and discussions. Additionally, the whole paper demonstrates the extreme expressiveness and flexibility of massively parallel computational approaches compared to other computational approaches. The paper consists of the introductory parts that are explaining CSs, self-organization and emergence, entropy, and CA. This allows readers to realize that there is a large variability in definitions and solutions of this class of models.

GPU-accelerated Double-stage Delay-multiply-and-sum Algorithm for Fast Photoacoustic Tomography Using LED Excitation and Linear Arrays.

Double-stage delay-multiply-and-sum (DS-DMAS) is an algorithm proposed for photoacoustic image reconstruction. The DS-DMAS algorithm offers a higher contrast than conventional delay-and-sum and delay-multiply and-sum but at the expense of higher computational complexity. Here, we utilized a compute unified device architecture (CUDA) graphics processing unit (GPU) parallel computation approach to address the high complexity of the DS-DMAS for photoacoustic image reconstruction generated from a commercial light-emitting diode (LED)-based photoacoustic scanner. In comparison with a single-threaded central processing unit (CPU), the GPU approach increased speeds by nearly 140-fold for 1024 × 1024 pixel image; there was no decrease in accuracy. The proposed implementation makes it possible to reconstruct photoacoustic images with frame rates of 250, 125, and 83.3 when the images are 64 × 64, 128 × 128, and 256 × 256, respectively. Thus, DS-DMAS can be efficiently used in clinical devices when coupled with CUDA GPU parallel computation.

A parallel modular computing approach to real‐time simulation of multiple fuel cells hybrid power system

A parallel modular computing approach to real‐time simulation of multiple fuel cells hybrid power system

Automated Neural-Based Modeling of Microwave Devices Using Parallel Computation and Interpolation Approaches

Automated model generation (AMG) is an automated artificial neural network (ANN) modeling algorithm, which integrates all the subtasks (including adaptive sampling/data generation, model structure adaptation, training, and testing) in neural model development into one unified framework. In existing AMG, most of the time is spent on data sampling and model structure adaptation due to the iterative neural network training and the sequential computation mechanism. In this paper, we propose an advanced AMG algorithm using parallel computation and interpolation approaches to speed up the neural modeling of microwave devices. Efficient interpolation approaches are incorporated to avoid repetitive training of the intermediate neural networks during adaptive sampling process in AMG. Parallel computation formulation based on a multi-processor environment is proposed to further save time during interpolation calculation, data generation, and model structure adaptation process. Examples of automated modeling of two microwave filters are presented to show the advantage of this paper.

A parallel computational approach for similarity search using Bloom filters

AbstractFinding similar items in a large and unstructured dataset is a challenging task in many applications of data science, such as searching, indexing, and retrieval. With the increasing data volume and demand for real time responses, similarity search has gained much consideration. In this paper, a parallel computational approach for similarity search using Bloom filters (PCASSB) has been proposed, which uses Bloom filter for the representation of features of document and comparison with user's query. Query features are stored in integer query array (IQA), an array of integer. The PCASSB, an approximate similarity search technique, has been implemented on graphics processing unit with compute unified device architecture as the programming platform. To compute the similarity score between query and reference dataset, Dice coefficient has been used as a baseline method. The accuracy of the results generated by PCASSB is compared with the baseline method and other state‐of‐the‐art methods. The experimental results show that the proposed technique is quite effective in processing large number of text documents as it takes less computational time.

Simulating coupled dynamics of a rigid-flexible multibody system and compressible fluid

As a subsequent work of previous studies of authors, a new parallel computation approach is proposed to simulate the coupled dynamics of a rigid-flexible multibody system and compressible fluid. In this approach, the smoothed particle hydrodynamics (SPH) method is used to model the compressible fluid, the natural coordinate formulation (NCF) and absolute nodal coordinate formulation (ANCF) are used to model the rigid and flexible bodies, respectively. In order to model the compressible fluid properly and efficiently via SPH method, three measures are taken as follows. The first is to use the Riemann solver to cope with the fluid compressibility, the second is to define virtual particles of SPH to model the dynamic interaction between the fluid and the multibody system, and the third is to impose the boundary conditions of periodical inflow and outflow to reduce the number of SPH particles involved in the computation process. Afterwards, a parallel computation strategy is proposed based on the graphics processing unit (GPU) to detect the neighboring SPH particles and to solve the dynamic equations of SPH particles in order to improve the computation efficiency. Meanwhile, the generalized-alpha algorithm is used to solve the dynamic equations of the multibody system. Finally, four case studies are given to validate the proposed parallel computation approach.

Method for Efficiency Increasing of Distributed Classification of the Images based on the Proactive Parallel Computing Approach

In this paper we propose a new clustering method based on alpha-procedure that differs with proactive computing of graphs and other possible factors superposition of classification. Th ...

Parallel O(N) Stokes' solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries.

An efficient parallel Stokes' solver has been developed for complete description of hydrodynamic interactions between Brownian particles in bulk and confined geometries. A Langevin description of the particle dynamics is adopted, where the long-range interactions are included using a Green's function formalism. A scalable parallel computational approach is presented, where the general geometry Stokeslet is calculated following a matrix-free algorithm using the general geometry Ewald-like method. Our approach employs a highly efficient iterative finite-element Stokes' solver for the accurate treatment of long-range hydrodynamic interactions in arbitrary confined geometries. A combination of mid-point time integration of the Brownian stochastic differential equation, the parallel Stokes' solver, and a Chebyshev polynomial approximation for the fluctuation-dissipation theorem leads to an O(N) parallel algorithm. We illustrate the new algorithm in the context of the dynamics of confined polymer solutions under equilibrium and non-equilibrium conditions. The method is then extended to treat suspended finite size particles of arbitrary shape in any geometry using an immersed boundary approach.