This study embarks on a comprehensive examination of optimization techniques within GPU-based parallel programming models,pivotal for advancing high-performance computing(HPC).Emphasizing the transition of GPUs from g...This study embarks on a comprehensive examination of optimization techniques within GPU-based parallel programming models,pivotal for advancing high-performance computing(HPC).Emphasizing the transition of GPUs from graphic-centric processors to versatile computing units,it delves into the nuanced optimization of memory access,thread management,algorithmic design,and data structures.These optimizations are critical for exploiting the parallel processing capabilities of GPUs,addressingboth the theoretical frameworks and practical implementations.By integrating advanced strategies such as memory coalescing,dynamic scheduling,and parallel algorithmic transformations,this research aims to significantly elevate computational efficiency and throughput.The findings underscore the potential of optimized GPU programming to revolutionize computational tasks across various domains,highlighting a pathway towards achieving unparalleled processing power and efficiency in HPC environments.The paper not only contributes to the academic discourse on GPU optimization but also provides actionable insights for developers,fostering advancements in computational sciences and technology.展开更多
Heterogeneous many-cores are now an integral part of modern computing systems ranging from embedding systems to supercomputers.While heterogeneous many-core design offers the potential for energy-efficient high-perfor...Heterogeneous many-cores are now an integral part of modern computing systems ranging from embedding systems to supercomputers.While heterogeneous many-core design offers the potential for energy-efficient high-performance,such potential can only be unlocked if the application programs are suitably parallel and can be made to match the underlying heterogeneous platform.In this article,we provide a comprehensive survey for parallel programming models for heterogeneous many-core architectures and review the compiling techniques of improving programmability and portability.We examine various software optimization techniques for minimizing the communicating overhead between heterogeneous computing devices.We provide a road map for a wide variety of different research areas.We conclude with a discussion on open issues in the area and potential research directions.This article provides both an accessible introduction to the fast-moving area of heterogeneous programming and a detailed bibliography of its main achievements.展开更多
Web service is a grid computing technology that promises greater ease-of-use and interoperability than previous distributed computing technologies. This paper proposed Group Service Framework, a grid computing platfor...Web service is a grid computing technology that promises greater ease-of-use and interoperability than previous distributed computing technologies. This paper proposed Group Service Framework, a grid computing platform based on Microsoft. NET that use web service to: (1) locate and harness volunteer computing resources for different applications, and (2) support multi-models such as Master/Slave, Divide and Conquer, Phase Parallel and so forth parallel programming paradigms in Grid environment, (3) allocate data and balance load dynamically and transparently for grid computing application. The Grid Service Framework based on Microsoft. NET was used to implement several simple parallel computing applications. The results show that the proposed Group Service Framework is suitable for generic parallel numerical computing.展开更多
Current HPC hardware presents the characteristics of heterogeneity and diversity.Portable parallel programming technologies are attractive for application developers.OP2 is a domain specific programming framework for ...Current HPC hardware presents the characteristics of heterogeneity and diversity.Portable parallel programming technologies are attractive for application developers.OP2 is a domain specific programming framework for unstructured applications.It supports unified programming and automatic code generation for multiple hardware platforms.However,current OP2 implementation is faced with some difficulties in programming application with complex data structures and function calls.To address this issue,we improve the implementation of OP2 framework in this paper.We modified the source-to-source translator and the runtime library of OP2,making it possible to automatically support applications with complex data structures and function calls during the generation of serial,OpenMP,CUDA,and MPI versions of codes.This avoids tedious manual code rewriting process for the OP2 application developers.HOUR2D,a high order and complex unstructured CFD application,is used as an example to verify the applicability of our extension to the OP2 framework.The results show that our extension enables OP2 to support portable programming for complex unstructured applications without changing its programming mode,ensures the correctness of the results,and achieves comparable or even better performance than manual parallelizations on Intel Xeon Gold CPU,HUAWEI Kunpeng CPU and NVIDIA V100 GPU.展开更多
The workload of the 3D magnetotelluric forward modeling algorithm is so large that the traditional serial algorithm costs an extremely large compute time. However, the 3D forward modeling algorithm can process the dat...The workload of the 3D magnetotelluric forward modeling algorithm is so large that the traditional serial algorithm costs an extremely large compute time. However, the 3D forward modeling algorithm can process the data in the frequency domain, which is very suitable for parallel computation. With the advantage of MPI and based on an analysis of the flow of the 3D magnetotelluric serial forward algorithm, we suggest the idea of parallel computation and apply it. Three theoretical models are tested and the execution efficiency is compared in different situations. The results indicate that the parallel 3D forward modeling computation is correct and the efficiency is greatly improved. This method is suitable for large size geophysical computations.展开更多
Modern power systems are evolving into sociotechnical systems with massive complexity, whose real-time operation and dispatch go beyond human capability. Thus,the need for developing and applying new intelligent power...Modern power systems are evolving into sociotechnical systems with massive complexity, whose real-time operation and dispatch go beyond human capability. Thus,the need for developing and applying new intelligent power system dispatch tools are of great practical significance. In this paper, we introduce the overall business model of power system dispatch, the top level design approach of an intelligent dispatch system, and the parallel intelligent technology with its dispatch applications. We expect that a new dispatch paradigm,namely the parallel dispatch, can be established by incorporating various intelligent technologies, especially the parallel intelligent technology, to enable secure operation of complex power grids,extend system operators' capabilities, suggest optimal dispatch strategies, and to provide decision-making recommendations according to power system operational goals.展开更多
Scale Invariant Feature Transform (SIFT) algorithm is a widely used computer vision algorithm that detects and extracts local feature descriptors from images. SIFT is computationally intensive, making it infeasible fo...Scale Invariant Feature Transform (SIFT) algorithm is a widely used computer vision algorithm that detects and extracts local feature descriptors from images. SIFT is computationally intensive, making it infeasible for single threaded im-plementation to extract local feature descriptors for high-resolution images in real time. In this paper, an approach to parallelization of the SIFT algorithm is demonstrated using NVIDIA’s Graphics Processing Unit (GPU). The parallel-ization design for SIFT on GPUs is divided into two stages, a) Algorithm de-sign-generic design strategies which focuses on data and b) Implementation de-sign-architecture specific design strategies which focuses on optimally using GPU resources for maximum occupancy. Increasing memory latency hiding, eliminating branches and data blocking achieve a significant decrease in aver-age computational time. Furthermore, it is observed via Paraver tools that our approach to parallelization while optimizing for maximum occupancy allows GPU to execute memory bound SIFT algorithm at optimal levels.展开更多
In recent years, the widespread adoption of parallel computing, especially in multi-core processors and high-performance computing environments, ushered in a new era of efficiency and speed. This trend was particularl...In recent years, the widespread adoption of parallel computing, especially in multi-core processors and high-performance computing environments, ushered in a new era of efficiency and speed. This trend was particularly noteworthy in the field of image processing, which witnessed significant advancements. This parallel computing project explored the field of parallel image processing, with a focus on the grayscale conversion of colorful images. Our approach involved integrating OpenMP into our framework for parallelization to execute a critical image processing task: grayscale conversion. By using OpenMP, we strategically enhanced the overall performance of the conversion process by distributing the workload across multiple threads. The primary objectives of our project revolved around optimizing computation time and improving overall efficiency, particularly in the task of grayscale conversion of colorful images. Utilizing OpenMP for concurrent processing across multiple cores significantly reduced execution times through the effective distribution of tasks among these cores. The speedup values for various image sizes highlighted the efficacy of parallel processing, especially for large images. However, a detailed examination revealed a potential decline in parallelization efficiency with an increasing number of cores. This underscored the importance of a carefully optimized parallelization strategy, considering factors like load balancing and minimizing communication overhead. Despite challenges, the overall scalability and efficiency achieved with parallel image processing underscored OpenMP’s effectiveness in accelerating image manipulation tasks.展开更多
The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to alig...The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.展开更多
HPC(high perfomance computing)based on clusters of multicores is one of the main research lines in parallel programming.It is important to study the impact of programming paradigms of shared memory,message passing or ...HPC(high perfomance computing)based on clusters of multicores is one of the main research lines in parallel programming.It is important to study the impact of programming paradigms of shared memory,message passing or a combination of both on these architectures in order to efficiently exploit the power of these architectures.The Smith-Waterman algorithm is used as study case for the local alignment of DNA sequences,which allows establishing the similarity degree between two sequences.In this paper,the Smith-Waterman algorithm is parallelized by means of a pipeline scheme due to the data dependencies that are inherent to the problem,using the various communication/synchronization models mentioned above and then carrying out a comparative analysis.Finally,experimental results are presented,as well as future research lines.展开更多
The solution of tension distributions is infinite for cable-driven parallel manipulators(CDPMs) with redundant cables. A rapid optimization method for determining the optimal tension distribution is presented. The n...The solution of tension distributions is infinite for cable-driven parallel manipulators(CDPMs) with redundant cables. A rapid optimization method for determining the optimal tension distribution is presented. The new optimization method is primarily based on the geometry properties of a polyhedron and convex analysis. The computational efficiency of the optimization method is improved by the designed projection algorithm, and a fast algorithm is proposed to determine which two of the lines are intersected at the optimal point. Moreover, a method for avoiding the operating point on the lower tension limit is developed. Simulation experiments are implemented on a six degree-of-freedom(6-DOF) CDPM with eight cables, and the results indicate that the new method is one order of magnitude faster than the standard simplex method. The optimal distribution of tension distribution is thus rapidly established on real-time by the proposed method.展开更多
Cyber-physical systems (CPS) represent a class of complex engineered systems where functionality and behavior emerge through the interaction between the computational and physical domains. Simulation provides design e...Cyber-physical systems (CPS) represent a class of complex engineered systems where functionality and behavior emerge through the interaction between the computational and physical domains. Simulation provides design engineers with quick and accurate feedback on the behaviors generated by their designs. However, as systems become more complex, simulating their behaviors becomes computation all complex. But, most modern simulation environments still execute on a single thread, which does not take advantage of the processing power available on modern multi-core CPUs. This paper investigates methods to partition and simulate differential equation-based models of cyber-physical systems using multiple threads on multi-core CPUs that can share data across threads. We describe model partitioning methods using fixed step and variable step numerical in-tegration methods that consider the multi-layer cache structure of these CPUs to avoid simulation performance degradation due to cache conflicts. We study the effectiveness of each parallel simu-lation algorithm by calculating the relative speedup compared to a serial simulation applied to a series of large electric circuit models. We also develop a series of guidelines for maximizing performance when developing parallel simulation software intended for use on multi-core CPUs.展开更多
Large scale optimization problems can only be solved in an efficient way, if their special structure is taken as the basis of algorithm design. In this paper we consider a very broad class of large-scale problems with...Large scale optimization problems can only be solved in an efficient way, if their special structure is taken as the basis of algorithm design. In this paper we consider a very broad class of large-scale problems with special structure, namely tree structured problems. We show how the exploitation of the structure leads to efficient decomposition algorithms and how it may be implemented in a parallel environment.展开更多
This study presents a parallel version of the string matching algorithms research tool(SMART)library,implemented on NVIDIA’s compute unified device architecture(CUDA)platform,and uses general-purpose computing on gra...This study presents a parallel version of the string matching algorithms research tool(SMART)library,implemented on NVIDIA’s compute unified device architecture(CUDA)platform,and uses general-purpose computing on graphics processing unit(GPGPU)programming concepts to enhance performance and gain insight into the parallel versions of these algorithms.We have developed the CUDA-enhanced SMART(CUSMART)library,which incorporates parallelized iterations of 64 string matching algorithms,leveraging the CUDA application programming interface.The performance of these algorithms has been assessed across various scenarios to ensure a comprehensive and impartial comparison,allowing for the identification of their strengths and weaknesses in specific application contexts.We have explored and established optimization techniques to gauge their influence on the performance of these algorithms.The results of this study highlight the potential of GPGPU computing in string matching applications through the scalability of algorithms,suggesting significant performance improvements.Furthermore,we have identified the best and worst performing algorithms in various scenarios.展开更多
Most modern technologies,such as social media,smart cities,and the internet of things(IoT),rely on big data.When big data is used in the real-world applications,two data challenges such as class overlap and class imba...Most modern technologies,such as social media,smart cities,and the internet of things(IoT),rely on big data.When big data is used in the real-world applications,two data challenges such as class overlap and class imbalance arises.When dealing with large datasets,most traditional classifiers are stuck in the local optimum problem.As a result,it’s necessary to look into new methods for dealing with large data collections.Several solutions have been proposed for overcoming this issue.The rapid growth of the available data threatens to limit the usefulness of many traditional methods.Methods such as oversampling and undersampling have shown great promises in addressing the issues of class imbalance.Among all of these techniques,Synthetic Minority Oversampling TechniquE(SMOTE)has produced the best results by generating synthetic samples for the minority class in creating a balanced dataset.The issue is that their practical applicability is restricted to problems involving tens of thousands or lower instances of each.In this paper,we have proposed a parallel mode method using SMOTE and MapReduce strategy,this distributes the operation of the algorithm among a group of computational nodes for addressing the aforementioned problem.Our proposed solution has been divided into three stages.Thefirst stage involves the process of splitting the data into different blocks using a mapping function,followed by a pre-processing step for each mapping block that employs a hybrid SMOTE algo-rithm for solving the class imbalanced problem.On each map block,a decision tree model would be constructed.Finally,the decision tree blocks would be com-bined for creating a classification model.We have used numerous datasets with up to 4 million instances in our experiments for testing the proposed scheme’s cap-abilities.As a result,the Hybrid SMOTE appears to have good scalability within the framework proposed,and it also cuts down the processing time.展开更多
The seismic reflection method is one of the most important methods in geophysical exploration.There are three stages in a seismic exploration survey:acquisition,processing,and interpretation.This paper focuses on a pr...The seismic reflection method is one of the most important methods in geophysical exploration.There are three stages in a seismic exploration survey:acquisition,processing,and interpretation.This paper focuses on a pre-processing tool,the Non-Local Means(NLM)filter algorithm,which is a powerful technique that can significantly suppress noise in seismic data.However,the domain of the NLM algorithm is the whole dataset and 3D seismic data being very large,often exceeding one terabyte(TB),it is impossible to store all the data in Random Access Memory(RAM).Furthermore,the NLM filter would require a considerably long runtime.These factors make a straightforward implementation of the NLM algorithm on real geophysical exploration data infeasible.This paper redesigned and implemented the NLM filter algorithm to fit the challenges of seismic exploration.The optimized implementation of the NLM filter is capable of processing production-size seismic data on modern clusters and is 87 times faster than the straightforward implementation of NLM.展开更多
本文用CORE-IAF(Coordinated Ocean-ice Reference Experiments–Interannual Forcing)外强迫场分别强迫LICOM3(LASG/IAP Climate System Ocean Model Version 3)和POP2(Parallel Ocean Program version 2)两个海洋模式,并分析了这两个...本文用CORE-IAF(Coordinated Ocean-ice Reference Experiments–Interannual Forcing)外强迫场分别强迫LICOM3(LASG/IAP Climate System Ocean Model Version 3)和POP2(Parallel Ocean Program version 2)两个海洋模式,并分析了这两个模式中太平洋北赤道逆流(NECC)的模拟结果。我们发现LICOM3和POP2模拟的NECC强度均弱于实测,这和Sun et al.(2019)的研究结果一致,也进一步证明了海洋模式中NECC偏弱是CORE-IAF外强迫场造成的,海表风应力及对应的风应力旋度是海洋模式准确模拟NECC的最主要因子。同时,我们也分析了NECC的模拟在动力机制上的差别,这里的动力强迫项包括风应力项、平流项和余项。我们发现模式的外强迫场虽然相同,但是两个模式中各动力强迫项(风应力项、平流项和余项)对NECC模拟的影响并不完全相同。展开更多
First, an asynchronous distributed parallel evolutionary modeling algorithm (PEMA) for building the model of system of ordinary differential equations for dynamical systems is proposed in this paper. Then a series of ...First, an asynchronous distributed parallel evolutionary modeling algorithm (PEMA) for building the model of system of ordinary differential equations for dynamical systems is proposed in this paper. Then a series of parallel experiments have been conducted to systematically test the influence of some important parallel control parameters on the performance of the algorithm. A lot of experimental results are obtained and we make some analysis and explanations to them.展开更多
In this paper they deal with the issue of specification and design of parallel communicatingprocesses. A trace-state based model is introduced to describe the behaviour of concurrent programs. They presenta formal sys...In this paper they deal with the issue of specification and design of parallel communicatingprocesses. A trace-state based model is introduced to describe the behaviour of concurrent programs. They presenta formal system based on that model to achieve hierarchical and modular development and verification methods. Anumber of refinement rules are used to decompose the specification into smaller ones and calculate program fromthe展开更多
摘要This study embarks on a comprehensive examination of optimization techniques within GPU-based parallel programming models,pivotal for advancing high-performance computing(HPC).Emphasizing the transition of GPUs from graphic-centric processors to versatile computing units,it delves into the nuanced optimization of memory access,thread management,algorithmic design,and data structures.These optimizations are critical for exploiting the parallel processing capabilities of GPUs,addressingboth the theoretical frameworks and practical implementations.By integrating advanced strategies such as memory coalescing,dynamic scheduling,and parallel algorithmic transformations,this research aims to significantly elevate computational efficiency and throughput.The findings underscore the potential of optimized GPU programming to revolutionize computational tasks across various domains,highlighting a pathway towards achieving unparalleled processing power and efficiency in HPC environments.The paper not only contributes to the academic discourse on GPU optimization but also provides actionable insights for developers,fostering advancements in computational sciences and technology.
基金partially funded by the National Key Research and Development Program of China under Grant No.2018YFB0204301the National Natural Science Foundation of China under Grant agreements 61972408,61602501 and 61872294a UK Royal Society International Collaboration Grant.
摘要Heterogeneous many-cores are now an integral part of modern computing systems ranging from embedding systems to supercomputers.While heterogeneous many-core design offers the potential for energy-efficient high-performance,such potential can only be unlocked if the application programs are suitably parallel and can be made to match the underlying heterogeneous platform.In this article,we provide a comprehensive survey for parallel programming models for heterogeneous many-core architectures and review the compiling techniques of improving programmability and portability.We examine various software optimization techniques for minimizing the communicating overhead between heterogeneous computing devices.We provide a road map for a wide variety of different research areas.We conclude with a discussion on open issues in the area and potential research directions.This article provides both an accessible introduction to the fast-moving area of heterogeneous programming and a detailed bibliography of its main achievements.
基金National Natural F oundation of China(No.60 173 0 13 )
摘要Web service is a grid computing technology that promises greater ease-of-use and interoperability than previous distributed computing technologies. This paper proposed Group Service Framework, a grid computing platform based on Microsoft. NET that use web service to: (1) locate and harness volunteer computing resources for different applications, and (2) support multi-models such as Master/Slave, Divide and Conquer, Phase Parallel and so forth parallel programming paradigms in Grid environment, (3) allocate data and balance load dynamically and transparently for grid computing application. The Grid Service Framework based on Microsoft. NET was used to implement several simple parallel computing applications. The results show that the proposed Group Service Framework is suitable for generic parallel numerical computing.
基金supported by the National Natural Science Foundation of China under Grant Nos.62272474 and 61561146395.
摘要Current HPC hardware presents the characteristics of heterogeneity and diversity.Portable parallel programming technologies are attractive for application developers.OP2 is a domain specific programming framework for unstructured applications.It supports unified programming and automatic code generation for multiple hardware platforms.However,current OP2 implementation is faced with some difficulties in programming application with complex data structures and function calls.To address this issue,we improve the implementation of OP2 framework in this paper.We modified the source-to-source translator and the runtime library of OP2,making it possible to automatically support applications with complex data structures and function calls during the generation of serial,OpenMP,CUDA,and MPI versions of codes.This avoids tedious manual code rewriting process for the OP2 application developers.HOUR2D,a high order and complex unstructured CFD application,is used as an example to verify the applicability of our extension to the OP2 framework.The results show that our extension enables OP2 to support portable programming for complex unstructured applications without changing its programming mode,ensures the correctness of the results,and achieves comparable or even better performance than manual parallelizations on Intel Xeon Gold CPU,HUAWEI Kunpeng CPU and NVIDIA V100 GPU.
基金This research is sponsored by the National Natural Science Foundation of China (No. 40374024).
摘要The workload of the 3D magnetotelluric forward modeling algorithm is so large that the traditional serial algorithm costs an extremely large compute time. However, the 3D forward modeling algorithm can process the data in the frequency domain, which is very suitable for parallel computation. With the advantage of MPI and based on an analysis of the flow of the 3D magnetotelluric serial forward algorithm, we suggest the idea of parallel computation and apply it. Three theoretical models are tested and the execution efficiency is compared in different situations. The results indicate that the parallel 3D forward modeling computation is correct and the efficiency is greatly improved. This method is suitable for large size geophysical computations.
基金supported by State Grid Corporation of China(SGCC)Science and Technology Project SGTJDK00DWJS1700060
摘要Modern power systems are evolving into sociotechnical systems with massive complexity, whose real-time operation and dispatch go beyond human capability. Thus,the need for developing and applying new intelligent power system dispatch tools are of great practical significance. In this paper, we introduce the overall business model of power system dispatch, the top level design approach of an intelligent dispatch system, and the parallel intelligent technology with its dispatch applications. We expect that a new dispatch paradigm,namely the parallel dispatch, can be established by incorporating various intelligent technologies, especially the parallel intelligent technology, to enable secure operation of complex power grids,extend system operators' capabilities, suggest optimal dispatch strategies, and to provide decision-making recommendations according to power system operational goals.
摘要Scale Invariant Feature Transform (SIFT) algorithm is a widely used computer vision algorithm that detects and extracts local feature descriptors from images. SIFT is computationally intensive, making it infeasible for single threaded im-plementation to extract local feature descriptors for high-resolution images in real time. In this paper, an approach to parallelization of the SIFT algorithm is demonstrated using NVIDIA’s Graphics Processing Unit (GPU). The parallel-ization design for SIFT on GPUs is divided into two stages, a) Algorithm de-sign-generic design strategies which focuses on data and b) Implementation de-sign-architecture specific design strategies which focuses on optimally using GPU resources for maximum occupancy. Increasing memory latency hiding, eliminating branches and data blocking achieve a significant decrease in aver-age computational time. Furthermore, it is observed via Paraver tools that our approach to parallelization while optimizing for maximum occupancy allows GPU to execute memory bound SIFT algorithm at optimal levels.
摘要In recent years, the widespread adoption of parallel computing, especially in multi-core processors and high-performance computing environments, ushered in a new era of efficiency and speed. This trend was particularly noteworthy in the field of image processing, which witnessed significant advancements. This parallel computing project explored the field of parallel image processing, with a focus on the grayscale conversion of colorful images. Our approach involved integrating OpenMP into our framework for parallelization to execute a critical image processing task: grayscale conversion. By using OpenMP, we strategically enhanced the overall performance of the conversion process by distributing the workload across multiple threads. The primary objectives of our project revolved around optimizing computation time and improving overall efficiency, particularly in the task of grayscale conversion of colorful images. Utilizing OpenMP for concurrent processing across multiple cores significantly reduced execution times through the effective distribution of tasks among these cores. The speedup values for various image sizes highlighted the efficacy of parallel processing, especially for large images. However, a detailed examination revealed a potential decline in parallelization efficiency with an increasing number of cores. This underscored the importance of a carefully optimized parallelization strategy, considering factors like load balancing and minimizing communication overhead. Despite challenges, the overall scalability and efficiency achieved with parallel image processing underscored OpenMP’s effectiveness in accelerating image manipulation tasks.
摘要The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.
摘要HPC(high perfomance computing)based on clusters of multicores is one of the main research lines in parallel programming.It is important to study the impact of programming paradigms of shared memory,message passing or a combination of both on these architectures in order to efficiently exploit the power of these architectures.The Smith-Waterman algorithm is used as study case for the local alignment of DNA sequences,which allows establishing the similarity degree between two sequences.In this paper,the Smith-Waterman algorithm is parallelized by means of a pipeline scheme due to the data dependencies that are inherent to the problem,using the various communication/synchronization models mentioned above and then carrying out a comparative analysis.Finally,experimental results are presented,as well as future research lines.
基金Supported by National Natural Science Foundation of China(Grant No.51275500)Research Project of State Key Laboratory of Mechanical System and Vibration(Grant No.MSV201502)+1 种基金USTC-COOGOO Robotics Research Center(Grant No.2015)Youth Innovation Promotion Association of Chinese Academy of Sciences(Grant No.2012321)
摘要The solution of tension distributions is infinite for cable-driven parallel manipulators(CDPMs) with redundant cables. A rapid optimization method for determining the optimal tension distribution is presented. The new optimization method is primarily based on the geometry properties of a polyhedron and convex analysis. The computational efficiency of the optimization method is improved by the designed projection algorithm, and a fast algorithm is proposed to determine which two of the lines are intersected at the optimal point. Moreover, a method for avoiding the operating point on the lower tension limit is developed. Simulation experiments are implemented on a six degree-of-freedom(6-DOF) CDPM with eight cables, and the results indicate that the new method is one order of magnitude faster than the standard simplex method. The optimal distribution of tension distribution is thus rapidly established on real-time by the proposed method.
摘要Cyber-physical systems (CPS) represent a class of complex engineered systems where functionality and behavior emerge through the interaction between the computational and physical domains. Simulation provides design engineers with quick and accurate feedback on the behaviors generated by their designs. However, as systems become more complex, simulating their behaviors becomes computation all complex. But, most modern simulation environments still execute on a single thread, which does not take advantage of the processing power available on modern multi-core CPUs. This paper investigates methods to partition and simulate differential equation-based models of cyber-physical systems using multiple threads on multi-core CPUs that can share data across threads. We describe model partitioning methods using fixed step and variable step numerical in-tegration methods that consider the multi-layer cache structure of these CPUs to avoid simulation performance degradation due to cache conflicts. We study the effectiveness of each parallel simu-lation algorithm by calculating the relative speedup compared to a serial simulation applied to a series of large electric circuit models. We also develop a series of guidelines for maximizing performance when developing parallel simulation software intended for use on multi-core CPUs.
基金Supported by the Austrin Science Fund as part of the Special Research Program AURORA(f0 11)
摘要Large scale optimization problems can only be solved in an efficient way, if their special structure is taken as the basis of algorithm design. In this paper we consider a very broad class of large-scale problems with special structure, namely tree structured problems. We show how the exploitation of the structure leads to efficient decomposition algorithms and how it may be implemented in a parallel environment.
基金Project supported by the Scientific and Technological Research Council of Türkiye(No.117E142)Open access funding provided by the Scientific and Technological Research Council of Türkiye(TÜBİTAK)。
摘要This study presents a parallel version of the string matching algorithms research tool(SMART)library,implemented on NVIDIA’s compute unified device architecture(CUDA)platform,and uses general-purpose computing on graphics processing unit(GPGPU)programming concepts to enhance performance and gain insight into the parallel versions of these algorithms.We have developed the CUDA-enhanced SMART(CUSMART)library,which incorporates parallelized iterations of 64 string matching algorithms,leveraging the CUDA application programming interface.The performance of these algorithms has been assessed across various scenarios to ensure a comprehensive and impartial comparison,allowing for the identification of their strengths and weaknesses in specific application contexts.We have explored and established optimization techniques to gauge their influence on the performance of these algorithms.The results of this study highlight the potential of GPGPU computing in string matching applications through the scalability of algorithms,suggesting significant performance improvements.Furthermore,we have identified the best and worst performing algorithms in various scenarios.
摘要Most modern technologies,such as social media,smart cities,and the internet of things(IoT),rely on big data.When big data is used in the real-world applications,two data challenges such as class overlap and class imbalance arises.When dealing with large datasets,most traditional classifiers are stuck in the local optimum problem.As a result,it’s necessary to look into new methods for dealing with large data collections.Several solutions have been proposed for overcoming this issue.The rapid growth of the available data threatens to limit the usefulness of many traditional methods.Methods such as oversampling and undersampling have shown great promises in addressing the issues of class imbalance.Among all of these techniques,Synthetic Minority Oversampling TechniquE(SMOTE)has produced the best results by generating synthetic samples for the minority class in creating a balanced dataset.The issue is that their practical applicability is restricted to problems involving tens of thousands or lower instances of each.In this paper,we have proposed a parallel mode method using SMOTE and MapReduce strategy,this distributes the operation of the algorithm among a group of computational nodes for addressing the aforementioned problem.Our proposed solution has been divided into three stages.Thefirst stage involves the process of splitting the data into different blocks using a mapping function,followed by a pre-processing step for each mapping block that employs a hybrid SMOTE algo-rithm for solving the class imbalanced problem.On each map block,a decision tree model would be constructed.Finally,the decision tree blocks would be com-bined for creating a classification model.We have used numerous datasets with up to 4 million instances in our experiments for testing the proposed scheme’s cap-abilities.As a result,the Hybrid SMOTE appears to have good scalability within the framework proposed,and it also cuts down the processing time.
摘要The seismic reflection method is one of the most important methods in geophysical exploration.There are three stages in a seismic exploration survey:acquisition,processing,and interpretation.This paper focuses on a pre-processing tool,the Non-Local Means(NLM)filter algorithm,which is a powerful technique that can significantly suppress noise in seismic data.However,the domain of the NLM algorithm is the whole dataset and 3D seismic data being very large,often exceeding one terabyte(TB),it is impossible to store all the data in Random Access Memory(RAM).Furthermore,the NLM filter would require a considerably long runtime.These factors make a straightforward implementation of the NLM algorithm on real geophysical exploration data infeasible.This paper redesigned and implemented the NLM filter algorithm to fit the challenges of seismic exploration.The optimized implementation of the NLM filter is capable of processing production-size seismic data on modern clusters and is 87 times faster than the straightforward implementation of NLM.
摘要本文用CORE-IAF(Coordinated Ocean-ice Reference Experiments–Interannual Forcing)外强迫场分别强迫LICOM3(LASG/IAP Climate System Ocean Model Version 3)和POP2(Parallel Ocean Program version 2)两个海洋模式,并分析了这两个模式中太平洋北赤道逆流(NECC)的模拟结果。我们发现LICOM3和POP2模拟的NECC强度均弱于实测,这和Sun et al.(2019)的研究结果一致,也进一步证明了海洋模式中NECC偏弱是CORE-IAF外强迫场造成的,海表风应力及对应的风应力旋度是海洋模式准确模拟NECC的最主要因子。同时,我们也分析了NECC的模拟在动力机制上的差别,这里的动力强迫项包括风应力项、平流项和余项。我们发现模式的外强迫场虽然相同,但是两个模式中各动力强迫项(风应力项、平流项和余项)对NECC模拟的影响并不完全相同。
基金Supported by the National Natural Science Foundation of China(60133010,70071042,60073043)
摘要First, an asynchronous distributed parallel evolutionary modeling algorithm (PEMA) for building the model of system of ordinary differential equations for dynamical systems is proposed in this paper. Then a series of parallel experiments have been conducted to systematically test the influence of some important parallel control parameters on the performance of the algorithm. A lot of experimental results are obtained and we make some analysis and explanations to them.
基金ESPRIT Basic Research ProCoS project 3104 and 7071
摘要In this paper they deal with the issue of specification and design of parallel communicatingprocesses. A trace-state based model is introduced to describe the behaviour of concurrent programs. They presenta formal system based on that model to achieve hierarchical and modular development and verification methods. Anumber of refinement rules are used to decompose the specification into smaller ones and calculate program fromthe