A parallel implementation of nearest neighbor analysis based on GPGPU

Graphics processing units (GPUs) 1 have enjoyed increasing popularity in recent years, which benefits from, for example, general-purpose GPU (GPGPU) for parallel programs and new computing paradigms, such as the Internet of Things (IoT). GPUs hold great potential in providing effective solutions for big data analytics while the demands for processing large quantities of data in real time are also increasing. However, the pervasive presence of GPUs on mobile devices presents great challenges for GPGPU, mainly because GPGPU integrates a large amount of processor arrays and concurrent executing threads (up to hundreds of thousands). In particular, the root causes of performance loss in a GPGPU program can not be revealed in detail by current approaches. In this article, we propose MiC (Multi-level Characterization), a framework that comprehensively characterizes GPGPU kernels at the instruction, Basic Block (BBL), and thread levels. Specifically, we devise Instruction Vectors (IV) and Basic Blocks Vectors (BBV), a Thread Similarity Matrix (TSM), and a Divergence Flow Statistics Graph (DFSG) to profile information in each level. We use MiC to provide insights into GPGPU kernels through the characterizations of 34 kernels from popular GPGPU benchmark suites such as Compute Unified Device Architecture (CUDA) Software Development Kit (SDK), Rodinia, and Parboil. In comparison with Central Processing Unit (CPU) workloads, we conclude the key findings as follows: (1) There are comparable Instruction-Level Parallelism (ILP); (2) The BBL count is significantly smaller than CPU workloads—only 22.8 on average; (3) The dynamic instruction count per thread varies from dozens to tens of thousands and it is extremely small compared to CPU benchmarks; (4) The Pareto principle (also called 90/10 rule) does not apply to GPGPU kernels while it pervasively exists in CPU programs; (5) The loop patterns are dramatically different from those in CPU workloads; (6) The branch ratio is lower than that of CPU programs but higher than pure GPU workloads. In addition, we have also shown how TSM and DFSG are used to characterize the branch divergence in a visual way, to enable the analysis of thread behavior in GPGPU programs. In addition, we show an optimization case for a GPGPU kernel from the bottleneck identified through its characterization result, which improves 16.8% performance.

Computational Fluid Dynamics (CFD) is widely used in industry and academic research to investigate complex fluid flow. The bottleneck of a realistic CFD simulation is its long simulation time. The simulation time is generally reduced by massively parallel Central Processing Unit (CPU) clusters, which are very expensive. In this paper, it is shown that the CFD simulation can be accelerated significantly by a novel hardware called General Purpose Computing on Graphical Processing Units (GPGPU). GPGPU is a cost-effective computing cluster, which uses the Compute Unified Device Architecture (CUDA) of NVIDIA devices to transform the GPU into a massively parallel processor. The paper demonstrates the faster computing ability of GPU compared to a traditional multi-core CPU. Two scenarios are simulated; one is a 2-dimensional simulation of regular wave and another one is a 3-dimensional motion of a floating ship on a regular wave. A smoothed particle hydrodynamics (SPH) based CFD solver is used for simulating the complex free-surface flow. The performance of a single GPU is compared against a commonly used 16 core CPU. For a large simulation of 6 degrees of freedom (DOF) ship motion simulation, the comparative study exhibits a speedup of more than an order of magnitude, reducing simulation time from 30 hours to about 2 hours. This indicates a CUDA enabled GPU card can be used as a cost-effective computing tool for a reliable and accurate SPH-based CFD simulation. The cost-benefit analysis of GPU over a CPU cluster is also discussed.

Purpose: For microdosimetric calculation event-by-event Monte Carlo (MC) simulation is considered the most accurate, but it is very time-consuming. In this work we present an event-by-event MC simulation of low energy electron and proton for accelerated microdosimetric MC simulations on a graphic processing unit (GPU). Methods: The MC simulation of particle was implemented in C and executed on a multi-core CPU, and a commercially available general purpose GPU using the compute unified device architecture (CUDA). Additionally, a hybrid implementation scheme was realized by employing OpenMP and CUDA so that both GPU and multi-core CPU were utilized simultaneously. The two implementation schemes have been tested and compared with the sequential single threaded MC simulation on the CPU. A calculation time comparison was established on the speed-up for a set of benchmarking cases of electron and proton. Results: Dosimetric results were obtained with both the parallel and serial MC codes. A GPU over CPU speed-up of 67.2 and 19.2 times was achieved for 300 eV and 2 keV electron tracks respectively. For proton tracks, the GPU-based code was approximately 5 times faster than the CPU-single-thread code. By incorporating a multi-core CPU and running the MC code simultaneously on the GPU and CPU, an increase of 2%-7% and 20% in the speedup was noticed for electrons and protons tracks respectively. A good dosimetric agreement between the CPU- and GPU-based MC methods was observed for both electrons and proton. Conclusions: A GPU-based MC method for microdosimetric calculations of low energy electron and proton has been presented. The results indicate the capability of our GPU-based implementation for accelerated MC simulations of both electron and proton without loss of accuracy. Lastly, the potential of a hybrid approach by utilizing simultaneously a GPU and a multi-core CPU for further acceleration of MC microdosimetric calculations has been demonstrated.

Starting from brief introduction to fast developing Multi-view Video Coding technology and Compute Unified Device Architecture (CUDA) of General-purpose computing on graphics processing units (GPGPU), we designed an Heterogeneous computing system plan with cooperation of CPU and parallel GPU to accelerate the MVC coding process. To take advantage of GPGPU, parallel MVC motion estimation approach on CUDA was interpreted. For further optimize the system efficiency, a cooperating mode between CPU and GPU are designed.

In today's era, there is a great importance to parallel programming to gain high performance in terms of time required for data computation. There are some constraints to achieve parallelism on CPU (Central Processing Unit). It is possible to achieve data parallelism by SIMD (Single Instruction Multiple Data) on General Purpose Graphics Processing Unit (GPGPU) integrated with Central Processing Unit (CPU). In Database processing, most of the research is going on. In this implementation, Linear Regression Algorithm is used to achieve parallelism in database processing on images using a programming model, Compute Unified Device Architecture (CUDA) which uses multithreading technique. Most of the time is required to perform various operations on huge content-based database e.g. to read big images, datasets, etc. Linear Regression is one of the algorithm to predict, forecast, mine huge amount of data. Linear Regression using CUDA can achieve high performance. Here, Linear Regression is implemented on Graphics Processing Unit (GPU) and on CPU to process image database for prediction of data by finding Covariance matrix, Eigen values and Eigen vectors. The strongest Eigen vector is the best fit line. The time spent for computation is compared in both the implementations.

This study introduces a practical approach to implement real-time signal processing algorithms for general surveillance radar based on NVIDIA graphical processing units (GPUs). The pulse compression algorithms are implemented using compute unified device architecture (CUDA) libraries such as CUDA basic linear algebra subroutines and CUDA fast Fourier transform library, which are adopted from open source libraries and optimized for the NVIDIA GPUs. For more advanced, adaptive processing algorithms such as adaptive pulse compression, customized kernel optimization is needed and investigated. A statistical optimization approach is developed for this purpose without needing much knowledge of the physical configurations of the kernels. It was found that the kernel optimization approach can significantly improve the performance. Benchmark performance is compared with the CPU performance in terms of processing accelerations. The proposed implementation framework can be used in various radar systems including ground-based phased array radar, airborne sense and avoid radar, and aerospace surveillance radar.

Fractal image coding is one of the most prominent compression technologies. It can be also used for industrial applications like image retrieval methods and image indexing methods. In addition, the adaptive approach can achieve the image compression with given quality level by changing the size of range blocks in any location, so the adaptive approach can achieve a high compression rate with less data than the non-adaptive method, but the naive parallel implementation may result in the inefficient parallelization due to the imbalance of work loads. On the other hand, GPGPU (General Purpose computing on Graphics Processing Unit) attracts a great deal of attention, which is used for general-purpose computations like numerical calculations as well as graphics processing. In this paper, we evaluate three parallel programs for the adaptive fractal image coding algorithm on GPUs by using CUDA (Compute Unified Device Architecture) on Nvidia GTX Titan GPU and discuss the effectiveness of parallel programs using index vectors and multithreading. Especially, the third program may enhance the occupancy of GPU computing by distributing the reduction computing over several processing cores.

Parallelization of the finite-difference time-domain method for room acoustics modelling based on CUDA

Abstract. Thanks to the nature of the graphics processing, the newly released products offer highly parallel processing units with high-memory bandwidth and computational power of more than teraflops per second. The modern GPUs are not only powerful graphic engines but also they are high level parallel programmable processors with very fast computing capabilities and high-memory bandwidth speed compared to central processing units (CPU). Data-parallel computations can be shortly described as mapping data elements to parallel processing threads. The rapid development of GPUs programmability and capabilities attracted the attentions of researchers dealing with complex problems which need high level calculations. This interest has revealed the concepts of “General Purpose Computation on Graphics Processing Units (GPGPU)” and “stream processing”. The graphic processors are powerful hardware which is really cheap and affordable. So the graphic processors became an alternative to computer processors. The graphic chips which were standard application hardware have been transformed into modern, powerful and programmable processors to meet the overall needs. Especially in recent years, the phenomenon of the usage of graphics processing units in general purpose computation has led the researchers and developers to this point. The biggest problem is that the graphics processing units use different programming models unlike current programming methods. Therefore, an efficient GPU programming requires re-coding of the current program algorithm by considering the limitations and the structure of the graphics hardware. Currently, multi-core processors can not be programmed by using traditional programming methods. Event procedure programming method can not be used for programming the multi-core processors. GPUs are especially effective in finding solution for repetition of the computing steps for many data elements when high accuracy is needed. Thus, it provides the computing process more quickly and accurately. Compared to the GPUs, CPUs which perform just one computing in a time according to the flow control are slower in performance. This structure can be evaluated for various applications of computer technology. In this study covers how general purpose parallel programming and computational power of the GPUs can be used in photogrammetric applications especially direct georeferencing. The direct georeferencing algorithm is coded by using GPGPU method and CUDA (Compute Unified Device Architecture) programming language. Results provided by this method were compared with the traditional CPU programming. In the other application the projective rectification is coded by using GPGPU method and CUDA programming language. Sample images of various sizes, as compared to the results of the program were evaluated. GPGPU method can be used especially in repetition of same computations on highly dense data, thus finding the solution quickly.

GPGPU (General Purpose computing on Graphic Processing Unit) attracts a great deal of attention, that is used for general-purpose computations like numerical calculations as well as graphic processing. In this paper, as an example of hierarchical clustering algorithms, we evaluate PNN (Pairwise Nearest Neighbor) on GPUs by using CUDA (Compute Unified Device Architecture). We also evaluate it from the viewpoint of the power consumption.

Fuzzy dark matter (FDM) is a promising candidate for dark matter (DM), characterized by its ultra-light mass, which gives rise to wave effects at astrophysical scales. These effects offer potential solutions to the small-scale issues encountered within the standard cold dark matter (CDM) paradigm. In this paper, we investigate the large-scale structure of the cosmic web using FDM simulations, comparing them to CDM-only simulations and a simulation incorporating baryonic effects. Our study employs the nearest neighbour (NN) analysis as a new statistical tool for examining the structure and statistics of the cosmic web in an FDM universe. This analysis could capture the information absent in the two-point correlation functions. In particular, we analyse data related to the spherical contact, nearest neighbour distances (NND), and the angle between the first and second nearest neighbours of haloes (NNA). Specifically, we utilize probability distribution functions, statistical moments, and fitting parameters, as well as G(x), F(x), and J(x) functions to analyse the above data. Remarkably, the results from the FDM simulations differ significantly from the others across these analyses, while no noticeable distinction is observed between the baryonic and CDM-only simulations. Moreover, the lower FDM mass leads to more significant deviations from the CDM simulations. These compelling results highlight the efficiency of the NN analysis – mainly through the use of the J(x) function, $s_3$, $l_{3}$, and $a_4$ parameters – as a prominent new tool for investigating FDM on large scales and making observational predictions.

Nowadays graphics processing units (GPUs) have become popular parallel computing platforms known as General-Purpose GPU (GPGPU) computing. GPUs thereby are chosen by some security researchers as cryptographic accelerators to secure massive volumes of transactions. However, their security issues are ignored in spite of their popularity and performance. There are some possible information leakages faced with malicious attacks or even in the normal GPU computing. Our objective is to secure the confidentiality of cryptographic keys in GPU computing environments and provide easy-to-use programming with few constraints. In this paper, we propose a prototype in Linux, a system of GPGPU computing solution empowered by GPU virtualization technology, which keeps encrypted keys in guest machine to protect secret keys from leakage even in the event of full system compromise. With the API interception and redirection of CUDA, applications in Virtual Machines (VMs) can access the GPU device in a transparent way. Besides, we use virtio, a dedicated virtual I/O device, to transfer data between virtual and host machines in high performance. In our current study, we evaluate our prototype with the GPU implementation of ECC. We show that it can protect private keys of GPU cryptographic computation and it also incurs low performance penalty compared with the native environment, therefore demonstrating the prototype is secure and requires reasonable overhead.

Fast computation of projection images is crucial in many applications such as medical image reconstruction and light field image processing. To do that, parallelization of the computation and efficient implementation of the computation using a parallel processor such as GPGPU (General-Purpose computing on Graphics Processing Units) is essential. In this research, we investigate methods for parallel computation of projection images and efficient implementation of the methods using CUDA (Compute Unified Device Architecture). We also study how to efficiently use the memory of GPU for the parallel processing.

DNA microarrays are used to simultaneously analyze the expression level of thousands of genes under multiple conditions; however, massive amount of data is generated making its analysis a challenge and an ideal candidate for massive parallel processing. Among the available technologies, the use of General Purpose computation on Graphics Processing Units (GPGPU) is an efficient cost-effective alternative, compared to a Central Processing Unit (CPU). This paper presents an implementation of algorithms using Compute Unified Device Architecture (CUDA) to determine statistical significance in the evaluation of gene expression levels for a microarray hybridization experiment designed and carried out at the Centro de Investigaciones Biologicas del Noroeste S.C. (CIBNOR). The obtained results are compared to traditional implementations.

Two benchmark tests were carried out to analyze the performance of OpenFOAM-based CFD solvers using General-Purpose computing on Graphics Processing Units(GPGPU). In the present study, RapidCFD, which is an implementation of OpenFOAM capable of running most of the functions of OpenFOAM on GPUs, was used to apply GPGPU to OpenFOAM. The numerical simulations of 1) 3D lid-driven cavity incompressible flows and 2) steady flows around a motorbike were conducted on two kinds of CPU, single-GPU, and multi-GPU systems, and the computational times were analyzed. For the test of cavity flows, as the number of cells increased, the performance and the scalability of GPGPU were improved. When the number of cells was 2503, a system with 8-GPUs showed the highest performance with 42 times of speedup over a CPU system. For the test of flows around a motorbike, a system with 8-GPUs showed the highest performance with 20 times of speedup over a CPU system. For both single precision and double precision calculations, the performance improvements using GPGPU were efficient. The results demonstrate that GPGPU would be more efficient than computing on CPUs when computing large-scale flows and practical problems that require massive parallelism.