A promising CUDA-accelerated vehicular area network simulator using NS-3

Watershed analysis, as a fundamental component of digital terrain analysis, is based on the Digital Elevation Model (DEM), which is a grid (raster) model of the Earth surface and topography. Watershed analysis consists of computationally and data intensive computing algorithms that need to be implemented by leveraging parallel and high-performance computing methods and techniques. In this paper, the Multiple Flow Direction (MFD) algorithm for watershed analysis is implemented and evaluated on multi-core Central Processing Units (CPU) and many-core Graphics Processing Units (GPU), which provides significant improvements in performance and energy usage. The implementation is based on NVIDIA CUDA (Compute Unified Device Architecture) implementation for GPU, as well as on OpenACC (Open ACCelerators), a parallel programming model, and a standard for parallel computing. Both phases of the MFD algorithm (i) iterative DEM preprocessing and (ii) iterative MFD algorithm, are parallelized and run over multi-core CPU and GPU. The evaluation of the proposed solutions is performed with respect to the execution time, energy consumption, and programming effort for algorithm parallelization for different sizes of input data. An experimental evaluation has shown not only the advantage of using OpenACC programming over CUDA programming in implementing the watershed analysis on a GPU in terms of performance, energy consumption, and programming effort, but also significant benefits in implementing it on the multi-core CPU.

Turbo Similarity Searching (TSS) is a two phases searching procedure that has been proven by previous works as one of the best searching method on chemical databases. TSS however consumes lots of computation time due to the number of searches and fusion carried out in the second phase of its procedure. Hence, TSS would not be able to cater the increase in the chemical database size due to this limitation. With the emergence of the parallel technology, this research looks into accelerating TSS on the widely-used many-cores i.e. the Graphics Processing Unit (GPU) and multi-cores platform. This would not only solve the computational time issue but also the cost as GPUs can be obtained at a lower cost. Hence, the implementation of TSS will help the medicinal chemist to execute the virtual screening in an accurate and fast manner. This study investigates the best possible method to parallelize TSS via experimentation of three parallel designs; two designs were implemented on GPU platform using the Compute Unified Device Architecture (CUDA) API namely CUDA 1 and CUDA 2 whilst one design was implemented on multi-core platform using OpenMP API. The CUDA 1 design had shown tremendous speedup and low GPU-memory utilization as compared to CUDA 2 design. In general observation, the parallel CUDA 1 was 131 times faster than sequential and 51 times faster than parallel OpenMP. This leads to the conclusion that CUDA 1 design as the best parallel design for TSS.

MSA Probs is a parallel algorithm developed to align multiple sequence alignment using a central processing unit (CPU). Whereas the CPU has some limitations, such as the inability to parallelize tasks in the processor (latency-oriented). To overcome these limitations, this paper proposes an improved version of MSA Probs that is compatible with a graphical Processing Unit (GPU). This idea helps in enhancing the performance of our algorithm (MSAprobs). To parallelize the sequential algorithm, Compute Unified Device Architecture (CUDA) or OpenCL is commonly used on GPUs. The NIVIDIA API is used to investigate the GPU's computing power. The results of using CPU only in MSAprobs versus the CPU and GPU are compared using two data sets from the Bali Base and OX Bench. The evaluation of the CPU and GPU is done using Threads 1,2 and 4. The results showed that by combining CPU and GPU, performance is improved and execution time is reduced.

Implementation of Image Enhancement Algorithms and Recursive Ray Tracing using CUDA

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.

The small slop approximation (SSA) is an accurate method to calculate the electromagnetic (EM) scattering properties of rough surfaces. However, its computational complexity restricts its application to smaller domains and there is always the need for speedup in very large cases using pure central processing units (CPUs) hardware. With the development of graphics processing units (GPUs), more processors are dedicated to perform independent calculations. In addition, NVIDIA introduced a parallel computing platform, compute unified device architecture (CUDA), which provides researchers an easy way to use processors on GPU. To calculate EM scattering properties on GPU, we reformulate the SSA method with CUDA to take advantage of GPU threads. Because each thread executes synchronously and deals with a corresponding point data of rough surface, the CUDA-based SSA method calculates faster than the pure-CPU equivalent. To overcome memory limitations, the data of large rough surface are stored on hard disk. Moreover, a subsidiary thread is used to deal with the process of data transmission between the memory and the hard disk and reduce transmitting time further. The factors, block size, data transfers, and register, are also discussed in the optimization of the CUDA application. Test cases running on a NVIDIA GTX 460 GPU indicate that two orders of magnitude speedup, including file input and output, is obtained with our new formulation.

GPU acceleration of MPAS microphysics WSM6 using OpenACC directives: Performance and verification

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.

The performance of computing systems has been improved significantly for several decades. However, increasing the throughput of recent CPUs (Central Processing Units) is restricted by power consumption and thermal issues. GPUs (Graphics Processing Units) are recognized as efficient computing platform with powerful hardware resources to support CPUs in computing systems. Unlike CPUs, there is a large number of CUDA (Compute Unified Device Architecture) cores in GPUs, hence, some cache blocks are referenced many times repeatedly. If those cache blocks reside in the cache for long time, hit rates can be improved. On the other hand, many cache blocks are referenced only once and never referenced again in the cache. These blocks waste cache memory space, resulting in reduced GPU performance. Conventional LRU replacement policy cannot consider the problems from non-reused cache blocks and frequently-reused cache blocks. In this paper, a new cache replacement policy based on the reuse pattern of cache blocks is proposed. The proposed cache replacement policy manages cache blocks by separating reused cache blocks and thrashing cache blocks. According to simulation results, the proposed cache reuse replacement policy can increase IPC by up to 4.4% compared to the conventional GPU architecture.

Cardiac magnetic resonance imaging (MRI) has become a crucial part of monitoring patients with congenital heart diseases. An important limitation of cardiac MRI using the prominent 3D steady-state free precession (3D-SSFP) sequence is its long scan time. Compressed sensing (CS) algorithm reduces the scan time by undersampling the data but increases the image reconstruction time because a non-linear optimization problem must be iteratively solved to estimate the missing data and reconstruct the images. The growing demand for reducing the examination time in cardiac MRI led us to investigate opportunities to accelerate this non-linear optimization problem to facilitate the migration of CS into the clinical environment. Using undersampled 3D-SSFP datasets acquired from five patients, we compared the speed and output quality of CS image reconstruction algorithm using a Central Processing Unit (CPU), a CPU with OpenMP parallelization, and two different Graphics Processing Unit (GPU) platforms. Reconstruction time had a mean of 13.1 minutes with a standard deviation of 3.8 minutes for the CPU, a mean of 11.5 minutes with a standard deviation of 3.6 minutes for the CPU with OpenMP parallelization, a mean of 2.2 minutes with a standard deviation of 0.3 minutes for the CPU with OpenMP plus NVIDIA k20m GPU, and a mean of 1.7 minutes with a standard deviation of 0.3 minutes for the CPU with OpenMP plus NVIDIA k40m GPU. The quality of images reconstructed on GPU and on CPU, as assessed by image subtraction, was comparable. Furthermore, necessary steps for implementation of rapid CS image reconstruction in the clinical environment are discussed.

Many geophysical problems are computationally expensive owing to their iterative nature or due to the programs processing to large datasets. Such problems are challenging and have to be approached with extreme caution because a wrong parameter selection will not only lead to wrong results but will also take up a lot of time. The Compute Unified Device Architecture (CUDA) introduced by NVIDIA has enabled programmers to execute tasks in parallel on a Graphics Processing Unit (GPU) using a high level language like C and C++. GPU's are massively parallel architectures with computing output several MFLOPS (10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> Floating Point Operations per second) higher than Central Processing Unit. They posses high memory bandwidth and low memory latency which makes it ideally suited for parallel computation. There are a number of geophysical processes which can benefit from reduced computing time. Iterative optimization procedures are one of them. We have implemented a CUDA version of the Particle Swarm Optimization (PSO) algorithm and used it to invert Self Potential, Magnetic and Resistivity data. The CUDA version of the algorithm was compared to an efficient CPU implementation of the same. We observed significant speed up compared to a CPU only version and the results of the CUDA version were as good as the CPU version.

The general-purpose graphics processing unit programming has been widely used and has achieved satisfactory results across many knowledge areas and it keeps evolving since its earlier stages. This paper presents an implementation of a modified Simplex method using the computational power brought from graphics processing unit (GPU) computing using the Nvidia framework for GPU programming, compute unified device architecture (CUDA). The results achieved shown that the parallel GPU implementation reached 15× and 22× maximum speedup measuring the overall time (data transfer plus kernel work time) and the kernel computation time respectively, in comparison with the standard sequential implementation using central processing unit (CPU).

Molecular dynamics simulation is currently a theoretical technique eligible in simulating of a wide range of systems, from soft condensed matter to biological systems. Excellent outcomes have resulted from using this technique; however, the implementation of this approach remains computationally expensive to some extent. Novel computing technologies may help reducing the computational simulation time, particularly, by using Graphical Processing Units (GPUs). Calculations on GPUs make possible to carry out simulations of large and complex molecular systems at a significantly reduced time. In this manuscript, the implementations of measure-preserving geometric integrator in the canonical ensemble coded in Compute Unified Device Architecture (CUDA) language are presented. The performance and validation of our High-throughput Molecular Dynamics (HIMD) code was done by calculating the thermodynamic properties of a Lennard-Jones fluid. From our tested systems, an excellent agreement was achieved with the reported of literature, compared with calculations carried out on Central Processing Units (CPUs). The implementation of the HIMD code performs time integration on Nosé-Hoover chains (NHC) faster in comparison to the NHC method implemented in LAMMPS code tested with one CPU vs one GPU. Along this work, the scope and limitations in performing simulations by using our HIMD code under rigorous statistical thermodynamics in the canonical ensemble are discussed and analyzed.KeywordsMolecular Dynamics (MD)Graphical Processing Units (GPUs)Nosé-Hoover Chains (NHC)Canonical Ensemble (NVT)

This paper presents a Reynolds equation solver for hydrostatic gas bearings, implemented to run on graphics processing units (GPUs). The original analysis code for the central processing unit (CPU) was modified for the GPU by using the compute unified device architecture (CUDA). The red-black Gauss-Seidel (RBGS) algorithm was employed instead of the original Gauss-Seidel algorithm for the iterative pressure solver, because the latter has data dependency between neighboring nodes. The implemented GPU program was tested on the nVidia GTX580 system and compared to the original CPU program on the AMD Llano system. In the iterative pressure calculation, the implemented GPU program showed 20-100 times faster performance than the original CPU codes. Comparison of the wall-clock times including all of pre/post processing codes showed that the GPU codes still delivered 4-12 times faster performance than the CPU code for our target problem.