GPU acceleration of conjugate gradient method obtaining Green's function for transport-property calculation

With the development of information technology and the increasing demand for data processing, the serial mode of the central processing unit (CPU) is difficult to efficiently transmit large-scale spatiotemporal data, and the processing effect for high-resolution images is not good. This paper designed a high-resolution image processing and spatiotemporal data transmission system based on graphics processing unit (GPU) acceleration to improve the processing efficiency of large-scale spatiotemporal data. In this paper, traffic spatiotemporal data was taken as an example for analysis. Large-scale traffic image data was collected by road monitoring equipment, and image compression was performed on the collected image. Fourier transform was used to eliminate image data redundancy, and GPU-accelerated parallel processing was used to achieve fast image defogging and data transmission. This paper selected 2TB of traffic spatiotemporal data with image resolutions of 540P, 720P, 1080P, 1440P, and 2160P. GPU acceleration was performed using the Compute Unified Device Architecture (CUDA). In images with a resolution of 2160P, the processing time for CPU and GPU acceleration was 2900ms and 28ms, respectively, with an acceleration ratio of 103.6. A high-resolution image processing and spatiotemporal data transmission system based on GPU acceleration can improve the efficiency of traffic spatiotemporal data processing and have excellent concurrent processing capabilities.

Multi-core platform enters the territory of high performance computing (HPC). Moreover, the NVIDA GT200 has 240 cores and performs thousands upon thousands of threads simultaneously. The role of the Graphics Processing Units (GPU)accelerator has become more and more important for scientific computing and computational fluid dynamic (CFD) to obtain result quickly and efficiently. In this paper we presented efficient computational scheme for solving parabolic partial differential equations on Multithreading and GPU accelerator. The purpose of this paper is to obtain the solutions as accurate and high speed-up using implicit scheme is convection-diffusion-reaction(CDR). In this paper we propose to CUDA-CDR solver to quickly solve big problem on GPU accelerator. The NVIDIA CUDATM is an extension of C language and has been implemented as a veteran environment since 2006. Our multithread version illustrates 2.5 times faster than those on a sequential code in Model Problem 1 with the problem size of 400x400. The performance of parallel version via CUDA C is 11 times faster than those on a sequential code in Model Problem 1 with the problem size of 400x400.

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

Most Computational Fluid Dynamics (CFD) applications solve the Naiver-Stokes equations using various discretization methods like Finite Difference Method (FDM), Finite Element Method (FEM), Finite Volume Method (FVM), etc. The most compute-intensive process in CFD algorithms is the pressure Poisson solver. Solving the pressure Poisson equation requires the solution of a set of linear simultaneous equations. As the problem size/complexity increases, so does the effort and time invested in solving the equations. This study presents fast and robust iterative solvers and the acceleration of the same using the Graphics Processing Unit (GPU) architecture. Serial versions of the codes are implemented in the C language and the parallelization on GPU is achieved using Compute Unified Device Architecture (CUDA). For this study, a two-dimensional heat conduction problem is considered. FDM is used for discretization. Iterative solvers Conjugate Gradient and Multi Grid methods have been implemented in serial and parallel. The performance enhancement with single GPU and CPU system over a single CPU in terms of computing time is reported. It is seen that multigrid algorithms are superior in convergence and nearly 13 times speed-up has been obtained through GPU acceleration using CUDA, for a grid size of 2048 X 2048. The tests have been done on a cluster with Intel(R) Xeon(R) CPU E5-2670 CPU and NVIDIA K10 GPU.

In recent years, Artificial Intelligence (AI) and Deep Learning (DL) Research and Development (R&D) work has picked up amongst academia, research community and industry. Training Deep Neural Network model (DNN) requires huge amount of data and computing resources, specially Graphics Processing Unit (GPU) accelerator along with DL framework like TensorFlow and programing language like Python. Different distribution of framework and programing language is available and optimized for GPU and Central Processing Unit (CPU). Many literature, article and studies are published for DNN training on GPU. However, only few article and studied are available for DNN training on CPU especially in HPC Cluster. This paper presents performance analysis and comparison between different distribution of Python and TensorFlow to verify which combination run optimally on available CPU only node of a HPC cluster. We used ResNet50 [1], ResNet101 [1] and Inceptionv3 [2] neural network model of tf_cnn_benchmarks [3] for performance comparison. We further tune best identified software combination using distributed training technique, across single and multiple nodes. We did performance comparison based on different processor and architectures. We were able to show up to 7x performance improvement using Intel Distribution for TensorFlow on single node and up to 15.7X speedup on 16 nodes on different CPU architecture.

<strong class="journal-contentHeaderColor">Abstract.</strong> With semiconductor technology gradually approaching its physical and thermal limits, Graphics processing unit (GPU) is becoming an attractive solution in many scientific applications due to their high performance. This paper presents an application of GPU accelerators in air quality model. We endeavor to demonstrate an approach that runs a PPM solver of horizontal advection (HADVPPM) for air quality model CAMx on GPU clusters. Specifically, we first convert the HADVPPM to a new Compute Unified Device Architecture C (CUDA C) code to make it computable on the GPU (GPU-HADVPPM). Then, a series of optimization measures are taken, including reducing the CPU-GPU communication frequency, increasing the size of data computation on GPU, optimizing the GPU memory access, and using thread and block indices in order to improve the overall computing performance of CAMx model coupled with GPU-HADVPPM (named as CAMx-CUDA model). Finally, a heterogeneous, hybrid programming paradigm is presented and utilized with the GPU-HADVPPM on GPU clusters with Massage Passing Interface (MPI) and CUDA. Offline experiment results show that running GPU-HADVPPM on one NVIDIA Tesla K40m and NVIDIA Tesla V100 GPU can achieve up to 845.4x and 1113.6x acceleration. By implementing a series of optimization schemes, the CAMx-CUDA model resulted in a 29.0x and 128.4x improvement in computational efficiency using a GPU accelerator card on a K40m and V100 cluster, respectively. In terms of the single-module computational efficiency of GPU-HADVPPM, it can achieve 1.3x and 19.4x speedup on NVIDIA Tesla K40m GPU and NVIDA Tesla V100 GPU respectively. The multi-GPU acceleration algorithm enables 4.5x speedup with 8 CPU cores and 8 GPU accelerators on V100 cluster.

<strong class="journal-contentHeaderColor">Abstract.</strong> With semiconductor technology gradually approaching its physical and thermal limits, Graphics processing unit (GPU) is becoming an attractive solution in many scientific applications due to their high performance. This paper presents an application of GPU accelerators in air quality model. We endeavor to demonstrate an approach that runs a PPM solver of horizontal advection (HADVPPM) for air quality model CAMx on GPU clusters. Specifically, we first convert the HADVPPM to a new Compute Unified Device Architecture C (CUDA C) code to make it computable on the GPU (GPU-HADVPPM). Then, a series of optimization measures are taken, including reducing the CPU-GPU communication frequency, increasing the size of data computation on GPU, optimizing the GPU memory access, and using thread and block indices in order to improve the overall computing performance of CAMx model coupled with GPU-HADVPPM (named as CAMx-CUDA model). Finally, a heterogeneous, hybrid programming paradigm is presented and utilized with the GPU-HADVPPM on GPU clusters with Massage Passing Interface (MPI) and CUDA. Offline experiment results show that running GPU-HADVPPM on one NVIDIA Tesla K40m and NVIDIA Tesla V100 GPU can achieve up to 845.4x and 1113.6x acceleration. By implementing a series of optimization schemes, the CAMx-CUDA model resulted in a 29.0x and 128.4x improvement in computational efficiency using a GPU accelerator card on a K40m and V100 cluster, respectively. In terms of the single-module computational efficiency of GPU-HADVPPM, it can achieve 1.3x and 19.4x speedup on NVIDIA Tesla K40m GPU and NVIDA Tesla V100 GPU respectively. The multi-GPU acceleration algorithm enables 4.5x speedup with 8 CPU cores and 8 GPU accelerators on V100 cluster.

We have implemented the Martini force field within Lawrence Livermore National Laboratory's molecular dynamics program, ddcMD. The program is extended to a heterogeneous programming model so that it can exploit graphics processing unit (GPU) accelerators. In addition to the Martini force field being ported to the GPU, the entire integration step, including thermostat, barostat, and constraint solver, is ported as well, which speeds up the simulations to 278-fold using one GPU vs one central processing unit (CPU) core. A benchmark study is performed with several test cases, comparing ddcMD and GROMACS Martini simulations. The average performance of ddcMD for a protein-lipid simulation system of 136k particles achieves 1.04 µs/day on one NVIDIA V100 GPU and aggregates 6.19 µs/day on one Summit node with six GPUs. The GPU implementation in ddcMD offloads all computations to the GPU and only requires one CPU core per simulation to manage the inputs and outputs, freeing up remaining CPU resources on the compute node for alternative tasks often required in complex simulation campaigns. The ddcMD code has been made open source and is available on GitHub at https://github.com/LLNL/ddcMD.

The singular value decomposition characteristic basis function method (SVD-CBFM) is usually used to solve the electromagnetic scattering problems. When the number of unknowns increases, the memory and computation time consumed become insufferable. The parallel SVD-CBFM solution on graphics processing unit (GPU) is implemented by the compute unified device architecture (CUDA) technology in this paper. The acceleration ratio of parallel SVD-CBFM comparing with traditional central processing unit (CPU) is also analyzed. Numerical results show that the speed of impedance matrix filling and reduced matrix filling is greatly improved.

The energetic fuel-coolant interaction (FCI) has been one of the primary safety concerns in nuclear power plants. Graphical processing unit (GPU) implementation of the moving particle semi-implicit (MPS) method is presented and used to simulate the fuel coolant interaction problem. The governing equations are discretized with the particle interaction model of MPS. Detailed implementation on single-GPU is introduced. The three-dimensional broken dam is simulated to verify the developed GPU acceleration MPS method. The proposed GPU acceleration algorithm and developed code are then used to simulate the FCI problem. As a summary of results, the developed GPU-MPS method showed a good agreement with the experimental observation and theoretical prediction.

Efficient methods for implementation of multi-level nonrigid mass-preserving image registration on GPUs and multi-threaded CPUs

This paper presents a parallel system capable of accelerating biological sequence alignment on the graphics processing unit (GPU) grid. The GPU grid in this paper is a desktop grid system that utilizes idle GPUs and CPUs in the office and home. Our parallel implementation employs a master-worker paradigm to accelerate an OpenGL-based algorithm that runs on a single GPU. We integrate this implementation into a screensaver-based grid system that detects idle resources on which the alignment code can run. We also show some experimental results comparing our implementation with three different implementations running on a single GPU, a single CPU, or multiple CPUs. As a result, we find that a single non-dedicated GPU can provide us almost the same throughput as two dedicated CPUs in our laboratory environment, where GPU-equipped machines are ordinarily used to develop GPU applications. In a dedicated environment, the GPU-accelerated code achieves five times higher throughput than the CPU-based code. Furthermore, a linear speedup of 30.7X is observed on a 32-node cluster of dedicated GPUs. We also implement a compute unified device architecture (CUDA) based algorithm to demonstrate further acceleration.

The prediction of a dielectric breakdown in a high-voltage device is based on criteria that evaluate the electric field along possible breakdown paths. For this purpose it is necessary to efficiently compute the electric field at arbitrary points in space. A boundary element method (BEM) based on an indirect formulation, realized with MPI-parallel collocation, has proven to cope very well with this requirement. It deploys surface meshes only, which are easy to generate even for complex industrial geometries. The assembly of the large dense BEM-matrix, as well as the iterative solution of the resulting system, and the evaluation along the field-lines all require to carry out the same type of calculation many times. Graphical Processing Units (GPUs) promise to be more efficient than Central Processing Units (CPUs) when it is possible to do the same type of calculations for large blocks of data in parallel. In this paper we therefore investigate if GPU acceleration is a measure to further speed up the established CPU-parallel BEM solver.

The key to preventing the COVID-19 is to diagnose patients quickly and accurately. Studies have shown that using Convolutional Neural Networks (CNN) to analyze chest Computed Tomography (CT) images is helpful for timely COVID-19 diagnosis. However, personal privacy issues, public chest CT data sets are relatively few, which has limited CNN's application to COVID-19 diagnosis. Also, many CNNs have complex structures and massive parameters. Even if equipped with the dedicated Graphics Processing Unit (GPU) for acceleration, it still takes a long time, which is not conductive to widespread application. To solve above problems, this paper proposes a lightweight CNN classification model based on transfer learning. Use the lightweight CNN MobileNetV2 as the backbone of the model to solve the shortage of hardware resources and computing power. In order to alleviate the problem of model overfitting caused by insufficient data set, transfer learning is used to train the model. The study first exploits the weight parameters trained on the ImageNet database to initialize the MobileNetV2 network, and then retrain the model based on the CT image data set provided by Kaggle. Experimental results on a computer equipped only with the Central Processing Unit (CPU) show that it consumes only 1.06 s on average to diagnose a chest CT image. Compared to other lightweight models, the proposed model has a higher classification accuracy and reliability while having a lightweight architecture and few parameters, which can be easily applied to computers without GPU acceleration. Code:github.com/ZhouJie-520/paper-codes.

Intelligent optimization algorithms such as particle swarm optimization (PSO) have been introduced into four-dimensional variational assimilation of atmospheric data to solve complex optimization problems. The time-varying double compression model can solve the problem of accuracy well. But when confronted with the problem of high accuracy, the long training time will become the weakness. Parallelization acceleration is one of the effective ways to solve the conundrum. And applying Graphic Processing Unit (GPU) to accelerate PSO algorithm in parallel has the advantage of low hardware cost. In this paper, a parallel time-varying double compression factor PSO algorithm based on GPU acceleration is proposed. The parallel operation of particle swarm optimization algorithm is carried out by GPU, in which the time can be improved with the same precision kept. Compared with the dynamic inertia weight algorithm and time-varying double compression factor algorithm, the experimental results display that the accuracy is better than the former and the consuming time is shorter than the latter, which proves that the method can process the prediction in a faster and more accurate way.KeywordsData assimilationGraphic Processing UnitTime-varying double compression factor PSO algorithmWeather forecast