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<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.

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.

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.

Overlapping computation and communication of three-dimensional FDTD on a GPU cluster

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

Recently, general-purpose computation on graphics processing units (GPGPU) has become an increasingly popular field of study as graphics processing units (GPUs) continue to be proposed as high performance and relatively low cost implementation platforms for scientific computing applications. Among these applications figure astrophysical N-bodysimulations, which form one of the most challenging problems in computational science. However, in most reported studies, a simple $ \mathcal{O}(N^{2})$ algorithm was used for GPGPUs, and the resulting performances were not observed to be better than those of conventional CPUs that were based on more optimized $ \mathcal{O}(N \log N)$ algorithms such as the tree algorithm or the particle-particle particle-mesh algorithm. Because of the difficulty in getting efficient implementations of such algorithms on GPUs, a GPU cluster had no practical advantage over general-purpose PC clusters for N-bodysimulations. In this paper, we report a new method for efficient parallel implementation of the tree algorithm on GPUs. Our novel tree code allows the realization of an N-bodysimulation on a GPU cluster at a much higher performance than that on general PC clusters. We practically performed a cosmological simulation with 562 million particles on a GPU cluster using 128 NVIDIA GeForce 8800GTS GPUs at an overall cost of 168172 $. We obtained a sustained performance of 20.1 Tflops, which when normalized against a general-purpose CPU implementation leads to a performance of 8.50 Tflops. The achieved cost/performance was hence a mere $19.8 /Gflops which shows the high competitiveness of GPGPUs.

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

The calculation of pairwise correlation coefficient on a dataset, known as the correlation matrix, is often used in data analysis, signal processing, pattern recognition, image processing, and bioinformatics. With the state-of-the-art Graphic Processing Units (GPUs) that consist of massive cores capable to do processing up to several Gflops, the calculation of correlation matrix can be accelerated several times over traditional CPUs. However, due to the rapid growth of the data in the digital era, the correlation matrix calculation becomes computing intensive which needs to be executed on multiple GPUs. As of now, GPUs are common components in data center at many institutions. Their GPU deployment tends towards a GPU cluster which each node is equipped with GPUs. In this paper, we propose a parallel computing based on the hybrid MPI/CUDA programming for fast and efficient Pearson correlation matrix calculation on GPU clusters. At coarse grain parallelism, the correlation matrix is partitioned into tiles which are distributed to execute concurrently on many GPUs using MPI. At fine grain level, the CUDA kernel function on each node performs massively parallel computing on a GPU. To balance load across all GPUs, we adopt the work pool model which there is a master node that manages tasks in the work pool and dynamically assign tasks to worker nodes. The result of the evaluation shows that the proposed work can ensure the load balance across different GPUs and thus gives better execution time than using a simple static data partitioning.

We present a set of algorithms for simulating and visualizing real-time crowds in GPU (Graphics Processing Units) clusters. First we will present crowd simulation and rendering techniques that take advantage of single GPU machines, then using as an example a wandering crowd behavior simulation algorithm, we explain how this kind of algorithms can be extended for their use in GPU cluster environments. We also present a visualization architecture that renders the simulation results using detailed 3D virtual characters. This architecture is adaptable in order to support the Barcelona Supercomputing Center (BSC) infrastructure. Results show that our algorithms are scalable in different hardware platforms including embedded systems, desktop GPUs and GPU clusters, in particular, the BSC's Minotauro cluster.

We evaluate a novel implementation of a Self-Organizing Map (SOM) on a Graphics Processing Unit (GPU) cluster. Using various combinations of OpenCL, CUDA, and two different graphics cards, we demonstrate the scalability of the SOM implementation on one to eight GPUs. Results indicate that while the algorithm scales well with the number of training samples and the map size, the benefits from using the data-parallel approaches offered by the GPU are severely limited when combined with the Message Passing Interface (MPI) in this setting, and comparable to speedups of GPU-based implementations as compared to optimized sequential code. Speedups achieved range from 3 to 32, for various map and training data sizes. We also observed a performance penalty for the OpenCL implementation as compared to CUDA.

Gravitational waves from the coalescences of black hole and neutron stars afford us the unique opportunity to determine the sources' properties, such as their masses and spins, with unprecedented accuracy. To do so, however, theoretical models of the emitted signal that are i) extremely accurate and ii) computationally highly efficient are necessary. The inclusion of more detailed physics such as higher-order multipoles and relativistic spin-induced orbital precession increases the complexity and hence also computational cost of waveform models, which presents a severe bottleneck to the parameter inference problem. A popular method to generate waveforms more efficiently is to build a fast surrogate model of a slower one. In this paper, we show that traditional surrogate modelling methods combined with artificial neural networks can be used to build a computationally highly efficient while still accurate emulation of multipolar time-domain waveform models of precessing binary black holes. We apply this method to the state-of-the-art waveform model SEOBNRv4PHM and find significant computational improvements: On a traditional CPU, the typical generation of a single waveform using our neural network surrogate SEOBNN_v4PHM_4dq2 takes 18ms for a binary black hole with a total mass of $44 M_{\odot}$ when generated from 20Hz. In comparison to SEOBNRv4PHM itself, this amounts to an improvement in computational efficiency by two orders of magnitude. Utilising additional GPU acceleration, we find that this speed-up can be increased further with the generation of batches of waveforms simultaneously. Even without additional GPU acceleration, this dramatic decrease in waveform generation cost can reduce the inference timescale from weeks to hours.

A novel block-structured Cartesian mesh method is developed that is well designed for the graphics processing unit (GPU) acceleration of flow simulations. The size of the mesh block is set based on the thread hierarchy in Compute Unified Device Architecture which is an easy-to-use GPU programming model. The mesh method is implemented in a finite-volume compressible flow solver, where the two-dimension steady Euler equations are solved by using the AUSM + scheme in spatial discretization and third-order total-variation-diminishing Runge–Kutta method in time discretization. For the GPU implementation, the redundant computation, data structure reorganization and Structure-of-Arrays (SoA) mesh layout are utilized to reduce the frequency and data size for information transfer between host and device. Two test cases, the supersonic flow over a circular cylinder and a NACA0012 airfoil, are presented to validate numerical approaches and valuate computational performance. Additionally, numerical experiments are carried out on a test case at different mesh sizes and execution configurations to investigate properties of the proposed method.

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.

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.