A Survey on GPU Techniques in Astronomical Data Processing

<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.

Based on the principle of QR loop iterations, this paper implements a parallel algorithm based on the hardware of GPU (Graphic Process Unit) by using routines from CUDA (Computer Unified Device Architecture) to find the eigenvalues of general matrices. CPU and GPU computing card form a client-server computing framework. Here, CPU can be regarded as a client and GPU card is considered as a computing server. For the experiment environment, this paper chooses a GPU card with the model of NVIDIA GeForce GTX460 as a server side and a CPU with the model of Intel Core i5-760 quad-core as a client side. Win7 64-bit is selected as the operating system. The parallel implementation consists of two parts:PA H and PA QR. PA H is a procedure that transforms a matrix A into the Hessenberg matrix B. PA QR is the actual parallel algorithm of the QR iterations that is imposed on the Hessenberg matrix B for finding eigenvalues of the general matrix A. The speedup ratio of the proposed algorithm is jarless when the number of iterations becomes greater. The experimental results show that the parallel implementation with CUDA on GPU only makes use of less running time than traditional sequential algorithms. The speedup ratio of PA H is between 1.79 and 7.81. The speedup ratio of PA QR is between 3.24 and 118.9. Especially, when the order of general matrix equals 8192, the amount of iterations becomes 10000. The speedup ratio of the PA-H and the PA QR can run up to 7.81 and 118.9 respectively.

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.

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.

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.

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.

Many algorithms for image processing and pattern recognition have recently been implemented on GPU (graphic processing unit) for faster computational times. However, the implementation using GPU encounters two problems. First, the programmer should master the fundamentals of the graphics shading languages that require the prior knowledge on computer graphics. Second, in a job which needs much cooperation between CPU and GPU, which is usual in image processings and pattern recognitions contrary to the graphics area, CPU should generate raw feature data for GPU processing as much as possible to effectively utilize GPU performance. This paper proposes more quick and efficient implementation of neural networks on both GPU and multi-core CPU. We use CUDA (compute unified device architecture) that can be easily programmed due to its simple C language-like style instead of GPU to solve the first problem. Moreover, OpenMP (Open Multi-Processing) is used to concurrently process multiple data with single instruction on multi-core CPU, which results ineffectively utilizing the memories of GPU. In the experiments, we implemented neural networks-based text detection system using the proposed architecture, and the computational times showed about 15 times faster than implementation using CPU and about 4 times faster than implementation on only GPU without OpenMP.

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.

Many-core framework, represented by Graphic Processing Unit (GPU), has been becoming more popular in scientific computing and data analysis, and Compute Unified Device Architecture (CUDA) allows developers to carry out computation on GPUs more conveniently. Matrix operation is one of the most important application scenarios of GPU computation and CUDA, widely appearing in domains like graph applications and artificial intelligence. This paper focuses on accelerating matrix power operation (MPO) process, which appears in many engineering problems and may be time-consuming when the scale of matrixes is large, with GPUs and CUDA. In this paper, three techniques are used to speed up the MPO process: matrix parallel reduction, matrix parallel multiplication and CUDA dynamic parallelism. The experiments were carried out on NVIDIA RTX 2080 Super and Intel(R) Core(TM) i7-10750H. The code is compiled and executed in Visual Studio 2019 community, the GPU driver version is 461.40, the CUDA version is 11.1, and the NVCC version is 11.1.74. With all three techniques, the MPO process can get hundreds of times speedup compared with the sequential multiplication process executed by Eigen library, even though the code of algorithm is hardly optimized. Moreover, with the number of power increasing, the efficiency of algorithm can be even higher because of the relatively fixed time consumed in data transmission and GPU memory allocation.

Implementation of Image Enhancement Algorithms and Recursive Ray Tracing using CUDA

This paper proposes a parallel ant colony optimization (ACO) for solving quadratic assignment problems (QAPs) on a graphics processing unit (GPU) by combining fast, 2-opt local search in compute unified device architecture (CUDA). In 2-opt for QAP, 2-opt moves can be divided into two groups based on computing cost. In one group, the computing cost is O(1) and in the other group, the computing cost is O(n). We compute these groups of 2-opt moves in parallel by assigning the computations to threads of CUDA. In this assignment, we propose an efficient method that can reduce disabling time in each thread of CUDA. The results show GPU computation with 2-opt produces a speedup of ×24.6 on average, compared to computation with CPU.

Data-parallel accelerator devices such as Graphical Processing Units (GPUs) are providing dramatic performance improvements over even multi-core CPUs for lattice-oriented applications in computational physics. Models such as the Ising and Potts models continue to play a role in investigating phase transitions on small-world and scale-free graph structures. These models are particularly well-suited to the performance gains possible using GPUs and relatively high-level device programming languages such as NVIDIA’s Compute Unified Device Architecture (CUDA). We report on algorithms and CUDA data-parallel programming techniques for implementing Metropolis Monte Carlo updates for the Ising model using bit-packing storage, and adjacency neighbour lists for various graph structures in addition to regular hypercubic lattices. We report on parallel performance gains and also memory and performance tradeoffs using GPU/CPU and algorithmic combinations.

This paper presents a computational acceleration of image inpainting using parallel processing based on Graphics Processing Unit (GPU) Compute Unified Device Architecture (CUDA). We use parabolic partial differential equation (PDE) called heat equation as the model equation. The heat equation is discretized numerically using Finite Difference method. Semi-algebraic equation that formed then solved by using Alternating-Direction Implicit (ADI) scheme. The numerical algorithm is implemented in GPU CUDA parallel computing to speed up the computational time. The computational process of the inpainting can be done using larger time-step. The computational time can be accelerated to 5.86 times faster using an image with 2736×1824 resolution.

Performance models for asynchronous data transfers on consumer Graphics Processing Units