High‐speed parallel implementations of the rainbow method based on perfect tables in a heterogeneous system

The computing power of graphics processing units (GPU) has increased rapidly, and there has been extensive research on general‐purpose computing on GPU (GPGPU) for cryptographic algorithms such as RSA, Elliptic Curve Cryptosystem (ECC), NTRU, and Advanced Encryption Standard. With the rise of GPGPU, commodity computers have become complex heterogeneous GPU+CPU systems. This new architecture poses new challenges and opportunities in high‐performance computing. In this paper, we present high‐speed parallel implementations of the rainbow method based on perfect tables, which is known as the most efficient time‐memory trade‐off, in the heterogeneous GPU+CPU system. We give a complete analysis of the effect of multiple checkpoints on reducing the cost of false alarms and take advantage of it for load balancing between GPU and CPU. For GTX460, our implementation is about 1.86 and 3.25 times faster than other GPU‐accelerated implementations, RainbowCrack and Cryptohaze, respectively, and for GTX580, 1.53 and 2.40 times faster. Copyright © 2014 John Wiley & Sons, Ltd.     

High Level Data Structures for GPGPU Programming in a Statically Typed Language

To increase software performance, it is now common to use hardware accelerators. Currently, GPUs are the most widespread accelerators that can handle general computations. This requires to use GPGPU frameworks such as Cuda or OpenCL. Both are very low-level and make the benefit of GPGPU programming difficult to achieve. In particular, they require to write programs as a combination of two subprograms, and, to manually manage devices and memory transfers. This increases the complexity of the overall software design. The idea we develop in this paper is to guarantee expressiveness and safety for CPU and GPU computations and memory managements with high-level data-structures and static type-checking. In this paper, we present how statically typed languages, compilers and libraries help harness high level GPGPU programming. In particular, we show how we added high-level user-defined data structures to a GPGPU programming framework based on a statically typed programming language: OCaml. Thus, we describe the introduction of records and tagged unions shared between the host program and GPGPU kernels described via a domain specific language as well as a simple pattern matching control structure to manage them. Examples, practical tests and comparisons with state of the art tools, show that our solutions improve code design, productivity, and safety while providing a high level of performance.     

Providing Source Code Level Portability Between CPU and GPU with MapCG

Graphics processing units (GPU) have taken an important role in the general purpose computing market in recent years.At present,the common approach to programming GPU units is to write GPU specific cod...     

The Implementation of a High Performance GPGPU Compiler

In this paper we present our experience in developing an optimizing compiler for general purpose computation on graphics processing units (GPGPU) based on the Cetus compiler framework. The input to our compiler is a naïve GPU kernel procedure, which is functionally correct but without any consideration for performance optimization. Our compiler applies a set of optimization techniques to the naive kernel and generates the optimized GPU kernel. Our compiler supports optimizations for GPU kernels using either global memory or texture memory. The implementation of our compiler is facilitated with a source-to-source compiler infrastructure, Cetus. The code transformation in the Cetus compiler framework is called a pass. We classify all the passes used in our work into two categories: functional passes and optimization passes. The functional passes translate input kernels into desired intermediate representation, which clearly represents memory access patterns and thread configurations. A series of optimization passes improve the performance of the kernels by adapting them to the target GPGPU architecture. Our experiments show that the optimized code achieves very high performance, either superior or very close to highly fine-tuned libraries.     

Compiler support for general-purpose computation on GPUs

In recent years, the GPU (graphics processing unit) has evolved into an extremely powerful and flexible processor, with it now representing an attractive platform for general-purpose computation. Moreover, changes to the design and programmability of GPUs provide the opportunity to perform general-purpose computation on a GPU (GPGPU). Even though many programming languages, software tools, and libraries have been proposed to facilitate GPGPU programming, the unusual and specific programming model of the GPU remains a significant barrier to writing GPGPU programs. In this paper, we introduce a novel compiler-based approach for GPGPU programming. Compiler directives are used to label code fragments that are to be executed on the GPU. Our GPGPU compiler, Guru, converts the labeled code fragments into ISO-compliant C code that contains appropriate OpenGL and Cg APIs. A native C compiler can then be used to compile it into the executable code for GPU. Our compiler is implemented based on the Open64 compiler infrastructure. Preliminary experimental results from selected benchmarks show that our compiler produces significant performance improvements for programs that exhibit a high degree of data parallelism.     

Object oriented framework for real-time image processing on GPU

General purpose computation on graphics processing unit (GPGPU) provides a significant gain in terms of the processing time compared with CPU. Images are particularly good subjects for massive parallel implementations on GPU. Thus, the processing time can be improved for computer vision and image/video processing algorithms. However, GPGPU has a fairly complex integration process in a framework and they evolve very rapidly. In this paper, we present a framework that provides all the desired primitives related to GPGPU-based image processing algorithms, which makes it easy and straightforward for the user to exploit. The proposed framework is object-oriented, and it utilizes design patterns. The user can benefit from all the advantages of object-oriented programming, such as code reusability/extensibility, flexibility, information hiding, and complexity hiding. This makes it possible to rapidly integrate new technologies and functionality as they appear.     

Computing prestack Kirchhoff time migration on general purpose GPU

This paper introduces how to optimize a practical prestack Kirchhoff time migration program by the Compute Unified Device Architecture (CUDA) on a general purpose GPU (GPGPU). A few useful optimization methods on GPGPU are demonstrated, such as how to increase the kernel thread numbers on GPU cores, and how to utilize the memory streams to overlap GPU kernel execution time, etc. The floating-point errors on CUDA and NVidia's GPUs are discussed in detail. Some effective methods that can be used to reduce the floating-point errors are introduced. The images generated by the practical prestack Kirchhoff time migration programs for the same real-world seismic data inputs on CPU and GPU are demonstrated. The final GPGPU approach on NVidia GTX 260 is more than 17 times faster than its original CPU version on Intel's P4 3.0G.     

Resolving the GPU responsiveness dilemma through program transformations

The emerging integrated CPU–GPU architectures facilitate short computational kernels to utilize GPU acceleration. Evidence has shown that, on such systems, the GPU control responsiveness (how soon the host program finds out about the completion of a GPU kernel) is essential for the overall performance. This study identifies the GPU responsiveness dilemma: host busy polling responds quickly, but at the expense of high energy consumption and interference with co-running CPU programs; interrupt-based notification minimizes energy and CPU interference costs, but suffers from substantial response delay. We present a program level solution that wakes up the host program in anticipation of GPU kernel completion. We systematically explore the design space of an anticipatory wakeup scheme through a timer-delayed wakeup or kernel splitting-based pre-completion notification. Experiments show that our proposed technique can achieve the best of both worlds, high responsiveness with low power and CPU costs, for a wide range of GPU workloads.     

Accelerating dissipative particle dynamics simulations on GPUs: Algorithms,numerics and applications

We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10–30 times speedup on a single GPU over 16 CPU cores and almost linear weak scaling across a thousand nodes. A unified framework is developed within which the efficient generation of the neighbor list and maintaining particle data locality are addressed. Our algorithm generates strictly ordered neighbor lists in parallel, while the construction is deterministic and makes no use of atomic operations or sorting. Such neighbor list leads to optimal data loading efficiency when combined with a two-level particle reordering scheme. A faster in situ generation scheme for Gaussian random numbers is proposed using precomputed binary signatures. We designed custom transcendental functions that are fast and accurate for evaluating the pairwise interaction. The correctness and accuracy of the code is verified through a set of test cases simulating Poiseuille flow and spontaneous vesicle formation. Computer benchmarks demonstrate the speedup of our implementation over the CPU implementation as well as strong and weak scalability. A large-scale simulation of spontaneous vesicle formation consisting of 128 million particles was conducted to further illustrate the practicality of our code in real-world applications.     

利用GPGPU进行快速稀疏磁共振数据重建

利用GPGPU（General Purpose GPU）强大的并行处理能力,基于NVIDIA CUDA框架对已有的稀疏磁共振（Sparse MRI）重建算法进行了并行化改造,使其能够适应实际应用的要求。稀疏磁共振成像的重建算法包含大量的浮点运算,计算耗时严重,难以应用于实际,必须对其进行加速和优化。实验结果显示,NVIDIA GTX275 GPU使运算时间从4分多钟缩短到3.4秒左右,与Intel Q8200 CPU相比,达到了76倍的加速。     

q-state Potts model metastability study using optimized GPU-based Monte Carlo algorithms

We implemented a GPU-based parallel code to perform Monte Carlo simulations of the two-dimensional q-state Potts model. The algorithm is based on a checkerboard update scheme and assigns independent random number generators to each thread. The implementation allows to simulate systems up to ～10⁹ spins with an average time per spin flip of 0.147 ns on the fastest GPU card tested, representing a speedup up to 155×, compared with an optimized serial code running on a high-end CPU.The possibility of performing high speed simulations at large enough system sizes allowed us to provide a positive numerical evidence about the existence of metastability on very large systems based on Binder?s criterion, namely, on the existence or not of specific heat singularities at spinodal temperatures different of the transition one.     

CU++: an object oriented framework for computational fluid dynamics applications using graphics processing units

The application of graphics processing units (GPU) to solve partial differential equations is gaining popularity with the advent of improved computer hardware. Various lower level interfaces exist that allow the user to access GPU specific functions. One such interface is NVIDIA’s Compute Unified Device Architecture (CUDA) library. However, porting existing codes to run on the GPU requires the user to write kernels that execute on multiple cores, in the form of Single Instruction Multiple Data (SIMD). In the present work, a higher level framework, termed CU++, has been developed that uses object oriented programming techniques available in C++ such as polymorphism, operator overloading, and template meta programming. Using this approach, CUDA kernels can be generated automatically during compile time. Briefly, CU++ allows a code developer with just C/C++ knowledge to write computer programs that will execute on the GPU without any knowledge of specific programming techniques in CUDA. This approach is tremendously beneficial for Computational Fluid Dynamics (CFD) code development because it mitigates the necessity of creating hundreds of GPU kernels for various purposes. In its current form, CU++ provides a framework for parallel array arithmetic, simplified data structures to interface with the GPU, and smart array indexing. An implementation of heterogeneous parallelism, i.e., utilizing multiple GPUs to simultaneously process a partitioned grid system with communication at the interfaces using Message Passing Interface (MPI) has been developed and tested.     

Multi-Kepler GPU vs. multi-Intel MIC for spin systems simulations

We present and compare the performances of two many-core architectures: the Nvidia Kepler and the Intel MIC both in a single system and in cluster configuration for the simulation of spin systems. As a benchmark we consider the time required to update a single spin of the 3D Heisenberg spin glass model by using the Over-relaxation algorithm. We present data also for a traditional high-end multi-core architecture: the Intel Sandy Bridge. The results show that although on the two Intel architectures it is possible to use basically the same code, the performances of a Intel MIC change dramatically depending on (apparently) minor details. Another issue is that to obtain a reasonable scalability with the Intel Phi coprocessor (Phi is the coprocessor that implements the MIC architecture) in a cluster configuration it is necessary to use the so-called offload mode which reduces the performances of the single system. As to the GPU, the Kepler architecture offers a clear advantage with respect to the previous Fermi architecture maintaining exactly the same source code. Scalability of the multi-GPU implementation remains very good by using the CPU as a communication co-processor of the GPU. All source codes are provided for inspection and for double-checking the results.     

Parallelization of the FMM on distributed-memory GPGPU systems for acoustic-scattering prediction

In this work, we carry out the parallelization of the single level Fast Multipole Method (FMM) for solving acoustic-scattering problems (using the Helmholtz equation) on distributed-memory GPGPU systems. With the aim of enlarging the scope of feasible simulations, the presented solution combines the techniques developed for our distributed-memory CPU solver with our shared-memory GPGPU solver. The performance of the developed solution is proved using two different GPGPU clusters: the first one consists of two workstations with NVIDIA GTX 480 GPUs linked by a Gigabit Ethernet network, and the second one comprises four nodes with NVIDIA Tesla M2090 GPUs linked by an Infiniband network.     

Resource-efficient utilization of CPU/GPU-based heterogeneous supercomputers for Bayesian phylogenetic inference

Bayesian inference is one of the most important methods for estimating phylogenetic trees in bioinformatics. Due to the potentially huge computational requirements, several parallel algorithms of Bayesian inference have been implemented to run on CPU-based clusters, multicore CPUs, or small clusters of CPUs and GPUs. To the best of our knowledge, however, none of the existing methods is able to simultaneously and fully utilize both CPUs and GPUs for the computations, leaving idle either the CPU part or the GPU part of modern heterogeneous supercomputers. Aiming at an optimized utilization of heterogeneous computing resources, which is a promising hardware architecture for future bioinformatics applications, we present a new hybrid parallel algorithm and implementation of Bayesian phylogenetic inference, which combines MPI, OpenMP, and CUDA programming. The novelty of our algorithm, denoted as oMC³, is its ability of using CPU cores simultaneously with GPUs for the computations, while ensuring a fair work division between the two types of hardware components. We have implemented oMC³ based on MrBayes, which is one of the most popular software packages for Bayesian phylogenetic inference. Numerical experiments show that oMC³ obtains 2.5× speedup over nMC³, which is a cutting-edge GPU implementation of MrBayes, on a single server consisting of two GPUs and sixteen CPU cores. Moreover, oMC³ scales nicely when 128 GPUs and 1536 CPU cores are in use.     

MinGPU: a minimum GPU library for computer vision

In the field of computer vision, it is becoming increasingly popular to implement algorithms, in sections or in their entirety, on a graphics processing unit (GPU). This is due to the superior speed GPUs offer compared to CPUs. In this paper, we present a GPU library, MinGPU, which contains all of the necessary functions to convert an existing CPU code to GPU. We have created GPU implementations of several well known computer vision algorithms, including the homography transformation between two 3D views. We provide timing charts and show that our MinGPU implementation of homography transformations performs approximately 600 times faster than its C++ CPU implementation.

Performance of CPU/GPU compiler directives on ISO/TTI kernels

GPUs are slowly becoming ubiquitous devices in High Performance Computing, as their capabilities to enhance the performance per watt of compute intensive algorithms as compared to multicore CPUs have been identified. The primary shortcoming of a GPU is usability, since vendor specific APIs are quite different from existing programming languages, and it requires a substantial knowledge of the device and programming interface to optimize applications. Hence, lately a growing number of higher level programming models are targeting GPUs to alleviate this problem. The ultimate goal for a high-level model is to expose an easy-to-use interface for the user to offload compute intensive portions of code (kernels) to the GPU, and tune the code according to the target accelerator to maximize overall performance with a reduced development effort. In this paper, we share our experiences of three of the notable high-level directive based GPU programming models—PGI, CAPS and OpenACC (from CAPS and PGI) on an Nvidia M2090 GPU. We analyze their performance and programmability against Isotropic (ISO)/Tilted Transversely Isotropic (TTI) finite difference kernels, which are primary components in the Reverse Time Migration (RTM) application used by oil and gas exploration for seismic imaging of the sub-surface. When ported to a single GPU using the mentioned directives, we observe an average 1.5–1.8x improvement in performance for both ISO and TTI kernels, when compared with optimized multi-threaded CPU implementations using OpenMP.     

基于CUDA的BP算法并行化与实例验证

CUDA是应用较广的GPU通用计算模型,BP算法是目前应用最广泛的神经网络模型之一。提出了用CUDA模型并行化BP算法的方法。用该方法训练BP神经网络,训练开始前将数据传到GPU,训练开始后计算隐含层和输出层的输入输出和误差,更新权重和偏倚的过程都在GPU上实现。将该方法用于手写数字图片训练练实验,与在四核CPU上的训练相比,加速比为6．12～8．17。分别用在CPU和GPU上训练得到的结果识别相同的测试集图片,GPU上的训练结果对图片的识别率比CPU上的高0．05％～0．22％。     

GPU accelerated tensor contractions in the plaquette renormalization scheme

We use the graphical processing unit (GPU) to accelerate the tensor contractions, which is the most time consuming operations in the variational method based on the plaquette renormalized states. Using a frustrated Heisenberg J₁–J₂ model on a square lattice as an example, we implement the algorithm based on the compute unified device architecture (CUDA). For a single plaquette contraction with the bond dimensions C = 3 of each rank of the tensor, results are obtained 25 times faster on GPU than on a current CPU core. This makes it possible to simulate systems with the size 8 × 8 and larger, which are extremely time consuming on a single CPU. This technology successfully relieves the computing time dependence with C, while in the CPU serial computation, the total required time scales both with C and the system size.     

Accelerated event-by-event Monte Carlo microdosimetric calculations of electrons and protons tracks on a multi-core CPU and a CUDA-enabled GPU

For microdosimetric calculations event-by-event Monte Carlo (MC) methods are considered the most accurate. The main shortcoming of those methods is the extensive requirement for computational time. In this work we present an event-by-event MC code of low projectile energy electron and proton tracks for accelerated microdosimetric MC simulations on a graphic processing unit (GPU). Additionally, a hybrid implementation scheme was realized by employing OpenMP and CUDA in such a way 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 code on the CPU. Performance comparison was established on the speed-up for a set of benchmarking cases of electron and proton tracks. A maximum speedup of 67.2 was achieved for the GPU-based MC code, while a further improvement of the speedup up to 20% was achieved for the hybrid approach. The results indicate the capability of our CPU–GPU implementation for accelerated MC microdosimetric calculations of both electron and proton tracks without loss of accuracy.