Evaluation of Image Pixels Similarity Measurement Algorithm Accelerated on GPU with OpenACC

OpenACC is a directive based parallel programming library that allows for easy acceleration of existing C, C++ and Fortran based applications with minimal code modifications. By annotating the bottleneck causing section of the code with OpenACC directives, the acceleration of the code can be simplified, leading for high portability of performance across different target Graphic Processing Units (GPUs). In this work, the portability of an implemented parallelizable chi-square based pixel similarity measurement algorithm has been evaluated on two consumer and professional grade GPUs. To our best knowledge, this is the first performance evaluation report that utilizes the OpenACC optimization clauses (collapse and tile) on different GPUs to process a less workload (low resolution image of 581x429 pixels) and a heavy workload (high resolution image of 4500 x 3500 pixels) to demonstrate the effectiveness and high portability of OpenACC

Evaluation of Image Pixels Similarity Measurement Algorithm Accelerated on GPU with OpenACC

OpenACC is a directive based parallel programming library that allows for the easy acceleration of existing C, C++ and Fortran based applications with minimal code modifications. By annotating the bottleneck causing a section of the code with OpenACC directives, the acceleration of the code can be simplified, leading for high portability of performance across different target Graphic Processing Units (GPUs). In this work, the portability of an implemented parallelizable chi-square based pixel similarity measurement algorithm has been evaluated on two consumer and professional grade GPUs. To our best knowledge, this is the first performance evaluation report that utilizes the OpenACC optimization clauses (collapse and tile) on different GPUs to process a less workload (low resolution image of 581x429 pixels) and a heavy workload (high resolution image of 4500 x 3500 pixels) to demonstrate the effectiveness and high portability of OpenACC

Fast algorithm for real-time rings reconstruction

The GAP project is dedicated to study the application of GPU in several contexts in which real-time response is important to take decisions. The definition of real-time depends on the application under study, ranging from answer time of μs up to several hours in case of very computing intensive task. During this conference we presented our work in low level triggers [1] [2] and high level triggers [3] in high energy physics experiments, and specific application for nuclear magnetic resonance (NMR) [4] [5] and cone-beam CT [6]. Apart from the study of dedicated solution to decrease the latency due to data transport and preparation, the computing algorithms play an essential role in any GPU application. In this contribution, we show an original algorithm developed for triggers application, to accelerate the ring reconstruction in RICH detector when it is not possible to have seeds for reconstruction from external trackers

Scheduling and Tuning Kernels for High-performance on Heterogeneous Processor Systems

Accelerated parallel computing techniques using devices such as GPUs and Xeon Phis (along with CPUs) have proposed promising solutions of extending the cutting edge of high-performance computer systems. A significant performance improvement can be achieved when suitable workloads are handled by the accelerator. Traditional CPUs can handle those workloads not well suited for accelerators. Combination of multiple types of processors in a single computer system is referred to as a heterogeneous system. This dissertation addresses tuning and scheduling issues in heterogeneous systems. The first section presents work on tuning scientific workloads on three different types of processors: multi-core CPU, Xeon Phi massively parallel processor, and NVIDIA GPU; common tuning methods and platform-specific tuning techniques are presented. Then, analysis is done to demonstrate the performance characteristics of the heterogeneous system on different input data. This section of the dissertation is part of the GeauxDock project, which prototyped a few state-of-art bioinformatics algorithms, and delivered a fast molecular docking program. The second section of this work studies the performance model of the GeauxDock computing kernel. Specifically, the work presents an extraction of features from the input data set and the target systems, and then uses various regression models to calculate the perspective computation time. This helps understand why a certain processor is faster for certain sets of tasks. It also provides the essential information for scheduling on heterogeneous systems. In addition, this dissertation investigates a high-level task scheduling framework for heterogeneous processor systems in which, the pros and cons of using different heterogeneous processors can complement each other. Thus a higher performance can be achieve on heterogeneous computing systems. A new scheduling algorithm with four innovations is presented: Ranked Opportunistic Balancing (ROB), Multi-subject Ranking (MR), Multi-subject Relative Ranking (MRR), and Automatic Small Tasks Rearranging (ASTR). The new algorithm consistently outperforms previously proposed algorithms with better scheduling results, lower computational complexity, and more consistent results over a range of performance prediction errors. Finally, this work extends the heterogeneous task scheduling algorithm to handle power capping feature. It demonstrates that a power-aware scheduler significantly improves the power efficiencies and saves the energy consumption. This suggests that, in addition to performance benefits, heterogeneous systems may have certain advantages on overall power efficiency

Development and application of real-time and interactive software for complex system

Soft materials have attracted considerable interest in recent years for predicting the characteristics of phase separation and self-assembly in nanoscale structures. A popular method for demonstrating and simulating the dynamic behaviour of particles (e.g. particle tracking) and to consider effects of simulation parameters is cell dynamic simulation (CDS). This is a cellular computerisation technique that can be used to investigate different aspects of morphological topographies of soft material systems. The acquisition of quantitative data from particles is a critical requirement in order to obtain a better understanding and of characterising their dynamic behaviour. To achieve this objective particle tracking methods considering quantitative data and focusing on different properties and components of particles is essential. Despite the availability of various types of particle tracking used in experimental work, there is no method available to consider uniform computational data. In order to achieve accurate and efficient computational results for cell dynamic simulation method and particle tracking, two factors are essential: computing/calculating time-scale and simulation system size. Consequently, finding available computing algorithms and resources such as sequential algorithm for implementing a complex technique and achieving precise results is critical and rather expensive. Therefore, it is highly desirable to consider a parallel algorithm and programming model to solve time-consuming and massive computational processing issues. Hence, the gaps between the experimental and computational works and solving time consuming for expensive computational calculations need to be filled in order to investigate a uniform computational technique for particle tracking and significant enhancements in speed and execution times. The work presented in this thesis details a new particle tracking method for integrating diblock copolymers in the form of spheres with a shear flow and a novel designed GPU-based parallel acceleration approach to cell dynamic simulation (CDS). In addition, the evaluation of parallel models and architectures (CPUs and GPUs) utilising the mixtures of application program interface, OpenMP and programming model, CUDA were developed. Finally, this study presents the performance enhancements achieved with GPU-CUDA of approximately ~2 times faster than multi-threading implementation and 13~14 times quicker than optimised sequential processing for the CDS computations/workloads respectively

GPU Array Access Auto-Tuning

GPUs have been used for years in compute intensive applications. Their massive parallel processing capabilities can speedup calculations significantly. However, to leverage this speedup it is necessary to rethink and develop new algorithms that allow parallel processing. These algorithms are only one piece to achieve high performance. Nearly as important as suitable algorithms is the actual implementation and the usage of special hardware features such as intra-warp communication, shared memory, caches, and memory access patterns. Optimizing these factors is usually a time consuming task that requires deep understanding of the algorithms and the underlying hardware. Unlike CPUs, the internal structure of GPUs has changed significantly and will likely change even more over the years. Therefore it does not suffice to optimize the code once during the development, but it has to be optimized for each new GPU generation that is released. To efficiently (re-)optimize code towards the underlying hardware, auto-tuning tools have been developed that perform these optimizations automatically, taking this burden from the programmer. In particular, NVIDIA -- the leading manufacturer for GPUs today -- applied significant changes to the memory hierarchy over the last four hardware generations. This makes the memory hierarchy an attractive objective for an auto-tuner. In this thesis we introduce the MATOG auto-tuner that automatically optimizes array access for NVIDIA CUDA applications. In order to achieve these optimizations, MATOG has to analyze the application to determine optimal parameter values. The analysis relies on empirical profiling combined with a prediction method and a data post-processing step. This allows to find nearly optimal parameter values in a minimal amount of time. Further, MATOG is able to automatically detect varying application workloads and can apply different optimization parameter settings at runtime. To show MATOG's capabilities, we evaluated it on a variety of different applications, ranging from simple algorithms up to complex applications on the last four hardware generations, with a total of 14 GPUs. MATOG is able to achieve equal or even better performance than hand-optimized code. Further, it is able to provide performance portability across different GPU types (low-, mid-, high-end and HPC) and generations. In some cases it is able to exceed the performance of hand-crafted code that has been specifically optimized for the tested GPU by dynamically changing data layouts throughout the execution