A novel parallel algorithm for surface editing and its FPGA implementation

A thesis submitted to the University of Bedfordshire in partial fulfilment of the requirements for the degree of Doctor of PhilosophySurface modelling and editing is one of important subjects in computer graphics. Decades of research in computer graphics has been carried out on both low-level, hardware-related algorithms and high-level, abstract software. Success of computer graphics has been seen in many application areas, such as multimedia, visualisation, virtual reality and the Internet. However, the hardware realisation of OpenGL architecture based on FPGA (field programmable gate array) is beyond the scope of most of computer graphics researches. It is an uncultivated research area where the OpenGL pipeline, from hardware through the whole embedded system (ES) up to applications, is implemented in an FPGA chip. This research proposes a hybrid approach to investigating both software and hardware methods. It aims at bridging the gap between methods of software and hardware, and enhancing the overall performance for computer graphics. It consists of four parts, the construction of an FPGA-based ES, Mesa-OpenGL implementation for FPGA-based ESs, parallel processing, and a novel algorithm for surface modelling and editing. The FPGA-based ES is built up. In addition to the Nios II soft processor and DDR SDRAM memory, it consists of the LCD display device, frame buffers, video pipeline, and algorithm-specified module to support the graphics processing. Since there is no implementation of OpenGL ES available for FPGA-based ESs, a specific OpenGL implementation based on Mesa is carried out. Because of the limited FPGA resources, the implementation adopts the fixed-point arithmetic, which can offer faster computing and lower storage than the floating point arithmetic, and the accuracy satisfying the needs of 3D rendering. Moreover, the implementation includes Bézier-spline curve and surface algorithms to support surface modelling and editing. The pipelined parallelism and co-processors are used to accelerate graphics processing in this research. These two parallelism methods extend the traditional computation parallelism in fine-grained parallel tasks in the FPGA-base ESs. The novel algorithm for surface modelling and editing, called Progressive and Mixing Algorithm (PAMA), is proposed and implemented on FPGA-based ES’s. Compared with two main surface editing methods, subdivision and deformation, the PAMA can eliminate the large storage requirement and computing cost of intermediated processes. With four independent shape parameters, the PAMA can be used to model and edit freely the shape of an open or closed surface that keeps globally the zero-order geometric continuity. The PAMA can be applied independently not only FPGA-based ESs but also other platforms. With the parallel processing, small size, and low costs of computing, storage and power, the FPGA-based ES provides an effective hybrid solution to surface modelling and editing

Acceleration of Biomolecular Simulations using FPGA-based Reconfigurable Computing

A paradigm shift is occurring in the way compute-intensive scientific applications are developed. Thanks to advancements in commercially viable hybrid architectures for High-Performance Computing (HPC), the focus has shifted from improving performance by merely scaling algorithms on von Neumann computing nodes to fully exploiting additional computational capabilities provided by accelerators such as FPGAs (Field Programmable Gate Arrays) and GPGPUs (General Purpose Graphical Processing Units). Computational chemists use Molecular Dynamics (MD) simulations like LAMMPS (Large Scale Atomic Molecular Massively Parallel Systems) and NAMD (NAnoscale Molecular Dynamics) to simulate biomolecular behaviour such as protein folding and small molecule docking to proteins. MD simulations are computationally complex n-body problems, which are time consuming to simulate in biologically relevant scales. Executing such simulations in best available HPC environments is critical for scientific advancements in the field. Thus, as HPC technology evolves, there is a need to update classical biomolecular simulation applications like LAMMPS to better suit the architecture. In this work, we modify LAMMPS (a classical molecular dynamics simulation program developed for CPU-only clusters) to execute on a reconfigurable computer system, SRC-7 H MAP. The SRC-7 H MAP consists of two Altera FPGA logic chips interfaced to a dual-core Intel Xeon processor. Users can benefit by offloading most compute-intensive tasks of the application to the FPGA logic. This work explores the challenges involved in effectively adapting a production level application code optimized for von Neumann architecture, to an FPGA-based hybrid architecture. We have successfully accelerated the non-bonded force computations, the most compute-intensive module in LAMMPS for biomolecular simulations, by 5.0x over a single 3.0 GHz Xeon processor. This performance includes the data transfer overheads and function calling overheads. Further, using the accelerated non-bonded force computations function, we achieve an overall application speed-up of 2.0x to 2.4

WCET Optimizations and Architectural Support for Hard Real-Time Systems

As time predictability is critical to hard real-time systems, it is not only necessary to accurately estimate the worst-case execution time (WCET) of the real-time tasks but also desirable to improve either the WCET of the tasks or time predictability of the system, because the real-time tasks with lower WCETs are easy to schedule and more likely to meat their deadlines. As a real-time system is an integration of software and hardware, the optimization can be achieved through two ways: software optimization and time-predictable architectural support. In terms of software optimization, we fi rst propose a loop-based instruction prefetching approach to further improve the WCET comparing with simple prefetching techniques such as Next-N-Line prefetching which can enhance both the average-case performance and the worst-case performance. Our prefetching approach can exploit the program controlow information to intelligently prefetch instructions that are most likely needed. Second, as inter-thread interferences in shared caches can signi cantly a ect the WCET of real-time tasks running on multicore processors, we study three multicore-aware code positioning methods to reduce the inter-core L2 cache interferences between co-running real-time threads. One strategy focuses on decreasing the longest WCET among the co-running threads, and two other methods aim at achieving fairness in terms of the amount or percentage of WCET reduction among co-running threads. In the aspect of time-predictable architectural support, we introduce the concept of architectural time predictability (ATP) to separate timing uncertainty concerns caused by hardware from software, which greatly facilitates the advancement of time-predictable processor design. We also propose a metric called Architectural Time-predictability Factor (ATF) to measure architectural time predictability quantitatively. Furthermore, while cache memories can generally improve average-case performance, they are harmful to time predictability and thus are not desirable for hard real-time and safety-critical systems. In contrast, Scratch-Pad Memories (SPMs) are time predictable, but they may lead to inferior performance. Guided by ATF, we propose and evaluate a variety of hybrid on-chip memory architectures to combine both caches and SPMs intelligently to achieve good time predictability and high performance. Detailed implementation and experimental results discussion are presented in this dissertation

On the Determinism of Multi-core Processors

Hard real time systems are evolving in order to respond to the increasing demand in complex functionalities while taking advantage of newer hardware. Software development for safety critical systems has to comply with strict requirements that will facilitate the certification process. During this process, each part of the system is evaluated, requiring a certain level of assurance in order to provide confidence in the product. In particular there must be a level of confidence that the system behaves deterministically that may be based on functionality, resources and time. The success of system verification depends greatly on the capacity to determine its exact behavior. Nonetheless, hardware evolved in order to maximize the average computation power throughput with little to no regard to the deterministic aspect. Therefore modern architectural features of processors, like pipelines, cache memories and co-processors, make it hard to verify that all the needed properties are respected. The multi-core is furthermore difficult to analyze as the architecture employs mechanisms that compromise strong spatial and temporal partitioning when using shared resources without rigorous access control like shared caches or shared input/outputs. In this paper we identify and analyze the main sources of nondeterminism of the multi-cores with regard to the timing estimation. Precise determination of the worst case execution time is a challenging task even in single-core architectures. The problems are accentuated in the multi-core context mainly due to the resource sharing that can lead to highly complex interactions or to nondeterminism. Most of the units that generate behaviors that are hard to take into account can be deactivated, but it is not always easy to predict the impact on the performance. Nevertheless some of the features cannot be disabled (such as the out of order execution or some nondeterministic crossbar access policies) which leads to the invalidation of the respective platform for applications with high criticality level. We will address the problematic units, propose configuration or architecture guidelines and estimate their impact on the performance and determinism of the system