Achieving High Speed CFD simulations: Optimization, Parallelization, and FPGA Acceleration for the unstructured DLR TAU Code

Today, large scale parallel simulations are fundamental tools to handle complex problems. The number of processors in current computation platforms has been recently increased and therefore it is necessary to optimize the application performance and to enhance the scalability of massively-parallel systems. In addition, new heterogeneous architectures, combining conventional processors with specific hardware, like FPGAs, to accelerate the most time consuming functions are considered as a strong alternative to boost the performance. In this paper, the performance of the DLR TAU code is analyzed and optimized. The improvement of the code efficiency is addressed through three key activities: Optimization, parallelization and hardware acceleration. At first, a profiling analysis of the most time-consuming processes of the Reynolds Averaged Navier Stokes flow solver on a three-dimensional unstructured mesh is performed. Then, a study of the code scalability with new partitioning algorithms are tested to show the most suitable partitioning algorithms for the selected applications. Finally, a feasibility study on the application of FPGAs and GPUs for the hardware acceleration of CFD simulations is presented

FPGA acceleration of sequence analysis tools in bioinformatics

Thesis (Ph.D.)--Boston UniversityWith advances in biotechnology and computing power, biological data are being produced at an exceptional rate. The purpose of this study is to analyze the application of FPGAs to accelerate high impact production biosequence analysis tools. Compared with other alternatives, FPGAs offer huge compute power, lower power consumption, and reasonable flexibility. BLAST has become the de facto standard in bioinformatic approximate string matching and so its acceleration is of fundamental importance. It is a complex highly-optimized system, consisting of tens of thousands of lines of code and a large number of heuristics. Our idea is to emulate the main phases of its algorithm on FPGA. Utilizing our FPGA engine, we quickly reduce the size of the database to a small fraction, and then use the original code to process the query. Using a standard FPGA-based system, we achieved 12x speedup over a highly optimized multithread reference code. Multiple Sequence Alignment (MSA)--the extension of pairwise Sequence Alignment to multiple Sequences--is critical to solve many biological problems. Previous attempts to accelerate Clustal-W, the most commonly used MSA code, have directly mapped a portion of the code to the FPGA. We use a new approach: we apply prefiltering of the kind commonly used in BLAST to perform the initial all-pairs alignments. This results in a speedup of from 8Ox to 190x over the CPU code (8 cores). The quality is comparable to the original according to a commonly used benchmark suite evaluated with respect to multiple distance metrics. The challenge in FPGA-based acceleration is finding a suitable application mapping. Unfortunately many software heuristics do not fall into this category and so other methods must be applied. One is restructuring: an entirely new algorithm is applied. Another is to analyze application utilization and develop accuracy/performance tradeoffs. Using our prefiltering approach and novel FPGA programming models we have achieved significant speedup over reference programs. We have applied approximation, seeding, and filtering to this end. The bulk of this study is to introduce the pros and cons of these acceleration models for biosequence analysis tools

Power and Energy Aware Heterogeneous Computing Platform

During the last decade, wireless technologies have experienced significant development, most notably in the form of mobile cellular radio evolution from GSM to UMTS/HSPA and thereon to Long-Term Evolution (LTE) for increasing the capacity and speed of wireless data networks. Considering the real-time constraints of the new wireless standards and their demands for parallel processing, reconfigurable architectures and in particular, multicore platforms are part of the most successful platforms due to providing high computational parallelism and throughput. In addition to that, by moving toward Internet-of-Things (IoT), the number of wireless sensors and IP-based high throughput network routers is growing at a rapid pace. Despite all the progression in IoT, due to power and energy consumption, a single chip platform for providing multiple communication standards and a large processing bandwidth is still missing.The strong demand for performing different sets of operations by the embedded systems and increasing the computational performance has led to the use of heterogeneous multicore architectures with the help of accelerators for computationally-intensive data-parallel tasks acting as coprocessors. Currently, highly heterogeneous systems are the most power-area efficient solution for performing complex signal processing systems. Additionally, the importance of IoT has increased significantly the need for heterogeneous and reconfigurable platforms.On the other hand, subsequent to the breakdown of the Dennardian scaling and due to the enormous heat dissipation, the performance of a single chip was obstructed by the utilization wall since all cores cannot be clocked at their maximum operating frequency. Therefore, a thermal melt-down might be happened as a result of high instantaneous power dissipation. In this context, a large fraction of the chip, which is switched-off (Dark) or operated at a very low frequency (Dim) is called Dark Silicon. The Dark Silicon issue is a constraint for the performance of computers, especially when the up-coming IoT scenario will demand a very high performance level with high energy efficiency. Among the suggested solution to combat the problem of Dark-Silicon, the use of application-specific accelerators and in particular Coarse-Grained Reconfigurable Arrays (CGRAs) are the main motivation of this thesis work.This thesis deals with design and implementation of Software Defined Radio (SDR) as well as High Efficiency Video Coding (HEVC) application-specific accelerators for computationally intensive kernels and data-parallel tasks. One of the most important data transmission schemes in SDR due to its ability of providing high data rates is Orthogonal Frequency Division Multiplexing (OFDM). This research work focuses on the evaluation of Heterogeneous Accelerator-Rich Platform (HARP) by implementing OFDM receiver blocks as designs for proof-of-concept. The HARP template allows the designer to instantiate a heterogeneous reconfigurable platform with a very large amount of custom-tailored computational resources while delivering a high performance in terms of many high-level metrics. The availability of this platform lays an excellent foundation to investigate techniques and methods to replace the Dark or Dim part of chip with high-performance silicon dissipating very low power and energy. Furthermore, this research work is also addressing the power and energy issues of the embedded computing systems by tailoring the HARP for self-aware and energy-aware computing models. In this context, the instantaneous power dissipation and therefore the heat dissipation of HARP are mitigated on FPGA/ASIC by using Dynamic Voltage and Frequency Scaling (DVFS) to minimize the dark/dim part of the chip. Upgraded HARP for self-aware and energy-aware computing can be utilized as an energy-efficient general-purpose transceiver platform that is cognitive to many radio standards and can provide high throughput while consuming as little energy as possible. The evaluation of HARP has shown promising results, which makes it a suitable platform for avoiding Dark Silicon in embedded computing platforms and also for diverse needs of IoT communications.In this thesis, the author designed the blocks of OFDM receiver by crafting templatebased CGRA devices and then attached them to HARP’s Network-on-Chip (NoC) nodes. The performance of application-specific accelerators generated from templatebased CGRAs, the performance of the entire platform subsequent to integrating the CGRA nodes on HARP and the NoC traffic are recorded in terms of several highlevel performance metrics. In evaluating HARP on FPGA prototype, it delivers a performance of 0.012 GOPS/mW. Because of the scalability and regularity in HARP, the author considered its value as architectural constant. In addition to showing the gain and the benefits of maximizing the number of reconfigurable processing resources on a platform in comparison to the scaled performance of several state-of-the-art platforms, HARP’s architectural constant ensures application-independent figure of merit. HARP is further evaluated by implementing various sizes of Discrete Cosine transform (DCT) and Discrete Sine Transform (DST) dedicated for HEVC standard, which showed its ability to sustain Full HD 1080p format at 30 fps on FPGA. The author also integrated self-aware computing model in HARP to mitigate the power dissipation of an OFDM receiver. In the case of FPGA implementation, the total power dissipation of the platform showed 16.8% reduction due to employing the Feedback Control System (FCS) technique with Dynamic Frequency Scaling (DFS). Furthermore, by moving to ASIC technology and scaling both frequency and voltage simultaneously, significant dynamic power reduction (up to 82.98%) was achieved, which proved the DFS/DVFS techniques as one step forward to mitigate the Dark Silicon issue

Architecture and Analysis for Next Generation Mobile Signal Processing.

Mobile devices have proliferated at a spectacular rate, with more than 3.3 billion active cell phones in the world. With sales totaling hundreds of billions every year, the mobile phone has arguably become the dominant computing platform, replacing the personal computer. Soon, improvements to today’s smart phones, such as high-bandwidth internet access, high-definition video processing, and human-centric interfaces that integrate voice recognition and video-conferencing will be commonplace. Cost effective and power efficient support for these applications will be required. Looking forward to the next generation of mobile computing, computation requirements will increase by one to three orders of magnitude due to higher data rates, increased complexity algorithms, and greater computation diversity but the power requirements will be just as stringent to ensure reasonable battery lifetimes. The design of the next generation of mobile platforms must address three critical challenges: efficiency, programmability, and adaptivity. The computational efficiency of existing solutions is inadequate and straightforward scaling by increasing the number of cores or the amount of data-level parallelism will not suffice. Programmability provides the opportunity for a single platform to support multiple applications and even multiple standards within each application domain. Programmability also provides: faster time to market as hardware and software development can proceed in parallel; the ability to fix bugs and add features after manufacturing; and, higher chip volumes as a single platform can support a family of mobile devices. Lastly, hardware adaptivity is necessary to maintain efficiency as the computational characteristics of the applications change. Current solutions are tailored specifically for wireless signal processing algorithms, but lose their efficiency when other application domains like high definition video are processed. This thesis addresses these challenges by presenting analysis of next generation mobile signal processing applications and proposing an advanced signal processing architecture to deal with the stringent requirements. An application-centric design approach is taken to design our architecture. First, a next generation wireless protocol and high definition video is analyzed and algorithmic characterizations discussed. From these characterizations, key architectural implications are presented, which form the basis for the advanced signal processor architecture, AnySP.Ph.D.Electrical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/86344/1/mwoh_1.pd

Embedded electronic systems driven by run-time reconfigurable hardware

Abstract This doctoral thesis addresses the design of embedded electronic systems based on run-time reconfigurable hardware technology –available through SRAM-based FPGA/SoC devices– aimed at contributing to enhance the life quality of the human beings. This work does research on the conception of the system architecture and the reconfiguration engine that provides to the FPGA the capability of dynamic partial reconfiguration in order to synthesize, by means of hardware/software co-design, a given application partitioned in processing tasks which are multiplexed in time and space, optimizing thus its physical implementation –silicon area, processing time, complexity, flexibility, functional density, cost and power consumption– in comparison with other alternatives based on static hardware (MCU, DSP, GPU, ASSP, ASIC, etc.). The design flow of such technology is evaluated through the prototyping of several engineering applications (control systems, mathematical coprocessors, complex image processors, etc.), showing a high enough level of maturity for its exploitation in the industry.Resumen Esta tesis doctoral abarca el diseño de sistemas electrónicos embebidos basados en tecnología hardware dinámicamente reconfigurable –disponible a través de dispositivos lógicos programables SRAM FPGA/SoC– que contribuyan a la mejora de la calidad de vida de la sociedad. Se investiga la arquitectura del sistema y del motor de reconfiguración que proporcione a la FPGA la capacidad de reconfiguración dinámica parcial de sus recursos programables, con objeto de sintetizar, mediante codiseño hardware/software, una determinada aplicación particionada en tareas multiplexadas en tiempo y en espacio, optimizando así su implementación física –área de silicio, tiempo de procesado, complejidad, flexibilidad, densidad funcional, coste y potencia disipada– comparada con otras alternativas basadas en hardware estático (MCU, DSP, GPU, ASSP, ASIC, etc.). Se evalúa el flujo de diseño de dicha tecnología a través del prototipado de varias aplicaciones de ingeniería (sistemas de control, coprocesadores aritméticos, procesadores de imagen, etc.), evidenciando un nivel de madurez viable ya para su explotación en la industria.Resum Aquesta tesi doctoral està orientada al disseny de sistemes electrònics empotrats basats en tecnologia hardware dinàmicament reconfigurable –disponible mitjançant dispositius lògics programables SRAM FPGA/SoC– que contribueixin a la millora de la qualitat de vida de la societat. S’investiga l’arquitectura del sistema i del motor de reconfiguració que proporcioni a la FPGA la capacitat de reconfiguració dinàmica parcial dels seus recursos programables, amb l’objectiu de sintetitzar, mitjançant codisseny hardware/software, una determinada aplicació particionada en tasques multiplexades en temps i en espai, optimizant així la seva implementació física –àrea de silici, temps de processat, complexitat, flexibilitat, densitat funcional, cost i potència dissipada– comparada amb altres alternatives basades en hardware estàtic (MCU, DSP, GPU, ASSP, ASIC, etc.). S’evalúa el fluxe de disseny d’aquesta tecnologia a través del prototipat de varies aplicacions d’enginyeria (sistemes de control, coprocessadors aritmètics, processadors d’imatge, etc.), demostrant un nivell de maduresa viable ja per a la seva explotació a la indústria

Energy-Efficient Computing for Mobile Signal Processing

Mobile devices have rapidly proliferated, and deployment of handheld devices continues to increase at a spectacular rate. As today's devices not only support advanced signal processing of wireless communication data but also provide rich sets of applications, contemporary mobile computing requires both demanding computation and efficiency. Most mobile processors combine general-purpose processors, digital signal processors, and hardwired application-specific integrated circuits to satisfy their high-performance and low-power requirements. However, such a heterogeneous platform is inefficient in area, power and programmability. Improving the efficiency of programmable mobile systems is a critical challenge and an active area of computer systems research. SIMD (single instruction multiple data) architectures are very effective for data-level-parallelism intense algorithms in mobile signal processing. However, new characteristics of advanced wireless/multimedia algorithms require architectural re-evaluation to achieve better energy efficiency. Therefore, fourth generation wireless protocol and high definition mobile video algorithms are analyzed to enhance a wide-SIMD architecture. The key enhancements include 1) programmable crossbar to support complex data alignment, 2) SIMD partitioning to support fine-grain SIMD computation, and 3) fused operation to support accelerating frequently used instruction pairs. Near-threshold computation has been attractive in low-power architecture research because it balances performance and power. To further improve energy efficiency in mobile computing, near-threshold computation is applied to a wide SIMD architecture. This proposed near-threshold wide SIMD architecture-Diet SODA-presents interesting architectural design decisions such as 1) very wide SIMD datapath to compensate for degraded performance induced by near-threshold computation and 2) scatter-gather data prefetcher to exploit large latency gap between memory and the SIMD datapath. Although near-threshold computation provides excellent energy efficiency, it suffers from increased delay variations. A systematic study of delay variations in near-threshold computing is performed and simple techniques-structural duplication and voltage/frequency margining-are explored to tolerate and mitigate the delay variations in near-threshold wide SIMD architectures. This dissertation analyzes representative wireless/multimedia mobile signal processing algorithms, proposes an energy-efficient programmable platform, and evaluates performance and power. A main theme of this dissertation is that the performance and efficiency of programmable embedded systems can be significantly improved with a combination of parallel SIMD and near-threshold computations.Ph.D.Electrical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/86356/1/swseo_1.pd

Manticore: Hardware-Accelerated RTL Simulation with Static Bulk-Synchronous Parallelism

The demise of Moore's Law and Dennard Scaling has revived interest in specialized computer architectures and accelerators. Verification and testing of this hardware heavily uses cycle-accurate simulation of register-transfer-level (RTL) designs. The best software RTL simulators can simulate designs at 1--1000~kHz, i.e., more than three orders of magnitude slower than hardware. Faster simulation can increase productivity by speeding design iterations and permitting more exhaustive exploration. One possibility is to use parallelism as RTL exposes considerable fine-grain concurrency. However, state-of-the-art RTL simulators generally perform best when single-threaded since modern processors cannot effectively exploit fine-grain parallelism. This work presents Manticore: a parallel computer designed to accelerate RTL simulation. Manticore uses a static bulk-synchronous parallel (BSP) execution model to eliminate runtime synchronization barriers among many simple processors. Manticore relies entirely on its compiler to schedule resources and communication. Because RTL code is practically free of long divergent execution paths, static scheduling is feasible. Communication and synchronization no longer incur runtime overhead, enabling efficient fine-grain parallelism. Moreover, static scheduling dramatically simplifies the physical implementation, significantly increasing the potential parallelism on a chip. Our 225-core FPGA prototype running at 475 MHz outperforms a state-of-the-art RTL simulator on an Intel Xeon processor running at $\approx$ 3.3 GHz by up to 27.9$\times$ (geomean 5.3$\times$) in nine Verilog benchmarks