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

Dynamically reconfigurable architecture for embedded computer vision systems

The objective of this research work is to design, develop and implement a new architecture which integrates on the same chip all the processing levels of a complete Computer Vision system, so that the execution is efficient without compromising the power consumption while keeping a reduced cost. For this purpose, an analysis and classification of different mathematical operations and algorithms commonly used in Computer Vision are carried out, as well as a in-depth review of the image processing capabilities of current-generation hardware devices. This permits to determine the requirements and the key aspects for an efficient architecture. A representative set of algorithms is employed as benchmark to evaluate the proposed architecture, which is implemented on an FPGA-based system-on-chip. Finally, the prototype is compared to other related approaches in order to determine its advantages and weaknesses

A Framework of Multi-Dimensional and Multi-Scale Modeling with Applications

In this dissertation, a framework for multi-dimensional and multi-scale modeling is proposed. The essential idea is based on oriented space curves, which can be represented as a 3D slender object or 1D step parameters. SMILES and Masks provide functionalities that extend slender objects into branched and other objects. We treat the conversion between 1D, 2D, 3D, and 4D representations as data unification. A mathematical analysis of different methods applied to helices (a special type of space curves) is also provided. Computational implementation utilizes Model-ViewController design principles to integrate data unification with graphical visualizations to create a dashboard. Applications of multi-dimensional and multi-scale modeling are provided to study “Magic Snake”, “Nanocar” and “Genome Dashboard”

Castell: a heterogeneous cmp architecture scalable to hundreds of processors

Technology improvements and power constrains have taken multicore architectures to dominate microprocessor designs over uniprocessors. At the same time, accelerator based architectures have shown that heterogeneous multicores are very efficient and can provide high throughput for parallel applications, but with a high-programming effort. We propose Castell a scalable chip multiprocessor architecture that can be programmed as uniprocessors, and provides the high throughput of accelerator-based architectures. Castell relies on task-based programming models that simplify software development. These models use a runtime system that dynamically finds, schedules, and adds hardware-specific features to parallel tasks. One of these features is DMA transfers to overlap computation and data movement, which is known as double buffering. This feature allows applications on Castell to tolerate large memory latencies and lets us design the memory system focusing on memory bandwidth. In addition to provide programmability and the design of the memory system, we have used a hierarchical NoC and added a synchronization module. The NoC design distributes memory traffic efficiently to allow the architecture to scale. The synchronization module is a consequence of the large performance degradation of application for large synchronization latencies. Castell is mainly an architecture framework that enables the definition of domain-specific implementations, fine-tuned to a particular problem or application. So far, Castell has been successfully used to propose heterogeneous multicore architectures for scientific kernels, video decoding (using H.264), and protein sequence alignment (using Smith-Waterman and clustalW). It has also been used to explore a number of architecture optimizations such as enhanced DMA controllers, and architecture support for task-based programming models. ii

Proceedings of the 5th International Workshop on Reconfigurable Communication-centric Systems on Chip 2010 - ReCoSoC\u2710 - May 17-19, 2010 Karlsruhe, Germany. (KIT Scientific Reports ; 7551)

ReCoSoC is intended to be a periodic annual meeting to expose and discuss gathered expertise as well as state of the art research around SoC related topics through plenary invited papers and posters. The workshop aims to provide a prospective view of tomorrow\u27s challenges in the multibillion transistor era, taking into account the emerging techniques and architectures exploring the synergy between flexible on-chip communication and system reconfigurability

Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció

Proceedings of the Second International Workshop on Sustainable Ultrascale Computing Systems (NESUS 2015) Krakow, Poland

Proceedings of: Second International Workshop on Sustainable Ultrascale Computing Systems (NESUS 2015). Krakow (Poland), September 10-11, 2015

High performance reconfigurable architectures for biological sequence alignment

Bioinformatics and computational biology (BCB) is a rapidly developing multidisciplinary field which encompasses a wide range of domains, including genomic sequence alignments. It is a fundamental tool in molecular biology in searching for homology between sequences. Sequence alignments are currently gaining close attention due to their great impact on the quality aspects of life such as facilitating early disease diagnosis, identifying the characteristics of a newly discovered sequence, and drug engineering. With the vast growth of genomic data, searching for a sequence homology over huge databases (often measured in gigabytes) is unable to produce results within a realistic time, hence the need for acceleration. Since the exponential increase of biological databases as a result of the human genome project (HGP), supercomputers and other parallel architectures such as the special purpose Very Large Scale Integration (VLSI) chip, Graphic Processing Unit (GPUs) and Field Programmable Gate Arrays (FPGAs) have become popular acceleration platforms. Nevertheless, there are always trade-off between area, speed, power, cost, development time and reusability when selecting an acceleration platform. FPGAs generally offer more flexibility, higher performance and lower overheads. However, they suffer from a relatively low level programming model as compared with off-the-shelf microprocessors such as standard microprocessors and GPUs. Due to the aforementioned limitations, the need has arisen for optimized FPGA core implementations which are crucial for this technology to become viable in high performance computing (HPC). This research proposes the use of state-of-the-art reprogrammable system-on-chip technology on FPGAs to accelerate three widely-used sequence alignment algorithms; the Smith-Waterman with affine gap penalty algorithm, the profile hidden Markov model (HMM) algorithm and the Basic Local Alignment Search Tool (BLAST) algorithm. The three novel aspects of this research are firstly that the algorithms are designed and implemented in hardware, with each core achieving the highest performance compared to the state-of-the-art. Secondly, an efficient scheduling strategy based on the double buffering technique is adopted into the hardware architectures. Here, when the alignment matrix computation task is overlapped with the PE configuration in a folded systolic array, the overall throughput of the core is significantly increased. This is due to the bound PE configuration time and the parallel PE configuration approach irrespective of the number of PEs in a systolic array. In addition, the use of only two configuration elements in the PE optimizes hardware resources and enables the scalability of PE systolic arrays without relying on restricted onboard memory resources. Finally, a new performance metric is devised, which facilitates the effective comparison of design performance between different FPGA devices and families. The normalized performance indicator (speed-up per area per process technology) takes out advantages of the area and lithography technology of any FPGA resulting in fairer comparisons. The cores have been designed using Verilog HDL and prototyped on the Alpha Data ADM-XRC-5LX card with the Virtex-5 XC5VLX110-3FF1153 FPGA. The implementation results show that the proposed architectures achieved giga cell updates per second (GCUPS) performances of 26.8, 29.5 and 24.2 respectively for the acceleration of the Smith-Waterman with affine gap penalty algorithm, the profile HMM algorithm and the BLAST algorithm. In terms of speed-up improvements, comparisons were made on performance of the designed cores against their corresponding software and the reported FPGA implementations. In the case of comparison with equivalent software execution, acceleration of the optimal alignment algorithm in hardware yielded an average speed-up of 269x as compared to the SSEARCH 35 software. For the profile HMM-based sequence alignment, the designed core achieved speed-up of 103x and 8.3x against the HMMER 2.0 and the latest version of HMMER (version 3.0) respectively. On the other hand, the implementation of the gapped BLAST with the two-hit method in hardware achieved a greater than tenfold speed-up compared to the latest NCBI BLAST software. In terms of comparison against other reported FPGA implementations, the proposed normalized performance indicator was used to evaluate the designed architectures fairly. The results showed that the first architecture achieved more than 50 percent improvement, while acceleration of the profile HMM sequence alignment in hardware gained a normalized speed-up of 1.34. In the case of the gapped BLAST with the two-hit method, the designed core achieved 11x speed-up after taking out advantages of the Virtex-5 FPGA. In addition, further analysis was conducted in terms of cost and power performances; it was noted that, the core achieved 0.46 MCUPS per dollar spent and 958.1 MCUPS per watt. This shows that FPGAs can be an attractive platform for high performance computation with advantages of smaller area footprint as well as represent economic ‘green’ solution compared to the other acceleration platforms. Higher throughput can be achieved by redeploying the cores on newer, bigger and faster FPGAs with minimal design effort