Efficient Molecular Dynamics Simulation on Reconfigurable Models with MultiGrid Method

In the field of biology, MD simulations are continuously used to investigate biological studies. A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. We are focusing on long-ranged interactions, since the calculation time is O(N^2) for an N particle system. In this dissertation, we are proposing two research directions for the MD simulation. First, we design a new variation of Multigrid (MG) algorithm called Multi-level charge assignment (MCA) that requires O(N) time for accurate and efficient calculation of the electrostatic forces. We apply MCA and back interpolation based on the structure of molecules to enhance the accuracy of the simulation. Our second research utilizes reconfigurable models to achieve fast calculation time. We have been working on exploiting two reconfigurable models. We design FPGA-based MD simulator implementing MCA method for Xilinx Virtex-IV. It performs about 10 to 100 times faster than software implementation depending on the simulation accuracy desired. We also design fast and scalable Reconfigurable mesh (R-Mesh) algorithms for MD simulations. This work demonstrates that the large scale biological studies can be simulated in close to real time. The R-Mesh algorithms we design highlight the feasibility of these models to evaluate potentials with faster calculation times. Specifically, we develop R-Mesh algorithms for both Direct method and Multigrid method. The Direct method evaluates exact potentials and forces, but requires O(N^2) calculation time for evaluating electrostatic forces on a general purpose processor. The MG method adopts an interpolation technique to reduce calculation time to O(N) for a given accuracy. However, our R-Mesh algorithms require only O(N) or O(logN) time complexity for the Direct method on N linear R-Mesh and N¡¿N R-Mesh, respectively and O(r)+O(logM) time complexity for the Multigrid method on an X¡¿Y¡¿Z R-Mesh. r is N/M and M = X¡¿Y¡¿Z is the number of finest grid points

An Energy-Efficient and Reliable Data Transmission Scheme for Transmitter-based Energy Harvesting Networks

Energy harvesting technology has been studied to overcome a limited power resource problem for a sensor network. This paper proposes a new data transmission period control and reliable data transmission algorithm for energy harvesting based sensor networks. Although previous studies proposed a communication protocol for energy harvesting based sensor networks, it still needs additional discussion. Proposed algorithm control a data transmission period and the number of data transmission dynamically based on environment information. Through this, energy consumption is reduced and transmission reliability is improved. The simulation result shows that the proposed algorithm is more efficient when compared with previous energy harvesting based communication standard, Enocean in terms of transmission success rate and residual energy.This research was supported by Basic Science Research Program through the National Research Foundation by Korea (NRF) funded by the Ministry of Education, Science and Technology(2012R1A1A3012227)

An automated OpenCL FPGA compilation framework targeting a configurable, VLIW chip multiprocessor

Modern system-on-chips augment their baseline CPU with coprocessors and accelerators to increase overall computational capacity and power efficiency, and thus have evolved into heterogeneous systems. Several languages have been developed to enable this paradigm shift, including CUDA and OpenCL. This thesis discusses a unified compilation environment to enable heterogeneous system design through the use of OpenCL and a customised VLIW chip multiprocessor (CMP) architecture, known as the LE1. An LLVM compilation framework was researched and a prototype developed to enable the execution of OpenCL applications on the LE1 CPU. The framework fully automates the compilation flow and supports work-item coalescing to better utilise the CPU cores and alleviate the effects of thread divergence. This thesis discusses in detail both the software stack and target hardware architecture and evaluates the scalability of the proposed framework on a highly precise cycle-accurate simulator. This is achieved through the execution of 12 benchmarks across 240 different machine configurations, as well as further results utilising an incomplete development branch of the compiler. It is shown that the problems generally scale well with the LE1 architecture, up to eight cores, when the memory system becomes a serious bottleneck. Results demonstrate superlinear performance on certain benchmarks (x9 for the bitonic sort benchmark with 8 dual-issue cores) with further improvements from compiler optimisations (x14 for bitonic with the same configuration

Probabilistic Image Models and their Massively Parallel Architectures : A Seamless Simulation- and VLSI Design-Framework Approach

Algorithmic robustness in real-world scenarios and real-time processing capabilities are the two essential and at the same time contradictory requirements modern image-processing systems have to fulfill to go significantly beyond state-of-the-art systems. Without suitable image processing and analysis systems at hand, which comply with the before mentioned contradictory requirements, solutions and devices for the application scenarios of the next generation will not become reality. This issue would eventually lead to a serious restraint of innovation for various branches of industry. This thesis presents a coherent approach to the above mentioned problem. The thesis at first describes a massively parallel architecture template and secondly a seamless simulation- and semiconductor-technology-independent design framework for a class of probabilistic image models, which are formulated on a regular Markovian processing grid. The architecture template is composed of different building blocks, which are rigorously derived from Markov Random Field theory with respect to the constraints of \it massively parallel processing \rm and \it technology independence\rm. This systematic derivation procedure leads to many benefits: it decouples the architecture characteristics from constraints of one specific semiconductor technology; it guarantees that the derived massively parallel architecture is in conformity with theory; and it finally guarantees that the derived architecture will be suitable for VLSI implementations. The simulation-framework addresses the unique hardware-relevant simulation needs of MRF based processing architectures. Furthermore the framework ensures a qualified representation for simulation of the image models and their massively parallel architectures by means of their specific simulation modules. This allows for systematic studies with respect to the combination of numerical, architectural, timing and massively parallel processing constraints to disclose novel insights into MRF models and their hardware architectures. The design-framework rests upon a graph theoretical approach, which offers unique capabilities to fulfill the VLSI demands of massively parallel MRF architectures: the semiconductor technology independence guarantees a technology uncommitted architecture for several design steps without restricting the design space too early; the design entry by means of behavioral descriptions allows for a functional representation without determining the architecture at the outset; and the topology-synthesis simplifies and separates the data- and control-path synthesis. Detailed results discussed in the particular chapters together with several additional results collected in the appendix will further substantiate the claims made in this thesis

Split and Shift Methodology: Overcoming Hardware Limitations on Cellular Processor Arrays for Image Processing

Na era multimedia, o procesado de imaxe converteuse nun elemento de singular importancia nos dispositivos electrónicos. Dende as comunicacións (p.e. telemedicina), a seguranza (p.e. recoñecemento retiniano) ou control de calidade e de procesos industriais (p.e. orientación de brazos articulados, detección de defectos do produto), pasando pola investigación (p.e. seguimento de partículas elementais) e diagnose médica (p.e. detección de células estrañas, identificaciónn de veas retinianas), hai un sinfín de aplicacións onde o tratamento e interpretación automáticas de imaxe e fundamental. O obxectivo último será o deseño de sistemas de visión con capacidade de decisión. As tendencias actuais requiren, ademais, a combinación destas capacidades en dispositivos pequenos e portátiles con resposta en tempo real. Isto propón novos desafíos tanto no deseño hardware como software para o procesado de imaxe, buscando novas estruturas ou arquitecturas coa menor area e consumo de enerxía posibles sen comprometer a funcionalidade e o rendemento

Parallel and Distributed Computing

The 14 chapters presented in this book cover a wide variety of representative works ranging from hardware design to application development. Particularly, the topics that are addressed are programmable and reconfigurable devices and systems, dependability of GPUs (General Purpose Units), network topologies, cache coherence protocols, resource allocation, scheduling algorithms, peertopeer networks, largescale network simulation, and parallel routines and algorithms. In this way, the articles included in this book constitute an excellent reference for engineers and researchers who have particular interests in each of these topics in parallel and distributed computing