Hardware implementation of non-bonded forces in molecular dynamics simulations

Molecular Dynamics is a computational method based on classical mechanics to describe the behavior of a molecular system. This method is used in biomolecular simulations, which are intended to contribute to the study and advance of nanotechnology, medicine, chemistry and biology. Software implementations of Molecular Dynamics simulations can spend most of time computing the non-bonded interactions. This work presents the design and implementation of an FPGA-based coprocessor that accelerates MD simulations by computing in parallel the non-bonded interactions, specifically, the van der Waals and the electrostatic interactions. These interactions are modeled as the Lennard-Jones 6-12 potential and the direct-space Ewald summation, respectively. In addition, this work introduces a novel variable transformation of the potential energy functions, and a novel interpolation method with pseudo-floating-point representation to compute the short-range forces. Also, it uses a combination of fixed-point and floating-point arithmetic to obtain the best of both representations. The FPGA coprocessor is a memory-mapped system connected to a host by PCI Express, and is provided with interruption capabilities to improve parallelization. Its main block is based on a single functional pipeline, and is connected via Avalon Bus to other peripherals such as the PCIe Hard-IP and the SG-DMA. It is implemented on an Altera¿s EP2AGX125EF35C4 device, can process 16k particles, and is configured to store up to 16 different types of particles. Simulations in a custom C-application for MD that only computes non-bonded forces become up to 12.5x faster using the FPGA coprocessor when considering 12500 atoms.PregradoINGENIERO(A) EN ELECTRÓNIC

Customisable arithmetic hardware designs

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Accelerated Financial Applications through Specialized Hardware, FPGA

This project will investigate Field Programmable Gate Array (FPGA) technology in financial applications. FPGA implementation in high performance computing is still in its infancy. Certain companies like XtremeData inc. advertized speed improvements of 50 to 1000 times for DNA sequencing using FPGAs, while using an FPGA as a coprocessor to handle specific tasks provides two to three times more processing power. FPGA technology increases performance by parallelizing calculations. This project will specifically address speed and accuracy improvements of both fundamental and transcendental functions when implemented using FPGA technology. The results of this project will lead to a series of recommendations for effective utilization of FPGA technology in financial applications

Mathematical model and implementation of rational processing

Precision in computations is a considerable challenge to adequately addressing many current scientific or engineering problems. The way in which the numbers are represented constitutes the first step to compute them and determines the validity of the results. The aim of this research is to provide a formal framework and a set of computational primitives to address high precision problems of mathematical calculation in engineering and numerical simulation. The main contribution of this research is a mathematical model to build an exact arithmetical unit able to represent without error rational numbers in positional notation system. The functions under consideration are addition and multiplication because they form an algebraic commutative ring which contains a multiplicative inverse for every non-zero element. This paper reviews other specialized arithmetic units based on existing formats to show ways to make high precision computing. It is proposed a formal framework of the whole arithmetic architecture in which the operators are based. Then, the design of the addition operation is detailed and its hardware implementation is described. Finally, extensive evaluation of this operator is performed to prove its ability for exact processing

Gbit/second lossless data compression hardware

This thesis investigates how to improve the performance of lossless data compression hardware as a tool to reduce the cost per bit stored in a computer system or transmitted over a communication network. Lossless data compression allows the exact reconstruction of the original data after decompression. Its deployment in some high-bandwidth applications has been hampered due to performance limitations in the compressing hardware that needs to match the performance of the original system to avoid becoming a bottleneck. Advancing the area of lossless data compression hardware, hence, offers a valid motivation with the potential of doubling the performance of the system that incorporates it with minimum investment. This work starts by presenting an analysis of current compression methods with the objective of identifying the factors that limit performance and also the factors that increase it. [Continues.

Hardware-software co-design of an iris recognition algorithm

This paper describes the implementation of an iris recognition algorithm based on hardware-software co-design. The system architecture consists of a general-purpose 32- bit microprocessor and several slave coprocessors that accelerate the most intensive calculations. The whole iris recognition algorithm has been implemented on a low-cost Spartan 3 FPGA, achieving significant reduction in execution time when compared to a conventional software-based application. Experimental results show that with a clock speed of 40 MHz, an IrisCode is obtained in less than 523 ms from an image of 640x480 pixels, which is just 20% of the total time needed by a software solution running on the same microprocessor embedded in the architecture.Peer ReviewedPreprin

Tuning the Computational Effort: An Adaptive Accuracy-aware Approach Across System Layers

This thesis introduces a novel methodology to realize accuracy-aware systems, which will help designers integrate accuracy awareness into their systems. It proposes an adaptive accuracy-aware approach across system layers that addresses current challenges in that domain, combining and tuning accuracy-aware methods on different system layers. To widen the scope of accuracy-aware computing including approximate computing for other domains, this thesis presents innovative accuracy-aware methods and techniques for different system layers. The required tuning of the accuracy-aware methods is integrated into a configuration layer that tunes the available knobs of the accuracy-aware methods integrated into a system