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Towards production FPGA-accelerated molecular dynamics: Progress and challenges

Towards production FPGA-accelerated molecular dynamics: Prog...

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International Workshop on High-Performance Reconfigurable Computing Technology and Applications, HPRCTA

作者： Matt Chiu Martin C. Herbordt Computer Architecture and Automated Design Laboratory Department of Electrical and Computer Engineering Boston University Boston MA USA

Recent work in the FPGA acceleration of molecular dynamics simulation has shown that including on-the-fly neighbor list calculation (particle filtering) in the device has the potential for an 80× per core speed-up over the CPU-based reference code and so to make the approach competitive with other computing technologies. In this paper we report on progress and challenges in advancing this work towards the creation of a production system, especially one capable of running on a large-scale system such as the Novo-G. The current version consists of an FPGA-accelerated NAMD-lite running on a PC with a Gidel PROCStar III. The most important implementation issues include software integration, handling exclusion, and modifying the force pipeline. In the last of these we have added support for Particle-Mesh-Ewald and augmented the Lennard-Jones calculation with a switching function. In experiments, we find that energy stability so far appears to be acceptable, but that longer simulations are needed. Due primarily to the added complexity of the force pipelines, performance is somewhat diminished from the previous study; we find, however, that porting to a newer (existing) device will more than compensate for this loss.

关键词： Force Pipelines Field programmable gate arrays Switches Computational modeling Acceleration computer architecture

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Symbolic descriptor and state space model of interconnected linear systems with algebraic loops

Symbolic descriptor and state space model of interconnected ...

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IEEE International Symposium on computer-aided Control System design

作者： Koga, Masanobu Anan, Satoru Department of Systems Design and Informatics Faculty of Computer Science and Systems Engineering Kyushu Institute of Technology 680-4 Kawazu Iizuka Fukuoka Japan Department of Creative Informatics Kyushu Institute of Technology 680-4 Kawazu Iizuka Fukuoka Japan

ISBN: (纸本)9781424453542

This paper proposes a method which gives symbolic model of the interconnected linear system using the adjacency matrix which represent the system. When there exist any algebraic loops in the system, they are reduced to the self loops by the edge contraction. If the weight matrix of the self loop is nonsingular, it is removed and the symbolic state space model is obtained, otherwise the symbolic descriptor model is obtained. We introduce a new interactive graphical software tool which have been developed for modeling and simulation of control systems using the proposed method. © 2010 IEEE.

关键词： Linear systems

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Fast binding site mapping using GPUs and CUDA

Fast binding site mapping using GPUs and CUDA

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IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)

作者： Bharat Sukhwani Martin C. Herbordt Computer Architecture and Automated Design Laboratory Department of Electrical and Computer Engineering Boston University Boston MA USA

ISBN: (纸本)9781424465330

Binding site mapping refers to the computational prediction of the regions on a protein surface that are likely to bind a small molecule with high affinity. The process involves flexibly docking a variety of small molecule probes and finding a consensus site that binds most of those probes. Due to the computational complexity of flexible docking, the process is often split into two steps: the first performs rigid docking between the protein and the probe; the second models the side chain flexibility by energy-minimizing the (few thousand) top scoring protein-probe complexes generated by the first step. Both these steps are computationally very expensive, requiring many hours of runtime per probe on a serial CPU. In the current article, we accelerate a production mapping software program using NVIDIA GPUs. We accelerate both the rigid-docking and the energy minimization steps of the program. The result is a 30× speedup on rigid docking and 12× on energy minimization, resulting in a 13× overall speedup over the current single core implementation.

关键词： Acceleration Probes Drugs Runtime Production Inhibitors computer architecture Laboratories Protein engineering Computational complexity

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An automatic test generation framework for digitally-assisted adaptive equalizers in high-speed serial links

An automatic test generation framework for digitally-assiste...

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design, Automation and Test in Europe Conference and Exhibition, DATE 2010

作者： Abbas, Mohamed Cheng, Kwang-Ting Furukawa, Yasuo Komatsu, Satoshi Asada, Kunihiro VLSI Design and Education Center University of Tokyo Tokyo 113-0032 Japan Department of Electrical and Computer Engineering University of California Santa Barbara CA United States ADVANTEST Corporation Gunma 370-0718 Japan

ISBN: (纸本)9783981080162

This paper presents a new analog ATPG (AATPG) framework that generates near-optimal test stimulus for the digitally-assisted adaptive equalizers in high-speed serial links. Based on the dynamic-signature-based testing scheme developed recently, our AATPG utilizes a Genetic Algorithm (GA) which attempts to maximize the difference between the fault-free and faulty dynamic signatures of the target fault. Our test generation framework takes into account process variations and signal noise in selecting the test stimulus, which minimizes the number of misclassified devices. The experimental results on a 5-tap feed-forward adaptive equalizer demonstrate that the GA-tests generated by our framework can effectively detect faults that are hard to detect by the hand-crafted tests. © 2010 EDAA.

关键词： Genetic algorithms

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Process modelling in process-oriented enterprise mashups

Process modelling in process-oriented enterprise mashups

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2010 2nd IEEE International Conference on Information Management and engineering, ICIME 2010

作者： Xie, Li Xu, Lai De Vrieze, Paul Department of Computer Science and Technology GuangDong Polytechnic Normal University Guangzhou China School of Design Engineering and Computing Bournemouth University Poole Dorset. BH12 5BB United Kingdom

ISBN: (纸本)9781424452644

The Internet and related technologies have created an interconnected world in which we can exchange information easily, process tasks collaboratively, and form communities among users with similar interests. This allows improved efficiency and performance. Mashups, a new web 2.0 technology, have become very important as Web applications to perform these tasks. Currently, the uses of mashups are often more data related than process related. In this paper we explore differences between data-oriented mashups and process-oriented enterprise mashups. Specific attention is paid to how to model end users' process mashup applications from both control flow and data flow perspectives. Based on our analysis, a lightweight process modelling approach is proposed. Further efforts are needed before we are able to easily connect existing web resources for implementing process-oriented enterprise mashups. © 2010 IEEE.

关键词： Systems engineering

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Development of a multi-granularity design support system using hierarchical clustering for non-dominated solutions

Development of a multi-granularity design support system usi...

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作者： Watanabe, Shinya Ohe, Shogo Minato, Ryoujiro College of Information and Systems Muroran Institute of Technology Japan Department of Computer Science and Systems Engineering Muroran Institute of Technology Japan College of Design and Manufacturing Technology Muroran Institute of Technology Japan

ISBN: (纸本)9781424496730

In this paper, an improved new design support system characterized by multigranularity is proposed. Previous studies has focused on only visualization of non-dominated solutions (NDSs), but our method aims to perform a feature extraction and a problem analysis by employing hierarchical clustering and intergroup comparison. The most distinctive feature of our system is an interactive granularity control according to user's preference. This feature enables a various granularity analysis for NDSs from macro to micro view points. In this paper, we examine the characteristics and effectiveness of the proposed approach through computational experiments on a design problem of a counter rotating axial fan turbojet engine. The design target of this problem is two fans and two turbines of the engine. We handle this task as a seven-objective design problem. © 2010 TSI Press.

关键词： Fans

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An intelligent model to construct specialized domain ontologies

An intelligent model to construct specialized domain ontolog...

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International Conference on computer Science and Information Technology (CSIT)

作者： A. Mooman O. Basir A. Younes Department of Electrical and Computer Engineering University of Waterloo Waterloo Canada Department of Systems Design Engineering University of Waterloo Waterloo Canada

Search engines and information retrieval (IR) systems provide a mechanism for users to access large amounts of information available through the Internet. However, in order to find the desired information, the user has to go through a staggering amount of information retrieved from highly dynamic resources. Experimental results show that the approach proposed for constructing specialized domains improves the precision of information retrieval. Our approach involves enriching the user's query with related linguistic semantic and statistical semantic related concept terms. We employ natural language process (NLP) techniques such as WordNet engine to enrich the user's query with semantic lexical synonymous terms and a probabilistic topic model such as latent dirichet allocation (LDA) to extract highly ranked topic from a query's retrieved information. Furthermore, an intelligent learning algorithm, reinforcement learning (RL) is integrated into the design to assist end users in selecting the concept domains that are most relevant to their needs.

关键词： Variable speed drives Ontologies

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Bilateral control with different inertia based on modal decomposition

Bilateral control with different inertia based on modal deco...

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2010 11th IEEE International Workshop on Advanced Motion Control, AMC2010

作者： Motoi, Naoki Kubo, Ryogo Shimono, Tomoyuki Ohnishi, Kouhei Department of System Design Engineering Keio University 3-14-1 Hiyoshi Kouhoku Yokohama Kanagawa 223-8522 Japan Division of Electrical and Computer Engineering Yokohama National University 79-5 Tokiwadai Hodogaya Yokohama Kanagawa 240-8501 Japan

ISBN: (纸本)9781424466696

A bilateral control robot is one of the master-slave teleoperation robots. Consider two robots, a master robot is manipulated by human operators and a slave robot contacts remote environment. Decoupling of a force control and a position control in bilateral control is realized using the mode transformation i.e. a force controller in the common mode and a position controller in the differential mode. In conventional method, high transparency in a bilateral control is obtained when the inertia of the master and slave robots are equal. However, high transparency is not achieved when the inertia of the master and slave robots is different. Additionally, transparency goes down in the case of the bilateral control with scaling. Since the common mode and the differential mode interfere when the inertia and scaling of the master robot slave robots are different. In this paper, modal space disturbance observer (MSDOB) is proposed to solve these interferential problems. MSDOB is disturbance observer in the modal space and is implemented in each mode. MSDOB eliminates these interferences and modeling error in the modal space. In the results, decoupling of the force control and the position control is realized. Therefore, high transparency is achieved even if the inertia and the scaling of the master and slave robots are different. From the simulation and experimental results, the validity of the proposed method was confirmed. © 2010 IEEE.

关键词： Slave robots

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Inference of performance annotations in web service composition models

Inference of performance annotations in web service composit...

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2nd International Workshop on Model-Driven Service engineering, MoSE 2010

作者： García-Domínguez, Antonio Medina-Bulo, Inmaculada Marcos-Bárcena, Mariano Department of Computer Languages and Systems University of Cádiz C/Chile 1 CP 11003 Cádiz Spain Department of Mechanical Engineering and Industrial Design University of Cádiz C/Chile 1 CP 11003 Cádiz Spain

High-quality services must keep working reliably and efficiently, and service compositions are no exception. As they integrate several internal and external services over the network, they need to be carefully designed to meet their performance requirements. Current approaches assist developers in estimating whether the selected services can fulfill those requirements. However, they do not help developers define requirements for services lacking performance constraints and historical data. Manually estimating these constraints is a time-consuming process which might underestimate or overestimate the required performance, incurring in additional costs. This work presents the first version of two algorithms which infer the missing performance constraints from a service composition model. The algorithms are designed to spread equally the load across the composition according to the probability and frequency each service is invoked, and to check the consistency of the performance constraints of each service with those of the composition.

关键词： Load testing

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Fusion Based Approach for Distributed Alarm Correlation in computer Networks

Fusion Based Approach for Distributed Alarm Correlation in C...

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International Conference on Communication Software and Networks, ICCSN

作者： Abduljalil A. Mohamed Otman Basir Department of Systems Design Engineering University of Waterloo Waterloo Canada Department of Electrical and Computer Engineering University of Waterloo Waterloo Canada

ISBN: (纸本)9781424457267;9780769539614

We propose a new distributed alarm correlation and fault identification in computer networks. The managed network is divided into a disjoint management domains and each management domain is assigned a dedicated intelligent agent. The intelligent agent is responsible for collecting, analyzing, and correlating alarms emitted form emitted from its constituent entities in its domain. In the framework of Dempster-Shafer evidence theory, each agent perceives each alarm as a piece of evidence in the occurrence of a certain fault hypothesis and correlates the received alarms into a single alarm called local composite alarm, which encapsulates the agent's partial view of the current status of the managed system. While the alarm correlation process is performed locally, each intelligent agent is able to correlate its alarms globally. These local composite alarms are, in turn, sent to a higher agent whose task is to fuse these alarms and form a global view of operation status of the running network. Extensive experimentations have demonstrated that the proposed approach is more alarm loss tolerant than the codebook based approaches and hence shown its effectiveness in a usually noisy network environment.

关键词： computer networks computer network management Fault diagnosis Protocols Intelligent agent ISO standards Fault detection Neural networks Management training Communication system software

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