Investigating grid computing technologies for use with commercial simulation packages

As simulation experimentation in industry become more computationally demanding, grid computing can be seen as a promising technology that has the potential to bind together the computational resources needed to quickly execute such simulations. To investigate how this might be possible, this paper reviews the grid technologies that can be used together with commercial-off-the-shelf simulation packages (CSPs) used in industry. The paper identifies two specific forms of grid computing (Public Resource Computing and Enterprise-wide Desktop Grid Computing) and the middleware associated with them (BOINC and Condor) as being suitable for grid-enabling existing CSPs. It further proposes three different CSP-grid integration approaches and identifies one of them to be the most appropriate. It is hoped that this research will encourage simulation practitioners to consider grid computing as a technologically viable means of executing CSP-based experiments faster

An FPGA-Based, Multi-model Simulation Method for Biochemical Systems

Modeling and simulation of a cellular system on computers are now becoming an essential process in biological researches. However, modern PCs can\u27t provide enough performance to simulate large-scale biochemical networks. ReCSiP is the alternative FPGA-based solution for biochemical simulations. In this paper, the novel method of biochemical simulation with multiple reaction models on an FPGA is proposed. The method generates optimal circuit and its optimal schedule for each simulation models written in SBML, the standard markup language in systems biology. ReCSiP has a Xilinx\u27s XC2VP70 and achieved over 20-fold speedup compared to Intel’s PentiumIII 1.13GHz.19th IEEE International Parallel and Distributed Processing Symposium (IPDPS\u2705), April 4-8, 2005, Denver, Colorad

Supporting simulation in industry through the application of grid computing

An increased need for collaborative research, together with continuing advances in communication technology and computer hardware, has facilitated the development of distributed systems that can provide users access to geographically dispersed computing resources that are administered in multiple computer domains. The term grid computing, or grids, is popularly used to refer to such distributed systems. Simulation is characterized by the need to run multiple sets of computationally intensive experiments. Large scale scientific simulations have traditionally been the primary benefactor of grid computing. The application of this technology to simulation in industry has, however, been negligible. This research investigates how grid technology can be effectively exploited by users to model simulations in industry. It introduces our desktop grid, WinGrid, and presents a case study conducted at a leading European investment bank. Results indicate that grid computing does indeed hold promise for simulation in industry

A review of High Performance Computing foundations for scientists

The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which otherwise would not be accessible, helps to improve experiments and provides new insights on systems which are analysed [3-6]. Knowing the fundamentals of computation can be very useful for scientists, for it can help them to improve the performance of their theoretical models and simulations. This review includes some technical essentials that can be useful to this end, and it is devised as a complement for researchers whose education is focused on scientific issues and not on technological respects. In this document we attempt to discuss the fundamentals of High Performance Computing (HPC) [7] in a way which is easy to understand without much previous background. We sketch the way standard computers and supercomputers work, as well as discuss distributed computing and discuss essential aspects to take into account when running scientific calculations in computers.Comment: 33 page

zCap: a zero configuration adaptive paging and mobility management mechanism

Today, cellular networks rely on fixed collections of cells (tracking areas) for user equipment localisation. Locating users within these areas involves broadcast search (paging), which consumes radio bandwidth but reduces the user equipment signalling required for mobility management. Tracking areas are today manually configured, hard to adapt to local mobility and influence the load on several key resources in the network. We propose a decentralised and self-adaptive approach to mobility management based on a probabilistic model of local mobility. By estimating the parameters of this model from observations of user mobility collected online, we obtain a dynamic model from which we construct local neighbourhoods of cells where we are most likely to locate user equipment. We propose to replace the static tracking areas of current systems with neighbourhoods local to each cell. The model is also used to derive a multi-phase paging scheme, where the division of neighbourhood cells into consecutive phases balances response times and paging cost. The complete mechanism requires no manual tracking area configuration and performs localisation efficiently in terms of signalling and response times. Detailed simulations show that significant potential gains in localisation effi- ciency are possible while eliminating manual configuration of mobility management parameters. Variants of the proposal can be implemented within current (LTE) standards

Adaptive Hierarchical Data Aggregation using Compressive Sensing (A-HDACS) for Non-smooth Data Field

Compressive Sensing (CS) has been applied successfully in a wide variety of applications in recent years, including photography, shortwave infrared cameras, optical system research, facial recognition, MRI, etc. In wireless sensor networks (WSNs), significant research work has been pursued to investigate the use of CS to reduce the amount of data communicated, particularly in data aggregation applications and thereby improving energy efficiency. However, most of the previous work in WSN has used CS under the assumption that data field is smooth with negligible white Gaussian noise. In these schemes signal sparsity is estimated globally based on the entire data field, which is then used to determine the CS parameters. In more realistic scenarios, where data field may have regional fluctuations or it is piecewise smooth, existing CS based data aggregation schemes yield poor compression efficiency. In order to take full advantage of CS in WSNs, we propose an Adaptive Hierarchical Data Aggregation using Compressive Sensing (A-HDACS) scheme. The proposed schemes dynamically chooses sparsity values based on signal variations in local regions. We prove that A-HDACS enables more sensor nodes to employ CS compared to the schemes that do not adapt to the changing field. The simulation results also demonstrate the improvement in energy efficiency as well as accurate signal recovery

Grid-enabled SIMAP utility: Motivation, integration technology and performance results

A biological system comprises large numbers of functionally diverse and frequently multifunctional sets of elements that interact selectively and nonlinearly to produce coherent behaviours. Such a system can be anything from an intracellular biological process (such as a biochemical reaction cycle, gene regulatory network or signal transduction pathway) to a cell, tissue, entire organism, or even an ecological web. Biochemical systems are responsible for processing environmental signals, inducing the appropriate cellular responses and sequence of internal events. However, such systems are not fully or even poorly understood. Systems biology is a scientific field that is concerned with the systematic study of biological and biochemical systems in terms of complex interactions rather than their individual molecular components. At the core of systems biology is computational modelling (also called mathematical modelling), which is the process of constructing and simulating an abstract model of a biological system for subsequent analysis. This methodology can be used to test hypotheses via insilico experiments, providing predictions that can be tested by in-vitro and in-vivo studies. For example, the ERbB1-4 receptor tyrosine kinases (RTKs) and the signalling pathways they activate, govern most core cellular processes such as cell division, motility and survival (Citri and Yarden, 2006) and are strongly linked to cancer when they malfunction due to mutations etc. An ODE (ordinary differential equation)-based mass action ErbB model has been constructed and analysed by Chen et al. (2009) in order to depict what roles of each protein plays and ascertain to how sets of proteins coordinate with each other to perform distinct physiological functions. The model comprises 499 species (molecules), 201 parameters and 828 reactions. These in silico experiments can often be computationally very expensive, e.g. when multiple biochemical factors are being considered or a variety of complex networks are being simulated simultaneously. Due to the size and complexity of the models and the requirement to perform comprehensive experiments it is often necessary to use high-performance computing (HPC) to keep the experimental time within tractable bounds. Based on this as part of an EC funded cancer research project, we have developed the SIMAP Utility that allows the SImulation modeling of the MAP kinase pathway (http://www.simap-project.org). In this paper we present experiences with Grid-enabling SIMAP using Condor

A fuzzy-based reliaility for JXTA-overlay P2P platform considering data download speed, peer congestion situation, number of interaction and packet loss parameters

(c) 2016 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.In this paper, we propose and evaluate a new fuzzy-based reliability system for Peer-to-Peer (P2P) communications in JXTA-Overlay platform considering as a new parameter the peer congestion situation. In our system, we considered four input parameters: Data Download Speed (DDS), Peer Congestion Situation (PCS), Number of Interactions (NI) and Packet Loss (PL) to decide the Peer Reliability (PR). We evaluate the proposed system by computer simulations. The simulation results have shown that the proposed system has a good performance and can choose reliable peers to connect in JXTA-Overlay platform.Peer ReviewedPostprint (author's final draft