Computer-aided solution of some problems relating to control of the complicated mechanical systems

Consideration was given to control of a complex object whose motion obeys a multivariable nonlinear nonstationary mathematical model. Rigid constraints were imposed on the object’s dynamic precision. The paper considered computer-aided generation of the current equations of object motion with regard for the actuators which differ from subsystem to subsystem. The object is controlled adaptively with regard for the computer-based realization. The algorithms of control system operation that maintain the guaranteed precision of object motion were constructed. Conditions for problem solvability were formulated. The freeflying space robot was discussed by way of example.     

Mathematical modeling of the pollutants overland flow and transport

Modeling of the natural and technogenic processes in diverse geomorphological environments is one of the basic tools for forecasting and preventing unfavorable development of the urban ecology. One of the causes of its deterioration lies in pollution. The paper considers mathematical modeling of the spread of pollutants transported with water. The complicated process of pollutant spread was modeled as an aggregate of four simpler models such as overland water flow, influent seepage, pollutants transport with surface runoff, and pollutant deposition (accumulation) on the land surface. The model relies on the diffusion equation with supplementary addends in the right-hand side of which one reflects the effect of the terrain relief and the other, which depends on the lithologic structure of the territory, defines the intensity of pollutant uptake rate by the land surface. This equation is satisfied in the two-dimensional domain corresponding physically to an area covered with water. Both the form of the boundary and topology of this area are time-dependent because of appearance of dry “islands” surrounded by water.     

Flexible modeling complex for the operator support systems of UPP’s with VVER-1000 reactor

Consideration was given to the main issues concerning development of a flexible modeling complex for the operator support system of a UPP power-generating unit with VVER reactor, as well as to the model for calculation of the dynamics of the neutron-physical parameters of the VVER-1000 core with the aim of using it in the flexible modeling complex.     

Distributed calculations and simulation of radar image-based navigation

Consideration was given to the simulation of navigation of a moving object by the terrain radar images. An algorithm to model the radar images was described, the problem of the radar image-based navigation was formulated, and the structure and implementation of the simulation software complex based on the distributed calculations in a network of Windows computers was discussed in detail.     

Productivity prediction of MPI programs based on models

A model of parallel program that can be effectively interpreted on the development computer guaranteeing the possibility of a sufficiently precise prediction of real run time for a simulated parallel program at the prescribed computer system is studied. The model is worked out for parallel programs with explicit message passing written in the Java language with MPI library access and is included into the composition of ParJava environment. The model is obtained by transforming the program control tree that can be constructed for Java programs by modifying the abstract syntax tree. To model communication functions, the model LogGP is used which allows taking into consideration the specific character of the communication network of the distributed computer system.     

Some models of qualitative dynamic cognitive maps with fuzzy states

Some models of dynamic cognitive maps, whose factors are determined in finite linearly ordered qualitative scales, are studied. Notions of fuzzy values and increments of factors and operations over them are determined. Specific features of defuzzification of fuzzy qualitative values are discussed. Basic behavior effects of these models, sources and forms of data fuzziness in the computing process, means for controlling this event, and confidence limits in the simulating process are studied.     

Off-lattice simulation of the solid phase DNA amplification

Recent simulations of the solid phase DNA amplification (SPA) by J.-F. Mercier et al. [Biophys. J. 85 (2003) 2075] are generalized to include two kinds of primers and the off-lattice character of the primer distribution on the surface. The sigmoidal character of the primer occupation by DNA, observed experimentally, is reproduced in the simulation. We discuss an influence of two parameters on the efficiency of the amplification process: the initial density p₀ of the occupied primers from the interfacial amplification and the ratio r of the molecule length to the average distance between primers. The number of cycles required for a complete saturation decreases with p₀ roughly as . For r=1.5, the number of occupied primers is reduced by a factor two, when compared to the case of longer molecules. Below r=1.4, the effectivity of SPA is reduced by a factor 100.     

A time saving algorithm for the Monte Carlo method of Metropolis

A time saving algorithm for the Monte Carlo method of Metropolis is presented. The technique is tested with different potential models and number of particles. The coupling of the method with neighbor lists, linked lists, Ewald sum and reaction field techniques is also analyzed. It is shown that the proposed algorithm is particularly suitable for computationally heavy intermolecular potentials.     

An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations

This paper focuses on the implementation and the performance analysis of a smooth particle mesh Ewald method on several parallel computers. We present the details of the algorithms and our implementation that are used to optimize parallel efficiency on such parallel computers.     

LCG MCDB—a knowledgebase of Monte-Carlo simulated events

In this paper we report on LCG Monte-Carlo Data Base (MCDB) and software which has been developed to operate MCDB. The main purpose of the LCG MCDB project is to provide a storage and documentation system for sophisticated event samples simulated for the LHC Collaborations by experts. In many cases, the modern Monte-Carlo simulation of physical processes requires expert knowledge in Monte-Carlo generators or significant amount of CPU time to produce the events. MCDB is a knowledgebase mainly dedicated to accumulate simulated events of this type. The main motivation behind LCG MCDB is to make the sophisticated MC event samples available for various physical groups. All the data from MCDB is accessible in several convenient ways. LCG MCDB is being developed within the CERN LCG Application Area Simulation project.

Program summary

Program title: LCG Monte-Carlo Data BaseCatalogue identifier: ADZX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU General Public LicenceNo. of lines in distributed program, including test data, etc.: 30 129No. of bytes in distributed program, including test data, etc.: 216 943Distribution format: tar.gzProgramming language: PerlComputer: CPU: Intel Pentium 4, RAM: 1 Gb, HDD: 100 GbOperating system: Scientific Linux CERN 3/4RAM: 1 073 741 824 bytes (1 Gb)Classification: 9External routines:

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perl >= 5.8.5;

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Perl modules

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DBD-mysql >= 2.9004,

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File::Basename,

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GD::SecurityImage,

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GD::SecurityImage::AC,

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Linux::Statistics,

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XML::LibXML > 1.6,

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XML::SAX,

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XML::NamespaceSupport;

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Apache HTTP Server >= 2.0.59;

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mod auth external >= 2.2.9;

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edg-utils-system RPM package;

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gd >= 2.0.28;

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rpm package CASTOR-client >= 2.1.2-4;

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arc-server (optional)

Nature of problem: Often, different groups of experimentalists prepare similar samples of particle collision events or turn to the same group of authors of Monte-Carlo (MC) generators to prepare the events. For example, the same MC samples of Standard Model (SM) processes can be employed for the investigations either in the SM analyses (as a signal) or in searches for new phenomena in Beyond Standard Model analyses (as a background). If the samples are made available publicly and equipped with corresponding and comprehensive documentation, it can speed up cross checks of the samples themselves and physical models applied. Some event samples require a lot of computing resources for preparation. So, a central storage of the samples prevents possible waste of researcher time and computing resources, which can be used to prepare the same events many times.Solution method: Creation of a special knowledgebase (MCDB) designed to keep event samples for the LHC experimental and phenomenological community. The knowledgebase is realized as a separate web-server (http://mcdb.cern.ch). All event samples are kept on types at CERN. Documentation describing the events is the main contents of MCDB. Users can browse the knowledgebase, read and comment articles (documentation), and download event samples. Authors can upload new event samples, create new articles, and edit own articles.Restrictions: The software is adopted to solve the problems, described in the article and there are no any additional restrictions.Unusual features: The software provides a framework to store and document large files with flexible authentication and authorization system. Different external storages with large capacity can be used to keep the files. The WEB Content Management System provides all of the necessary interfaces for the authors of the files, end-users and administrators.Running time: Real time operations.References:[1] The main LCG MCDB server, http://mcdb.cern.ch/.[2] P. Bartalini, L. Dudko, A. Kryukov, I.V. Selyuzhenkov, A. Sherstnev, A. Vologdin, LCG Monte-Carlo data base, hep-ph/0404241.[3] J.P. Baud, B. Couturier, C. Curran, J.D. Durand, E. Knezo, S. Occhetti, O. Barring, CASTOR: status and evolution, cs.oh/0305047.     

Development of a Geant4 solid for stereo mini-jet cells in a cylindrical drift chamber

Stereo mini-jet cells will be indispensable components of a future e⁺e⁻ linear collider central tracker such as JLC-CDC. There is, however, no official Geant4 solid available at present to describe such geometrical objects, which had been a major obstacle for us to develop a full Geant4-based simulator with stereo cells built in. We have thus extended Geant4 to include a new solid (TwistedTubs), which consists of three kinds of surfaces: two end planes, inner and outer hyperboloidal surfaces, and two so-called twisted surfaces that make slant and twisted φ-boundaries. Design philosophy and its realization in the Geant4 framework are described together with algorithmic details. We have implemented stereo cells with the new solid, and tested them using geantinos and Pythia events (e⁺e⁻→ZH at  GeV). The performance was found reasonable: the stereo cells consumed only 25% more CPU time than ordinary axial cells.     

Parallelization issues of a code for physically-based simulation of fabrics

The simulation of fabrics, clothes, and flexible materials is an essential topic in computer animation of realistic virtual humans and dynamic sceneries. New emerging technologies, as interactive digital TV and multimedia products, make necessary the development of powerful tools to perform real-time simulations. Parallelism is one of such tools. When analyzing computationally fabric simulations we found these codes belonging to the complex class of irregular applications. Frequently this kind of codes includes reduction operations in their core, so that an important fraction of the computational time is spent on such operations. In fabric simulators these operations appear when evaluating forces, giving rise to the equation system to be solved. For this reason, this paper discusses only this phase of the simulation. This paper analyzes and evaluates different irregular reduction parallelization techniques on ccNUMA shared memory machines, applied to a real, physically-based, fabric simulator we have developed. Several issues are taken into account in order to achieve high code performance, as exploitation of data access locality and parallelism, as well as careful use of memory resources (memory overhead). In this paper we use the concept of data affinity to develop various efficient algorithms for reduction parallelization exploiting data locality.     

TIERRAS: A package to simulate high energy cosmic ray showers underground, underwater and under-ice

In this paper we present TIERRAS, a Monte Carlo simulation program based on the well-known AIRES air shower simulations system that enables the propagation of particle cascades underground, providing a tool to study particles arriving underground from a primary cosmic ray on the atmosphere or to initiate cascades directly underground and propagate them, exiting into the atmosphere if necessary. We show several cross-checks of its results against CORSIKA, FLUKA, GEANT and ZHS simulations and we make some considerations regarding its possible use and limitations. The first results of full underground shower simulations are presented, as an example of the package capabilities.

Program summary

Program title: TIERRAS for AIRESCatalogue identifier: AEFO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFO_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 36 489No. of bytes in distributed program, including test data, etc.: 3 261 669Distribution format: tar.gzProgramming language: Fortran 77 and CComputer: PC, Alpha, IBM, HP, Silicon Graphics and Sun workstationsOperating system: Linux, DEC Unix, AIX, SunOS, Unix System VRAM: 22 Mb bytesClassification: 1.1External routines: TIERRAS requires AIRES 2.8.4 to be installed on the system. AIRES 2.8.4 can be downloaded from http://www.fisica.unlp.edu.ar/auger/aires/eg_AiresDownload.html.Nature of problem: Simulation of high and ultra high energy underground particle showers.Solution method: Modification of the AIRES 2.8.4 code to accommodate underground conditions.Restrictions: In AIRES some processes that are not statistically significant on the atmosphere are not simulated. In particular, it does not include muon photonuclear processes. This imposes a limitation on the application of this package to a depth of 1 km of standard rock (or 2.5 km of water equivalent). Neutrinos are not tracked on the simulation, but their energy is taken into account in decays.Running time: A TIERRAS for AIRES run of a ¹⁰²⁰ eV shower with statistical sampling (thinning) below ¹⁰¹² eV and 0.2 weight factor (see [1]) uses approximately 1 h of CPU time on an Intel Core 2 Quad Q6600 at 2.4 GHz. It uses only one core, so 4 simultaneous simulations can be run on this computer. Aires includes a spooling system to run several simultaneous jobs of any type.References:

[1]

S. Sciutto, AIRES 2.6 User Manual, http://www.fisica.unlp.edu.ar/auger/aires/.

     

A handy tool for history keeping of Geant4 tracks - J4HistoryKeeper

The Particle Flow Analysis (PFA) is currently under intense studies as the most promising way to achieve precision jet energy measurements required at the future linear e⁺e⁻ collider. In order to optimize detector configurations and to tune up the PFA it is crucial to identify factors that limit the PFA performance and clarify the fundamental limits on the jet energy resolution that remain even with the perfect PFA and an infinitely granular calorimeter. This necessitates a tool to connect each calorimeter hit in particle showers to its parent charged track, if any, and eventually all the way back to its corresponding primary particle, while identifying possible interactions and decays along the way. In order to realize this with a realistic memory space, we have developed a set of C++ classes that facilitates history keeping of particle tracks within the framework of Geant4. This software tool, hereafter called J4HistoryKeeper, comes in handy in particular when one needs to stop this history keeping for memory space economy at multiple geometrical boundaries beyond which a particle shower is expected to start. In this paper this software tool is described and applied to a generic detector model to demonstrate its functionality.     

Regional research exploitation of the LHC: A case-study of the required computing resources

A simulation study to evaluate the required computing resources for a research exploitation of the Large Hadron Collider (LHC) has been performed. The evaluation was done as a case study, assuming existence of a Nordic regional centre and using the requirements for performing a specific physics analysis as a yard-stick. Other input parameters were: assumption for the distribution of researchers at the institutions involved, an analysis model, and two different functional structures of the computing resources.     

PANMIN: sequential and parallel global optimization procedures with a variety of options for the local search strategy

We present two sequential and one parallel global optimization codes, that belong to the stochastic class, and an interface routine that enables the use of the Merlin/MCL environment as a non-interactive local optimizer. This interface proved extremely important, since it provides flexibility, effectiveness and robustness to the local search task that is in turn employed by the global procedures. We demonstrate the use of the parallel code to a molecular conformation problem.

Program summary

Title of program: PANMINCatalogue identifier: ADSUProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSUProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer for which the program is designed and others on which it has been tested: PANMIN is designed for UNIX machines. The parallel code runs on either shared memory architectures or on a distributed system. The code has been tested on a SUN Microsystems ENTERPRISE 450 with four CPUs, and on a 48-node cluster under Linux, with both the GNU g77 and the Portland group compilers. The parallel implementation is based on MPI and has been tested with LAM MPI and MPICHInstallation: University of Ioannina, GreeceProgramming language used: Fortran-77Memory required to execute with typical data: Approximately O(n²) words, where n is the number of variablesNo. of bits in a word: 64No. of processors used: 1 or manyHas the code been vectorised or parallelized?: Parallelized using MPINo. of bytes in distributed program, including test data, etc.: 147163No. of lines in distributed program, including the test data, etc.: 14366Distribution format: gzipped tar fileNature of physical problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques can be trapped in any local minimum. Global Optimization is then the appropriate tool. For example, solving a non-linear system of equations via optimization, one may encounter many local minima that do not correspond to solutions, i.e. they are far from zeroMethod of solution: PANMIN is a suite of programs for Global Optimization that take advantage of the Merlin/MCL optimization environment [1,2]. We offer implementations of two algorithms that belong to the stochastic class and use local searches either as intermediate steps or as solution refinementRestrictions on the complexity of the problem: The only restriction is set by the available memory of the hardware configuration. The software can handle bound constrained problems. The Merlin Optimization environment must be installed. Availability of an MPI installation is necessary for executing the parallel codeTypical running time: Depending on the objective functionReferences: [1] D.G. Papageorgiou, I.N. Demetropoulos, I.E. Lagaris, Merlin-3.0. A multidimensional optimization environment, Comput. Phys. Commun. 109 (1998) 227-249. [2] D.G. Papageorgiou, I.N. Demetropoulos, I.E. Lagaris, The Merlin Control Language for strategic optimization, Comput. Phys. Commun. 109 (1998) 250-275.     

Investigation of performance of programming approaches and languages used for numerical simulation of granular material by the discrete element method

Performance of programming approaches and languages used for the development of software codes for numerical simulation of granular material dynamics by the discrete element method (DEM) is investigated. The granular material considered represents a space filled with discrete spherical visco-elastic particles, and the behaviour of material under imposed conditions is simulated using the DEM. The object-oriented programming approach (implemented via C++) was compared with the procedural approach (using FORTRAN 90 and OBJECT PASCAL) in order to test their efficiency. The identical neighbour-searching algorithm, contact forces model and time integration method were implemented in all versions of codes.Two identical representative examples of the dynamic behaviour of granular material on a personal computer (compatible with IBM PC) were solved. The results show that software based on procedural approach runs faster in compare with software based on OOP, and software developed by FORTRAN 90 runs faster in compare with software developed by OBJECT PASCAL.     

Stochastic optimization for a tip-tilt adaptive correcting system

We present computer simulations of a tip-tilt adaptive optics system, where stochastic optimization is applied to the problem of dynamic compensation of atmospheric turbulence. The system uses a simple measure of the light intensity that passes through a mask and is recorded on the image plane, to generate signals for the tip-tilt mirror. A feedback system rotates the mirror adaptively and in phase with the rapidly changing atmospheric conditions. Computer simulations and a series of numerical experiments investigate the implementation of the method in the presence of drifting atmosphere. In particular, the study examines the system's sensitivity to the rate of change of the atmospheric conditions and investigates the optimal size of the mirror's masking area and the algorithm's optimal degree of stochasticity.     

Control of the medical treatment of AIDS

This work deals with the statement and the solution of problems of optimal control of the human immune system affected by a human immunodeficiency virus (HIV). The solution is performed by the numerical methods of optimal control on the basis of a dynamic model of the development of an infection in the organism of a human being. The results illustrate the possibilities for the use of mathematical methods in the problem of extending the life of HIV-infected patients.     

Stochastic optimization for the calculation of the time dependency of the physiological demand during exercise and recovery

The stochastic optimization method ALOPEX IV is successfully applied to the problem of estimating the time dependency of the physiological demand in response to exercise. This is a fundamental and unsolved problem in the area of exercise physiology, where the lack of appropriate tools and techniques forces the assumption and the use of a constant demand during exercise. By the use of an appropriate partition of the physiological time series and by means of stochastic optimization, the time dependency of the physiological demand during heavy intensity exercise and its subsequent recovery is, for the first time, revealed.