Cooperative and competitive concurrency in scientific computing. A full open-source upgrade of the program for dynamical calculations of RHEED intensity oscillations

A computational model is a computer program, which attempts to simulate an abstract model of a particular system. Computational models use enormous calculations and often require supercomputer speed. As personal computers are becoming more and more powerful, more laboratory experiments can be converted into computer models that can be interactively examined by scientists and students without the risk and cost of the actual experiments. The future of programming is concurrent programming. The threaded programming model provides application programmers with a useful abstraction of concurrent execution of multiple tasks. The objective of this release is to address the design of architecture for scientific application, which may execute as multiple threads execution, as well as implementations of the related shared data structures.

New version program summary

Program title: GrowthCPCatalogue identifier: ADVL_v4_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVL_v4_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.: 32 269No. of bytes in distributed program, including test data, etc.: 8 234 229Distribution format: tar.gzProgramming language: Free Object PascalComputer: multi-core x64-based PCOperating system: Windows XP, Vista, 7Has the code been vectorised or parallelized?: NoRAM: More than 1 GB. The program requires a 32-bit or 64-bit processor to run the generated code. Memory is addressed using 32-bit (on 32-bit processors) or 64-bit (on 64-bit processors with 64-bit addressing) pointers. The amount of addressed memory is limited only by the available amount of virtual memory.Supplementary material: The figures mentioned in the “Summary of revisions” section can be obtained here.Classification: 4.3, 7.2, 6.2, 8, 14External routines: Lazarus [1]Catalogue identifier of previous version: ADVL_v3_0Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 709Does the new version supersede the previous version?: YesNature of problem: Reflection high-energy electron diffraction (RHEED) is an important in-situ analysis technique, which is capable of giving quantitative information about the growth process of thin layers and its control. It can be used to calibrate growth rate, analyze surface morphology, calibrate surface temperature, monitor the arrangement of the surface atoms, and provide information about growth kinetics. Such control allows the development of structures where the electrons can be confined in space, giving quantum wells or even quantum dots. In order to determine the atomic positions of atoms in the first few layers, the RHEED intensity must be measured as a function of the scattering angles and then compared with dynamic calculations. The objective of this release is to address the design of architecture for application that simulates the rocking curves RHEED intensities during hetero-epitaxial growth process of thin films.Solution method: The GrowthCP is a complex numerical model that uses multiple threads for simulation of epitaxial growth of thin layers. This model consists of two transactional parts. The first part is a mathematical model being based on the Runge–Kutta method with adaptive step-size control. The second part represents first-principles of the one-dimensional RHEED computational model. This model is based on solving a one-dimensional Schrödinger equation. Several problems can arise when applications contain a mixture of data access code, numerical code, and presentation code. Such applications are difficult to maintain, because interdependencies between all the components cause strong ripple effects whenever a change is made anywhere. Adding new data views often requires reimplementing a numerical code, which then requires maintenance in multiple places. In order to solve problems of this type, the computational and threading layers of the project have been implemented in the form of one design pattern as a part of Model-View-Controller architecture.Reasons for new version: Responding to the users? feedback the Growth09 project has been upgraded to a standard that allows the carrying out of sample computations of the RHEED intensities for a disordered surface for a wide range of single- and epitaxial hetero-structures. The design pattern on which the project is based has also been improved. It is shown that this model can be effectively used for multithreaded growth simulations of thin epitaxial layers and corresponding RHEED intensities for a wide range of single- and hetero-structures. Responding to the users? feedback the present release has been implemented using a well-documented free compiler [1] not requiring the special configuration and installation additional libraries.Summary of revisions:

• 1. 

  The logical structure of the Growth09 program has been modified according to the scheme showed in Fig. 1.1 The class diagram in Fig. 11 is a static view of the main platform-specific elements of the GrowthCP architecture. Fig. 21 provides a dynamic view by showing the creation and destruction simplistic sequence diagram for the process.

• 2. 

  The program requires the user to provide the appropriate parameters in the form of a knowledge base for the crystal structures under investigation. These parameters are loaded from the parameters.ini files at run-time. Instructions to prepare the .ini files can be found in the new distribution.

• 3. 

  The program enables carrying out different growth models and one-dimensional dynamical RHEED calculations for the fcc lattice with basis of three-atoms, fcc lattice with basis of two-atoms, fcc lattice with single atom basis, Zinc-Blende, Sodium Chloride, and Wurtzite crystalline structures and hetero-structures, but yet the Fourier component of the scattering potential in the TRHEEDCalculations.crystPotUgXXX() procedure can be modified and implemented according to users? specific application requirements. The Fourier component of the scattering potential of the whole crystalline hetero-structures can be determined as a sum of contributions coming from all thin slices of individual atomic layers. To carry out one-dimensional calculations of the scattering potentials, the program uses properly constructed self-consistent procedures.

• 4. 

  Each component of the system shown in Figs. 11 and 21 is fully extendable and can easily be adapted to new changeable requirements. Two essential logical elements of the system, i.e. TGrowthTransaction and TRHEEDCalculations classes, were designed and implemented in this way for them to pass the information to themselves without the need to use the data-exchange files given. In consequence each of them can be independently modified and/or extended. Implementing other types of differential equations and the different algorithm for solving them in the TGrowthTransaction class does not require another implementation of the TRHEEDCalculations class. Similarly, implementing other forms of scattering potential and different algorithm for RHEED calculation stays without the influence on the TGrowthTransaction class construction.

Unusual features: The program is distributed in the form of main project GrowthCP.lpr, with associated files, and should be compiled using Lazarus IDE. The program should be compiled with English/USA regional and language options.Running time: The typical running time is machine and user-parameters dependent.References:

• [1] 

  http://sourceforge.net/projects/lazarus/files/.

     

Trade-offs Between the Size of Advice and Broadcasting Time in Trees

We study the problem of the amount of information required to perform fast broadcasting in tree networks. The source located at the root of a tree has to disseminate a message to all nodes. In each round each informed node can transmit to one child. Nodes do not know the topology of the tree but an oracle knowing it can give a string of bits of advice to the source which can then pass it down the tree with the source message. The quality of a broadcasting algorithm with advice is measured by its competitive ratio: the worst case ratio, taken over n-node trees, between the time of this algorithm and the optimal broadcasting time in the given tree. Our goal is to find a trade-off between the size of advice and the best competitive ratio of a broadcasting algorithm for n-node trees. We establish such a trade-off with an approximation factor of O(n ^ε ), for an arbitrarily small positive constant ε. This is the first communication problem for which a trade-off between the size of advice and the efficiency of the solution is shown for arbitrary size of advice.     

Information systems in modeling interactive computations on granules

In this paper, we discuss the importance of information systems in modeling interactive computations performed on (complex) granules and we propose a formal approach to interactive computations based on generalized information systems and rough sets which can be combined with other soft computing paradigms such as fuzzy sets or evolutionary computing, but also with machine learning and data mining techniques. Information systems are treated as dynamic granules used for representing the results of the interaction of attributes with the environment. Two kinds of attributes are distinguished, namely, the perception attributes, including sensory attributes, and the action attributes. Sensory attributes are the basic perception attributes, other perception attributes are constructed on the basis of the sensory ones. Actions are activated when their guards, being often complex and vague concepts, are satisfied to a satisfactory degree. The guards can be approximated on the basis of measurements performed by sensory attributes rather than defined exactly. Satisfiability degrees for guards are results of reasoning called the adaptive judgment. The approximations are induced using hierarchical modeling. We show that information systems can be used for modeling more advanced forms of interactions in hierarchical modeling. The role of hierarchical interactions is emphasized in the modeling of interactive computations. Some illustrative examples of interactions used in the ACT-R 6.0 system are reported. ACT-R 6.0 is based on a cognitive architecture and can be treated as an example of a highly interactive complex granule which can be involved in hierarchical interactions. For modeling of interactive computations, we propose much more general information systems than the studied dynamic information systems (see, e.g., Ciucci (2010) [8] and Pa?asiński and Pancerz (2010) [32]). For example, the dynamic information systems are making it possible to consider incremental changes in information systems. However, they do not contain the perception and action attributes necessary for modeling interactive computations, in particular for modeling intrastep interactions.     

Optimal Deterministic Broadcasting in Known Topology Radio Networks

We consider deterministic broadcasting in radio networks whose nodes have full topological information about the network. The aim is to design a polynomial algorithm, which, given a graph G with source s, produces a fast broadcast scheme in the radio network represented by G. The problem of finding a fastest broadcast scheme for a given graph is NP-hard, hence it is only possible to get an approximation algorithm. We give a deterministic polynomial algorithm which produces a broadcast scheme of length , for every n-node graph of diameter D, thus improving a result of Gąsieniec et al. (PODC 2005) [17] and solving a problem stated there. Unless the inclusion NP BPTIME( holds, the length of a polynomially constructible deterministic broadcast scheme is optimal.A preliminary version of this paper (with a weaker result) appeared in the Proc. 7th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX’2004), August 2004, Harvard University, Cambridge, USA, LNCS 3122, 171–182. Research of the second author supported in part by NSERC discovery grant and by the Research Chair in Distributed Computing of the Université du Québec en Outaouais. Part of this work was done during the second author’s visit at the Max-Planck-Institut für Informatik.     

Learning about psychological professions with the world-wide web

Abstract Teaching with the world-wide web is becoming a common practice in modern education. The web serves two main interrelated functions, namely, retrieval and publication of information. To enhance learning and motivation, the student-as-teacher (SAT) principle was adopted in the study reported in this paper. Students were given the role of teacher of high school students and the general public about the subject matter they learned on a course. To achieve this goal, the students created educational web sites featuring two selected psychological professions. Being the major assignment for the course, the web sites created by students received higher scores than the assignments of their peers who learned the same materials through traditional pedagogical approaches. Course evaluation confirmed that the web implementation of the SAT principle enhanced learning, increased motivation and provided a transfer-able skill, without compromising accomplishment of major course goals.     

Discover dependency pattern among attributes by using a new type of nonlinear multiregression

Multiregression is one of the most common approaches used to discover dependency pattern among attributes in a database. Nonadditive set functions have been applied to deal with the interactive predictive attributes involved, and some nonlinear integrals with respect to nonadditive set functions are employed to establish a nonlinear multiregression model describing the relation between the objective attribute and predictive attributes. The values of the nonadditive set function play a role of unknown regression coefficients in the model and are determined by an adaptive genetic algorithm from the data of predictive and objective attributes. Furthermore, such a model is now improved by a new numericalization technique such that the model can accommodate both categorical and continuous numerical attributes. The traditional dummy binary method dealing with the mixed type data can be regarded as a very special case of our model when there is no interaction among the predictive attributes and the Choquet integral is used. When running the algorithm, to avoid a premature during the evolutionary procedure, a technique of maintaining diversity in the population is adopted. A test example shows that the algorithm and the relevant program have a good reversibility for the data. © 2001 John Wiley & Sons, Inc.16: 949–962 (2001)     

Kernel PCA for Feature Extraction and De-Noising in Nonlinear Regression

In this paper, we propose the application of the Kernel Principal Component Analysis (PCA) technique for feature selection in a high-dimensional feature space, where input variables are mapped by a Gaussian kernel. The extracted features are employed in the regression problems of chaotic Mackey–Glass time-series prediction in a noisy environment and estimating human signal detection performance from brain event-related potentials elicited by task relevant signals. We compared results obtained using either Kernel PCA or linear PCA as data preprocessing steps. On the human signal detection task, we report the superiority of Kernel PCA feature extraction over linear PCA. Similar to linear PCA, we demonstrate de-noising of the original data by the appropriate selection of various nonlinear principal components. The theoretical relation and experimental comparison of Kernel Principal Components Regression, Kernel Ridge Regression and ε-insensitive Support Vector Regression is also provided.     

Isocube: exploiting the cubemap hardware

This paper proposes a novel six-face spherical map, isocube, that fully utilizes the cubemap hardware built in most GPUs. Unlike the cubemap, the proposed isocube uniformly samples the unit sphere (uniformly distributed), and all samples span the same solid angle (equally important). Its mapping computation contains only a small overhead. By feeding the cubemap hardware with the six-face isocube map, the isocube can exploit all built-in texturing operators tailored for the cubemap and achieve a very high frame rate. In addition, we develop an anisotropic filtering that compensates aliasing artifacts due to texture magnification. This filtering technique extends the existing hardware anisotropic filtering and can be applied not only to the proposed isocube, but also to other texture mapping applications.     

Pilot mental workload: how well do pilots really perform?

The purpose of this study was to investigate the effects of increasing mental demands on various aspects of aircrew performance. In particular, the robustness of the prioritization and allocation hierarchy of aviate-navigate-communicate was examined, a hierarchy commonly used within the aviation industry. A total of 42 trainee pilots were divided into three workload groups (low, medium, high) to complete a desktop, computer-based exercise that simulated combinations of generic flight deck activities: flight control manipulation, rule-based actions and higher level cognitive processing, in addition to Air Traffic Control instructions that varied in length from one chunk of auditory information to seven chunks. It was found that as mental workload and auditory input increased, participants experienced considerable difficulty in carrying out the primary manipulation task. A similar decline in prioritization was also observed. Moreover, when pilots were under a high mental workload their ability to comprehend more than two chunks of auditory data deteriorated rapidly.