Java Computer Research Articles

Clinical implications of amathematical-geometrical model to predict changes in the anterior arch dimension.

Anterior arch length (AL) and the alterations in its dimension following incisor movements were shown to be predictable for an individual patient using amathematical-geometrical model based on athird-degree parabola. Although the model has been validated previously, it is hard to apply in daily orthodontic routine. Thus, the aim of this study was to modify the model using different approaches to allow its establishment in daily routine. This retrospective study was based on astudy collective, which was described previously and consisted of 50randomly chosen dental casts and lateral cephalograms taken before (T0) and after (T1) orthodontic treatment with fixed appliances. AJAVA computer program (Oracle, Austin, TX, USA) was developed to predict AL changes following therapeutic changes of arch width, depth or incisor inclination/position, taking the type of tooth movement into account. Performing exemplary AL calculations with the computer program, general rules and nomograms were set up, followed by multiple linear regression analyses to establish easy-to-use regression equations. The JAVA computer program is available for download. Sagittal changes showed more effect on AL than transverse modifications. Protruding incisors increased AL, but also reduced overbite. The extent of alteration in AL depended on the initial depth, width, incisor inclination, tooth movement type and distance between the incisal edge and the centre of rotation. The computer program precisely predicts individual changes in AL but is time-consuming. The presented regression equations and nomograms, considering metric variables, are easier to apply clinically and the differences compared to the AL calculated by the computer program are negligible.

Performance evaluation of Java/PCJ implementation of parallel algorithms on the cloud (extended version)

AbstractLarge‐scale computing and data processing with cloud resources is gaining popularity. However, the usage of the cloud differs from traditional high‐performance computing (HPC) systems and both algorithms and codes have to be adjusted. This work is often time‐consuming and performance is not guaranteed. To address this problem we have developed the PCJ library (parallel computing in Java), a novel tool for scalable HPC and big data processing in Java. In this article, we present a performance evaluation of parallel applications implemented in Java using the PCJ library. The performance evaluation is based on the examples of highly scalable applications of different characteristics focusing on CPU, communication or I/O. They run on the traditional HPC system and Amazon web services Cloud as well as Linaro Developer Cloud. For the clouds, we have used Intel x86 and ARM processors for running Java codes without changing any line of the program code and without the need for time‐consuming recompilation. Presented applications have been parallelized using the partitioned global address space programming model and its realization in the PCJ library. Our results prove that the PCJ library, due to its performance and ability to create simple portable code, has great promise to be successful for the parallelization of various applications and run them on the cloud with a performance close to HPC systems.

PCJ Java library as a solution to integrate HPC, Big Data and Artificial Intelligence workloads

With the development of peta- and exascale size computational systems there is growing interest in running Big Data and Artificial Intelligence (AI) applications on them. Big Data and AI applications are implemented in Java, Scala, Python and other languages that are not widely used in High-Performance Computing (HPC) which is still dominated by C and Fortran. Moreover, they are based on dedicated environments such as Hadoop or Spark which are difficult to integrate with the traditional HPC management systems. We have developed the Parallel Computing in Java (PCJ) library, a tool for scalable high-performance computing and Big Data processing in Java. In this paper, we present the basic functionality of the PCJ library with examples of highly scalable applications running on the large resources. The performance results are presented for different classes of applications including traditional computational intensive (HPC) workloads (e.g. stencil), as well as communication-intensive algorithms such as Fast Fourier Transform (FFT). We present implementation details and performance results for Big Data type processing running on petascale size systems. The examples of large scale AI workloads parallelized using PCJ are presented.

Jas4pp — A data-analysis framework for physics and detector studies

This paper describes the Jas4pp framework for exploring physics cases and for detector-performance studies of future particle collision experiments. Jas4pp is a multi-platform Java program for numeric calculations, scientific visualization in 2D and 3D, storing data in various file formats and displaying collision events and detector geometries. It also includes complex data-analysis algorithms for function minimization, regression analysis, event reconstruction (such as jet reconstruction), limit settings and other libraries widely used in particle physics. The framework can be used with several scripting languages, such as Python/Jython, Groovy and JShell. Several benchmark tests discussed in the paper illustrate significant improvements in the performance of the Groovy and JShell scripting languages compared to the standard Python implementation in C. The improvements for numeric computations in Java are attributed to recent enhancements in the Java Virtual Machine. Program summaryProgram title: Jas4ppCPC Library link to program files:https://doi.org/10.17632/jzvddk26cy.1Developer’s repository link:https://atlaswww.hep.anl.gov/asc/jas4pp/Licensing provisions: GNU General Public License 3Programming language: Java, Jython, GroovyNature of problem: Develop a platform-independent data-analysis framework for high-energy and nuclear physics (HEP and NP) with a support of fast dynamically-typed scripting languages, comprehensive data-visualisation and I/O libraries.Solution method: The solution adopted here is to use Java and the scripting languages integrated with Java VM.Additional comments: All 3rd party Java libraries included with this program are licensed by GPLv3, GNU Lesser General Public License (LGPL) or by other licenses compatible with the GPLv3 license, and adhere to Mendeley Data approved open-source software licenses. These licenses files are includes with the program.

Comparison of sort algorithms in Hadoop and PCJ

Sorting algorithms are among the most commonly used algorithms in computer science and modern software. Having efficient implementation of sorting is necessary for a wide spectrum of scientific applications. This paper describes the sorting algorithm written using the partitioned global address space (PGAS) model, implemented using the Parallel Computing in Java (PCJ) library. The iterative implementation description is used to outline the possible performance issues and provide means to resolve them. The key idea of the implementation is to have an efficient building block that can be easily integrated into many application codes. This paper also presents the performance comparison of the PCJ implementation with the MapReduce approach, using Apache Hadoop TeraSort implementation. The comparison serves to show that the performance of the implementation is good enough, as the PCJ implementation shows similar efficiency to the Hadoop implementation.

Design and Development of Learn Your Way Out: A Gamified Content for Basic Java Computer Programming

Learning computer programming requires problem-solving skills, coding skills and algorithmic skills which are complex and difficult to master. Computer programming is difficult because of its essence in creating a solution that requires translating it in a language understood only by the computer. This poses barriers like anxiety, panic, stress, grief and frustration to novice programmers. The purpose of this study was to design and develop a gamified content for selected topics of basic Java computer programming for freshman college students of Mindanao State University Tawi-Tawi College of Technology and Oceanography. The game follows the Player-Centered, Iterative, Interdisciplinary and Integrated framework. The idea of using Gamification was adopted in the development of the gamified content. The game was evaluated using Octalysis by seven subject experts from the Institute of Information and Communications Technology. The overall rating of the game resulted to have proper motivation for Gamification.

Risk model of tree stand damage by winds and its evaluation based on damage caused by cyclone “Xaver”

Aim of study: To develop and evaluate the forest’s wind-risk model, dedicated for stand damage level.Area of study: Model was tested in the northeastern Poland.Material and methods: A risk model referring to the damage of forest stands by wind specifies, for every stand in a selected forest district, the risk factor within the range of 0 to 3. The higher value of the factor, the greater risk of damage, if wind occurs. The model was based on 11 features: average size of a tree stand, mean diameter breast high in the specified features’ ratio, species composition, degree of stand density, age of stand, forest site type, amount of damage caused by wind in the last 10-year period, location of forest district in the region of Poland, and three features for mountains: stand’s altitude above sea level, direction, and slope. The model used information from the State Forests’ Information System database (SILP), and since it was developed in JAVA computer language, the processing of data for one forest district lasted less than one minute.Main results: The model can create a forest district digital map, in which stands characterized by specific risk values are presented with high prediction accuracy.Research highlights: The risk model of tree stand damage by winds uses data provided by the SILP and what was proven in below study, can be used as an effective tool in a forestry practice.

Massively Parallel Implementation of Sequence Alignment with Basic Local Alignment Search Tool Using Parallel Computing in Java Library.

Basic Local Alignment Search Tool (BLAST) is an essential algorithm that researchers use for sequence alignment analysis. The National Center for Biotechnology Information (NCBI)-BLAST application is the most popular implementation of the BLAST algorithm. It can run on a single multithreading node. However, the volume of nucleotide and protein data is fast growing, making single node insufficient. It is more and more important to develop high-performance computing solutions, which could help researchers to analyze genetic data in a fast and scalable way. This article presents execution of the BLAST algorithm on high performance computing (HPC) clusters and supercomputers in a massively parallel manner using thousands of processors. The Parallel Computing in Java (PCJ) library has been used to implement the optimal splitting up of the input queries, the work distribution, and search management. It is used with the nonmodified NCBI-BLAST package, which is an additional advantage for the users. The result application-PCJ-BLAST-is responsible for reading sequence for comparison, splitting it up and starting multiple NCBI-BLAST executables. Since I/O performance could limit sequence analysis performance, the article contains an investigation of this problem. The obtained results show that using Java and PCJ library it is possible to perform sequence analysis using hundreds of nodes in parallel. We have achieved excellent performance and efficiency and we have significantly reduced the time required for sequence analysis. Our work also proved that PCJ library could be used as an effective tool for fast development of the scalable applications.

Thoth: Software for data visualization & statistics

Thoth is a standalone software application with a graphical user interface for making it easy to query, display, visualize, and analyze tabular data stored in relational databases and data files. From imported data tables, it can create pie charts, bar charts, scatter plots, and many other kinds of data graphs with simple menus and mouse clicks (no programming required), by leveraging the open-source JFreeChart library. It also computes useful table-column data statistics. A mature tool, having underwent development and testing over several years, it is written in the Java computer language, and hence can be run on any computing platform that has a Java Virtual Machine and graphical-display capability. It can be downloaded and used by anyone free of charge, and has general applicability in science, engineering, medical, business, and other fields. Special tools and features for common tasks in astronomy and astrophysical research are included in the software.

Java Computer Animation for Effective Learning of the Cholesky Algorithm with Transportation Engineering Applications

In this paper, the well-known Cholesky Algorithm (for solving simultaneous linear equations, or SLE) is re-visited, with the ultimate goal of developing a simple, user-friendly, attractive, and useful Java Visualization and Animation Graphical User Inter-face (GUI) software as an additional teaching tool for students to learn the Cholesky factorization in a step-by-step fashion with computer voice and animation. A demo video of the Cholesky Decomposition (or factorization) animation and result can be viewed online from the website: http://www.lions.odu.edu/~imako001/cholesky/demo/index.html. The software tool developed from this work can be used for both students and their instructors not only to master this technical subject, but also to provide a dynamic/valuable tool for obtaining the solutions for homework assignments, class examinations, self-assessment studies, and other coursework related activities. Various transportation engineering applications of SLE are cited. Engineering educators who have adopted “flipped classroom instruction” can also utilize this Java Visualization and Animation software for students to “self-learning” these algorithms at their own time (and at their preferable locations), and use valuable class-meeting time for more challenging (real-life) problems’ discussions. Statistical data for comparisons of students’ performance with and without using the developed Java computer animation are also included.

Evolution of crack paths and compliance in round bars under cyclic tension and bending

The aim of this paper is to calculate how the surface crack front and the dimensionless compliance evolve in cylindrical bars containing a transverse edge crack subjected to cyclic tension or bending with different initial crack geometries (crack depths and aspect ratios). A Java computer program was developed and implemented to obtain the crack path evolution (changes of crack depth and aspect ratio), as well as the progress of mechanical compliance, by discretizing the crack front (characterized with elliptical shape) and calculating the crack front changes on the basis of the Paris law, and using a three-parameter stress intensity factor (SIF). The results show that in fatigue crack propagation, relative crack depth influences more on dimensionless compliance than the aspect ratio, because the crack front tends to converge when the crack propagates from different initial geometries, showing greater values of dimensionless compliance for tension than for bending. Furthermore, during fatigue crack growth, materials with higher values of the exponent of the Paris law produce slightly greater dimensionless compliance and a better convergence between the results for straight-fronted and circular initial cracks.

J-Circos: an interactive Circos plotter.

Circos plots are graphical outputs that display three dimensional chromosomal interactions and fusion transcripts. However, the Circos plot tool is not an interactive visualization tool, but rather a figure generator. For example, it does not enable data to be added dynamically nor does it provide information for specific data points interactively. Recently, an R-based Circos tool (RCircos) has been developed to integrate Circos to R, but similarly, Rcircos can only be used to generate plots. Thus, we have developed a Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable, it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the Graphical user interface (GUI). J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data. J-circos and its manual are freely available at http://www.australianprostatecentre.org/research/software/jcircos j.an@qut.edu.au Supplementary data are available at Bioinformatics online.

Multilevel Analysis of Factors Predicting Self Efficacy in Computer Programming

This study used multilevel analysis to determine the predictive value of selected intrinsic factors (gender, computer ownership, mathematics background and computer experience) and institutional type (an extrinsic factor) on undergraduates’ Self Efficacy in Java Computer Programming (SEiJCP) in South – West, Nigeria. The study adopted a correlational design. Purposive Sampling was used to select 254 computer science undergraduates from four universities (three federal-owned and one state-owned) in south-west, Nigeria. Three research questions were answered. Two research instruments namely, Computer experience scale (r = 0.84) and Java Programming Self Efficacy Scale (JPSES, r = 0.96) were used to collect data. Data were analysed using descriptive statistics, and null and linear growth model (LGM) procedures. The intercorrelation coefficients among the extrinsic factor, intrinsic factors and SEiJCP were moderate. Null model shows that the variations in SEiJCP accounted for by insitutional level differences was 99.0%. The fixed part of the LGM of intrinsic factors showed that only mathematical backgroung contributed significantly (p < 0.05) to the prediction of SEiJCP. The random part of the LGM showed no significant contributions of the interactions of the intrinsic factors, to the prediction of SEiJCP. About 60.0% of the student level variation in SEiJCP is explained by the differences in intrinsic factors. The institution – level variable had large predictive value on programming self efficacy. Computer science departments should increase the number of mathematics courses in their curriculum.

A Java-Based Package for Genetic Algorithm

Genetic algorithm is a very important and popular kind of algorithm of evolution computing. In order to use this algorithm better and platform-independently, this paper introduces an implement package which is coded in Java, an object-oriented and platform-independent advanced computer programming language, for genetic algorithm. This package includes several sub-packages. In each sub-package, there are some classes with different roles and functions. After the test, these classes can work properly and efficiently in together. The good effect has been received through using this algorithm in four function optimization problems. For the further goal, some studies even need to be carried out in the future.

Overview of Real-Time Java Computing

This paper presents a complete survey of recent techniques that are applied in the field of real-time Java computing. It focuses on the issues that are especially important for hard real-time applications, which include time predictable garbage collection, worst-case execution time analysis of Java programs, real-time Java threads scheduling and compiler techniques designed for real-time purpose. It also evaluates experimental frameworks that can be used for researching real-time Java. This overview is expected to help researchers understand the state-of-the-art and advance the research in real-time Java computing.

Active Condition Monitoring of a Marine Gas Turbine through Rotor Shaft Vibration Analysis

While preventive and predictive maintenance have played their part in engine health monitoring, the problem of downtime maintenance has truly reached a serious level. Also, most companies have found out that their maintenance costs can be cut drastically by establishing a proactive line of defence. Most imminent faults in gas turbines often result from the vibration of the rotor shaft of the engine. Some of these faults that could lead to catastrophy include misalignment, imbalance, cracks and eccentricity. These defects are equally likely to lead to unscheduled downtime resulting to large economic losses. It is on this backdrop that the rotor shaft of a marine gas turbine system was isolated and used for condition monitoring to enunciate methods to reduce downtime. The need to study vibration which is one of the biggest threats to rotating equipment has become much required now than ever before. This project thus presents a case to monitor the condition of the gas turbine through its thermodynamic and rotor shaft vibration analyses. Selected measurements from an industrial gas turbine to detect changes in operating conditions of the plant were of immense help in setting the proactive measures for the plant. Simulation and analysis were achieved using high level java computer programming language and data collected from a gas turbine plant. The work shows that vibration reduces the active load of the engine. Thus, proactive maintenance monitoring programs should be employed in gas turbine usage to avoid the effects of vibration.

TIM, a ray-tracing program for METATOY research and its dissemination

TIM (The Interactive METATOY) is a ray-tracing program specifically tailored towards our research in METATOYs, which are optical components that appear to be able to create wave-optically forbidden light-ray fields. For this reason, TIM possesses features not found in other ray-tracing programs. TIM can either be used interactively or by modifying the openly available source code; in both cases, it can easily be run as an applet embedded in a web page. Here we describe the basic structure of TIMʼs source code and how to extend it, and we give examples of how we have used TIM in our own research. Program summary Program title: TIM Catalogue identifier: AEKY_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKY_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 124 478 No. of bytes in distributed program, including test data, etc.: 4 120 052 Distribution format: tar.gz Programming language: Java Computer: Any computer capable of running the Java Virtual Machine (JVM) 1.6 Operating system: Any; developed under Mac OS X Version 10.6 RAM: Typically 145 MB (interactive version running under Mac OS X Version 10.6) Classification: 14, 18 External routines: JAMA [1] (source code included) Nature of problem: Visualisation of scenes that include scene objects that create wave-optically forbidden light-ray fields. Solution method: Ray tracing. Unusual features: Specifically designed to visualise wave-optically forbidden light-ray fields; can visualise ray trajectories; can visualise geometric optic transformations; can create anaglyphs (for viewing with coloured “3D glasses”) and random-dot autostereograms of the scene; integrable into web pages. Running time: Problem-dependent; typically seconds for a simple scene.

Rebuilding the Great Pyramids: A Method for Identifying Control Relations in Complex Ownership Structures

Identifying the corporate controller (controlling shareholder, ultimate owner) is an essential prerequisite for any debate on the corporate governance of a specific firm and of entire markets. This paper aims to provide a comprehensive, precise and economically sound method for identifying control relations on the corporate level and especially in complex ownership structures. We apply weighted voting games literature as a theoretical framework for our analysis and use the Shapley-Shubik and the Banzhaf power indices to determine control rights. The core element of the proposed method, distinguishing our study from others, in solving the puzzle of corporate control, is the simultaneous analysis of both the specific ownership map within the corporation and the corporate network in which the firm is embedded. We implemented our algorithm into a Java computer program and tested it on a real-world data set of corporate ownership in the Israeli market. The direct product of the analysis of these data is a comprehensive map of control relations at every time point. We find that the corporate control relations identified by our method are richer and more accurate than those provided by different official sources.

Device level communication libraries for high-performance computing in Java

Since its release, the Java programming language has attracted considerable attention from the high-performance computing (HPC) community because of its portability, high programming productivity, and built-in multithreading and networking support. As a consequence, several initiatives have been taken to develop a high-performance Java message-passing library to program distributed memory architectures, such as clusters. The performance of Java message-passing applications relies heavily on the communications performance. Thus, the design and implementation of low-level communication devices that support message-passing libraries is an important research issue in Java for HPC. MPJ Express is our Java message-passing implementation for developing high-performance parallel Java applications. Its public release currently contains three communication devices: the first one is built using the Java New Input/Output (NIO) package for the TCP/IP; the second one is specifically designed for the Myrinet Express library on Myrinet; and the third one supports thread-based shared memory communications. Although these devices have been successfully deployed in many production environments, previous performance evaluations of MPJ Express suggest that the buffering layer, tightly coupled with these devices, incurs a certain degree of copying overhead, which represents one of the main performance penalties. This paper presents a more efficient Java message-passing communications device, based on Java Input/Output sockets, that avoids this buffering overhead. Moreover, this device implements several strategies, both in the communication protocol and in the HPC hardware support, which optimizes Java message-passing communications. In order to evaluate its benefits, this paper analyzes the performance of this device comparatively with other Java and native message-passing libraries on various high-speed networks, such as Gigabit Ethernet, Scalable Coherent Interface, Myrinet, and InfiniBand, as well as on a shared memory multicore scenario. The reported communication overhead reduction encourages the upcoming incorporation of this device in MPJ Express (). Copyright © 2011 John Wiley & Sons, Ltd.

HATHOR – HAdronic Top and Heavy quarks crOss section calculatoR

We present a program to calculate the total cross section for top-quark pair production in hadronic collisions. The program takes into account recent theoretical developments such as approximate next-to-next-to-leading order perturbative QCD corrections and it allows for studies of the theoretical uncertainty by separate variations of the factorization and renormalization scales. In addition it offers the possibility to obtain the cross section as a function of the running top-quark mass. The program can also be applied to a hypothetical fourth quark family provided the QCD couplings are standard. Program summary Program title: Hathor Catalogue identifier: AEID_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEID_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL 3 No. of lines in distributed program, including test data, etc.: 5405 No. of bytes in distributed program, including test data, etc.: 327 718 Distribution format: tar.gz Programming language: C++, Fortran, Java Computer: Standard PCs (x86, x86_64 processors) Operating system: Linux RAM: 256 MB Classification: 11.1 External routines: Interface to LHAPDF for the user's choice of parton distribution functions, see http://projects.hepforge.org/lhapdf/ Nature of problem: Computation of total cross section in perturbative QCD. Solution method: Numerical integration of hard parton cross section convoluted with parton distribution functions. Running time: A few seconds to a few minutes on standard desktop PCs or notebooks, depending on the chosen options.