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The Feasibility of Multicasting in RMI

Description: Due to the growing need of the Internet and networking technologies, simple, powerful, easily maintained distributed applications needed to be developed. These kinds of applications can benefit greatly from distributed computing concepts. Despite its powerful mechanisms, Jini has yet to be accepted in mainstream Java development. Until that happens, we need to find better Remote Method Invocation (RMI) solutions. Feasibility of implementation of Multicasting in RMI is worked in this paper. Multicasting capability can be used in RMI using Jini-like technique. Support of Multicast over Unicast reference layer is also studied. A piece of code explaining how it can be done, is added.
Date: May 2003
Creator: Ujjinihavildar, Vinay
Partner: UNT Libraries


Description: The XMGR5 graphing package [1] for drawing RELAP5 [2] plots is being re-written in Java [3]. Java is a robust programming language that is available at no cost for most computer platforms from Sun Microsystems, Inc. XMGR5 is an extension of an XY plotting tool called ACE/gr extended to plot data from several US Nuclear Regulatory Commission (NRC) applications. It is also the most popular graphing package worldwide for making RELAP5 plots. In Section 1, a short review of XMGR5 is given, followed by a brief overview of Java. In Section 2, shortcomings of both tkXMGR [4] and XMGR5 are discussed and the value of converting to Java is given. Details of the conversion to Java are given in Section 3. The progress to date, some conclusions and future work are given in Section 4. Some screen shots of the Java version are shown.
Date: August 1, 2004
Creator: Mesina, Dr. George L. & Miller, Steven P.
Partner: UNT Libraries Government Documents Department

Grid Logging: Best Practices Guide

Description: The purpose of this document is to help developers of Grid middleware and application software generate log files that will be useful to Grid administrators, users, developers and Grid middleware itself. Currently, most of the currently generated log files are only useful to the author of the program. Good logging practices are instrumental to performance analysis, problem diagnosis, and security auditing tasks such as incident tracing and damage assessment. This document does not discuss the issue of a logging API. It is assumed that a standard log API such as syslog (C), log4j (Java), or logger (Python) is being used. Other custom logging API or even printf could be used. The key point is that the logs must contain the required information in the required format. At a high level of abstraction, the best practices for Grid logging are: (1) Consistently structured, typed, log events; (2) A standard high-resolution timestamp; (3) Use of logging levels and categories to separate logs by detail and purpose; (4) Consistent use of global and local identifiers; and (5) Use of some regular, newline-delimited ASCII text format. The rest of this document describes each of these recommendations in detail.
Date: April 1, 2008
Creator: Tierney, Brian L; Tierney, Brian L & Gunter, Dan
Partner: UNT Libraries Government Documents Department

Babel Fortran 2003 Binding for Structured Data Types

Description: Babel is a tool aimed at the high-performance computing community that addresses the need for mixing programming languages (Java, Python, C, C++, Fortran 90, FORTRAN 77) in order to leverage the specific benefits of those languages. Scientific codes often rely on structured data types (structs, derived data types) to encapsulate data, and Babel has been lacking in this type of support until recently. We present a new language binding that focuses on their interoperability of C/C++ with Fortran 2003. The new binding builds on the existing Fortran 90 infrastructure by using the iso-c-binding module defined in the Fortran 2003 standard as the basis for C/C++ interoperability. We present the technical approach for the new binding and discuss our initial experiences in applying the binding in FACETS (Framework Application for Core-Edge Transport Simulations) to integrate C++ with legacy Fortran codes.
Date: May 2, 2008
Creator: Muszala, S; Epperly, T & Wang, N
Partner: UNT Libraries Government Documents Department

Java Metadata Facility

Description: The Java Metadata Facility is introduced by Java Specification Request (JSR) 175 [1], and incorporated into the Java language specification [2] in version 1.5 of the language. The specification allows annotations on Java program elements: classes, interfaces, methods, and fields. Annotations give programmers a uniform way to add metadata to program elements that can be used by code checkers, code generators, or other compile-time or runtime components. Annotations are defined by annotation types. These are defined the same way as interfaces, but with the symbol {at} preceding the interface keyword. There are additional restrictions on defining annotation types: (1) They cannot be generic; (2) They cannot extend other annotation types or interfaces; (3) Methods cannot have any parameters; (4) Methods cannot have type parameters; (5) Methods cannot throw exceptions; and (6) The return type of methods of an annotation type must be a primitive, a String, a Class, an annotation type, or an array, where the type of the array is restricted to one of the four allowed types. See [2] for additional restrictions and syntax. The methods of an annotation type define the elements that may be used to parameterize the annotation in code. Annotation types may have default values for any of its elements. For example, an annotation that specifies a defect report could initialize an element defining the defect outcome submitted. Annotations may also have zero elements. This could be used to indicate serializability for a class (as opposed to the current Serializability interface).
Date: March 6, 2008
Creator: Buttler, D. J.
Partner: UNT Libraries Government Documents Department

Generic Optimization Program User Manual Version 3.0.0

Description: GenOpt is an optimization program for the minimization of a cost function that is evaluated by an external simulation program. It has been developed for optimization problems where the cost function is computationally expensive and its derivatives are not available or may not even exist. GenOpt can be coupled to any simulation program that reads its input from text files and writes its output to text files. The independent variables can be continuous variables (possibly with lower and upper bounds), discrete variables, or both, continuous and discrete variables. Constraints on dependent variables can be implemented using penalty or barrier functions. GenOpt uses parallel computing to evaluate the simulations. GenOpt has a library with local and global multi-dimensional and one-dimensional optimization algorithms, and algorithms for doing parametric runs. An algorithm interface allows adding new minimization algorithms without knowing the details of the program structure. GenOpt is written in Java so that it is platform independent. The platform independence and the general interface make GenOpt applicable to a wide range of optimization problems. GenOpt has not been designed for linear programming problems, quadratic programming problems, and problems where the gradient of the cost function is available. For such problems, as well as for other problems, special tailored software exists that is more efficient.
Date: May 11, 2009
Creator: Wetter, Michael
Partner: UNT Libraries Government Documents Department

Grid-based asynchronous migration of execution context in Java virtual machines

Description: Previous research efforts for building thread migration systems have concentrated on the development of frameworks dealing with a small local environment controlled by a single user. Computational Grids provide the opportunity to utilize a large-scale environment controlled over different organizational boundaries. Using this class of large-scale computational resources as part of a thread migration system provides a significant challenge previously not addressed by this community. In this paper the authors present a framework that integrates Grid services to enhance the functionality of a thread migration system. To accommodate future Grid services, the design of the framework is both flexible and extensible. Currently, the thread migration system contains Grid services for authentication, registration, lookup, and automatic software installation. In the context of distributed applications executed on a Grid-based infrastructure, the asynchronous migration of an execution context can help solve problems such as remote execution, load balancing, and the development of mobile agents. The prototype is based on the migration of Java threads, allowing asynchronous and heterogeneous migration of the execution context of the running code.
Date: June 15, 2000
Creator: von Laszewski, G.; Shudo, K. & Muraoka, Y.
Partner: UNT Libraries Government Documents Department

Extensions to Jinni Mobile Agent Architecture

Description: We extend the Jinni mobile agent architecture with a multicast network transport layer, an agent-to-agent delegation mechanism and a reflection based Prolog-to-Java interface. To ensure that our agent infrastructure runs efficiently, independently of router-level multicast support, we describe a blackboard based algorithm for locating a randomly roaming agent. As part of the agent-to-agent delegation mechanism, we describe an alternative to code-fetching mechanism for stronger mobility of mobile agents with less network overhead. In the context of direct and reflection based extension mechanisms for Jinni, we describe the design and the implementation of a reflection based Prolog-to-Java interface. The presence of subtyping and method overloading makes finding the most specific method corresponding to a Prolog call pattern fairly difficult. We describe a run-time algorithm which provides accurate handling of overloaded methods beyond Java's reflection package's limitations.
Date: May 2001
Creator: Tyagi, Satyam
Partner: UNT Libraries

Bal. Pulse = 1'

Description: Thesis written by a student in the UNT Honors College discussing the Gamelan orchestra of Indonesia, its instruments, a musical piece composed in the style, and scanned photographs of the instruments.
Date: Spring 1994
Creator: Murphy, Kevin
Partner: UNT Honors College

Prototyping Faithful Execution in a Java virtual machine.

Description: This report presents the implementation of a stateless scheme for Faithful Execution, the design for which is presented in a companion report, ''Principles of Faithful Execution in the Implementation of Trusted Objects'' (SAND 2003-2328). We added a simple cryptographic capability to an already simplified class loader and its associated Java Virtual Machine (JVM) to provide a byte-level implementation of Faithful Execution. The extended class loader and JVM we refer to collectively as the Sandia Faithfully Executing Java architecture (or JavaFE for short). This prototype is intended to enable exploration of more sophisticated techniques which we intend to implement in hardware.
Date: September 1, 2003
Creator: Tarman, Thomas David; Campbell, Philip LaRoche & Pierson, Lyndon George
Partner: UNT Libraries Government Documents Department

Phylo-VISTA: An interactive visualization tool for multiple DNAsequence alignments

Description: Motivation. The power of multi-sequence comparison forbiological discovery is well established and sequence data from a growinglist of organisms is becoming available. Thus, a need exists forcomputational strategies to visually compare multiple aligned sequencesto support conservation analysis across various species. To be efficientthese visualization algorithms require the ability to universally handlea wide range of evolutionary distances while taking into accountphylogeny Results. We have developed Phylo-VISTA, an interactive tool foranalyzing multiple alignments by visualizing the similarity of DNAsequences among multiple species while considering their phylogenicrelationships. Features include a broad spectrum of resolution parametersfor examining the alignment and the ability to easily compare any subtreeof sequences within a complete alignment dataset. Phylo-VISTA uses VISTAconcepts that have been successfully applied previously to a wide rangeof comparative genomics data analysis problems. Availability Phylo-VISTAis an interactive java applet available for downloading athttp://graphics.cs.ucdavis.edu/~;nyshah/Phylo-VISTA. It is also availableon-line at http://www-gsd.lbl.gov/phylovista and is integrated with theglobal alignment program LAGAN athttp://lagan.stanford.edu.Contactphylovista@lbl.gov
Date: April 25, 2003
Creator: Shah, Nameeta; Couronne, Olivier; Pennacchio, Len A.; Brudno,Michael; Batzoglou, Serafim; Bethel, E. Wes et al.
Partner: UNT Libraries Government Documents Department

New results on the resistivity structure of Merapi Volcano(Indonesia), derived from 3D restricted inversion of long-offsettransient electromagnetic data

Description: Three long-offset transient electromagnetic (LOTEM) surveyswerecarried out at the active volcano Merapi in Central Java (Indonesia)during the years 1998, 2000, and 2001. The measurements focused on thegeneral resistivity structure of the volcanic edifice at depths of 0.5-2km and the further investigation of a southside anomaly. The measurementswere insufficient for a full 3D inversion scheme, which could enable theimaging of finely discretized resistivity distributions. Therefore, astable, damped least-squares joint-inversion approach is used to optimize3D models with a limited number of parameters. The mode ls feature therealistic simulation of topography, a layered background structure, andadditional coarse 3D blocks representing conductivity anomalies.Twenty-eight LOTEM transients, comprising both horizontal and verticalcomponents of the magnetic induction time derivative, were analyzed. Inview of the few unknowns, we were able to achieve reasonable data fits.The inversion results indicate an upwelling conductor below the summit,suggesting hydrothermal activity in the central volcanic complex. Ashallow conductor due to a magma-filled chamber, at depths down to 1 kmbelow the summit, suggested by earlier seismic studies, is not indicatedby the inversion results. In conjunction with an anomalous-density model,derived from arecent gravity study, our inversion results provideinformation about the southern geological structure resulting from amajor sector collapse during the Middle Merapi period. The density modelallows to assess a porosity range andthus an estimated vertical salinityprofile to explain the high conductivities on a larger scale, extendingbeyond the foothills of Merapi.
Date: June 14, 2006
Creator: Commer, Michael; Helwig, Stefan, L.; Hordt, Andreas; Scholl,Carsten & Tezkan, Bulent
Partner: UNT Libraries Government Documents Department


Description: Recording setting changes within an accelerator facility provides information that can be used to answer questions about when, why, and how changes were made to some accelerator system. This can be very useful during normal operations, but can also aid with security concerns and in detecting unusual software behavior. The Set History System (SHS) is a new client-server system developed at the Collider-Accelerator Department of Brookhaven National Laboratory to provide these capabilities. The SHS has been operational for over two years and currently stores about IOOK settings per day into a commercial database management system. The SHS system consists of a server written in Java, client tools written in both Java and C++, and a web interface for querying the database of setting changes. The design of the SHS focuses on performance, portability, and a minimal impact on database resources. In this paper, we present an overview of the system design along with benchmark results showing the performance and reliability of the SHS over the last year.
Date: October 15, 2007
Creator: D OTTAVIO,T.; FU, W. & OTTAVIO, D.P.
Partner: UNT Libraries Government Documents Department

DOECGF 2010 Site Report

Description: The Data group provides data analysis and visualization support to its customers. This consists primarily of the development and support of VisIt, a data analysis and visualization tool. Support ranges from answering questions about the tool, providing classes on how to use the tool, and performing data analysis and visualization for customers. The Information Management and Graphics Group supports and develops tools that enhance our ability to access, display, and understand large, complex data sets. Activities include applying visualization software for large scale data exploration; running video production labs on two networks; supporting graphics libraries and tools for end users; maintaining PowerWalls and assorted other displays; and developing software for searching and managing scientific data. Researchers in the Center for Applied Scientific Computing (CASC) work on various projects including the development of visualization techniques for large scale data exploration that are funded by the ASC program, among others. The researchers also have LDRD projects and collaborations with other lab researchers, academia, and industry. The IMG group is located in the Terascale Simulation Facility, home to Dawn, Atlas, BGL, and others, which includes both classified and unclassified visualization theaters, a visualization computer floor and deployment workshop, and video production labs. We continued to provide the traditional graphics group consulting and video production support. We maintained five PowerWalls and many other displays. We deployed a 576-node Opteron/IB cluster with 72 TB of memory providing a visualization production server on our classified network. We continue to support a 128-node Opteron/IB cluster providing a visualization production server for our unclassified systems and an older 256-node Opteron/IB cluster for the classified systems, as well as several smaller clusters to drive the PowerWalls. The visualization production systems includes NFS servers to provide dedicated storage for data analysis and visualization. The ASC projects have delivered new versions ...
Date: April 12, 2010
Creator: Springmeyer, R. R.; Brugger, E. & Cook, R.
Partner: UNT Libraries Government Documents Department

JAGUAR developer's manual.

Description: JAGUAR (JAva GUi for Applied Research) is a Java software tool providing an advanced text editor and graphical user interface (GUI) to manipulate DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) input specifications. This document focuses on the technical background necessary for a developer to understand JAGUAR.
Date: June 1, 2011
Creator: Chan, Ethan
Partner: UNT Libraries Government Documents Department

Summary Report for the SINBAD Search Tool Project

Description: The Shielding Integral Benchmark Archive Database (SINBAD) Search Tool has been developed to serve as an interface with the SINBAD database to facilitate a simple and quick means of searching for information related to experimental benchmark problems. The Search Tool is written in Java and provides a better and efficient way to retrieve information from the SINBAD database. Searches can be performed quickly and easily. With regard to improvements, users are no longer required to know the name of the benchmarks to search the database. Instead, a search can be performed by specifying the experimental facility, constituents of the experimental benchmark, etc. In summary, a new powerful database search tool has been developed for SINBAD.
Date: June 1, 2012
Creator: Cunha Da Silva, Alice
Partner: UNT Libraries Government Documents Department

Teaching object concepts for XML-based representations.

Description: Students learned about object-oriented design concepts and knowledge representation through the use of a set of toy blocks. The blocks represented a limited and focused domain of knowledge and one that was physical and tangible. The blocks helped the students to better visualize, communicate, and understand the domain of knowledge as well as how to perform object decomposition. The blocks were further abstracted to an engineering design kit for water park design. This helped the students to work on techniques for abstraction and conceptualization. It also led the project from tangible exercises into software and programming exercises. Students employed XML to create object-based knowledge representations and Java to use the represented knowledge. The students developed and implemented software allowing a lay user to design and create their own water slide and then to take a simulated ride on their slide.
Date: January 1, 2002
Creator: Kelsey, R. L. (Robert L.)
Partner: UNT Libraries Government Documents Department

The CMS dataset bookkeeping service

Description: The CMS Dataset Bookkeeping Service (DBS) has been developed to catalog all CMS event data from Monte Carlo and Detector sources. It provides the ability to identify MC or trigger source, track data provenance, construct datasets for analysis, and discover interesting data. CMS requires processing and analysis activities at various service levels and the DBS system provides support for localized processing or private analysis, as well as global access for CMS users at large. Catalog entries can be moved among the various service levels with a simple set of migration tools, thus forming a loose federation of databases. DBS is available to CMS users via a Python API, Command Line, and a Discovery web page interfaces. The system is built as a multi-tier web application with Java servlets running under Tomcat, with connections via JDBC to Oracle or MySQL database backends. Clients connect to the service through HTTP or HTTPS with authentication provided by GRID certificates and authorization through VOMS. DBS is an integral part of the overall CMS Data Management and Workflow Management systems.
Date: October 1, 2007
Creator: Afaq, Anzar,; /Fermilab; Dolgert, Andrew; /Cornell U., Phys. Dept.; Guo, Yuyi; /Fermilab et al.
Partner: UNT Libraries Government Documents Department

DAKOTA JAGUAR 2.1 user's Manual.

Description: JAGUAR (JAva GUi for Applied Research) is a Java software tool providing an advanced text editor and graphical user interface (GUI) to manipulate DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) input specifications. This document focuses on the features necessary for a user to use JAGUAR.
Date: June 1, 2011
Creator: Adams, Brian M.; Lefantzi, Sophia; Chan, Ethan & Ruthruff, Joseph R.
Partner: UNT Libraries Government Documents Department

CartaBlanca-rapid prototyping development environment for non-linear systems on unstructured grids.

Description: This talk describes a component-based nonlinear physical system simulation prototyping package written entirely in Java using objectoriented design, The package provides scientists and engineers a 'developer-friendly' software environment for large-scale computational algorithm and physical model development, on the Jacobian-Free Newton-Krylov solution method surrounding a finite-volume treatment of conservation equations. This enables a clean component-like implementation. We first provide motivation for the development of the software and then discuss software structure. Discussion .includes a description of the use of Java's built-in thread facility that enables parallel, shared-memory computations on a wide variety of unstructured grids with triangular, quadrilateral, tetrahedral and hexahedral elements. We also discuss the use of Java's inheritance mechanism in the construction of a hierarchy of physics systems objects and linear and nonlinear solver objects that simplify development and foster software re-use. Following this, we show results from example calculations and then discuss plans including the extension of the software to distributed memory computer systems.
Date: January 1, 2002
Creator: VanderHeyden, W. B. (William Brian); Livescu, D. (Daniel) & Padial-Collins, N. T. (Nely T.)
Partner: UNT Libraries Government Documents Department

Drag and drop display & builder

Description: The Drag and Drop (DnD) Display & Builder is a component-oriented system that allows users to create visual representations of data received from data acquisition systems. It is an upgrade of a Synoptic Display mechanism used at Fermilab since 2002. Components can be graphically arranged and logically interconnected in the web-startable Project Builder. Projects can be either lightweight AJAX- and SVG-based web pages, or they can be started as Java applications. The new version was initiated as a response to discussions between the LHC Controls Group and Fermilab.
Date: December 1, 2007
Creator: Bolshakov, Timofei B. & Petrov, Andrey D.
Partner: UNT Libraries Government Documents Department

An evaluation of Java's I/O capabilities for high-performance computing.

Description: Java is quickly becoming the preferred language for writing distributed applications because of its inherent support for programming on distributed platforms. In particular, Java provides compile-time and run-time security, automatic garbage collection, inherent support for multithreading, support for persistent objects and object migration, and portability. Given these significant advantages of Java, there is a growing interest in using Java for high-performance computing applications. To be successful in the high-performance computing domain, however, Java must have the capability to efficiently handle the significant I/O requirements commonly found in high-performance computing applications. While there has been significant research in high-performance I/O using languages such as C, C++, and Fortran, there has been relatively little research into the I/O capabilities of Java. In this paper, we evaluate the I/O capabilities of Java for high-performance computing. We examine several approaches that attempt to provide high-performance I/O--many of which are not obvious at first glance--and investigate their performance in both parallel and multithreaded environments. We also provide suggestions for expanding the I/O capabilities of Java to better support the needs of high-performance computing applications.
Date: November 10, 2000
Creator: Dickens, P. M. & Thakur, R.
Partner: UNT Libraries Government Documents Department

Moving the Hazard Prediction and Assessment Capability to a Distributed, Portable Architecture

Description: The Hazard Prediction and Assessment Capability (HPAC) has been re-engineered from a Windows application with tight binding between computation and a graphical user interface (GUI) to a new distributed object architecture. The key goals of this new architecture are platform portability, extensibility, deployment flexibility, client-server operations, easy integration with other systems, and support for a new map-based GUI. Selection of Java as the development and runtime environment is the major factor in achieving each of the goals, platform portability in particular. Portability is further enforced by allowing only Java components in the client. Extensibility is achieved via Java's dynamic binding and class loading capabilities and a design by interface approach. HPAC supports deployment on a standalone host, as a heavy client in client-server mode with data stored on the client but calculations performed on the server host, and as a thin client with data and calculations on the server host. The principle architectural element supporting deployment flexibility is the use of Universal Resource Locators (URLs) for all file references. Java WebStart{trademark} is used for thin client deployment. Although there were many choices for the object distribution mechanism, the Common Object Request Broker Architecture (CORBA) was chosen to support HPAC client server operation. HPAC complies with version 2.0 of the CORBA standard and does not assume support for pass-by-value method arguments. Execution in standalone mode is expedited by having most server objects run in the same process as client objects, thereby bypassing CORBA object transport. HPAC provides four levels for access by other tools and systems, starting with a Windows library providing transport and dispersion (T&D) calculations and output generation, detailed and more abstract sets of CORBA services, and reusable Java components.
Date: September 5, 2002
Creator: Lee, RW
Partner: UNT Libraries Government Documents Department

Applying Loop Optimizations to Object-oriented Abstractions Through General Classification of Array Semantics

Description: Optimizing compilers have a long history of applying loop transformations to C and Fortran scientific applications. However, such optimizations are rare in compilers for object-oriented languages such as C++ or Java, where loops operating on user-defined types are left unoptimized due to their unknown semantics. Our goal is to reduce the performance penalty of using high-level object-oriented abstractions. We propose an approach that allows the explicit communication between programmers and compilers. We have extended the traditional Fortran loop optimizations with an open interface. Through this interface, we have developed techniques to automatically recognize and optimize user-defined array abstractions. In addition, we have developed an adapted constant-propagation algorithm to automatically propagate properties of abstractions. We have implemented these techniques in a C++ source-to-source translator and have applied them to optimize several kernels written using an array-class library. Our experimental results show that using our approach, applications using high-level abstractions can achieve comparable, and in cases superior, performance to that achieved by efficient low-level hand-written codes.
Date: March 5, 2004
Creator: Yi, Q & Quinlan, D
Partner: UNT Libraries Government Documents Department