Introduction to an open source internet-based testing program for medical student examinations.

PubMed

Lee, Yoon-Hwan

2009-12-20

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education.

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

PubMed

Buske, Fabian A; French, Hugh J; Smith, Martin A; Clark, Susan J; Bauer, Denis C

2014-05-15

The initial steps in the analysis of next-generation sequencing data can be automated by way of software 'pipelines'. However, individual components depreciate rapidly because of the evolving technology and analysis methods, often rendering entire versions of production informatics pipelines obsolete. Constructing pipelines from Linux bash commands enables the use of hot swappable modular components as opposed to the more rigid program call wrapping by higher level languages, as implemented in comparable published pipelining systems. Here we present Next Generation Sequencing ANalysis for Enterprises (NGSANE), a Linux-based, high-performance-computing-enabled framework that minimizes overhead for set up and processing of new projects, yet maintains full flexibility of custom scripting when processing raw sequence data. Ngsane is implemented in bash and publicly available under BSD (3-Clause) licence via GitHub at https://github.com/BauerLab/ngsane. Denis.Bauer@csiro.au Supplementary data are available at Bioinformatics online.

NSTX-U Advances in Real-Time C++11 on Linux

NASA Astrophysics Data System (ADS)

Erickson, Keith G.

2015-08-01

Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11 standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) will serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.

MYRaf: An Easy Aperture Photometry GUI for IRAF

NASA Astrophysics Data System (ADS)

Niaei, M. S.; KiliÇ, Y.; Özeren, F. F.

2015-07-01

We describe the design and development of MYRaf, a GUI (Graphical User Interface) that aims to be completely open-source under General Public License (GPL). MYRaf is an easy to use, reliable, and a fast IRAF aperture photometry GUI tool for those who are conversant with text-based software and command-line procedures in GNU/Linux OSs. MYRaf uses IRAF, PyRAF, matplotlib, ginga, alipy, and SExtractor with the general-purpose and high-level programming language Python, and uses the Qt framework.

Towards a new Mercator Observatory Control System

NASA Astrophysics Data System (ADS)

Pessemier, W.; Raskin, G.; Prins, S.; Saey, P.; Merges, F.; Padilla, J. P.; Van Winckel, H.; Waelkens, C.

2010-07-01

A new control system is currently being developed for the 1.2-meter Mercator Telescope at the Roque de Los Muchachos Observatory (La Palma, Spain). Formerly based on transputers, the new Mercator Observatory Control System (MOCS) consists of a small network of Linux computers complemented by a central industrial controller and an industrial real-time data communication network. Python is chosen as the high-level language to develop flexible yet powerful supervisory control and data acquisition (SCADA) software for the Linux computers. Specialized applications such as detector control, auto-guiding and middleware management are also integrated in the same Python software package. The industrial controller, on the other hand, is connected to the majority of the field devices and is targeted to run various control loops, some of which are real-time critical. Independently of the Linux distributed control system (DCS), this controller makes sure that high priority tasks such as the telescope motion, mirror support and hydrostatic bearing control are carried out in a reliable and safe way. A comparison is made between different controller technologies including a LabVIEW embedded system, a PROFINET Programmable Logic Controller (PLC) and motion controller, and an EtherCAT embedded PC (soft-PLC). As the latter is chosen as the primary platform for the lower level control, a substantial part of the software is being ported to the IEC 61131-3 standard programming languages. Additionally, obsolete hardware is gradually being replaced by standard industrial alternatives with fast EtherCAT communication. The use of Python as a scripting language allows a smooth migration to the final MOCS: finished parts of the new control system can readily be commissioned to replace the corresponding transputer units of the old control system with minimal downtime. In this contribution, we give an overview of the systems design, implementation details and the current status of the project.

Pressure Ratio to Thermal Environments

NASA Technical Reports Server (NTRS)

Lopez, Pedro; Wang, Winston

2012-01-01

A pressure ratio to thermal environments (PRatTlE.pl) program is a Perl language code that estimates heating at requested body point locations by scaling the heating at a reference location times a pressure ratio factor. The pressure ratio factor is the ratio of the local pressure at the reference point and the requested point from CFD (computational fluid dynamics) solutions. This innovation provides pressure ratio-based thermal environments in an automated and traceable method. Previously, the pressure ratio methodology was implemented via a Microsoft Excel spreadsheet and macro scripts. PRatTlE is able to calculate heating environments for 150 body points in less than two minutes. PRatTlE is coded in Perl programming language, is command-line-driven, and has been successfully executed on both the HP and Linux platforms. It supports multiple concurrent runs. PRatTlE contains error trapping and input file format verification, which allows clear visibility into the input data structure and intermediate calculations.

NSTX-U Advances in Real-Time C++11 on Linux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erickson, Keith G.

Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) willmore » serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.« less

NSTX-U Advances in Real-Time C++11 on Linux

DOE PAGES

Erickson, Keith G.

2015-08-14

Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) willmore » serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.« less

Open discovery: An integrated live Linux platform of Bioinformatics tools.

PubMed

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

Turning a remotely controllable observatory into a fully autonomous system

NASA Astrophysics Data System (ADS)

Swindell, Scott; Johnson, Chris; Gabor, Paul; Zareba, Grzegorz; Kubánek, Petr; Prouza, Michael

2014-08-01

We describe a complex process needed to turn an existing, old, operational observatory - The Steward Observatory's 61" Kuiper Telescope - into a fully autonomous system, which observers without an observer. For this purpose, we employed RTS2,1 an open sourced, Linux based observatory control system, together with other open sourced programs and tools (GNU compilers, Python language for scripting, JQuery UI for Web user interface). This presentation provides a guide with time estimates needed for a newcomers to the field to handle such challenging tasks, as fully autonomous observatory operations.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations.

PubMed

Tchantchaleishvili, Vakhtang; Schmitto, Jan D

2011-10-22

Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux.

Open discovery: An integrated live Linux platform of Bioinformatics tools

PubMed Central

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery ‐ a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. Availability The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in PMID:19238235

Internet Distribution of Spacecraft Telemetry Data

NASA Technical Reports Server (NTRS)

Specht, Ted; Noble, David

2006-01-01

Remote Access Multi-mission Processing and Analysis Ground Environment (RAMPAGE) is a Java-language server computer program that enables near-real-time display of spacecraft telemetry data on any authorized client computer that has access to the Internet and is equipped with Web-browser software. In addition to providing a variety of displays of the latest available telemetry data, RAMPAGE can deliver notification of an alarm by electronic mail. Subscribers can then use RAMPAGE displays to determine the state of the spacecraft and formulate a response to the alarm, if necessary. A user can query spacecraft mission data in either binary or comma-separated-value format by use of a Web form or a Practical Extraction and Reporting Language (PERL) script to automate the query process. RAMPAGE runs on Linux and Solaris server computers in the Ground Data System (GDS) of NASA's Jet Propulsion Laboratory and includes components designed specifically to make it compatible with legacy GDS software. The client/server architecture of RAMPAGE and the use of the Java programming language make it possible to utilize a variety of competitive server and client computers, thereby also helping to minimize costs.

Integrating a Trusted Computing Base Extension Server and Secure Session Server into the LINUX Operating System

DTIC Science & Technology

2001-09-01

Readily Available Linux has been copyrighted under the terms of the GNU General Public 5 License (GPL)1. This is a license written by the Free...GNOME and KDE . d. Portability Linux is highly compatible with many common operating systems. For...using suitable libraries, Linux is able to run programs written for other operating systems. [Ref. 8] 1 The GNU Project is coordinated by the

Preparing a scientific manuscript in Linux: Today's possibilities and limitations

PubMed Central

2011-01-01

Background Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Findings Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux. PMID:22018246

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

PubMed

Prins, Pjotr; Goto, Naohisa; Yates, Andrew; Gautier, Laurent; Willis, Scooter; Fields, Christopher; Katayama, Toshiaki

2012-01-01

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, BioJava, and R/Bioconductor. In this chapter, we compare the two principal approaches for sharing software between different programming languages: either by remote procedure call (RPC) or by sharing a local call stack. RPC provides a language-independent protocol over a network interface; examples are RSOAP and Rserve. The local call stack provides a between-language mapping not over the network interface, but directly in computer memory; examples are R bindings, RPy, and languages sharing the Java Virtual Machine stack. This functionality provides strategies for sharing of software between Bio* projects, which can be exploited more often. Here, we present cross-language examples for sequence translation, and measure throughput of the different options. We compare calling into R through native R, RSOAP, Rserve, and RPy interfaces, with the performance of native BioPerl, Biopython, BioJava, and BioRuby implementations, and with call stack bindings to BioJava and the European Molecular Biology Open Software Suite. In general, call stack approaches outperform native Bio* implementations and these, in turn, outperform RPC-based approaches. To test and compare strategies, we provide a downloadable BioNode image with all examples, tools, and libraries included. The BioNode image can be run on VirtualBox-supported operating systems, including Windows, OSX, and Linux.

LevelScheme: A level scheme drawing and scientific figure preparation system for Mathematica

NASA Astrophysics Data System (ADS)

Caprio, M. A.

2005-09-01

LevelScheme is a scientific figure preparation system for Mathematica. The main emphasis is upon the construction of level schemes, or level energy diagrams, as used in nuclear, atomic, molecular, and hadronic physics. LevelScheme also provides a general infrastructure for the preparation of publication-quality figures, including support for multipanel and inset plotting, customizable tick mark generation, and various drawing and labeling tasks. Coupled with Mathematica's plotting functions and powerful programming language, LevelScheme provides a flexible system for the creation of figures combining diagrams, mathematical plots, and data plots. Program summaryTitle of program:LevelScheme Catalogue identifier:ADVZ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVZ Operating systems:Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux Programming language used:Mathematica 4 Number of bytes in distributed program, including test and documentation:3 051 807 Distribution format:tar.gz Nature of problem:Creation of level scheme diagrams. Creation of publication-quality multipart figures incorporating diagrams and plots. Method of solution:A set of Mathematica packages has been developed, providing a library of level scheme drawing objects, tools for figure construction and labeling, and control code for producing the graphics.

owlcpp: a C++ library for working with OWL ontologies.

PubMed

Levin, Mikhail K; Cowell, Lindsay G

2015-01-01

The increasing use of ontologies highlights the need for a library for working with ontologies that is efficient, accessible from various programming languages, and compatible with common computational platforms. We developed owlcpp, a library for storing and searching RDF triples, parsing RDF/XML documents, converting triples into OWL axioms, and reasoning. The library is written in ISO-compliant C++ to facilitate efficiency, portability, and accessibility from other programming languages. Internally, owlcpp uses the Raptor RDF Syntax library for parsing RDF/XML and the FaCT++ library for reasoning. The current version of owlcpp is supported under Linux, OSX, and Windows platforms and provides an API for Python. The results of our evaluation show that, compared to other commonly used libraries, owlcpp is significantly more efficient in terms of memory usage and searching RDF triple stores. owlcpp performs strict parsing and detects errors ignored by other libraries, thus reducing the possibility of incorrect semantic interpretation of ontologies. owlcpp is available at http://owl-cpp.sf.net/ under the Boost Software License, Version 1.0.

New Version of SeismicHandler (SHX) based on ObsPy

NASA Astrophysics Data System (ADS)

Stammler, Klaus; Walther, Marcus

2016-04-01

The command line version of SeismicHandler (SH), a scientific analysis tool for seismic waveform data developed around 1990, has been redesigned in the recent years, based on a project funded by the Deutsche Forschungsgemeinschaft (DFG). The aim was to address new data access techniques, simplified metadata handling and a modularized software design. As a result the program was rewritten in Python in its main parts, taking advantage of simplicity of this script language and its variety of well developed software libraries, including ObsPy. SHX provides an easy access to waveforms and metadata via arclink and FDSN webservice protocols, also access to event catalogs is implemented. With single commands whole networks or stations within a certain area may be read in, the metadata are retrieved from the servers and stored in a local database. For data processing the large set of SH commands is available, as well as the SH scripting language. Via this SH language scripts or additional Python modules the command set of SHX is easily extendable. The program is open source, tested on Linux operating systems, documentation and download is found at URL "https://www.seismic-handler.org/".

Architecture Adaptive Computing Environment

NASA Technical Reports Server (NTRS)

Dorband, John E.

2006-01-01

Architecture Adaptive Computing Environment (aCe) is a software system that includes a language, compiler, and run-time library for parallel computing. aCe was developed to enable programmers to write programs, more easily than was previously possible, for a variety of parallel computing architectures. Heretofore, it has been perceived to be difficult to write parallel programs for parallel computers and more difficult to port the programs to different parallel computing architectures. In contrast, aCe is supportable on all high-performance computing architectures. Currently, it is supported on LINUX clusters. aCe uses parallel programming constructs that facilitate writing of parallel programs. Such constructs were used in single-instruction/multiple-data (SIMD) programming languages of the 1980s, including Parallel Pascal, Parallel Forth, C*, *LISP, and MasPar MPL. In aCe, these constructs are extended and implemented for both SIMD and multiple- instruction/multiple-data (MIMD) architectures. Two new constructs incorporated in aCe are those of (1) scalar and virtual variables and (2) pre-computed paths. The scalar-and-virtual-variables construct increases flexibility in optimizing memory utilization in various architectures. The pre-computed-paths construct enables the compiler to pre-compute part of a communication operation once, rather than computing it every time the communication operation is performed.

LORES: Low resolution shape program for the calculation of small angle scattering profiles for biological macromolecules in solution

NASA Astrophysics Data System (ADS)

Zhou, J.; Deyhim, A.; Krueger, S.; Gregurick, S. K.

2005-08-01

A program for determining the low resolution shape of biological macromolecules, based on the optimization of a small angle neutron scattering profile to experimental data, is presented. This program, termed LORES, relies on a Monte Carlo optimization procedure and will allow for multiple scattering length densities of complex structures. It is therefore more versatile than utilizing a form factor approach to produce low resolution structural models. LORES is easy to compile and use, and allows for structural modeling of biological samples in real time. To illustrate the effectiveness and versatility of the program, we present four specific biological examples, Apoferritin (shell model), Ribonuclease S (ellipsoidal model), a 10-mer dsDNA (duplex helix) and a construct of a 10-mer DNA/PNA duplex helix (heterogeneous structure). These examples are taken from protein and nucleic acid SANS studies, of both large and small scale structures. We find, in general, that our program will accurately reproduce the geometric shape of a given macromolecule, when compared with the known crystallographic structures. We also present results to illustrate the lower limit of the experimental resolution which the LORES program is capable of modeling. Program summaryTitle of program:LORES Catalogue identifier: ADVC Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVC Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer:SGI Origin200, SGI Octane, SGI Linux, Intel Pentium PC Operating systems:UNIX64 6.5 and LINUX 2.4.7 Programming language used:C Memory required to execute with typical data:8 MB No. of lines in distributed program, including test data, etc.:2270 No. of bytes in distributed program, including test data, etc.:13 302 Distribution format:tar.gz External subprograms used:The entire code must be linked with the MATH library

MPPhys—A many-particle simulation package for computational physics education

NASA Astrophysics Data System (ADS)

Müller, Thomas

2014-03-01

In a first course to classical mechanics elementary physical processes like elastic two-body collisions, the mass-spring model, or the gravitational two-body problem are discussed in detail. The continuation to many-body systems, however, is deferred to graduate courses although the underlying equations of motion are essentially the same and although there is a strong motivation for high-school students in particular because of the use of particle systems in computer games. The missing link between the simple and the more complex problem is a basic introduction to solve the equations of motion numerically which could be illustrated, however, by means of the Euler method. The many-particle physics simulation package MPPhys offers a platform to experiment with simple particle simulations. The aim is to give a principle idea how to implement many-particle simulations and how simulation and visualization can be combined for interactive visual explorations. Catalogue identifier: AERR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERR_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 111327 No. of bytes in distributed program, including test data, etc.: 608411 Distribution format: tar.gz Programming language: C++, OpenGL, GLSL, OpenCL. Computer: Linux and Windows platforms with OpenGL support. Operating system: Linux and Windows. RAM: Source Code 4.5 MB Complete package 242 MB Classification: 14, 16.9. External routines: OpenGL, OpenCL Nature of problem: Integrate N-body simulations, mass-spring models Solution method: Numerical integration of N-body-simulations, 3D-Rendering via OpenGL. Running time: Problem dependent

Performance and scalability evaluation of "Big Memory" on Blue Gene Linux.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoshii, K.; Iskra, K.; Naik, H.

2011-05-01

We address memory performance issues observed in Blue Gene Linux and discuss the design and implementation of 'Big Memory' - an alternative, transparent memory space introduced to eliminate the memory performance issues. We evaluate the performance of Big Memory using custom memory benchmarks, NAS Parallel Benchmarks, and the Parallel Ocean Program, at a scale of up to 4,096 nodes. We find that Big Memory successfully resolves the performance issues normally encountered in Blue Gene Linux. For the ocean simulation program, we even find that Linux with Big Memory provides better scalability than does the lightweight compute node kernel designed solelymore » for high-performance applications. Originally intended exclusively for compute node tasks, our new memory subsystem dramatically improves the performance of certain I/O node applications as well. We demonstrate this performance using the central processor of the LOw Frequency ARray radio telescope as an example.« less

Collaboration rules.

PubMed

Evans, Philip; Wolf, Bob

2005-01-01

Corporate leaders seeking to boost growth, learning, and innovation may find the answer in a surprising place: the Linux open-source software community. Linux is developed by an essentially volunteer, self-organizing community of thousands of programmers. Most leaders would sell their grandmothers for workforces that collaborate as efficiently, frictionlessly, and creatively as the self-styled Linux hackers. But Linux is software, and software is hardly a model for mainstream business. The authors have, nonetheless, found surprising parallels between the anarchistic, caffeinated, hirsute world of Linux hackers and the disciplined, tea-sipping, clean-cut world of Toyota engineering. Specifically, Toyota and Linux operate by rules that blend the self-organizing advantages of markets with the low transaction costs of hierarchies. In place of markets' cash and contracts and hierarchies' authority are rules about how individuals and groups work together (with rigorous discipline); how they communicate (widely and with granularity); and how leaders guide them toward a common goal (through example). Those rules, augmented by simple communication technologies and a lack of legal barriers to sharing information, create rich common knowledge, the ability to organize teams modularly, extraordinary motivation, and high levels of trust, which radically lowers transaction costs. Low transaction costs, in turn, make it profitable for organizations to perform more and smaller transactions--and so increase the pace and flexibility typical of high-performance organizations. Once the system achieves critical mass, it feeds on itself. The larger the system, the more broadly shared the knowledge, language, and work style. The greater individuals' reputational capital, the louder the applause and the stronger the motivation. The success of Linux is evidence of the power of that virtuous circle. Toyota's success is evidence that it is also powerful in conventional companies.

Scalable and Accurate SMT-Based Model Checking of Data Flow Systems

DTIC Science & Technology

2013-10-31

accessed from C, C++, Java, and OCaml , and provisions have been made to support other languages . CVC4 can be compiled and run on various flavors of...be accessed from C, C++, Java, and OCaml , and provisions have been made to support other languages . CVC4 can be compiled and run on various flavors of...C, C++, Java, and OCaml , and provisions have been made to support other languages . CVC4 can be compiled and run on various flavors of Linux, Mac OS

Three-Dimensional Audio Client Library

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.

2005-01-01

The Three-Dimensional Audio Client Library (3DAudio library) is a group of software routines written to facilitate development of both stand-alone (audio only) and immersive virtual-reality application programs that utilize three-dimensional audio displays. The library is intended to enable the development of three-dimensional audio client application programs by use of a code base common to multiple audio server computers. The 3DAudio library calls vendor-specific audio client libraries and currently supports the AuSIM Gold-Server and Lake Huron audio servers. 3DAudio library routines contain common functions for (1) initiation and termination of a client/audio server session, (2) configuration-file input, (3) positioning functions, (4) coordinate transformations, (5) audio transport functions, (6) rendering functions, (7) debugging functions, and (8) event-list-sequencing functions. The 3DAudio software is written in the C++ programming language and currently operates under the Linux, IRIX, and Windows operating systems.

The Linux operating system: An introduction

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.

1995-01-01

Linux is a Unix-like operating system for Intel 386/486/Pentium based IBM-PCs and compatibles. The kernel of this operating system was written from scratch by Linus Torvalds and, although copyrighted by the author, may be freely distributed. A world-wide group has collaborated in developing Linux on the Internet. Linux can run the powerful set of compilers and programming tools of the Free Software Foundation, and XFree86, a port of the X Window System from MIT. Most capabilities associated with high performance workstations, such as networking, shared file systems, electronic mail, TeX, LaTeX, etc. are freely available for Linux. It can thus transform cheap IBM-PC compatible machines into Unix workstations with considerable capabilities. The author explains how Linux may be obtained, installed and networked. He also describes some interesting applications for Linux that are freely available. The enormous consumer market for IBM-PC compatible machines continually drives down prices of CPU chips, memory, hard disks, CDROMs, etc. Linux can convert such machines into powerful workstations that can be used for teaching, research and software development. For professionals who use Unix based workstations at work, Linux permits virtually identical working environments on their personal home machines. For cost conscious educational institutions Linux can create world-class computing environments from cheap, easily maintained, PC clones. Finally, for university students, it provides an essentially cost-free path away from DOS into the world of Unix and X Windows.

Kernel-based Linux emulation for Plan 9.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minnich, Ronald G.

2010-09-01

CNKemu is a kernel-based system for the 9k variant of the Plan 9 kernel. It is designed to provide transparent binary support for programs compiled for IBM's Compute Node Kernel (CNK) on the Blue Gene series of supercomputers. This support allows users to build applications with the standard Blue Gene toolchain, including C++ and Fortran compilers. While the CNK is not Linux, IBM designed the CNK so that the user interface has much in common with the Linux 2.0 system call interface. The Plan 9 CNK emulator hence provides the foundation of kernel-based Linux system call support on Plan 9.more » In this paper we discuss cnkemu's implementation and some of its more interesting features, such as the ability to easily intermix Plan 9 and Linux system calls.« less

Line-by-line spectroscopic simulations on graphics processing units

NASA Astrophysics Data System (ADS)

Collange, Sylvain; Daumas, Marc; Defour, David

2008-01-01

We report here on software that performs line-by-line spectroscopic simulations on gases. Elaborate models (such as narrow band and correlated-K) are accurate and efficient for bands where various components are not simultaneously and significantly active. Line-by-line is probably the most accurate model in the infrared for blends of gases that contain high proportions of H 2O and CO 2 as this was the case for our prototype simulation. Our implementation on graphics processing units sustains a speedup close to 330 on computation-intensive tasks and 12 on memory intensive tasks compared to implementations on one core of high-end processors. This speedup is due to data parallelism, efficient memory access for specific patterns and some dedicated hardware operators only available in graphics processing units. It is obtained leaving most of processor resources available and it would scale linearly with the number of graphics processing units in parallel machines. Line-by-line simulation coupled with simulation of fluid dynamics was long believed to be economically intractable but our work shows that it could be done with some affordable additional resources compared to what is necessary to perform simulations on fluid dynamics alone. Program summaryProgram title: GPU4RE Catalogue identifier: ADZY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 62 776 No. of bytes in distributed program, including test data, etc.: 1 513 247 Distribution format: tar.gz Programming language: C++ Computer: x86 PC Operating system: Linux, Microsoft Windows. Compilation requires either gcc/g++ under Linux or Visual C++ 2003/2005 and Cygwin under Windows. It has been tested using gcc 4.1.2 under Ubuntu Linux 7.04 and using Visual C++ 2005 with Cygwin 1.5.24 under Windows XP. RAM: 1 gigabyte Classification: 21.2 External routines: OpenGL ( http://www.opengl.org) Nature of problem: Simulating radiative transfer on high-temperature high-pressure gases. Solution method: Line-by-line Monte-Carlo ray-tracing. Unusual features: Parallel computations are moved to the GPU. Additional comments: nVidia GeForce 7000 or ATI Radeon X1000 series graphics processing unit is required. Running time: A few minutes.

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

PubMed

Bonnal, Raoul J P; Aerts, Jan; Githinji, George; Goto, Naohisa; MacLean, Dan; Miller, Chase A; Mishima, Hiroyuki; Pagani, Massimiliano; Ramirez-Gonzalez, Ricardo; Smant, Geert; Strozzi, Francesco; Syme, Rob; Vos, Rutger; Wennblom, Trevor J; Woodcroft, Ben J; Katayama, Toshiaki; Prins, Pjotr

2012-04-01

Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html bonnal@ingm.org.

FLY MPI-2: a parallel tree code for LSS

NASA Astrophysics Data System (ADS)

Becciani, U.; Comparato, M.; Antonuccio-Delogu, V.

2006-04-01

New version program summaryProgram title: FLY 3.1 Catalogue identifier: ADSC_v2_0 Licensing provisions: yes Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSC_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland No. of lines in distributed program, including test data, etc.: 158 172 No. of bytes in distributed program, including test data, etc.: 4 719 953 Distribution format: tar.gz Programming language: Fortran 90, C Computer: Beowulf cluster, PC, MPP systems Operating system: Linux, Aix RAM: 100M words Catalogue identifier of previous version: ADSC_v1_0 Journal reference of previous version: Comput. Phys. Comm. 155 (2003) 159 Does the new version supersede the previous version?: yes Nature of problem: FLY is a parallel collisionless N-body code for the calculation of the gravitational force Solution method: FLY is based on the hierarchical oct-tree domain decomposition introduced by Barnes and Hut (1986) Reasons for the new version: The new version of FLY is implemented by using the MPI-2 standard: the distributed version 3.1 was developed by using the MPICH2 library on a PC Linux cluster. Today the FLY performance allows us to consider the FLY code among the most powerful parallel codes for tree N-body simulations. Another important new feature regards the availability of an interface with hydrodynamical Paramesh based codes. Simulations must follow a box large enough to accurately represent the power spectrum of fluctuations on very large scales so that we may hope to compare them meaningfully with real data. The number of particles then sets the mass resolution of the simulation, which we would like to make as fine as possible. The idea to build an interface between two codes, that have different and complementary cosmological tasks, allows us to execute complex cosmological simulations with FLY, specialized for DM evolution, and a code specialized for hydrodynamical components that uses a Paramesh block structure. Summary of revisions: The parallel communication schema was totally changed. The new version adopts the MPICH2 library. Now FLY can be executed on all Unix systems having an MPI-2 standard library. The main data structure, is declared in a module procedure of FLY (fly_h.F90 routine). FLY creates the MPI Window object for one-sided communication for all the shared arrays, with a call like the following: CALL MPI_WIN_CREATE(POS, SIZE, REAL8, MPI_INFO_NULL, MPI_COMM_WORLD, WIN_POS, IERR) the following main window objects are created: win_pos, win_vel, win_acc: particles positions velocities and accelerations, win_pos_cell, win_mass_cell, win_quad, win_subp, win_grouping: cells positions, masses, quadrupole momenta, tree structure and grouping cells. Other windows are created for dynamic load balance and global counters. Restrictions: The program uses the leapfrog integrator schema, but could be changed by the user. Unusual features: FLY uses the MPI-2 standard: the MPICH2 library on Linux systems was adopted. To run this version of FLY the working directory must be shared among all the processors that execute FLY. Additional comments: Full documentation for the program is included in the distribution in the form of a README file, a User Guide and a Reference manuscript. Running time: IBM Linux Cluster 1350, 512 nodes with 2 processors for each node and 2 GB RAM for each processor, at Cineca, was adopted to make performance tests. Processor type: Intel Xeon Pentium IV 3.0 GHz and 512 KB cache (128 nodes have Nocona processors). Internal Network: Myricom LAN Card "C" Version and "D" Version. Operating System: Linux SuSE SLES 8. The code was compiled using the mpif90 compiler version 8.1 and with basic optimization options in order to have performances that could be useful compared with other generic clusters Processors

Computing and combustion

NASA Technical Reports Server (NTRS)

Thompson, Daniel

2004-01-01

Coming into the Combustion Branch of the Turbomachinery and Propulsion Systems Division, there was not any set project planned out for me to work on. This was understandable, considering I am only at my sophmore year in college. Also, my mentor was a division chief and it was expected that I would be passed down the line. It took about a week for me to be placed with somebody who could use me. My first project was to write a macro for TecPlot. Commonly, a person would have a 3D contour volume modeling something such as a combustion engine. This 3D volume needed to have slices extracted from it and made into 2D scientific plots with all of the appropriate axis and titles. This was very tedious to do by hand. My macro needed to automate the process. There was some education I needed before I could start, however. First, TecPlot ran on Unix and Linux, like a growing majority of scientific applications. I knew a little about Linux, but I would need to know more to use the software at hand. I took two classes at the Learning Center on Unix and am now comfortable with Linux and Unix. I already had taken Computer Science I and II, and had undergone the transformation from Computer Programmer to Procedural Epistemologist. I knew how to design efficient algorithms, I just needed to learn the macro language. After a little less than a week, I had learned the basics of the language. Like most languages, the best way to learn more of it was by using it. It was decided that it was best that I do the macro in layers, starting simple and adding features as I went. The macro started out slicing with respect to only one axis, and did not make 2D plots out of the slices. Instead, it lined them up inside the solid. Next, I allowed for more than one axis and placed each slice in a separate frame. After this, I added code that transformed each individual slice-frame into a scientific plot. I also made frames for composite volumes, which showed all of the slices in the same XYZ space. I then designed an addition companion macro that exported each frame into its own image file. I then distributed the macros to a test group, and am awaiting feedback. In the meantime, a am researching the possible applications of distributed computing on the National Combustor Code. Many of our Linux boxes were idle for most of the day. The department thinks that it would be wonderful if we could get all of these idle processors to work on a problem under the NCC code. The client software would have to be easily distributed, such as in screensaver format or as a program that only ran when the computer was not in use. This project proves to be an interesting challenge.

Scilab software package for the study of dynamical systems

NASA Astrophysics Data System (ADS)

Bordeianu, C. C.; Beşliu, C.; Jipa, Al.; Felea, D.; Grossu, I. V.

2008-05-01

This work presents a new software package for the study of chaotic flows and maps. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well known examples are implemented, with the capability of the users inserting their own ODE. Program summaryProgram title: Chaos Catalogue identifier: AEAP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 885 No. of bytes in distributed program, including test data, etc.: 5925 Distribution format: tar.gz Programming language: Scilab 3.1.1 Computer: PC-compatible running Scilab on MS Windows or Linux Operating system: Windows XP, Linux RAM: below 100 Megabytes Classification: 6.2 Nature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE). Solution method: Numerical solving of ordinary differential equations. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincaré sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies. Restrictions: The package routines are normally able to handle ODE systems of high orders (up to order twelve and possibly higher), depending on the nature of the problem. Running time: 10 to 20 seconds for problems that do not involve Lyapunov exponents calculation; 60 to 1000 seconds for problems that involve high orders ODE and Lyapunov exponents calculation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayan Ghosh, Jeff Hammond

OpenSHMEM is a community effort to unifyt and standardize the SHMEM programming model. MPI (Message Passing Interface) is a well-known community standard for parallel programming using distributed memory. The most recen t release of MPI, version 3.0, was designed in part to support programming models like SHMEM.OSHMPI is an implementation of the OpenSHMEM standard using MPI-3 for the Linux operating system. It is the first implementation of SHMEM over MPI one-sided communication and has the potential to be widely adopted due to the portability and widely availability of Linux and MPI-3. OSHMPI has been tested on a variety of systemsmore » and implementations of MPI-3, includingInfiniBand clusters using MVAPICH2 and SGI shared-memory supercomputers using MPICH. Current support is limited to Linux but may be extended to Apple OSX if there is sufficient interest. The code is opensource via https://github.com/jeffhammond/oshmpi« less

Cloudy's Journey from FORTRAN to C, Why and How

NASA Astrophysics Data System (ADS)

Ferland, G. J.

Cloudy is a large-scale plasma simulation code that is widely used across the astronomical community as an aid in the interpretation of spectroscopic data. The cover of the ADAS VI book featured predictions of the code. The FORTRAN 77 source code has always been freely available on the Internet, contributing to its widespread use. The coming of PCs and Linux has fundamentally changed the computing environment. Modern Fortran compilers (F90 and F95) are not freely available. A common-use code must be written in either FORTRAN 77 or C to be Open Source/GNU/Linux friendly. F77 has serious drawbacks - modern language constructs cannot be used, students do not have skills in this language, and it does not contribute to their future employability. It became clear that the code would have to be ported to C to have a viable future. I describe the approach I used to convert Cloudy from FORTRAN 77 with MILSPEC extensions to ANSI/ISO 89 C. Cloudy is now openly available as a C code, and will evolve to C++ as gcc and standard C++ mature. Cloudy looks to a bright future with a modern language.

JaxoDraw: A graphical user interface for drawing Feynman diagrams

NASA Astrophysics Data System (ADS)

Binosi, D.; Theußl, L.

2004-08-01

JaxoDraw is a Feynman graph plotting tool written in Java. It has a complete graphical user interface that allows all actions to be carried out via mouse click-and-drag operations in a WYSIWYG fashion. Graphs may be exported to postscript/EPS format and can be saved in XML files to be used for later sessions. One of JaxoDraw's main features is the possibility to create ? code that may be used to generate graphics output, thus combining the powers of ? with those of a modern day drawing program. With JaxoDraw it becomes possible to draw even complicated Feynman diagrams with just a few mouse clicks, without the knowledge of any programming language. Program summaryTitle of program: JaxoDraw Catalogue identifier: ADUA Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUA Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar gzip file Operating system: Any Java-enabled platform, tested on Linux, Windows ME, XP, Mac OS X Programming language used: Java License: GPL Nature of problem: Existing methods for drawing Feynman diagrams usually require some 'hard-coding' in one or the other programming or scripting language. It is not very convenient and often time consuming, to generate relatively simple diagrams. Method of solution: A program is provided that allows for the interactive drawing of Feynman diagrams with a graphical user interface. The program is easy to learn and use, produces high quality output in several formats and runs on any operating system where a Java Runtime Environment is available. Number of bytes in distributed program, including test data: 2 117 863 Number of lines in distributed program, including test data: 60 000 Restrictions: Certain operations (like internal latex compilation, Postscript preview) require the execution of external commands that might not work on untested operating systems. Typical running time: As an interactive program, the running time depends on the complexity of the diagram to be drawn.

VPython: Writing Real-time 3D Physics Programs

NASA Astrophysics Data System (ADS)

Chabay, Ruth

2001-06-01

VPython (http://cil.andrew.cmu.edu/projects/visual) combines the Python programming language with an innovative 3D graphics module called Visual, developed by David Scherer. Designed to make 3D physics simulations accessible to novice programmers, VPython allows the programmer to write a purely computational program without any graphics code, and produces an interactive realtime 3D graphical display. In a program 3D objects are created and their positions modified by computational algorithms. Running in a separate thread, the Visual module monitors the positions of these objects and renders them many times per second. Using the mouse, one can zoom and rotate to navigate through the scene. After one hour of instruction, students in an introductory physics course at Carnegie Mellon University, including those who have never programmed before, write programs in VPython to model the behavior of physical systems and to visualize fields in 3D. The Numeric array processing module allows the construction of more sophisticated simulations and models as well. VPython is free and open source. The Visual module is based on OpenGL, and runs on Windows, Linux, and Macintosh.

Chicks in Charge: Andrea Baker & Amy Daniels--Airport High School Media Center, Columbia, SC

ERIC Educational Resources Information Center

Library Journal, 2004

2004-01-01

This article briefly discusses two librarians exploration of Linux. Andrea Baker and Amy Daniels were tired of telling their students that new technology items were not in the budget. They explored Linux, which is a program that recycles older computers, installs free operating systems and free software.

Precision studies of the NNLO DGLAP evolution at the LHC with Candia

NASA Astrophysics Data System (ADS)

Cafarella, Alessandro; Corianò, Claudio; Guzzi, Marco

2008-11-01

We summarize the theoretical approach to the solution of the NNLO DGLAP equations using methods based on the logarithmic expansions in x-space and their implementation into the C program CANDIA 1.0. We present the various options implemented in the program and discuss the different solutions. The user can choose the order of the evolution, the type of the solution, which can be either exact or truncated, and the evolution either with a fixed or a varying flavor number, implemented in the varying-flavor-number scheme (VFNS). The renormalization and factorization scale dependencies are treated separately. In the non-singlet sector the program implements an exact NNLO solution. Program summaryProgram title: CANDIA Catalogue identifier: AEBK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 101 376 No. of bytes in distributed program, including test data, etc.: 5 865 234 Distribution format: tar.gz Programming language: C and Fortran Computer: All Operating system: Linux RAM: In the given examples, it ranges from 4 to 490 MB Classification: 11.1, 11.5 Nature of problem: The program provided here solves the DGLAP evolution equations for the parton distribution functions up to NNLO. Solution method: The algorithm implemented is based on the theory of the logarithmic expansions in Bjorken x-space. Additional comments: To be sure of getting the latest version of the program, the authors suggest downloading the code from their official CANDIA website ( http://www.le.infn.it/candia). Running time: In the given examples, it ranges from 1 to 40 minutes. The jobs have been executed on an Intel Core 2 Duo T7250 CPU at 2 GHz with a 64 bit Linux kernel. The test run script included in the package contains 5 sample runs and may take a number of hours to process, depending on the speed of the processor used and the size of the available RAM. http://www.le.infn.it/candia.

MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.

PubMed

Bunk, Boyke; Kucklick, Martin; Jonas, Rochus; Münch, Richard; Schobert, Max; Jahn, Dieter; Hiller, Karsten

2006-12-01

MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual intervention. The integration of a self-acting calibration function allows the parallel and fast calibration for several metabolites simultaneously. Finally, MetaQuant is able to import GC/MS data in the common NetCDF format and to export the results of the quantification into Systems Biology Markup Language (SBML), Comma Separated Values (CSV) or Microsoft Excel (XLS) format. MetaQuant is written in Java and is available under an open source license. Precompiled packages for the installation on Windows or Linux operating systems are freely available for download. The source code as well as the installation packages are available at http://bioinformatics.org/metaquant

Parallel Processing at the High School Level.

ERIC Educational Resources Information Center

Sheary, Kathryn Anne

This study investigated the ability of high school students to cognitively understand and implement parallel processing. Data indicates that most parallel processing is being taught at the university level. Instructional modules on C, Linux, and the parallel processing language, P4, were designed to show that high school students are highly…

BOKASUN: A fast and precise numerical program to calculate the Master Integrals of the two-loop sunrise diagrams

NASA Astrophysics Data System (ADS)

Caffo, Michele; Czyż, Henryk; Gunia, Michał; Remiddi, Ettore

2009-03-01

We present the program BOKASUN for fast and precise evaluation of the Master Integrals of the two-loop self-mass sunrise diagram for arbitrary values of the internal masses and the external four-momentum. We use a combination of two methods: a Bernoulli accelerated series expansion and a Runge-Kutta numerical solution of a system of linear differential equations. Program summaryProgram title: BOKASUN Catalogue identifier: AECG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 9404 No. of bytes in distributed program, including test data, etc.: 104 123 Distribution format: tar.gz Programming language: FORTRAN77 Computer: Any computer with a Fortran compiler accepting FORTRAN77 standard. Tested on various PC's with LINUX Operating system: LINUX RAM: 120 kbytes Classification: 4.4 Nature of problem: Any integral arising in the evaluation of the two-loop sunrise Feynman diagram can be expressed in terms of a given set of Master Integrals, which should be calculated numerically. The program provides a fast and precise evaluation method of the Master Integrals for arbitrary (but not vanishing) masses and arbitrary value of the external momentum. Solution method: The integrals depend on three internal masses and the external momentum squared p. The method is a combination of an accelerated expansion in 1/p in its (pretty large!) region of fast convergence and of a Runge-Kutta numerical solution of a system of linear differential equations. Running time: To obtain 4 Master Integrals on PC with 2 GHz processor it takes 3 μs for series expansion with pre-calculated coefficients, 80 μs for series expansion without pre-calculated coefficients, from a few seconds up to a few minutes for Runge-Kutta method (depending on the required accuracy and the values of the physical parameters).

Linux OS Jitter Measurements at Large Node Counts using a BlueGene/L

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R; Tauferner, Mr. Andrew; Inglett, Mr. Todd

2010-01-01

We present experimental results for a coordinated scheduling implementation of the Linux operating system. Results were collected on an IBM Blue Gene/L machine at scales up to 16K nodes. Our results indicate coordinated scheduling was able to provide a dramatic improvement in scaling performance for two applications characterized as bulk synchronous parallel programs.

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

PubMed

Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian; Hippler, Michael

2011-04-15

We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily. Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at http://www.proteomatic.org. michael.specht@uni-muenster.de Supplementary data are available at Bioinformatics online.

ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases.

PubMed

Khan, Mohd Shoaib; Gupta, Amit Kumar; Kumar, Manoj

2016-01-01

To develop a computational resource for viral epigenomic methylation profiles from diverse diseases. Methylation patterns of Epstein-Barr virus and hepatitis B virus genomic regions are provided as web platform developed using open source Linux-Apache-MySQL-PHP (LAMP) bundle: programming and scripting languages, that is, HTML, JavaScript and PERL. A comprehensive and integrated web resource ViralEpi v1.0 is developed providing well-organized compendium of methylation events and statistical analysis associated with several diseases. Additionally, it also facilitates 'Viral EpiGenome Browser' for user-affable browsing experience using JavaScript-based JBrowse. This web resource would be helpful for research community engaged in studying epigenetic biomarkers for appropriate prognosis and diagnosis of diseases and its various stages.

SpecPad: device-independent NMR data visualization and processing based on the novel DART programming language and Html5 Web technology.

PubMed

Guigas, Bruno

2017-09-01

SpecPad is a new device-independent software program for the visualization and processing of one-dimensional and two-dimensional nuclear magnetic resonance (NMR) time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks. Another topic of interest is whether this technique also effectively supports the required sophisticated graphical and computational algorithms. SpecPad is device-independent because DART's compiled executable code is JavaScript and can, therefore, be run by the browsers of PCs and tablets. Because of Html5 browser cache technology, SpecPad may be operated off-line. Network access is only required during data import or export, e.g. via a Cloud service, or for software updates. A professional and easy to use graphical user interface consistent across all hardware platforms supports touch screen features on mobile devices for zooming and panning and for NMR-related interactive operations such as phasing, integration, peak picking, or atom assignment. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The orbifolder: A tool to study the low-energy effective theory of heterotic orbifolds

NASA Astrophysics Data System (ADS)

Nilles, H. P.; Ramos-Sánchez, S.; Vaudrevange, P. K. S.; Wingerter, A.

2012-06-01

The orbifolder is a program developed in C++ that computes and analyzes the low-energy effective theory of heterotic orbifold compactifications. The program includes routines to compute the massless spectrum, to identify the allowed couplings in the superpotential, to automatically generate large sets of orbifold models, to identify phenomenologically interesting models (e.g. MSSM-like models) and to analyze their vacuum configurations. Program summaryProgram title: orbifolder Catalogue identifier: AELR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 145 572 No. of bytes in distributed program, including test data, etc.: 930 517 Distribution format: tar.gz Programming language:C++ Computer: Personal computer Operating system: Tested on Linux (Fedora 15, Ubuntu 11, SuSE 11) Word size: 32 bits or 64 bits Classification: 11.1 External routines: Boost (http://www.boost.org/), GSL (http://www.gnu.org/software/gsl/) Nature of problem: Calculating the low-energy spectrum of heterotic orbifold compactifications. Solution method: Quadratic equations on a lattice; representation theory; polynomial algebra. Running time: Less than a second per model.

VizieR Online Data Catalog: Habitable zones around main-sequence stars (Kopparapu+, 2014)

NASA Astrophysics Data System (ADS)

Kopparapu, R. K.; Ramirez, R. M.; Schottelkotte, J.; Kasting, J. F.; Domagal-Goldman, S.; Eymet, V.

2017-08-01

Language: Fortran 90 Code tested under the following compilers/operating systems: ifort/CentOS linux Description of input data: No input necessary. Description of output data: Output files: HZs.dat, HZ_coefficients.dat System requirements: No major system requirement. Fortran compiler necessary. Calls to external routines: None. Additional comments: None (1 data file).

Real Time Linux - The RTOS for Astronomy?

NASA Astrophysics Data System (ADS)

Daly, P. N.

The BoF was attended by about 30 participants and a free CD of real time Linux-based upon RedHat 5.2-was available. There was a detailed presentation on the nature of real time Linux and the variants for hard real time: New Mexico Tech's RTL and DIAPM's RTAI. Comparison tables between standard Linux and real time Linux responses to time interval generation and interrupt response latency were presented (see elsewhere in these proceedings). The present recommendations are to use RTL for UP machines running the 2.0.x kernels and RTAI for SMP machines running the 2.2.x kernel. Support, both academically and commercially, is available. Some known limitations were presented and the solutions reported e.g., debugging and hardware support. The features of RTAI (scheduler, fifos, shared memory, semaphores, message queues and RPCs) were described. Typical performance statistics were presented: Pentium-based oneshot tasks running > 30kHz, 486-based oneshot tasks running at ~ 10 kHz, periodic timer tasks running in excess of 90 kHz with average zero jitter peaking to ~ 13 mus (UP) and ~ 30 mus (SMP). Some detail on kernel module programming, including coding examples, were presented showing a typical data acquisition system generating simulated (random) data writing to a shared memory buffer and a fifo buffer to communicate between real time Linux and user space. All coding examples were complete and tested under RTAI v0.6 and the 2.2.12 kernel. Finally, arguments were raised in support of real time Linux: it's open source, free under GPL, enables rapid prototyping, has good support and the ability to have a fully functioning workstation capable of co-existing hard real time performance. The counter weight-the negatives-of lack of platforms (x86 and PowerPC only at present), lack of board support, promiscuous root access and the danger of ignorance of real time programming issues were also discussed. See ftp://orion.tuc.noao.edu/pub/pnd/rtlbof.tgz for the StarOffice overheads for this presentation.

Adaptive Multilevel Middleware for Object Systems

DTIC Science & Technology

2006-12-01

the system at the system-call level or using the CORBA-standard Extensible Transport Framework ( ETF ). Transparent insertion is highly desirable from an...often as it needs to. This is remedied by using the real-time scheduling class in a stock Linux kernel. We used schedsetscheduler system call (with...real-time scheduling class (SCHEDFIFO) for all the ML-NFD programs, later experiments with CPU load indicate that a stock Linux kernel is not

Proposal of Network-Based Multilingual Space Dictionary Database System

NASA Astrophysics Data System (ADS)

Yoshimitsu, T.; Hashimoto, T.; Ninomiya, K.

2002-01-01

The International Academy of Astronautics (IAA) is now constructing a multilingual dictionary database system of space-friendly terms. The database consists of a lexicon and dictionaries of multiple languages. The lexicon is a table which relates corresponding terminology in different languages. Each language has a dictionary which contains terms and their definitions. The database assumes the use on the internet. Updating and searching the terms and definitions are conducted via the network. Maintaining the database is conducted by the international cooperation. A new word arises day by day, thus to easily input new words and their definitions to the database is required for the longstanding success of the system. The main key of the database is an English term which is approved at the table held once or twice with the working group members. Each language has at lease one working group member who is responsible of assigning the corresponding term and the definition of the term of his/her native language. Inputting and updating terms and their definitions can be conducted via the internet from the office of each member which may be located at his/her native country. The system is constructed by freely distributed database server program working on the Linux operating system, which will be installed at the head office of IAA. Once it is installed, it will be open to all IAA members who can search the terms via the internet. Currently the authors are constructing the prototype system which is described in this paper.

BOOK REVIEW: Numerical Recipes in C++: The Art of Scientific Computing (2nd edn)1 Numerical Recipes Example Book (C++) (2nd edn)2 Numerical Recipes Multi-Language Code CD ROM with LINUX or UNIX Single-Screen License Revised Version3Numerical Recipes in C++: The Art of Scientific Computing (2nd edn) Numerical Recipes Example Book (C++) (2nd edn) Numerical Recipes Multi-Language Code CD ROM with LINUX or UNIX Single-Screen License Revised Version

NASA Astrophysics Data System (ADS)

Press, William H.; Teukolsky, Saul A.; Vettering, William T.; Flannery, Brian P.

2003-05-01

The two Numerical Recipes books are marvellous. The principal book, The Art of Scientific Computing, contains program listings for almost every conceivable requirement, and it also contains a well written discussion of the algorithms and the numerical methods involved. The Example Book provides a complete driving program, with helpful notes, for nearly all the routines in the principal book. The first edition of Numerical Recipes: The Art of Scientific Computing was published in 1986 in two versions, one with programs in Fortran, the other with programs in Pascal. There were subsequent versions with programs in BASIC and in C. The second, enlarged edition was published in 1992, again in two versions, one with programs in Fortran (NR(F)), the other with programs in C (NR(C)). In 1996 the authors produced Numerical Recipes in Fortran 90: The Art of Parallel Scientific Computing as a supplement, called Volume 2, with the original (Fortran) version referred to as Volume 1. Numerical Recipes in C++ (NR(C++)) is another version of the 1992 edition. The numerical recipes are also available on a CD ROM: if you want to use any of the recipes, I would strongly advise you to buy the CD ROM. The CD ROM contains the programs in all the languages. When the first edition was published I bought it, and have also bought copies of the other editions as they have appeared. Anyone involved in scientific computing ought to have a copy of at least one version of Numerical Recipes, and there also ought to be copies in every library. If you already have NR(F), should you buy the NR(C++) and, if not, which version should you buy? In the preface to Volume 2 of NR(F), the authors say 'C and C++ programmers have not been far from our minds as we have written this volume, and we think that you will find that time spent in absorbing its principal lessons will be amply repaid in the future as C and C++ eventually develop standard parallel extensions'. In the preface and introduction to NR(C++), the authors point out some of the problems in the use of C++ in scientific computing. I have not found any mention of parallel computing in NR(C++). Fortran has quite a lot going for it. As someone who has used it in most of its versions from Fortran II, I have seen it develop and leave behind other languages promoted by various enthusiasts: who now uses Algol or Pascal? I think it unlikely that C++ will disappear: it was devised as a systems language, and can also be used for other purposes such as scientific computing. It is possible that Fortran will disappear, but Fortran has the strengths that it can develop, that there are extensive Fortran subroutine libraries, and that it has been developed for parallel computing. To argue with programmers as to which is the best language to use is sterile. If you wish to use C++, then buy NR(C++), but you should also look at volume 2 of NR(F). If you are a Fortran programmer, then make sure you have NR(F), volumes 1 and 2. But whichever language you use, make sure you have one version or the other, and the CD ROM. The Example Book provides listings of complete programs to run nearly all the routines in NR, frequently based on cases where an anlytical solution is available. It is helpful when developing a new program incorporating an unfamiliar routine to see that routine actually working, and this is what the programs in the Example Book achieve. I started teaching computational physics before Numerical Recipes was published. If I were starting again, I would make heavy use of both The Art of Scientific Computing and of the Example Book. Every computational physics teaching laboratory should have both volumes: the programs in the Example Book are included on the CD ROM, but the extra commentary in the book itself is of considerable value. P Borcherds

Development of EPA Protocol Information Enquiry Service System Based on Embedded ARM Linux

NASA Astrophysics Data System (ADS)

Peng, Daogang; Zhang, Hao; Weng, Jiannian; Li, Hui; Xia, Fei

Industrial Ethernet is a new technology for industrial network communications developed in recent years. In the field of industrial automation in China, EPA is the first standard accepted and published by ISO, and has been included in the fourth edition IEC61158 Fieldbus of NO.14 type. According to EPA standard, Field devices such as industrial field controller, actuator and other instruments are all able to realize communication based on the Ethernet standard. The Atmel AT91RM9200 embedded development board and open source embedded Linux are used to develop an information inquiry service system of EPA protocol based on embedded ARM Linux in this paper. The system is capable of designing an EPA Server program for EPA data acquisition procedures, the EPA information inquiry service is available for programs in local or remote host through Socket interface. The EPA client can access data and information of other EPA equipments on the EPA network when it establishes connection with the monitoring port of the server.

ALPHACAL: A new user-friendly tool for the calibration of alpha-particle sources.

PubMed

Timón, A Fernández; Vargas, M Jurado; Gallardo, P Álvarez; Sánchez-Oro, J; Peralta, L

2018-05-01

In this work, we present and describe the program ALPHACAL, specifically developed for the calibration of alpha-particle sources. It is therefore more user-friendly and less time-consuming than multipurpose codes developed for a wide range of applications. The program is based on the recently developed code AlfaMC, which simulates specifically the transport of alpha particles. Both cylindrical and point sources mounted on the surface of polished backings can be simulated, as is the convention in experimental measurements of alpha-particle sources. In addition to the efficiency calculation and determination of the backscattering coefficient, some additional tools are available to the user, like the visualization of energy spectrum, use of energy cut-off or low-energy tail corrections. ALPHACAL has been implemented in C++ language using QT library, so it is available for Windows, MacOs and Linux platforms. It is free and can be provided under request to the authors. Copyright © 2018 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wahanani, Nursinta Adi, E-mail: sintaadi@batan.go.id; Natsir, Khairina, E-mail: sintaadi@batan.go.id; Hartini, Entin, E-mail: sintaadi@batan.go.id

Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this softwaremore » 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu{sup 239} and Pu{sup 241}. Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis.« less

FORM version 4.0

NASA Astrophysics Data System (ADS)

Kuipers, J.; Ueda, T.; Vermaseren, J. A. M.; Vollinga, J.

2013-05-01

We present version 4.0 of the symbolic manipulation system FORM. The most important new features are manipulation of rational polynomials and the factorization of expressions. Many other new functions and commands are also added; some of them are very general, while others are designed for building specific high level packages, such as one for Gröbner bases. New is also the checkpoint facility, that allows for periodic backups during long calculations. Finally, FORM 4.0 has become available as open source under the GNU General Public License version 3. Program summaryProgram title: FORM. Catalogue identifier: AEOT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 151599 No. of bytes in distributed program, including test data, etc.: 1 078 748 Distribution format: tar.gz Programming language: The FORM language. FORM itself is programmed in a mixture of C and C++. Computer: All. Operating system: UNIX, LINUX, Mac OS, Windows. Classification: 5. Nature of problem: FORM defines a symbolic manipulation language in which the emphasis lies on fast processing of very large formulas. It has been used successfully for many calculations in Quantum Field Theory and mathematics. In speed and size of formulas that can be handled it outperforms other systems typically by an order of magnitude. Special in this version: The version 4.0 contains many new features. Most important are factorization and rational arithmetic. The program has also become open source under the GPL. The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes. Solution method: See "Nature of Problem", above. Additional comments: NOTE: The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes.

PLATYPUS: A code for reaction dynamics of weakly-bound nuclei at near-barrier energies within a classical dynamical model

NASA Astrophysics Data System (ADS)

Diaz-Torres, Alexis

2011-04-01

A self-contained Fortran-90 program based on a three-dimensional classical dynamical reaction model with stochastic breakup is presented, which is a useful tool for quantifying complete and incomplete fusion, and breakup in reactions induced by weakly-bound two-body projectiles near the Coulomb barrier. The code calculates (i) integrated complete and incomplete fusion cross sections and their angular momentum distribution, (ii) the excitation energy distribution of the primary incomplete-fusion products, (iii) the asymptotic angular distribution of the incomplete-fusion products and the surviving breakup fragments, and (iv) breakup observables, such as angle, kinetic energy and relative energy distributions. Program summaryProgram title: PLATYPUS Catalogue identifier: AEIG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 332 342 No. of bytes in distributed program, including test data, etc.: 344 124 Distribution format: tar.gz Programming language: Fortran-90 Computer: Any Unix/Linux workstation or PC with a Fortran-90 compiler Operating system: Linux or Unix RAM: 10 MB Classification: 16.9, 17.7, 17.8, 17.11 Nature of problem: The program calculates a wide range of observables in reactions induced by weakly-bound two-body nuclei near the Coulomb barrier. These include integrated complete and incomplete fusion cross sections and their spin distribution, as well as breakup observables (e.g. the angle, kinetic energy, and relative energy distributions of the fragments). Solution method: All the observables are calculated using a three-dimensional classical dynamical model combined with the Monte Carlo sampling of probability-density distributions. See Refs. [1,2] for further details. Restrictions: The program is suited for a weakly-bound two-body projectile colliding with a stable target. The initial orientation of the segment joining the two breakup fragments is considered to be isotropic. Additional comments: Several source routines from Numerical Recipies, and the Mersenne Twister random number generator package are included to enable independent compilation. Running time: About 75 minutes for input provided, using a PC with 1.5 GHz processor.

Switching the JLab Accelerator Operations Environment from an HP-UX Unix-based to a PC/Linux-based environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mcguckin, Theodore

2008-10-01

The Jefferson Lab Accelerator Controls Environment (ACE) was predominantly based on the HP-UX Unix platform from 1987 through the summer of 2004. During this period the Accelerator Machine Control Center (MCC) underwent a major renovation which included introducing Redhat Enterprise Linux machines, first as specialized process servers and then gradually as general login servers. As computer programs and scripts required to run the accelerator were modified, and inherent problems with the HP-UX platform compounded, more development tools became available for use with Linux and the MCC began to be converted over. In May 2008 the last HP-UX Unix login machinemore » was removed from the MCC, leaving only a few Unix-based remote-login servers still available. This presentation will explore the process of converting an operational Control Room environment from the HP-UX to Linux platform as well as the many hurdles that had to be overcome throughout the transition period (including a discussion of« less

A PC parallel port button box provides millisecond response time accuracy under Linux.

PubMed

Stewart, Neil

2006-02-01

For psychologists, it is sometimes necessary to measure people's reaction times to the nearest millisecond. This article describes how to use the PC parallel port to receive signals from a button box to achieve millisecond response time accuracy. The workings of the parallel port, the corresponding port addresses, and a simple Linux program for controlling the port are described. A test of the speed and reliability of button box signal detection is reported. If the reader is moderately familiar with Linux, this article should provide sufficient instruction for him or her to build and test his or her own parallel port button box. This article also describes how the parallel port could be used to control an external apparatus.

A Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing (SAPE)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2009-01-01

SAPE is a Python-based multidisciplinary analysis tool for systems analysis of planetary entry, descent, and landing (EDL) for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. The purpose of SAPE is to provide a variable-fidelity capability for conceptual and preliminary analysis within the same framework. SAPE includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and structural sizing. SAPE uses the Python language-a platform-independent open-source software for integration and for the user interface. The development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE runs on Microsoft Windows and Apple Mac OS X and has been partially tested on Linux.

WebBio, a web-based management and analysis system for patient data of biological products in hospital.

PubMed

Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

2011-08-01

We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

Development of EnergyPlus Utility to Batch Simulate Building Energy Performance on a National Scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valencia, Jayson F.; Dirks, James A.

2008-08-29

EnergyPlus is a simulation program that requires a large number of details to fully define and model a building. Hundreds or even thousands of lines in a text file are needed to run the EnergyPlus simulation depending on the size of the building. To manually create these files is a time consuming process that would not be practical when trying to create input files for thousands of buildings needed to simulate national building energy performance. To streamline the process needed to create the input files for EnergyPlus, two methods were created to work in conjunction with the National Renewable Energymore » Laboratory (NREL) Preprocessor; this reduced the hundreds of inputs needed to define a building in EnergyPlus to a small set of high-level parameters. The first method uses Java routines to perform all of the preprocessing on a Windows machine while the second method carries out all of the preprocessing on the Linux cluster by using an in-house built utility called Generalized Parametrics (GPARM). A comma delimited (CSV) input file is created to define the high-level parameters for any number of buildings. Each method then takes this CSV file and uses the data entered for each parameter to populate an extensible markup language (XML) file used by the NREL Preprocessor to automatically prepare EnergyPlus input data files (idf) using automatic building routines and macro templates. Using a Linux utility called “make”, the idf files can then be automatically run through the Linux cluster and the desired data from each building can be aggregated into one table to be analyzed. Creating a large number of EnergyPlus input files results in the ability to batch simulate building energy performance and scale the result to national energy consumption estimates.« less

Enhancements to the Sentinel Fireball Network Video Software

NASA Astrophysics Data System (ADS)

Watson, Wayne

2009-05-01

The Sentinel Fireball Network that supports meteor imaging of bright meteors (fireballs) has been in existence for over ten years. Nearly five years ago it moved from gathering meteor data with a camera and VCR video tape to a fisheye lens attached to a hardware device, the Sentinel box, which allowed meteor data to be recorded on a PC operating under real-time Linux. In 2006, that software, sentuser, was made available on Apple, Linux, and Window operating systems using the Python computer language. It provides basic video and management functionality and a small amount of analytic software capability. This paper describes the new and attractive future features of the software, and, additionally, it reviews some of the research and networks from the past and present using video equipment to collect and analyze fireball data that have applicability to sentuser.

Space Communications Emulation Facility

NASA Technical Reports Server (NTRS)

Hill, Chante A.

2004-01-01

Establishing space communication between ground facilities and other satellites is a painstaking task that requires many precise calculations dealing with relay time, atmospheric conditions, and satellite positions, to name a few. The Space Communications Emulation Facility (SCEF) team here at NASA is developing a facility that will approximately emulate the conditions in space that impact space communication. The emulation facility is comprised of a 32 node distributed cluster of computers; each node representing a satellite or ground station. The objective of the satellites is to observe the topography of the Earth (water, vegetation, land, and ice) and relay this information back to the ground stations. Software originally designed by the University of Kansas, labeled the Emulation Manager, controls the interaction of the satellites and ground stations, as well as handling the recording of data. The Emulation Manager is installed on a Linux Operating System, employing both Java and C++ programming codes. The emulation scenarios are written in extensible Markup Language, XML. XML documents are designed to store, carry, and exchange data. With XML documents data can be exchanged between incompatible systems, which makes it ideal for this project because Linux, MAC and Windows Operating Systems are all used. Unfortunately, XML documents cannot display data like HTML documents. Therefore, the SCEF team uses XML Schema Definition (XSD) or just schema to describe the structure of an XML document. Schemas are very important because they have the capability to validate the correctness of data, define restrictions on data, define data formats, and convert data between different data types, among other things. At this time, in order for the Emulation Manager to open and run an XML emulation scenario file, the user must first establish a link between the schema file and the directory under which the XML scenario files are saved. This procedure takes place on the command line on the Linux Operating System. Once this link has been established the Emulation manager validates all the XML files in that directory against the schema file, before the actual scenario is run. Using some very sophisticated commercial software called the Satellite Tool Kit (STK) installed on the Linux box, the Emulation Manager is able to display the data and graphics generated by the execution of a XML emulation scenario file. The Emulation Manager software is written in JAVA programming code. Since the SCEF project is in the developmental stage, the source code for this type of software is being modified to better fit the requirements of the SCEF project. Some parameters for the emulation are hard coded, set at fixed values. Members of the SCEF team are altering the code to allow the user to choose the values of these hard coded parameters by inserting a toolbar onto the preexisting GUI.

Video-Game-Like Engine for Depicting Spacecraft Trajectories

NASA Technical Reports Server (NTRS)

Upchurch, Paul R.

2009-01-01

GoView is a video-game-like software engine, written in the C and C++ computing languages, that enables real-time, three-dimensional (3D)-appearing visual representation of spacecraft and trajectories (1) from any perspective; (2) at any spatial scale from spacecraft to Solar-system dimensions; (3) in user-selectable time scales; (4) in the past, present, and/or future; (5) with varying speeds; and (6) forward or backward in time. GoView constructs an interactive 3D world by use of spacecraft-mission data from pre-existing engineering software tools. GoView can also be used to produce distributable application programs for depicting NASA orbital missions on personal computers running the Windows XP, Mac OsX, and Linux operating systems. GoView enables seamless rendering of Cartesian coordinate spaces with programmable graphics hardware, whereas prior programs for depicting spacecraft trajectories variously require non-Cartesian coordinates and/or are not compatible with programmable hardware. GoView incorporates an algorithm for nonlinear interpolation between arbitrary reference frames, whereas the prior programs are restricted to special classes of inertial and non-inertial reference frames. Finally, whereas the prior programs present complex user interfaces requiring hours of training, the GoView interface provides guidance, enabling use without any training.

Processable Data Making in the Remote Server Sent by Android Phone as a GIS Data Collecting Tool

NASA Astrophysics Data System (ADS)

Karaagac, Abdullah; Bostancı, Bulent

2016-04-01

Mobile technologies are improving and getting cheaper everyday. Not only smart phones are improved much but also new types of mobile applications and sensors come with the smart phone together. Maps and navigation applications one of the most popular types of applications on these types. Most of these applications uses location services including GNSS, Wi Fi, cellular data and beacon services. Although these coordinate precision not very high, it is appropriate for many applications to utilize. Android is a mobile operating system based on Linux Kernel. It is compatible for varies mobile devices like smart phones, tablets, smart TV's, wearable technologies etc. Android has large capability for application development by using the open source libraries and device sensors like gyroscope, GNSS etc. Android Studio is the most popular integrated development environment (IDE) for Android devices, mainly developing by Google. It had been announced on May 16, 2013 at Google I/O conference. Android Studio is built upon Gradle architecture which is written in Java language. SQLite is a relational database operating system which has so common usage for mobile devices. It developed by using C programming library. It is mostly used via embedding into a software or application. It supports many operating systems including Android. Remote servers can be in several forms from high complexity to simplicity. For this project we will use a open source quad core board computer named Raspberry Pi 2. This device includes 900 MHz ARMv7 compatible quad core CPU, VideoCore IV GPU and 1 GB RAM. Although Raspberry Pi 2's main operating system is Raspbian, we use Debian which are both Linux based operating systems. Raspberry is compatible for many programming language, however some languages are optimized for this device. These are Python, Java, C, C++, Ruby, Perl and Squeak Smalltalk. In this paper, a mobile application will be developed to send coordinate and string data to a SQL database embedded to a remote server. The application will run on Android Operating System running mobile phone. The application will get the location information from the GNSS and cellular data. The user will enter the other information individually. These information will send by clicking a button to remote server which runs SQLite. All these informations will be convertible to any type of measure like type of coordinates could be converted from WGS 84 to ITRF.

AESS: Accelerated Exact Stochastic Simulation

NASA Astrophysics Data System (ADS)

Jenkins, David D.; Peterson, Gregory D.

2011-12-01

The Stochastic Simulation Algorithm (SSA) developed by Gillespie provides a powerful mechanism for exploring the behavior of chemical systems with small species populations or with important noise contributions. Gene circuit simulations for systems biology commonly employ the SSA method, as do ecological applications. This algorithm tends to be computationally expensive, so researchers seek an efficient implementation of SSA. In this program package, the Accelerated Exact Stochastic Simulation Algorithm (AESS) contains optimized implementations of Gillespie's SSA that improve the performance of individual simulation runs or ensembles of simulations used for sweeping parameters or to provide statistically significant results. Program summaryProgram title: AESS Catalogue identifier: AEJW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: University of Tennessee copyright agreement No. of lines in distributed program, including test data, etc.: 10 861 No. of bytes in distributed program, including test data, etc.: 394 631 Distribution format: tar.gz Programming language: C for processors, CUDA for NVIDIA GPUs Computer: Developed and tested on various x86 computers and NVIDIA C1060 Tesla and GTX 480 Fermi GPUs. The system targets x86 workstations, optionally with multicore processors or NVIDIA GPUs as accelerators. Operating system: Tested under Ubuntu Linux OS and CentOS 5.5 Linux OS Classification: 3, 16.12 Nature of problem: Simulation of chemical systems, particularly with low species populations, can be accurately performed using Gillespie's method of stochastic simulation. Numerous variations on the original stochastic simulation algorithm have been developed, including approaches that produce results with statistics that exactly match the chemical master equation (CME) as well as other approaches that approximate the CME. Solution method: The Accelerated Exact Stochastic Simulation (AESS) tool provides implementations of a wide variety of popular variations on the Gillespie method. Users can select the specific algorithm considered most appropriate. Comparisons between the methods and with other available implementations indicate that AESS provides the fastest known implementation of Gillespie's method for a variety of test models. Users may wish to execute ensembles of simulations to sweep parameters or to obtain better statistical results, so AESS supports acceleration of ensembles of simulation using parallel processing with MPI, SSE vector units on x86 processors, and/or using NVIDIA GPUs with CUDA.

PyEPL: a cross-platform experiment-programming library.

PubMed

Geller, Aaron S; Schlefer, Ian K; Sederberg, Per B; Jacobs, Joshua; Kahana, Michael J

2007-11-01

PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments forspatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL.

PyEPL: A cross-platform experiment-programming library

PubMed Central

Geller, Aaron S.; Schleifer, Ian K.; Sederberg, Per B.; Jacobs, Joshua; Kahana, Michael J.

2009-01-01

PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments for spatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL. PMID:18183912

Reduze - Feynman integral reduction in C++

NASA Astrophysics Data System (ADS)

Studerus, C.

2010-07-01

Reduze is a computer program for reducing Feynman integrals to master integrals employing a Laporta algorithm. The program is written in C++ and uses classes provided by the GiNaC library to perform the simplifications of the algebraic prefactors in the system of equations. Reduze offers the possibility to run reductions in parallel. Program summaryProgram title:Reduze Catalogue identifier: AEGE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:: yes No. of lines in distributed program, including test data, etc.: 55 433 No. of bytes in distributed program, including test data, etc.: 554 866 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Unix/Linux Number of processors used: The number of processors is problem dependent. More than one possible but not arbitrary many. RAM: Depends on the complexity of the system. Classification: 4.4, 5 External routines: CLN ( http://www.ginac.de/CLN/), GiNaC ( http://www.ginac.de/) Nature of problem: Solving large systems of linear equations with Feynman integrals as unknowns and rational polynomials as prefactors. Solution method: Using a Gauss/Laporta algorithm to solve the system of equations. Restrictions: Limitations depend on the complexity of the system (number of equations, number of kinematic invariants). Running time: Depends on the complexity of the system.

Software for Processing of Digitized Astronegatives from Archives and Databases of Virtual Observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Yu. I.; Andruk, V. N.; Kazantseva, L. V.

The paper discusses and illustrates the steps of basic processing of digitized image of astro negatives. Software for obtaining of a rectangular coordinates and photometric values of objects on photographic plates was created in the environment LINUX / MIDAS / ROMAFOT. The program can automatically process the specified number of files in FITS format with sizes up to 20000 x 20000 pixels. Other programs were made in FORTRAN and PASCAL with the ability to work in an environment of LINUX or WINDOWS. They were used for: identification of stars, separation and exclusion of diffraction satellites and double and triple exposures, elimination of image defects, reduction to the equatorial coordinates and magnitudes of a reference catalogs.

mr: A C++ library for the matching and running of the Standard Model parameters

NASA Astrophysics Data System (ADS)

Kniehl, Bernd A.; Pikelner, Andrey F.; Veretin, Oleg L.

2016-09-01

We present the C++ program library mr that allows us to reliably calculate the values of the running parameters in the Standard Model at high energy scales. The initial conditions are obtained by relating the running parameters in the MS bar renormalization scheme to observables at lower energies with full two-loop precision. The evolution is then performed in accordance with the renormalization group equations with full three-loop precision. Pure QCD corrections to the matching and running are included through four loops. We also provide a Mathematica interface for this program library. Catalogue identifier: AFAI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFAI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 517613 No. of bytes in distributed program, including test data, etc.: 2358729 Distribution format: tar.gz Programming language: C++. Computer: IBM PC. Operating system: Linux, Mac OS X. RAM: 1 GB Classification: 11.1. External routines: TSIL [1], OdeInt [2], boost [3] Nature of problem: The running parameters of the Standard Model renormalized in the MS bar scheme at some high renormalization scale, which is chosen by the user, are evaluated in perturbation theory as precisely as possible in two steps. First, the initial conditions at the electroweak energy scale are evaluated from the Fermi constant GF and the pole masses of the W, Z, and Higgs bosons and the bottom and top quarks including the full two-loop threshold corrections. Second, the evolution to the high energy scale is performed by numerically solving the renormalization group evolution equations through three loops. Pure QCD corrections to the matching and running are included through four loops. Solution method: Numerical integration of analytic expressions Additional comments: Available for download from URL: http://apik.github.io/mr/. The MathLink interface is tested to work with Mathematica 7-9 and, with an additional flag, also with Mathematica 10 under Linux and with Mathematica 10 under Mac OS X. Running time: less than 1 second References: [1] S. P. Martin and D. G. Robertson, Comput. Phys. Commun. 174 (2006) 133-151 [hep-ph/0501132]. [2] K. Ahnert and M. Mulansky, AIP Conf. Proc. 1389 (2011) 1586-1589 [arxiv:1110.3397 [cs.MS

jSynthesizer: A Java based first-motion synthetic seismogram tool

NASA Astrophysics Data System (ADS)

Sullivan, Mark

2009-10-01

Both researchers and educators need software tools to create synthetic seismograms to model earthquake sources. We have developed a program that generates first-motion synthetic seismograms that is highly interactive and suited to the needs of both research and education audiences. Implemented in the Java programming language, our program is available for use on Windows, Mac OS X and Linux operating systems. Our program allows the user to input the fault parameters strike, dip and slip angle, numerically or graphically using a lower hemisphere equal-area stereographic projection of the focal sphere of the earthquake. This representation is familiar to geologists and seismologists as the standard way of displaying the orientation of a fault in space. The user is also able to enter the relative location of the seismograph and the depth and crustal velocity structure in the vicinity of the earthquake. The direct P wave along with reflections off of layer boundaries near the source are generated using a constant ray-parameter approximation. The instrument response functions used by the Worldwide Standardized Seismogram Network and the attenuation response of the Earth's mantle are generated in the frequency domain and applied to generate the synthetic seismogram. Planned enhancements to this program will allow the simultaneous generation of seismograms at many stations as well as more complicated crustal structures.

Progress on China nuclear data processing code system

NASA Astrophysics Data System (ADS)

Liu, Ping; Wu, Xiaofei; Ge, Zhigang; Li, Songyang; Wu, Haicheng; Wen, Lili; Wang, Wenming; Zhang, Huanyu

2017-09-01

China is developing the nuclear data processing code Ruler, which can be used for producing multi-group cross sections and related quantities from evaluated nuclear data in the ENDF format [1]. The Ruler includes modules for reconstructing cross sections in all energy range, generating Doppler-broadened cross sections for given temperature, producing effective self-shielded cross sections in unresolved energy range, calculating scattering cross sections in thermal energy range, generating group cross sections and matrices, preparing WIMS-D format data files for the reactor physics code WIMS-D [2]. Programming language of the Ruler is Fortran-90. The Ruler is tested for 32-bit computers with Windows-XP and Linux operating systems. The verification of Ruler has been performed by comparison with calculation results obtained by the NJOY99 [3] processing code. The validation of Ruler has been performed by using WIMSD5B code.

Geospatial Authentication

NASA Technical Reports Server (NTRS)

Lyle, Stacey D.

2009-01-01

A software package that has been designed to allow authentication for determining if the rover(s) is/are within a set of boundaries or a specific area to access critical geospatial information by using GPS signal structures as a means to authenticate mobile devices into a network wirelessly and in real-time has been developed. The advantage lies in that the system only allows those with designated geospatial boundaries or areas into the server. The Geospatial Authentication software has two parts Server and Client. The server software is a virtual private network (VPN) developed in Linux operating system using Perl programming language. The server can be a stand-alone VPN server or can be combined with other applications and services. The client software is a GUI Windows CE software, or Mobile Graphical Software, that allows users to authenticate into a network. The purpose of the client software is to pass the needed satellite information to the server for authentication.

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs.

PubMed

Mishima, Hiroyuki; Lidral, Andrew C; Ni, Jun

2008-05-28

Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4-15.9 times faster, while Unphased jobs performed 1.1-18.6 times faster compared to the accumulated computation duration. Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance.

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs

PubMed Central

Mishima, Hiroyuki; Lidral, Andrew C; Ni, Jun

2008-01-01

Background Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Results Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4–15.9 times faster, while Unphased jobs performed 1.1–18.6 times faster compared to the accumulated computation duration. Conclusion Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance. PMID:18541045

A Business Case Study of Open Source Software

DTIC Science & Technology

2001-07-01

LinuxPPC LinuxPPC www.linuxppc.com MandrakeSoft Linux -Mandrake www.linux-mandrake.com/ en / CLE Project CLE cle.linux.org.tw/CLE/e_index.shtml Red Hat... en Coyote Linux www2.vortech.net/coyte/coyte.htm MNIS www.mnis.fr Data-Portal www.data-portal.com Mr O’s Linux Emporium www.ouin.com DLX Linux www.wu...1998 1999 Year S h ip m en ts ( in m ill io n s) Source: IDC, 2000. Figure 11. Worldwide New Linux Shipments (Client and Server) 3.2.2 Market

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

PubMed

Takeuchi, Toshiki; Yamada, Atsuo; Aoki, Takashi; Nishimura, Kunihiro

2016-01-01

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required. We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure. Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.

Improvement of the software Bernese for SLR data processing in the Main Metrological Centre of the State Time and Frequency Service

NASA Astrophysics Data System (ADS)

Tsyba, E.; Kaufman, M.

2015-08-01

Preparatory works for resuming operational calculations of the Earth rotation parameters based on the results of satellite laser ranging data processing (LAGEOS 1, LAGEOS 2) are to be completed in the Main Metrology Centre Of The State Time And Frequency Service (VNIIFTRI) in 2014. For this purpose BERNESE 5.2 software (Dach & Walser, 2014) was chosen as a base software which has been used for many years in the Main Metrological Centre of the State Time and Frequency Service to process phase observations of GLONASS and GPS satellites. Although in the BERNESE 5.2 software announced presentation the possibility of the SLR data processing is declared, it has not been fully implemented. In particular there is no such an essential element as corrective action (as input or resulting parameters) in the local time scale ("time bias"), etc. Therefore, additional program blocks have been developed and integrated into the BERNESE 5.2 software environment. The program blocks are written in Perl and Matlab program languages and can be used both for Windows and Linux, 32-bit and 64-bit platforms.

Software for Displaying Data from Planetary Rovers

NASA Technical Reports Server (NTRS)

Powell, Mark; Backers, Paul; Norris, Jeffrey; Vona, Marsette; Steinke, Robert

2003-01-01

Science Activity Planner (SAP) DownlinkBrowser is a computer program that assists in the visualization of processed telemetric data [principally images, image cubes (that is, multispectral images), and spectra] that have been transmitted to Earth from exploratory robotic vehicles (rovers) on remote planets. It is undergoing adaptation to (1) the Field Integrated Design and Operations (FIDO) rover (a prototype Mars-exploration rover operated on Earth as a test bed) and (2) the Mars Exploration Rover (MER) mission. This program has evolved from its predecessor - the Web Interface for Telescience (WITS) software - and surpasses WITS in the processing, organization, and plotting of data. SAP DownlinkBrowser creates Extensible Markup Language (XML) files that organize data files, on the basis of content, into a sortable, searchable product database, without the overhead of a relational database. The data-display components of SAP DownlinkBrowser (descriptively named ImageView, 3DView, OrbitalView, PanoramaView, ImageCubeView, and SpectrumView) are designed to run in a memory footprint of at least 256MB on computers that utilize the Windows, Linux, and Solaris operating systems.

Grid Visualization Tool

NASA Technical Reports Server (NTRS)

Chouinard, Caroline; Fisher, Forest; Estlin, Tara; Gaines, Daniel; Schaffer, Steven

2005-01-01

The Grid Visualization Tool (GVT) is a computer program for displaying the path of a mobile robotic explorer (rover) on a terrain map. The GVT reads a map-data file in either portable graymap (PGM) or portable pixmap (PPM) format, representing a gray-scale or color map image, respectively. The GVT also accepts input from path-planning and activity-planning software. From these inputs, the GVT generates a map overlaid with one or more rover path(s), waypoints, locations of targets to be explored, and/or target-status information (indicating success or failure in exploring each target). The display can also indicate different types of paths or path segments, such as the path actually traveled versus a planned path or the path traveled to the present position versus planned future movement along a path. The program provides for updating of the display in real time to facilitate visualization of progress. The size of the display and the map scale can be changed as desired by the user. The GVT was written in the C++ language using the Open Graphics Library (OpenGL) software. It has been compiled for both Sun Solaris and Linux operating systems.

XVD Image Display Program

NASA Technical Reports Server (NTRS)

Deen, Robert G.; Andres, Paul M.; Mortensen, Helen B.; Parizher, Vadim; McAuley, Myche; Bartholomew, Paul

2009-01-01

The XVD [X-Windows VICAR (video image communication and retrieval) Display] computer program offers an interactive display of VICAR and PDS (planetary data systems) images. It is designed to efficiently display multiple-GB images and runs on Solaris, Linux, or Mac OS X systems using X-Windows.

Migration of the Three-dimensional Wind Field (3DWF) Model from Linux to Windows and Mobile Platforms

DTIC Science & Technology

2017-11-01

7 Fig. 10 Build executable code ........................................................................... 8 Fig. 11 3DWF GUI’s main web ...can be designed in any Windows operating system with internet access via Microsoft’s Internet Explorer (IE) web browser. For this particular project...Therefore, it is advised to have network security safeguards in place and operate only in a trusted PC. The GUI’s Hypertext Markup Language (HTML) web

Mapping, Awareness, and Virtualization Network Administrator Training Tool (MAVNATT) Architecture and Framework

DTIC Science & Technology

2015-06-01

unit may setup and teardown the entire tactical infrastructure multiple times per day. This tactical network administrator training is a critical...language and runs on Linux and Unix based systems. All provisioning is based around the Nagios Core application, a powerful backend solution for network...start up a large number of virtual machines quickly. CORE supports the simulation of fixed and mobile networks. CORE is open-source, written in Python

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

NASA Astrophysics Data System (ADS)

Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

2010-09-01

The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full documentation is provided in the distribution file. This includes an INSTALL file giving details of how to build the package. A set of test runs is provided in the examples directory. The distribution file for this program is over 90 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or ab-initio molecular dynamics simulation on hundreds of atoms.

Runwien: a text-based interface for the WIEN package

NASA Astrophysics Data System (ADS)

Otero de la Roza, A.; Luaña, Víctor

2009-05-01

A new text-based interface for WIEN2k, the full-potential linearized augmented plane-waves (FPLAPW) program, is presented. This code provides an easy to use, yet powerful way of generating arbitrarily large sets of calculations. Thus, properties over a potential energy surface and WIEN2k parameter exploration can be calculated using a simple input text file. This interface also provides new capabilities to the WIEN2k package, such as the calculation of elastic constants on hexagonal systems or the automatic gathering of relevant information. Additionally, runwien is modular, flexible and intuitive. Program summaryProgram title: runwien Catalogue identifier: AECM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL version 3 No. of lines in distributed program, including test data, etc.: 62 567 No. of bytes in distributed program, including test data, etc.: 610 973 Distribution format: tar.gz Programming language: gawk (with locale POSIX or similar) Computer: All running Unix, Linux Operating system: Unix, GNU/Linux Classification: 7.3 External routines: WIEN2k ( http://www.wien2k.at/), GAWK ( http://www.gnu.org/software/gawk/), rename by L. Wall, a Perl script which renames files, modified by R. Barker to check for the existence of target files, gnuplot ( http://www.gnuplot.info/) Subprograms used:Cat Id: ADSY_v1_0/AECB_v1_0, Title: GIBBS/CRITIC, Reference: CPC 158 (2004) 57/CPC 999 (2009) 999 Nature of problem: Creation of a text-based, batch-oriented interface for the WIEN2k package. Solution method: WIEN2k solves the Kohn-Sham equations of a solid using the FPLAPW formalism. Runwien interprets an input file containing the description of the geometry and structure of the solid and drives the execution of the WIEN2k programs. The input is simplified thanks to the default values of the WIEN2k parameters known to runwien. Additional comments: Designed for WIEN2k versions 06.4, 07.2, 08.2, and 08.3. Running time: For the test case (TiC), a single geometry takes 5 to 10 minutes on a typical desktop PC (Intel Pentium 4, 3.4 GHz, 1 GB RAM). The full example including the calculation of the elastic constants and the equation of state, takes 9 hours and 32 minutes.

LXtoo: an integrated live Linux distribution for the bioinformatics community

PubMed Central

2012-01-01

Background Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Findings Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. Conclusions LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo. PMID:22813356

LXtoo: an integrated live Linux distribution for the bioinformatics community.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

2012-07-19

Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

Modules based on the geochemical model PHREEQC for use in scripting and programming languages

USGS Publications Warehouse

Charlton, Scott R.; Parkhurst, David L.

2011-01-01

The geochemical model PHREEQC is capable of simulating a wide range of equilibrium reactions between water and minerals, ion exchangers, surface complexes, solid solutions, and gases. It also has a general kinetic formulation that allows modeling of nonequilibrium mineral dissolution and precipitation, microbial reactions, decomposition of organic compounds, and other kinetic reactions. To facilitate use of these reaction capabilities in scripting languages and other models, PHREEQC has been implemented in modules that easily interface with other software. A Microsoft COM (component object model) has been implemented, which allows PHREEQC to be used by any software that can interface with a COM server—for example, Excel®, Visual Basic®, Python, or MATLAB". PHREEQC has been converted to a C++ class, which can be included in programs written in C++. The class also has been compiled in libraries for Linux and Windows that allow PHREEQC to be called from C++, C, and Fortran. A limited set of methods implements the full reaction capabilities of PHREEQC for each module. Input methods use strings or files to define reaction calculations in exactly the same formats used by PHREEQC. Output methods provide a table of user-selected model results, such as concentrations, activities, saturation indices, and densities. The PHREEQC module can add geochemical reaction capabilities to surface-water, groundwater, and watershed transport models. It is possible to store and manipulate solution compositions and reaction information for many cells within the module. In addition, the object-oriented nature of the PHREEQC modules simplifies implementation of parallel processing for reactive-transport models. The PHREEQC COM module may be used in scripting languages to fit parameters; to plot PHREEQC results for field, laboratory, or theoretical investigations; or to develop new models that include simple or complex geochemical calculations.

Modules based on the geochemical model PHREEQC for use in scripting and programming languages

USGS Publications Warehouse

Charlton, S.R.; Parkhurst, D.L.

2011-01-01

The geochemical model PHREEQC is capable of simulating a wide range of equilibrium reactions between water and minerals, ion exchangers, surface complexes, solid solutions, and gases. It also has a general kinetic formulation that allows modeling of nonequilibrium mineral dissolution and precipitation, microbial reactions, decomposition of organic compounds, and other kinetic reactions. To facilitate use of these reaction capabilities in scripting languages and other models, PHREEQC has been implemented in modules that easily interface with other software. A Microsoft COM (component object model) has been implemented, which allows PHREEQC to be used by any software that can interface with a COM server-for example, Excel??, Visual Basic??, Python, or MATLAB??. PHREEQC has been converted to a C++ class, which can be included in programs written in C++. The class also has been compiled in libraries for Linux and Windows that allow PHREEQC to be called from C++, C, and Fortran. A limited set of methods implements the full reaction capabilities of PHREEQC for each module. Input methods use strings or files to define reaction calculations in exactly the same formats used by PHREEQC. Output methods provide a table of user-selected model results, such as concentrations, activities, saturation indices, and densities. The PHREEQC module can add geochemical reaction capabilities to surface-water, groundwater, and watershed transport models. It is possible to store and manipulate solution compositions and reaction information for many cells within the module. In addition, the object-oriented nature of the PHREEQC modules simplifies implementation of parallel processing for reactive-transport models. The PHREEQC COM module may be used in scripting languages to fit parameters; to plot PHREEQC results for field, laboratory, or theoretical investigations; or to develop new models that include simple or complex geochemical calculations. ?? 2011.

PhAst: A Flexible IDL Astronomical Image Viewer

NASA Astrophysics Data System (ADS)

Rehnberg, Morgan; Crawford, R.; Trueblood, M.; Mighell, K.

2012-01-01

We present near-Earth asteroid data analyzed with PhAst, a new IDL astronomical image viewer based on the existing application ATV. PhAst opens, displays, and analyzes an arbitrary number of FITS images. Analysis packages include image calibration, photometry, and astrometry (provided through an interface with SExtractor, SCAMP, and missFITS). PhAst has been designed to generate reports for Minor Planet Center reporting. PhAst is cross platform (Linux/Mac OSX/Windows for image viewing and Linux/Mac OSX for image analysis) and can be downloaded from the following website at NOAO: http://www.noao.edu/staff/mighell/phast/. Rehnberg was supported by the NOAO/KPNO Research Experiences for Undergraduates (REU) Program which is funded by the National Science Foundation Research Experiences for Undergraduates Program and the Department of Defense ASSURE program through Scientific Program Order No. 13 (AST-0754223) of the Cooperative Agreement No. AST-0132798 between the Association of Universities for Research in Astronomy (AURA) and the NSF.

Java application for the superposition T-matrix code to study the optical properties of cosmic dust aggregates

NASA Astrophysics Data System (ADS)

Halder, P.; Chakraborty, A.; Deb Roy, P.; Das, H. S.

2014-09-01

In this paper, we report the development of a java application for the Superposition T-matrix code, JaSTA (Java Superposition T-matrix App), to study the light scattering properties of aggregate structures. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precession superposition codes for multi-sphere clusters in random orientation developed by Mackowski and Mischenko (1996). It consists of a graphical user interface (GUI) in the front hand and a database of related data in the back hand. Both the interactive GUI and database package directly enable a user to model by self-monitoring respective input parameters (namely, wavelength, complex refractive indices, grain size, etc.) to study the related optical properties of cosmic dust (namely, extinction, polarization, etc.) instantly, i.e., with zero computational time. This increases the efficiency of the user. The database of JaSTA is now created for a few sets of input parameters with a plan to create a large database in future. This application also has an option where users can compile and run the scattering code directly for aggregates in GUI environment. The JaSTA aims to provide convenient and quicker data analysis of the optical properties which can be used in different fields like planetary science, atmospheric science, nano science, etc. The current version of this software is developed for the Linux and Windows platform to study the light scattering properties of small aggregates which will be extended for larger aggregates using parallel codes in future. Catalogue identifier: AETB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 571570 No. of bytes in distributed program, including test data, etc.: 120226886 Distribution format: tar.gz Programming language: Java, Fortran95. Computer: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler; Developed on 2.40 GHz Intel Core i3. Operating system: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler. RAM: Ranging from a few Mbytes to several Gbytes, depending on the input parameters. Classification: 1.3. External routines: jfreechart-1.0.14 [1] (free plotting library for java), j3d-jre-1.5.2 [2] (3D visualization). Nature of problem: Optical properties of cosmic dust aggregates. Solution method: Java application based on Mackowski and Mischenko's Superposition T-Matrix code. Restrictions: The program is designed for single processor systems. Additional comments: The distribution file for this program is over 120 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Ranging from few minutes to several hours, depending on the input parameters. References: [1] http://www.jfree.org/index.html [2] https://java3d.java.net/

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.

PubMed

Excoffier, Laurent; Lischer, Heidi E L

2010-05-01

We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework. © 2010 Blackwell Publishing Ltd.

Lightweight application for generating clinical research information systems: MAGIC.

PubMed

Leskošek, Brane; Pajntar, Marjan

2015-12-01

Our purpose was to build and test a lightweight solution for generating clinical research information systems (CRIS) that would allow non-IT professionals with basic knowledge of computer usage to quickly define and build a ready-to-use, safe and secure web-based clinical research system for data management. We use the acronym MAGIC (Medical Application Generator InteraCtive) for the system. The generated CRIS should be very easy to build and use, so a common LAMP (Linux Apache MySQL Perl) platform was used, which also enables short development cycles. The application was built and tested using eXtreme Programming (XP) principles by a small development team consisting of one informatics specialist, one physician and one graphical designer/programmer. The parameter and graphical user interface (GUI) definitions for the CRIS can be made by non-IT professionals using an intuitive English-language-like formalism called application definition language (ADL). From these definitions, the MAGIC builds an end-user CRIS that can be used on a wide variety of platforms (from standard workstations to hand-held devices). A working example of a national health-care-quality assessment program is presented to illustrate this process. The lightweight application for generating CRIS (MAGIC) has proven to be useful for both clinical and analytical users in real working environment. To achieve better performance and interoperability, we are planning to recompile the application using XML schemas (XSD) in HL7 CDA or openEHR archetypes formats used for parameters definition and for data interchange between different information systems.

Milne, a routine for the numerical solution of Milne's problem

NASA Astrophysics Data System (ADS)

Rawat, Ajay; Mohankumar, N.

2010-11-01

The routine Milne provides accurate numerical values for the classical Milne's problem of neutron transport for the planar one speed and isotropic scattering case. The solution is based on the Case eigen-function formalism. The relevant X functions are evaluated accurately by the Double Exponential quadrature. The calculated quantities are the extrapolation distance and the scalar and the angular fluxes. Also, the H function needed in astrophysical calculations is evaluated as a byproduct. Program summaryProgram title: Milne Catalogue identifier: AEGS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 701 No. of bytes in distributed program, including test data, etc.: 6845 Distribution format: tar.gz Programming language: Fortran 77 Computer: PC under Linux or Windows Operating system: Ubuntu 8.04 (Kernel version 2.6.24-16-generic), Windows-XP Classification: 4.11, 21.1, 21.2 Nature of problem: The X functions are integral expressions. The convergence of these regular and Cauchy Principal Value integrals are impaired by the singularities of the integrand in the complex plane. The DE quadrature scheme tackles these singularities in a robust manner compared to the standard Gauss quadrature. Running time: The test included in the distribution takes a few seconds to run.

Introduction to LINUX OS for new LINUX users - Basic Information Before Using The Kurucz Codes Under LINUX-.

NASA Astrophysics Data System (ADS)

Çay, M. Taşkin

Recently the ATLAS suite (Kurucz) was ported to LINUX OS (Sbordone et al.). Those users of the suite unfamiliar with LINUX need to know some basic information to use these versions. This paper is a quick overview and introduction to LINUX OS. The reader is highly encouraged to own a book on LINUX OS for comprehensive use. Although the subjects and examples in this paper are for general use, they to help with the installation and running the ATLAS suite.

Monte Carlo event generators in atomic collisions: A new tool to tackle the few-body dynamics

NASA Astrophysics Data System (ADS)

Ciappina, M. F.; Kirchner, T.; Schulz, M.

2010-04-01

We present a set of routines to produce theoretical event files, for both single and double ionization of atoms by ion impact, based on a Monte Carlo event generator (MCEG) scheme. Such event files are the theoretical counterpart of the data obtained from a kinematically complete experiment; i.e. they contain the momentum components of all collision fragments for a large number of ionization events. Among the advantages of working with theoretical event files is the possibility to incorporate the conditions present in a real experiment, such as the uncertainties in the measured quantities. Additionally, by manipulating them it is possible to generate any type of cross sections, specially those that are usually too complicated to compute with conventional methods due to a lack of symmetry. Consequently, the numerical effort of such calculations is dramatically reduced. We show examples for both single and double ionization, with special emphasis on a new data analysis tool, called four-body Dalitz plots, developed very recently. Program summaryProgram title: MCEG Catalogue identifier: AEFV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2695 No. of bytes in distributed program, including test data, etc.: 18 501 Distribution format: tar.gz Programming language: FORTRAN 77 with parallelization directives using scripting Computer: Single machines using Linux and Linux servers/clusters (with cores with any clock speed, cache memory and bits in a word) Operating system: Linux (any version and flavor) and FORTRAN 77 compilers Has the code been vectorised or parallelized?: Yes RAM: 64-128 kBytes (the codes are very cpu intensive) Classification: 2.6 Nature of problem: The code deals with single and double ionization of atoms by ion impact. Conventional theoretical approaches aim at a direct calculation of the corresponding cross sections. This has the important shortcoming that it is difficult to account for the experimental conditions when comparing results to measured data. In contrast, the present code generates theoretical event files of the same type as are obtained in a real experiment. From these event files any type of cross sections can be easily extracted. The theoretical schemes are based on distorted wave formalisms for both processes of interest. Solution method: The codes employ a Monte Carlo Event Generator based on theoretical formalisms to generate event files for both single and double ionization. One of the main advantages of having access to theoretical event files is the possibility of adding the conditions present in real experiments (parameter uncertainties, environmental conditions, etc.) and to incorporate additional physics in the resulting event files (e.g. elastic scattering or other interactions absent in the underlying calculations). Additional comments: The computational time can be dramatically reduced if a large number of processors is used. Since the codes has no communication between processes it is possible to achieve an efficiency of a 100% (this number certainly will be penalized by the queuing waiting time). Running time: Times vary according to the process, single or double ionization, to be simulated, the number of processors and the type of theoretical model. The typical running time is between several hours and up to a few weeks.

Generating heavy particles with energy and momentum conservation

NASA Astrophysics Data System (ADS)

Mereš, Michal; Melo, Ivan; Tomášik, Boris; Balek, Vladimír; Černý, Vladimír

2011-12-01

We propose a novel algorithm, called REGGAE, for the generation of momenta of a given sample of particle masses, evenly distributed in Lorentz-invariant phase space and obeying energy and momentum conservation. In comparison to other existing algorithms, REGGAE is designed for the use in multiparticle production in hadronic and nuclear collisions where many hadrons are produced and a large part of the available energy is stored in the form of their masses. The algorithm uses a loop simulating multiple collisions which lead to production of configurations with reasonably large weights. Program summaryProgram title: REGGAE (REscattering-after-Genbod GenerAtor of Events) Catalogue identifier: AEJR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1523 No. of bytes in distributed program, including test data, etc.: 9608 Distribution format: tar.gz Programming language: C++ Computer: PC Pentium 4, though no particular tuning for this machine was performed. Operating system: Originally designed on Linux PC with g++, but it has been compiled and ran successfully on OS X with g++ and MS Windows with Microsoft Visual C++ 2008 Express Edition, as well. RAM: This depends on the number of particles which are generated. For 10 particles like in the attached example it requires about 120 kB. Classification: 11.2 Nature of problem: The task is to generate momenta of a sample of particles with given masses which obey energy and momentum conservation. Generated samples should be evenly distributed in the available Lorentz-invariant phase space. Solution method: In general, the algorithm works in two steps. First, all momenta are generated with the GENBOD algorithm. There, particle production is modeled as a sequence of two-body decays of heavy resonances. After all momenta are generated this way, they are reshuffled. Each particle undergoes a collision with some other partner such that in the pair center of mass system the new directions of momenta are distributed isotropically. After each particle collides only a few times, the momenta are distributed evenly across the whole available phase space. Starting with GENBOD is not essential for the procedure but it improves the performance. Running time: This depends on the number of particles and number of events one wants to generate. On a LINUX PC with 2 GHz processor, generation of 1000 events with 10 particles each takes about 3 s.

The Grid[Way] Job Template Manager, a tool for parameter sweeping

NASA Astrophysics Data System (ADS)

Lorca, Alejandro; Huedo, Eduardo; Llorente, Ignacio M.

2011-04-01

Parameter sweeping is a widely used algorithmic technique in computational science. It is specially suited for high-throughput computing since the jobs evaluating the parameter space are loosely coupled or independent. A tool that integrates the modeling of a parameter study with the control of jobs in a distributed architecture is presented. The main task is to facilitate the creation and deletion of job templates, which are the elements describing the jobs to be run. Extra functionality relies upon the GridWay Metascheduler, acting as the middleware layer for job submission and control. It supports interesting features like multi-dimensional sweeping space, wildcarding of parameters, functional evaluation of ranges, value-skipping and job template automatic indexation. The use of this tool increases the reliability of the parameter sweep study thanks to the systematic bookkeeping of job templates and respective job statuses. Furthermore, it simplifies the porting of the target application to the grid reducing the required amount of time and effort. Program summaryProgram title: Grid[Way] Job Template Manager (version 1.0) Catalogue identifier: AEIE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Apache license 2.0 No. of lines in distributed program, including test data, etc.: 3545 No. of bytes in distributed program, including test data, etc.: 126 879 Distribution format: tar.gz Programming language: Perl 5.8.5 and above Computer: Any (tested on PC x86 and x86_64) Operating system: Unix, GNU/Linux (tested on Ubuntu 9.04, Scientific Linux 4.7, centOS 5.4), Mac OS X (tested on Snow Leopard 10.6) RAM: 10 MB Classification: 6.5 External routines: The GridWay Metascheduler [1]. Nature of problem: To parameterize and manage an application running on a grid or cluster. Solution method: Generation of job templates as a cross product of the input parameter sets. Also management of the job template files including the job submission to the grid, control and information retrieval. Restrictions: The parameter sweep is limited by disk space during generation of the job templates. The wild-carding of parameters cannot be done in decreasing order. Job submission, control and information is delegated to the GridWay Metascheduler. Running time: From half a second in the simplest operation to a few minutes for thousands of exponential sampling parameters.

GLoBES: General Long Baseline Experiment Simulator

NASA Astrophysics Data System (ADS)

Huber, Patrick; Kopp, Joachim; Lindner, Manfred; Rolinec, Mark; Winter, Walter

2007-09-01

GLoBES (General Long Baseline Experiment Simulator) is a flexible software package to simulate neutrino oscillation long baseline and reactor experiments. On the one hand, it contains a comprehensive abstract experiment definition language (AEDL), which allows to describe most classes of long baseline experiments at an abstract level. On the other hand, it provides a C-library to process the experiment information in order to obtain oscillation probabilities, rate vectors, and Δχ-values. Currently, GLoBES is available for GNU/Linux. Since the source code is included, the port to other operating systems is in principle possible. GLoBES is an open source code that has previously been described in Computer Physics Communications 167 (2005) 195 and in Ref. [7]). The source code and a comprehensive User Manual for GLoBES v3.0.8 is now available from the CPC Program Library as described in the Program Summary below. The home of GLobES is http://www.mpi-hd.mpg.de/~globes/. Program summaryProgram title: GLoBES version 3.0.8 Catalogue identifier: ADZI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 145 295 No. of bytes in distributed program, including test data, etc.: 1 811 892 Distribution format: tar.gz Programming language: C Computer: GLoBES builds and installs on 32bit and 64bit Linux systems Operating system: 32bit or 64bit Linux RAM: Typically a few MBs Classification: 11.1, 11.7, 11.10 External routines: GSL—The GNU Scientific Library, www.gnu.org/software/gsl/ Nature of problem: Neutrino oscillations are now established as the leading flavor transition mechanism for neutrinos. In a long history of many experiments, see, e.g., [1], two oscillation frequencies have been identified: The fast atmospheric and the slow solar oscillations, which are driven by the respective mass squared differences. In addition, there could be interference effects between these two oscillations, provided that the coupling given by the small mixing angle θ is large enough. Such interference effects include, for example, leptonic CP violation. In order to test the unknown oscillation parameters, i.e. the mixing angle θ, the leptonic CP phase, and the neutrino mass hierarchy, new long-baseline and reactor experiments are proposed. These experiments send an artificial neutrino beam to a detector, or detect the neutrinos produced by a nuclear fission reactor. However, the presence of multiple solutions which are intrinsic to neutrino oscillation probabilities [2-5] affect these measurements. Thus optimization strategies are required which maximally exploit complementarity between experiments. Therefore, a modern, complete experiment simulation and analysis tool does not only need to have a highly accurate beam and detector simulation, but also powerful means to analyze correlations and degeneracies, especially for the combination of several experiments. The GLoBES software package is such a tool [6,7]. Solution method: GLoBES is a flexible software tool to simulate and analyze neutrino oscillation long-baseline and reactor experiments using a complete three-flavor description. On the one hand, it contains a comprehensive abstract experiment definition language (AEDL), which makes it possible to describe most classes of long baseline and reactor experiments at an abstract level. On the other hand, it provides a C-library to process the experiment information in order to obtain oscillation probabilities, rate vectors, and Δχ-values. In addition, it provides a binary program to test experiment definitions very quickly, before they are used by the application software. Restrictions: Currently restricted to discrete sets of sources and detectors. For example, the simulation of an atmospheric neutrino flux is not supported. Unusual features: Clear separation between experiment description and the simulation software. Additional comments: To find information on the latest version of the software and user manual, please check the author's web site, http://www.mpi-hd.mpg.de/~globes Running time: The examples included in the distribution take only a few minutes to complete. More sophisticated problems can take up to several days. References [1] V. Barger, D. Marfatia, K. Whisnant, Int. J. Mod. Phys. E 12 (2003) 569, hep-ph/0308123, and references therein. [2] G.L. Fogli, E. Lisi, Phys. Rev. D 54 (1996) 3667, hep-ph/9604415. [3] J. Burguet-Castell, M.B. Gavela, J.J. Gomez-Cadenas, P. Hernandez, O. Mena, Nucl. Phys. B 608 (2001) 301, hep-ph/0103258. [4] H. Minakata, H. Nunokawa, JHEP 0110 (2001) 001, hep-ph/0108085. [5] V. Barger, D. Marfatia, K. Whisnant, Phys. Rev. D 65 (2002) 073023, hep-ph/0112119. [6] P. Huber, M. Lindner, W. Winter, Comput. Phys. Commun. 167 (2005) 195. [7] P. Huber, J. Kopp, M. Lindner, M. Rolinec, W. Winter, Comput. Phys. Commun. 177 (2007) 432.

MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity

NASA Astrophysics Data System (ADS)

Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.

2012-08-01

We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Catalogue identifier: AEMF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon processors) Operating system: Linux/Unix/Mac OS RAM: 2 Mbytes Classification: 16.3, 16.12, 23 Nature of problem: Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperatures) of complex molecules involving multiple torsional motions. Solution method: The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation [1]. Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multi-torsional problems for which one can afford to calculate all the conformations and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes and six utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomain defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 24 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 seconds. J. Zheng, T. Yu, E. Papajak, I.M. Alecu, S.L. Mielke, D.G. Truhlar, Practical methods for including torsional anharmonicity in thermochemical calculations of complex molecules: The internal-coordinate multi-structural approximation, Phys. Chem. Chem. Phys. 13 (2011) 10885-10907.

Molecular t-matrices for Low-Energy Electron Diffraction (TMOL v1.1)

NASA Astrophysics Data System (ADS)

Blanco-Rey, Maria; de Andres, Pedro; Held, Georg; King, David A.

2004-08-01

We describe a FORTRAN-90 program that computes scattering t-matrices for a molecule. These can be used in a Low-Energy Electron Diffraction program to solve the molecular structural problem very efficiently. The intramolecular multiple scattering is computed within a Dyson-like approach, using free space Green propagators in a basis of spherical waves. The advantage of this approach is related to exploiting the chemical identity of the molecule, and to the simplicity to translate and rotate these t-matrices without performing a new multiple-scattering calculation for each configuration. FORTRAN-90 routines for rotating the resulting t-matrices using Wigner matrices are also provided. Program summaryTitle of program: TMOL Catalogue number: ADUF Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUF Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland. Computers: Alpha ev6-21264 (700 MHz) and Pentium-IV. Operating systems: Digital UNIX V5.0 and Linux (Red Hat 8.0). Programming language: FORTRAN-90/95 (Compaq True64 compiler, and Intel Fortran Compiler 7.0 for Linux). High-speed storage required for the test run: minimum 64 Mbytes, it can grow to more depending on the system considered. Disk storage required: None. No. of bits in a word: 64 and 32. No. of lines in distributed program, including test data etc.: 5404 No. of bytes in distributed program, including test data etc.: 59 856 Distribution format: tar.gz Nature of problem: We describe the FORTRAN-90 program TMOL (v1.1) for the computation of non-diagonal scattering t-matrices for molecules or any other poly-atomic sub-unit of surface structures. These matrices can be used in an standard Low-Energy Electron Diffraction program, such as LEED90 or CLEED. Method of solution: A general non-diagonal t-matrix is assumed for the atoms or more general scatterers forming the molecule. The molecular t-matrix is solved adding the possible intramolecular multiple scattering events using Green's propagator formalism. The resulting t-matrix is referred to the mass centre of the molecule and can be easily translated with these propagators and rotated applying Wigner matrices. Typical running time: Calculating the t-matrix for a single energy takes a few seconds. Time depends on the maximum angular momentum quantum number, lmax, and the number of scatterers in the molecule, N. Running time scales as lmax6 and N3. References: [1] S. Andersson, J.B. Pendry, J. Phys. C: Solid St. Phys. 13 (1980) 3547. [2] A. Gonis, W.H. Butler, Multiple Scattering in Solids, Springer-Verlag, Berlin/New York, 2000.

AIRE-Linux

NASA Astrophysics Data System (ADS)

Zhou, Jianfeng; Xu, Benda; Peng, Chuan; Yang, Yang; Huo, Zhuoxi

2015-08-01

AIRE-Linux is a dedicated Linux system for astronomers. Modern astronomy faces two big challenges: massive observed raw data which covers the whole electromagnetic spectrum, and overmuch professional data processing skill which exceeds personal or even a small team's abilities. AIRE-Linux, which is a specially designed Linux and will be distributed to users by Virtual Machine (VM) images in Open Virtualization Format (OVF), is to help astronomers confront the challenges. Most astronomical software packages, such as IRAF, MIDAS, CASA, Heasoft etc., will be integrated into AIRE-Linux. It is easy for astronomers to configure and customize the system and use what they just need. When incorporated into cloud computing platforms, AIRE-Linux will be able to handle data intensive and computing consuming tasks for astronomers. Currently, a Beta version of AIRE-Linux is ready for download and testing.

A Set of Free Cross-Platform Authoring Programs for Flexible Web-Based CALL Exercises

ERIC Educational Resources Information Center

O'Brien, Myles

2012-01-01

The Mango Suite is a set of three freely downloadable cross-platform authoring programs for flexible network-based CALL exercises. They are Adobe Air applications, so they can be used on Windows, Macintosh, or Linux computers, provided the freely-available Adobe Air has been installed on the computer. The exercises which the programs generate are…

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.

PubMed

Ibarra, Ignacio L; Melo, Francisco

2010-07-01

Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm version and the gap opening/extension penalties. We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications. The software is freely available at: http:/melolab.org/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX. All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl.

Vectorized data acquisition and fast triple-correlation integrals for Fluorescence Triple Correlation Spectroscopy

NASA Astrophysics Data System (ADS)

Ridgeway, William K.; Millar, David P.; Williamson, James R.

2013-04-01

Fluorescence Correlation Spectroscopy (FCS) is widely used to quantify reaction rates and concentrations of molecules in vitro and in vivo. We recently reported Fluorescence Triple Correlation Spectroscopy (F3CS), which correlates three signals together instead of two. F3CS can analyze the stoichiometries of complex mixtures and detect irreversible processes by identifying time-reversal asymmetries. Here we report the computational developments that were required for the realization of F3CS and present the results as the Triple Correlation Toolbox suite of programs. Triple Correlation Toolbox is a complete data analysis pipeline capable of acquiring, correlating and fitting large data sets. Each segment of the pipeline handles error estimates for accurate error-weighted global fitting. Data acquisition was accelerated with a combination of off-the-shelf counter-timer chips and vectorized operations on 128-bit registers. This allows desktop computers with inexpensive data acquisition cards to acquire hours of multiple-channel data with sub-microsecond time resolution. Off-line correlation integrals were implemented as a two delay time multiple-tau scheme that scales efficiently with multiple processors and provides an unprecedented view of linked dynamics. Global fitting routines are provided to fit FCS and F3CS data to models containing up to ten species. Triple Correlation Toolbox is a complete package that enables F3CS to be performed on existing microscopes. Catalogue identifier: AEOP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOP_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 50189 No. of bytes in distributed program, including test data, etc.: 6135283 Distribution format: tar.gz Programming language: C/Assembly. Computer: Any with GCC and library support. Operating system: Linux and OS X (data acq. for Linux only due to library availability), not tested on Windows. RAM: ≥512 MB. Classification: 16.4. External routines: NIDAQmx (National Instruments), Gnu Scientific Library, GTK+, PLplot (optional) Nature of problem: Fluorescence Triple Correlation Spectroscopy required three things: data acquisition at faster speeds than were possible without expensive custom hardware, triple-correlation routines that could process 1/2 TB data sets rapidly, and fitting routines capable of handling several to a hundred fit parameters and 14,000 + data points, each with error estimates. Solution method: A novel data acquisition concept mixed signal processing with off-the-shelf hardware and data-parallel processing using 128-bit registers found in desktop CPUs. Correlation algorithms used fractal data structures and multithreading to reduce data analysis times. Global fitting was implemented with robust minimization routines and provides feedback that allows the user to critically inspect initial guesses and fits. Restrictions: Data acquisition only requires a National Instruments data acquisition card (it was tested on Linux using card PCIe-6251) and a simple home-built circuit. Unusual features: Hand-coded ×86-64 assembly for data acquisition loops (platform-independent C code also provided). Additional comments: A complete collection of tools to perform Fluorescence Triple Correlation Spectroscopy-from data acquisition to two-tau correlation of large data sets, to model fitting. Running time: 1-5 h of data analysis per hour of data collected. Varies depending on data-acquisition length, time resolution, data density and number of cores used for correlation integrals.

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

The GNAT: A new tool for processing NMR data.

PubMed

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A; Morris, Gareth A; Nilsson, Mathias

2018-06-01

The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T 1 /T 2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. © 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

MCdevelop - a universal framework for Stochastic Simulations

NASA Astrophysics Data System (ADS)

Slawinska, M.; Jadach, S.

2011-03-01

We present MCdevelop, a universal computer framework for developing and exploiting the wide class of Stochastic Simulations (SS) software. This powerful universal SS software development tool has been derived from a series of scientific projects for precision calculations in high energy physics (HEP), which feature a wide range of functionality in the SS software needed for advanced precision Quantum Field Theory calculations for the past LEP experiments and for the ongoing LHC experiments at CERN, Geneva. MCdevelop is a "spin-off" product of HEP to be exploited in other areas, while it will still serve to develop new SS software for HEP experiments. Typically SS involve independent generation of large sets of random "events", often requiring considerable CPU power. Since SS jobs usually do not share memory it makes them easy to parallelize. The efficient development, testing and running in parallel SS software requires a convenient framework to develop software source code, deploy and monitor batch jobs, merge and analyse results from multiple parallel jobs, even before the production runs are terminated. Throughout the years of development of stochastic simulations for HEP, a sophisticated framework featuring all the above mentioned functionality has been implemented. MCdevelop represents its latest version, written mostly in C++ (GNU compiler gcc). It uses Autotools to build binaries (optionally managed within the KDevelop 3.5.3 Integrated Development Environment (IDE)). It uses the open-source ROOT package for histogramming, graphics and the mechanism of persistency for the C++ objects. MCdevelop helps to run multiple parallel jobs on any computer cluster with NQS-type batch system. Program summaryProgram title:MCdevelop Catalogue identifier: AEHW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 48 136 No. of bytes in distributed program, including test data, etc.: 355 698 Distribution format: tar.gz Programming language: ANSI C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system. Operating system: Most UNIX systems, Linux. The application programs were thoroughly tested under Ubuntu 7.04, 8.04 and CERN Scientific Linux 5. Has the code been vectorised or parallelised?: Tools (scripts) for optional parallelisation on a PC farm are included. RAM: 500 bytes Classification: 11.3 External routines: ROOT package version 5.0 or higher ( http://root.cern.ch/drupal/). Nature of problem: Developing any type of stochastic simulation program for high energy physics and other areas. Solution method: Object Oriented programming in C++ with added persistency mechanism, batch scripts for running on PC farms and Autotools.

Millisecond accuracy video display using OpenGL under Linux.

PubMed

Stewart, Neil

2006-02-01

To measure people's reaction times to the nearest millisecond, it is necessary to know exactly when a stimulus is displayed. This article describes how to display stimuli with millisecond accuracy on a normal CRT monitor, using a PC running Linux. A simple C program is presented to illustrate how this may be done within X Windows using the OpenGL rendering system. A test of this system is reported that demonstrates that stimuli may be consistently displayed with millisecond accuracy. An algorithm is presented that allows the exact time of stimulus presentation to be deduced, even if there are relatively large errors in measuring the display time.

XOP: a multiplatform graphical user interface for synchrotron radiation spectral and optics calculations

NASA Astrophysics Data System (ADS)

Sanchez del Rio, Manuel; Dejus, Roger J.

1997-11-01

XOP (X-ray OPtics utilities) is a graphical user interface (GUI) created to execute several computer programs that calculate the basic information needed by a synchrotron beamline scientist (designer or experimentalist). Typical examples of such calculations are: insertion device (undulator or wiggler) spectral and angular distributions, mirror and multilayer reflectivities, and crystal diffraction profiles. All programs are provided to the user under a unified GUI, which greatly simplifies their execution. The XOP optics applications (especially mirror calculations) take their basic input (optical constants, compound and mixture tables) from a flexible file-oriented database, which allows the user to select data from a large number of choices and also to customize their own data sets. XOP includes many mathematical and visualization capabilities. It also permits the combination of reflectivities from several mirrors and filters, and their effect, onto a source spectrum. This feature is very useful when calculating thermal load on a series of optical elements. The XOP interface is written in the IDL (Interactive Data Language). An embedded version of XOP, which freely runs under most Unix platforms (HP, Sun, Dec, Linux, etc) and under Windows95 and NT, is available upon request.

Efficient Comparison between Windows and Linux Platform Applicable in a Virtual Architectural Walkthrough Application

NASA Astrophysics Data System (ADS)

Thubaasini, P.; Rusnida, R.; Rohani, S. M.

This paper describes Linux, an open source platform used to develop and run a virtual architectural walkthrough application. It proposes some qualitative reflections and observations on the nature of Linux in the concept of Virtual Reality (VR) and on the most popular and important claims associated with the open source approach. The ultimate goal of this paper is to measure and evaluate the performance of Linux used to build the virtual architectural walkthrough and develop a proof of concept based on the result obtain through this project. Besides that, this study reveals the benefits of using Linux in the field of virtual reality and reflects a basic comparison and evaluation between Windows and Linux base operating system. Windows platform is use as a baseline to evaluate the performance of Linux. The performance of Linux is measured based on three main criteria which is frame rate, image quality and also mouse motion.

A programmable optimization environment using the GAMESS-US and MERLIN/MCL packages. Applications on intermolecular interaction energies

NASA Astrophysics Data System (ADS)

Kalatzis, Fanis G.; Papageorgiou, Dimitrios G.; Demetropoulos, Ioannis N.

2006-09-01

The Merlin/MCL optimization environment and the GAMESS-US package were combined so as to offer an extended and efficient quantum chemistry optimization system, capable of implementing complex optimization strategies for generic molecular modeling problems. A communication and data exchange interface was established between the two packages exploiting all Merlin features such as multiple optimizers, box constraints, user extensions and a high level programming language. An important feature of the interface is its ability to perform dimer computations by eliminating the basis set superposition error using the counterpoise (CP) method of Boys and Bernardi. Furthermore it offers CP-corrected geometry optimizations using analytic derivatives. The unified optimization environment was applied to construct portions of the intermolecular potential energy surface of the weakly bound H-bonded complex C 6H 6-H 2O by utilizing the high level Merlin Control Language. The H-bonded dimer HF-H 2O was also studied by CP-corrected geometry optimization. The ab initio electronic structure energies were calculated using the 6-31G ** basis set at the Restricted Hartree-Fock and second-order Moller-Plesset levels, while all geometry optimizations were carried out using a quasi-Newton algorithm provided by Merlin. Program summaryTitle of program: MERGAM Catalogue identifier:ADYB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYB_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The program is designed for machines running the UNIX operating system. It has been tested on the following architectures: IA32 (Linux with gcc/g77 v.3.2.3), AMD64 (Linux with the Portland group compilers v.6.0), SUN64 (SunOS 5.8 with the Sun Workshop compilers v.5.2) and SGI64 (IRIX 6.5 with the MIPSpro compilers v.7.4) Installations: University of Ioannina, Greece Operating systems or monitors under which the program has been tested: UNIX Programming language used: ANSI C, ANSI Fortran-77 No. of lines in distributed program, including test data, etc.:11 282 No. of bytes in distributed program, including test data, etc.: 49 458 Distribution format: tar.gz Memory required to execute with typical data: Memory requirements mainly depend on the selection of a GAMESS-US basis set and the number of atoms No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: no Nature of physical problem: Multidimensional geometry optimization is of great importance in any ab initio calculation since it usually is one of the most CPU-intensive tasks, especially on large molecular systems. For example, the geometric and energetic description of van der Waals and weakly bound H-bonded complexes requires the construction of related important portions of the multidimensional intermolecular potential energy surface (IPES). So the various held views about the nature of these bonds can be quantitatively tested. Method of solution: The Merlin/MCL optimization environment was interconnected with the GAMESS-US package to facilitate geometry optimization in quantum chemistry problems. The important portions of the IPES require the capability to program optimization strategies. The Merlin/MCL environment was used for the implementation of such strategies. In this work, a CP-corrected geometry optimization was performed on the HF-H 2O complex and an MCL program was developed to study portions of the potential energy surface of the C 6H 6-H 2O complex. Restrictions on the complexity of the problem: The Merlin optimization environment and the GAMESS-US package must be installed. The MERGAM interface requires GAMESS-US input files that have been constructed in Cartesian coordinates. This restriction occurs from a design-time requirement to not allow reorientation of atomic coordinates; this rule holds always true when applying the COORD = UNIQUE keyword in a GAMESS-US input file. Typical running time: It depends on the size of the molecular system, the size of the basis set and the method of electron correlation. Execution of the test run took approximately 5 min on a 2.8 GHz Intel Pentium CPU.

Development of Automatic Live Linux Rebuilding System with Flexibility in Science and Engineering Education and Applying to Information Processing Education

NASA Astrophysics Data System (ADS)

Sonoda, Jun; Yamaki, Kota

We develop an automatic Live Linux rebuilding system for science and engineering education, such as information processing education, numerical analysis and so on. Our system is enable to easily and automatically rebuild a customized Live Linux from a ISO image of Ubuntu, which is one of the Linux distribution. Also, it is easily possible to install/uninstall packages and to enable/disable init daemons. When we rebuild a Live Linux CD using our system, we show number of the operations is 8, and the rebuilding time is about 33 minutes on CD version and about 50 minutes on DVD version. Moreover, we have applied the rebuilded Live Linux CD in a class of information processing education in our college. As the results of a questionnaires survey from our 43 students who used the Live Linux CD, we obtain that the our Live Linux is useful for about 80 percents of students. From these results, we conclude that our system is able to easily and automatically rebuild a useful Live Linux in short time.

Development of a platform-independent receiver control system for SISIFOS

NASA Astrophysics Data System (ADS)

Lemke, Roland; Olberg, Michael

1998-05-01

Up to now receiver control software was a time consuming development usually written by receiver engineers who had mainly the hardware in mind. We are presenting a low-cost and very flexible system which uses a minimal interface to the real hardware, and which makes it easy to adapt to new receivers. Our system uses Tcl/Tk as a graphical user interface (GUI), SpecTcl as a GUI builder, Pgplot as plotting software, a simple query language (SQL) database for information storage and retrieval, Ethernet socket to socket communication and SCPI as a command control language. The complete system is in principal platform independent but for cost saving reasons we are using it actually on a PC486 running Linux 2.0.30, which is a copylefted Unix. The only hardware dependent part are the digital input/output boards, analog to digital and digital to analog convertors. In the case of the Linux PC we are using a device driver development kit to integrate the boards fully into the kernel of the operating system, which indeed makes them look like an ordinary device. The advantage of this system is firstly the low price and secondly the clear separation between the different software components which are available for many operating systems. If it is not possible, due to CPU performance limitations, to run all the software in a single machine,the SQL-database or the graphical user interface could be installed on separate computers.

Browndye: A software package for Brownian dynamics

NASA Astrophysics Data System (ADS)

Huber, Gary A.; McCammon, J. Andrew

2010-11-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. Program summaryProgram title: Browndye Catalogue identifier: AEGT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license, included in distribution No. of lines in distributed program, including test data, etc.: 143 618 No. of bytes in distributed program, including test data, etc.: 1 067 861 Distribution format: tar.gz Programming language: C++, OCaml ( http://caml.inria.fr/) Computer: PC, Workstation, Cluster Operating system: Linux Has the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreads RAM: Depends linearly on size of physical system Classification: 3 External routines: uses the output of APBS [1] ( http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained and installed separately. Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne Twister. These are included in the Browndye distribution. Nature of problem: Exploration and determination of rate constants of bimolecular interactions involving large biological molecules. Solution method: Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces. Running time: Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.

Generating and using truly random quantum states in Mathematica

NASA Astrophysics Data System (ADS)

Miszczak, Jarosław Adam

2012-01-01

The problem of generating random quantum states is of a great interest from the quantum information theory point of view. In this paper we present a package for Mathematica computing system harnessing a specific piece of hardware, namely Quantis quantum random number generator (QRNG), for investigating statistical properties of quantum states. The described package implements a number of functions for generating random states, which use Quantis QRNG as a source of randomness. It also provides procedures which can be used in simulations not related directly to quantum information processing. Program summaryProgram title: TRQS Catalogue identifier: AEKA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 7924 No. of bytes in distributed program, including test data, etc.: 88 651 Distribution format: tar.gz Programming language: Mathematica, C Computer: Requires a Quantis quantum random number generator (QRNG, http://www.idquantique.com/true-random-number-generator/products-overview.html) and supporting a recent version of Mathematica Operating system: Any platform supporting Mathematica; tested with GNU/Linux (32 and 64 bit) RAM: Case dependent Classification: 4.15 Nature of problem: Generation of random density matrices. Solution method: Use of a physical quantum random number generator. Running time: Generating 100 random numbers takes about 1 second, generating 1000 random density matrices takes more than a minute.

Calculation of four-particle harmonic-oscillator transformation brackets

NASA Astrophysics Data System (ADS)

Germanas, D.; Kalinauskas, R. K.; Mickevičius, S.

2010-02-01

A procedure for precise calculation of the three- and four-particle harmonic-oscillator (HO) transformation brackets is presented. The analytical expressions of the four-particle HO transformation brackets are given. The computer code for the calculations of HO transformation brackets proves to be quick, efficient and produces results with small numerical uncertainties. Program summaryProgram title: HOTB Catalogue identifier: AEFQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1247 No. of bytes in distributed program, including test data, etc.: 6659 Distribution format: tar.gz Programming language: FORTRAN 90 Computer: Any computer with FORTRAN 90 compiler Operating system: Windows, Linux, FreeBSD, True64 Unix RAM: 8 MB Classification: 17.17 Nature of problem: Calculation of the three-particle and four-particle harmonic-oscillator transformation brackets. Solution method: The method is based on compact expressions of the three-particle harmonics oscillator brackets, presented in [1] and expressions of the four-particle harmonics oscillator brackets, presented in this paper. Restrictions: The three- and four-particle harmonic-oscillator transformation brackets up to the e=28. Unusual features: Possibility of calculating the four-particle harmonic-oscillator transformation brackets. Running time: Less than one second for the single harmonic-oscillator transformation bracket. References:G.P. Kamuntavičius, R.K. Kalinauskas, B.R. Barret, S. Mickevičius, D. Germanas, Nuclear Physics A 695 (2001) 191.

MsSpec-1.0: A multiple scattering package for electron spectroscopies in material science

NASA Astrophysics Data System (ADS)

Sébilleau, Didier; Natoli, Calogero; Gavaza, George M.; Zhao, Haifeng; Da Pieve, Fabiana; Hatada, Keisuke

2011-12-01

We present a multiple scattering package to calculate the cross-section of various spectroscopies namely photoelectron diffraction (PED), Auger electron diffraction (AED), X-ray absorption (XAS), low-energy electron diffraction (LEED) and Auger photoelectron coincidence spectroscopy (APECS). This package is composed of three main codes, computing respectively the cluster, the potential and the cross-section. In the latter case, in order to cover a range of energies as wide as possible, three different algorithms are provided to perform the multiple scattering calculation: full matrix inversion, series expansion or correlation expansion of the multiple scattering matrix. Numerous other small Fortran codes or bash/csh shell scripts are also provided to perform specific tasks. The cross-section code is built by the user from a library of subroutines using a makefile. Program summaryProgram title: MsSpec-1.0 Catalogue identifier: AEJT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 504 438 No. of bytes in distributed program, including test data, etc.: 14 448 180 Distribution format: tar.gz Programming language: Fortran 77 Computer: Any Operating system: Linux, MacOs RAM: Bytes Classification: 7.2 External routines: Lapack ( http://www.netlib.org/lapack/) Nature of problem: Calculation of the cross-section of various spectroscopies. Solution method: Multiple scattering. Running time: The test runs provided only take a few seconds to run.

Optimized multiple quantum MAS lineshape simulations in solid state NMR

NASA Astrophysics Data System (ADS)

Brouwer, William J.; Davis, Michael C.; Mueller, Karl T.

2009-10-01

The majority of nuclei available for study in solid state Nuclear Magnetic Resonance have half-integer spin I>1/2, with corresponding electric quadrupole moment. As such, they may couple with a surrounding electric field gradient. This effect introduces anisotropic line broadening to spectra, arising from distinct chemical species within polycrystalline solids. In Multiple Quantum Magic Angle Spinning (MQMAS) experiments, a second frequency dimension is created, devoid of quadrupolar anisotropy. As a result, the center of gravity of peaks in the high resolution dimension is a function of isotropic second order quadrupole and chemical shift alone. However, for complex materials, these parameters take on a stochastic nature due in turn to structural and chemical disorder. Lineshapes may still overlap in the isotropic dimension, complicating the task of assignment and interpretation. A distributed computational approach is presented here which permits simulation of the two-dimensional MQMAS spectrum, generated by random variates from model distributions of isotropic chemical and quadrupole shifts. Owing to the non-convex nature of the residual sum of squares (RSS) function between experimental and simulated spectra, simulated annealing is used to optimize the simulation parameters. In this manner, local chemical environments for disordered materials may be characterized, and via a re-sampling approach, error estimates for parameters produced. Program summaryProgram title: mqmasOPT Catalogue identifier: AEEC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3650 No. of bytes in distributed program, including test data, etc.: 73 853 Distribution format: tar.gz Programming language: C, OCTAVE Computer: UNIX/Linux Operating system: UNIX/Linux Has the code been vectorised or parallelized?: Yes RAM: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 3.5M, SMP AMD opteron Classification: 2.3 External routines: OCTAVE ( http://www.gnu.org/software/octave/), GNU Scientific Library ( http://www.gnu.org/software/gsl/), OPENMP ( http://openmp.org/wp/) Nature of problem: The optimal simulation and modeling of multiple quantum magic angle spinning NMR spectra, for general systems, especially those with mild to significant disorder. The approach outlined and implemented in C and OCTAVE also produces model parameter error estimates. Solution method: A model for each distinct chemical site is first proposed, for the individual contribution of crystallite orientations to the spectrum. This model is averaged over all powder angles [1], as well as the (stochastic) parameters; isotropic chemical shift and quadrupole coupling constant. The latter is accomplished via sampling from a bi-variate Gaussian distribution, using the Box-Muller algorithm to transform Sobol (quasi) random numbers [2]. A simulated annealing optimization is performed, and finally the non-linear jackknife [3] is applied in developing model parameter error estimates. Additional comments: The distribution contains a script, mqmasOpt.m, which runs in the OCTAVE language workspace. Running time: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 58.35 seconds, SMP AMD opteron. References:S.K. Zaremba, Annali di Matematica Pura ed Applicata 73 (1966) 293. H. Niederreiter, Random Number Generation and Quasi-Monte Carlo Methods, SIAM, 1992. T. Fox, D. Hinkley, K. Larntz, Technometrics 22 (1980) 29.

SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

USGS Publications Warehouse

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

USGS Publications Warehouse

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data.

PubMed

Miller, Mark P; Knaus, Brian J; Mullins, Thomas D; Haig, Susan M

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25 bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

Tri-Laboratory Linux Capacity Cluster 2007 SOW

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seager, M

2007-03-22

The Advanced Simulation and Computing (ASC) Program (formerly know as Accelerated Strategic Computing Initiative, ASCI) has led the world in capability computing for the last ten years. Capability computing is defined as a world-class platform (in the Top10 of the Top500.org list) with scientific simulations running at scale on the platform. Example systems are ASCI Red, Blue-Pacific, Blue-Mountain, White, Q, RedStorm, and Purple. ASC applications have scaled to multiple thousands of CPUs and accomplished a long list of mission milestones on these ASC capability platforms. However, the computing demands of the ASC and Stockpile Stewardship programs also include a vastmore » number of smaller scale runs for day-to-day simulations. Indeed, every 'hero' capability run requires many hundreds to thousands of much smaller runs in preparation and post processing activities. In addition, there are many aspects of the Stockpile Stewardship Program (SSP) that can be directly accomplished with these so-called 'capacity' calculations. The need for capacity is now so great within the program that it is increasingly difficult to allocate the computer resources required by the larger capability runs. To rectify the current 'capacity' computing resource shortfall, the ASC program has allocated a large portion of the overall ASC platforms budget to 'capacity' systems. In addition, within the next five to ten years the Life Extension Programs (LEPs) for major nuclear weapons systems must be accomplished. These LEPs and other SSP programmatic elements will further drive the need for capacity calculations and hence 'capacity' systems as well as future ASC capability calculations on 'capability' systems. To respond to this new workload analysis, the ASC program will be making a large sustained strategic investment in these capacity systems over the next ten years, starting with the United States Government Fiscal Year 2007 (GFY07). However, given the growing need for 'capability' systems as well, the budget demands are extreme and new, more cost effective ways of fielding these systems must be developed. This Tri-Laboratory Linux Capacity Cluster (TLCC) procurement represents the ASC first investment vehicle in these capacity systems. It also represents a new strategy for quickly building, fielding and integrating many Linux clusters of various sizes into classified and unclassified production service through a concept of Scalable Units (SU). The programmatic objective is to dramatically reduce the overall Total Cost of Ownership (TCO) of these 'capacity' systems relative to the best practices in Linux Cluster deployments today. This objective only makes sense in the context of these systems quickly becoming very robust and useful production clusters under the crushing load that will be inflicted on them by the ASC and SSP scientific simulation capacity workload.« less

TICK: Transparent Incremental Checkpointing at Kernel Level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrini, Fabrizio; Gioiosa, Roberto

2004-10-25

TICK is a software package implemented in Linux 2.6 that allows the save and restore of user processes, without any change to the user code or binary. With TICK a process can be suspended by the Linux kernel upon receiving an interrupt and saved in a file. This file can be later thawed in another computer running Linux (potentially the same computer). TICK is implemented as a Linux kernel module, in the Linux version 2.6.5

Potential performance bottleneck in Linux TCP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wenji; Crawford, Matt; /Fermilab

2006-12-01

TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system tomore » its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.« less

Large-scale parallel lattice Boltzmann-cellular automaton model of two-dimensional dendritic growth

NASA Astrophysics Data System (ADS)

Jelinek, Bohumir; Eshraghi, Mohsen; Felicelli, Sergio; Peters, John F.

2014-03-01

An extremely scalable lattice Boltzmann (LB)-cellular automaton (CA) model for simulations of two-dimensional (2D) dendritic solidification under forced convection is presented. The model incorporates effects of phase change, solute diffusion, melt convection, and heat transport. The LB model represents the diffusion, convection, and heat transfer phenomena. The dendrite growth is driven by a difference between actual and equilibrium liquid composition at the solid-liquid interface. The CA technique is deployed to track the new interface cells. The computer program was parallelized using the Message Passing Interface (MPI) technique. Parallel scaling of the algorithm was studied and major scalability bottlenecks were identified. Efficiency loss attributable to the high memory bandwidth requirement of the algorithm was observed when using multiple cores per processor. Parallel writing of the output variables of interest was implemented in the binary Hierarchical Data Format 5 (HDF5) to improve the output performance, and to simplify visualization. Calculations were carried out in single precision arithmetic without significant loss in accuracy, resulting in 50% reduction of memory and computational time requirements. The presented solidification model shows a very good scalability up to centimeter size domains, including more than ten million of dendrites. Catalogue identifier: AEQZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, UK Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 29,767 No. of bytes in distributed program, including test data, etc.: 3131,367 Distribution format: tar.gz Programming language: Fortran 90. Computer: Linux PC and clusters. Operating system: Linux. Has the code been vectorized or parallelized?: Yes. Program is parallelized using MPI. Number of processors used: 1-50,000 RAM: Memory requirements depend on the grid size Classification: 6.5, 7.7. External routines: MPI (http://www.mcs.anl.gov/research/projects/mpi/), HDF5 (http://www.hdfgroup.org/HDF5/) Nature of problem: Dendritic growth in undercooled Al-3 wt% Cu alloy melt under forced convection. Solution method: The lattice Boltzmann model solves the diffusion, convection, and heat transfer phenomena. The cellular automaton technique is deployed to track the solid/liquid interface. Restrictions: Heat transfer is calculated uncoupled from the fluid flow. Thermal diffusivity is constant. Unusual features: Novel technique, utilizing periodic duplication of a pre-grown “incubation” domain, is applied for the scaleup test. Running time: Running time varies from minutes to days depending on the domain size and number of computational cores.

CADNA_C: A version of CADNA for use with C or C++ programs

NASA Astrophysics Data System (ADS)

Lamotte, Jean-Luc; Chesneaux, Jean-Marie; Jézéquel, Fabienne

2010-11-01

The CADNA library enables one to estimate round-off error propagation using a probabilistic approach. The CADNA_C version enables this estimation in C or C++ programs, while the previous version had been developed for Fortran programs. The CADNA_C version has the same features as the previous one: with CADNA the numerical quality of any simulation program can be controlled. Furthermore by detecting all the instabilities which may occur at run time, a numerical debugging of the user code can be performed. CADNA provides new numerical types on which round-off errors can be estimated. Slight modifications are required to control a code with CADNA, mainly changes in variable declarations, input and output. New version program summaryProgram title: CADNA_C Catalogue identifier: AEGQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 60 075 No. of bytes in distributed program, including test data, etc.: 710 781 Distribution format: tar.gz Programming language: C++ Computer: PC running LINUX with an i686 or an ia64 processor, UNIX workstations including SUN, IBM Operating system: LINUX, UNIX Classification: 6.5 Catalogue identifier of previous version: AEAT_v1_0 Journal reference of previous version: Comput. Phys. Comm. 178 (2008) 933 Does the new version supersede the previous version?: No Nature of problem: A simulation program which uses floating-point arithmetic generates round-off errors, due to the rounding performed at each assignment and at each arithmetic operation. Round-off error propagation may invalidate the result of a program. The CADNA library enables one to estimate round-off error propagation in any simulation program and to detect all numerical instabilities that may occur at run time. Solution method: The CADNA library [1-3] implements Discrete Stochastic Arithmetic [4,5] which is based on a probabilistic model of round-off errors. The program is run several times with a random rounding mode generating different results each time. From this set of results, CADNA estimates the number of exact significant digits in the result that would have been computed with standard floating-point arithmetic. Reasons for new version: The previous version (AEAT_v1_0) enables the estimation of round-off error propagation in Fortran programs [2]. The new version has been developed to enable this estimation in C or C++ programs. Summary of revisions: The CADNA_C source code consists of one assembly language file (cadna_rounding.s) and twenty-three C++ language files (including three header files). cadna_rounding.s is a symbolic link to the assembly file corresponding to the processor and the C++ compiler used. This assembly file contains routines which are frequently called in the CADNA_C C++ files to change the rounding mode. The C++ language files contain the definition of the stochastic types on which the control of accuracy can be performed, CADNA_C specific functions (for instance to enable or disable the detection of numerical instabilities), the definition of arithmetic and relational operators which are overloaded for stochastic variables and the definition of mathematical functions which can be used with stochastic arguments. As a remark, on 64-bit processors, the mathematical library associated with the GNU C++ compiler may provide incorrect results or generate severe bugs with rounding towards -∞ and +∞, which the random rounding mode is based on. Therefore, if CADNA_C is used on a 64-bit processor with the GNU C++ compiler, mathematical functions are computed with rounding to the nearest, otherwise they are computed with the random rounding mode. It must be pointed out that the knowledge of the accuracy of the argument of a mathematical function is never lost. Additional comments: In the library archive, users are advised to read the INSTALL file first. The doc directory contains a user guide named ug.cadna.pdf and a reference guide named, ref_cadna.pdf. The user guide shows how to control the numerical accuracy of a program using CADNA, provides installation instructions and describes test runs.The reference guide briefly describes each function of the library. The source code (which consists of C++ and assembly files) is located in the src directory. The examples directory contains seven test runs which illustrate the use of the CADNA library and the benefits of Discrete Stochastic Arithmetic. Running time: The version of a code which uses CADNA runs at least three times slower than its floating-point version. This cost depends on the computer architecture and can be higher if the detection of numerical instabilities is enabled. In this case, the cost may be related to the number of instabilities detected.

A new version of the CADNA library for estimating round-off error propagation in Fortran programs

NASA Astrophysics Data System (ADS)

Jézéquel, Fabienne; Chesneaux, Jean-Marie; Lamotte, Jean-Luc

2010-11-01

The CADNA library enables one to estimate, using a probabilistic approach, round-off error propagation in any simulation program. CADNA provides new numerical types, the so-called stochastic types, on which round-off errors can be estimated. Furthermore CADNA contains the definition of arithmetic and relational operators which are overloaded for stochastic variables and the definition of mathematical functions which can be used with stochastic arguments. On 64-bit processors, depending on the rounding mode chosen, the mathematical library associated with the GNU Fortran compiler may provide incorrect results or generate severe bugs. Therefore the CADNA library has been improved to enable the numerical validation of programs on 64-bit processors. New version program summaryProgram title: CADNA Catalogue identifier: AEAT_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAT_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 28 488 No. of bytes in distributed program, including test data, etc.: 463 778 Distribution format: tar.gz Programming language: Fortran NOTE: A C++ version of this program is available in the Library as AEGQ_v1_0 Computer: PC running LINUX with an i686 or an ia64 processor, UNIX workstations including SUN, IBM Operating system: LINUX, UNIX Classification: 6.5 Catalogue identifier of previous version: AEAT_v1_0 Journal reference of previous version: Comput. Phys. Commun. 178 (2008) 933 Does the new version supersede the previous version?: Yes Nature of problem: A simulation program which uses floating-point arithmetic generates round-off errors, due to the rounding performed at each assignment and at each arithmetic operation. Round-off error propagation may invalidate the result of a program. The CADNA library enables one to estimate round-off error propagation in any simulation program and to detect all numerical instabilities that may occur at run time. Solution method: The CADNA library [1-3] implements Discrete Stochastic Arithmetic [4,5] which is based on a probabilistic model of round-off errors. The program is run several times with a random rounding mode generating different results each time. From this set of results, CADNA estimates the number of exact significant digits in the result that would have been computed with standard floating-point arithmetic. Reasons for new version: On 64-bit processors, the mathematical library associated with the GNU Fortran compiler may provide incorrect results or generate severe bugs with rounding towards -∞ and +∞, which the random rounding mode is based on. Therefore a particular definition of mathematical functions for stochastic arguments has been included in the CADNA library to enable its use with the GNU Fortran compiler on 64-bit processors. Summary of revisions: If CADNA is used on a 64-bit processor with the GNU Fortran compiler, mathematical functions are computed with rounding to the nearest, otherwise they are computed with the random rounding mode. It must be pointed out that the knowledge of the accuracy of the stochastic argument of a mathematical function is never lost. Restrictions: CADNA requires a Fortran 90 (or newer) compiler. In the program to be linked with the CADNA library, round-off errors on complex variables cannot be estimated. Furthermore array functions such as product or sum must not be used. Only the arithmetic operators and the abs, min, max and sqrt functions can be used for arrays. Additional comments: In the library archive, users are advised to read the INSTALL file first. The doc directory contains a user guide named ug.cadna.pdf which shows how to control the numerical accuracy of a program using CADNA, provides installation instructions and describes test runs. The source code, which is located in the src directory, consists of one assembly language file (cadna_rounding.s) and eighteen Fortran language files. cadna_rounding.s is a symbolic link to the assembly file corresponding to the processor and the Fortran compiler used. This assembly file contains routines which are frequently called in the CADNA Fortran files to change the rounding mode. The Fortran language files contain the definition of the stochastic types on which the control of accuracy can be performed, CADNA specific functions (for instance to enable or disable the detection of numerical instabilities), the definition of arithmetic and relational operators which are overloaded for stochastic variables and the definition of mathematical functions which can be used with stochastic arguments. The examples directory contains seven test runs which illustrate the use of the CADNA library and the benefits of Discrete Stochastic Arithmetic. Running time: The version of a code which uses CADNA runs at least three times slower than its floating-point version. This cost depends on the computer architecture and can be higher if the detection of numerical instabilities is enabled. In this case, the cost may be related to the number of instabilities detected.

Arc4nix: A cross-platform geospatial analytical library for cluster and cloud computing

NASA Astrophysics Data System (ADS)

Tang, Jingyin; Matyas, Corene J.

2018-02-01

Big Data in geospatial technology is a grand challenge for processing capacity. The ability to use a GIS for geospatial analysis on Cloud Computing and High Performance Computing (HPC) clusters has emerged as a new approach to provide feasible solutions. However, users lack the ability to migrate existing research tools to a Cloud Computing or HPC-based environment because of the incompatibility of the market-dominating ArcGIS software stack and Linux operating system. This manuscript details a cross-platform geospatial library "arc4nix" to bridge this gap. Arc4nix provides an application programming interface compatible with ArcGIS and its Python library "arcpy". Arc4nix uses a decoupled client-server architecture that permits geospatial analytical functions to run on the remote server and other functions to run on the native Python environment. It uses functional programming and meta-programming language to dynamically construct Python codes containing actual geospatial calculations, send them to a server and retrieve results. Arc4nix allows users to employ their arcpy-based script in a Cloud Computing and HPC environment with minimal or no modification. It also supports parallelizing tasks using multiple CPU cores and nodes for large-scale analyses. A case study of geospatial processing of a numerical weather model's output shows that arcpy scales linearly in a distributed environment. Arc4nix is open-source software.

View_SPECPR: Software for Plotting Spectra (Installation Manual and User's Guide, Version 1.2)

USGS Publications Warehouse

Kokaly, Raymond F.

2008-01-01

This document describes procedures for installing and using the 'View_SPECPR' software system to plot spectra stored in SPECPR (SPECtrum Processing Routines) files. The View_SPECPR software is comprised of programs written in IDL (Interactive Data Language) that run within the ENVI (ENvironment for Visualizing Images) image processing system. SPECPR files are used by earth-remote-sensing scientists and planetary scientists for storing spectra collected by laboratory, field, and remote sensing instruments. A widely distributed SPECPR file is the U.S. Geological Survey (USGS) spectral library that contains thousands of spectra of minerals, vegetation, and man-made materials (Clark and others, 2007). SPECPR files contain reflectance data and associated wavelength and spectral resolution data, as well as meta-data on the time and date of collection and spectrometer settings. Furthermore, the SPECPR file automatically tracks changes to data records through its 'history' fields. For more details on the format and content of SPECPR files, see Clark (1993). For more details on ENVI, see ITT (2008). This program has been updated using an ENVI 4.5/IDL7.0 full license operating on a Windows XP operating system and requires the installation of the iTools components of IDL7.0; however, this program should work with full licenses on UNIX/LINUX systems. This software has not been tested with ENVI licenses on Windows Vista or Apple Operating Systems.

Using ParaView Software on the Peregrine System | High-Performance

Science.gov Websites

come pre-installed on most Linux and Mac systems. On Windows the ssh and terminal functions are provided by the programs plink.exe and cmd.exe, of which only cmd.exe will come pre-installed. The ssh

Abstract of talk for Silicon Valley Linux Users Group

NASA Technical Reports Server (NTRS)

Clanton, Sam

2003-01-01

The use of Linux for research at NASA Ames is discussed.Topics include:work with the Atmospheric Physics branch on software for a spectrometer to be used in the CRYSTAL-FACE mission this summer; work on in the Neuroengineering Lab with code IC including an introduction to the extension of the human senses project,advantages with using linux for real-time biological data processing,algorithms utilized on a linux system, goals of the project,slides of people with Neuroscan caps on, and progress that has been made and how linux has helped.

An integrated tool for loop calculations: AITALC

NASA Astrophysics Data System (ADS)

Lorca, Alejandro; Riemann, Tord

2006-01-01

AITALC, a new tool for automating loop calculations in high energy physics, is described. The package creates Fortran code for two-fermion scattering processes automatically, starting from the generation and analysis of the Feynman graphs. We describe the modules of the tool, the intercommunication between them and illustrate its use with three examples. Program summaryTitle of the program:AITALC version 1.2.1 (9 August 2005) Catalogue identifier:ADWO Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWO Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Computer:PC i386 Operating system:GNU/ LINUX, tested on different distributions SuSE 8.2 to 9.3, Red Hat 7.2, Debian 3.0, Ubuntu 5.04. Also on SOLARIS Programming language used:GNU MAKE, DIANA, FORM, FORTRAN77 Additional programs/libraries used:DIANA 2.35 ( QGRAF 2.0), FORM 3.1, LOOPTOOLS 2.1 ( FF) Memory required to execute with typical data:Up to about 10 MB No. of processors used:1 No. of lines in distributed program, including test data, etc.:40 926 No. of bytes in distributed program, including test data, etc.:371 424 Distribution format:tar gzip file High-speed storage required:from 1.5 to 30 MB, depending on modules present and unfolding of examples Nature of the physical problem:Calculation of differential cross sections for ee annihilation in one-loop approximation. Method of solution:Generation and perturbative analysis of Feynman diagrams with later evaluation of matrix elements and form factors. Restriction of the complexity of the problem:The limit of application is, for the moment, the 2→2 particle reactions in the electro-weak standard model. Typical running time:Few minutes, being highly depending on the complexity of the process and the FORTRAN compiler.

Parallel implementation of an adaptive and parameter-free N-body integrator

NASA Astrophysics Data System (ADS)

Pruett, C. David; Ingham, William H.; Herman, Ralph D.

2011-05-01

Previously, Pruett et al. (2003) [3] described an N-body integrator of arbitrarily high order M with an asymptotic operation count of O(MN). The algorithm's structure lends itself readily to data parallelization, which we document and demonstrate here in the integration of point-mass systems subject to Newtonian gravitation. High order is shown to benefit parallel efficiency. The resulting N-body integrator is robust, parameter-free, highly accurate, and adaptive in both time-step and order. Moreover, it exhibits linear speedup on distributed parallel processors, provided that each processor is assigned at least a handful of bodies. Program summaryProgram title: PNB.f90 Catalogue identifier: AEIK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3052 No. of bytes in distributed program, including test data, etc.: 68 600 Distribution format: tar.gz Programming language: Fortran 90 and OpenMPI Computer: All shared or distributed memory parallel processors Operating system: Unix/Linux Has the code been vectorized or parallelized?: The code has been parallelized but has not been explicitly vectorized. RAM: Dependent upon N Classification: 4.3, 4.12, 6.5 Nature of problem: High accuracy numerical evaluation of trajectories of N point masses each subject to Newtonian gravitation. Solution method: Parallel and adaptive extrapolation in time via power series of arbitrary degree. Running time: 5.1 s for the demo program supplied with the package.

An upgraded version of the generator BCVEGPY2.0 for hadronic production of B meson and its excited states

NASA Astrophysics Data System (ADS)

Chang, Chao-Hsi; Wang, Jian-Xiong; Wu, Xing-Gang

2006-11-01

An upgraded version of the package BCVEGPY2.0: [C.-H. Chang, J.-X. Wang, X.-G. Wu, Comput. Phys. Commun. 174 (2006) 241] is presented, which works under LINUX system and is named as BCVEGPY2.1. With the version and a GNU C compiler additionally, users may simulate the B-events in various experimental environments very conveniently. It has been manipulated in better modularity and code reusability (less cross communication among various modules) than BCVEGPY2.0 has. Furthermore, in the upgraded version a special execution is arranged as that the GNU command make compiles a requested code with the help of a master makefile in main code directory, and then builds an executable file with the default name run. Finally, this paper may also be considered as an erratum, i.e., typo errors in BCVEGPY2.0 and corrections accordingly have been listed. New version program (BCVEGPY2.1) summaryTitle of program: BCVEGPY2.1 Catalogue identifier: ADTJ_v2_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTJ_v2_1 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Reference to original program: BCVEGPY2.0 Reference in CPC: Comput. Phys. Commun. 174 (2006) 241 Does the new version supersede the old program: No Computer: Any LINUX based on PC with FORTRAN 77 or FORTRAN 90 and GNU C compiler as well Operating systems: LINUX Programming language used: FORTRAN 77/90 Memory required to execute with typical data: About 2.0 MB No. of lines in distributed program, including test data, etc.: 31 521 No. of bytes in distributed program, including test data, etc.: 1 310 179 Distribution format: tar.gz Nature of physical problem: Hadronic production of B meson itself and its excited states Method of solution: The code with option can generate weighted and unweighted events. An interface to PYTHIA is provided to meet the needs of jets hadronization in the production. Restrictions on the complexity of the problem: The hadronic production of (cb¯)-quarkonium in S-wave and P-wave states via the mechanism of gluon-gluon fusion are given by the so-called 'complete calculation' approach. Reasons for new version: Responding to the feedback from users, we rearrange the program in a convenient way and then it can be easily adopted by the users to do the simulations according to their own experimental environment (e.g. detector acceptances and experimental cuts). We have paid many efforts to rearrange the program into several modules with less cross communication among the modules, the main program is slimmed down and all the further actions are decoupled from the main program and can be easily called for various purposes. Typical running time: The typical running time is machine and user-parameters dependent. Typically, for production of the S-wave (cb¯)-quarkonium, when IDWTUP = 1, it takes about 20 hour on a 1.8 GHz Intel P4-processor machine to generate 1000 events; however, when IDWTUP = 3, to generate 10 6 events it takes about 40 minutes only. Of the production, the time for the P-wave (cb¯)-quarkonium will take almost two times longer than that for its S-wave quarkonium. Summary of the changes (improvements): (1) The structure and organization of the program have been changed a lot. The new version package BCVEGPY2.1 has been divided into several modules with less cross communication among the modules (some old version source files are divided into several parts for the purpose). The main program is slimmed down and all the further actions are decoupled from the main program so that they can be easily called for various applications. All of the Fortran codes are organized in the main code directory named as bcvegpy2.1, which contains the main program, all of its prerequisite files and subsidiary 'folders' (subdirectory to the main code directory). The method for setting the parameter is the same as that of the previous versions [C.-H. Chang, C. Driouich, P. Eerola, X.-G. Wu, Comput. Phys. Commun. 159 (2004) 192, hep-ph/0309120. [1

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.

PubMed

Thakur, Shalabh; Guttman, David S

2016-06-30

Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation. We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available. DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/ .

SLHAplus: A library for implementing extensions of the standard model

NASA Astrophysics Data System (ADS)

Bélanger, G.; Christensen, Neil D.; Pukhov, A.; Semenov, A.

2011-03-01

We provide a library to facilitate the implementation of new models in codes such as matrix element and event generators or codes for computing dark matter observables. The library contains an SLHA reader routine as well as diagonalisation routines. This library is available in CalcHEP and micrOMEGAs. The implementation of models based on this library is supported by LanHEP and FeynRules. Program summaryProgram title: SLHAplus_1.3 Catalogue identifier: AEHX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 6283 No. of bytes in distributed program, including test data, etc.: 52 119 Distribution format: tar.gz Programming language: C Computer: IBM PC, MAC Operating system: UNIX (Linux, Darwin, Cygwin) RAM: 2000 MB Classification: 11.1 Nature of problem: Implementation of extensions of the standard model in matrix element and event generators and codes for dark matter observables. Solution method: For generic extensions of the standard model we provide routines for reading files that adopt the standard format of the SUSY Les Houches Accord (SLHA) file. The procedure has been generalized to take into account an arbitrary number of blocks so that the reader can be used in generic models including non-supersymmetric ones. The library also contains routines to diagonalize real and complex mass matrices with either unitary or bi-unitary transformations as well as routines for evaluating the running strong coupling constant, running quark masses and effective quark masses. Running time: 0.001 sec

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

PubMed

Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

2003-12-01

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

A machine vision system for micro-EDM based on linux

NASA Astrophysics Data System (ADS)

Guo, Rui; Zhao, Wansheng; Li, Gang; Li, Zhiyong; Zhang, Yong

2006-11-01

Due to the high precision and good surface quality that it can give, Electrical Discharge Machining (EDM) is potentially an important process for the fabrication of micro-tools and micro-components. However, a number of issues remain unsolved before micro-EDM becomes a reliable process with repeatable results. To deal with the difficulties in micro electrodes on-line fabrication and tool wear compensation, a micro-EDM machine vision system is developed with a Charge Coupled Device (CCD) camera, with an optical resolution of 1.61μm and an overall magnification of 113~729. Based on the Linux operating system, an image capturing program is developed with the V4L2 API, and an image processing program is exploited by using OpenCV. The contour of micro electrodes can be extracted by means of the Canny edge detector. Through the system calibration, the micro electrodes diameter can be measured on-line. Experiments have been carried out to prove its performance, and the reasons of measurement error are also analyzed.

System for Automated Geoscientific Analyses (SAGA) v. 2.1.4

NASA Astrophysics Data System (ADS)

Conrad, O.; Bechtel, B.; Bock, M.; Dietrich, H.; Fischer, E.; Gerlitz, L.; Wehberg, J.; Wichmann, V.; Böhner, J.

2015-02-01

The System for Automated Geoscientific Analyses (SAGA) is an open-source Geographic Information System (GIS), mainly licensed under the GNU General Public License. Since its first release in 2004, SAGA has rapidly developed from a specialized tool for digital terrain analysis to a comprehensive and globally established GIS platform for scientific analysis and modeling. SAGA is coded in C++ in an object oriented design and runs under several operating systems including Windows and Linux. Key functional features of the modular organized software architecture comprise an application programming interface for the development and implementation of new geoscientific methods, an easily approachable graphical user interface with many visualization options, a command line interpreter, and interfaces to scripting and low level programming languages like R and Python. The current version 2.1.4 offers more than 700 tools, which are implemented in dynamically loadable libraries or shared objects and represent the broad scopes of SAGA in numerous fields of geoscientific endeavor and beyond. In this paper, we inform about the system's architecture, functionality, and its current state of development and implementation. Further, we highlight the wide spectrum of scientific applications of SAGA in a review of published studies with special emphasis on the core application areas digital terrain analysis, geomorphology, soil science, climatology and meteorology, as well as remote sensing.

3DProIN: Protein-Protein Interaction Networks and Structure Visualization.

PubMed

Li, Hui; Liu, Chunmei

2014-06-14

3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view. It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network. Properties such as color, shape and name of each node (protein) of the network can be edited in either 2D or 3D views. 3DProIN is implemented using 3D Java and C programming languages. The internet crawl technique is also used to parse dynamically grasped protein interactions from protein data bank (PDB). It is a java applet component that is embedded in the web page and it can be used on different platforms including Linux, Mac and Window using web browsers such as Firefox, Internet Explorer, Chrome and Safari. It also was converted into a mac app and submitted to the App store as a free app. Mac users can also download the app from our website. 3DProIN is available for academic research at http://bicompute.appspot.com.

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.

PubMed

McMurdie, Paul J; Holmes, Susan

2015-01-15

We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user's session, allowing the user to archive, share and reproduce the sequence of steps that created their result-without writing any new code themselves. Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny--phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at http://joey711.github.io/shiny-phyloseq/. © The Author 2014. Published by Oxford University Press.

Chronology of DIC technique based on the fundamental mathematical modeling and dehydration impact.

PubMed

Alias, Norma; Saipol, Hafizah Farhah Saipan; Ghani, Asnida Che Abd

2014-12-01

A chronology of mathematical models for heat and mass transfer equation is proposed for the prediction of moisture and temperature behavior during drying using DIC (Détente Instantanée Contrôlée) or instant controlled pressure drop technique. DIC technique has the potential as most commonly used dehydration method for high impact food value including the nutrition maintenance and the best possible quality for food storage. The model is governed by the regression model, followed by 2D Fick's and Fourier's parabolic equation and 2D elliptic-parabolic equation in a rectangular slice. The models neglect the effect of shrinkage and radiation effects. The simulations of heat and mass transfer equations with parabolic and elliptic-parabolic types through some numerical methods based on finite difference method (FDM) have been illustrated. Intel®Core™2Duo processors with Linux operating system and C programming language have been considered as a computational platform for the simulation. Qualitative and quantitative differences between DIC technique and the conventional drying methods have been shown as a comparative.

DPEMC: A Monte Carlo for double diffraction

NASA Astrophysics Data System (ADS)

Boonekamp, M.; Kúcs, T.

2005-05-01

We extend the POMWIG Monte Carlo generator developed by B. Cox and J. Forshaw, to include new models of central production through inclusive and exclusive double Pomeron exchange in proton-proton collisions. Double photon exchange processes are described as well, both in proton-proton and heavy-ion collisions. In all contexts, various models have been implemented, allowing for comparisons and uncertainty evaluation and enabling detailed experimental simulations. Program summaryTitle of the program:DPEMC, version 2.4 Catalogue identifier: ADVF Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVF Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: any computer with the FORTRAN 77 compiler under the UNIX or Linux operating systems Operating system: UNIX; Linux Programming language used: FORTRAN 77 High speed storage required:<25 MB No. of lines in distributed program, including test data, etc.: 71 399 No. of bytes in distributed program, including test data, etc.: 639 950 Distribution format: tar.gz Nature of the physical problem: Proton diffraction at hadron colliders can manifest itself in many forms, and a variety of models exist that attempt to describe it [A. Bialas, P.V. Landshoff, Phys. Lett. B 256 (1991) 540; A. Bialas, W. Szeremeta, Phys. Lett. B 296 (1992) 191; A. Bialas, R.A. Janik, Z. Phys. C 62 (1994) 487; M. Boonekamp, R. Peschanski, C. Royon, Phys. Rev. Lett. 87 (2001) 251806; Nucl. Phys. B 669 (2003) 277; R. Enberg, G. Ingelman, A. Kissavos, N. Timneanu, Phys. Rev. Lett. 89 (2002) 081801; R. Enberg, G. Ingelman, L. Motyka, Phys. Lett. B 524 (2002) 273; R. Enberg, G. Ingelman, N. Timneanu, Phys. Rev. D 67 (2003) 011301; B. Cox, J. Forshaw, Comput. Phys. Comm. 144 (2002) 104; B. Cox, J. Forshaw, B. Heinemann, Phys. Lett. B 540 (2002) 26; V. Khoze, A. Martin, M. Ryskin, Phys. Lett. B 401 (1997) 330; Eur. Phys. J. C 14 (2000) 525; Eur. Phys. J. C 19 (2001) 477; Erratum, Eur. Phys. J. C 20 (2001) 599; Eur. Phys. J. C 23 (2002) 311]. This program implements some of the more significant ones, enabling the simulation of central particle production through color singlet exchange between interacting protons or antiprotons. Method of solution: The Monte Carlo method is used to simulate all elementary 2→2 and 2→1 processes available in HERWIG. The color singlet exchanges implemented in DPEMC are implemented as functions reweighting the photon flux already present in HERWIG. Restriction on the complexity of the problem: The program relying extensively on HERWIG, the limitations are the same as in [G. Marchesini, B.R. Webber, G. Abbiendi, I.G. Knowles, M.H. Seymour, L. Stanco, Comput. Phys. Comm. 67 (1992) 465; G. Corcella, I.G. Knowles, G. Marchesini, S. Moretti, K. Odagiri, P. Richardson, M. Seymour, B. Webber, JHEP 0101 (2001) 010]. Typical running time: Approximate times on a 800 MHz Pentium III: 5-20 min per 10 000 unweighted events, depending on the process under consideration.

BerkeleyGW: A massively parallel computer package for the calculation of the quasiparticle and optical properties of materials and nanostructures

NASA Astrophysics Data System (ADS)

Deslippe, Jack; Samsonidze, Georgy; Strubbe, David A.; Jain, Manish; Cohen, Marvin L.; Louie, Steven G.

2012-06-01

BerkeleyGW is a massively parallel computational package for electron excited-state properties that is based on the many-body perturbation theory employing the ab initio GW and GW plus Bethe-Salpeter equation methodology. It can be used in conjunction with many density-functional theory codes for ground-state properties, including PARATEC, PARSEC, Quantum ESPRESSO, SIESTA, and Octopus. The package can be used to compute the electronic and optical properties of a wide variety of material systems from bulk semiconductors and metals to nanostructured materials and molecules. The package scales to 10 000s of CPUs and can be used to study systems containing up to 100s of atoms. Program summaryProgram title: BerkeleyGW Catalogue identifier: AELG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open source BSD License. See code for licensing details. No. of lines in distributed program, including test data, etc.: 576 540 No. of bytes in distributed program, including test data, etc.: 110 608 809 Distribution format: tar.gz Programming language: Fortran 90, C, C++, Python, Perl, BASH Computer: Linux/UNIX workstations or clusters Operating system: Tested on a variety of Linux distributions in parallel and serial as well as AIX and Mac OSX RAM: (50-2000) MB per CPU (Highly dependent on system size) Classification: 7.2, 7.3, 16.2, 18 External routines: BLAS, LAPACK, FFTW, ScaLAPACK (optional), MPI (optional). All available under open-source licenses. Nature of problem: The excited state properties of materials involve the addition or subtraction of electrons as well as the optical excitations of electron-hole pairs. The excited particles interact strongly with other electrons in a material system. This interaction affects the electronic energies, wavefunctions and lifetimes. It is well known that ground-state theories, such as standard methods based on density-functional theory, fail to correctly capture this physics. Solution method: We construct and solve the Dyson's equation for the quasiparticle energies and wavefunctions within the GW approximation for the electron self-energy. We additionally construct and solve the Bethe-Salpeter equation for the correlated electron-hole (exciton) wavefunctions and excitation energies. Restrictions: The material size is limited in practice by the computational resources available. Materials with up to 500 atoms per periodic cell can be studied on large HPCs. Additional comments: The distribution file for this program is approximately 110 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: 1-1000 minutes (depending greatly on system size and processor number).

Automated evaluation of matrix elements between contracted wavefunctions: A Mathematica version of the FRODO program

NASA Astrophysics Data System (ADS)

Angeli, C.; Cimiraglia, R.

2013-02-01

A symbolic program performing the Formal Reduction of Density Operators (FRODO), formerly developed in the MuPAD computer algebra system with the purpose of evaluating the matrix elements of the electronic Hamiltonian between internally contracted functions in a complete active space (CAS) scheme, has been rewritten in Mathematica. New version : A program summaryProgram title: FRODO Catalogue identifier: ADV Y _v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVY_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3878 No. of bytes in distributed program, including test data, etc.: 170729 Distribution format: tar.gz Programming language: Mathematica Computer: Any computer on which the Mathematica computer algebra system can be installed Operating system: Linux Classification: 5 Catalogue identifier of previous version: ADV Y _v1_0 Journal reference of previous version: Comput. Phys. Comm. 171(2005)63 Does the new version supersede the previous version?: No Nature of problem. In order to improve on the CAS-SCF wavefunction one can resort to multireference perturbation theory or configuration interaction based on internally contracted functions (ICFs) which are obtained by application of the excitation operators to the reference CAS-SCF wavefunction. The previous formulation of such matrix elements in the MuPAD computer algebra system, has been rewritten using Mathematica. Solution method: The method adopted consists in successively eliminating all occurrences of inactive orbital indices (core and virtual) from the products of excitation operators which appear in the definition of the ICFs and in the electronic Hamiltonian expressed in the second quantization formalism. Reasons for new version: Some years ago we published in this journal a couple of papers [1, 2] hereafter to be referred to as papers I and II, respectively dedicated to the automated evaluation of the matrix elements of the molecular electronic Hamiltonian between internally contracted functions [3] (ICFs). In paper II the program FRODO (after Formal Reduction Of Density Operators) was presented with the purpose of providing working formulas for each occurrence of the ICFs. The original FRODO program was written in the MuPAD computer algebra system [4] and was actively used in our group for the generation of the matrix elements to be employed in the third-order n-electron valence state perturbation theory (NEVPT) [5-8] as well as in the internally contracted configuration interaction (IC-CI) [9]. We present a new version of the program FRODO written in the Mathematica system [10]. The reason for the rewriting of the program lies in the fact that, on the one hand, MuPAD does not seem to be any longer available as a stand-alone system and, on the other hand, Mathematica, due to its ubiquitousness, appears to be increasingly the computer algebra system most widely used nowadays. Restrictions: The program is limited to no more than doubly excited ICFs. Running time: The examples described in the Readme file take a few seconds to run. References: [1] C. Angeli, R. Cimiraglia, Comp. Phys. Comm. 166 (2005) 53. [2] C. Angeli, R. Cimiraglia, Comp. Phys. Comm. 171 (2005) 63. [3] H.-J. Werner, P. J. Knowles, Adv. Chem. Phys. 89 (1988) 5803. [4] B. Fuchssteiner, W. Oevel: http://www.mupad.de Mupad research group, university of Paderborn. Mupad version 2.5.3 for Linux. [5] C. Angeli, R. Cimiraglia, S. Evangelisti, T. Leininger, J.-P. Malrieu, J. Chem. Phys. 114 (2001) 10252. [6] C. Angeli, R. Cimiraglia, J.-P. Malrieu, J. Chem. Phys. 117 (2002) 9138. [7] C. Angeli, B. Bories, A. Cavallini, R. Cimiraglia, J. Chem. Phys. 124 (2006) 054108. [8] C. Angeli, M. Pastore, R. Cimiraglia, Theor. Chem. Acc. 117 (2007) 743. [9] C. Angeli, R. Cimiraglia, Mol. Phys. in press, DOI:10.1080/00268976.2012.689872 [10] http://www.wolfram.com/Mathematica. Mathematica version 8 for Linux.

Building CHAOS: An Operating System for Livermore Linux Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garlick, J E; Dunlap, C M

2003-02-21

The Livermore Computing (LC) Linux Integration and Development Project (the Linux Project) produces and supports the Clustered High Availability Operating System (CHAOS), a cluster operating environment based on Red Hat Linux. Each CHAOS release begins with a set of requirements and ends with a formally tested, packaged, and documented release suitable for use on LC's production Linux clusters. One characteristic of CHAOS is that component software packages come from different sources under varying degrees of project control. Some are developed by the Linux Project, some are developed by other LC projects, some are external open source projects, and some aremore » commercial software packages. A challenge to the Linux Project is to adhere to release schedules and testing disciplines in a diverse, highly decentralized development environment. Communication channels are maintained for externally developed packages in order to obtain support, influence development decisions, and coordinate/understand release schedules. The Linux Project embraces open source by releasing locally developed packages under open source license, by collaborating with open source projects where mutually beneficial, and by preferring open source over proprietary software. Project members generally use open source development tools. The Linux Project requires system administrators and developers to work together to resolve problems that arise in production. This tight coupling of production and development is a key strategy for making a product that directly addresses LC's production requirements. It is another challenge to balance support and development activities in such a way that one does not overwhelm the other.« less

ALOHA: Automatic libraries of helicity amplitudes for Feynman diagram computations

NASA Astrophysics Data System (ADS)

de Aquino, Priscila; Link, William; Maltoni, Fabio; Mattelaer, Olivier; Stelzer, Tim

2012-10-01

We present an application that automatically writes the HELAS (HELicity Amplitude Subroutines) library corresponding to the Feynman rules of any quantum field theory Lagrangian. The code is written in Python and takes the Universal FeynRules Output (UFO) as an input. From this input it produces the complete set of routines, wave-functions and amplitudes, that are needed for the computation of Feynman diagrams at leading as well as at higher orders. The representation is language independent and currently it can output routines in Fortran, C++, and Python. A few sample applications implemented in the MADGRAPH 5 framework are presented. Program summary Program title: ALOHA Catalogue identifier: AEMS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: http://www.opensource.org/licenses/UoI-NCSA.php No. of lines in distributed program, including test data, etc.: 6094320 No. of bytes in distributed program, including test data, etc.: 7479819 Distribution format: tar.gz Programming language: Python2.6 Computer: 32/64 bit Operating system: Linux/Mac/Windows RAM: 512 Mbytes Classification: 4.4, 11.6 Nature of problem: An effcient numerical evaluation of a squared matrix element can be done with the help of the helicity routines implemented in the HELAS library [1]. This static library contains a limited number of helicity functions and is therefore not always able to provide the needed routine in the presence of an arbitrary interaction. This program provides a way to automatically create the corresponding routines for any given model. Solution method: ALOHA takes the Feynman rules associated to the vertex obtained from the model information (in the UFO format [2]), and multiplies it by the different wavefunctions or propagators. As a result the analytical expression of the helicity routines is obtained. Subsequently, this expression is automatically written in the requested language (Python, Fortran or C++) Restrictions: The allowed fields are currently spin 0, 1/2, 1 and 2, and the propagators of these particles are canonical. Running time: A few seconds for the SM and the MSSM, and up to a few minutes for models with spin 2 particles. References: [1] Murayama, H. and Watanabe, I. and Hagiwara, K., HELAS: HELicity Amplitude Subroutines for Feynman diagram evaluations, KEK-91-11, (1992) http://www-lib.kek.jp/cgi-bin/img_index?199124011 [2] C. Degrande, C. Duhr, B. Fuks, D. Grellscheid, O. Mattelaer, et al., UFO— The Universal FeynRules Output, Comput. Phys. Commun. 183 (2012) 1201-1214. arXiv:1108.2040, doi:10.1016/j.cpc.2012.01.022.

Mars Science Laboratory Workstation Test Set

NASA Technical Reports Server (NTRS)

Henriquez, David A.; Canham, Timothy K.; Chang, Johnny T.; Villaume, Nathaniel

2009-01-01

The Mars Science Laboratory developed the Workstation TestSet (WSTS) is a computer program that enables flight software development on virtual MSL avionics. The WSTS is the non-real-time flight avionics simulator that is designed to be completely software-based and run on a workstation class Linux PC.

Development of an Autonomous Navigation Technology Test Vehicle

DTIC Science & Technology

2004-08-01

as an independent thread on processors using the Linux operating system. The computer hardware selected for the nodes that host the MRS threads...communications system design. Linux was chosen as the operating system for all of the single board computers used on the Mule. Linux was specifically...used for system analysis and development. The simple realization of multi-thread processing and inter-process communications in Linux made it a

Development of new on-line statistical program for the Korean Society for Radiation Oncology

PubMed Central

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Choi, Eun Kyung; Cho, Kwan Ho

2015-01-01

Purpose To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. Materials and Methods The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Results Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. Conclusion The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology. PMID:26157684

Development of new on-line statistical program for the Korean Society for Radiation Oncology.

PubMed

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Shin, Kyung Hwan; Choi, Eun Kyung; Cho, Kwan Ho

2015-06-01

To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology.

Research about Memory Detection Based on the Embedded Platform

NASA Astrophysics Data System (ADS)

Sun, Hao; Chu, Jian

As is known to us all, the resources of memory detection of the embedded systems are very limited. Taking the Linux-based embedded arm as platform, this article puts forward two efficient memory detection technologies according to the characteristics of the embedded software. Especially for the programs which need specific libraries, the article puts forwards portable memory detection methods to help program designers to reduce human errors,improve programming quality and therefore make better use of the valuable embedded memory resource.

Scaling Concolic Execution of Binary Programs for Security Applications

DTIC Science & Technology

2013-08-01

Byte Array “<><><>” “<>” (89 times) 4/5 672 1 Sendmail 2 struct passwd (Linux) (“”,“root”,0,0,“root”,“”,“”) (“”,“root”,0,0,“rootroo”,“”,“”) 1/1 526

An algorithm of a real time image tracking system using a camera with pan/tilt motors on an embedded system

NASA Astrophysics Data System (ADS)

Kim, Hie-Sik; Nam, Chul; Ha, Kwan-Yong; Ayurzana, Odgeral; Kwon, Jong-Won

2005-12-01

The embedded systems have been applied to many fields, including households and industrial sites. The user interface technology with simple display on the screen was implemented more and more. The user demands are increasing and the system has more various applicable fields due to a high penetration rate of the Internet. Therefore, the demand for embedded system is tend to rise. An embedded system for image tracking was implemented. This system is used a fixed IP for the reliable server operation on TCP/IP networks. Using an USB camera on the embedded Linux system developed a real time broadcasting of video image on the Internet. The digital camera is connected at the USB host port of the embedded board. All input images from the video camera are continuously stored as a compressed JPEG file in a directory at the Linux web-server. And each frame image data from web camera is compared for measurement of displacement Vector. That used Block matching algorithm and edge detection algorithm for past speed. And the displacement vector is used at pan/tilt motor control through RS232 serial cable. The embedded board utilized the S3C2410 MPU, which used the ARM 920T core form Samsung. The operating system was ported to embedded Linux kernel and mounted of root file system. And the stored images are sent to the client PC through the web browser. It used the network function of Linux and it developed a program with protocol of the TCP/IP.

a Linux PC Cluster for Lattice QCD with Exact Chiral Symmetry

NASA Astrophysics Data System (ADS)

Chiu, Ting-Wai; Hsieh, Tung-Han; Huang, Chao-Hsi; Huang, Tsung-Ren

A computational system for lattice QCD with overlap Dirac quarks is described. The platform is a home-made Linux PC cluster, built with off-the-shelf components. At present the system constitutes of 64 nodes, with each node consisting of one Pentium 4 processor (1.6/2.0/2.5 GHz), one Gbyte of PC800/1066 RDRAM, one 40/80/120 Gbyte hard disk, and a network card. The computationally intensive parts of our program are written in SSE2 codes. The speed of our system is estimated to be 70 Gflops, and its price/performance ratio is better than $1.0/Mflops for 64-bit (double precision) computations in quenched QCD. We discuss how to optimize its hardware and software for computing propagators of overlap Dirac quarks.

Tuning Linux to meet real time requirements

NASA Astrophysics Data System (ADS)

Herbel, Richard S.; Le, Dang N.

2007-04-01

There is a desire to use Linux in military systems. Customers are requesting contractors to use open source to the maximal possible extent in contracts. Linux is probably the best operating system of choice to meet this need. It is widely used. It is free. It is royalty free, and, best of all, it is completely open source. However, there is a problem. Linux was not originally built to be a real time operating system. There are many places where interrupts can and will be blocked for an indeterminate amount of time. There have been several attempts to bridge this gap. One of them is from RTLinux, which attempts to build a microkernel underneath Linux. The microkernel will handle all interrupts and then pass it up to the Linux operating system. This does insure good interrupt latency; however, it is not free [1]. Another is RTAI, which provides a similar typed interface; however, the PowerPC platform, which is used widely in real time embedded community, was stated as "recovering" [2]. Thus this is not suited for military usage. This paper provides a method for tuning a standard Linux kernel so it can meet the real time requirement of an embedded system.

g_contacts: Fast contact search in bio-molecular ensemble data

NASA Astrophysics Data System (ADS)

Blau, Christian; Grubmuller, Helmut

2013-12-01

Short-range interatomic interactions govern many bio-molecular processes. Therefore, identifying close interaction partners in ensemble data is an essential task in structural biology and computational biophysics. A contact search can be cast as a typical range search problem for which efficient algorithms have been developed. However, none of those has yet been adapted to the context of macromolecular ensembles, particularly in a molecular dynamics (MD) framework. Here a set-decomposition algorithm is implemented which detects all contacting atoms or residues in maximum O(Nlog(N)) run-time, in contrast to the O(N2) complexity of a brute-force approach. Catalogue identifier: AEQA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQA_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 8945 No. of bytes in distributed program, including test data, etc.: 981604 Distribution format: tar.gz Programming language: C99. Computer: PC. Operating system: Linux. RAM: ≈Size of input frame Classification: 3, 4.14. External routines: Gromacs 4.6[1] Nature of problem: Finding atoms or residues that are closer to one another than a given cut-off. Solution method: Excluding distant atoms from distance calculations by decomposing the given set of atoms into disjoint subsets. Running time:≤O(Nlog(N)) References: [1] S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J.C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and Erik Lindahl, Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29 (7) (2013).

SLAM, a Mathematica interface for SUSY spectrum generators

NASA Astrophysics Data System (ADS)

Marquard, Peter; Zerf, Nikolai

2014-03-01

We present and publish a Mathematica package, which can be used to automatically obtain any numerical MSSM input parameter from SUSY spectrum generators, which follow the SLHA standard, like SPheno, SOFTSUSY, SuSeFLAV or Suspect. The package enables a very comfortable way of numerical evaluations within the MSSM using Mathematica. It implements easy to use predefined high scale and low scale scenarios like mSUGRA or mhmax and if needed enables the user to directly specify the input required by the spectrum generators. In addition it supports an automatic saving and loading of SUSY spectra to and from a SQL data base, avoiding the rerun of a spectrum generator for a known spectrum. Catalogue identifier: AERX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERX_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 4387 No. of bytes in distributed program, including test data, etc.: 37748 Distribution format: tar.gz Programming language: Mathematica. Computer: Any computer where Mathematica version 6 or higher is running providing bash and sed. Operating system: Linux. Classification: 11.1. External routines: A SUSY spectrum generator such as SPheno, SOFTSUSY, SuSeFLAV or SUSPECT Nature of problem: Interfacing published spectrum generators for automated creation, saving and loading of SUSY particle spectra. Solution method: SLAM automatically writes/reads SLHA spectrum generator input/output and is able to save/load generated data in/from a data base. Restrictions: No general restrictions, specific restrictions are given in the manuscript. Running time: A single spectrum calculation takes much less than one second on a modern PC.

QuTiP: An open-source Python framework for the dynamics of open quantum systems

NASA Astrophysics Data System (ADS)

Johansson, J. R.; Nation, P. D.; Nori, Franco

2012-08-01

We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum object class, and then passed on to a choice of master equation or Monte Carlo solvers. We give an overview of the basic structure for the framework before detailing the numerical simulation of open system dynamics. Several examples are given to illustrate the build up to a complete calculation. Finally, we measure the performance of our library against that of current implementations. The framework described here is particularly well suited to the fields of quantum optics, superconducting circuit devices, nanomechanics, and trapped ions, while also being ideal for use in classroom instruction. Catalogue identifier: AEMB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 16 482 No. of bytes in distributed program, including test data, etc.: 213 438 Distribution format: tar.gz Programming language: Python Computer: i386, x86-64 Operating system: Linux, Mac OSX, Windows RAM: 2+ Gigabytes Classification: 7 External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.org/), Matplotlib (http://matplotlib.sourceforge.net/) Nature of problem: Dynamics of open quantum systems. Solution method: Numerical solutions to Lindblad master equation or Monte Carlo wave function method. Restrictions: Problems must meet the criteria for using the master equation in Lindblad form. Running time: A few seconds up to several tens of minutes, depending on size of underlying Hilbert space.

QRAP: A numerical code for projected (Q)uasiparticle (RA)ndom (P)hase approximation

NASA Astrophysics Data System (ADS)

Samana, A. R.; Krmpotić, F.; Bertulani, C. A.

2010-06-01

A computer code for quasiparticle random phase approximation - QRPA and projected quasiparticle random phase approximation - PQRPA models of nuclear structure is explained in details. The residual interaction is approximated by a simple δ-force. An important application of the code consists in evaluating nuclear matrix elements involved in neutrino-nucleus reactions. As an example, cross sections for 56Fe and 12C are calculated and the code output is explained. The application to other nuclei and the description of other nuclear and weak decay processes are also discussed. Program summaryTitle of program: QRAP ( Quasiparticle RAndom Phase approximation) Computers: The code has been created on a PC, but also runs on UNIX or LINUX machines Operating systems: WINDOWS or UNIX Program language used: Fortran-77 Memory required to execute with typical data: 16 Mbytes of RAM memory and 2 MB of hard disk space No. of lines in distributed program, including test data, etc.: ˜ 8000 No. of bytes in distributed program, including test data, etc.: ˜ 256 kB Distribution format: tar.gz Nature of physical problem: The program calculates neutrino- and antineutrino-nucleus cross sections as a function of the incident neutrino energy, and muon capture rates, using the QRPA or PQRPA as nuclear structure models. Method of solution: The QRPA, or PQRPA, equations are solved in a self-consistent way for even-even nuclei. The nuclear matrix elements for the neutrino-nucleus interaction are treated as the beta inverse reaction of odd-odd nuclei as function of the transfer momentum. Typical running time: ≈ 5 min on a 3 GHz processor for Data set 1.

A Matlab-based finite-difference solver for the Poisson problem with mixed Dirichlet-Neumann boundary conditions

NASA Astrophysics Data System (ADS)

Reimer, Ashton S.; Cheviakov, Alexei F.

2013-03-01

A Matlab-based finite-difference numerical solver for the Poisson equation for a rectangle and a disk in two dimensions, and a spherical domain in three dimensions, is presented. The solver is optimized for handling an arbitrary combination of Dirichlet and Neumann boundary conditions, and allows for full user control of mesh refinement. The solver routines utilize effective and parallelized sparse vector and matrix operations. Computations exhibit high speeds, numerical stability with respect to mesh size and mesh refinement, and acceptable error values even on desktop computers. Catalogue identifier: AENQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3.0 No. of lines in distributed program, including test data, etc.: 102793 No. of bytes in distributed program, including test data, etc.: 369378 Distribution format: tar.gz Programming language: Matlab 2010a. Computer: PC, Macintosh. Operating system: Windows, OSX, Linux. RAM: 8 GB (8, 589, 934, 592 bytes) Classification: 4.3. Nature of problem: To solve the Poisson problem in a standard domain with “patchy surface”-type (strongly heterogeneous) Neumann/Dirichlet boundary conditions. Solution method: Finite difference with mesh refinement. Restrictions: Spherical domain in 3D; rectangular domain or a disk in 2D. Unusual features: Choice between mldivide/iterative solver for the solution of large system of linear algebraic equations that arise. Full user control of Neumann/Dirichlet boundary conditions and mesh refinement. Running time: Depending on the number of points taken and the geometry of the domain, the routine may take from less than a second to several hours to execute.

Open Radio Communications Architecture Core Framework V1.1.0 Volume 1 Software Users Manual

DTIC Science & Technology

2005-02-01

on a PC utilizing the KDE desktop that comes with Red Hat Linux . The default desktop for most Red Hat Linux installations is the GNOME desktop. The...SCA) v2.2. The software was designed for a desktop computer running the Linux operating system (OS). It was developed in C++, uses ACE/TAO for CORBA...middleware, Xerces for the XML parser, and Red Hat Linux for the Operating System. The software is referred to as, Open Radio Communication

Content Documents Management

NASA Technical Reports Server (NTRS)

Muniz, R.; Hochstadt, J.; Boelke J.; Dalton, A.

2011-01-01

The Content Documents are created and managed under the System Software group with. Launch Control System (LCS) project. The System Software product group is lead by NASA Engineering Control and Data Systems branch (NEC3) at Kennedy Space Center. The team is working on creating Operating System Images (OSI) for different platforms (i.e. AIX, Linux, Solaris and Windows). Before the OSI can be created, the team must create a Content Document which provides the information of a workstation or server, with the list of all the software that is to be installed on it and also the set where the hardware belongs. This can be for example in the LDS, the ADS or the FR-l. The objective of this project is to create a User Interface Web application that can manage the information of the Content Documents, with all the correct validations and filters for administrator purposes. For this project we used one of the most excellent tools in agile development applications called Ruby on Rails. This tool helps pragmatic programmers develop Web applications with Rails framework and Ruby programming language. It is very amazing to see how a student can learn about OOP features with the Ruby language, manage the user interface with HTML and CSS, create associations and queries with gems, manage databases and run a server with MYSQL, run shell commands with command prompt and create Web frameworks with Rails. All of this in a real world project and in just fifteen weeks!

HARE: Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mckie, Jim

2012-01-09

This report documents the results of work done over a 6 year period under the FAST-OS programs. The first effort was called Right-Weight Kernels, (RWK) and was concerned with improving measurements of OS noise so it could be treated quantitatively; and evaluating the use of two operating systems, Linux and Plan 9, on HPC systems and determining how these operating systems needed to be extended or changed for HPC, while still retaining their general-purpose nature. The second program, HARE, explored the creation of alternative runtime models, building on RWK. All of the HARE work was done on Plan 9. Themore » HARE researchers were mindful of the very good Linux and LWK work being done at other labs and saw no need to recreate it. Even given this limited funding, the two efforts had outsized impact: _ Helped Cray decide to use Linux, instead of a custom kernel, and provided the tools needed to make Linux perform well _ Created a successor operating system to Plan 9, NIX, which has been taken in by Bell Labs for further development _ Created a standard system measurement tool, Fixed Time Quantum or FTQ, which is widely used for measuring operating systems impact on applications _ Spurred the use of the 9p protocol in several organizations, including IBM _ Built software in use at many companies, including IBM, Cray, and Google _ Spurred the creation of alternative runtimes for use on HPC systems _ Demonstrated that, with proper modifications, a general purpose operating systems can provide communications up to 3 times as effective as user-level libraries Open source was a key part of this work. The code developed for this project is in wide use and available at many places. The core Blue Gene code is available at https://bitbucket.org/ericvh/hare. We describe details of these impacts in the following sections. The rest of this report is organized as follows: First, we describe commercial impact; next, we describe the FTQ benchmark and its impact in more detail; operating systems and runtime research follows; we discuss infrastructure software; and close with a description of the new NIX operating system, future work, and conclusions.« less

Linux thin-client conversion in a large cardiology practice: initial experience.

PubMed

Echt, Martin P; Rosen, Jordan

2004-01-01

Capital Cardiology Associates (CCA) is a single-specialty cardiology practice with offices in New York and Massachusetts. In 2003, CCA converted its IT system from a Microsoft-based network to a Linux network employing Linux thin-client technology with overall positive outcomes.

OpenMx: An Open Source Extended Structural Equation Modeling Framework

ERIC Educational Resources Information Center

Boker, Steven; Neale, Michael; Maes, Hermine; Wilde, Michael; Spiegel, Michael; Brick, Timothy; Spies, Jeffrey; Estabrook, Ryne; Kenny, Sarah; Bates, Timothy; Mehta, Paras; Fox, John

2011-01-01

OpenMx is free, full-featured, open source, structural equation modeling (SEM) software. OpenMx runs within the "R" statistical programming environment on Windows, Mac OS-X, and Linux computers. The rationale for developing OpenMx is discussed along with the philosophy behind the user interface. The OpenMx data structures are…

A Design and Development of Multi-Purpose CCD Camera System with Thermoelectric Cooling: Software

NASA Astrophysics Data System (ADS)

Oh, S. H.; Kang, Y. W.; Byun, Y. I.

2007-12-01

We present a software which we developed for the multi-purpose CCD camera. This software can be used on the all 3 types of CCD - KAF-0401E (768×512), KAF-1602E (15367times;1024), KAF-3200E (2184×1472) made in KODAK Co.. For the efficient CCD camera control, the software is operated with two independent processes of the CCD control program and the temperature/shutter operation program. This software is designed to fully automatic operation as well as manually operation under LINUX system, and is controled by LINUX user signal procedure. We plan to use this software for all sky survey system and also night sky monitoring and sky observation. As our results, the read-out time of each CCD are about 15sec, 64sec, 134sec for KAF-0401E, KAF-1602E, KAF-3200E., because these time are limited by the data transmission speed of parallel port. For larger format CCD, the data transmission is required more high speed. we are considering this control software to one using USB port for high speed data transmission.

Development and Testing of a High-Speed Real-Time Kinematic Precise DGPS Positioning System Between Two Aircraft

DTIC Science & Technology

2006-09-01

work-horse for this thesis. He spent hours writing some of the more tedious code, and as much time helping me learn C++ and Linux . He was always there...compared with C++, and the need to use Linux as the operating system, the filter was coded using C++ and KDevelop [28] in SUSE LINUX Professional 9.2 [42...The driving factor for using Linux was the operating system’s ability to access the serial ports in a reliable fashion. Under the original MATLAB® and

FTAP: a Linux-based program for tapping and music experiments.

PubMed

Finney, S A

2001-02-01

This paper describes FTAP, a flexible data collection system for tapping and music experiments. FTAP runs on standard PC hardware with the Linux operating system and can process input keystrokes and auditory output with reliable millisecond resolution. It uses standard MIDI devices for input and output and is particularly flexible in the area of auditory feedback manipulation. FTAP can run a wide variety of experiments, including synchronization/continuation tasks (Wing & Kristofferson, 1973), synchronization tasks combined with delayed auditory feedback (Aschersleben & Prinz, 1997), continuation tasks with isolated feedback perturbations (Wing, 1977), and complex alterations of feedback in music performance (Finney, 1997). Such experiments have often been implemented with custom hardware and software systems, but with FTAP they can be specified by a simple ASCII text parameter file. FTAP is available at no cost in source-code form.

A Fault-Oblivious Extreme-Scale Execution Environment (FOX)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Hensbergen, Eric; Speight, William; Xenidis, Jimi

IBM Research’s contribution to the Fault Oblivious Extreme-scale Execution Environment (FOX) revolved around three core research deliverables: • collaboration with Boston University around the Kittyhawk cloud infrastructure which both enabled a development and deployment platform for the project team and provided a fault-injection testbed to evaluate prototypes • operating systems research focused on exploring role-based operating system technologies through collaboration with Sandia National Labs on the NIX research operating system and collaboration with the broader IBM Research community around a hybrid operating system model which became known as FusedOS • IBM Research also participated in an advisory capacity with themore » Boston University SESA project, the core of which was derived from the K42 operating system research project funded in part by DARPA’s HPCS program. Both of these contributions were built on a foundation of previous operating systems research funding by the Department of Energy’s FastOS Program. Through the course of the X-stack funding we were able to develop prototypes, deploy them on production clusters at scale, and make them available to other researchers. As newer hardware, in the form of BlueGene/Q, came online, we were able to port the prototypes to the new hardware and release the source code for the resulting prototypes as open source to the community. In addition to the open source coded for the Kittyhawk and NIX prototypes, we were able to bring the BlueGene/Q Linux patches up to a more recent kernel and contribute them for inclusion by the broader Linux community. The lasting impact of the IBM Research work on FOX can be seen in its effect on the shift of IBM’s approach to HPC operating systems from Linux and Compute Node Kernels to role-based approaches as prototyped by the NIX and FusedOS work. This impact can be seen beyond IBM in follow-on ideas being incorporated into the proposals for the Exasacale Operating Systems/Runtime program.« less

MOLAR: Modular Linux and Adaptive Runtime Support for HEC OS/R Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frank Mueller

2009-02-05

MOLAR is a multi-institution research effort that concentrates on adaptive, reliable,and efficient operating and runtime system solutions for ultra-scale high-end scientific computing on the next generation of supercomputers. This research addresses the challenges outlined by the FAST-OS - forum to address scalable technology for runtime and operating systems --- and HECRTF --- high-end computing revitalization task force --- activities by providing a modular Linux and adaptable runtime support for high-end computing operating and runtime systems. The MOLAR research has the following goals to address these issues. (1) Create a modular and configurable Linux system that allows customized changes based onmore » the requirements of the applications, runtime systems, and cluster management software. (2) Build runtime systems that leverage the OS modularity and configurability to improve efficiency, reliability, scalability, ease-of-use, and provide support to legacy and promising programming models. (3) Advance computer reliability, availability and serviceability (RAS) management systems to work cooperatively with the OS/R to identify and preemptively resolve system issues. (4) Explore the use of advanced monitoring and adaptation to improve application performance and predictability of system interruptions. The overall goal of the research conducted at NCSU is to develop scalable algorithms for high-availability without single points of failure and without single points of control.« less

Development and application of remote video monitoring system for combine harvester based on embedded Linux

NASA Astrophysics Data System (ADS)

Chen, Jin; Wang, Yifan; Wang, Xuelei; Wang, Yuehong; Hu, Rui

2017-01-01

Combine harvester usually works in sparsely populated areas with harsh environment. In order to achieve the remote real-time video monitoring of the working state of combine harvester. A remote video monitoring system based on ARM11 and embedded Linux is developed. The system uses USB camera for capturing working state video data of the main parts of combine harvester, including the granary, threshing drum, cab and cut table. Using JPEG image compression standard to compress video data then transferring monitoring screen to remote monitoring center over the network for long-range monitoring and management. At the beginning of this paper it describes the necessity of the design of the system. Then it introduces realization methods of hardware and software briefly. And then it describes detailedly the configuration and compilation of embedded Linux operating system and the compiling and transplanting of video server program are elaborated. At the end of the paper, we carried out equipment installation and commissioning on combine harvester and then tested the system and showed the test results. In the experiment testing, the remote video monitoring system for combine harvester can achieve 30fps with the resolution of 800x600, and the response delay in the public network is about 40ms.

Plasma Interactions With Spacecraft (I)

DTIC Science & Technology

2009-04-01

with the Windows, Red hat LINUX, and MacOS X environments. We wrote N2kScriptRunner, a C++ code that runs a Nascap-2k script outside of the Java ...console-based and with a Java interface), a stand alone program that reads and writes Nascap-2k database files. This program has proved invaluable...surface currents for DSX and prototyped it in Java . A description of the algorithm and the prototype implementation is in Section 3. 1.5. DSX

Research and Design of Embedded Wireless Meal Ordering System Based on SQLite

NASA Astrophysics Data System (ADS)

Zhang, Jihong; Chen, Xiaoquan

The paper describes features and internal architecture and developing method of SQLite. And then it gives a design and program of meal ordering system. The system realizes the information interaction among the users and embedded devices with SQLite as database system. The embedded database SQLite manages the data and achieves wireless communication by using Bluetooth. A system program based on Qt/Embedded and Linux drivers realizes the local management of environmental data.

Development of small scale cluster computer for numerical analysis

NASA Astrophysics Data System (ADS)

Zulkifli, N. H. N.; Sapit, A.; Mohammed, A. N.

2017-09-01

In this study, two units of personal computer were successfully networked together to form a small scale cluster. Each of the processor involved are multicore processor which has four cores in it, thus made this cluster to have eight processors. Here, the cluster incorporate Ubuntu 14.04 LINUX environment with MPI implementation (MPICH2). Two main tests were conducted in order to test the cluster, which is communication test and performance test. The communication test was done to make sure that the computers are able to pass the required information without any problem and were done by using simple MPI Hello Program where the program written in C language. Additional, performance test was also done to prove that this cluster calculation performance is much better than single CPU computer. In this performance test, four tests were done by running the same code by using single node, 2 processors, 4 processors, and 8 processors. The result shows that with additional processors, the time required to solve the problem decrease. Time required for the calculation shorten to half when we double the processors. To conclude, we successfully develop a small scale cluster computer using common hardware which capable of higher computing power when compare to single CPU processor, and this can be beneficial for research that require high computing power especially numerical analysis such as finite element analysis, computational fluid dynamics, and computational physics analysis.

The program LOPT for least-squares optimization of energy levels

NASA Astrophysics Data System (ADS)

Kramida, A. E.

2011-02-01

The article describes a program that solves the least-squares optimization problem for finding the energy levels of a quantum-mechanical system based on a set of measured energy separations or wavelengths of transitions between those energy levels, as well as determining the Ritz wavelengths of transitions and their uncertainties. The energy levels are determined by solving the matrix equation of the problem, and the uncertainties of the Ritz wavenumbers are determined from the covariance matrix of the problem. Program summaryProgram title: LOPT Catalogue identifier: AEHM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 19 254 No. of bytes in distributed program, including test data, etc.: 427 839 Distribution format: tar.gz Programming language: Perl v.5 Computer: PC, Mac, Unix workstations Operating system: MS Windows (XP, Vista, 7), Mac OS X, Linux, Unix (AIX) RAM: 3 Mwords or more Word size: 32 or 64 Classification: 2.2 Nature of problem: The least-squares energy-level optimization problem, i.e., finding a set of energy level values that best fits the given set of transition intervals. Solution method: The solution of the least-squares problem is found by solving the corresponding linear matrix equation, where the matrix is constructed using a new method with variable substitution. Restrictions: A practical limitation on the size of the problem N is imposed by the execution time, which scales as N and depends on the computer. Unusual features: Properly rounds the resulting data and formats the output in a format suitable for viewing with spreadsheet editing software. Estimates numerical errors resulting from the limited machine precision. Running time: 1 s for N=100, or 60 s for N=400 on a typical PC.

Critic: a new program for the topological analysis of solid-state electron densities

NASA Astrophysics Data System (ADS)

Otero-de-la-Roza, A.; Blanco, M. A.; Pendás, A. Martín; Luaña, Víctor

2009-01-01

In this paper we introduce CRITIC, a new program for the topological analysis of the electron densities of crystalline solids. Two different versions of the code are provided, one adapted to the LAPW (Linear Augmented Plane Wave) density calculated by the WIEN2K package and the other to the ab initio Perturbed Ion ( aiPI) density calculated with the PI7 code. Using the converged ground state densities, CRITIC can locate their critical points, determine atomic basins and integrate properties within them, and generate several graphical representations which include topological atomic basins and primary bundles, contour maps of ρ and ∇ρ, vector maps of ∇ρ, chemical graphs, etc. Program summaryProgram title: CRITIC Catalogue identifier: AECB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL, version 3 No. of lines in distributed program, including test data, etc.: 1 206 843 No. of bytes in distributed program, including test data, etc.: 12 648 065 Distribution format: tar.gz Programming language: FORTRAN 77 and 90 Computer: Any computer capable of compiling Fortran Operating system: Unix, GNU/Linux Classification: 7.3 Nature of problem: Topological analysis of the electron density in periodic solids. Solution method: The automatic localization of the electron density critical points is based on a recursive partitioning of the Wigner-Seitz cell into tetrahedra followed by a Newton search from significant points on each tetrahedra. Plotting of and integration on the atomic basins is currently based on a new implementation of Keith's promega algorithm. Running time: Variable, depending on the task. From seconds to a few minutes for the localization of critical points. Hours to days for the determination of the atomic basins shape and properties. Times correspond to a typical 2007 PC.

SLURM: Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Grondona, M

2002-12-19

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. This paper presents an overview of the SLURM architecture and functionality.

SLURM: Simplex Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Grondona, M

2003-04-22

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling, and stream copy modules. This paper presents an overview of the SLURM architecture and functionality.

77 FR 5864 - BluePoint Linux Software Corp., China Bottles Inc., Long-e International, Inc., and Nano...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] BluePoint Linux Software Corp., China Bottles Inc., Long-e International, Inc., and Nano Superlattice Technology, Inc.; Order of Suspension of... current and accurate information concerning the securities of BluePoint Linux Software Corp. because it...

The Research on Linux Memory Forensics

NASA Astrophysics Data System (ADS)

Zhang, Jun; Che, ShengBing

2018-03-01

Memory forensics is a branch of computer forensics. It does not depend on the operating system API, and analyzes operating system information from binary memory data. Based on the 64-bit Linux operating system, it analyzes system process and thread information from physical memory data. Using ELF file debugging information and propose a method for locating kernel structure member variable, it can be applied to different versions of the Linux operating system. The experimental results show that the method can successfully obtain the sytem process information from physical memory data, and can be compatible with multiple versions of the Linux kernel.

Project Golden Gate: towards real-time Java in space missions

NASA Technical Reports Server (NTRS)

Dvorak, Daniel; Bollella, Greg; Canham, Tim; Carson, Vanessa; Champlin, Virgil; Giovannoni, Brian; Indictor, Mark; Meyer, Kenny; Murray, Alex; Reinholtz, Kirk

2004-01-01

This paper describes the problem domain and our experimentation with the first commercial implementation of the Real Time Specification for Java. The two main issues explored in this report are: (1) the effect of RTSJ's non-heap memory on the programming model, and (2) performance benchmarking of RTSJ/Linux relative to C++/VxWorks.

Peregrine System User Basics | High-Performance Computing | NREL

Science.gov Websites

peregrine.hpc.nrel.gov or to one of the login nodes. Example commands to access Peregrine from a Linux or Mac OS X system Code Example Create a file called hello.F90 containing the following code: program hello write(6 information by enclosing it in brackets < >. For example: $ ssh -Y

XTALOPT: An open-source evolutionary algorithm for crystal structure prediction

NASA Astrophysics Data System (ADS)

Lonie, David C.; Zurek, Eva

2011-02-01

The implementation and testing of XTALOPT, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XTALOPT are optimized using a novel benchmarking scheme. XTALOPT is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface. Program summaryProgram title:XTALOPT Catalogue identifier: AEGX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.1 or later [1] No. of lines in distributed program, including test data, etc.: 36 849 No. of bytes in distributed program, including test data, etc.: 1 149 399 Distribution format: tar.gz Programming language: C++ Computer: PCs, workstations, or clusters Operating system: Linux Classification: 7.7 External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7]. Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics. Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XTALOPT, is freely available to the scientific community for use and collaboration under the GNU Public License. Running time: User dependent. The program runs until stopped by the user.

Moment distributions of clusters and molecules in the adiabatic rotor model

NASA Astrophysics Data System (ADS)

Ballentine, G. E.; Bertsch, G. F.; Onishi, N.; Yabana, K.

2008-01-01

We present a Fortran program to compute the distribution of dipole moments of free particles for use in analyzing molecular beams experiments that measure moments by deflection in an inhomogeneous field. The theory is the same for magnetic and electric dipole moments, and is based on a thermal ensemble of classical particles that are free to rotate and that have moment vectors aligned along a principal axis of rotation. The theory has two parameters, the ratio of the magnetic (or electric) dipole energy to the thermal energy, and the ratio of moments of inertia of the rotor. Program summaryProgram title:AdiabaticRotor Catalogue identifier:ADZO_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZO_v1_0.html Program obtainable from:CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.:479 No. of bytes in distributed program, including test data, etc.:4853 Distribution format:tar.gz Programming language:Fortran 90 Computer:Pentium-IV, Macintosh Power PC G4 Operating system:Linux, Mac OS X RAM:600 Kbytes Word size:64 bits Classification:2.3 Nature of problem:The system considered is a thermal ensemble of rotors having a magnetic or electric moment aligned along one of the principal axes. The ensemble is placed in an external field which is turned on adiabatically. The problem is to find the distribution of moments in the presence of the external field. Solution method:There are three adiabatic invariants. The only nontrivial one is the action associated with the polar angle of the rotor axis with respect to external field. It is found by Newton's method. Running time:3 min on a 3 GHz Pentium IV processor.

QDENSITY—A Mathematica Quantum Computer simulation

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Burdis, Joseph M.; Tabakin, Frank

2006-06-01

This Mathematica 5.2 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. Selected examples of the basic commands are presented here and a tutorial notebook, Tutorial.nb is provided with the package (available on our website) that serves as a full guide to the package. Finally, application is made to a variety of relevant cases, including Teleportation, Quantum Fourier transform, Grover's search and Shor's algorithm, in separate notebooks: QFT.nb, Teleportation.nb, Grover.nb and Shor.nb where each algorithm is explained in detail. Finally, two examples of the construction and manipulation of cluster states, which are part of "one way computing" ideas, are included as an additional tool in the notebook Cluster.nb. A Mathematica palette containing most commands in QDENSITY is also included: QDENSpalette.nb. Program summaryTitle of program: QDENSITY Catalogue identifier: ADXH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v1_0 Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Operating systems: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4 Programming language used: Mathematica 5.2 No. of bytes in distributed program, including test data, etc.: 180 581 No. of lines in distributed program, including test data, etc.: 19 382 Distribution format: tar.gz Method of solution: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed. QDENSITY is available at http://www.pitt.edu/~tabakin/QDENSITY.

xPerm: fast index canonicalization for tensor computer algebra

NASA Astrophysics Data System (ADS)

Martín-García, José M.

2008-10-01

We present a very fast implementation of the Butler-Portugal algorithm for index canonicalization with respect to permutation symmetries. It is called xPerm, and has been written as a combination of a Mathematica package and a C subroutine. The latter performs the most demanding parts of the computations and can be linked from any other program or computer algebra system. We demonstrate with tests and timings the effectively polynomial performance of the Butler-Portugal algorithm with respect to the number of indices, though we also show a case in which it is exponential. Our implementation handles generic tensorial expressions with several dozen indices in hundredths of a second, or one hundred indices in a few seconds, clearly outperforming all other current canonicalizers. The code has been already under intensive testing for several years and has been essential in recent investigations in large-scale tensor computer algebra. Program summaryProgram title: xPerm Catalogue identifier: AEBH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 93 582 No. of bytes in distributed program, including test data, etc.: 1 537 832 Distribution format: tar.gz Programming language: C and Mathematica (version 5.0 or higher) Computer: Any computer running C and Mathematica (version 5.0 or higher) Operating system: Linux, Unix, Windows XP, MacOS RAM:: 20 Mbyte Word size: 64 or 32 bits Classification: 1.5, 5 Nature of problem: Canonicalization of indexed expressions with respect to permutation symmetries. Solution method: The Butler-Portugal algorithm. Restrictions: Multiterm symmetries are not considered. Running time: A few seconds with generic expressions of up to 100 indices. The xPermDoc.nb notebook supplied with the distribution takes approximately one and a half hours to execute in full.

Strongdeco: Expansion of analytical, strongly correlated quantum states into a many-body basis

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Graß, Tobias

2012-03-01

We provide a Mathematica code for decomposing strongly correlated quantum states described by a first-quantized, analytical wave function into many-body Fock states. Within them, the single-particle occupations refer to the subset of Fock-Darwin functions with no nodes. Such states, commonly appearing in two-dimensional systems subjected to gauge fields, were first discussed in the context of quantum Hall physics and are nowadays very relevant in the field of ultracold quantum gases. As important examples, we explicitly apply our decomposition scheme to the prominent Laughlin and Pfaffian states. This allows for easily calculating the overlap between arbitrary states with these highly correlated test states, and thus provides a useful tool to classify correlated quantum systems. Furthermore, we can directly read off the angular momentum distribution of a state from its decomposition. Finally we make use of our code to calculate the normalization factors for Laughlin's famous quasi-particle/quasi-hole excitations, from which we gain insight into the intriguing fractional behavior of these excitations. Program summaryProgram title: Strongdeco Catalogue identifier: AELA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5475 No. of bytes in distributed program, including test data, etc.: 31 071 Distribution format: tar.gz Programming language: Mathematica Computer: Any computer on which Mathematica can be installed Operating system: Linux, Windows, Mac Classification: 2.9 Nature of problem: Analysis of strongly correlated quantum states. Solution method: The program makes use of the tools developed in Mathematica to deal with multivariate polynomials to decompose analytical strongly correlated states of bosons and fermions into a standard many-body basis. Operations with polynomials, determinants and permanents are the basic tools. Running time: The distributed notebook takes a couple of minutes to run.

Automated symbolic calculations in nonequilibrium thermodynamics

NASA Astrophysics Data System (ADS)

Kröger, Martin; Hütter, Markus

2010-12-01

We cast the Jacobi identity for continuous fields into a local form which eliminates the need to perform any partial integration to the expense of performing variational derivatives. This allows us to test the Jacobi identity definitely and efficiently and to provide equations between different components defining a potential Poisson bracket. We provide a simple Mathematica TM notebook which allows to perform this task conveniently, and which offers some additional functionalities of use within the framework of nonequilibrium thermodynamics: reversible equations of change for fields, and the conservation of entropy during the reversible dynamics. Program summaryProgram title: Poissonbracket.nb Catalogue identifier: AEGW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 227 952 No. of bytes in distributed program, including test data, etc.: 268 918 Distribution format: tar.gz Programming language: Mathematica TM 7.0 Computer: Any computer running Mathematica TM 6.0 and later versions Operating system: Linux, MacOS, Windows RAM: 100 Mb Classification: 4.2, 5, 23 Nature of problem: Testing the Jacobi identity can be a very complex task depending on the structure of the Poisson bracket. The Mathematica TM notebook provided here solves this problem using a novel symbolic approach based on inherent properties of the variational derivative, highly suitable for the present tasks. As a by product, calculations performed with the Poisson bracket assume a compact form. Solution method: The problem is first cast into a form which eliminates the need to perform partial integration for arbitrary functionals at the expense of performing variational derivatives. The corresponding equations are conveniently obtained using the symbolic programming environment Mathematica TM. Running time: For the test cases and most typical cases in the literature, the running time is of the order of seconds or minutes, respectively.

KAnalyze: a fast versatile pipelined K-mer toolkit

PubMed Central

Audano, Peter; Vannberg, Fredrik

2014-01-01

Motivation: Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language. Results: As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes. Availability and implementation: KAnalyze is available on SourceForge: https://sourceforge.net/projects/kanalyze/ Contact: fredrik.vannberg@biology.gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24642064

KAnalyze: a fast versatile pipelined k-mer toolkit.

PubMed

Audano, Peter; Vannberg, Fredrik

2014-07-15

Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language. As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes. KAnalyze is available on SourceForge: https://sourceforge.net/projects/kanalyze/. © The Author 2014. Published by Oxford University Press.

Developing the science product algorithm testbed for Chinese next-generation geostationary meteorological satellites: Fengyun-4 series

NASA Astrophysics Data System (ADS)

Min, Min; Wu, Chunqiang; Li, Chuan; Liu, Hui; Xu, Na; Wu, Xiao; Chen, Lin; Wang, Fu; Sun, Fenglin; Qin, Danyu; Wang, Xi; Li, Bo; Zheng, Zhaojun; Cao, Guangzhen; Dong, Lixin

2017-08-01

Fengyun-4A (FY-4A), the first of the Chinese next-generation geostationary meteorological satellites, launched in 2016, offers several advances over the FY-2: more spectral bands, faster imaging, and infrared hyperspectral measurements. To support the major objective of developing the prototypes of FY-4 science algorithms, two science product algorithm testbeds for imagers and sounders have been developed by the scientists in the FY-4 Algorithm Working Group (AWG). Both testbeds, written in FORTRAN and C programming languages for Linux or UNIX systems, have been tested successfully by using Intel/g compilers. Some important FY-4 science products, including cloud mask, cloud properties, and temperature profiles, have been retrieved successfully through using a proxy imager, Himawari-8/Advanced Himawari Imager (AHI), and sounder data, obtained from the Atmospheric InfraRed Sounder, thus demonstrating their robustness. In addition, in early 2016, the FY-4 AWG was developed based on the imager testbed—a near real-time processing system for Himawari-8/AHI data for use by Chinese weather forecasters. Consequently, robust and flexible science product algorithm testbeds have provided essential and productive tools for popularizing FY-4 data and developing substantial improvements in FY-4 products.

A multipurpose camera system for monitoring Kīlauea Volcano, Hawai'i

USGS Publications Warehouse

Patrick, Matthew R.; Orr, Tim R.; Lee, Lopaka; Moniz, Cyril J.

2015-01-01

We describe a low-cost, compact multipurpose camera system designed for field deployment at active volcanoes that can be used either as a webcam (transmitting images back to an observatory in real-time) or as a time-lapse camera system (storing images onto the camera system for periodic retrieval during field visits). The system also has the capability to acquire high-definition video. The camera system uses a Raspberry Pi single-board computer and a 5-megapixel low-light (near-infrared sensitive) camera, as well as a small Global Positioning System (GPS) module to ensure accurate time-stamping of images. Custom Python scripts control the webcam and GPS unit and handle data management. The inexpensive nature of the system allows it to be installed at hazardous sites where it might be lost. Another major advantage of this camera system is that it provides accurate internal timing (independent of network connection) and, because a full Linux operating system and the Python programming language are available on the camera system itself, it has the versatility to be configured for the specific needs of the user. We describe example deployments of the camera at Kīlauea Volcano, Hawai‘i, to monitor ongoing summit lava lake activity. 

Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

Systems analysis of a planetary entry (SAPE), descent, and landing (EDL) is a multidisciplinary activity in nature. SAPE improves the performance of the systems analysis team by automating and streamlining the process, and this improvement can reduce the errors that stem from manual data transfer among discipline experts. SAPE is a multidisciplinary tool for systems analysis of planetary EDL for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. It performs EDL systems analysis for any planet, operates cross-platform (i.e., Windows, Mac, and Linux operating systems), uses existing software components and open-source software to avoid software licensing issues, performs low-fidelity systems analysis in one hour on a computer that is comparable to an average laptop, and keeps discipline experts in the analysis loop. SAPE uses Python, a platform-independent, open-source language, for integration and for the user interface. Development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE currently includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and interface for structural sizing.

CADNA: a library for estimating round-off error propagation

NASA Astrophysics Data System (ADS)

Jézéquel, Fabienne; Chesneaux, Jean-Marie

2008-06-01

The CADNA library enables one to estimate round-off error propagation using a probabilistic approach. With CADNA the numerical quality of any simulation program can be controlled. Furthermore by detecting all the instabilities which may occur at run time, a numerical debugging of the user code can be performed. CADNA provides new numerical types on which round-off errors can be estimated. Slight modifications are required to control a code with CADNA, mainly changes in variable declarations, input and output. This paper describes the features of the CADNA library and shows how to interpret the information it provides concerning round-off error propagation in a code. Program summaryProgram title:CADNA Catalogue identifier:AEAT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAT_v1_0.html Program obtainable from:CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.:53 420 No. of bytes in distributed program, including test data, etc.:566 495 Distribution format:tar.gz Programming language:Fortran Computer:PC running LINUX with an i686 or an ia64 processor, UNIX workstations including SUN, IBM Operating system:LINUX, UNIX Classification:4.14, 6.5, 20 Nature of problem:A simulation program which uses floating-point arithmetic generates round-off errors, due to the rounding performed at each assignment and at each arithmetic operation. Round-off error propagation may invalidate the result of a program. The CADNA library enables one to estimate round-off error propagation in any simulation program and to detect all numerical instabilities that may occur at run time. Solution method:The CADNA library [1] implements Discrete Stochastic Arithmetic [2-4] which is based on a probabilistic model of round-off errors. The program is run several times with a random rounding mode generating different results each time. From this set of results, CADNA estimates the number of exact significant digits in the result that would have been computed with standard floating-point arithmetic. Restrictions:CADNA requires a Fortran 90 (or newer) compiler. In the program to be linked with the CADNA library, round-off errors on complex variables cannot be estimated. Furthermore array functions such as product or sum must not be used. Only the arithmetic operators and the abs, min, max and sqrt functions can be used for arrays. Running time:The version of a code which uses CADNA runs at least three times slower than its floating-point version. This cost depends on the computer architecture and can be higher if the detection of numerical instabilities is enabled. In this case, the cost may be related to the number of instabilities detected. References:The CADNA library, URL address: http://www.lip6.fr/cadna. J.-M. Chesneaux, L'arithmétique Stochastique et le Logiciel CADNA, Habilitation á diriger des recherches, Université Pierre et Marie Curie, Paris, 1995. J. Vignes, A stochastic arithmetic for reliable scientific computation, Math. Comput. Simulation 35 (1993) 233-261. J. Vignes, Discrete stochastic arithmetic for validating results of numerical software, Numer. Algorithms 37 (2004) 377-390.

Continuous-time quantum Monte Carlo impurity solvers

NASA Astrophysics Data System (ADS)

Gull, Emanuel; Werner, Philipp; Fuchs, Sebastian; Surer, Brigitte; Pruschke, Thomas; Troyer, Matthias

2011-04-01

Continuous-time quantum Monte Carlo impurity solvers are algorithms that sample the partition function of an impurity model using diagrammatic Monte Carlo techniques. The present paper describes codes that implement the interaction expansion algorithm originally developed by Rubtsov, Savkin, and Lichtenstein, as well as the hybridization expansion method developed by Werner, Millis, Troyer, et al. These impurity solvers are part of the ALPS-DMFT application package and are accompanied by an implementation of dynamical mean-field self-consistency equations for (single orbital single site) dynamical mean-field problems with arbitrary densities of states. Program summaryProgram title: dmft Catalogue identifier: AEIL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: ALPS LIBRARY LICENSE version 1.1 No. of lines in distributed program, including test data, etc.: 899 806 No. of bytes in distributed program, including test data, etc.: 32 153 916 Distribution format: tar.gz Programming language: C++ Operating system: The ALPS libraries have been tested on the following platforms and compilers: Linux with GNU Compiler Collection (g++ version 3.1 and higher), and Intel C++ Compiler (icc version 7.0 and higher) MacOS X with GNU Compiler (g++ Apple-version 3.1, 3.3 and 4.0) IBM AIX with Visual Age C++ (xlC version 6.0) and GNU (g++ version 3.1 and higher) compilers Compaq Tru64 UNIX with Compq C++ Compiler (cxx) SGI IRIX with MIPSpro C++ Compiler (CC) HP-UX with HP C++ Compiler (aCC) Windows with Cygwin or coLinux platforms and GNU Compiler Collection (g++ version 3.1 and higher) RAM: 10 MB-1 GB Classification: 7.3 External routines: ALPS [1], BLAS/LAPACK, HDF5 Nature of problem: (See [2].) Quantum impurity models describe an atom or molecule embedded in a host material with which it can exchange electrons. They are basic to nanoscience as representations of quantum dots and molecular conductors and play an increasingly important role in the theory of "correlated electron" materials as auxiliary problems whose solution gives the "dynamical mean field" approximation to the self-energy and local correlation functions. Solution method: Quantum impurity models require a method of solution which provides access to both high and low energy scales and is effective for wide classes of physically realistic models. The continuous-time quantum Monte Carlo algorithms for which we present implementations here meet this challenge. Continuous-time quantum impurity methods are based on partition function expansions of quantum impurity models that are stochastically sampled to all orders using diagrammatic quantum Monte Carlo techniques. For a review of quantum impurity models and their applications and of continuous-time quantum Monte Carlo methods for impurity models we refer the reader to [2]. Additional comments: Use of dmft requires citation of this paper. Use of any ALPS program requires citation of the ALPS [1] paper. Running time: 60 s-8 h per iteration.

Wrapping up BLAST and other applications for use on Unix clusters.

PubMed

Hokamp, Karsten; Shields, Denis C; Wolfe, Kenneth H; Caffrey, Daniel R

2003-02-12

We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.

Data Collection and Recording on the Wisconsin/GSFC X-ray Quantum Calorimeter

NASA Astrophysics Data System (ADS)

O'Neill, Laura; X-ray Astrophysics Group at the University of Wisconsin-Madison

2016-01-01

The Wisconsin/GSFC X-ray Quantum Calorimeter (XQC) is an astronomical X-ray sounding rocket payload which uses a micro-calorimeter array to detect low (less than1keV) X-rays. Three different devices were evaluated to upgrade XQC's data collection and recording system. The system takes incoming data from XQC's pixel sensors and stores it to a memory card. The upgrade is a much smaller board and much more compact storage device. The Terasic DE0-Nano, Terasic DE0-Nano SoC, and the BeagleBone Black were tested to determine which would suit the needs of XQC best. The device needed to take incoming data, store it to an SD card, and be able to output it through a USB connection. The Terasic DE0-Nano is a simple FPGA, but needed some peripheral additions for an SD card slot and USB readout. The Terasic DE0-Nano SoC was a powerful FPGA and hard processor running Linux combined. It was able to do what was needed, but pulled too much power in the process. The BeagleBone Black had a microcontroller and also ran Linux. This last device ended up being the best choice, as it did not require too much power and had a very easy system already in place for USB readout. The only difficulty to deal with was programming the microcontroller in assembly language. This device is necessary due to the telemetry on XQC not being able to send all of the data down during the flight. It records valuable data about low energy X-rays so that the X-ray Astrophysics Groups at the University of Wisconsin-Madison and Goddard Space Flight Center can analyze and resolve the spectrum of the soft X-ray background.Later, using the digital logic on a Terasic DE0-Nano FPGA, a data simulator for the BeagleBone Black data collection and recording device was created. Programmed with Quartus II, the simulator uses basic digital logic components to fabricate trackable data signals and related timing signals to send to the data management device, as well as other timing signals that are asynchronous to the rest of the circuit, a failsafe enable for outputs, and several user feedback components

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

SLURM: Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Dunlap, C; Garlick, J

2002-07-08

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. The design also includes a scalable, general-purpose communication infrastructure. This paper presents a overview of the SLURM architecture and functionality.

XMDS2: Fast, scalable simulation of coupled stochastic partial differential equations

NASA Astrophysics Data System (ADS)

Dennis, Graham R.; Hope, Joseph J.; Johnsson, Mattias T.

2013-01-01

XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The equations are described in a high-level XML-based script, and the package generates low-level optionally parallelised C++ code for the efficient solution of those equations. It combines the advantages of high-level simulations, namely fast and low-error development, with the speed, portability and scalability of hand-written code. XMDS2 is a complete redesign of the XMDS package, and features support for a much wider problem space while also producing faster code. Program summaryProgram title: XMDS2 Catalogue identifier: AENK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 2 No. of lines in distributed program, including test data, etc.: 872490 No. of bytes in distributed program, including test data, etc.: 45522370 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer with a Unix-like system, a C++ compiler and Python. Operating system: Any Unix-like system; developed under Mac OS X and GNU/Linux. RAM: Problem dependent (roughly 50 bytes per grid point) Classification: 4.3, 6.5. External routines: The external libraries required are problem-dependent. Uses FFTW3 Fourier transforms (used only for FFT-based spectral methods), dSFMT random number generation (used only for stochastic problems), MPI message-passing interface (used only for distributed problems), HDF5, GNU Scientific Library (used only for Bessel-based spectral methods) and a BLAS implementation (used only for non-FFT-based spectral methods). Nature of problem: General coupled initial-value stochastic partial differential equations. Solution method: Spectral method with method-of-lines integration Running time: Determined by the size of the problem

TU-F-CAMPUS-I-05: Semi-Automated, Open Source MRI Quality Assurance and Quality Control Program for Multi-Unit Institution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yung, J; Stefan, W; Reeve, D

2015-06-15

Purpose: Phantom measurements allow for the performance of magnetic resonance (MR) systems to be evaluated. Association of Physicists in Medicine (AAPM) Report No. 100 Acceptance Testing and Quality Assurance Procedures for MR Imaging Facilities, American College of Radiology (ACR) MR Accreditation Program MR phantom testing, and ACR MRI quality control (QC) program documents help to outline specific tests for establishing system performance baselines as well as system stability over time. Analyzing and processing tests from multiple systems can be time-consuming for medical physicists. Besides determining whether tests are within predetermined limits or criteria, monitoring longitudinal trends can also help preventmore » costly downtime of systems during clinical operation. In this work, a semi-automated QC program was developed to analyze and record measurements in a database that allowed for easy access to historical data. Methods: Image analysis was performed on 27 different MR systems of 1.5T and 3.0T field strengths from GE and Siemens manufacturers. Recommended measurements involved the ACR MRI Accreditation Phantom, spherical homogenous phantoms, and a phantom with an uniform hole pattern. Measurements assessed geometric accuracy and linearity, position accuracy, image uniformity, signal, noise, ghosting, transmit gain, center frequency, and magnetic field drift. The program was designed with open source tools, employing Linux, Apache, MySQL database and Python programming language for the front and backend. Results: Processing time for each image is <2 seconds. Figures are produced to show regions of interests (ROIs) for analysis. Historical data can be reviewed to compare previous year data and to inspect for trends. Conclusion: A MRI quality assurance and QC program is necessary for maintaining high quality, ACR MRI Accredited MR programs. A reviewable database of phantom measurements assists medical physicists with processing and monitoring of large datasets. Longitudinal data can reveal trends that although are within passing criteria indicate underlying system issues.« less

Elegent—An elastic event generator

NASA Astrophysics Data System (ADS)

Kašpar, J.

2014-03-01

Although elastic scattering of nucleons may look like a simple process, it presents a long-lasting challenge for theory. Due to missing hard energy scale, the perturbative QCD cannot be applied. Instead, many phenomenological/theoretical models have emerged. In this paper we present a unified implementation of some of the most prominent models in a C++ library, moreover extended to account for effects of the electromagnetic interaction. The library is complemented with a number of utilities. For instance, programs to sample many distributions of interest in four-momentum transfer squared, t, impact parameter, b, and collision energy √{s}. These distributions at ISR, Spp¯S, RHIC, Tevatron and LHC energies are available for download from the project web site. Both in the form of ROOT files and PDF figures providing comparisons among the models. The package includes also a tool for Monte-Carlo generation of elastic scattering events, which can easily be embedded in any other program framework. Catalogue identifier: AERT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERT_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 10551 No. of bytes in distributed program, including test data, etc.: 126316 Distribution format: tar.gz Programming language: C++. Computer: Any in principle, tested on x86-64 architecture. Operating system: Any in principle, tested on GNU/Linux. RAM: Strongly depends on the task, but typically below 20MB Classification: 11.6. External routines: ROOT, HepMC Nature of problem: Monte-Carlo simulation of elastic nucleon-nucleon collisions Solution method: Implementation of some of the most prominent phenomenological/theoretical models providing cumulative distribution function that is used for random event generation. Running time: Strongly depends on the task, but typically below 1 h.

Construction of SO(5)⊃SO(3) spherical harmonics and Clebsch-Gordan coefficients

NASA Astrophysics Data System (ADS)

Caprio, M. A.; Rowe, D. J.; Welsh, T. A.

2009-07-01

The SO(5)⊃SO(3) spherical harmonics form a natural basis for expansion of nuclear collective model angular wave functions. They underlie the recently-proposed algebraic method for diagonalization of the nuclear collective model Hamiltonian in an SU(1,1)×SO(5) basis. We present a computer code for explicit construction of the SO(5)⊃SO(3) spherical harmonics and use them to compute the Clebsch-Gordan coefficients needed for collective model calculations in an SO(3)-coupled basis. With these Clebsch-Gordan coefficients it becomes possible to compute the matrix elements of collective model observables by purely algebraic methods. Program summaryProgram title: GammaHarmonic Catalogue identifier: AECY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 346 421 No. of bytes in distributed program, including test data, etc.: 16 037 234 Distribution format: tar.gz Programming language: Mathematica 6 Computer: Any which supports Mathematica Operating system: Any which supports Mathematica; tested under Microsoft Windows XP and Linux Classification: 4.2 Nature of problem: Explicit construction of SO(5) ⊃ SO(3) spherical harmonics on S. Evaluation of SO(3)-reduced matrix elements and SO(5) ⊃ SO(3) Clebsch-Gordan coefficients (isoscalar factors). Solution method: Construction of SO(5) ⊃ SO(3) spherical harmonics by orthonormalization, obtained from a generating set of functions, according to the method of Rowe, Turner, and Repka [1]. Matrix elements and Clebsch-Gordan coefficients follow by construction and integration of SO(3) scalar products. Running time: Depends strongly on the maximum SO(5) and SO(3) representation labels involved. A few minutes for the calculation in the Mathematica notebook. References: [1] D.J. Rowe, P.S. Turner, J. Repka, J. Math. Phys. 45 (2004) 2761.

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi.

PubMed

Sapes, Jordi; Solsona, Francesc

2016-02-06

Nowadays, researchers are paying increasing attention to embedding systems. Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard. Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products. This paper presents a low-cost fingerprint recognition system embedded into a Raspberry Pi with Linux.

Virtualizing access to scientific applications with the Application Hosting Environment

NASA Astrophysics Data System (ADS)

Zasada, S. J.; Coveney, P. V.

2009-12-01

The growing power and number of high performance computing resources made available through computational grids present major opportunities as well as a number of challenges to the user. At issue is how these resources can be accessed and how their power can be effectively exploited. In this paper we first present our views on the usability of contemporary high-performance computational resources. We introduce the concept of grid application virtualization as a solution to some of the problems with grid-based HPC usability. We then describe a middleware tool that we have developed to realize the virtualization of grid applications, the Application Hosting Environment (AHE), and describe the features of the new release, AHE 2.0, which provides access to a common platform of federated computational grid resources in standard and non-standard ways. Finally, we describe a case study showing how AHE supports clinical use of whole brain blood flow modelling in a routine and automated fashion. Program summaryProgram title: Application Hosting Environment 2.0 Catalogue identifier: AEEJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public Licence, Version 2 No. of lines in distributed program, including test data, etc.: not applicable No. of bytes in distributed program, including test data, etc.: 1 685 603 766 Distribution format: tar.gz Programming language: Perl (server), Java (Client) Computer: x86 Operating system: Linux (Server), Linux/Windows/MacOS (Client) RAM: 134 217 728 (server), 67 108 864 (client) bytes Classification: 6.5 External routines: VirtualBox (server), Java (client) Nature of problem: The middleware that makes grid computing possible has been found by many users to be too unwieldy, and presents an obstacle to use rather than providing assistance [1,2]. Such problems are compounded when one attempts to harness the power of a grid, or a federation of different grids, rather than just a single resource on the grid. Solution method: To address the above problem, we have developed AHE, a lightweight interface, designed to simplify the process of running scientific codes on a grid of HPC and local resources. AHE does this by introducing a layer of middleware between the user and the grid, which encapsulates much of the complexity associated with launching grid applications. Unusual features: The server is distributed as a VirtualBox virtual machine. VirtualBox ( http://www.virtualbox.org) must be downloaded and installed in order to run the AHE server virtual machine. Details of how to do this are given in the AHE 2.0 Quick Start Guide. Running time: Not applicable References:J. Chin, P.V. Coveney, Towards tractable toolkits for the grid: A plea for lightweight, useable middleware, NeSC Technical Report, 2004, http://nesc.ac.uk/technical_papers/UKeS-2004-01.pdf. P.V. Coveney, R.S. Saksena, S.J. Zasada, M. McKeown, S. Pickles, The Application Hosting Environment: Lightweight middleware for grid-based computational science, Computer Physics Communications 176 (2007) 406-418.

Computers in Libraries, 2000: Proceedings (15th, Washington, D.C., March 15-17, 2000).

ERIC Educational Resources Information Center

Nixon, Carol, Comp.; Burmood, Jennifer, Comp.

Topics of the Proceedings of the 15th Annual Computers in Libraries Conference (March 15-17, 2000) include: Linux and open source software in an academic library; a Master Trainer Program; what educators need to know about multimedia and copyright; how super searchers find business information online; managing print costs; new technologies in wide…

MCR Container Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haas, Nicholas Q; Gillen, Robert E; Karnowski, Thomas P

MathWorks' MATLAB is widely used in academia and industry for prototyping, data analysis, data processing, etc. Many users compile their programs using the MATLAB Compiler to run on workstations/computing clusters via the free MATLAB Compiler Runtime (MCR). The MCR facilitates the execution of code calling Application Programming Interfaces (API) functions from both base MATLAB and MATLAB toolboxes. In a Linux environment, a sizable number of third-party runtime dependencies (i.e. shared libraries) are necessary. Unfortunately, to the MTLAB community's knowledge, these dependencies are not documented, leaving system administrators and/or end-users to find/install the necessary libraries either as runtime errors resulting frommore » them missing or by inspecting the header information of Executable and Linkable Format (ELF) libraries of the MCR to determine which ones are missing from the system. To address various shortcomings, Docker Images based on Community Enterprise Operating System (CentOS) 7, a derivative of Redhat Enterprise Linux (RHEL) 7, containing recent (2015-2017) MCR releases and their dependencies were created. These images, along with a provided sample Docker Compose YAML Script, can be used to create a simulated computing cluster where MATLAB Compiler created binaries can be executed using a sample Slurm Workload Manager script.« less

‘tripleint_cc’: A program for 2-centre variational leptonic Coulomb potential matrix elements using Hylleraas-type trial functions, with a performance optimization study

NASA Astrophysics Data System (ADS)

Plummer, M.; Armour, E. A. G.; Todd, A. C.; Franklin, C. P.; Cooper, J. N.

2009-12-01

We present a program used to calculate intricate three-particle integrals for variational calculations of solutions to the leptonic Schrödinger equation with two nuclear centres in which inter-leptonic distances (electron-electron and positron-electron) are included directly in the trial functions. The program has been used so far in calculations of He-H¯ interactions and positron H 2 scattering, however the precisely defined integrals are applicable to other situations. We include a summary discussion of how the program has been optimized from a 'legacy'-type code to a more modern high-performance code with a performance improvement factor of up to 1000. Program summaryProgram title: tripleint.cc Catalogue identifier: AEEV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 12 829 No. of bytes in distributed program, including test data, etc.: 91 798 Distribution format: tar.gz Programming language: Fortran 95 (fixed format) Computer: Modern PC (tested on AMD processor) [1], IBM Power5 [2] Cray XT4 [3], similar Operating system: Red Hat Linux [1], IBM AIX [2], UNICOS [3] Has the code been vectorized or parallelized?: Serial (multi-core shared memory may be needed for some large jobs) RAM: Dependent on parameter sizes and option to use intermediate I/O. Estimates for practical use: 0.5-2 GBytes (with intermediate I/O); 1-4 GBytes (all-memory: the preferred option). Classification: 2.4, 2.6, 2.7, 2.9, 16.5, 16.10, 20 Nature of problem: The 'tripleint.cc' code evaluates three-particle integrals needed in certain variational (in particular: Rayleigh-Ritz and generalized-Kohn) matrix elements for solution of the Schrödinger equation with two fixed centres (the solutions may then be used in subsequent dynamic nuclear calculations). Specifically the integrals are defined by Eq. (16) in the main text and contain terms proportional to r×r/r,i≠j,i≠k,j≠k, with r the distance between leptons i and j. The article also briefly describes the performance optimizations used to increase the speed of evaluation of the integrals enough to allow detailed testing and mapping of the effect of varying non-linear parameters in the variational trial functions. Solution method: Each integral is solved using prolate spheroidal coordinates and series expansions (with cut-offs) of the many-lepton expressions. 1-d integrals and sub-integrals are solved analytically by various means (the program automatically chooses the most accurate of the available methods for each set of parameters and function arguments), while two of the three integrations over the prolate spheroidal coordinates ' λ' are carried out numerically. Many similar integrals with identical non-linear variational parameters may be calculated with one call of the code. Restrictions: There are limits to the number of points for the numerical integrations, to the cut-off variable itaumax for the many-lepton series expansions, and to the maximum powers of Slater-like input functions. For runs near the limit of the cut-off variable and with certain small-magnitude values of variational non-linear parameters, the code can require large amounts of memory (an option using some intermediate I/O is included to offset this). Unusual features: In addition to the program, we also present a summary description of the techniques and ideology used to optimize the code, together with accuracy tests and indications of performance improvement. Running time: The test runs take 1-15 minutes on HPCx [2] as indicated in Section 5 of the main text. A practical run with 729 integrals, 40 quadrature points per dimension and itaumax = 8 took 150 minutes on a PC (e.g., [1]): a similar run with 'medium' accuracy, e.g. for parameter optimization (see Section 2 of the main text), with 30 points per dimension and itaumax = 6 took 35 minutes. References:PC: Memory: 2.72 GB, CPU: AMD Opteron 246 dual-core, 2×2 GHz, OS: GNU/Linux, kernel: Linux 2.6.9-34.0.2.ELsmp. HPCx, IBM eServer 575 running IBM AIX, http://www.hpcx.ac.uk/ (visited May 2009). HECToR, CRAY XT4 running UNICOS/lc, http://www.hector.ac.uk/ (visited May 2009).

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

PubMed

Beltrame, Luca; Calura, Enrica; Popovici, Razvan R; Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-08-01

Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.

PubMed

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI).

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System

PubMed Central

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C.; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI). PMID:28381997

Source Code Analysis Laboratory (SCALe)

DTIC Science & Technology

2012-04-01

Versus Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8...is inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with software for a particular...servers support a collection of virtual machines (VMs) that can be configured to support analysis in various environments, such as Windows XP and Linux . A

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi

PubMed Central

Sapes, Jordi; Solsona, Francesc

2016-01-01

Nowadays, researchers are paying increasing attention to embedding systems. Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard. Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products. This paper presents a low-cost fingerprint recognition system embedded into a Raspberry Pi with Linux. PMID:26861340

Improving Block-level Efficiency with scsi-mq

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caldwell, Blake A

2015-01-01

Current generation solid-state storage devices are exposing a new bottlenecks in the SCSI and block layers of the Linux kernel, where IO throughput is limited by lock contention, inefficient interrupt handling, and poor memory locality. To address these limitations, the Linux kernel block layer underwent a major rewrite with the blk-mq project to move from a single request queue to a multi-queue model. The Linux SCSI subsystem rework to make use of this new model, known as scsi-mq, has been merged into the Linux kernel and work is underway for dm-multipath support in the upcoming Linux 4.0 kernel. These piecesmore » were necessary to make use of the multi-queue block layer in a Lustre parallel filesystem with high availability requirements. We undertook adding support of the 3.18 kernel to Lustre with scsi-mq and dm-multipath patches to evaluate the potential of these efficiency improvements. In this paper we evaluate the block-level performance of scsi-mq with backing storage hardware representative of a HPC-targerted Lustre filesystem. Our findings show that SCSI write request latency is reduced by as much as 13.6%. Additionally, when profiling the CPU usage of our prototype Lustre filesystem, we found that CPU idle time increased by a factor of 7 with Linux 3.18 and blk-mq as compared to a standard 2.6.32 Linux kernel. Our findings demonstrate increased efficiency of the multi-queue block layer even with disk-based caching storage arrays used in existing parallel filesystems.« less

Linux Kernel Co-Scheduling and Bulk Synchronous Parallelism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R

2012-01-01

This paper describes a kernel scheduling algorithm that is based on coscheduling principles and that is intended for parallel applications running on 1000 cores or more. Experimental results for a Linux implementation on a Cray XT5 machine are presented. The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

THERMINATOR: THERMal heavy-IoN generATOR

NASA Astrophysics Data System (ADS)

Kisiel, Adam; Tałuć, Tomasz; Broniowski, Wojciech; Florkowski, Wojciech

2006-04-01

THERMINATOR is a Monte Carlo event generator designed for studying of particle production in relativistic heavy-ion collisions performed at such experimental facilities as the SPS, RHIC, or LHC. The program implements thermal models of particle production with single freeze-out. It performs the following tasks: (1) generation of stable particles and unstable resonances at the chosen freeze-out hypersurface with the local phase-space density of particles given by the statistical distribution factors, (2) subsequent space-time evolution and decays of hadronic resonances in cascades, (3) calculation of the transverse-momentum spectra and numerous other observables related to the space-time evolution. The geometry of the freeze-out hypersurface and the collective velocity of expansion may be chosen from two successful models, the Cracow single-freeze-out model and the Blast-Wave model. All particles from the Particle Data Tables are used. The code is written in the object-oriented c++ language and complies to the standards of the ROOT environment. Program summaryProgram title:THERMINATOR Catalogue identifier:ADXL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXL_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland RAM required to execute with typical data:50 Mbytes Number of processors used:1 Computer(s) for which the program has been designed: PC, Pentium III, IV, or Athlon, 512 MB RAM not hardware dependent (any computer with the c++ compiler and the ROOT environment [R. Brun, F. Rademakers, Nucl. Instrum. Methods A 389 (1997) 81, http://root.cern.ch] Operating system(s) for which the program has been designed:Linux: Mandrake 9.0, Debian 3.0, SuSE 9.0, Red Hat FEDORA 3, etc., Windows XP with Cygwin ver. 1.5.13-1 and gcc ver. 3.3.3 (cygwin special)—not system dependent External routines/libraries used: ROOT ver. 4.02.00 Programming language:c++ Size of the package: (324 KB directory 40 KB compressed distribution archive), without the ROOT libraries (see http://root.cern.ch for details on the ROOT [R. Brun, F. Rademakers, Nucl. Instrum. Methods A 389 (1997) 81, http://root.cern.ch] requirements). The output files created by the code need 1.1 GB for each 500 events. Distribution format: tar gzip file Number of lines in distributed program, including test data, etc.: 6534 Number of bytes in ditribution program, including test data, etc.:41 828 Nature of the physical problem: Statistical models have proved to be very useful in the description of soft physics in relativistic heavy-ion collisions [P. Braun-Munzinger, K. Redlich, J. Stachel, 2003, nucl-th/0304013. [2

PHANTOM: A Monte Carlo event generator for six parton final states at high energy colliders

NASA Astrophysics Data System (ADS)

Ballestrero, Alessandro; Belhouari, Aissa; Bevilacqua, Giuseppe; Kashkan, Vladimir; Maina, Ezio

2009-03-01

PHANTOM is a tree level Monte Carlo for six parton final states at proton-proton, proton-antiproton and electron-positron colliders at O(αEM6) and O(αEM4αS2) including possible interferences between the two sets of diagrams. This comprehends all purely electroweak contributions as well as all contributions with one virtual or two external gluons. It can generate unweighted events for any set of processes and it is interfaced to parton shower and hadronization packages via the latest Les Houches Accord protocol. It can be used to analyze the physics of boson-boson scattering, Higgs boson production in boson-boson fusion, tt¯ and three boson production. Program summaryProgram title:PHANTOM (V. 1.0) Catalogue identifier: AECE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 175 787 No. of bytes in distributed program, including test data, etc.: 965 898 Distribution format: tar.gz Programming language: Fortran 77 Computer: Any with a UNIX, LINUX compatible Fortran compiler Operating system: UNIX, LINUX RAM: 500 MB Classification: 11.1 External routines: LHAPDF (Les Houches Accord PDF Interface, http://projects.hepforge.org/lhapdf/), CIRCE (beamstrahlung for ee ILC collider). Nature of problem: Six fermion final state processes have become important with the increase of collider energies and are essential for the study of top, Higgs and electroweak symmetry breaking physics at high energy colliders. Since thousands of Feynman diagrams contribute in a single process and events corresponding to hundreds of different final states need to be generated, a fast and stable calculation is needed. Solution method:PHANTOM is a tree level Monte Carlo for six parton final states at proton-proton, proton-antiproton and electron-positron colliders. It computes all amplitudes at O(αEM6) and O(αEM4αs2) including possible interferences between the two sets of diagrams. The matrix elements are computed with the helicity formalism implemented in the program PHACT [1]. The integration makes use of an iterative-adaptive multichannel method which, relying on adaptivity, allows the use of only a few channels per process. Unweighted event generation can be performed for any set of processes and it is interfaced to parton shower and hadronization packages via the latest Les Houches Accord protocol. Restrictions: All Feynman diagrams are computed al LO. Unusual features: Phantom is written in Fortran 77 but it makes use of structures. The g77 compiler cannot compile it as it does not recognize the structures. The Intel, Portland Group, True64 HP Fortran 77 or Fortran 90 compilers have been tested and can be used. Running time: A few hours for a cross section integration of one process at per mille accuracy. One hour for one thousand unweighted events. References:A. Ballestrero, E. Maina, Phys. Lett. B 350 (1995) 225, hep-ph/9403244; A. Ballestrero, PHACT 1.0, Program for helicity amplitudes Calculations with Tau matrices, hep-ph/9911318, in: B.B. Levchenko, V.I. Savrin (Eds.), Proceedings of the 14th International Workshop on High Energy Physics and Quantum Field Theory (QFTHEP 99), SINP MSU, Moscow, p. 303.

CPsuperH2.0: An improved computational tool for Higgs phenomenology in the MSSM with explicit CP violation

NASA Astrophysics Data System (ADS)

Lee, J. S.; Carena, M.; Ellis, J.; Pilaftsis, A.; Wagner, C. E. M.

2009-02-01

We describe the Fortran code CPsuperH2.0, which contains several improvements and extensions of its predecessor CPsuperH. It implements improved calculations of the Higgs-boson pole masses, notably a full treatment of the 4×4 neutral Higgs propagator matrix including the Goldstone boson and a more complete treatment of threshold effects in self-energies and Yukawa couplings, improved treatments of two-body Higgs decays, some important three-body decays, and two-loop Higgs-mediated contributions to electric dipole moments. CPsuperH2.0 also implements an integrated treatment of several B-meson observables, including the branching ratios of B→μμ, B→ττ, B→τν, B→Xγ and the latter's CP-violating asymmetry A, and the supersymmetric contributions to the Bs,d0-B¯s,d0 mass differences. These additions make CPsuperH2.0 an attractive integrated tool for analyzing supersymmetric CP and flavour physics as well as searches for new physics at high-energy colliders such as the Tevatron, LHC and linear colliders. Program summaryProgram title: CPsuperH2.0 Catalogue identifier: ADSR_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSR_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 13 290 No. of bytes in distributed program, including test data, etc.: 89 540 Distribution format: tar.gz Programming language: Fortran 77 Computer: PC running under Linux and computers in Unix environment Operating system: Linux RAM: 32 Mbytes Classification: 11.1 Catalogue identifier of the previous version: ADSR_v1_0 Journal reference of the previous version: CPC 156 (2004) 283 Does the new version supersede the previous version?: Yes Nature of problem: The calculations of mass spectrum, decay widths and branching ratios of the neutral and charged Higgs bosons in the Minimal Supersymmetric Standard Model with explicit CP violation have been improved. The program is based on recent renormalization-group-improved diagrammatic calculations that include dominant higher-order logarithmic and threshold corrections, b-quark Yukawa-coupling resummation effects and improved treatment of Higgs-boson pole-mass shifts. The couplings of the Higgs bosons to the Standard Model gauge bosons and fermions, to their supersymmetric partners and all the trilinear and quartic Higgs-boson self-couplings are also calculated. The new implementations include a full treatment of the 4×4(2×2) neutral (charged) Higgs propagator matrix together with the center-of-mass dependent Higgs-boson couplings to gluons and photons, two-loop Higgs-mediated contributions to electric dipole moments, and an integrated treatment of several B-meson observables. Solution method: One-dimensional numerical integration for several Higgs-decay modes, iterative treatment of the threshold corrections and Higgs-boson pole masses, and the numerical diagonalization of the neutralino mass matrix. Reasons for new version: Mainly to provide a coherent numerical framework which calculates consistently observables for both low- and high-energy experiments. Summary of revisions: Improved treatment of Higgs-boson masses and propagators. Improved treatment of Higgs-boson couplings and decays. Higgs-mediated two-loop electric dipole moments. B-meson observables. Running time: Less than 0.1 seconds. The program may be obtained from http://www.hep.man.ac.uk/u/jslee/CPsuperH.html.

The VOLSCAT package for electron and positron scattering of molecular targets: A new high throughput approach to cross-section and resonances computation

NASA Astrophysics Data System (ADS)

Sanna, N.; Baccarelli, I.; Morelli, G.

2009-12-01

VOLSCAT is a computer program which implements the Single Center Expansion (SCE) method to solve the scattering equation for the elastic collision of electrons/positrons off molecular targets. The scattering potential needed is calculated by on-the-fly calls to the external SCELib library for molecular properties, recently ported to GPU computing environment and ClearSpeed platforms, and made available by means of an Application Program Interface (SCELib-API) which is also provided with the VOLSCAT package in a beta version. The result is a high throughput approach to the solution of the complex e/e-molecule scattering problem, with allows for intensive calculations both for the number of systems which can be studied and for their size. Accurate partial and total elastic cross sections are produced in output together with the associated eigenphase sums. Indirect scattering processes arising from the formation of temporary negative ions can also be analyzed through the computation of the resonances' parameters. Program summaryProgram title: VOLSCAT V1.0 Catalogue identifier: AEEW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 4 618 353 No. of bytes in distributed program, including test data, etc.: 120 307 536 Distribution format: tar.gz Programming language: Fortran90 Computer: All SMP platforms based on AIX, Linux and SUNOS operating systems over SPARC, POWER, Intel Itanium2, X86, em64t and Opteron processors Operating system: SUNOS, IBM AIX, Linux RedHat (Enterprise), Linux SuSE (SLES) Has the code been vectorized or parallelized?: Yes. The parallel version in the present release of the code is limited to the OpenMP calculation of the exchange potential V or V. The number of OpenMP threads can then be set in the input script. RAM: For a typical (isolated) biomolecule (e.g. Cytosine or Ribose) a converged calculation would require from 320 MB up to 2.5 GB. Word size: 64 bits Classification: 16.5 External routines: LAPACK (dsyev, dgetri, dgetrf) ( http://www.netlib.org/lapack/) Nature of problem: In this set of codes an efficient procedure is implemented to calculate partial cross section for the scattering between an electron/positron and a molecular target as a function of the collision energies. Solution method: The scattering equations are derived in the framework of the Single Center Expansion (SCE) procedure which allows the reduction of the original three-dimensional problem to a radial (one-dimensional) equation through the expansion of the scattering potential and the system wavefunction in a set of symmetry-adapted (real) spherical harmonics. The local part of the electrostatic interaction between the charged projectile (electron/positron) and the molecular target is provided in input by the SCELib library, which also provides the correlation and polarization corrections for the short-range and long-range part, respectively, of the interaction. A proper Application Programming Interface (API) is used by VOLSCAT to load the energy-independent part of the potential while the non-local exchange contribution is approximated by a local form and calculated on the fly in the VOLSCAT run for each desired collision energy. The resulting SCE one-dimensional homogeneous scattering equation is rewritten in an integral form by means of the standard Green's function technique resulting in a set of Volterra coupled equations which are solved to give the phase shifts and cross sections for any desired impact energy in terms of the partial components defined by the irreducible representations of the symmetry point group to which the target molecule belongs. The total cross section can then be straightforwardly calculated by summing over all the partial cross sections produced in the output. By the Breit-Wigner analysis of the eigenphase sum produced as a function of the energy one can also get information on the location of possible resonance states arising in the collision process. Restrictions: Depending on the molecular system under study and on the operating conditions the program may or may not fit into available RAM memory. Additional comments: A beta version of SCELib-API is included in the distribution package. Running time: The execution time strongly depends on the molecular target description and on the hardware/OS chosen, it is directly proportional to the (r,θ,φ) grid size and to the number of angular basis functions used.

Construct exploit constraint in crash analysis by bypassing canary

NASA Astrophysics Data System (ADS)

Huang, Ning; Huang, Shuguang; Huang, Hui; Chang, Chao

2017-08-01

Selective symbolic execution is a common program testing technology. Developed on the basis of it, some crash analysis systems are often used to test the fragility of the program by constructing exploit constraints, such as CRAX. From the study of crash analysis based on symbolic execution, this paper find that this technology cannot bypass the canary stack protection mechanisms. This paper makes the improvement uses the API hook in Linux. Experimental results show that the use of API hook can effectively solve the problem that crash analysis cannot bypass the canary protection.

Elan4/SPARC V9 Cross Loader and Dynamic Linker

DOE Office of Scientific and Technical Information (OSTI.GOV)

anf Fabien Lebaillif-Delamare, Fabrizio Petrini

2004-10-25

The Elan4/Sparc V9 Croos Loader and Liner is a part of the Linux system software that allows the dynamic loading and linking of user code in the network interface Quadrics QsNETII, also called as Elan4 Quadrics. Elan44 uses a thread processor that is based on the assembly instruction set of the Sparc V9. All this software is integrated as a Linux kernel module in the Linux 2.6.5 release.

Memory Analysis of the KBeast Linux Rootkit: Investigating Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2015-06-01

examine how a computer forensic investigator/incident handler, without specialised computer memory or software reverse engineering skills , can successfully...memory images and malware, this new series of reports will be directed at those who must analyse Linux malware-infected memory images. The skills ...disable 1287 1000 1000 /usr/lib/policykit-1-gnome/polkit-gnome-authentication- agent-1 1310 1000 1000 /usr/lib/pulseaudio/pulse/gconf- helper 1350

Semi-Automated Identification of Rocks in Images

NASA Technical Reports Server (NTRS)

Bornstein, Benjamin; Castano, Andres; Anderson, Robert

2006-01-01

Rock Identification Toolkit Suite is a computer program that assists users in identifying and characterizing rocks shown in images returned by the Mars Explorer Rover mission. Included in the program are components for automated finding of rocks, interactive adjustments of outlines of rocks, active contouring of rocks, and automated analysis of shapes in two dimensions. The program assists users in evaluating the surface properties of rocks and soil and reports basic properties of rocks. The program requires either the Mac OS X operating system running on a G4 (or more capable) processor or a Linux operating system running on a Pentium (or more capable) processor, plus at least 128MB of random-access memory.

Markovian Monte Carlo program EvolFMC v.2 for solving QCD evolution equations

NASA Astrophysics Data System (ADS)

Jadach, S.; Płaczek, W.; Skrzypek, M.; Stokłosa, P.

2010-02-01

We present the program EvolFMC v.2 that solves the evolution equations in QCD for the parton momentum distributions by means of the Monte Carlo technique based on the Markovian process. The program solves the DGLAP-type evolution as well as modified-DGLAP ones. In both cases the evolution can be performed in the LO or NLO approximation. The quarks are treated as massless. The overall technical precision of the code has been established at 5×10. This way, for the first time ever, we demonstrate that with the Monte Carlo method one can solve the evolution equations with precision comparable to the other numerical methods. New version program summaryProgram title: EvolFMC v.2 Catalogue identifier: AEFN_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFN_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including binary test data, etc.: 66 456 (7407 lines of C++ code) No. of bytes in distributed program, including test data, etc.: 412 752 Distribution format: tar.gz Programming language: C++ Computer: PC, Mac Operating system: Linux, Mac OS X RAM: Less than 256 MB Classification: 11.5 External routines: ROOT ( http://root.cern.ch/drupal/) Nature of problem: Solution of the QCD evolution equations for the parton momentum distributions of the DGLAP- and modified-DGLAP-type in the LO and NLO approximations. Solution method: Monte Carlo simulation of the Markovian process of a multiple emission of partons. Restrictions:Limited to the case of massless partons. Implemented in the LO and NLO approximations only. Weighted events only. Unusual features: Modified-DGLAP evolutions included up to the NLO level. Additional comments: Technical precision established at 5×10. Running time: For the 10 6 events at 100 GeV: DGLAP NLO: 27s; C-type modified DGLAP NLO: 150s (MacBook Pro with Mac OS X v.10.5.5, 2.4 GHz Intel Core 2 Duo, gcc 4.2.4, single thread).

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.

PubMed

De Oliveira, T; Miller, R; Tarin, M; Cassol, S

2003-01-01

Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).

High precision series solutions of differential equations: Ordinary and regular singular points of second order ODEs

NASA Astrophysics Data System (ADS)

Noreen, Amna; Olaussen, Kåre

2012-10-01

A subroutine for a very-high-precision numerical solution of a class of ordinary differential equations is provided. For a given evaluation point and equation parameters the memory requirement scales linearly with precision P, and the number of algebraic operations scales roughly linearly with P when P becomes sufficiently large. We discuss results from extensive tests of the code, and how one, for a given evaluation point and equation parameters, may estimate precision loss and computing time in advance. Program summary Program title: seriesSolveOde1 Catalogue identifier: AEMW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 991 No. of bytes in distributed program, including test data, etc.: 488116 Distribution format: tar.gz Programming language: C++ Computer: PC's or higher performance computers. Operating system: Linux and MacOS RAM: Few to many megabytes (problem dependent). Classification: 2.7, 4.3 External routines: CLN — Class Library for Numbers [1] built with the GNU MP library [2], and GSL — GNU Scientific Library [3] (only for time measurements). Nature of problem: The differential equation -s2({d2}/{dz2}+{1-ν+-ν-}/{z}{d}/{dz}+{ν+ν-}/{z2})ψ(z)+{1}/{z} ∑n=0N vnznψ(z)=0, is solved numerically to very high precision. The evaluation point z and some or all of the equation parameters may be complex numbers; some or all of them may be represented exactly in terms of rational numbers. Solution method: The solution ψ(z), and optionally ψ'(z), is evaluated at the point z by executing the recursion A(z)={s-2}/{(m+1+ν-ν+)(m+1+ν-ν-)} ∑n=0N Vn(z)A(z), ψ(z)=ψ(z)+A(z), to sufficiently large m. Here ν is either ν+ or ν-, and Vn(z)=vnz. The recursion is initialized by A(z)=δzν,for n=0,1,…,N ψ(z)=A0(z). Restrictions: No solution is computed if z=0, or s=0, or if ν=ν- (assuming Reν+≥Reν-) with ν+-ν- an integer, except when ν+-ν-=1 and v =0 (i.e. when z is an ordinary point for zψ(z)). Additional comments: The code of the main algorithm is in the file seriesSolveOde1.cc, which "#include" the file checkForBreakOde1.cc. These routines, and the programs using them, must "#include" the file seriesSolveOde1.cc. Running time: On a Linux PC that is a few years old, at y=√{10} to an accuracy of P=200 decimal digits, evaluating the ground state wavefunction of the anharmonic oscillator (with the eigenvalue known in advance); (cf. Eq. (6)) takes about 2 ms, and about 40 min at an accuracy of P=100000 decimal digits. References: [1] B. Haible and R.B. Kreckel, CLN — Class Library for Numbers, http://www.ginac.de/CLN/ [2] T. Granlund and collaborators, GMP — The GNU Multiple Precision Arithmetic Library, http://gmplib.org/ [3] M. Galassi et al., GNU Scientific Library Reference Manual (3rd Ed.), ISBN 0954612078., http://www.gnu.org/software/gsl/

Linux Kernel Co-Scheduling For Bulk Synchronous Parallel Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R

2011-01-01

This paper describes a kernel scheduling algorithm that is based on co-scheduling principles and that is intended for parallel applications running on 1000 cores or more where inter-node scalability is key. Experimental results for a Linux implementation on a Cray XT5 machine are presented.1 The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

Develop, Build, and Test a Virtual Lab to Support a Vulnerability Training System

DTIC Science & Technology

2004-09-01

docs.us.dell.com/support/edocs/systems/pe1650/ en /it/index.htm> (20 August 2004) “HOWTO: Installing Web Services with Linux /Tomcat/Apache/Struts...configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web server was configured as the external interface to...1650, dual processor, blade servers were configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web

RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.

PubMed

Garcia-Martin, Juan Antonio; Dotu, Ivan; Clote, Peter

2015-07-01

Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

System for Automated Geoscientific Analyses (SAGA) v. 2.1.4

NASA Astrophysics Data System (ADS)

Conrad, O.; Bechtel, B.; Bock, M.; Dietrich, H.; Fischer, E.; Gerlitz, L.; Wehberg, J.; Wichmann, V.; Böhner, J.

2015-07-01

The System for Automated Geoscientific Analyses (SAGA) is an open source geographic information system (GIS), mainly licensed under the GNU General Public License. Since its first release in 2004, SAGA has rapidly developed from a specialized tool for digital terrain analysis to a comprehensive and globally established GIS platform for scientific analysis and modeling. SAGA is coded in C++ in an object oriented design and runs under several operating systems including Windows and Linux. Key functional features of the modular software architecture comprise an application programming interface for the development and implementation of new geoscientific methods, a user friendly graphical user interface with many visualization options, a command line interpreter, and interfaces to interpreted languages like R and Python. The current version 2.1.4 offers more than 600 tools, which are implemented in dynamically loadable libraries or shared objects and represent the broad scopes of SAGA in numerous fields of geoscientific endeavor and beyond. In this paper, we inform about the system's architecture, functionality, and its current state of development and implementation. Furthermore, we highlight the wide spectrum of scientific applications of SAGA in a review of published studies, with special emphasis on the core application areas digital terrain analysis, geomorphology, soil science, climatology and meteorology, as well as remote sensing.

Software for Photometric and Astrometric Reduction of Video Meteors

NASA Astrophysics Data System (ADS)

Atreya, Prakash; Christou, Apostolos

2007-12-01

SPARVM is a Software for Photometric and Astrometric Reduction of Video Meteors being developed at Armagh Observatory. It is written in Interactive Data Language (IDL) and is designed to run primarily under Linux platform. The basic features of the software will be derivation of light curves, estimation of angular velocity and radiant position for single station data. For double station data, calculation of 3D coordinates of meteors, velocity, brightness, and estimation of meteoroid's orbit including uncertainties. Currently, the software supports extraction of time and date from video frames, estimation of position of cameras (Azimuth, Altitude), finding stellar sources in video frames and transformation of coordinates from video, frames to Horizontal coordinate system (Azimuth, Altitude), and Equatorial coordinate system (RA, Dec).

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Sailfish: A flexible multi-GPU implementation of the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Januszewski, M.; Kostur, M.

2014-09-01

We present Sailfish, an open source fluid simulation package implementing the lattice Boltzmann method (LBM) on modern Graphics Processing Units (GPUs) using CUDA/OpenCL. We take a novel approach to GPU code implementation and use run-time code generation techniques and a high level programming language (Python) to achieve state of the art performance, while allowing easy experimentation with different LBM models and tuning for various types of hardware. We discuss the general design principles of the code, scaling to multiple GPUs in a distributed environment, as well as the GPU implementation and optimization of many different LBM models, both single component (BGK, MRT, ELBM) and multicomponent (Shan-Chen, free energy). The paper also presents results of performance benchmarks spanning the last three NVIDIA GPU generations (Tesla, Fermi, Kepler), which we hope will be useful for researchers working with this type of hardware and similar codes. Catalogue identifier: AETA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Lesser General Public License, version 3 No. of lines in distributed program, including test data, etc.: 225864 No. of bytes in distributed program, including test data, etc.: 46861049 Distribution format: tar.gz Programming language: Python, CUDA C, OpenCL. Computer: Any with an OpenCL or CUDA-compliant GPU. Operating system: No limits (tested on Linux and Mac OS X). RAM: Hundreds of megabytes to tens of gigabytes for typical cases. Classification: 12, 6.5. External routines: PyCUDA/PyOpenCL, Numpy, Mako, ZeroMQ (for multi-GPU simulations), scipy, sympy Nature of problem: GPU-accelerated simulation of single- and multi-component fluid flows. Solution method: A wide range of relaxation models (LBGK, MRT, regularized LB, ELBM, Shan-Chen, free energy, free surface) and boundary conditions within the lattice Boltzmann method framework. Simulations can be run in single or double precision using one or more GPUs. Restrictions: The lattice Boltzmann method works for low Mach number flows only. Unusual features: The actual numerical calculations run exclusively on GPUs. The numerical code is built dynamically at run-time in CUDA C or OpenCL, using templates and symbolic formulas. The high-level control of the simulation is maintained by a Python process. Additional comments: !!!!! The distribution file for this program is over 45 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!! Running time: Problem-dependent, typically minutes (for small cases or short simulations) to hours (large cases or long simulations).

Cyber Fundamental Exercises

DTIC Science & Technology

2013-03-01

the /bin, /sbin, /etc, /var/log, /home, /proc, /root, /dev, /tmp, and /lib directories • Describe the purpose of the /etc/shadow and /etc/ passwd ...UNLIMITED 19 2.6.2 /etc/ passwd and /etc/shadow The /etc/shadow file didn’t exist on early Linux distributions. Originally only root could access the...etc/ passwd file, which stored user names, user configuration information, and passwords. However, when common programs such as ls running under

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

PubMed Central

2010-01-01

Background Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. Description An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date. Conclusions Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms. PMID:21210976

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics.

PubMed

Taylor, Ronald C

2010-12-21

Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date. Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms.

ObsPy: A Python Toolbox for Seismology

NASA Astrophysics Data System (ADS)

Wassermann, J. M.; Krischer, L.; Megies, T.; Barsch, R.; Beyreuther, M.

2013-12-01

Python combines the power of a full-blown programming language with the flexibility and accessibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. ObsPy is a community-driven, open-source project extending Python's capabilities to fit the specific needs that arise when working with seismological data. It a) comes with a continuously growing signal processing toolbox that covers most tasks common in seismological analysis, b) provides read and write support for many common waveform, station and event metadata formats and c) enables access to various data centers, webservices and databases to retrieve waveform data and station/event metadata. In combination with mature and free Python packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy makes it possible to develop complete workflows in Python, ranging from reading locally stored data or requesting data from one or more different data centers via signal analysis and data processing to visualization in GUI and web applications, output of modified/derived data and the creation of publication-quality figures. All functionality is extensively documented and the ObsPy Tutorial and Gallery give a good impression of the wide range of possible use cases. ObsPy is tested and running on Linux, OS X and Windows and comes with installation routines for these systems. ObsPy is developed in a test-driven approach and is available under the LGPLv3 open source licence. Users are welcome to request help, report bugs, propose enhancements or contribute code via either the user mailing list or the project page on GitHub.

HEP Computing

Science.gov Websites

Computing Visitors who do not need a HEP linux account Visitors with laptops can use wireless network HEP linux account Step 1: Click Here for New Account Application After submitting the application, you

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Neutrino oscillation parameter sampling with MonteCUBES

NASA Astrophysics Data System (ADS)

Blennow, Mattias; Fernandez-Martinez, Enrique

2010-01-01

We present MonteCUBES ("Monte Carlo Utility Based Experiment Simulator"), a software package designed to sample the neutrino oscillation parameter space through Markov Chain Monte Carlo algorithms. MonteCUBES makes use of the GLoBES software so that the existing experiment definitions for GLoBES, describing long baseline and reactor experiments, can be used with MonteCUBES. MonteCUBES consists of two main parts: The first is a C library, written as a plug-in for GLoBES, implementing the Markov Chain Monte Carlo algorithm to sample the parameter space. The second part is a user-friendly graphical Matlab interface to easily read, analyze, plot and export the results of the parameter space sampling. Program summaryProgram title: MonteCUBES (Monte Carlo Utility Based Experiment Simulator) Catalogue identifier: AEFJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 69 634 No. of bytes in distributed program, including test data, etc.: 3 980 776 Distribution format: tar.gz Programming language: C Computer: MonteCUBES builds and installs on 32 bit and 64 bit Linux systems where GLoBES is installed Operating system: 32 bit and 64 bit Linux RAM: Typically a few MBs Classification: 11.1 External routines: GLoBES [1,2] and routines/libraries used by GLoBES Subprograms used:Cat Id ADZI_v1_0, Title GLoBES, Reference CPC 177 (2007) 439 Nature of problem: Since neutrino masses do not appear in the standard model of particle physics, many models of neutrino masses also induce other types of new physics, which could affect the outcome of neutrino oscillation experiments. In general, these new physics imply high-dimensional parameter spaces that are difficult to explore using classical methods such as multi-dimensional projections and minimizations, such as those used in GLoBES [1,2]. Solution method: MonteCUBES is written as a plug-in to the GLoBES software [1,2] and provides the necessary methods to perform Markov Chain Monte Carlo sampling of the parameter space. This allows an efficient sampling of the parameter space and has a complexity which does not grow exponentially with the parameter space dimension. The integration of the MonteCUBES package with the GLoBES software makes sure that the experimental definitions already in use by the community can also be used with MonteCUBES, while also lowering the learning threshold for users who already know GLoBES. Additional comments: A Matlab GUI for interpretation of results is included in the distribution. Running time: The typical running time varies depending on the dimensionality of the parameter space, the complexity of the experiment, and how well the parameter space should be sampled. The running time for our simulations [3] with 15 free parameters at a Neutrino Factory with O(10) samples varied from a few hours to tens of hours. References:P. Huber, M. Lindner, W. Winter, Comput. Phys. Comm. 167 (2005) 195, hep-ph/0407333. P. Huber, J. Kopp, M. Lindner, M. Rolinec, W. Winter, Comput. Phys. Comm. 177 (2007) 432, hep-ph/0701187. S. Antusch, M. Blennow, E. Fernandez-Martinez, J. Lopez-Pavon, arXiv:0903.3986 [hep-ph].

Tcl as a Software Environment for a TCS

NASA Astrophysics Data System (ADS)

Terrett, David L.

2002-12-01

This paper describes how the Tcl scripting language and C API has been used as the software environment for a telescope pointing kernel so that new pointing algorithms and software architectures can be developed and tested without needing a real-time operating system or real-time software environment. It has enabled development to continue outside the framework of a specific telescope project while continuing to build a system that is sufficiently complete to be capable of controlling real hardware but expending minimum effort on replacing the services that would normally by provided by a real-time software environment. Tcl is used as a scripting language for configuring the system at startup and then as the command interface for controlling the running system; the Tcl C language API is used to provided a system independent interface to file and socket I/O and other operating system services. The pointing algorithms themselves are implemented as a set of C++ objects calling C library functions that implement the algorithms described in [2]. Although originally designed as a test and development environment, the system, running as a soft real-time process on Linux, has been used to test the SOAR mount control system and will be used as the pointing kernel of the SOAR telescope control system

QDENSITY—A Mathematica quantum computer simulation

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Burdis, Joseph M.; Tabakin, Frank

2009-03-01

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. New version program summaryProgram title: QDENSITY 2.0 Catalogue identifier: ADXH_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 26 055 No. of bytes in distributed program, including test data, etc.: 227 540 Distribution format: tar.gz Programming language: Mathematica 6.0 Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4 Catalogue identifier of previous version: ADXH_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914 Classification: 4.15 Does the new version supersede the previous version?: Offers an alternative, more up to date, implementation Nature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters. Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed. Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0 Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0 Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.

RELAP5-3D developmental assessment: Comparison of version 4.2.1i on Linux and Windows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayless, Paul D.

2014-06-01

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.2i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

RELAP5-3D Developmental Assessment. Comparison of Version 4.3.4i on Linux and Windows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayless, Paul David

2015-10-01

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.3i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

Container-Based Clinical Solutions for Portable and Reproducible Image Analysis.

PubMed

Matelsky, Jordan; Kiar, Gregory; Johnson, Erik; Rivera, Corban; Toma, Michael; Gray-Roncal, William

2018-05-08

Medical imaging analysis depends on the reproducibility of complex computation. Linux containers enable the abstraction, installation, and configuration of environments so that software can be both distributed in self-contained images and used repeatably by tool consumers. While several initiatives in neuroimaging have adopted approaches for creating and sharing more reliable scientific methods and findings, Linux containers are not yet mainstream in clinical settings. We explore related technologies and their efficacy in this setting, highlight important shortcomings, demonstrate a simple use-case, and endorse the use of Linux containers for medical image analysis.

bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.

PubMed

Lindenbaum, Pierre; Redon, Richard

2018-04-01

Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard Linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries. In this study, we developed a set of tools namely bioalcidae, samjs and vcffilterjs that reformat or filter files using a JavaScript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk). https://github.com/lindenb/jvarkit. pierre.lindenbaum@univ-nantes.fr.

A General Purpose High Performance Linux Installation Infrastructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wachsmann, Alf

2002-06-17

With more and more and larger and larger Linux clusters, the question arises how to install them. This paper addresses this question by proposing a solution using only standard software components. This installation infrastructure scales well for a large number of nodes. It is also usable for installing desktop machines or diskless Linux clients, thus, is not designed for cluster installations in particular but is, nevertheless, highly performant. The infrastructure proposed uses PXE as the network boot component on the nodes. It uses DHCP and TFTP servers to get IP addresses and a bootloader to all nodes. It then usesmore » kickstart to install Red Hat Linux over NFS. We have implemented this installation infrastructure at SLAC with our given server hardware and installed a 256 node cluster in 30 minutes. This paper presents the measurements from this installation and discusses the bottlenecks in our installation.« less

Demonstration of the DSST State Transition Matrix Time-Update Properties Using the Linux GTDS Program

DTIC Science & Technology

2011-09-01

by a single mean equinoctial element set . EGP Orbit Determination Test Cases Rev 25 14 All of the EGP test cases employ the same observation...the non-singular equinoctial mean elements is more linear and this has positive implications for orbit determination processes based on the semi...by a single mean equinoctial element set . 5. CONCLUSIONS The GTDS Semi-analytical Satellite Theory (DSST) architecture has been extended to

A Comparison of Satellite Conjunction Analysis Screening Tools

DTIC Science & Technology

2011-09-01

visualization tool. Version 13.1.4 for Linux was tested. The SOAP conjunction analysis function does not have the capacity to perform the large...was examined by SOAP to confirm the conjunction. STK Advanced CAT STK Advanced CAT (Conjunction Analysis Tools) is an add-on module for the STK ...run with each tool. When attempting to perform the seven day all vs all analysis with STK Advanced CAT, the program consistently crashed during report

Scalable Unix commands for parallel processors : a high-performance implementation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ong, E.; Lusk, E.; Gropp, W.

2001-06-22

We describe a family of MPI applications we call the Parallel Unix Commands. These commands are natural parallel versions of common Unix user commands such as ls, ps, and find, together with a few similar commands particular to the parallel environment. We describe the design and implementation of these programs and present some performance results on a 256-node Linux cluster. The Parallel Unix Commands are open source and freely available.

A Trusted Path Design and Implementation for Security Enhanced Linux

DTIC Science & Technology

2004-09-01

functionality by a member of the team? Witten, et al., [21] provides an excellent discussion of some aspects of the subject. Ultimately, open vs ...terminal window is a program like gnome - terminal that provides a TTY-like environment as a window inside an X Windows session. The phrase computer...Editors selected No sound or video No graphics Check all development boxes except KDE Administrative tools System tools No printing support

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

PubMed

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Free and open source software for the manipulation of digital images.

PubMed

Solomon, Robert W

2009-06-01

Free and open source software is a type of software that is nearly as powerful as commercial software but is freely downloadable. This software can do almost everything that the expensive programs can. GIMP (gnu image manipulation program) is the free program that is comparable to Photoshop, and versions are available for Windows, Macintosh, and Linux platforms. This article briefly describes how GIMP can be installed and used to manipulate radiology images. It is no longer necessary to budget large amounts of money for high-quality software to achieve the goals of image processing and document creation because free and open source software is available for the user to download at will.

LAMMPS framework for dynamic bonding and an application modeling DNA

NASA Astrophysics Data System (ADS)

Svaneborg, Carsten

2012-08-01

We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework. Catalogue identifier: AEME_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 2 243 491 No. of bytes in distributed program, including test data, etc.: 771 Distribution format: tar.gz Programming language: C++ Computer: Single and multiple core servers Operating system: Linux/Unix/Windows Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives. RAM: 1 Gb Classification: 16.11, 16.12 Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds. Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent. Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Hours to days. The examples provided in the distribution take just seconds to run.

Plato: A localised orbital based density functional theory code

NASA Astrophysics Data System (ADS)

Kenny, S. D.; Horsfield, A. P.

2009-12-01

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation. Program summaryProgram title: Plato Catalogue identifier: AEFC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 219 974 No. of bytes in distributed program, including test data, etc.: 1 821 493 Distribution format: tar.gz Programming language: C/MPI and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux and Mac OS X Has the code been vectorised or parallelised?: Yes, up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Nature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces. Solution method: Localised orbital based density functional theory. Restrictions: Tight-binding and density functional theory only, no exact exchange. Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater-Koster tables for accuracy. Running time: Test cases will run in a few minutes, large calculations may run for several days.

[Study for lung sound acquisition module based on ARM and Linux].

PubMed

Lu, Qiang; Li, Wenfeng; Zhang, Xixue; Li, Junmin; Liu, Longqing

2011-07-01

A acquisition module with ARM and Linux as a core was developed. This paper presents the hardware configuration and the software design. It is shown that the module can extract human lung sound reliably and effectively.

Language-Through-Literature; A Literary Language/Language Arts Program for Bilingual Education, ESL and Other Activities in Early Childhood. Books 1 and 2.

ERIC Educational Resources Information Center

King, Paul; King, Eva

This language-through-literature program is designed to be used as a native language program (language arts/reading readiness), as a second language program, or as a combined native and second language program in early childhood education. Sequentially developed over the year and within each unit, the program is subdivided into 14 units of about…

PhyLIS: a simple GNU/Linux distribution for phylogenetics and phyloinformatics.

PubMed

Thomson, Robert C

2009-07-30

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/.

PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics

PubMed Central

Thomson, Robert C.

2009-01-01

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/. PMID:19812729

Awakening the Languages. Challenges of Enduring Language Programs: Field Reports from 15 Programs from Arizona, New Mexico and Oklahoma.

ERIC Educational Resources Information Center

Linn, Mary S.; Naranjo, Tessie; Nicholas, Sheilah; Slaughter, Inee; Yamamoto, Akira; Zepeda, Ofelia

The Indigenous Language Institute (ILI) collaborates with indigenous language communities to combat language decline. ILI facilitates community-based language programs, increases public awareness of language endangerment, and disseminates information on language preservation and successful language revitalization programs. In response to numerous…

BioBlend: automating pipeline analyses within Galaxy and CloudMan.

PubMed

Sloggett, Clare; Goonasekera, Nuwan; Afgan, Enis

2013-07-01

We present BioBlend, a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs. BioBlend makes it easy for bioinformaticians to automate end-to-end large data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provide the required infrastructure and automate complex analyses over large datasets within the familiar Galaxy environment. http://bioblend.readthedocs.org/. Automated installation of BioBlend is available via PyPI (e.g. pip install bioblend). Alternatively, the source code is available from the GitHub repository (https://github.com/afgane/bioblend) under the MIT open source license. The library has been tested and is working on Linux, Macintosh and Windows-based systems.

Report on IVS-WG4

NASA Astrophysics Data System (ADS)

Gipson, John

2011-07-01

I describe the proposed data structure for storing, archiving and processing VLBI data. In this scheme, most VLBI data is stored in NetCDF files. NetCDF has the advantage that there are interfaces to most common computer languages including Fortran, Fortran-90, C, C++, Perl, etc, and the most common operating systems including linux, Windows and Mac. The data files for a particular session are organized by special ASCII "wrapper" files which contain pointers to the data files. This allows great flexibility in the processing and analysis of VLBI data, and also allows for extending the types of data used, e.g., source maps. I discuss the use of the new format in calc/solve and other VLBI analysis packages. I also discuss plans for transitioning to the new structure.

2DRMP: A suite of two-dimensional R-matrix propagation codes

NASA Astrophysics Data System (ADS)

Scott, N. S.; Scott, M. P.; Burke, P. G.; Stitt, T.; Faro-Maza, V.; Denis, C.; Maniopoulou, A.

2009-12-01

The R-matrix method has proved to be a remarkably stable, robust and efficient technique for solving the close-coupling equations that arise in electron and photon collisions with atoms, ions and molecules. During the last thirty-four years a series of related R-matrix program packages have been published periodically in CPC. These packages are primarily concerned with low-energy scattering where the incident energy is insufficient to ionise the target. In this paper we describe 2DRMP, a suite of two-dimensional R-matrix propagation programs aimed at creating virtual experiments on high performance and grid architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies. Program summaryProgram title: 2DRMP Catalogue identifier: AEEA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 196 717 No. of bytes in distributed program, including test data, etc.: 3 819 727 Distribution format: tar.gz Programming language: Fortran 95, MPI Computer: Tested on CRAY XT4 [1]; IBM eServer 575 [2]; Itanium II cluster [3] Operating system: Tested on UNICOS/lc [1]; IBM AIX [2]; Red Hat Linux Enterprise AS [3] Has the code been vectorised or parallelised?: Yes. 16 cores were used for small test run Classification: 2.4 External routines: BLAS, LAPACK, PBLAS, ScaLAPACK Subprograms used: ADAZ_v1_1 Nature of problem: 2DRMP is a suite of programs aimed at creating virtual experiments on high performance architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies. Solution method: Two-dimensional R-matrix propagation theory. The (r,r) space of the internal region is subdivided into a number of subregions. Local R-matrices are constructed within each subregion and used to propagate a global R-matrix, ℜ, across the internal region. On the boundary of the internal region ℜ is transformed onto the IERM target state basis. Thus, the two-dimensional R-matrix propagation technique transforms an intractable problem into a series of tractable problems enabling the internal region to be extended far beyond that which is possible with the standard one-sector codes. A distinctive feature of the method is that both electrons are treated identically and the R-matrix basis states are constructed to allow for both electrons to be in the continuum. The subregion size is flexible and can be adjusted to accommodate the number of cores available. Restrictions: The implementation is currently restricted to electron scattering from H-like atoms and ions. Additional comments: The programs have been designed to operate on serial computers and to exploit the distributed memory parallelism found on tightly coupled high performance clusters and supercomputers. 2DRMP has been systematically and comprehensively documented using ROBODoc [4] which is an API documentation tool that works by extracting specially formatted headers from the program source code and writing them to documentation files. Running time: The wall clock running time for the small test run using 16 cores and performed on [3] is as follows: bp (7 s); rint2 (34 s); newrd (32 s); diag (21 s); amps (11 s); prop (24 s). References:HECToR, CRAY XT4 running UNICOS/lc, http://www.hector.ac.uk/, accessed 22 July, 2009. HPCx, IBM eServer 575 running IBM AIX, http://www.hpcx.ac.uk/, accessed 22 July, 2009. HP Cluster, Itanium II cluster running Red Hat Linux Enterprise AS, Queen s University Belfast, http://www.qub.ac.uk/directorates/InformationServices/Research/HighPerformanceComputing/Services/Hardware/HPResearch/, accessed 22 July, 2009. Automating Software Documentation with ROBODoc, http://www.xs4all.nl/~rfsber/Robo/, accessed 22 July, 2009.

A web-server of cell type discrimination system.

PubMed

Wang, Anyou; Zhong, Yan; Wang, Yanhua; He, Qianchuan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells.

A Web-Server of Cell Type Discrimination System

PubMed Central

Zhong, Yan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells. PMID:24578634

I/O performance evaluation of a Linux-based network-attached storage device

NASA Astrophysics Data System (ADS)

Sun, Zhaoyan; Dong, Yonggui; Wu, Jinglian; Jia, Huibo; Feng, Guanping

2002-09-01

In a Local Area Network (LAN), clients are permitted to access the files on high-density optical disks via a network server. But the quality of read service offered by the conventional server is not satisfied because of the multiple functions on the server and the overmuch caller. This paper develops a Linux-based Network-Attached Storage (NAS) server. The Operation System (OS), composed of an optimized kernel and a miniaturized file system, is stored in a flash memory. After initialization, the NAS device is connected into the LAN. The administrator and users could configure the access the server through the web page respectively. In order to enhance the quality of access, the management of buffer cache in file system is optimized. Some benchmark programs are peformed to evaluate the I/O performance of the NAS device. Since data recorded in optical disks are usually for reading accesses, our attention is focused on the reading throughput of the device. The experimental results indicate that the I/O performance of our NAS device is excellent.

GNU Data Language (GDL) - a free and open-source implementation of IDL

NASA Astrophysics Data System (ADS)

Arabas, Sylwester; Schellens, Marc; Coulais, Alain; Gales, Joel; Messmer, Peter

2010-05-01

GNU Data Language (GDL) is developed with the aim of providing an open-source drop-in replacement for the ITTVIS's Interactive Data Language (IDL). It is free software developed by an international team of volunteers led by Marc Schellens - the project's founder (a list of contributors is available on the project's website). The development is hosted on SourceForge where GDL continuously ranks in the 99th percentile of most active projects. GDL with its library routines is designed as a tool for numerical data analysis and visualisation. As its proprietary counterparts (IDL and PV-WAVE), GDL is used particularly in geosciences and astronomy. GDL is dynamically-typed, vectorized and has object-oriented programming capabilities. The library routines handle numerical calculations, data visualisation, signal/image processing, interaction with host OS and data input/output. GDL supports several data formats such as netCDF, HDF4, HDF5, GRIB, PNG, TIFF, DICOM, etc. Graphical output is handled by X11, PostScript, SVG or z-buffer terminals, the last one allowing output to be saved in a variety of raster graphics formats. GDL is an incremental compiler with integrated debugging facilities. It is written in C++ using the ANTLR language-recognition framework. Most of the library routines are implemented as interfaces to open-source packages such as GNU Scientific Library, PLPlot, FFTW, ImageMagick, and others. GDL features a Python bridge (Python code can be called from GDL; GDL can be compiled as a Python module). Extensions to GDL can be written in C++, GDL, and Python. A number of open software libraries written in IDL, such as the NASA Astronomy Library, MPFIT, CMSVLIB and TeXtoIDL are fully or partially functional under GDL. Packaged versions of GDL are available for several Linux distributions and Mac OS X. The source code compiles on some other UNIX systems, including BSD and OpenSolaris. The presentation will cover the current status of the project, the key accomplishments, and the weaknesses - areas where contributions and users' feedback are welcome! While still being in beta-stage of development, GDL proved to be a useful tool for classroom work on data analysis. Its usage for teaching meteorological-data processing at the University of Warsaw will serve as an example.

Accelerating numerical solution of stochastic differential equations with CUDA

NASA Astrophysics Data System (ADS)

Januszewski, M.; Kostur, M.

2010-01-01

Numerical integration of stochastic differential equations is commonly used in many branches of science. In this paper we present how to accelerate this kind of numerical calculations with popular NVIDIA Graphics Processing Units using the CUDA programming environment. We address general aspects of numerical programming on stream processors and illustrate them by two examples: the noisy phase dynamics in a Josephson junction and the noisy Kuramoto model. In presented cases the measured speedup can be as high as 675× compared to a typical CPU, which corresponds to several billion integration steps per second. This means that calculations which took weeks can now be completed in less than one hour. This brings stochastic simulation to a completely new level, opening for research a whole new range of problems which can now be solved interactively. Program summaryProgram title: SDE Catalogue identifier: AEFG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu GPL v3 No. of lines in distributed program, including test data, etc.: 978 No. of bytes in distributed program, including test data, etc.: 5905 Distribution format: tar.gz Programming language: CUDA C Computer: any system with a CUDA-compatible GPU Operating system: Linux RAM: 64 MB of GPU memory Classification: 4.3 External routines: The program requires the NVIDIA CUDA Toolkit Version 2.0 or newer and the GNU Scientific Library v1.0 or newer. Optionally gnuplot is recommended for quick visualization of the results. Nature of problem: Direct numerical integration of stochastic differential equations is a computationally intensive problem, due to the necessity of calculating multiple independent realizations of the system. We exploit the inherent parallelism of this problem and perform the calculations on GPUs using the CUDA programming environment. The GPU's ability to execute hundreds of threads simultaneously makes it possible to speed up the computation by over two orders of magnitude, compared to a typical modern CPU. Solution method: The stochastic Runge-Kutta method of the second order is applied to integrate the equation of motion. Ensemble-averaged quantities of interest are obtained through averaging over multiple independent realizations of the system. Unusual features: The numerical solution of the stochastic differential equations in question is performed on a GPU using the CUDA environment. Running time: < 1 minute

BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.

PubMed

Abrahamsson, Erik; Plotkin, Steven S

2009-09-01

Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which may be output from molecular dynamics simulations that include orientation output in either quaternion or ANISOU format, and can render frames of the trajectory in several common image formats for subsequent concatenation into a movie file. The BioVEC program is written in C++, uses the OpenGL API for rendering, and is open source. It is lightweight, allows for user-defined settings for and texture, and runs on either Windows or Linux platforms.

25 CFR 39.132 - Can a school integrate Language Development programs into its regular instructional program?

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false Can a school integrate Language Development programs into... Language Development Programs § 39.132 Can a school integrate Language Development programs into its regular instructional program? A school may offer Language Development programs to students as part of its...

25 CFR 39.132 - Can a school integrate Language Development programs into its regular instructional program?

Code of Federal Regulations, 2011 CFR

2011-04-01

... 25 Indians 1 2011-04-01 2011-04-01 false Can a school integrate Language Development programs into... Language Development Programs § 39.132 Can a school integrate Language Development programs into its regular instructional program? A school may offer Language Development programs to students as part of its...

Stochastic hyperfine interactions modeling library

NASA Astrophysics Data System (ADS)

Zacate, Matthew O.; Evenson, William E.

2011-04-01

The stochastic hyperfine interactions modeling library (SHIML) provides a set of routines to assist in the development and application of stochastic models of hyperfine interactions. The library provides routines written in the C programming language that (1) read a text description of a model for fluctuating hyperfine fields, (2) set up the Blume matrix, upon which the evolution operator of the system depends, and (3) find the eigenvalues and eigenvectors of the Blume matrix so that theoretical spectra of experimental techniques that measure hyperfine interactions can be calculated. The optimized vector and matrix operations of the BLAS and LAPACK libraries are utilized; however, there was a need to develop supplementary code to find an orthonormal set of (left and right) eigenvectors of complex, non-Hermitian matrices. In addition, example code is provided to illustrate the use of SHIML to generate perturbed angular correlation spectra for the special case of polycrystalline samples when anisotropy terms of higher order than A can be neglected. Program summaryProgram title: SHIML Catalogue identifier: AEIF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIF_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.: 8224 No. of bytes in distributed program, including test data, etc.: 312 348 Distribution format: tar.gz Programming language: C Computer: Any Operating system: LINUX, OS X RAM: Varies Classification: 7.4 External routines: TAPP [1], BLAS [2], a C-interface to BLAS [3], and LAPACK [4] Nature of problem: In condensed matter systems, hyperfine methods such as nuclear magnetic resonance (NMR), Mössbauer effect (ME), muon spin rotation (μSR), and perturbed angular correlation spectroscopy (PAC) measure electronic and magnetic structure within Angstroms of nuclear probes through the hyperfine interaction. When interactions fluctuate at rates comparable to the time scale of a hyperfine method, there is a loss in signal coherence, and spectra are damped. The degree of damping can be used to determine fluctuation rates, provided that theoretical expressions for spectra can be derived for relevant physical models of the fluctuations. SHIML provides routines to help researchers quickly develop code to incorporate stochastic models of fluctuating hyperfine interactions in calculations of hyperfine spectra. Solution method: Calculations are based on the method for modeling stochastic hyperfine interactions for PAC by Winkler and Gerdau [5]. The method is extended to include other hyperfine methods following the work of Dattagupta [6]. The code provides routines for reading model information from text files, allowing researchers to develop new models quickly without the need to modify computer code for each new model to be considered. Restrictions: In the present version of the code, only methods that measure the hyperfine interaction on one probe spin state, such as PAC, μSR, and NMR, are supported. Running time: Varies

25 CFR 39.136 - What is the WSU for Language Development programs?

Code of Federal Regulations, 2011 CFR

2011-04-01

... 25 Indians 1 2011-04-01 2011-04-01 false What is the WSU for Language Development programs? 39.136... EQUALIZATION PROGRAM Indian School Equalization Formula Language Development Programs § 39.136 What is the WSU for Language Development programs? Language Development programs are funded at 0.13 WSUs per student. ...

GENXICC2.0: An upgraded version of the generator for hadronic production of double heavy baryons Ξ, Ξ and Ξ

NASA Astrophysics Data System (ADS)

Chang, Chao-Hsi; Wang, Jian-Xiong; Wu, Xing-Gang

2010-06-01

An upgraded (second) version of the package GENXICC (A Generator for Hadronic Production of the Double Heavy Baryons Ξ, Ξ and Ξ by C.H. Chang, J.X. Wang and X.G. Wu [its first version in: Comput. Phys. Comm. 177 (2007) 467]) is presented. Users, with this version being implemented in PYTHIA and a GNU C compiler, may simulate full events of these processes in various experimental environments conveniently. In comparison with the previous version, in order to implement it in PYTHIA properly, a subprogram for the fragmentation of the produced double heavy diquark to the relevant baryon is supplied and the interface of the generator to PYTHIA is changed accordingly. In the subprogram, with explanation, certain necessary assumptions (approximations) are made in order to conserve the momenta and the QCD 'color' flow for the fragmentation. Program summaryProgram title: GENXICC2.0 Catalogue identifier: ADZJ_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZJ_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 102 482 No. of bytes in distributed program, including test data, etc.: 1 469 519 Distribution format: tar.gz Programming language: Fortran 77/90 Computer: Any LINUX based on PC with FORTRAN 77 or FORTRAN 90 and GNU C compiler as well Operating system: Linux RAM: About 2.0 MByte Classification: 11.2 Catalogue identifier of previous version: ADZJ_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 467 Does the new version supersede the previous version?: No Nature of problem: Hadronic production of double heavy baryons Ξ, Ξ and Ξ Solution method: The code is based on NRQCD framework. With proper options, it can generate weighted and un-weighted events of hadronic double heavy baryon production. When the hadronizations of the produced jets and double heavy diquark are taken into account in the production, the upgraded version with proper interface to PYTHIA can generate full events. Reasons for new version: Responding to the feedback from users, we improve the generator mainly by carefully completing the 'final non-perturbative process', i.e. the formulation of the double heavy baryon from relevant intermediate diquark. In the present version, the information for fragmentation about momentum-flow and the color-flow, that is necessary for PYTHIA to generate full events, is retained although reasonable approximations are made. In comparison with the original version, the upgraded one can implement it in PYTHIA properly to do the full event simulation of the double heavy baryon production. Summary of revisions:We try to explain the treatment of the momentum distribution of the process more clearly than the original version, and show how the final baryon is generated through the typical intermediate diquark precisely. We present color flow of the involved processes precisely and the corresponding changes for the program are made. The corresponding changes of the program are explained in the paper. Restrictions: The color flow, particularly, in the piece of code programming of the fragmentation from the produced colorful double heavy diquark into a relevant double heavy baryon, is treated carefully so as to implement it in PYTHIA properly. Running time: It depends on which option is chosen to configure PYTHIA when generating full events and also on which mechanism is chosen to generate the events. Typically, for the most complicated case with gluon-gluon fusion mechanism to generate the mixed events via the intermediate diquark in (cc)[ and (cc)[ states, under the option, IDWTUP=1, to generate 1000 events, takes about 20 hours on a 1.8 GHz Intel P4-processor machine, whereas under the option, IDWTUP=3, even to generate 106 events takes about 40 minutes on the same machine.

Linux Incident Response Volatile Data Analysis Framework

ERIC Educational Resources Information Center

McFadden, Matthew

2013-01-01

Cyber incident response is an emphasized subject area in cybersecurity in information technology with increased need for the protection of data. Due to ongoing threats, cybersecurity imposes many challenges and requires new investigative response techniques. In this study a Linux Incident Response Framework is designed for collecting volatile data…

Onboard Flow Sensing For Downwash Detection and Avoidance On Small Quadrotor Helicopters

DTIC Science & Technology

2015-01-01

onboard computers, one for flight stabilization and a Linux computer for sensor integration and control calculations . The Linux computer runs Robot...Hirokawa, D. Kubo , S. Suzuki, J. Meguro, and T. Suzuki. Small uav for immediate hazard map generation. In AIAA Infotech@Aerospace Conf, May 2007. 8F

Cross platform development using Delphi and Kylix

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDonald, J.L.; Nishimura, H.; Timossi, C.

2002-10-08

A cross platform component for EPICS Simple Channel Access (SCA) has been developed for the use with Delphi on Windows and Kylix on Linux. An EPICS controls GUI application developed on Windows runs on Linux by simply rebuilding it, and vice versa. This paper describes the technical details of the component.

Assessing Foreign Language Proficiency of Undergraduates. Issues in Language Program Direction: A Series of Annual Volumes.

ERIC Educational Resources Information Center

Teschner, Richard V., Ed.

This collection of papers includes: "Foreign Language Testing Today: Issues in Language Program Direction" (Frank Nuessel); "Assessing the Problems of Assessment" (M. Peter Hagiwara); "Testing in Foreign Language Programs and Testing Programs in Foreign Language Departments: Reflections and Recommendations" (Elizabeth…

PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.

PubMed

Müller, Paul; Schwille, Petra; Weidemann, Thomas

2014-09-01

We present a graphical user interface (PyCorrFit) for the fitting of theoretical model functions to experimental data obtained by fluorescence correlation spectroscopy (FCS). The program supports many data file formats and features a set of tools specialized in FCS data evaluation. The Python source code is freely available for download from the PyCorrFit web page at http://pycorrfit.craban.de. We offer binaries for Ubuntu Linux, Mac OS X and Microsoft Windows. © The Author 2014. Published by Oxford University Press.

APEX 3: a multi-purpose test platform for auditory psychophysical experiments.

PubMed

Francart, Tom; van Wieringen, Astrid; Wouters, Jan

2008-07-30

APEX 3 is a software test platform for auditory behavioral experiments. It provides a generic means of setting up experiments without any programming. The supported output devices include sound cards and cochlear implants from Cochlear Corporation and Advanced Bionics Corporation. Many psychophysical procedures are provided and there is an interface to add custom procedures. Plug-in interfaces are provided for data filters and external controllers. APEX 3 is supported under Linux and Windows and is available free of charge.

GANGA: A tool for computational-task management and easy access to Grid resources

NASA Astrophysics Data System (ADS)

Mościcki, J. T.; Brochu, F.; Ebke, J.; Egede, U.; Elmsheuser, J.; Harrison, K.; Jones, R. W. L.; Lee, H. C.; Liko, D.; Maier, A.; Muraru, A.; Patrick, G. N.; Pajchel, K.; Reece, W.; Samset, B. H.; Slater, M. W.; Soroko, A.; Tan, C. L.; van der Ster, D. C.; Williams, M.

2009-11-01

In this paper, we present the computational task-management tool GANGA, which allows for the specification, submission, bookkeeping and post-processing of computational tasks on a wide set of distributed resources. GANGA has been developed to solve a problem increasingly common in scientific projects, which is that researchers must regularly switch between different processing systems, each with its own command set, to complete their computational tasks. GANGA provides a homogeneous environment for processing data on heterogeneous resources. We give examples from High Energy Physics, demonstrating how an analysis can be developed on a local system and then transparently moved to a Grid system for processing of all available data. GANGA has an API that can be used via an interactive interface, in scripts, or through a GUI. Specific knowledge about types of tasks or computational resources is provided at run-time through a plugin system, making new developments easy to integrate. We give an overview of the GANGA architecture, give examples of current use, and demonstrate how GANGA can be used in many different areas of science. Catalogue identifier: AEEN_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEN_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL No. of lines in distributed program, including test data, etc.: 224 590 No. of bytes in distributed program, including test data, etc.: 14 365 315 Distribution format: tar.gz Programming language: Python Computer: personal computers, laptops Operating system: Linux/Unix RAM: 1 MB Classification: 6.2, 6.5 Nature of problem: Management of computational tasks for scientific applications on heterogenous distributed systems, including local, batch farms, opportunistic clusters and Grids. Solution method: High-level job management interface, including command line, scripting and GUI components. Restrictions: Access to the distributed resources depends on the installed, 3rd party software such as batch system client or Grid user interface.

25 CFR 39.131 - What is a Language Development Program?

Code of Federal Regulations, 2014 CFR

2014-04-01

... EQUALIZATION PROGRAM Indian School Equalization Formula Language Development Programs § 39.131 What is a Language Development Program? A Language Development program is one that serves students who either: (a...

25 CFR 39.131 - What is a Language Development Program?

Code of Federal Regulations, 2013 CFR

2013-04-01

... EQUALIZATION PROGRAM Indian School Equalization Formula Language Development Programs § 39.131 What is a Language Development Program? A Language Development program is one that serves students who either: (a...

25 CFR 39.131 - What is a Language Development Program?

Code of Federal Regulations, 2012 CFR

2012-04-01

... EQUALIZATION PROGRAM Indian School Equalization Formula Language Development Programs § 39.131 What is a Language Development Program? A Language Development program is one that serves students who either: (a...

Research Issues and Language Program Direction. Issues in Language Program Direction: A Series of Annual Volumes.

ERIC Educational Resources Information Center

Heilenman, L. Kathy, Ed.

This collection of papers is divided into two parts. After "Introduction" (L. Kathy Heilenman), Part 1, "Research and Language Program Directors: The Relationship," includes "Research Domains and Language Program Direction" (Bill VanPatten); "Language Program Direction and the Modernist Agenda" (Celeste…

MADANALYSIS 5, a user-friendly framework for collider phenomenology

NASA Astrophysics Data System (ADS)

Conte, Eric; Fuks, Benjamin; Serret, Guillaume

2013-01-01

We present MADANALYSIS 5, a new framework for phenomenological investigations at particle colliders. Based on a C++ kernel, this program allows us to efficiently perform, in a straightforward and user-friendly fashion, sophisticated physics analyses of event files such as those generated by a large class of Monte Carlo event generators. MADANALYSIS 5 comes with two modes of running. The first one, easier to handle, uses the strengths of a powerful PYTHON interface in order to implement physics analyses by means of a set of intuitive commands. The second one requires one to implement the analyses in the C++ programming language, directly within the core of the analysis framework. This opens unlimited possibilities concerning the level of complexity which can be reached, being only limited by the programming skills and the originality of the user. Program summaryProgram title: MadAnalysis 5 Catalogue identifier: AENO_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENO_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Permission to use, copy, modify and distribute this program is granted under the terms of the GNU General Public License. No. of lines in distributed program, including test data, etc.: 31087 No. of bytes in distributed program, including test data, etc.: 399105 Distribution format: tar.gz Programming language: PYTHON, C++. Computer: All platforms on which Python version 2.7, Root version 5.27 and the g++ compiler are available. Compatibility with newer versions of these programs is also ensured. However, the Python version must be below version 3.0. Operating system: Unix, Linux and Mac OS operating systems on which the above-mentioned versions of Python and Root, as well as g++, are available. Classification: 11.1. External routines: ROOT (http://root.cern.ch/drupal/) Nature of problem: Implementing sophisticated phenomenological analyses in high-energy physics through a flexible, efficient and straightforward fashion, starting from event files such as those produced by Monte Carlo event generators. The event files can have been matched or not to parton-showering and can have been processed or not by a (fast) simulation of a detector. According to the sophistication level of the event files (parton-level, hadron-level, reconstructed-level), one must note that several input formats are possible. Solution method: We implement an interface allowing the production of predefined as well as user-defined histograms for a large class of kinematical distributions after applying a set of event selection cuts specified by the user. This therefore allows us to devise robust and novel search strategies for collider experiments, such as those currently running at the Large Hadron Collider at CERN, in a very efficient way. Restrictions: Unsupported event file format. Unusual features: The code is fully based on object representations for events, particles, reconstructed objects and cuts, which facilitates the implementation of an analysis. Running time: It depends on the purposes of the user and on the number of events to process. It varies from a few seconds to the order of the minute for several millions of events.

A dynamic kernel modifier for linux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minnich, R. G.

2002-09-03

Dynamic Kernel Modifier, or DKM, is a kernel module for Linux that allows user-mode programs to modify the execution of functions in the kernel without recompiling or modifying the kernel source in any way. Functions may be traced, either function entry only or function entry and exit; nullified; or replaced with some other function. For the tracing case, function execution results in the activation of a watchpoint. When the watchpoint is activated, the address of the function is logged in a FIFO buffer that is readable by external applications. The watchpoints are time-stamped with the resolution of the processor highmore » resolution timers, which on most modem processors are accurate to a single processor tick. DKM is very similar to earlier systems such as the SunOS trace device or Linux TT. Unlike these two systems, and other similar systems, DKM requires no kernel modifications. DKM allows users to do initial probing of the kernel to look for performance problems, or even to resolve potential problems by turning functions off or replacing them. DKM watchpoints are not without cost: it takes about 200 nanoseconds to make a log entry on an 800 Mhz Pentium-Ill. The overhead numbers are actually competitive with other hardware-based trace systems, although it has less 'Los Alamos National Laboratory is operated by the University of California for the National Nuclear Security Administration of the United States Department of Energy under contract W-7405-ENG-36. accuracy than an In-Circuit Emulator such as the American Arium. Once the user has zeroed in on a problem, other mechanisms with a higher degree of accuracy can be used.« less

CASS—CFEL-ASG software suite

NASA Astrophysics Data System (ADS)

Foucar, Lutz; Barty, Anton; Coppola, Nicola; Hartmann, Robert; Holl, Peter; Hoppe, Uwe; Kassemeyer, Stephan; Kimmel, Nils; Küpper, Jochen; Scholz, Mirko; Techert, Simone; White, Thomas A.; Strüder, Lothar; Ullrich, Joachim

2012-10-01

The Max Planck Advanced Study Group (ASG) at the Center for Free Electron Laser Science (CFEL) has created the CFEL-ASG Software Suite CASS to view, process and analyse multi-parameter experimental data acquired at Free Electron Lasers (FELs) using the CFEL-ASG Multi Purpose (CAMP) instrument Strüder et al. (2010) [6]. The software is based on a modular design so that it can be adjusted to accommodate the needs of all the various experiments that are conducted with the CAMP instrument. In fact, this allows the use of the software in all experiments where multiple detectors are involved. One of the key aspects of CASS is that it can be used either 'on-line', using a live data stream from the free-electron laser facility's data acquisition system to guide the experiment, and 'off-line', on data acquired from a previous experiment which has been saved to file. Program summary Program title: CASS Catalogue identifier: AEMP_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence, version 3 No. of lines in distributed program, including test data, etc.: 167073 No. of bytes in distributed program, including test data, etc.: 1065056 Distribution format: tar.gz Programming language: C++. Computer: Intel x86-64. Operating system: GNU/Linux (for information about restrictions see outlook). RAM: >8 GB Classification: 2.3, 3, 15, 16.4. External routines: Qt-Framework[1], SOAP[2], (optional HDF5[3], VIGRA[4], ROOT[5], QWT[6]) Nature of problem: Analysis and visualisation of scientific data acquired at Free-Electron-Lasers Solution method: Generalise data access and storage so that a variety of small programming pieces can be linked to form a complex analysis chain. Unusual features: Complex analysis chains can be built without recompiling the program Additional comments: An updated extensive documentation of CASS is available at [7]. Running time: Depending on the data size and complexity of analysis algorithms. References: [1] http://qt.nokia.com [2] http://www.cs.fsu.edu/~engelen/soap.html [3] http://www.hdfgroup.org/HDF5/ [4] http://hci.iwr.uni-heidelberg.de/vigra/ [5] http://root.cern.ch [6] http://qwt.sourceforge.net/ [7] http://www.mpi-hd.mpg.de/personalhomes/gitasg/cass

SLURM: Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Dunlap, C; Garlick, J

2002-04-24

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, and scheduling modules. The design also includes a scalable, general-purpose communication infrastructure. Development will take place in four phases: Phase I results in a solid infrastructure; Phase II produces a functional but limited interactive job initiation capability without use of the interconnect/switch; Phase III provides switch support and documentation; Phase IV provides job status, fault-tolerance, and job queuing and control through Livermore's Distributed Productionmore » Control System (DPCS), a meta-batch and resource management system.« less

Implementation of image transmission server system using embedded Linux

NASA Astrophysics Data System (ADS)

Park, Jong-Hyun; Jung, Yeon Sung; Nam, Boo Hee

2005-12-01

In this paper, we performed the implementation of image transmission server system using embedded system that is for the specified object and easy to install and move. Since the embedded system has lower capability than the PC, we have to reduce the quantity of calculation of the baseline JPEG image compression and transmission. We used the Redhat Linux 9.0 OS at the host PC and the target board based on embedded Linux. The image sequences are obtained from the camera attached to the FPGA (Field Programmable Gate Array) board with ALTERA cooperation chip. For effectiveness and avoiding some constraints from the vendor's own, we made the device driver using kernel module.

A survey of functional programming language principles

NASA Technical Reports Server (NTRS)

Holloway, C. M.

1986-01-01

Research in the area of functional programming languages has intensified in the 8 years since John Backus' Turing Award Lecture on the topic was published. The purpose of this paper is to present a survey of the ideas of functional programming languages. The paper assumes the reader is comfortable with mathematics and has knowledge of the basic principles of traditional programming languages, but does not assume any prior knowledge of the ideas of functional languages. A simple functional language is defined and used to illustrate the basic ideas. Topics discussed include the reasons for developing functional languages, methods of expressing concurrency, the algebra of functional programming languages, program transformation techniques, and implementations of functional languages. Existing functional languages are also mentioned. The paper concludes with the author's opinions as to the future of functional languages. An annotated bibliography on the subject is also included.

25 CFR 39.137 - May schools operate a language development program without a specific appropriation from Congress?

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false May schools operate a language development program... Formula Language Development Programs § 39.137 May schools operate a language development program without a specific appropriation from Congress? Yes, a school may operate a language development program...

34 CFR 658.1 - What is the Undergraduate International Studies and Foreign Language Program?

Code of Federal Regulations, 2011 CFR

2011-07-01

... Foreign Language Program? 658.1 Section 658.1 Education Regulations of the Offices of the Department of... STUDIES AND FOREIGN LANGUAGE PROGRAM General § 658.1 What is the Undergraduate International Studies and Foreign Language Program? The Undergraduate International Studies and Foreign Language Program is designed...

34 CFR 669.1 - What is the Language Resource Centers Program?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 3 2010-07-01 2010-07-01 false What is the Language Resource Centers Program? 669.1... POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION LANGUAGE RESOURCE CENTERS PROGRAM General § 669.1 What is the Language Resource Centers Program? The Language Resource Centers Program makes awards, through grants or...

34 CFR 658.1 - What is the Undergraduate International Studies and Foreign Language Program?

Code of Federal Regulations, 2010 CFR

2010-07-01

... Foreign Language Program? 658.1 Section 658.1 Education Regulations of the Offices of the Department of... STUDIES AND FOREIGN LANGUAGE PROGRAM General § 658.1 What is the Undergraduate International Studies and Foreign Language Program? The Undergraduate International Studies and Foreign Language Program is designed...

34 CFR 669.1 - What is the Language Resource Centers Program?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 34 Education 3 2011-07-01 2011-07-01 false What is the Language Resource Centers Program? 669.1... POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION LANGUAGE RESOURCE CENTERS PROGRAM General § 669.1 What is the Language Resource Centers Program? The Language Resource Centers Program makes awards, through grants or...

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

PubMed Central

Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-01-01

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. Results: The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and ‘wet lab’ scientists. Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X. Contact: duccio.cavalieri@unifi.it; sorin@wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21653523

Linux Adventures on a Laptop. Computers in Small Libraries

ERIC Educational Resources Information Center

Roberts, Gary

2005-01-01

This article discusses the pros and cons of open source software, such as Linux. It asserts that despite the technical difficulties of installing and maintaining this type of software, ultimately it is helpful in terms of knowledge acquisition and as a beneficial investment librarians can make in themselves, their libraries, and their patrons.…

Drowning in PC Management: Could a Linux Solution Save Us?

ERIC Educational Resources Information Center

Peters, Kathleen A.

2004-01-01

Short on funding and IT staff, a Western Canada library struggled to provide adequate public computing resources. Staff turned to a Linux-based solution that supports up to 10 users from a single computer, and blends Web browsing and productivity applications with session management, Internet filtering, and user authentication. In this article,…

78 FR 57648 - Notice of Issuance of Final Determination Concerning Video Teleconferencing Server

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-19

... the Chinese- origin Video Board and the Filter Board, impart the essential character to the video... includes the codec; a network filter electronic circuit board (``Filter Board''); a housing case; a power... (``Linux software''). The Linux software allows the Filter Board to inspect each Ethernet packet of...

Impact of the Shodan Computer Search Engine on Internet-facing Industrial Control System Devices

DTIC Science & Technology

2014-03-27

bridge implementation. The transparent bridge is designed using a Raspberry Pi configured with Linux IPtables and bridge-utils to bridge the on board...Ethernet card and a second USB Ethernet adapter. A Raspberry Pi is a credit-card-sized single-board computer running a version of Debian Linux. There

Diversifying the Department of Defense Network Enterprise with Linux

DTIC Science & Technology

2010-03-01

Cyberspace, Cyberwar, Legacy, Inventory, Acquisition, Competitive Advantage, Coalition Communications, Ubiquitous, Strategic, Centricity, Kaizen , ISO... Kaizen , ISO, Outsource CLASSIFICATION: Unclassified Historically, the United States and its closest allies have grown increasingly reliant...control through the use of continuous improvement processes ( Kaizen )34. In choosing the Linux client operating system, the move encourages open standards

Development of a portable Linux-based ECG measurement and monitoring system.

PubMed

Tan, Tan-Hsu; Chang, Ching-Su; Huang, Yung-Fa; Chen, Yung-Fu; Lee, Cheng

2011-08-01

This work presents a portable Linux-based electrocardiogram (ECG) signals measurement and monitoring system. The proposed system consists of an ECG front end and an embedded Linux platform (ELP). The ECG front end digitizes 12-lead ECG signals acquired from electrodes and then delivers them to the ELP via a universal serial bus (USB) interface for storage, signal processing, and graphic display. The proposed system can be installed anywhere (e.g., offices, homes, healthcare centers and ambulances) to allow people to self-monitor their health conditions at any time. The proposed system also enables remote diagnosis via Internet. Additionally, the system has a 7-in. interactive TFT-LCD touch screen that enables users to execute various functions, such as scaling a single-lead or multiple-lead ECG waveforms. The effectiveness of the proposed system was verified by using a commercial 12-lead ECG signal simulator and in vivo experiments. In addition to its portability, the proposed system is license-free as Linux, an open-source code, is utilized during software development. The cost-effectiveness of the system significantly enhances its practical application for personal healthcare.

Managing a Real-Time Embedded Linux Platform with Buildroot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diamond, J.; Martin, K.

2015-01-01

Developers of real-time embedded software often need to build the operating system, kernel, tools and supporting applications from source to work with the differences in their hardware configuration. The first attempts to introduce Linux-based real-time embedded systems into the Fermilab accelerator controls system used this approach but it was found to be time-consuming, difficult to maintain and difficult to adapt to different hardware configurations. Buildroot is an open source build system with a menu-driven configuration tool (similar to the Linux kernel build system) that automates this process. A customized Buildroot [1] system has been developed for use in the Fermilabmore » accelerator controls system that includes several hardware configuration profiles (including Intel, ARM and PowerPC) and packages for Fermilab support software. A bootable image file is produced containing the Linux kernel, shell and supporting software suite that varies from 3 to 20 megabytes large – ideal for network booting. The result is a platform that is easier to maintain and deploy in diverse hardware configurations« less

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Conway, Darrel, J.

2007-01-01

Early in 2002, Goddard Space Flight Center (GSFC) began to identify requirements for the flight dynamics software needed to fly upcoming missions that use formations of spacecraft to collect data. These requirements ranged from low level modeling features to large scale interoperability requirements. In 2003 we began work on a system designed to meet these requirement; this system is GMAT. The General Mission Analysis Tool (GMAT) is a general purpose flight dynamics modeling tool built on open source principles. The GMAT code is written in C++, and uses modern C++ constructs extensively. GMAT can be run through either a fully functional Graphical User Interface (GUI) or as a command line program with minimal user feedback. The system is built and runs on Microsoft Windows, Linux, and Macintosh OS X platforms. The GMAT GUI is written using wxWidgets, a cross platform library of components that streamlines the development and extension of the user interface Flight dynamics modeling is performed in GMAT by building components that represent the players in the analysis problem that is being modeled. These components interact through the sequential execution of instructions, embodied in the GMAT Mission Sequence. A typical Mission Sequence will model the trajectories of a set of spacecraft evolving over time, calculating relevant parameters during this propagation, and maneuvering individual spacecraft to maintain a set of mission constraints as established by the mission analyst. All of the elements used in GMAT for mission analysis can be viewed in the GMAT GUI or through a custom scripting language. Analysis problems modeled in GMAT are saved as script files, and these files can be read into GMAT. When a script is read into the GMAT GUI, the corresponding user interface elements are constructed in the GMAT GUI. The GMAT system was developed from the ground up to run in a platform agnostic environment. The source code compiles on numerous different platforms, and is regularly exercised running on Windows, Linux and Macintosh computers by the development and analysis teams working on the project. The system can be run using either a graphical user interface, written using the open source wxWidgets framework, or from a text console. The GMAT source code was written using open source tools. GSFC has released the code using the NASA open source license.

The new version 2.12 of BKG Ntrip Client (BNC)

NASA Astrophysics Data System (ADS)

Stürze, Andrea; Mervart, Leos; Weber, Georg; Rülke, Axel; Wiesensarter, Erwin; Neumaier, Peter

2016-04-01

A new version of the BKG Ntrip Client (BNC) has been released. Originally developed in cooperation of the Federal Agency for Cartography and Geodesy (BKG) and the Czech Technical University (CTU) with a focus on multi-stream real-time access to GPS observations, the software has once again been substantially extended. Promoting Open Standards as recommended by the Radio Technical Commission for Maritime Services (RTCM) remains the prime subject. Beside its Graphical User Interface (GUI), the real-time software for Windows, Linux, Mac, and Linux platforms now comes with complete Command Line Interface (CLI) and considerable post processing functionality. RINEX Version 3 file editing & Quality Check (QC) with full support of Galileo, BeiDou, and SBAS - besides GPS and GLONASS - is part of the new features. Comparison of satellite orbit/clock files in SP3 format is another fresh ability of BNC. Simultaneous multi-station Precise Point Positioning (PPP) for real-time displacement-monitoring of entire reference station networks is one more recent addition to BNC. Implemented RTCM messages for PPP (under development) comprise satellite orbit and clock corrections, code and phase observation biases, and the Vertical Total Electron Content (VTEC) of the ionosphere. The well established, mature codebase is mostly written in C++ language. Its publication under GNU GPL is thought to be well-suited for test, validation and demonstration of new approaches in precise real-time satellite navigation when IP streaming is involved. The poster highlights BNC features which are new in version 2.12 and beneficial to IAG institutions and services such as IGS/RT-IGS and to the interested public in general.

NSTX-U Control System Upgrades

DOE PAGES

Erickson, K. G.; Gates, D. A.; Gerhardt, S. P.; ...

2014-06-01

The National Spherical Tokamak Experiment (NSTX) is undergoing a wealth of upgrades (NSTX-U). These upgrades, especially including an elongated pulse length, require broad changes to the control system that has served NSTX well. A new fiber serial Front Panel Data Port input and output (I/O) stream will supersede the aging copper parallel version. Driver support for the new I/O and cyber security concerns require updating the operating system from Redhat Enterprise Linux (RHEL) v4 to RedHawk (based on RHEL) v6. While the basic control system continues to use the General Atomics Plasma Control System (GA PCS), the effort to forwardmore » port the entire software package to run under 64-bit Linux instead of 32-bit Linux included PCS modifications subsequently shared with GA and other PCS users. Software updates focused on three key areas: (1) code modernization through coding standards (C99/C11), (2) code portability and maintainability through use of the GA PCS code generator, and (3) support of 64-bit platforms. Central to the control system upgrade is the use of a complete real time (RT) Linux platform provided by Concurrent Computer Corporation, consisting of a computer (iHawk), an operating system and drivers (RedHawk), and RT tools (NightStar). Strong vendor support coupled with an extensive RT toolset influenced this decision. The new real-time Linux platform, I/O, and software engineering will foster enhanced capability and performance for NSTX-U plasma control.« less

Flight program language requirements. Volume 2: Requirements and evaluations

NASA Technical Reports Server (NTRS)

1972-01-01

The efforts and results are summarized for a study to establish requirements for a flight programming language for future onboard computer applications. Several different languages were available as potential candidates for future NASA flight programming efforts. The study centered around an evaluation of the four most pertinent existing aerospace languages. Evaluation criteria were established, and selected kernels from the current Saturn 5 and Skylab flight programs were used as benchmark problems for sample coding. An independent review of the language specifications incorporated anticipated future programming requirements into the evaluation. A set of detailed language requirements was synthesized from these activities. The details of program language requirements and of the language evaluations are described.

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

A molecular dynamics implementation of the 3D Mercedes-Benz water model

NASA Astrophysics Data System (ADS)

Hynninen, T.; Dias, C. L.; Mkrtchyan, A.; Heinonen, V.; Karttunen, M.; Foster, A. S.; Ala-Nissila, T.

2012-02-01

The three-dimensional Mercedes-Benz model was recently introduced to account for the structural and thermodynamic properties of water. It treats water molecules as point-like particles with four dangling bonds in tetrahedral coordination, representing H-bonds of water. Its conceptual simplicity renders the model attractive in studies where complex behaviors emerge from H-bond interactions in water, e.g., the hydrophobic effect. A molecular dynamics (MD) implementation of the model is non-trivial and we outline here the mathematical framework of its force-field. Useful routines written in modern Fortran are also provided. This open source code is free and can easily be modified to account for different physical context. The provided code allows both serial and MPI-parallelized execution. Program summaryProgram title: CASHEW (Coarse Approach Simulator for Hydrogen-bonding Effects in Water) Catalogue identifier: AEKM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 20 501 No. of bytes in distributed program, including test data, etc.: 551 044 Distribution format: tar.gz Programming language: Fortran 90 Computer: Program has been tested on desktop workstations and a Cray XT4/XT5 supercomputer. Operating system: Linux, Unix, OS X Has the code been vectorized or parallelized?: The code has been parallelized using MPI. RAM: Depends on size of system, about 5 MB for 1500 molecules. Classification: 7.7 External routines: A random number generator, Mersenne Twister ( http://www.math.sci.hiroshima-u.ac.jp/m-mat/MT/VERSIONS/FORTRAN/mt95.f90), is used. A copy of the code is included in the distribution. Nature of problem: Molecular dynamics simulation of a new geometric water model. Solution method: New force-field for water molecules, velocity-Verlet integration, representation of molecules as rigid particles with rotations described using quaternion algebra. Restrictions: Memory and cpu time limit the size of simulations. Additional comments: Software web site: https://gitorious.org/cashew/. Running time: Depends on the size of system. The sample tests provided only take a few seconds.

The FTS atomic spectrum tool (FAST) for rapid analysis of line spectra

NASA Astrophysics Data System (ADS)

Ruffoni, M. P.

2013-07-01

The FTS Atomic Spectrum Tool (FAST) is an interactive graphical program designed to simplify the analysis of atomic emission line spectra obtained from Fourier transform spectrometers. Calculated, predicted and/or known experimental line parameters are loaded alongside experimentally observed spectral line profiles for easy comparison between new experimental data and existing results. Many such line profiles, which could span numerous spectra, may be viewed simultaneously to help the user detect problems from line blending or self-absorption. Once the user has determined that their experimental line profile fits are good, a key feature of FAST is the ability to calculate atomic branching fractions, transition probabilities, and oscillator strengths-and their uncertainties-which is not provided by existing analysis packages. Program SummaryProgram title: FAST: The FTS Atomic Spectrum Tool Catalogue identifier: AEOW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEOW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 293058 No. of bytes in distributed program, including test data, etc.: 13809509 Distribution format: tar.gz Programming language: C++. Computer: Intel x86-based systems. Operating system: Linux/Unix/Windows. RAM: 8 MB minimum. About 50-200 MB for a typical analysis. Classification: 2.2, 2.3, 21.2. Nature of problem: Visualisation of atomic line spectra including the comparison of theoretical line parameters with experimental atomic line profiles. Accurate intensity calibration of experimental spectra, and the determination of observed relative line intensities that are needed for calculating atomic branching fractions and oscillator strengths. Solution method: FAST is centred around a graphical interface, where a user may view sets of experimental line profiles and compare them to calculated data (such as from the Kurucz database [1]), predicted line parameters, and/or previously known experimental results. With additional information on the spectral response of the spectrometer, obtained from a calibrated standard light source, FT spectra may be intensity calibrated. In turn, this permits the user to calculate atomic branching fractions and oscillator strengths, and their respective uncertainties. Running time: Open ended. Defined by the user. References: [1] R.L. Kurucz (2007). URL http://kurucz.harvard.edu/atoms/.

A high-performance Fortran code to calculate spin- and parity-dependent nuclear level densities

NASA Astrophysics Data System (ADS)

Sen'kov, R. A.; Horoi, M.; Zelevinsky, V. G.

2013-01-01

A high-performance Fortran code is developed to calculate the spin- and parity-dependent shell model nuclear level densities. The algorithm is based on the extension of methods of statistical spectroscopy and implies exact calculation of the first and second Hamiltonian moments for different configurations at fixed spin and parity. The proton-neutron formalism is used. We have applied the method for calculating the level densities for a set of nuclei in the sd-, pf-, and pf+g- model spaces. Examples of the calculations for 28Si (in the sd-model space) and 64Ge (in the pf+g-model space) are presented. To illustrate the power of the method we estimate the ground state energy of 64Ge in the larger model space pf+g, which is not accessible to direct shell model diagonalization due to the prohibitively large dimension, by comparing with the nuclear level densities at low excitation energy calculated in the smaller model space pf. Program summaryProgram title: MM Catalogue identifier: AENM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 193181 No. of bytes in distributed program, including test data, etc.: 1298585 Distribution format: tar.gz Programming language: Fortran 90, MPI. Computer: Any architecture with a Fortran 90 compiler and MPI. Operating system: Linux. RAM: Proportional to the system size, in our examples, up to 75Mb Classification: 17.15. External routines: MPICH2 (http://www.mcs.anl.gov/research/projects/mpich2/) Nature of problem: Calculating of the spin- and parity-dependent nuclear level density. Solution method: The algorithm implies exact calculation of the first and second Hamiltonian moments for different configurations at fixed spin and parity. The code is parallelized using the Message Passing Interface and a master-slaves dynamical load-balancing approach. Restrictions: The program uses two-body interaction in a restricted single-level basis. For example, GXPF1A in the pf-valence space. Running time: Depends on the system size and the number of processors used (from 1 min to several hours).

Image Classification Workflow Using Machine Learning Methods

NASA Astrophysics Data System (ADS)

Christoffersen, M. S.; Roser, M.; Valadez-Vergara, R.; Fernández-Vega, J. A.; Pierce, S. A.; Arora, R.

2016-12-01

Recent increases in the availability and quality of remote sensing datasets have fueled an increasing number of scientifically significant discoveries based on land use classification and land use change analysis. However, much of the software made to work with remote sensing data products, specifically multispectral images, is commercial and often prohibitively expensive. The free to use solutions that are currently available come bundled up as small parts of much larger programs that are very susceptible to bugs and difficult to install and configure. What is needed is a compact, easy to use set of tools to perform land use analysis on multispectral images. To address this need, we have developed software using the Python programming language with the sole function of land use classification and land use change analysis. We chose Python to develop our software because it is relatively readable, has a large body of relevant third party libraries such as GDAL and Spectral Python, and is free to install and use on Windows, Linux, and Macintosh operating systems. In order to test our classification software, we performed a K-means unsupervised classification, Gaussian Maximum Likelihood supervised classification, and a Mahalanobis Distance based supervised classification. The images used for testing were three Landsat rasters of Austin, Texas with a spatial resolution of 60 meters for the years of 1984 and 1999, and 30 meters for the year 2015. The testing dataset was easily downloaded using the Earth Explorer application produced by the USGS. The software should be able to perform classification based on any set of multispectral rasters with little to no modification. Our software makes the ease of land use classification using commercial software available without an expensive license.

Expyriment: a Python library for cognitive and neuroscientific experiments.

PubMed

Krause, Florian; Lindemann, Oliver

2014-06-01

Expyriment is an open-source and platform-independent lightweight Python library for designing and conducting timing-critical behavioral and neuroimaging experiments. The major goal is to provide a well-structured Python library for script-based experiment development, with a high priority being the readability of the resulting program code. Expyriment has been tested extensively under Linux and Windows and is an all-in-one solution, as it handles stimulus presentation, the recording of input/output events, communication with other devices, and the collection and preprocessing of data. Furthermore, it offers a hierarchical design structure, which allows for an intuitive transition from the experimental design to a running program. It is therefore also suited for students, as well as for experimental psychologists and neuroscientists with little programming experience.

minimega

DOE Office of Scientific and Technical Information (OSTI.GOV)

David Fritz, John Floren

2013-08-27

Minimega is a simple emulytics platform for creating testbeds of networked devices. The platform consists of easily deployable tools to facilitate bringing up large networks of virtual machines including Windows, Linux, and Android. Minimega attempts to allow experiments to be brought up quickly with nearly no configuration. Minimega also includes tools for simple cluster management, as well as tools for creating Linux based virtual machine images.

Malware Memory Analysis of the Jynx2 Linux Rootkit (Part 1): Investigating a Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2014-10-01

indication that not a single scanner was able to detect the rootkit as malicious or infected. SHA256 ...clear indication that not a single scanner was able detect it as malicious, infected or associated to the Jynx2 rootkit. SHA256

Teaching Hands-On Linux Host Computer Security

ERIC Educational Resources Information Center

Shumba, Rose

2006-01-01

In the summer of 2003, a project to augment and improve the teaching of information assurance courses was started at IUP. Thus far, ten hands-on exercises have been developed. The exercises described in this article, and presented in the appendix, are based on actions required to secure a Linux host. Publicly available resources were used to…

Will Your Next Supercomputer Come from Costco?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farber, Rob

2007-04-15

A fun topic for April, one that is not an April fool’s joke, is that you can purchase a commodity 200+ Gflop (single-precision) Linux supercomputer for around $600 from your favorite electronic vendor. Yes, it’s true. Just walk in and ask for a Sony Playstation 3 (PS3), take it home and install Linux on it. IBM has provided an excellent tutorial for installing Linux and building applications at http://www-128.ibm.com/developerworks/power/library/pa-linuxps3-1. If you want to raise some eyebrows at work, then submit a purchase request for a Sony PS3 game console and watch the reactions as your paperwork wends its way throughmore » the procurement process.« less

Learning through an Aboriginal Language: The Impact on Students' English and Aboriginal Language Skills

ERIC Educational Resources Information Center

Usborne, Esther; Peck, Josephine; Smith, Donna-Lee; Taylor, Donald M.

2011-01-01

Aboriginal communities across Canada are implementing Aboriginal language programs in their schools. In the present research, we explore the impact of learning through an Aboriginal language on students' English and Aboriginal language skills by contrasting a Mi'kmaq language immersion program with a Mi'kmaq as a second language program. The…

GENXICC2.1: An improved version of GENXICC for hadronic production of doubly heavy baryons

NASA Astrophysics Data System (ADS)

Wang, Xian-You; Wu, Xing-Gang

2013-03-01

We present an improved version of GENXICC, which is a generator for hadronic production of the doubly heavy baryons Ξcc, Ξbc and Ξbb and has been introduced by C.H. Chang, J.X. Wang and X.G. Wu [Comput. Phys. Commun. 177 (2007) 467; Comput. Phys. Commun. 181 (2010) 1144]. In comparison with the previous GENXICC versions, we update the program in order to generate the unweighted baryon events more effectively under various simulation environments, whose distributions are now generated according to the probability proportional to the integrand. One Les Houches Event (LHE) common block has been added to produce a standard LHE data file that contains useful information of the doubly heavy baryon and its accompanying partons. Such LHE data can be conveniently imported into PYTHIA to do further hadronization and decay simulation, especially, the color-flow problem can be solved with PYTHIA8.0. NEW VERSION PROGRAM SUMMARYTitle of program: GENXICC2.1 Program obtained from: CPC Program Library Reference to original program: GENXICC Reference in CPC: Comput. Phys. Commun. 177, 467 (2007); Comput. Phys. Commun. 181, 1144 (2010) Does the new version supersede the old program: No Computer: Any LINUX based on PC with FORTRAN 77 or FORTRAN 90 and GNU C compiler as well Operating systems: LINUX Programming language used: FORTRAN 77/90 Memory required to execute with typical data: About 2.0 MB No. of bytes in distributed program: About 2 MB, including PYTHIA6.4 Distribution format: .tar.gz Nature of physical problem: Hadronic production of doubly heavy baryons Ξcc, Ξbc and Ξbb. Method of solution: The upgraded version with a proper interface to PYTHIA can generate full production and decay events, either weighted or unweighted, conveniently and effectively. Especially, the unweighted events are generated by using an improved hit-and-miss approach. Reasons for new version: Responding to the feedback from users of CMS and LHCb groups at the Large Hadron Collider, and based on the recent improvements of PYTHIA on the color-flow problem, we improve the efficiency for generating the unweighted events, and also improve the color-flow part for further hadronization. Especially, an interface has been added to import the output production events into a suitable form for PYTHIA8.0 simulation, in which the color-flow during the simulation can be correctly set. Typical running time: It depends on which option is chosen to match PYTHIA when generating the full events and also on which mechanism is chosen to generate the events. Typically, for the dominant gluon-gluon fusion mechanism to generate the mixed events via the intermediate diquarks in (cc)[3S1]3¯ and (cc)[1S0]6 states, setting IDWTUP=3 and unwght =.true., it takes 30 min to generate 105 unweighted events on a 2.27 GHz Intel Xeon E5520 processor machine; setting IDWTUP=3 and unwght =.false. or IDWTUP=1 and IGENERATE=0, it only needs 2 min to generate the 105 baryon events (the fastest way, for theoretical purposes only). As a comparison, for previous GENXICC versions, if setting IDWTUP=1 and IGENERATE=1, it takes about 22 hours to generate 1000 unweighted events. Keywords: Event generator; Doubly heavy baryons; Hadronic production. Summary of the changes (improvements): (1) The scheme for generating unweighted events has been improved; (2) One Les Houches Event (LHE) common block has been added to record the standard LHE data in order to be the correct input for PYTHIA8.0 for later simulation; (3) We present the code for connecting GENXICC to PYTHIA8.0, where three color-flows have to be correctly set for later simulation. More specifically, we present the changes together with their detailed explanations in the following:

MC-TESTER: a universal tool for comparisons of Monte Carlo predictions for particle decays in high energy physics

NASA Astrophysics Data System (ADS)

Golonka, P.; Pierzchała, T.; Waş, Z.

2004-02-01

Theoretical predictions in high energy physics are routinely provided in the form of Monte Carlo generators. Comparisons of predictions from different programs and/or different initialization set-ups are often necessary. MC-TESTER can be used for such tests of decays of intermediate states (particles or resonances) in a semi-automated way. Our test consists of two steps. Different Monte Carlo programs are run; events with decays of a chosen particle are searched, decay trees are analyzed and appropriate information is stored. Then, at the analysis step, a list of all found decay modes is defined and branching ratios are calculated for both runs. Histograms of all scalar Lorentz-invariant masses constructed from the decay products are plotted and compared for each decay mode found in both runs. For each plot a measure of the difference of the distributions is calculated and its maximal value over all histograms for each decay channel is printed in a summary table. As an example of MC-TESTER application, we include a test with the τ lepton decay Monte Carlo generators, TAUOLA and PYTHIA. The HEPEVT (or LUJETS) common block is used as exclusive source of information on the generated events. Program summaryTitle of the program:MC-TESTER, version 1.1 Catalogue identifier: ADSM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: PC, two Intel Xeon 2.0 GHz processors, 512MB RAM Operating system: Linux Red Hat 6.1, 7.2, and also 8.0 Programming language used:C++, FORTRAN77: gcc 2.96 or 2.95.2 (also 3.2) compiler suite with g++ and g77 Size of the package: 7.3 MB directory including example programs (2 MB compressed distribution archive), without ROOT libraries (additional 43 MB). No. of bytes in distributed program, including test data, etc.: 2 024 425 Distribution format: tar gzip file Additional disk space required: Depends on the analyzed particle: 40 MB in the case of τ lepton decays (30 decay channels, 594 histograms, 82-pages booklet). Keywords: particle physics, decay simulation, Monte Carlo methods, invariant mass distributions, programs comparison Nature of the physical problem: The decays of individual particles are well defined modules of a typical Monte Carlo program chain in high energy physics. A fast, semi-automatic way of comparing results from different programs is often desirable, for the development of new programs, to check correctness of the installations or for discussion of uncertainties. Method of solution: A typical HEP Monte Carlo program stores the generated events in the event records such as HEPEVT or PYJETS. MC-TESTER scans, event by event, the contents of the record and searches for the decays of the particle under study. The list of the found decay modes is successively incremented and histograms of all invariant masses which can be calculated from the momenta of the particle decay products are defined and filled. The outputs from the two runs of distinct programs can be later compared. A booklet of comparisons is created: for every decay channel, all histograms present in the two outputs are plotted and parameter quantifying shape difference is calculated. Its maximum over every decay channel is printed in the summary table. Restrictions on the complexity of the problem: For a list of limitations see Section 6. Typical running time: Varies substantially with the analyzed decay particle. On a PC/Linux with 2.0 GHz processors MC-TESTER increases the run time of the τ-lepton Monte Carlo program TAUOLA by 4.0 seconds for every 100 000 analyzed events (generation itself takes 26 seconds). The analysis step takes 13 seconds; ? processing takes additionally 10 seconds. Generation step runs may be executed simultaneously on multi-processor machines. Accessibility: web page: http://cern.ch/Piotr.Golonka/MC/MC-TESTER e-mails: Piotr.Golonka@CERN.CH, T.Pierzchala@friend.phys.us.edu.pl, Zbigniew.Was@CERN.CH.

A brief description and comparison of programming languages FORTRAN, ALGOL, COBOL, PL/1, and LISP 1.5 from a critical standpoint

NASA Technical Reports Server (NTRS)

Mathur, F. P.

1972-01-01

Several common higher level program languages are described. FORTRAN, ALGOL, COBOL, PL/1, and LISP 1.5 are summarized and compared. FORTRAN is the most widely used scientific programming language. ALGOL is a more powerful language for scientific programming. COBOL is used for most commercial programming applications. LISP 1.5 is primarily a list-processing language. PL/1 attempts to combine the desirable features of FORTRAN, ALGOL, and COBOL into a single language.

Symbolic computation of the Hartree-Fock energy from a chiral EFT three-nucleon interaction at N 2LO

NASA Astrophysics Data System (ADS)

Gebremariam, B.; Bogner, S. K.; Duguet, T.

2010-06-01

We present the first of a two-part Mathematica notebook collection that implements a symbolic approach for the application of the density matrix expansion (DME) to the Hartree-Fock (HF) energy from a chiral effective field theory (EFT) three-nucleon interaction at N 2LO. The final output from the notebooks is a Skyrme-like energy density functional that provides a quasi-local approximation to the non-local HF energy. In this paper, we discuss the derivation of the HF energy and its simplification in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix. Furthermore, a set of steps is described and illustrated on how to extend the approach to other three-nucleon interactions. Program summaryProgram title: SymbHFNNN Catalogue identifier: AEGC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 96 666 No. of bytes in distributed program, including test data, etc.: 378 083 Distribution format: tar.gz Programming language: Mathematica 7.1 Computer: Any computer running Mathematica 6.0 and later versions Operating system: Windows Xp, Linux/Unix RAM: 256 Mb Classification: 5, 17.16, 17.22 Nature of problem: The calculation of the HF energy from the chiral EFT three-nucleon interaction at N 2LO involves tremendous spin-isospin algebra. The problem is compounded by the need to eventually obtain a quasi-local approximation to the HF energy, which requires the HF energy to be expressed in terms of scalar/vector-isoscalar/isovector parts of the one-body density matrix. The Mathematica notebooks discussed in this paper solve the latter issue. Solution method: The HF energy from the chiral EFT three-nucleon interaction at N 2LO is cast into a form suitable for an automatic simplification of the spin-isospin traces. Several Mathematica functions and symbolic manipulation techniques are used to obtain the result in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix. Running time: Several hours

Flight program language requirements. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1972-01-01

The activities and results of a study for the definition of flight program language requirements are described. A set of detailed requirements are presented for a language capable of supporting onboard application programming for the Marshall Space Flight Center's anticipated future activities in the decade of 1975-85. These requirements are based, in part, on the evaluation of existing flight programming language designs to determine the applicability of these designs to flight programming activities which are anticipated. The coding of benchmark problems in the selected programming languages is discussed. These benchmarks are in the form of program kernels selected from existing flight programs. This approach was taken to insure that the results of the study would reflect state of the art language capabilities, as well as to determine whether an existing language design should be selected for adaptation.

25 CFR 39.130 - Can ISEF funds be used for Language Development Programs?

Code of Federal Regulations, 2010 CFR

2010-04-01

... INDIAN SCHOOL EQUALIZATION PROGRAM Indian School Equalization Formula Language Development Programs § 39.130 Can ISEF funds be used for Language Development Programs? Yes, schools can use ISEF funds to... 25 Indians 1 2010-04-01 2010-04-01 false Can ISEF funds be used for Language Development Programs...

25 CFR 39.130 - Can ISEF funds be used for Language Development Programs?

Code of Federal Regulations, 2011 CFR

2011-04-01

... 25 Indians 1 2011-04-01 2011-04-01 false Can ISEF funds be used for Language Development Programs... INDIAN SCHOOL EQUALIZATION PROGRAM Indian School Equalization Formula Language Development Programs § 39.130 Can ISEF funds be used for Language Development Programs? Yes, schools can use ISEF funds to...

C++ Programming Language

NASA Technical Reports Server (NTRS)

Shaykhian, Gholam Ali

2007-01-01

C++ Programming Language: The C++ seminar covers the fundamentals of C++ programming language. The C++ fundamentals are grouped into three parts where each part includes both concept and programming examples aimed at for hands-on practice. The first part covers the functional aspect of C++ programming language with emphasis on function parameters and efficient memory utilization. The second part covers the essential framework of C++ programming language, the object-oriented aspects. Information necessary to evaluate various features of object-oriented programming; including encapsulation, polymorphism and inheritance will be discussed. The last part of the seminar covers template and generic programming. Examples include both user defined and standard templates.

A Real-Time Linux for Multicore Platforms

DTIC Science & Technology

2013-12-20

under ARO support) to obtain a fully-functional OS for supporting real-time workloads on multicore platforms. This system, called LITMUS -RT...to be specified as plugin components. LITMUS -RT is open-source software (available at The views, opinions and/or findings contained in this report... LITMUS -RT (LInux Testbed for MUltiprocessor Scheduling in Real-Time systems), allows different multiprocessor real-time scheduling and

Computer-Aided Design of Drugs on Emerging Hybrid High Performance Computers

DTIC Science & Technology

2013-09-01

solutions to virtualization include lightweight, user-level implementations on Linux operating systems , but these solutions are often dependent on a...virtualization include lightweight, user-level implementations on Linux operating systems , but these solutions are often dependent on a specific version of...Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA, 22202-4302

Millisecond timing on PCs and Macs.

PubMed

MacInnes, W J; Taylor, T L

2001-05-01

A real-time, object-oriented solution for displaying stimuli on Windows 95/98, MacOS and Linux platforms is presented. The program, written in C++, utilizes a special-purpose window class (GLWindow), OpenGL, and 32-bit graphics acceleration; it avoids display timing uncertainty by substituting the new window class for the default window code for each system. We report the outcome of tests for real-time capability across PC and Mac platforms running a variety of operating systems. The test program, which can be used as a shell for programming real-time experiments and testing specific processors, is available at http://www.cs.dal.ca/~macinnwj. We propose to provide researchers with a sense of the usefulness of our program, highlight the ability of many multitasking environments to achieve real time, as well as caution users about systems that may not achieve real time, even under optimal conditions.

Interactivity vs. fairness in networked linux systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wenji; Crawford, Matt; /Fermilab

In general, the Linux 2.6 scheduler can ensure fairness and provide excellent interactive performance at the same time. However, our experiments and mathematical analysis have shown that the current Linux interactivity mechanism tends to incorrectly categorize non-interactive network applications as interactive, which can lead to serious fairness or starvation issues. In the extreme, a single process can unjustifiably obtain up to 95% of the CPU! The root cause is due to the facts that: (1) network packets arrive at the receiver independently and discretely, and the 'relatively fast' non-interactive network process might frequently sleep to wait for packet arrival. Thoughmore » each sleep lasts for a very short period of time, the wait-for-packet sleeps occur so frequently that they lead to interactive status for the process. (2) The current Linux interactivity mechanism provides the possibility that a non-interactive network process could receive a high CPU share, and at the same time be incorrectly categorized as 'interactive.' In this paper, we propose and test a possible solution to address the interactivity vs. fairness problems. Experiment results have proved the effectiveness of the proposed solution.« less

The Trajectory of Language Policy: The First Language Maintenance and Development Program in South Australia

ERIC Educational Resources Information Center

Liddicoat, Anthony J.; Curnow, Timothy Jowan; Scarino, Angela

2016-01-01

This paper examines the development of the First Language Maintenance and Development (FLMD) program in South Australia. This program is the main language policy activity that specifically focuses on language maintenance in government primary schools and has existed since 1986. During this time, the program has evolved largely as the result of ad…

HepML, an XML-based format for describing simulated data in high energy physics

NASA Astrophysics Data System (ADS)

Belov, S.; Dudko, L.; Kekelidze, D.; Sherstnev, A.

2010-10-01

In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summaryProgram title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high energy physics is divided into several stages. Various programs exist for these stages. In this article we are interested in interfacing different Monte Carlo event generators via data files, in particular, Matrix Element (ME) generators and Showering and Hadronization (SH) generators. There is a widely accepted format for data files for such interfaces - Les Houches Event Format (LHEF). Although information kept in an LHEF file is enough for proper working of SH generators, it is insufficient for understanding how events in the LHEF file have been prepared and which physical model has been applied. In this paper we propose an extension of the format for keeping additional information available in generators. We propose to add a new information block, marked up with XML tags, to the LHEF file. This block describes events in the file in more detail. In particular, it stores information about a physical model, kinematical cuts, generator, etc. This helps to make LHEF files self-documented. Certainly, HepML can be applied in more general context, not in LHEF files only. Solution method: In order to overcome drawbacks of the original LHEF accord we propose to add a new information block of HepML tags. HepML is an XML-based markup language. We designed several XML Schemas for all tags in the language. Any HepML document should follow rules of the Schemas. The language is equipped with a library for operation with HepML tags and documents. This C++ library, called libhepml, consists of classes for HepML objects, which represent a HepML document in computer memory, parsing classes, serializating classes, and some auxiliary classes. Restrictions: The software is adapted for solving problems, described in the article. There are no additional restrictions. Running time: Tests have been done on a computer with Intel(R) Core(TM)2 Solo, 1.4 GHz. Parsing of a HepML file: 6 ms (size of the HepML files is 12.5 Kb) Writing of a HepML block to file: 14 ms (file size 12.5 Kb) Merging of two HepML blocks and writing to file: 18 ms (file size - 25.0 Kb).

Ascent/Descent Software

NASA Technical Reports Server (NTRS)

Brown, Charles; Andrew, Robert; Roe, Scott; Frye, Ronald; Harvey, Michael; Vu, Tuan; Balachandran, Krishnaiyer; Bly, Ben

2012-01-01

The Ascent/Descent Software Suite has been used to support a variety of NASA Shuttle Program mission planning and analysis activities, such as range safety, on the Integrated Planning System (IPS) platform. The Ascent/Descent Software Suite, containing Ascent Flight Design (ASC)/Descent Flight Design (DESC) Configuration items (Cis), lifecycle documents, and data files used for shuttle ascent and entry modeling analysis and mission design, resides on IPS/Linux workstations. A list of tools in Navigation (NAV)/Prop Software Suite represents tool versions established during or after the IPS Equipment Rehost-3 project.

Artificial Potential Field Controllers for Robust Communications in a Network of Swarm Robots

DTIC Science & Technology

2005-05-18

vectors are less than 90◦ apart. Algorithm 1 The Algorithm for generating a feasible set of vectors P ← set of high priority vectors Csum ← [( LOS1 +R1...the 46 C program was finished reading and writing the values to the serial line it would delete the timing file. Only after the timing file had been... deleted would the base station write new values for the wheel velocities. The timing file kept both the Linux PC and the base station synchronized so

The Roots of Beowulf

NASA Technical Reports Server (NTRS)

Fischer, James R.

2014-01-01

The first Beowulf Linux commodity cluster was constructed at NASA's Goddard Space Flight Center in 1994 and its origins are a part of the folklore of high-end computing. In fact, the conditions within Goddard that brought the idea into being were shaped by rich historical roots, strategic pressures brought on by the ramp up of the Federal High-Performance Computing and Communications Program, growth of the open software movement, microprocessor performance trends, and the vision of key technologists. This multifaceted story is told here for the first time from the point of view of NASA project management.

X-LUNA: Extending Free/Open Source Real Time Executive for On-Board Space Applications

NASA Astrophysics Data System (ADS)

Braga, P.; Henriques, L.; Zulianello, M.

2008-08-01

In this paper we present xLuna, a system based on the RTEMS [1] Real-Time Operating System that is able to run on demand a GNU/Linux Operating System [2] as RTEMS' lowest priority task. Linux runs in user-mode and in a different memory partition. This allows running Hard Real-Time tasks and Linux applications on the same system sharing the Hardware resources while keeping a safe isolation and the Real-Time characteristics of RTEMS. Communication between both Systems is possible through a loose coupled mechanism based on message queues. Currently only SPARC LEON2 processor with Memory Management Unit (MMU) is supported. The advantage in having two isolated systems is that non critical components are quickly developed or simply ported reducing time-to-market and budget.

Spanish-language community-based mental health treatment programs, policy-required language-assistance programming, and mental health treatment access among Spanish-speaking clients.

PubMed

Snowden, Lonnie R; McClellan, Sean R

2013-09-01

We investigated the extent to which implementing language assistance programming through contracting with community-based organizations improved the accessibility of mental health care under Medi-Cal (California's Medicaid program) for Spanish-speaking persons with limited English proficiency, and whether it reduced language-based treatment access disparities. Using a time series nonequivalent control group design, we studied county-level penetration of language assistance programming over 10 years (1997-2006) for Spanish-speaking persons with limited English proficiency covered under Medi-Cal. We used linear regression with county fixed effects to control for ongoing trends and other influences. When county mental health plans contracted with community-based organizations, those implementing language assistance programming increased penetration rates of Spanish-language mental health services under Medi-Cal more than other plans (0.28 percentage points, a 25% increase on average; P < .05). However, the increase was insufficient to significantly reduce language-related disparities. Mental health treatment programs operated by community-based organizations may have moderately improved access after implementing required language assistance programming, but the programming did not reduce entrenched disparities in the accessibility of mental health services.

Spanish-Language Community-Based Mental Health Treatment Programs, Policy-Required Language-Assistance Programming, and Mental Health Treatment Access Among Spanish-Speaking Clients

PubMed Central

McClellan, Sean R.

2013-01-01

Objectives. We investigated the extent to which implementing language assistance programming through contracting with community-based organizations improved the accessibility of mental health care under Medi-Cal (California’s Medicaid program) for Spanish-speaking persons with limited English proficiency, and whether it reduced language-based treatment access disparities. Methods. Using a time series nonequivalent control group design, we studied county-level penetration of language assistance programming over 10 years (1997–2006) for Spanish-speaking persons with limited English proficiency covered under Medi-Cal. We used linear regression with county fixed effects to control for ongoing trends and other influences. Results. When county mental health plans contracted with community-based organizations, those implementing language assistance programming increased penetration rates of Spanish-language mental health services under Medi-Cal more than other plans (0.28 percentage points, a 25% increase on average; P < .05). However, the increase was insufficient to significantly reduce language-related disparities. Conclusions. Mental health treatment programs operated by community-based organizations may have moderately improved access after implementing required language assistance programming, but the programming did not reduce entrenched disparities in the accessibility of mental health services. PMID:23865663

Nociones de la programacion de lenguas extranjeras (Ensayo metodologico) (Programming Foreign Languages [A Methodological Study])

ERIC Educational Resources Information Center

Feldman, David

1975-01-01

Stresses the importance of language laboratories and other technical devices used in foreign language teaching, particularly in programed language instruction. Illustrates, by means of taxonomies, the various stages a foreign language learning program should follow. (Text is in Spanish.) (DS)

LCG MCDB—a knowledgebase of Monte-Carlo simulated events

NASA Astrophysics Data System (ADS)

Belov, S.; Dudko, L.; Galkin, E.; Gusev, A.; Pokorski, W.; Sherstnev, A.

2008-02-01

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 summaryProgram title: LCG Monte-Carlo Data Base Catalogue identifier: ADZX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 30 129 No. of bytes in distributed program, including test data, etc.: 216 943 Distribution format: tar.gz Programming language: Perl Computer: CPU: Intel Pentium 4, RAM: 1 Gb, HDD: 100 Gb Operating system: Scientific Linux CERN 3/4 RAM: 1 073 741 824 bytes (1 Gb) Classification: 9 External routines:perl >= 5.8.5; Perl modules DBD-mysql >= 2.9004, File::Basename, GD::SecurityImage, GD::SecurityImage::AC, Linux::Statistics, XML::LibXML > 1.6, XML::SAX, XML::NamespaceSupport; Apache HTTP Server >= 2.0.59; mod auth external >= 2.2.9; edg-utils-system RPM package; gd >= 2.0.28; rpm package CASTOR-client >= 2.1.2-4; 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.

MCNP Output Data Analysis with ROOT (MODAR)

NASA Astrophysics Data System (ADS)

Carasco, C.

2010-06-01

MCNP Output Data Analysis with ROOT (MODAR) is a tool based on CERN's ROOT software. MODAR has been designed to handle time-energy data issued by MCNP simulations of neutron inspection devices using the associated particle technique. MODAR exploits ROOT's Graphical User Interface and functionalities to visualize and process MCNP simulation results in a fast and user-friendly way. MODAR allows to take into account the detection system time resolution (which is not possible with MCNP) as well as detectors energy response function and counting statistics in a straightforward way. Program summaryProgram title: MODAR Catalogue identifier: AEGA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 155 373 No. of bytes in distributed program, including test data, etc.: 14 815 461 Distribution format: tar.gz Programming language: C++ Computer: Most Unix workstations and PC Operating system: Most Unix systems, Linux and windows, provided the ROOT package has been installed. Examples where tested under Suse Linux and Windows XP. RAM: Depends on the size of the MCNP output file. The example presented in the article, which involves three two-dimensional 139×740 bins histograms, allocates about 60 MB. These data are running under ROOT and include consumption by ROOT itself. Classification: 17.6 External routines: ROOT version 5.24.00 ( http://root.cern.ch/drupal/) Nature of problem: The output of an MCNP simulation is an ASCII file. The data processing is usually performed by copying and pasting the relevant parts of the ASCII file into Microsoft Excel. Such an approach is satisfactory when the quantity of data is small but is not efficient when the size of the simulated data is large, for example when time-energy correlations are studied in detail such as in problems involving the associated particle technique. In addition, since the finite time resolution of the simulated detector cannot be modeled with MCNP, systems in which time-energy correlation is crucial cannot be described in a satisfactory way. Finally, realistic particle energy deposit in detectors is calculated with MCNP in a two-step process involving type-5 then type-8 tallies. In the first step, the photon flux energy spectrum associated to a time region is selected and serves as a source energy distribution for the second step. Thus, several files must be manipulated before getting the result, which can be time consuming if one needs to study several time regions or different detectors performances. In the same way, modeling counting statistics obtained in a limited acquisition time requires several steps and can also be time consuming. Solution method: In order to overcome the previous limitations, the MODAR C++ code has been written to make use of CERN's ROOT data analysis software. MCNP output data are read from the MCNP output file with dedicated routines. Two-dimensional histograms are filled and can be handled efficiently within the ROOT framework. To keep a user friendly analysis tool, all processing and data display can be done by means of ROOT Graphical User Interface. Specific routines have been written to include detectors finite time resolution and energy response function as well as counting statistics in a straightforward way. Additional comments: The possibility of adding tallies has also been incorporated in MODAR in order to describe systems in which the signal from several detectors can be summed. Moreover, MODAR can be adapted to handle other problems involving two-dimensional data. Running time: The CPU time needed to smear a two-dimensional histogram depends on the size of the histogram. In the presented example, the time-energy smearing of one of the 139×740 two-dimensional histograms takes 3 minutes with a DELL computer equipped with INTEL Core 2.

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.

PubMed

Jossinet, Fabrice; Westhof, Eric

2005-08-01

Efficient RNA sequence manipulations (such as multiple alignments) need to be constrained by rules of RNA structure folding. The structural knowledge has increased dramatically in the last years with the accumulation of several large RNA structures similar to those of the bacterial ribosome subunits. However, no tool in the RNA community provides an easy way to link and integrate progress made at the sequence level using the available three-dimensional information. Sequence to Structure (S2S) proposes a framework in which an user can easily display, manipulate and interconnect heterogeneous RNA data, such as multiple sequence alignments, secondary and tertiary structures. S2S has been implemented using the Java language and has been developed and tested under UNIX systems, such as Linux and MacOSX. S2S is available at http://bioinformatics.org/S2S/.

An IBM 370 assembly language program verifier

NASA Technical Reports Server (NTRS)

Maurer, W. D.

1977-01-01

The paper describes a program written in SNOBOL which verifies the correctness of programs written in assembly language for the IBM 360 and 370 series of computers. The motivation for using assembly language as a source language for a program verifier was the realization that many errors in programs are caused by misunderstanding or ignorance of the characteristics of specific computers. The proof of correctness of a program written in assembly language must take these characteristics into account. The program has been compiled and is currently running at the Center for Academic and Administrative Computing of The George Washington University.

Educator Language Ideologies and a Top-Down Dual Language Program

ERIC Educational Resources Information Center

Fitzsimmons-Doolan, Shannon; Palmer, Deborah; Henderson, Kathryn

2017-01-01

Dual language bilingual education (DLBE) programs are framed to reflect pluralist discourses (de Jong, E. [2013]. "Policy Discourses and U.S. Language in Education Policies." "Peabody Journal of Education" 88 (1): 98-111) and affiliated language ideologies. The continued expansion of DLBE programs not surprisingly brings to…

Teaching Adaptability of Object-Oriented Programming Language Curriculum

ERIC Educational Resources Information Center

Zhu, Xiao-dong

2012-01-01

The evolution of object-oriented programming languages includes update of their own versions, update of development environments, and reform of new languages upon old languages. In this paper, the evolution analysis of object-oriented programming languages is presented in term of the characters and development. The notion of adaptive teaching upon…

Innovative Second Language Education: Bilingual Immersion Programs.

ERIC Educational Resources Information Center

Snow, Marguerite Ann

Bilingual immersion programs combine second language immersion for language majority children and bilingual education for language minority children. The programs are based on the underlying assumption of the immersion model: that a second language is best learned as a medium of instruction, not as the object of instruction. However, they are not…

The BASIC Instructional Program: Conversion into MAINSAIL Language.

ERIC Educational Resources Information Center

Dageforde, Mary L.

This report summarizes the rewriting of the BASIC Instructional Program (BIP) (a "hands-on laboratory" that teaches elementary programming in the BASIC language) from SAIL (a programming language available only on PDP-10 computers) into MAINSAIL (a language designed for portability on a broad class of computers). Four sections contain…

NATAL-74; Towards a Common Programming Language for CAL.

ERIC Educational Resources Information Center

Brahan, J. W.; Colpitts, B. A.

NATAL-74 is a programing language designed for Canadian computer aided learning (CAL) programs. The language has two fundamental elements: the UNIT provides the interface between the student and the subject matter, and the PROCEDURE element embodies teaching strategy. Desirable features of several programing languages have been adapted to cope…

A high level language for a high performance computer

NASA Technical Reports Server (NTRS)

Perrott, R. H.

1978-01-01

The proposed computational aerodynamic facility will join the ranks of the supercomputers due to its architecture and increased execution speed. At present, the languages used to program these supercomputers have been modifications of programming languages which were designed many years ago for sequential machines. A new programming language should be developed based on the techniques which have proved valuable for sequential programming languages and incorporating the algorithmic techniques required for these supercomputers. The design objectives for such a language are outlined.

CRITIC2: A program for real-space analysis of quantum chemical interactions in solids

NASA Astrophysics Data System (ADS)

Otero-de-la-Roza, A.; Johnson, Erin R.; Luaña, Víctor

2014-03-01

We present CRITIC2, a program for the analysis of quantum-mechanical atomic and molecular interactions in periodic solids. This code, a greatly improved version of the previous CRITIC program (Otero-de-la Roza et al., 2009), can: (i) find critical points of the electron density and related scalar fields such as the electron localization function (ELF), Laplacian, … (ii) integrate atomic properties in the framework of Bader’s Atoms-in-Molecules theory (QTAIM), (iii) visualize non-covalent interactions in crystals using the non-covalent interactions (NCI) index, (iv) generate relevant graphical representations including lines, planes, gradient paths, contour plots, atomic basins, … and (v) perform transformations between file formats describing scalar fields and crystal structures. CRITIC2 can interface with the output produced by a variety of electronic structure programs including WIEN2k, elk, PI, abinit, Quantum ESPRESSO, VASP, Gaussian, and, in general, any other code capable of writing the scalar field under study to a three-dimensional grid. CRITIC2 is parallelized, completely documented (including illustrative test cases) and publicly available under the GNU General Public License. Catalogue identifier: AECB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 11686949 No. of bytes in distributed program, including test data, etc.: 337020731 Distribution format: tar.gz Programming language: Fortran 77 and 90. Computer: Workstations. Operating system: Unix, GNU/Linux. Has the code been vectorized or parallelized?: Shared-memory parallelization can be used for most tasks. Classification: 7.3. Catalogue identifier of previous version: AECB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 157 Nature of problem: Analysis of quantum-chemical interactions in periodic solids by means of atoms-in-molecules and related formalisms. Solution method: Critical point search using Newton’s algorithm, atomic basin integration using bisection, qtree and grid-based algorithms, diverse graphical representations and computation of the non-covalent interactions index on a three-dimensional grid. Additional comments: !!!!! The distribution file for this program is over 330 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!! Running time: Variable, depending on the crystal and the source of the underlying scalar field.

mm_par2.0: An object-oriented molecular dynamics simulation program parallelized using a hierarchical scheme with MPI and OPENMP

NASA Astrophysics Data System (ADS)

Oh, Kwang Jin; Kang, Ji Hoon; Myung, Hun Joo

2012-02-01

We have revised a general purpose parallel molecular dynamics simulation program mm_par using the object-oriented programming. We parallelized the revised version using a hierarchical scheme in order to utilize more processors for a given system size. The benchmark result will be presented here. New version program summaryProgram title: mm_par2.0 Catalogue identifier: ADXP_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXP_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2 390 858 No. of bytes in distributed program, including test data, etc.: 25 068 310 Distribution format: tar.gz Programming language: C++ Computer: Any system operated by Linux or Unix Operating system: Linux Classification: 7.7 External routines: We provide wrappers for FFTW [1], Intel MKL library [2] FFT routine, and Numerical recipes [3] FFT, random number generator, and eigenvalue solver routines, SPRNG [4] random number generator, Mersenne Twister [5] random number generator, space filling curve routine. Catalogue identifier of previous version: ADXP_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 560 Does the new version supersede the previous version?: Yes Nature of problem: Structural, thermodynamic, and dynamical properties of fluids and solids from microscopic scales to mesoscopic scales. Solution method: Molecular dynamics simulation in NVE, NVT, and NPT ensemble, Langevin dynamics simulation, dissipative particle dynamics simulation. Reasons for new version: First, object-oriented programming has been used, which is known to be open for extension and closed for modification. It is also known to be better for maintenance. Second, version 1.0 was based on atom decomposition and domain decomposition scheme [6] for parallelization. However, atom decomposition is not popular due to its poor scalability. On the other hand, domain decomposition scheme is better for scalability. It still has a limitation in utilizing a large number of cores on recent petascale computers due to the requirement that the domain size is larger than the potential cutoff distance. To go beyond such a limitation, a hierarchical parallelization scheme has been adopted in this new version and implemented using MPI [7] and OPENMP [8]. Summary of revisions: (1) Object-oriented programming has been used. (2) A hierarchical parallelization scheme has been adopted. (3) SPME routine has been fully parallelized with parallel 3D FFT using volumetric decomposition scheme [9]. K.J.O. thanks Mr. Seung Min Lee for useful discussion on programming and debugging. Running time: Running time depends on system size and methods used. For test system containing a protein (PDB id: 5DHFR) with CHARMM22 force field [10] and 7023 TIP3P [11] waters in simulation box having dimension 62.23 Å×62.23 Å×62.23 Å, the benchmark results are given in Fig. 1. Here the potential cutoff distance was set to 12 Å and the switching function was applied from 10 Å for the force calculation in real space. For the SPME [12] calculation, K, K, and K were set to 64 and the interpolation order was set to 4. To do the fast Fourier transform, we used Intel MKL library. All bonds including hydrogen atoms were constrained using SHAKE/RATTLE algorithms [13,14]. The code was compiled using Intel compiler version 11.1 and mvapich2 version 1.5. Fig. 2 shows performance gains from using CUDA-enabled version [15] of mm_par for 5DHFR simulation in water on Intel Core2Quad 2.83 GHz and GeForce GTX 580. Even though mm_par2.0 is not ported yet for GPU, its performance data would be useful to expect mm_par2.0 performance on GPU. Timing results for 1000 MD steps. 1, 2, 4, and 8 in the figure mean the number of OPENMP threads. Timing results for 1000 MD steps from double precision simulation on CPU, single precision simulation on GPU, and double precision simulation on GPU.

Linux containers for fun and profit in HPC

DOE PAGES

Priedhorsky, Reid; Randles, Timothy C.

2017-10-01

This article outlines options for user-defined software stacks from an HPC perspective. Here, we argue that a lightweight approach based on Linux containers is most suitable for HPC centers because it provides the best balance between maximizing service of user needs and minimizing risks. We also discuss how containers work and several implementations, including Charliecloud, our own open-source solution developed at Los Alamos.

Linux containers for fun and profit in HPC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Priedhorsky, Reid; Randles, Timothy C.

This article outlines options for user-defined software stacks from an HPC perspective. Here, we argue that a lightweight approach based on Linux containers is most suitable for HPC centers because it provides the best balance between maximizing service of user needs and minimizing risks. We also discuss how containers work and several implementations, including Charliecloud, our own open-source solution developed at Los Alamos.

A resistive magnetohydrodynamics solver using modern C++ and the Boost library

NASA Astrophysics Data System (ADS)

Einkemmer, Lukas

2016-09-01

In this paper we describe the implementation of our C++ resistive magnetohydrodynamics solver. The framework developed facilitates the separation of the code implementing the specific numerical method and the physical model from the handling of boundary conditions and the management of the computational domain. In particular, this will allow us to use finite difference stencils which are only defined in the interior of the domain (the boundary conditions are handled automatically). We will discuss this and other design considerations and their impact on performance in some detail. In addition, we provide a documentation of the code developed and demonstrate that a performance comparable to Fortran can be achieved, while still maintaining a maximum of code readability and extensibility. Catalogue identifier: AFAH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFAH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 592774 No. of bytes in distributed program, including test data, etc.: 43771395 Distribution format: tar.gz Programming language: C++03. Computer: PC, HPC systems. Operating system: POSIX compatible (extensively tested on various Linux systems). In fact only the timing class requires POSIX routines; all other parts of the program can be run on any system where a C++ compiler, Boost, CVODE, and an implementation of BLAS are available. RAM: Hundredths of Kilobytes to Gigabytes (depending on the problem size) Classification: 19.10, 4.3. External routines: Boost, CVODE, either a BLAS library or Intel MKL Nature of problem: An approximate solution to the equations of resistive magnetohydrodynamics for a given initial value and given boundary conditions is computed. Solution method: The discretization is performed using a finite difference approximation in space and the CVODE library in time (which employs a scheme based on the backward differentiation formulas). Restrictions: We consider the 2.5 dimensional case; that is, the magnetic field and the velocity field are three dimensional but all quantities depend only on x and y (but not z). Unusual features: We provide an implementation in C++ using the Boost library that combines high level techniques (which greatly increases code maintainability and extensibility) with performance that is comparable to Fortran implementations. Running time: From seconds to weeks (depending on the problem size).

TmoleX--a graphical user interface for TURBOMOLE.

PubMed

Steffen, Claudia; Thomas, Klaus; Huniar, Uwe; Hellweg, Arnim; Rubner, Oliver; Schroer, Alexander

2010-12-01

We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers. © 2010 Wiley Periodicals, Inc.

Survey of Speech-Language Pathology Graduate Program Training in Outer and Middle Ear Screening.

PubMed

Serpanos, Yula C; Senzer, Deborah

2015-08-01

The purpose of this study was to determine the national training practices of speech-language pathology graduate programs in outer and middle ear screening. Directors of all American Speech-Language-Hearing Association-accredited speech-language pathology graduate programs (N = 254; Council on Academic Accreditation in Audiology and Speech-Language Pathology, 2013) were surveyed on instructional formats in outer and middle ear screening. The graduate speech-language pathology program survey yielded 84 (33.1%) responses. Results indicated that some programs do not provide any training in the areas of conventional screening otoscopy using a handheld otoscope (15.5%; n = 13) or screening tympanometry (11.9%; n = 10), whereas close to one half (46.4%; n = 39) reported no training in screening video otoscopy. Outcomes revealed that approximately one third or more of speech-language pathology graduate programs do not provide experiential opportunities in screening handheld otoscopy (36.9%) or tympanometry (32.1%), and most (78.6%) do not provide experiential opportunities in video otoscopy. The implication from the graduate speech-language pathology program survey findings is that some speech-language pathologists will graduate from academic programs without the acquired knowledge or experiential learning required to establish skill in 1 or more areas of screening otoscopy and tympanometry. Graduate speech-language pathology programs should consider appropriate training opportunities for students to acquire and demonstrate skill in outer and middle ear screening.

Investigating Principals' Knowledge and Perceptions of Second Language Programs for English Language Learners

ERIC Educational Resources Information Center

Padron, Yolanda N.; Waxman, Hersh C.

2016-01-01

This study examined principals' knowledge and perceptions of second language programs for English language learners (ELLs) operating in their schools. An open-ended survey and in-depth interviews were used to examine elementary school principals' knowledge of the second language programs implemented at their schools. The survey asked principals…

Teachers' Perspectives on Academic Achievement and Educational Growth of U.S.-Born Hispanic Students in a Midwestern Spanish Language Immersion Program

ERIC Educational Resources Information Center

Salgado, Herlinda Arlene Galve

2016-01-01

Elementary Spanish language immersion programs have become more popular in the educational field in the United States to support the academic achievement of minority students. The final goal of immersion programs is to develop proficiency in the home language and dominant language, identified as first language (L1) and second language (L2), to…

Python to learn programming

NASA Astrophysics Data System (ADS)

Bogdanchikov, A.; Zhaparov, M.; Suliyev, R.

2013-04-01

Today we have a lot of programming languages that can realize our needs, but the most important question is how to teach programming to beginner students. In this paper we suggest using Python for this purpose, because it is a programming language that has neatly organized syntax and powerful tools to solve any task. Moreover it is very close to simple math thinking. Python is chosen as a primary programming language for freshmen in most of leading universities. Writing code in python is easy. In this paper we give some examples of program codes written in Java, C++ and Python language, and we make a comparison between them. Firstly, this paper proposes advantages of Python language in relation to C++ and JAVA. Then it shows the results of a comparison of short program codes written in three different languages, followed by a discussion on how students understand programming. Finally experimental results of students' success in programming courses are shown.

Usability Issues in the Design of Novice Programming Systems,

DTIC Science & Technology

1996-08-01

lists this as a design principle for novice programming environments. In traditional compiled languages, beginners are also confused by the need to...programming task external knowledge that might interfere with correct under- standing of the language. Most beginner programming errors can be...language for text editing, but [Curtis 1988] found that a textual pseudocode and graphical flowcharts were both bet- ter than natural language in program

Programming Languages.

ERIC Educational Resources Information Center

Tesler, Lawrence G.

1984-01-01

Discusses the nature of programing languages, considering the features of BASIC, LOGO, PASCAL, COBOL, FORTH, APL, and LISP. Also discusses machine/assembly codes, the operation of a compiler, and trends in the evolution of programing languages (including interest in notational systems called object-oriented languages). (JN)

A Common Programming Language for the Department of Defense--Background and Technical Requirements

DTIC Science & Technology

1976-06-01

Method Findings I. Introduction A. The Problem 1. Software Costs 2. Programming Language 3. Lack of Comrr.onality 4. Common Language 5...accessible soft- ware tools and aids. There are a number of widely held perceptions about the ill effects of the lack of programming language ...cost- effective (at lea~t during development) than de- velopi~g a new programming language specialized to the project. On the other hand,

What Is a Programming Language?

ERIC Educational Resources Information Center

Wold, Allen

1983-01-01

Explains what a computer programing language is in general, the differences between machine language, assembler languages, and high-level languages, and the functions of compilers and interpreters. High-level languages mentioned in the article are: BASIC, FORTRAN, COBOL, PILOT, LOGO, LISP, and SMALLTALK. (EAO)

Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals

NASA Astrophysics Data System (ADS)

Patriarca, M.; Kuronen, A.; Robles, M.; Kaski, K.

2007-01-01

The study of crystal defects and the complex processes underlying their formation and time evolution has motivated the development of the program ALINE for interactive molecular dynamics experiments. This program couples a molecular dynamics code to a Graphical User Interface and runs on a UNIX-X11 Window System platform with the MOTIF library, which is contained in many standard Linux releases. ALINE is written in C, thus giving the user the possibility to modify the source code, and, at the same time, provides an effective and user-friendly framework for numerical experiments, in which the main parameters can be interactively varied and the system visualized in various ways. We illustrate the main features of the program through some examples of detection and dynamical tracking of point-defects, linear defects, and planar defects, such as stacking faults in lattice-mismatched heterostructures. Program summaryTitle of program:ALINE Catalogue identifier:ADYJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYJ_v1_0 Program obtainable from: CPC Program Library, Queen University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers:DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers Installations:Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland Operating systems under which the program has been tested:True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4 Programming language used:Standard C and MOTIF libraries Memory required to execute with typical data:6 Mbytes but may be larger depending on the system size No. of lines in distributed program, including test data, etc.:16 901 No. of bytes in distributed program, including test data, etc.:449 559 Distribution format:tar.gz Nature of physical problem:Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are difficult to detect and track even within numerical experiments, especially when one is interested in studying their dynamical properties and time evolution. Furthermore, traditional simulation methods require the storage of a huge amount of data which in turn may imply a long work for their analysis. Method of solution:Simplifications of the simulation work described above strongly depend also on the computer performance. It has now become possible to realize some of such simplifications thanks to the real possibility of using interactive programs. The solution proposed here is based on the development of an interactive graphical simulation program both for avoiding large storage of data and the subsequent elaboration and analysis as well as for visualizing and tracking many phenomena inside three-dimensional samples. However, the full computational power of traditional simulation programs may not be available in general in programs with graphical user interfaces, due to their interactive nature. Nevertheless interactive programs can still be very useful for detecting processes difficult to visualize, restricting the range or making a fine tuning of the parameters, and tailoring the faster programs toward precise targets. Restrictions on the complexity of the problem:The restrictions on the applicability of the program are related to the computer resources available. The graphical interface and interactivity demand computational resources that depend on the particular numerical simulation to be performed. To preserve a balance between speed and resources, the choice of the number of atoms to be simulated is critical. With an average current computer, simulations of systems with more than 10 5 atoms may not be easily feasible on an interactive scheme. Another restriction is related to the fact that the program was originally designed to simulate systems in the solid phase, so that problems in the simulation may occur if some particular physical quantities are computed beyond the melting point. Typical running time:It depends on the machine architecture, system size, and user needs. Unusual features of the program:In the program, besides the window in which the system is represented in real space, an additional graphical window presenting the real time distribution histogram for different physical variables (such as kinetic or potential energy) is included. Such tool is very interesting for making demonstrative numerical experiments for teaching purposes as well as for research, e.g., for detecting and tracking crystal defects. The program includes: an initial condition builder, an interactive display of the simulation, a set of tools which allow the user to filter through different physical quantities the information—either displayed in real time or printed in the output files—and to perform an efficient search of the interesting regions of parameter space.

Gener: a minimal programming module for chemical controllers based on DNA strand displacement

PubMed Central

Kahramanoğulları, Ozan; Cardelli, Luca

2015-01-01

Summary: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research’s DSD tool as well as to LaTeX. Availability and implementation: Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. Contact: ozan@cosbi.eu PMID:25957353

Gener: a minimal programming module for chemical controllers based on DNA strand displacement.

PubMed

Kahramanoğulları, Ozan; Cardelli, Luca

2015-09-01

: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research's DSD tool as well as to LaTeX. Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. ozan@cosbi.eu. © The Author 2015. Published by Oxford University Press.

Total Immersion Language Program: A New Approach to Foreign Language Instruction. Technical Report.

ERIC Educational Resources Information Center

Morel, Stefano

A three-year experimental program established in 1966 in Spanish language instruction at the secondary level is reported in this study. Students at Commack High School North, New York, participated in a total immersion language program in Spanish, taking two to four classes of instruction in the target language per day. Classes included regular…

34 CFR 658.4 - What definitions apply to the Undergraduate International Studies and Foreign Language Program?

Code of Federal Regulations, 2010 CFR

2010-07-01

... International Studies and Foreign Language Program? 658.4 Section 658.4 Education Regulations of the Offices of... UNDERGRADUATE INTERNATIONAL STUDIES AND FOREIGN LANGUAGE PROGRAM General § 658.4 What definitions apply to the Undergraduate International Studies and Foreign Language Program? The definitions in 34 CFR 655.4 apply to this...

34 CFR 658.4 - What definitions apply to the Undergraduate International Studies and Foreign Language Program?

Code of Federal Regulations, 2011 CFR

2011-07-01

... International Studies and Foreign Language Program? 658.4 Section 658.4 Education Regulations of the Offices of... UNDERGRADUATE INTERNATIONAL STUDIES AND FOREIGN LANGUAGE PROGRAM General § 658.4 What definitions apply to the Undergraduate International Studies and Foreign Language Program? The definitions in 34 CFR 655.4 apply to this...

Students' Perspective on the First Programming Language: C-Like or Pascal-Like Languages?

ERIC Educational Resources Information Center

Xinogalos, Stelios; Pitner, Tomáš; Ivanovic, Mirjana; Savic, Miloš

2018-01-01

The choice of the first programming language (FPL) has been a controversial issue for several decades. Nearly everyone agrees that the FPL is important and affects students' subsequent education on programming. The study presented in this article investigates the suitability of various C-like and Pascal-like programming languages as a FPL.…

HAL/SM language specification. [programming languages and computer programming for space shuttles

NASA Technical Reports Server (NTRS)

Williams, G. P. W., Jr.; Ross, C.

1975-01-01

A programming language is presented for the flight software of the NASA Space Shuttle program. It is intended to satisfy virtually all of the flight software requirements of the space shuttle. To achieve this, it incorporates a wide range of features, including applications-oriented data types and organizations, real time control mechanisms, and constructs for systems programming tasks. It is a higher order language designed to allow programmers, analysts, and engineers to communicate with the computer in a form approximating natural mathematical expression. Parts of the English language are combined with standard notation to provide a tool that readily encourages programming without demanding computer hardware expertise. Block diagrams and flow charts are included. The semantics of the language is discussed.

VizieR Online Data Catalog: RefleX : X-ray-tracing code (Paltani+, 2017)

NASA Astrophysics Data System (ADS)

Paltani, S.; Ricci, C.

2017-11-01

We provide here the RefleX executable, for both Linux and MacOSX, together with the User Manual and example script file and output file Running (for instance): reflex_linux will produce the file reflex.out Note that the results may differ slightly depending on the OS, because of slight differences in some implementations numerical computations. The difference are scientifically meaningless. (5 data files).

NAVO MSRC Navigator. Fall 2006

DTIC Science & Technology

2006-01-01

UNIX Manual Pages: xdm (1x). 7. Buddenhagen, Oswald, “The KDM Handbook,” KDE Documentation, http://docs.kde.org/development/ en /kdebase/kdm/. 8... Linux Opteron cluster was recently determined through a series of simulations that employed both fixed and adaptive meshes. The fixed-mesh scalability...approximately eight in the total number of cells in the 3-D simulation. The fixed-mesh and AMR scalability results on the Linux Opteron cluster are

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

Swan: A tool for porting CUDA programs to OpenCL

NASA Astrophysics Data System (ADS)

Harvey, M. J.; De Fabritiis, G.

2011-04-01

The use of modern, high-performance graphical processing units (GPUs) for acceleration of scientific computation has been widely reported. The majority of this work has used the CUDA programming model supported exclusively by GPUs manufactured by NVIDIA. An industry standardisation effort has recently produced the OpenCL specification for GPU programming. This offers the benefits of hardware-independence and reduced dependence on proprietary tool-chains. Here we describe a source-to-source translation tool, "Swan" for facilitating the conversion of an existing CUDA code to use the OpenCL model, as a means to aid programmers experienced with CUDA in evaluating OpenCL and alternative hardware. While the performance of equivalent OpenCL and CUDA code on fixed hardware should be comparable, we find that a real-world CUDA application ported to OpenCL exhibits an overall 50% increase in runtime, a reduction in performance attributable to the immaturity of contemporary compilers. The ported application is shown to have platform independence, running on both NVIDIA and AMD GPUs without modification. We conclude that OpenCL is a viable platform for developing portable GPU applications but that the more mature CUDA tools continue to provide best performance. Program summaryProgram title: Swan Catalogue identifier: AEIH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public License version 2 No. of lines in distributed program, including test data, etc.: 17 736 No. of bytes in distributed program, including test data, etc.: 131 177 Distribution format: tar.gz Programming language: C Computer: PC Operating system: Linux RAM: 256 Mbytes Classification: 6.5 External routines: NVIDIA CUDA, OpenCL Nature of problem: Graphical Processing Units (GPUs) from NVIDIA are preferentially programed with the proprietary CUDA programming toolkit. An alternative programming model promoted as an industry standard, OpenCL, provides similar capabilities to CUDA and is also supported on non-NVIDIA hardware (including multicore ×86 CPUs, AMD GPUs and IBM Cell processors). The adaptation of a program from CUDA to OpenCL is relatively straightforward but laborious. The Swan tool facilitates this conversion. Solution method:Swan performs a translation of CUDA kernel source code into an OpenCL equivalent. It also generates the C source code for entry point functions, simplifying kernel invocation from the host program. A concise host-side API abstracts the CUDA and OpenCL APIs. A program adapted to use Swan has no dependency on the CUDA compiler for the host-side program. The converted program may be built for either CUDA or OpenCL, with the selection made at compile time. Restrictions: No support for CUDA C++ features Running time: Nominal

Artificial intelligence programming languages for computer aided manufacturing

NASA Technical Reports Server (NTRS)

Rieger, C.; Samet, H.; Rosenberg, J.

1979-01-01

Eight Artificial Intelligence programming languages (SAIL, LISP, MICROPLANNER, CONNIVER, MLISP, POP-2, AL, and QLISP) are presented and surveyed, with examples of their use in an automated shop environment. Control structures are compared, and distinctive features of each language are highlighted. A simple programming task is used to illustrate programs in SAIL, LISP, MICROPLANNER, and CONNIVER. The report assumes reader knowledge of programming concepts, but not necessarily of the languages surveyed.

Web Services Provide Access to SCEC Scientific Research Application Software

NASA Astrophysics Data System (ADS)

Gupta, N.; Gupta, V.; Okaya, D.; Kamb, L.; Maechling, P.

2003-12-01

Web services offer scientific communities a new paradigm for sharing research codes and communicating results. While there are formal technical definitions of what constitutes a web service, for a user community such as the Southern California Earthquake Center (SCEC), we may conceptually consider a web service to be functionality provided on-demand by an application which is run on a remote computer located elsewhere on the Internet. The value of a web service is that it can (1) run a scientific code without the user needing to install and learn the intricacies of running the code; (2) provide the technical framework which allows a user's computer to talk to the remote computer which performs the service; (3) provide the computational resources to run the code; and (4) bundle several analysis steps and provide the end results in digital or (post-processed) graphical form. Within an NSF-sponsored ITR project coordinated by SCEC, we are constructing web services using architectural protocols and programming languages (e.g., Java). However, because the SCEC community has a rich pool of scientific research software (written in traditional languages such as C and FORTRAN), we also emphasize making existing scientific codes available by constructing web service frameworks which wrap around and directly run these codes. In doing so we attempt to broaden community usage of these codes. Web service wrapping of a scientific code can be done using a "web servlet" construction or by using a SOAP/WSDL-based framework. This latter approach is widely adopted in IT circles although it is subject to rapid evolution. Our wrapping framework attempts to "honor" the original codes with as little modification as is possible. For versatility we identify three methods of user access: (A) a web-based GUI (written in HTML and/or Java applets); (B) a Linux/OSX/UNIX command line "initiator" utility (shell-scriptable); and (C) direct access from within any Java application (and with the correct API interface from within C++ and/or C/Fortran). This poster presentation will provide descriptions of the following selected web services and their origin as scientific application codes: 3D community velocity models for Southern California, geocoordinate conversions (latitude/longitude to UTM), execution of GMT graphical scripts, data format conversions (Gocad to Matlab format), and implementation of Seismic Hazard Analysis application programs that calculate hazard curve and hazard map data sets.

SPheno 3.1: extensions including flavour, CP-phases and models beyond the MSSM

NASA Astrophysics Data System (ADS)

Porod, W.; Staub, F.

2012-11-01

We describe recent extensions of the program SPhenoincluding flavour aspects, CP-phases, R-parity violation and low energy observables. In case of flavour mixing all masses of supersymmetric particles are calculated including the complete flavour structure and all possible CP-phases at the 1-loop level. We give details on implemented seesaw models, low energy observables and the corresponding extension of the SUSY Les Houches Accord. Moreover, we comment on the possibilities to include MSSM extensions in SPheno. Catalogue identifier: ADRV_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADRV_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 154062 No. of bytes in distributed program, including test data, etc.: 1336037 Distribution format: tar.gz Programming language: Fortran95. Computer: PC running under Linux, should run in every Unix environment. Operating system: Linux, Unix. Classification: 11.6. Catalogue identifier of previous version: ADRV_v1_0 Journal reference of previous version: Comput. Phys. Comm. 153(2003)275 Does the new version supersede the previous version?: Yes Nature of problem: The first issue is the determination of the masses and couplings of supersymmetric particles in various supersymmetric models, the R-parity conserved MSSM with generation mixing and including CP-violating phases, various seesaw extensions of the MSSM and the MSSM with bilinear R-parity breaking. Low energy data on Standard Model fermion masses, gauge couplings and electroweak gauge boson masses serve as constraints. Radiative corrections from supersymmetric particles to these inputs must be calculated. Theoretical constraints on the soft SUSY breaking parameters from a high scale theory are imposed and the parameters at the electroweak scale are obtained from the high scale parameters by evaluating the corresponding renormalisation group equations. These parameters must be consistent with the requirement of correct electroweak symmetry breaking. The second issue is to use the obtained masses and couplings for calculating decay widths and branching ratios of supersymmetric particles as well as the cross sections for these particles in electron-positron annihilation. The third issue is to calculate low energy constraints in the B-meson sector such as BR(b s), MB s, rare lepton decays, such as BR(e), the SUSY contributions to anomalous magnetic moments and electric dipole moments of leptons, the SUSY contributions to the ρ parameter as well as lepton flavour violating Z decays. Solution method: The renormalisation connecting a high scale and the electroweak scale is calculated by the Runge-Kutta method. Iteration provides a solution consistent with the multi-boundary conditions. In case of three-body decays and for the calculation of initial state radiation Gaussian quadrature is used for the numerical solution of the integrals. Reasons for new version: Inclusion of new models as well as additional observables. Moreover, a new standard for data transfer had been established, which is now supported. Summary of revisions: The already existing models have been extended to include also CP-violation and flavour mixing. The data transfer is done using the so-called SLHA2 standard. In addition new models have been included: all three types of seesaw models as well as bilinear R-parity violation. Moreover, additional observables are calculated: branching ratios for flavour violating lepton decays, EDMs of leptons and of the neutron, CP-violating mass difference in the B-meson sector and branching ratios for flavour violating b-quark decays. Restrictions: In case of R-parity violation the cross sections are not calculated. Running time: 0.2 seconds on an Intel(R) Core(TM)2 Duo CPU T9900 with 3.06 GHz

Heritage Language Education: Valuing the Languages, Literacies, and Cultural Competencies of Immigrant Youth

ERIC Educational Resources Information Center

Seals, Corinne A.; Peyton, Joy Kreeft

2017-01-01

This article argues for the value of heritage language programs and the micro-level language policies that support them, focusing on a case study of a program in the USA to make this argument. We also argue for the importance of recognizing students' heritage languages, cultures, and individual goals and identities in mainstream school programs.…

Do They Make a Difference? The Impact of English Language Programs on Second Language Students in Canadian Universities

ERIC Educational Resources Information Center

Fox, Janna; Cheng, Liying; Zumbo, Bruno D.

2014-01-01

Few studies have investigated the impact of English language programs on second language (L2) students studying in Canadian universities (Cheng & Fox, 2008; Fox, 2005, 2009). This article reports on questionnaire responses of 641 L2 students studying in 36 English language programs in 26 Canadian universities. The researchers identified…

An Evaluation Framework and Comparative Analysis of the Widely Used First Programming Languages

PubMed Central

Farooq, Muhammad Shoaib; Khan, Sher Afzal; Ahmad, Farooq; Islam, Saeed; Abid, Adnan

2014-01-01

Computer programming is the core of computer science curriculum. Several programming languages have been used to teach the first course in computer programming, and such languages are referred to as first programming language (FPL). The pool of programming languages has been evolving with the development of new languages, and from this pool different languages have been used as FPL at different times. Though the selection of an appropriate FPL is very important, yet it has been a controversial issue in the presence of many choices. Many efforts have been made for designing a good FPL, however, there is no ample way to evaluate and compare the existing languages so as to find the most suitable FPL. In this article, we have proposed a framework to evaluate the existing imperative, and object oriented languages for their suitability as an appropriate FPL. Furthermore, based on the proposed framework we have devised a customizable scoring function to compute a quantitative suitability score for a language, which reflects its conformance to the proposed framework. Lastly, we have also evaluated the conformance of the widely used FPLs to the proposed framework, and have also computed their suitability scores. PMID:24586449

An evaluation framework and comparative analysis of the widely used first programming languages.

PubMed

Farooq, Muhammad Shoaib; Khan, Sher Afzal; Ahmad, Farooq; Islam, Saeed; Abid, Adnan

2014-01-01

Computer programming is the core of computer science curriculum. Several programming languages have been used to teach the first course in computer programming, and such languages are referred to as first programming language (FPL). The pool of programming languages has been evolving with the development of new languages, and from this pool different languages have been used as FPL at different times. Though the selection of an appropriate FPL is very important, yet it has been a controversial issue in the presence of many choices. Many efforts have been made for designing a good FPL, however, there is no ample way to evaluate and compare the existing languages so as to find the most suitable FPL. In this article, we have proposed a framework to evaluate the existing imperative, and object oriented languages for their suitability as an appropriate FPL. Furthermore, based on the proposed framework we have devised a customizable scoring function to compute a quantitative suitability score for a language, which reflects its conformance to the proposed framework. Lastly, we have also evaluated the conformance of the widely used FPLs to the proposed framework, and have also computed their suitability scores.

Knowledge, programming, and programming cultures: LISP, C, and Ada

NASA Technical Reports Server (NTRS)

Rochowiak, Daniel

1990-01-01

The results of research 'Ada as an implementation language for knowledge based systems' are presented. The purpose of the research was to compare Ada to other programming languages. The report focuses on the programming languages Ada, C, and Lisp, the programming cultures that surround them, and the programming paradigms they support.

Numerical modeling of exciton-polariton Bose-Einstein condensate in a microcavity

NASA Astrophysics Data System (ADS)

Voronych, Oksana; Buraczewski, Adam; Matuszewski, Michał; Stobińska, Magdalena

2017-06-01

A novel, optimized numerical method of modeling of an exciton-polariton superfluid in a semiconductor microcavity was proposed. Exciton-polaritons are spin-carrying quasiparticles formed from photons strongly coupled to excitons. They possess unique properties, interesting from the point of view of fundamental research as well as numerous potential applications. However, their numerical modeling is challenging due to the structure of nonlinear differential equations describing their evolution. In this paper, we propose to solve the equations with a modified Runge-Kutta method of 4th order, further optimized for efficient computations. The algorithms were implemented in form of C++ programs fitted for parallel environments and utilizing vector instructions. The programs form the EPCGP suite which has been used for theoretical investigation of exciton-polaritons. Catalogue identifier: AFBQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFBQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: BSD-3 No. of lines in distributed program, including test data, etc.: 2157 No. of bytes in distributed program, including test data, etc.: 498994 Distribution format: tar.gz Programming language: C++ with OpenMP extensions (main numerical program), Python (helper scripts). Computer: Modern PC (tested on AMD and Intel processors), HP BL2x220. Operating system: Unix/Linux and Windows. Has the code been vectorized or parallelized?: Yes (OpenMP) RAM: 200 MB for single run Classification: 7, 7.7. Nature of problem: An exciton-polariton superfluid is a novel, interesting physical system allowing investigation of high temperature Bose-Einstein condensation of exciton-polaritons-quasiparticles carrying spin. They have brought a lot of attention due to their unique properties and potential applications in polariton-based optoelectronic integrated circuits. This is an out-of-equilibrium quantum system confined within a semiconductor microcavity. It is described by a set of nonlinear differential equations similar in spirit to the Gross-Pitaevskii (GP) equation, but their unique properties do not allow standard GP solving frameworks to be utilized. Finding an accurate and efficient numerical algorithm as well as development of optimized numerical software is necessary for effective theoretical investigation of exciton-polaritons. Solution method: A Runge-Kutta method of 4th order was employed to solve the set of differential equations describing exciton-polariton superfluids. The method was fitted for the exciton-polariton equations and further optimized. The C++ programs utilize OpenMP extensions and vector operations in order to fully utilize the computer hardware. Running time: 6h for 100 ps evolution, depending on the values of parameters

The African Language Program at Michigan State University.

ERIC Educational Resources Information Center

Dwyer, David

1979-01-01

Describes the African language program at Michigan State University, which provides (1) supervised, individualized instruction for high-demand languages, on two levels; (2) regular classroom instruction for Swahili and Hausa; and (3) non-credit, self-instructional programs for low-demand languages. Sample forms are appended. (AM)

Computer Programming Languages for Health Care

PubMed Central

O'Neill, Joseph T.

1979-01-01

This paper advocates the use of standard high level programming languages for medical computing. It recommends that U.S. Government agencies having health care missions implement coordinated policies that encourage the use of existing standard languages and the development of new ones, thereby enabling them and the medical computing community at large to share state-of-the-art application programs. Examples are based on a model that characterizes language and language translator influence upon the specification, development, test, evaluation, and transfer of application programs.

Flight program language requirements. Volume 3: Appendices

NASA Technical Reports Server (NTRS)

1972-01-01

Government-sponsored study and development efforts were directed toward design and implementation of high level programming languages suitable for future aerospace applications. The study centered around an evaluation of the four most pertinent existing aerospace languages. Evaluation criteria were established, and selected kernels from the current Saturn 5 and Skylab flight programs were used as benchmark problems for sample coding. An independent review of the language specifications incorporated anticipated future programming requirements into the evaluation. A set of language requirements was synthesized from these activities.

Praxis language reference manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, J.H.

1981-01-01

This document is a language reference manual for the programming language Praxis. The document contains the specifications that must be met by any compiler for the language. The Praxis language was designed for systems programming in real-time process applications. Goals for the language and its implementations are: (1) highly efficient code generated by the compiler; (2) program portability; (3) completeness, that is, all programming requirements can be met by the language without needing an assembler; and (4) separate compilation to aid in design and management of large systems. The language does not provide any facilities for input/output, stack and queuemore » handling, string operations, parallel processing, or coroutine processing. These features can be implemented as routines in the language, using machine-dependent code to take advantage of facilities in the control environment on different machines.« less

Numerical simulation code for self-gravitating Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Madarassy, Enikő J. M.; Toth, Viktor T.

2013-04-01

We completed the development of simulation code that is designed to study the behavior of a conjectured dark matter galactic halo that is in the form of a Bose-Einstein Condensate (BEC). The BEC is described by the Gross-Pitaevskii equation, which can be solved numerically using the Crank-Nicholson method. The gravitational potential, in turn, is described by Poisson’s equation, that can be solved using the relaxation method. Our code combines these two methods to study the time evolution of a self-gravitating BEC. The inefficiency of the relaxation method is balanced by the fact that in subsequent time iterations, previously computed values of the gravitational field serve as very good initial estimates. The code is robust (as evidenced by its stability on coarse grids) and efficient enough to simulate the evolution of a system over the course of 109 years using a finer (100×100×100) spatial grid, in less than a day of processor time on a contemporary desktop computer. Catalogue identifier: AEOR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOR_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5248 No. of bytes in distributed program, including test data, etc.: 715402 Distribution format: tar.gz Programming language: C++ or FORTRAN. Computer: PCs or workstations. Operating system: Linux or Windows. Classification: 1.5. Nature of problem: Simulation of a self-gravitating Bose-Einstein condensate by simultaneous solution of the Gross-Pitaevskii and Poisson equations in three dimensions. Solution method: The Gross-Pitaevskii equation is solved numerically using the Crank-Nicholson method; Poisson’s equation is solved using the relaxation method. The time evolution of the system is governed by the Gross-Pitaevskii equation; the solution of Poisson’s equation at each time step is used as an initial estimate for the next time step, which dramatically increases the efficiency of the relaxation method. Running time: Depends on the chosen size of the problem. On a typical personal computer, a 100×100×100 grid can be solved with a time span of 10 Gyr in approx. a day of running time.

Visual Programming: A Programming Tool for Increasing Mathematics Achivement

ERIC Educational Resources Information Center

Swanier, Cheryl A.; Seals, Cheryl D.; Billionniere, Elodie V.

2009-01-01

This paper aims to address the need of increasing student achievement in mathematics using a visual programming language such as Scratch. This visual programming language facilitates creating an environment where students in K-12 education can develop mathematical simulations while learning a visual programming language at the same time.…

Alcator C-Mod Digital Plasma Control System

NASA Astrophysics Data System (ADS)

Wolfe, S. M.

2005-10-01

A new digital plasma control system (DPCS) has been implemented for Alcator C-Mod. The new system was put into service at the start of the 2005 run campaign and has been in routine operation since. The system consists of two 64-input, 16-output cPCI digitizers attached to a rack-mounted single-CPU Linux server, which performs both the I/O and the computation. During initial operation, the system was set up to directly emulate the original C-Mod ``Hybrid'' MIMO linear control system. Compatibility with the previous control system allows the existing user interface software and data structures to be used with the new hardware. The control program is written in IDL and runs under standard Linux. Interrupts are disabled during the plasma pulses to achieve real-time operation. A synchronous loop is executed with a nominal cycle rate of 10 kHz. Emulation of the original linear control algorithms requires 50 μsec per iteration, with the time evenly split between I/O and computation, so rates of about 20 KHz are achievable. Reliable vertical position control has been demonstrated with cycle rates as low as 5 KHz. Additional computations, including non-linear algorithms and adaptive response, are implemented as optional procedure calls within the main real-time loop.

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Soft Real-Time PID Control on a VME Computer

NASA Technical Reports Server (NTRS)

Karayan, Vahag; Sander, Stanley; Cageao, Richard

2007-01-01

microPID (uPID) is a computer program for real-time proportional + integral + derivative (PID) control of a translation stage in a Fourier-transform ultraviolet spectrometer. microPID implements a PID control loop over a position profile at sampling rate of 8 kHz (sampling period 125microseconds). The software runs in a strippeddown Linux operating system on a VersaModule Eurocard (VME) computer operating in real-time priority queue using an embedded controller, a 16-bit digital-to-analog converter (D/A) board, and a laser-positioning board (LPB). microPID consists of three main parts: (1) VME device-driver routines, (2) software that administers a custom protocol for serial communication with a control computer, and (3) a loop section that obtains the current position from an LPB-driver routine, calculates the ideal position from the profile, and calculates a new voltage command by use of an embedded PID routine all within each sampling period. The voltage command is sent to the D/A board to control the stage. microPID uses special kernel headers to obtain microsecond timing resolution. Inasmuch as microPID implements a single-threaded process and all other processes are disabled, the Linux operating system acts as a soft real-time system.

OPSO - The OpenGL based Field Acquisition and Telescope Guiding System

NASA Astrophysics Data System (ADS)

Škoda, P.; Fuchs, J.; Honsa, J.

2006-07-01

We present OPSO, a modular pointing and auto-guiding system for the coudé spectrograph of the Ondřejov observatory 2m telescope. The current field and slit viewing CCD cameras with image intensifiers are giving only standard TV video output. To allow the acquisition and guiding of very faint targets, we have designed an image enhancing system working in real time on TV frames grabbed by BT878-based video capture card. Its basic capabilities include the sliding averaging of hundreds of frames with bad pixel masking and removal of outliers, display of median of set of frames, quick zooming, contrast and brightness adjustment, plotting of horizontal and vertical cross cuts of seeing disk within given intensity range and many more. From the programmer's point of view, the system consists of three tasks running in parallel on a Linux PC. One C task controls the video capturing over Video for Linux (v4l2) interface and feeds the frames into the large block of shared memory, where the core image processing is done by another C program calling the OpenGL library. The GUI is, however, dynamically built in Python from XML description of widgets prepared in Glade. All tasks are exchanging information by IPC calls using the shared memory segments.

Problems for a Sign Language Planning Agency

ERIC Educational Resources Information Center

Covington, Virginia

1977-01-01

American Sign Language is chiefly untaught and nonstandardized. The Communicative Skills Program of the National Association of the Deaf aims to provide sign language classes for hearing personnel and to increase interpreting services. Programs, funding and aims of the Program are outlined. A government sign language planning agency is proposed.…

A Year-Round Professional Development Model for World Language Educators

ERIC Educational Resources Information Center

Steele, Tracy M.; Peterson, Margaret D.; Silva, Duarte M.; Padilla, Amado M.

2009-01-01

The Bay Area Foreign Language Program (BAFLP), one of nine regional sites of the California Foreign Language Project, offers ongoing, year-round professional development programs for world language educators. In addition, its leadership program prepares selected educators to assume leadership positions at their school sites, building capacity for…

Quantitative Model for Choosing Programming Language for Online Instruction

ERIC Educational Resources Information Center

Sherman, Steven J.; Shehane, Ronald F.; Todd, Dewey W.

2018-01-01

Colleges are increasingly offering online courses, including computer programming courses for business school students. Programming languages that are most useful to students are those that are widely used in the job market. However, the most popular computer languages change at least every three years. Therefore, the language used for instruction…

Foreign Language K-12. Program Evaluation 1991-92.

ERIC Educational Resources Information Center

Wadden, Jerry M.

The Des Moines (Iowa) Public Schools foreign language program for K-12 is described and evaluated. The evaluation report focuses on six areas, including: (1) school district mission and philosophy of foreign language instruction; (2) context (state policies and standards, foreign language program overview and enrollment, fiber-optic communication…

Les programmes de base: des principes a la realite (Core Programs: From Principles to Reality).

ERIC Educational Resources Information Center

Calve, Pierre

1985-01-01

The recent evolution of second language teaching theory regarding language, learning, communication, and teaching is summarized, and factors contributing to resistance to core second language programs are examined. They include tradition, school programs, time of instruction, language of instruction, teacher training, attitudes, and…

77 FR 30045 - 30-Day Notice of Proposed Information Collection: English Language Evaluation Surveys

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-21

...] 30-Day Notice of Proposed Information Collection: English Language Evaluation Surveys ACTION: Notice... clearance will allow ECA/P/V, as part of the English Language Evaluation, to conduct surveys of participants in the ETA Program, E-Teacher Scholarship program, and the English Language Specialist Program...

Listen! Native Radio Can Save Languages.

ERIC Educational Resources Information Center

Martin, Kallen

1996-01-01

In the United States and Canada, the number of radio stations operated by Native Americans has greatly increased in recent years, as have the amount of programming in native languages and the number of native language instructional programs. Such programming can play a role in maintaining vigorous native languages and revitalizing endangered…

Synchronization in Scratch: A Case Study with Education Science Students

ERIC Educational Resources Information Center

Nikolos, Dimitris; Komis, Vassilis

2015-01-01

The Scratch programming language is an introductory programming language for students. It is also a visual concurrent programming language, where multiple threads are executed simultaneously. Synchronization in concurrent languages is a complex task for novices to understand. Our research is focused on strategies and methods applied by novice…

Source Code Analysis Laboratory (SCALe) for Energy Delivery Systems

DTIC Science & Technology

2010-12-01

the software for reevaluation. Once the ree- valuation process is completed, CERT provides the client a report detailing the software’s con - formance...Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8% Wine...inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with energy system software will help

Reactive Aggregate Model Protecting Against Real-Time Threats

DTIC Science & Technology

2014-09-01

on the underlying functionality of three core components. • MS SQL server 2008 backend database. • Microsoft IIS running on Windows server 2008...services. The capstone tested a Linux-based Apache web server with the following software implementations: • MySQL as a Linux-based backend server for...malicious compromise. 1. Assumptions • GINA could connect to a backend MS SQL database through proper configuration of DotNetNuke. • GINA had access

Covert Android Rootkit Detection: Evaluating Linux Kernel Level Rootkits on the Android Operating System

DTIC Science & Technology

2012-06-14

the attacker . Thus, this race condition causes a privilege escalation . 2.2.5 Summary This section reviewed software exploitation of a Linux kernel...has led to increased targeting by malware writers. Android attacks have naturally sparked interest in researching protections for Android . This...release, Android 4.0 Ice Cream Sandwich. These rootkits focused on covert techniques to hide the presence of data used by an attacker to infect a

The Ubuntu Chat Corpus for Multiparticipant Chat Analysis

DTIC Science & Technology

2013-03-01

Intelligence (www.aaai.org). All rights reserved. the # LINUX corpus (Elsner and Charniak 2010), and the #IPHONE/#PHYSICS/#PYTHON corpus (Adams 2008). For many...made publicly available, making it difficult to comparatively evaluate dif- ferent techniques. Corpus Description Ubuntu, a Linux -based operating...Kubuntu (Ubuntu with KDE ) support #ubuntu-devel 2 112 074 12 140 53.7 2004-10-01 Developmental team coordination #ubuntu+1 1 621 680 26 805 52.6 2007-04-04

MVC for Content Management on the Cloud

DTIC Science & Technology

2011-09-01

Windows, Linux , MacOS, PalmOS and other customized ones (Qiu). Figure 20 illustrates implementation of MVC architecture. Qiu examines a “universal...Listing of Unzipped Text Document (From O’Reilly & Associates, Inc, 2005) Figure 37 shows the results of unzipping this file in Linux . The contents of the...ODF Adoption TC, and the ODF Alliance include members from Adobe, BBC, Bristol City Council, Bull, Corel, EDS, EMC, GNOME, IBM, Intel, KDE , MySQL

[Making a low cost IPSec router on Linux and the assessment for practical use].

PubMed

Amiki, M; Horio, M

2001-09-01

We installed Linux and FreeS/WAN on a PC/AT compatible machine to make an IPSec router. We measured the time of ping/ftp, only in the university, between the university and the external network. Between the university and the external network (the Internet), there were no differences. Therefore, we concluded that CPU load was not remarkable at low speed networks, because packets exchanged via the Internet are small, or compressions of VPN are more effective than encoding and decoding. On the other hand, in the university, the IPSec router performed down about 20-30% compared with normal IP communication, but this is not a serious problem for practical use. Recently, VPN machines are becoming cheaper, but they do not function sufficiently to create a fundamental VPN environment. Therefore, if one wants a fundamental VPN environment at a low cost, we believe you should select a VPN router on Linux.

Timing characterization and analysis of the Linux-based, closed loop control computer for the Subaru Telescope laser guide star adaptive optics system

NASA Astrophysics Data System (ADS)

Dinkins, Matthew; Colley, Stephen

2008-07-01

Hardware and software specialized for real time control reduce the timing jitter of executables when compared to off-the-shelf hardware and software. However, these specialized environments are costly in both money and development time. While conventional systems have a cost advantage, the jitter in these systems is much larger and potentially problematic. This study analyzes the timing characterstics of a standard Dell server running a fully featured Linux operating system to determine if such a system would be capable of meeting the timing requirements for closed loop operations. Investigations are preformed on the effectiveness of tools designed to make off-the-shelf system performance closer to specialized real time systems. The Gnu Compiler Collection (gcc) is compared to the Intel C Compiler (icc), compiler optimizations are investigated, and real-time extensions to Linux are evaluated.

Web-based Quality Control Tool used to validate CERES products on a cluster of Linux servers

NASA Astrophysics Data System (ADS)

Chu, C.; Sun-Mack, S.; Heckert, E.; Chen, Y.; Mlynczak, P.; Mitrescu, C.; Doelling, D.

2014-12-01

There have been a few popular desktop tools used in the Earth Science community to validate science data. Because of the limitation on the capacity of desktop hardware such as disk space and CPUs, those softwares are not able to display large amount of data from files.This poster will talk about an in-house developed web-based software built on a cluster of Linux servers. That allows users to take advantage of a few Linux servers working in parallel to generate hundreds images in a short period of time. The poster will demonstrate:(1) The hardware and software architecture is used to provide high throughput of images. (2) The software structure that can incorporate new products and new requirement quickly. (3) The user interface about how users can manipulate the data and users can control how the images are displayed.

At the Crossroads of Learning and Culture: Identifying a Construct for Effective Computer-Assisted Language Learning for English Language Learners

ERIC Educational Resources Information Center

Shaw, Yun

2010-01-01

Many of the commercial Computer-Assisted Language Learning (CALL) programs available today typically take a generic approach. This approach standardizes the program so that it can be used to teach any language merely by translating the content from one language to another. These CALL programs rarely consider the cultural background or preferred…

Towards the Automatic Generation of Programmed Foreign-Language Instructional Materials.

ERIC Educational Resources Information Center

Van Campen, Joseph A.

The purpose of this report is to describe a set of programs which either perform certain tasks useful in the generation of programed foreign-language instructional material or facilitate the writing of such task-oriented programs by other researchers. The programs described are these: (1) a PDP-10 assembly language program for the selection from a…

Programming Language Use in US Academia and Industry

ERIC Educational Resources Information Center

Ben Arfa Rabai, Latifa; Cohen, Barry; Mili, Ali

2015-01-01

In the same way that natural languages influence and shape the way we think, programming languages have a profound impact on the way a programmer analyzes a problem and formulates its solution in the form of a program. To the extent that a first programming course is likely to determine the student's approach to program design, program analysis,…

Teacher and Student Language Practices and Ideologies in a Third-Grade Two-Way Dual Language Program Implementation

ERIC Educational Resources Information Center

Henderson, Kathryn I.; Palmer, Deborah K.

2015-01-01

This article provides an in-depth exploration of the language ecologies of two classrooms attempting to implement a two-way dual language (TWDL) program and its mediating conditions. Drawing on ethnographic methods and a sociocultural understanding of language, we examined both teachers' and students' language ideologies and language practices,…

Chief Dull Knife Community Is Strengthening the Northern Cheyenne Language and Culture.

ERIC Educational Resources Information Center

Littlebear, Richard E.

2003-01-01

Language revitalization programs should focus on whether they want to teach the language, teach about the language, teach with the language, or teach the language for academic credit. A program at Chief Dull Knife College (Montana) teaches the Cheyenne language using the Total Physical Response method, which replicates the manner in which first…

Language plus for international graduate students in nursing.

PubMed

Julian, M A; Keane, A; Davidson, K

1999-01-01

To provide information about an English-language support program that focuses on the needs of international graduate nursing students. The growing presence of these students coincides with the increasing numbers of universities committed to world health. Crucial social and language competence affect the success and progress of international students in graduate nursing programs. Reviewed literature was 1980 to 1998, in nursing and applied linguistic research including second-language acquisition, phonology, discourse analysis, and language pragmatics to identify social and language phenomena. Investigators suggest essential elements such as conventions of academic writing, reading comprehension, vocabulary, and pronunciation skills be included in the supportive Language Plus program. Ongoing development of the Language Plus program can promote collaboration between nurses and linguists and increase the success of international graduate nursing students.

WaveAR: A software tool for calculating parameters for water waves with incident and reflected components

NASA Astrophysics Data System (ADS)

Landry, Blake J.; Hancock, Matthew J.; Mei, Chiang C.; García, Marcelo H.

2012-09-01

The ability to determine wave heights and phases along a spatial domain is vital to understanding a wide range of littoral processes. The software tool presented here employs established Stokes wave theory and sampling methods to calculate parameters for the incident and reflected components of a field of weakly nonlinear waves, monochromatic at first order in wave slope and propagating in one horizontal dimension. The software calculates wave parameters over an entire wave tank and accounts for reflection, weak nonlinearity, and a free second harmonic. Currently, no publicly available program has such functionality. The included MATLAB®-based open source code has also been compiled for Windows®, Mac® and Linux® operating systems. An additional companion program, VirtualWave, is included to generate virtual wave fields for WaveAR. Together, the programs serve as ideal analysis and teaching tools for laboratory water wave systems.

Benchmark Comparison of Dual- and Quad-Core Processor Linux Clusters with Two Global Climate Modeling Workloads

NASA Technical Reports Server (NTRS)

McGalliard, James

2008-01-01

This viewgraph presentation details the science and systems environments that NASA High End computing program serves. Included is a discussion of the workload that is involved in the processing for the Global Climate Modeling. The Goddard Earth Observing System Model, Version 5 (GEOS-5) is a system of models integrated using the Earth System Modeling Framework (ESMF). The GEOS-5 system was used for the Benchmark tests, and the results of the tests are shown and discussed. Tests were also run for the Cubed Sphere system, results for these test are also shown.

Interfacing the Controllogics PLC over Ethernet/IP.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kasemir, K. U.; Dalesio, L. R.

2001-01-01

The Allen-Bradley ControlLogix [1] line of programmable logic controllers (PLCs) offers several interfaces: Ethernet, ControlNet, DeviceNet, RS-232 and others. The ControlLogix Ethernet interface module 1756-ENET uses EtherNet/IP, the ControlNet protocol [2], encapsulated in Ethernet packages, with specific service codes [3]. A driver for the Experimental Physics and Industrial Control System (EPICS) has been developed that utilizes this EtherNet/IP protocol for controllers running the vxWorks RTOS as well as a Win32 and Unix/Linux test program. Features, performance and limitations of this interface are presented.

cloudPEST - A python module for cloud-computing deployment of PEST, a program for parameter estimation

USGS Publications Warehouse

Fienen, Michael N.; Kunicki, Thomas C.; Kester, Daniel E.

2011-01-01

This report documents cloudPEST-a Python module with functions to facilitate deployment of the model-independent parameter estimation code PEST on a cloud-computing environment. cloudPEST makes use of low-level, freely available command-line tools that interface with the Amazon Elastic Compute Cloud (EC2(TradeMark)) that are unlikely to change dramatically. This report describes the preliminary setup for both Python and EC2 tools and subsequently describes the functions themselves. The code and guidelines have been tested primarily on the Windows(Registered) operating system but are extensible to Linux(Registered).

Nuclear Data Online Services at Peking University

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fan, T.S.; Guo, Z.Y.; Ye, W.G.

2005-05-24

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

Nuclear Data Online Services at Peking University

NASA Astrophysics Data System (ADS)

Fan, T. S.; Guo, Z. Y.; Ye, W. G.; Liu, W. L.; Liu, T. J.; Liu, C. X.; Chen, J. X.; Tang, G. Y.; Shi, Z. M.; Huang, X. L.; Chen, J. E.

2005-05-01

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

Toolkit for testing scientific CCD cameras

NASA Astrophysics Data System (ADS)

Uzycki, Janusz; Mankiewicz, Lech; Molak, Marcin; Wrochna, Grzegorz

2006-03-01

The CCD Toolkit (1) is a software tool for testing CCD cameras which allows to measure important characteristics of a camera like readout noise, total gain, dark current, 'hot' pixels, useful area, etc. The application makes a statistical analysis of images saved in files with FITS format, commonly used in astronomy. A graphical interface is based on the ROOT package, which offers high functionality and flexibility. The program was developed in a way to ensure future compatibility with different operating systems: Windows and Linux. The CCD Toolkit was created for the "Pie of the Sky" project collaboration (2).

A strategy for automatically generating programs in the lucid programming language

NASA Technical Reports Server (NTRS)

Johnson, Sally C.

1987-01-01

A strategy for automatically generating and verifying simple computer programs is described. The programs are specified by a precondition and a postcondition in predicate calculus. The programs generated are in the Lucid programming language, a high-level, data-flow language known for its attractive mathematical properties and ease of program verification. The Lucid programming is described, and the automatic program generation strategy is described and applied to several example problems.

Award-Winning Foreign Language Programs: Prescriptions for Success.

ERIC Educational Resources Information Center

Sims, William D.; Hammond, Sandra B.

The study reviews 50 foreign language programs in the United States that are said to be both inspirational and useful for providing concrete information about the creation and preservation of successful language programs. The programs cited are exemplary and can serve as models for educators and administrators to study and visit. Program selection…

Laboratory automation in a functional programming language.

PubMed

Runciman, Colin; Clare, Amanda; Harkness, Rob

2014-12-01

After some years of use in academic and research settings, functional languages are starting to enter the mainstream as an alternative to more conventional programming languages. This article explores one way to use Haskell, a functional programming language, in the development of control programs for laboratory automation systems. We give code for an example system, discuss some programming concepts that we need for this example, and demonstrate how the use of functional programming allows us to express and verify properties of the resulting code. © 2014 Society for Laboratory Automation and Screening.

Language Program Evaluation

ERIC Educational Resources Information Center

Norris, John M.

2016-01-01

Language program evaluation is a pragmatic mode of inquiry that illuminates the complex nature of language-related interventions of various kinds, the factors that foster or constrain them, and the consequences that ensue. Program evaluation enables a variety of evidence-based decisions and actions, from designing programs and implementing…

Testing as a Way to Monitor English as a Foreign Language Learning

ERIC Educational Resources Information Center

Becker, Anthony; Nekrasova-Beker, Tatiana; Petrashova, Tamara

2017-01-01

This study was conducted at a large technical university in Russia, which offers English language courses to students majoring in nine different degree programs. Each degree program develops and delivers its own English language curriculum. While all degree programs followed the same curriculum development model to design language courses, each…

A Program That Acquires Language Using Positive and Negative Feedback.

ERIC Educational Resources Information Center

Brand, James

1987-01-01

Describes the language learning program "Acquire," which is a sample of grammar induction. It is a learning algorithm based on a pattern-matching scheme, using both a positive and negative network to reduce overgeneration. Language learning programs may be useful as tutorials for learning the syntax of a foreign language. (Author/LMO)

The English Language in the School Program.

ERIC Educational Resources Information Center

Hogan, Robert F., Ed.

The 22 papers in this publication, drawn from the 1963 and 1964 NCTE Spring Institutes on Language, Linguistics, and School Programs, concentrate on the relevance of recent scholarship for English language programs in elementary and secondary schools. Language theory is the focus of articles by Harold B. Allen, Sumner Ives, Albert H. Marckwardt,…

A Career-Oriented Foreign Language Program for Keystone Oaks School District, Pittsburgh, Pennsylvania.

ERIC Educational Resources Information Center

Grubesky, Marcia R.

A career-oriented foreign language program is discussed that takes into account marketable skills of foreign language majors for a number of careers. The program is threefold. First, it recognizes the need for language skills to supplement technical, business, and professional skills to expand educational knowledge; capabilities in diplomacy and…

Injecting Artificial Memory Errors Into a Running Computer Program

NASA Technical Reports Server (NTRS)

Bornstein, Benjamin J.; Granat, Robert A.; Wagstaff, Kiri L.

2008-01-01

Single-event upsets (SEUs) or bitflips are computer memory errors caused by radiation. BITFLIPS (Basic Instrumentation Tool for Fault Localized Injection of Probabilistic SEUs) is a computer program that deliberately injects SEUs into another computer program, while the latter is running, for the purpose of evaluating the fault tolerance of that program. BITFLIPS was written as a plug-in extension of the open-source Valgrind debugging and profiling software. BITFLIPS can inject SEUs into any program that can be run on the Linux operating system, without needing to modify the program s source code. Further, if access to the original program source code is available, BITFLIPS offers fine-grained control over exactly when and which areas of memory (as specified via program variables) will be subjected to SEUs. The rate of injection of SEUs is controlled by specifying either a fault probability or a fault rate based on memory size and radiation exposure time, in units of SEUs per byte per second. BITFLIPS can also log each SEU that it injects and, if program source code is available, report the magnitude of effect of the SEU on a floating-point value or other program variable.

The Effects of Web 2.0 Technologies Usage in Programming Languages Lesson on the Academic Success, Interrogative Learning Skills and Attitudes of Students towards Programming Languages

ERIC Educational Resources Information Center

Gençtürk, Abdullah Tarik; Korucu, Agah Tugrul

2017-01-01

It is observed that teacher candidates receiving education in the department of Computer and Instructional Technologies Education are not able to gain enough experience and knowledge in "Programming Languages" lesson. The goal of this study is to analyse the effects of web 2.0 technologies usage in programming languages lesson on the…

The Australian Language Levels (ALL) Project--A Response to Curriculum Needs in Australia.

ERIC Educational Resources Information Center

Scarino, Angela; McKay, Penny

Australia has a unique range of language communities and language education needs. A variety of languages is currently offered to different groups of learners through diverse programs. Language teaching may be provided through bilingual education, limited-exposure programs, or compulsory language instruction. Federal and state education agencies,…

MULTI2D - a computer code for two-dimensional radiation hydrodynamics

NASA Astrophysics Data System (ADS)

Ramis, R.; Meyer-ter-Vehn, J.; Ramírez, J.

2009-06-01

Simulation of radiation hydrodynamics in two spatial dimensions is developed, having in mind, in particular, target design for indirectly driven inertial confinement energy (IFE) and the interpretation of related experiments. Intense radiation pulses by laser or particle beams heat high-Z target configurations of different geometries and lead to a regime which is optically thick in some regions and optically thin in others. A diffusion description is inadequate in this situation. A new numerical code has been developed which describes hydrodynamics in two spatial dimensions (cylindrical R-Z geometry) and radiation transport along rays in three dimensions with the 4 π solid angle discretized in direction. Matter moves on a non-structured mesh composed of trilateral and quadrilateral elements. Radiation flux of a given direction enters on two (one) sides of a triangle and leaves on the opposite side(s) in proportion to the viewing angles depending on the geometry. This scheme allows to propagate sharply edged beams without ray tracing, though at the price of some lateral diffusion. The algorithm treats correctly both the optically thin and optically thick regimes. A symmetric semi-implicit (SSI) method is used to guarantee numerical stability. Program summaryProgram title: MULTI2D Catalogue identifier: AECV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 151 098 No. of bytes in distributed program, including test data, etc.: 889 622 Distribution format: tar.gz Programming language: C Computer: PC (32 bits architecture) Operating system: Linux/Unix RAM: 2 Mbytes Word size: 32 bits Classification: 19.7 External routines: X-window standard library (libX11.so) and corresponding heading files (X11/*.h) are required. Nature of problem: In inertial confinement fusion and related experiments with lasers and particle beams, energy transport by thermal radiation becomes important. Under these conditions, the radiation field strongly interacts with the hydrodynamic motion through emission and absorption processes. Solution method: The equations of radiation transfer coupled with Lagrangian hydrodynamics, heat diffusion and beam tracing (laser or ions) are solved, in two-dimensional axial-symmetric geometry ( R-Z coordinates) using a fractional step scheme. Radiation transfer is solved with angular resolution. Matter properties are either interpolated from tables (equations-of-state and opacities) or computed by user routines (conductivities and beam attenuation). Restrictions: The code has been designed for typical conditions prevailing in inertial confinement fusion (ns time scale, matter states close to local thermodynamical equilibrium, negligible radiation pressure, …). Although a wider range of situations can be treated, extrapolations to regions beyond this design range need special care. Unusual features: A special computer language, called r94, is used at top levels of the code. These parts have to be converted to standard C by a translation program (supplied as part of the package). Due to the complexity of code (hydro-code, grid generation, user interface, graphic post-processor, translator program, installation scripts) extensive manuals are supplied as part of the package. Running time: 567 seconds for the example supplied.

GenomeDiagram: a python package for the visualization of large-scale genomic data.

PubMed

Pritchard, Leighton; White, Jennifer A; Birch, Paul R J; Toth, Ian K

2006-03-01

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

PubMed

Couvin, David; Bernheim, Aude; Toffano-Nioche, Claire; Touchon, Marie; Michalik, Juraj; Néron, Bertrand; C Rocha, Eduardo P; Vergnaud, Gilles; Gautheret, Daniel; Pourcel, Christine

2018-05-22

CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

A HyperCard Program for Business German.

ERIC Educational Resources Information Center

Paulsell, Patricia R.

Although the use of computer-assisted language instruction software has been mainly limited to grammatical/syntactical drills, the increasing number of language professionals with programming skills is leading to the development of more sophisticated language education programs. This report describes the generation of such a program using the…

Programming languages for synthetic biology.

PubMed

Umesh, P; Naveen, F; Rao, Chanchala Uma Maheswara; Nair, Achuthsankar S

2010-12-01

In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented.

Developing and Benchmarking Native Linux Applications on Android

NASA Astrophysics Data System (ADS)

Batyuk, Leonid; Schmidt, Aubrey-Derrick; Schmidt, Hans-Gunther; Camtepe, Ahmet; Albayrak, Sahin

Smartphones get increasingly popular where more and more smartphone platforms emerge. Special attention was gained by the open source platform Android which was presented by the Open Handset Alliance (OHA) hosting members like Google, Motorola, and HTC. Android uses a Linux kernel and a stripped-down userland with a custom Java VM set on top. The resulting system joins the advantages of both environments, while third-parties are intended to develop only Java applications at the moment.

System Data Model (SDM) Source Code

DTIC Science & Technology

2012-08-23

CROSS_COMPILE=/opt/gumstix/build_arm_nofpu/staging_dir/bin/arm-linux-uclibcgnueabi- 8 : CC=$(CROSS_COMPILE)gcc 9: CXX=$(CROSS_COMPILE)g++ 10 : AR...and flags to pass to it 6: LEX=flex 7: LEXFLAGS=-B 8 : 9: ## The parser generator to invoke and flags to pass to it 10 : YACC=bison 11: YACCFLAGS...5: # Point to default PetaLinux root directory 6: ifndef ROOTDIR 7: ROOTDIR=$(PETALINUX)/software/petalinux-dist 8 : endif 9: 10 : PATH:=$(PATH

The database design of LAMOST based on MYSQL/LINUX

NASA Astrophysics Data System (ADS)

Li, Hui-Xian, Sang, Jian; Wang, Sha; Luo, A.-Li

2006-03-01

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) will be set up in the coming years. A fully automated software system for reducing and analyzing the spectra has to be developed with the telescope. This database system is an important part of the software system. The requirements for the database of the LAMOST, the design of the LAMOST database system based on MYSQL/LINUX and performance tests of this system are described in this paper.

Navigation/Prop Software Suite

NASA Technical Reports Server (NTRS)

Bruchmiller, Tomas; Tran, Sanh; Lee, Mathew; Bucker, Scott; Bupane, Catherine; Bennett, Charles; Cantu, Sergio; Kwong, Ping; Propst, Carolyn

2012-01-01

Navigation (Nav)/Prop software is used to support shuttle mission analysis, production, and some operations tasks. The Nav/Prop suite containing configuration items (CIs) resides on IPS/Linux workstations. It features lifecycle documents, and data files used for shuttle navigation and propellant analysis for all flight segments. This suite also includes trajectory server, archive server, and RAT software residing on MCC/Linux workstations. Navigation/Prop represents tool versions established during or after IPS Equipment Rehost-3 or after the MCC Rehost.

Malware Memory Analysis of the IVYL Linux Rootkit: Investigating a Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2015-04-01

report is to examine how a computer forensic investigator/incident handler, without specialised computer memory or software reverse engineering skills ...The skills amassed by incident handlers and investigators alike while using Volatility to examine Windows memory images will be of some help...bin/pulseaudio --start --log-target=syslog 1362 1000 1000 nautilus 1366 1000 1000 /usr/lib/pulseaudio/pulse/gconf- helper 1370 1000 1000 nm-applet

Approaches in highly parameterized inversion—PEST++ Version 3, a Parameter ESTimation and uncertainty analysis software suite optimized for large environmental models

USGS Publications Warehouse

Welter, David E.; White, Jeremy T.; Hunt, Randall J.; Doherty, John E.

2015-09-18

The PEST++ Version 3 software suite can be compiled for Microsoft Windows®4 and Linux®5 operating systems; the source code is available in a Microsoft Visual Studio®6 2013 solution; Linux Makefiles are also provided. PEST++ Version 3 continues to build a foundation for an open-source framework capable of producing robust and efficient parameter estimation tools for large environmental models.

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

Software For Least-Squares And Robust Estimation

NASA Technical Reports Server (NTRS)

Jeffreys, William H.; Fitzpatrick, Michael J.; Mcarthur, Barbara E.; Mccartney, James

1990-01-01

GAUSSFIT computer program includes full-featured programming language facilitating creation of mathematical models solving least-squares and robust-estimation problems. Programming language designed to make it easy to specify complex reduction models. Written in 100 percent C language.

Learning Through Survival: An Approach to Foreign Language Teaching. A Program Description and Evaluation.

ERIC Educational Resources Information Center

Travers, Claudia S.; Reilly, Joseph T. M.

A foreign travel program for eighth grade French language students from Shoreham, New York was developed to provide language speaking practice in Quebec, Canada. The program was designed to allow students to spend as much time as possible speaking the language and interacting with the people. The following "survival through speaking"…

Linking Language and Culture in the Language and Cultural Program of the Lauder Institute: The French Perspective.

ERIC Educational Resources Information Center

Lahaeye, Marie-Noelle

The University of Pennsylvania's Lauder Institute of Management and International Studies introduced a cultural segment into its second language program in 1986 to enable students to use language purposefully within the foreign culture. During the program's 2 years, students are exposed to eight different cultural segments taught by language…

A Systematic Meta-Analytic Review of Evidence for the Effectiveness of the "Fast ForWord" Language Intervention Program

ERIC Educational Resources Information Center

Strong, Gemma K.; Torgerson, Carole J.; Torgerson, David; Hulme, Charles

2011-01-01

Background: Fast ForWord is a suite of computer-based language intervention programs designed to improve children's reading and oral language skills. The programs are based on the hypothesis that oral language difficulties often arise from a rapid auditory temporal processing deficit that compromises the development of phonological…

New Dimensions in Language Training: The Dartmouth College Experiment.

ERIC Educational Resources Information Center

Rassias, John A.

The expanded foreign study and foreign language programs offered at Dartmouth are examined with emphasis on the influence of Peace Corps language programs during the last half-dozen years on American college campuses. The impact of the programs at Dartmouth since 1964 is discussed in terms of: (1) a brief history of language instruction at…

Uses of Technology in the Instruction of Adult English Language Learners. CAELA Network Brief

ERIC Educational Resources Information Center

Moore, Sarah Catherine K.

2009-01-01

In program year 2006-2007, 46 percent of the adults enrolled in federally funded, state-administered adult education programs in the United States were enrolled in English as a Second Language (ESL) programs. These adult English language learners represent a wide range of ages, nationalities, native languages, and English proficiency levels. In…

HAL/S language specification

NASA Technical Reports Server (NTRS)

Newbold, P. M.

1974-01-01

A programming language for the flight software of the NASA space shuttle program was developed and identified as HAL/S. The language is intended to satisfy virtually all of the flight software requirements of the space shuttle. The language incorporates a wide range of features, including applications-oriented data types and organizations, real time control mechanisms, and constructs for systems programming tasks.

A Multicultural Awareness Program To Improve Language and Thinking Skills to a Group of Language Deficient Preschool Students.

ERIC Educational Resources Information Center

Altamura, Marilyn T.

This practicum project exposed seven preschool students with language deficiencies to multicultural experiences and strategies, resulting in improvements in both language and thinking skills. The children were included in a regular preschool program serving low-income families. The program was based on a multicultural awareness curriculum which…

The Dual Language Program Planner: A Guide for Designing and Implementing Dual Language Programs.

ERIC Educational Resources Information Center

Howard, Elizabeth R.; Olague, Natalie; Rogers, David

This guide offers a framework to facilitate the planning process for dual language programs, assuming at least a basic working knowledge of the central characteristics and essential features of dual language models. It provides an overview of the various models that serve linguistically diverse student populations, defining the term dual language…

25 CFR 39.131 - What is a Language Development Program?

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false What is a Language Development Program? 39.131 Section 39.131 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR EDUCATION THE INDIAN SCHOOL EQUALIZATION PROGRAM Indian School Equalization Formula Language Development Programs § 39.131 What is a...

34 CFR 658.11 - What projects and activities may a grantee conduct under this program?

Code of Federal Regulations, 2014 CFR

2014-07-01

... STUDIES AND FOREIGN LANGUAGE PROGRAM What Kinds of Projects Does the Secretary Assist Under This Program... program to improve undergraduate instruction in international studies and foreign languages. These include... studies and foreign languages; (b) Teaching, research, curriculum development, faculty training in the...

34 CFR 658.11 - What projects and activities may a grantee conduct under this program?

Code of Federal Regulations, 2013 CFR

2013-07-01

... STUDIES AND FOREIGN LANGUAGE PROGRAM What Kinds of Projects Does the Secretary Assist Under This Program... program to improve undergraduate instruction in international studies and foreign languages. These include... studies and foreign languages; (b) Teaching, research, curriculum development, faculty training in the...

34 CFR 658.11 - What projects and activities may a grantee conduct under this program?

Code of Federal Regulations, 2012 CFR

2012-07-01

... STUDIES AND FOREIGN LANGUAGE PROGRAM What Kinds of Projects Does the Secretary Assist Under This Program... program to improve undergraduate instruction in international studies and foreign languages. These include... studies and foreign languages; (b) Teaching, research, curriculum development, faculty training in the...

The Dynamics of Language Program Direction. Issues in Language Program Direction: A Series of Annual Volumes.

ERIC Educational Resources Information Center

Benseler, David P., Ed.

This collection papers begins with "Introduction: The Dynamics of Successful Leadership in Foreign Language Programs," then features the following: "The Undergraduate Program: Autonomy and Empowerment" (Wilga M. Rivers); "TA Supervision: Are We Preparing a Future Professoriate?" (Cathy Pons); "Applied Scholarship…

[Union-Endicott Schools: Foreign Language Program.

ERIC Educational Resources Information Center

O'Connell, Raymond S.

This brochure describing language programs to both parents and prospective high school language students in Endicott, New York focuses on developing student motivation and interest. Topics discussed include: (1) reasons for studying foreign language, (2) stages of foreign language learning, (3) course offerings, (4) homework, and (5) examinations.…

Author Languages, Authoring Systems, and Their Relation to the Changing Focus of Computer-Aided Language Learning.

ERIC Educational Resources Information Center

Sussex, Roland

1991-01-01

Considers how the effectiveness of computer-assisted language learning (CALL) has been hampered by language teachers who lack programing and software engineering expertise, and explores the limitations and potential contributions of author languages, programs, and environments in increasing the range of options for language teachers who are not…

More than Words, A Way of Life: Language Restoration Programs Reach beyond Tribal Colleges and Universities

ERIC Educational Resources Information Center

Paskus, Laura

2013-01-01

In North America, and worldwide, Indigenous languages are disappearing at an alarming rate. There are, however, models of success for language revitalization in immersion language programs, usually found in tribal colleges and universities. Whether the language learners are tribal college students greeting one another in their native language,…

Real-Time Multiprocessor Programming Language (RTMPL) user's manual

NASA Technical Reports Server (NTRS)

Arpasi, D. J.

1985-01-01

A real-time multiprocessor programming language (RTMPL) has been developed to provide for high-order programming of real-time simulations on systems of distributed computers. RTMPL is a structured, engineering-oriented language. The RTMPL utility supports a variety of multiprocessor configurations and types by generating assembly language programs according to user-specified targeting information. Many programming functions are assumed by the utility (e.g., data transfer and scaling) to reduce the programming chore. This manual describes RTMPL from a user's viewpoint. Source generation, applications, utility operation, and utility output are detailed. An example simulation is generated to illustrate many RTMPL features.

Should bilingual children learn reading in two languages at the same time or in sequence?

PubMed Central

Berens, Melody S.; Kovelman, Ioulia; Petitto, Laura-Ann

2013-01-01

Is it best to learn reading in two languages simultaneously or sequentially? We observed 2nd and 3rd grade children in two-way dual-language learning contexts: (i) 50:50 or Simultaneous dual-language (two languages within same developmental period) and (ii) 90:10 or Sequential dual-language (one language, followed gradually by the other). They were compared to matched monolingual English-only children in single-language English schools. Bilinguals (home language was Spanish only, English-only, or Spanish and English in dual-language schools), were tested in both languages, and monolingual children were tested in English using standardized reading and language tasks. Bilinguals in 50:50 programs performed better than bilinguals in 90:10 programs on English Irregular Words and Passage Comprehension tasks, suggesting language and reading facilitation for underlying grammatical class and linguistic structure analyses. By contrast, bilinguals in 90:10 programs performed better than bilinguals in the 50:50 programs on English Phonological Awareness and Reading Decoding tasks, suggesting language and reading facilitation for surface phonological regularity analysis. Notably, children from English-only homes in dual-language learning contexts performed equally well, or better than, children from monolingual English-only homes in single-language learning contexts. Overall, the findings provide tantalizing evidence that dual-language learning during the same developmental period may provide bilingual reading advantages. PMID:23794952

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

PubMed

Krampis, Konstantinos; Booth, Tim; Chapman, Brad; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E

2012-03-19

A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

PubMed Central

2012-01-01

Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them. PMID:22429538

The Advantages and Disadvantages of Computer Technology in Second Language Acquisition

ERIC Educational Resources Information Center

Lai, Cheng-Chieh; Kritsonis, William Allan

2006-01-01

The purpose of this article is to discuss the advantages and disadvantages of computer technology and Computer Assisted Language Learning (CALL) programs for current second language learning. According to the National Clearinghouse for English Language Acquisition & Language Instruction Educational Programs' report (2002), more than nine million…

Online Collaborative Communities of Learning for Pre-Service Teachers of Languages

ERIC Educational Resources Information Center

Morgan, Anne-Marie

2015-01-01

University programs for preparing preservice teachers of languages for teaching in schools generally involve generic pedagogy, methodology, curriculum, programming and issues foci, that provide a bridge between the study of languages (or recognition of existing language proficiency) and the teaching of languages. There is much territory to cover…

A Whole Language Flight Plan: An Interview with Three Teachers.

ERIC Educational Resources Information Center

Griffith, Priscilla L.; Klesius, Janell

1990-01-01

Provides suggestions to teachers planning to implement a whole language program, based on interviews with three whole language teachers. Focuses on support for the whole language program; decisions about curriculum and evaluation; development of vocabulary and comprehension; strengths and weaknesses of the whole language approach; and preparation…

Programming parallel architectures: The BLAZE family of languages

NASA Technical Reports Server (NTRS)

Mehrotra, Piyush

1988-01-01

Programming multiprocessor architectures is a critical research issue. An overview is given of the various approaches to programming these architectures that are currently being explored. It is argued that two of these approaches, interactive programming environments and functional parallel languages, are particularly attractive since they remove much of the burden of exploiting parallel architectures from the user. Also described is recent work by the author in the design of parallel languages. Research on languages for both shared and nonshared memory multiprocessors is described, as well as the relations of this work to other current language research projects.

Defense Contracting: Actions Needed to Explore Additional Opportunities to Gain Efficiencies in Acquiring Foreign Language Support

DTIC Science & Technology

2013-02-25

Directive 5160.41E, Defense Language Program . 10GAO-11-456. Page 5 GAO-13-251R Defense Contracting types of foreign language support that DOD has acquired...Language Transformation Roadmap, (January 2005), and Department of Defense Directive 5160.41E, Defense Language Program . Page 15 GAO-13-251R Defense...examines the use of public funds; evaluates federal programs and policies; and provides analyses, recommendations, and other assistance to help