sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine.

PubMed

Gómez-Martín, Cristina; Lebrón, Ricardo; Rueda, Antonio; Oliver, José L; Hackenberg, Michael

2017-01-01

High-throughput sequencing (HTS) data for small RNAs (noncoding RNA molecules that are 20-250 nucleotides in length) can now be routinely generated by minimally equipped wet laboratories; however, the bottleneck in HTS-based research has shifted now to the analysis of such huge amount of data. One of the reasons is that many analysis types require a Linux environment but computers, system administrators, and bioinformaticians suppose additional costs that often cannot be afforded by small to mid-sized groups or laboratories. Web servers are an alternative that can be used if the data is not subjected to privacy issues (what very often is an important issue with medical data). However, in any case they are less flexible than stand-alone programs limiting the number of workflows and analysis types that can be carried out.We show in this protocol how virtual machines can be used to overcome those problems and limitations. sRNAtoolboxVM is a virtual machine that can be executed on all common operating systems through virtualization programs like VirtualBox or VMware, providing the user with a high number of preinstalled programs like sRNAbench for small RNA analysis without the need to maintain additional servers and/or operating systems.

GRIDVIEW: Recent Improvements in Research and Education Software for Exploring Mars Topography

NASA Technical Reports Server (NTRS)

Roark, J. H.; Masuoka, C. M.; Frey, H. V.

2004-01-01

GRIDVIEW is being developed by the GEODYNAMICS Branch at NASA's Goddard Space Flight Center and can be downloaded on the web at http://geodynamics.gsfc.nasa.gov/gridview/. The program is very mature and has been successfully used for more than four years, but is still under development as we add new features for data analysis and visualization. The software can run on any computer supported by the IDL virtual machine application supplied by RSI. The virtual machine application is currently available for recent versions of MS Windows, MacOS X, Red Hat Linux and UNIX. Minimum system memory requirement is 32 MB, however loading large data sets may require larger amounts of RAM to function adequately.

Staghorn: An Automated Large-Scale Distributed System Analysis Platform

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

Gabert, Kasimir; Burns, Ian; Elliott, Steven

2016-09-01

Conducting experiments on large-scale distributed computing systems is becoming significantly easier with the assistance of emulation. Researchers can now create a model of a distributed computing environment and then generate a virtual, laboratory copy of the entire system composed of potentially thousands of virtual machines, switches, and software. The use of real software, running at clock rate in full virtual machines, allows experiments to produce meaningful results without necessitating a full understanding of all model components. However, the ability to inspect and modify elements within these models is bound by the limitation that such modifications must compete with the model,more » either running in or alongside it. This inhibits entire classes of analyses from being conducted upon these models. We developed a mechanism to snapshot an entire emulation-based model as it is running. This allows us to \\freeze time" and subsequently fork execution, replay execution, modify arbitrary parts of the model, or deeply explore the model. This snapshot includes capturing packets in transit and other input/output state along with the running virtual machines. We were able to build this system in Linux using Open vSwitch and Kernel Virtual Machines on top of Sandia's emulation platform Firewheel. This primitive opens the door to numerous subsequent analyses on models, including state space exploration, debugging distributed systems, performance optimizations, improved training environments, and improved experiment repeatability.« less

Improving the Automated Detection and Analysis of Secure Coding Violations

DTIC Science & Technology

2014-06-01

eliminating software vulnerabilities and other flaws. The CERT Division produces books and courses that foster a security mindset in developers, and...website also provides a virtual machine containing a complete build of the Rosecheckers project on Linux . The Rosecheckers project leverages the...Compass/ROSE6 project developed at Law- rence Livermore National Laboratory. This project provides a high-level API for accessing the abstract syntax tree

Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-09-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reprint of: Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-11-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Scaling NS-3 DCE Experiments on Multi-Core Servers

DTIC Science & Technology

2016-06-15

that work well together. 3.2 Simulation Server Details We ran the simulations on a Dell® PowerEdge M520 blade server[8] running Ubuntu Linux 14.04...To minimize the amount of time needed to complete all of the simulations, we planned to run multiple simulations at the same time on a blade server...MacBook was running the simulation inside a virtual machine (Ubuntu 14.04), while the blade server was running the same operating system directly on

Implementation of Grid Tier 2 and Tier 3 facilities on a Distributed OpenStack Cloud

NASA Astrophysics Data System (ADS)

Limosani, Antonio; Boland, Lucien; Coddington, Paul; Crosby, Sean; Huang, Joanna; Sevior, Martin; Wilson, Ross; Zhang, Shunde

2014-06-01

The Australian Government is making a AUD 100 million investment in Compute and Storage for the academic community. The Compute facilities are provided in the form of 30,000 CPU cores located at 8 nodes around Australia in a distributed virtualized Infrastructure as a Service facility based on OpenStack. The storage will eventually consist of over 100 petabytes located at 6 nodes. All will be linked via a 100 Gb/s network. This proceeding describes the development of a fully connected WLCG Tier-2 grid site as well as a general purpose Tier-3 computing cluster based on this architecture. The facility employs an extension to Torque to enable dynamic allocations of virtual machine instances. A base Scientific Linux virtual machine (VM) image is deployed in the OpenStack cloud and automatically configured as required using Puppet. Custom scripts are used to launch multiple VMs, integrate them into the dynamic Torque cluster and to mount remote file systems. We report on our experience in developing this nation-wide ATLAS and Belle II Tier 2 and Tier 3 computing infrastructure using the national Research Cloud and storage facilities.

KNBD: A Remote Kernel Block Server for Linux

NASA Technical Reports Server (NTRS)

Becker, Jeff

1999-01-01

I am developing a prototype of a Linux remote disk block server whose purpose is to serve as a lower level component of a parallel file system. Parallel file systems are an important component of high performance supercomputers and clusters. Although supercomputer vendors such as SGI and IBM have their own custom solutions, there has been a void and hence a demand for such a system on Beowulf-type PC Clusters. Recently, the Parallel Virtual File System (PVFS) project at Clemson University has begun to address this need (1). Although their system provides much of the functionality of (and indeed was inspired by) the equivalent file systems in the commercial supercomputer market, their system is all in user-space. Migrating their 10 services to the kernel could provide a performance boost, by obviating the need for expensive system calls. Thanks to Pavel Machek, the Linux kernel has provided the network block device (2) with kernels 2.1.101 and later. You can configure this block device to redirect reads and writes to a remote machine's disk. This can be used as a building block for constructing a striped file system across several nodes.

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

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.

PubMed

Tristão Ramos, Ravi José; de Azevedo Martins, Allan Cézar; da Silva Delgado, Gabrielle; Ionescu, Crina-Maria; Ürményi, Turán Peter; Silva, Rosane; Koca, Jaroslav

2017-11-15

CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss. CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine. jkoca@ceitec.cz. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Parallel implementation of D-Phylo algorithm for maximum likelihood clusters.

PubMed

Malik, Shamita; Sharma, Dolly; Khatri, Sunil Kumar

2017-03-01

This study explains a newly developed parallel algorithm for phylogenetic analysis of DNA sequences. The newly designed D-Phylo is a more advanced algorithm for phylogenetic analysis using maximum likelihood approach. The D-Phylo while misusing the seeking capacity of k -means keeps away from its real constraint of getting stuck at privately conserved motifs. The authors have tested the behaviour of D-Phylo on Amazon Linux Amazon Machine Image(Hardware Virtual Machine)i2.4xlarge, six central processing unit, 122 GiB memory, 8  ×  800 Solid-state drive Elastic Block Store volume, high network performance up to 15 processors for several real-life datasets. Distributing the clusters evenly on all the processors provides us the capacity to accomplish a near direct speed if there should arise an occurrence of huge number of processors.

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.

Secure Video Surveillance System Acquisition Software

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

2009-12-04

The SVSS Acquisition Software collects and displays video images from two cameras through a VPN, and store the images onto a collection controller. The software is configured to allow a user to enter a time window to display up to 2 1/2, hours of video review. The software collects images from the cameras at a rate of 1 image per second and automatically deletes images older than 3 hours. The software code operates in a linux environment and can be run in a virtual machine on Windows XP. The Sandia software integrates the different COTS software together to build themore » video review system.« less

SplicePlot: a utility for visualizing splicing quantitative trait loci.

PubMed

Wu, Eric; Nance, Tracy; Montgomery, Stephen B

2014-04-01

RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility that produces intuitive visualization of sQTLs and their effects. SplicePlot takes mapped RNA sequencing reads in BAM format and genotype data in VCF format as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure. Source code and detailed documentation are available at http://montgomerylab.stanford.edu/spliceplot/index.html under Resources and at Github. SplicePlot is implemented in Python and is supported on Linux and Mac OS. A VirtualBox virtual machine running Ubuntu with SplicePlot already installed is also available.

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.

Virtual network computing: cross-platform remote display and collaboration software.

PubMed

Konerding, D E

1999-04-01

VNC (Virtual Network Computing) is a computer program written to address the problem of cross-platform remote desktop/application display. VNC uses a client/server model in which an image of the desktop of the server is transmitted to the client and displayed. The client collects mouse and keyboard input from the user and transmits them back to the server. The VNC client and server can run on Windows 95/98/NT, MacOS, and Unix (including Linux) operating systems. VNC is multi-user on Unix machines (any number of servers can be run are unrelated to the primary display of the computer), while it is effectively single-user on Macintosh and Windows machines (only one server can be run, displaying the contents of the primary display of the server). The VNC servers can be configured to allow more than one client to connect at one time, effectively allowing collaboration through the shared desktop. I describe the function of VNC, provide details of installation, describe how it achieves its goal, and evaluate the use of VNC for molecular modelling. VNC is an extremely useful tool for collaboration, instruction, software development, and debugging of graphical programs with remote users.

Dynamic provisioning of a HEP computing infrastructure on a shared hybrid HPC system

NASA Astrophysics Data System (ADS)

Meier, Konrad; Fleig, Georg; Hauth, Thomas; Janczyk, Michael; Quast, Günter; von Suchodoletz, Dirk; Wiebelt, Bernd

2016-10-01

Experiments in high-energy physics (HEP) rely on elaborate hardware, software and computing systems to sustain the high data rates necessary to study rare physics processes. The Institut fr Experimentelle Kernphysik (EKP) at KIT is a member of the CMS and Belle II experiments, located at the LHC and the Super-KEKB accelerators, respectively. These detectors share the requirement, that enormous amounts of measurement data must be processed and analyzed and a comparable amount of simulated events is required to compare experimental results with theoretical predictions. Classical HEP computing centers are dedicated sites which support multiple experiments and have the required software pre-installed. Nowadays, funding agencies encourage research groups to participate in shared HPC cluster models, where scientist from different domains use the same hardware to increase synergies. This shared usage proves to be challenging for HEP groups, due to their specialized software setup which includes a custom OS (often Scientific Linux), libraries and applications. To overcome this hurdle, the EKP and data center team of the University of Freiburg have developed a system to enable the HEP use case on a shared HPC cluster. To achieve this, an OpenStack-based virtualization layer is installed on top of a bare-metal cluster. While other user groups can run their batch jobs via the Moab workload manager directly on bare-metal, HEP users can request virtual machines with a specialized machine image which contains a dedicated operating system and software stack. In contrast to similar installations, in this hybrid setup, no static partitioning of the cluster into a physical and virtualized segment is required. As a unique feature, the placement of the virtual machine on the cluster nodes is scheduled by Moab and the job lifetime is coupled to the lifetime of the virtual machine. This allows for a seamless integration with the jobs sent by other user groups and honors the fairshare policies of the cluster. The developed thin integration layer between OpenStack and Moab can be adapted to other batch servers and virtualization systems, making the concept also applicable for other cluster operators. This contribution will report on the concept and implementation of an OpenStack-virtualized cluster used for HEP workflows. While the full cluster will be installed in spring 2016, a test-bed setup with 800 cores has been used to study the overall system performance and dedicated HEP jobs were run in a virtualized environment over many weeks. Furthermore, the dynamic integration of the virtualized worker nodes, depending on the workload at the institute's computing system, will be described.

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

PubMed Central

Saeed, Isaam; Wong, Stephen Q.; Mar, Victoria; Goode, David L.; Caramia, Franco; Doig, Ken; Ryland, Georgina L.; Thompson, Ella R.; Hunter, Sally M.; Halgamuge, Saman K.; Ellul, Jason; Dobrovic, Alexander; Campbell, Ian G.; Papenfuss, Anthony T.; McArthur, Grant A.; Tothill, Richard W.

2014-01-01

Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/. PMID:24752294

Implementing Journaling in a Linux Shared Disk File System

NASA Technical Reports Server (NTRS)

Preslan, Kenneth W.; Barry, Andrew; Brassow, Jonathan; Cattelan, Russell; Manthei, Adam; Nygaard, Erling; VanOort, Seth; Teigland, David; Tilstra, Mike; O'Keefe, Matthew;

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

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.

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.

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.

[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.

Running GUI Applications on Peregrine from OSX | High-Performance Computing

Science.gov Websites

Learn how to use Virtual Network Computing to access a Linux graphical desktop environment on Peregrine local port (on, e.g., your laptop), starts a VNC server process that manages a virtual desktop on your virtual desktop. This is persistent, so remember it-you will use this password whenever accessing

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.

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters.

PubMed

Abreu, Rui Mv; Froufe, Hugo Jc; Queiroz, Maria João Rp; Ferreira, Isabel Cfr

2010-10-28

Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.

How do I resolve problems reading the binary data?

Atmospheric Science Data Center

2014-12-08

... affecting compilation would be differing versions of the operating system and compilers the read software are being run on. Big ... Unix machines are Big Endian architecture while Linux systems are Little Endian architecture. Data generated on a Unix machine are ...

SU-E-T-314: The Application of Cloud Computing in Pencil Beam Scanning Proton Therapy Monte Carlo Simulation

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

Wang, Z; Gao, M

Purpose: Monte Carlo simulation plays an important role for proton Pencil Beam Scanning (PBS) technique. However, MC simulation demands high computing power and is limited to few large proton centers that can afford a computer cluster. We study the feasibility of utilizing cloud computing in the MC simulation of PBS beams. Methods: A GATE/GEANT4 based MC simulation software was installed on a commercial cloud computing virtual machine (Linux 64-bits, Amazon EC2). Single spot Integral Depth Dose (IDD) curves and in-air transverse profiles were used to tune the source parameters to simulate an IBA machine. With the use of StarCluster softwaremore » developed at MIT, a Linux cluster with 2–100 nodes can be conveniently launched in the cloud. A proton PBS plan was then exported to the cloud where the MC simulation was run. Results: The simulated PBS plan has a field size of 10×10cm{sup 2}, 20cm range, 10cm modulation, and contains over 10,000 beam spots. EC2 instance type m1.medium was selected considering the CPU/memory requirement and 40 instances were used to form a Linux cluster. To minimize cost, master node was created with on-demand instance and worker nodes were created with spot-instance. The hourly cost for the 40-node cluster was $0.63 and the projected cost for a 100-node cluster was $1.41. Ten million events were simulated to plot PDD and profile, with each job containing 500k events. The simulation completed within 1 hour and an overall statistical uncertainty of < 2% was achieved. Good agreement between MC simulation and measurement was observed. Conclusion: Cloud computing is a cost-effective and easy to maintain platform to run proton PBS MC simulation. When proton MC packages such as GATE and TOPAS are combined with cloud computing, it will greatly facilitate the pursuing of PBS MC studies, especially for newly established proton centers or individual researchers.« less

DOVIS: an implementation for high-throughput virtual screening using AutoDock.

PubMed

Zhang, Shuxing; Kumar, Kamal; Jiang, Xiaohui; Wallqvist, Anders; Reifman, Jaques

2008-02-27

Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried. DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.

Plancton: an opportunistic distributed computing project based on Docker containers

NASA Astrophysics Data System (ADS)

Concas, Matteo; Berzano, Dario; Bagnasco, Stefano; Lusso, Stefano; Masera, Massimo; Puccio, Maximiliano; Vallero, Sara

2017-10-01

The computing power of most modern commodity computers is far from being fully exploited by standard usage patterns. In this work we describe the development and setup of a virtual computing cluster based on Docker containers used as worker nodes. The facility is based on Plancton: a lightweight fire-and-forget background service. Plancton spawns and controls a local pool of Docker containers on a host with free resources, by constantly monitoring its CPU utilisation. It is designed to release the resources allocated opportunistically, whenever another demanding task is run by the host user, according to configurable policies. This is attained by killing a number of running containers. One of the advantages of a thin virtualization layer such as Linux containers is that they can be started almost instantly upon request. We will show how fast the start-up and disposal of containers eventually enables us to implement an opportunistic cluster based on Plancton daemons without a central control node, where the spawned Docker containers behave as job pilots. Finally, we will show how Plancton was configured to run up to 10 000 concurrent opportunistic jobs on the ALICE High-Level Trigger facility, by giving a considerable advantage in terms of management compared to virtual machines.

Computer network defense system

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

Urias, Vincent; Stout, William M. S.; Loverro, Caleb

A method and apparatus for protecting virtual machines. A computer system creates a copy of a group of the virtual machines in an operating network in a deception network to form a group of cloned virtual machines in the deception network when the group of the virtual machines is accessed by an adversary. The computer system creates an emulation of components from the operating network in the deception network. The components are accessible by the group of the cloned virtual machines as if the group of the cloned virtual machines was in the operating network. The computer system moves networkmore » connections for the group of the virtual machines in the operating network used by the adversary from the group of the virtual machines in the operating network to the group of the cloned virtual machines, enabling protecting the group of the virtual machines from actions performed by the adversary.« less

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

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

Simple re-instantiation of small databases using cloud computing.

PubMed

Tan, Tin Wee; Xie, Chao; De Silva, Mark; Lim, Kuan Siong; Patro, C Pawan K; Lim, Shen Jean; Govindarajan, Kunde Ramamoorthy; Tong, Joo Chuan; Choo, Khar Heng; Ranganathan, Shoba; Khan, Asif M

2013-01-01

Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.

Simple re-instantiation of small databases using cloud computing

PubMed Central

2013-01-01

Background Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. Results We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Conclusions Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear. PMID:24564380

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

Scalable computing for evolutionary genomics.

PubMed

Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert

2012-01-01

Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project, BioNode encourages creating free and open source VM images, for multiple targets, through one central project. BioNode can be deployed on Windows, OSX, Linux, and in the Cloud. Next to the downloadable BioNode images, we provide tutorials online, which empower bioinformaticians to install and run BioNode in different environments, as well as information for future initiatives, on creating and building such images.

Integrating multiple scientific computing needs via a Private Cloud infrastructure

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Brunetti, R.; Lusso, S.; Vallero, S.

2014-06-01

In a typical scientific computing centre, diverse applications coexist and share a single physical infrastructure. An underlying Private Cloud facility eases the management and maintenance of heterogeneous use cases such as multipurpose or application-specific batch farms, Grid sites catering to different communities, parallel interactive data analysis facilities and others. It allows to dynamically and efficiently allocate resources to any application and to tailor the virtual machines according to the applications' requirements. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques; for example, rolling updates can be performed easily and minimizing the downtime. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 site and a dynamically expandable PROOF-based Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The Private Cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem (used in two different configurations for worker- and service-class hypervisors) and the OpenWRT Linux distribution (used for network virtualization). A future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and by using mainstream contextualization tools like CloudInit.

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.

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.

Virtual Manufacturing Techniques Designed and Applied to Manufacturing Activities in the Manufacturing Integration and Technology Branch

NASA Technical Reports Server (NTRS)

Shearrow, Charles A.

1999-01-01

One of the identified goals of EM3 is to implement virtual manufacturing by the time the year 2000 has ended. To realize this goal of a true virtual manufacturing enterprise the initial development of a machinability database and the infrastructure must be completed. This will consist of the containment of the existing EM-NET problems and developing machine, tooling, and common materials databases. To integrate the virtual manufacturing enterprise with normal day to day operations the development of a parallel virtual manufacturing machinability database, virtual manufacturing database, virtual manufacturing paradigm, implementation/integration procedure, and testable verification models must be constructed. Common and virtual machinability databases will include the four distinct areas of machine tools, available tooling, common machine tool loads, and a materials database. The machine tools database will include the machine envelope, special machine attachments, tooling capacity, location within NASA-JSC or with a contractor, and availability/scheduling. The tooling database will include available standard tooling, custom in-house tooling, tool properties, and availability. The common materials database will include materials thickness ranges, strengths, types, and their availability. The virtual manufacturing databases will consist of virtual machines and virtual tooling directly related to the common and machinability databases. The items to be completed are the design and construction of the machinability databases, virtual manufacturing paradigm for NASA-JSC, implementation timeline, VNC model of one bridge mill and troubleshoot existing software and hardware problems with EN4NET. The final step of this virtual manufacturing project will be to integrate other production sites into the databases bringing JSC's EM3 into a position of becoming a clearing house for NASA's digital manufacturing needs creating a true virtual manufacturing enterprise.

Review of Enabling Technologies to Facilitate Secure Compute Customization

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

Aderholdt, Ferrol; Caldwell, Blake A; Hicks, Susan Elaine

High performance computing environments are often used for a wide variety of workloads ranging from simulation, data transformation and analysis, and complex workflows to name just a few. These systems may process data for a variety of users, often requiring strong separation between job allocations. There are many challenges to establishing these secure enclaves within the shared infrastructure of high-performance computing (HPC) environments. The isolation mechanisms in the system software are the basic building blocks for enabling secure compute enclaves. There are a variety of approaches and the focus of this report is to review the different virtualization technologies thatmore » facilitate the creation of secure compute enclaves. The report reviews current operating system (OS) protection mechanisms and modern virtualization technologies to better understand the performance/isolation properties. We also examine the feasibility of running ``virtualized'' computing resources as non-privileged users, and providing controlled administrative permissions for standard users running within a virtualized context. Our examination includes technologies such as Linux containers (LXC [32], Docker [15]) and full virtualization (KVM [26], Xen [5]). We categorize these different approaches to virtualization into two broad groups: OS-level virtualization and system-level virtualization. The OS-level virtualization uses containers to allow a single OS kernel to be partitioned to create Virtual Environments (VE), e.g., LXC. The resources within the host's kernel are only virtualized in the sense of separate namespaces. In contrast, system-level virtualization uses hypervisors to manage multiple OS kernels and virtualize the physical resources (hardware) to create Virtual Machines (VM), e.g., Xen, KVM. This terminology of VE and VM, detailed in Section 2, is used throughout the report to distinguish between the two different approaches to providing virtualized execution environments. As part of our technology review we analyzed several current virtualization solutions to assess their vulnerabilities. This included a review of common vulnerabilities and exposures (CVEs) for Xen, KVM, LXC and Docker to gauge their susceptibility to different attacks. The complete details are provided in Section 5 on page 33. Based on this review we concluded that system-level virtualization solutions have many more vulnerabilities than OS level virtualization solutions. As such, security mechanisms like sVirt (Section 3.3) should be considered when using system-level virtualization solutions in order to protect the host against exploits. The majority of vulnerabilities related to KVM, LXC, and Docker are in specific regions of the system. Therefore, future "zero day attacks" are likely to be in the same regions, which suggests that protecting these areas can simplify the protection of the host and maintain the isolation between users. The evaluations of virtualization technologies done thus far are discussed in Section 4. This includes experiments with 'user' namespaces in VEs, which provides the ability to isolate user privileges and allow a user to run with different UIDs within the container while mapping them to non-privileged UIDs in the host. We have identified Linux namespaces as a promising mechanism to isolate shared resources, while maintaining good performance. In Section 4.1 we describe our tests with LXC as a non-root user and leveraging namespaces to control UID/GID mappings and support controlled sharing of parallel file-systems. We highlight several of these namespace capabilities in Section 6.2.3. The other evaluations that were performed during this initial phase of work provide baseline performance data for comparing VEs and VMs to purely native execution. In Section 4.2 we performed tests using the High-Performance Computing Conjugate Gradient (HPCCG) benchmark to establish baseline performance for a scientific application when run on the Native (host) machine in contrast with execution under Docker and KVM. Our tests verified prior studies showing roughly 2-4% overheads in application execution time & MFlops when running in hypervisor-base environments (VMs) as compared to near native performance with VEs. For more details, see Figures 4.5 (page 28), 4.6 (page 28), and 4.7 (page 29). Additionally, in Section 4.3 we include network measurements for TCP bandwidth performance over the 10GigE interface in our testbed. The Native and Docker based tests achieved >= ~9Gbits/sec, while the KVM configuration only achieved 2.5Gbits/sec (Table 4.6 on page 32). This may be a configuration issue with our KVM installation, and is a point for further testing as we refine the network settings in the testbed. The initial network tests were done using a bridged networking configuration. The report outline is as follows: - Section 1 introduces the report and clarifies the scope of the proj...« less

Modeling and simulation of five-axis virtual machine based on NX

NASA Astrophysics Data System (ADS)

Li, Xiaoda; Zhan, Xianghui

2018-04-01

Virtual technology in the machinery manufacturing industry has shown the role of growing. In this paper, the Siemens NX software is used to model the virtual CNC machine tool, and the parameters of the virtual machine are defined according to the actual parameters of the machine tool so that the virtual simulation can be carried out without loss of the accuracy of the simulation. How to use the machine builder of the CAM module to define the kinematic chain and machine components of the machine is described. The simulation of virtual machine can provide alarm information of tool collision and over cutting during the process to users, and can evaluate and forecast the rationality of the technological process.

TinyONet: A Cache-Based Sensor Network Bridge Enabling Sensing Data Reusability and Customized Wireless Sensor Network Services

PubMed Central

Jung, Eui-Hyun; Park, Yong-Jin

2008-01-01

In recent years, a few protocol bridge research projects have been announced to enable a seamless integration of Wireless Sensor Networks (WSNs) with the TCP/IP network. These studies have ensured the transparent end-to-end communication between two network sides in the node-centric manner. Researchers expect this integration will trigger the development of various application domains. However, prior research projects have not fully explored some essential features for WSNs, especially the reusability of sensing data and the data-centric communication. To resolve these issues, we suggested a new protocol bridge system named TinyONet. In TinyONet, virtual sensors play roles as virtual counterparts of physical sensors and they dynamically group to make a functional entity, Slice. Instead of direct interaction with individual physical sensors, each sensor application uses its own WSN service provided by Slices. If a new kind of service is required in TinyONet, the corresponding function can be dynamically added at runtime. Beside the data-centric communication, it also supports the node-centric communication and the synchronous access. In order to show the effectiveness of the system, we implemented TinyONet on an embedded Linux machine and evaluated it with several experimental scenarios. PMID:27873968

Toward Millions of File System IOPS on Low-Cost, Commodity Hardware

PubMed Central

Zheng, Da; Burns, Randal; Szalay, Alexander S.

2013-01-01

We describe a storage system that removes I/O bottlenecks to achieve more than one million IOPS based on a user-space file abstraction for arrays of commodity SSDs. The file abstraction refactors I/O scheduling and placement for extreme parallelism and non-uniform memory and I/O. The system includes a set-associative, parallel page cache in the user space. We redesign page caching to eliminate CPU overhead and lock-contention in non-uniform memory architecture machines. We evaluate our design on a 32 core NUMA machine with four, eight-core processors. Experiments show that our design delivers 1.23 million 512-byte read IOPS. The page cache realizes the scalable IOPS of Linux asynchronous I/O (AIO) and increases user-perceived I/O performance linearly with cache hit rates. The parallel, set-associative cache matches the cache hit rates of the global Linux page cache under real workloads. PMID:24402052

Toward Millions of File System IOPS on Low-Cost, Commodity Hardware.

PubMed

Zheng, Da; Burns, Randal; Szalay, Alexander S

2013-01-01

We describe a storage system that removes I/O bottlenecks to achieve more than one million IOPS based on a user-space file abstraction for arrays of commodity SSDs. The file abstraction refactors I/O scheduling and placement for extreme parallelism and non-uniform memory and I/O. The system includes a set-associative, parallel page cache in the user space. We redesign page caching to eliminate CPU overhead and lock-contention in non-uniform memory architecture machines. We evaluate our design on a 32 core NUMA machine with four, eight-core processors. Experiments show that our design delivers 1.23 million 512-byte read IOPS. The page cache realizes the scalable IOPS of Linux asynchronous I/O (AIO) and increases user-perceived I/O performance linearly with cache hit rates. The parallel, set-associative cache matches the cache hit rates of the global Linux page cache under real workloads.

Effects of virtualization on a scientific application - Running a hyperspectral radiative transfer code on virtual machines.

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

Tikotekar, Anand A; Vallee, Geoffroy R; Naughton III, Thomas J

2008-01-01

The topic of system-level virtualization has recently begun to receive interest for high performance computing (HPC). This is in part due to the isolation and encapsulation offered by the virtual machine. These traits enable applications to customize their environments and maintain consistent software configurations in their virtual domains. Additionally, there are mechanisms that can be used for fault tolerance like live virtual machine migration. Given these attractive benefits to virtualization, a fundamental question arises, how does this effect my scientific application? We use this as the premise for our paper and observe a real-world scientific code running on a Xenmore » virtual machine. We studied the effects of running a radiative transfer simulation, Hydrolight, on a virtual machine. We discuss our methodology and report observations regarding the usage of virtualization with this application.« less

Comparison of fMRI data analysis by SPM99 on different operating systems.

PubMed

Shinagawa, Hideo; Honda, Ei-ichi; Ono, Takashi; Kurabayashi, Tohru; Ohyama, Kimie

2004-09-01

The hardware chosen for fMRI data analysis may depend on the platform already present in the laboratory or the supporting software. In this study, we ran SPM99 software on multiple platforms to examine whether we could analyze fMRI data by SPM99, and to compare their differences and limitations in processing fMRI data, which can be attributed to hardware capabilities. Six normal right-handed volunteers participated in a study of hand-grasping to obtain fMRI data. Each subject performed a run that consisted of 98 images. The run was measured using a gradient echo-type echo planar imaging sequence on a 1.5T apparatus with a head coil. We used several personal computer (PC), Unix and Linux machines to analyze the fMRI data. There were no differences in the results obtained on several PC, Unix and Linux machines. The only limitations in processing large amounts of the fMRI data were found using PC machines. This suggests that the results obtained with different machines were not affected by differences in hardware components, such as the CPU, memory and hard drive. Rather, it is likely that the limitations in analyzing a huge amount of the fMRI data were due to differences in the operating system (OS).

Managing virtual machines with Vac and Vcycle

NASA Astrophysics Data System (ADS)

McNab, A.; Love, P.; MacMahon, E.

2015-12-01

We compare the Vac and Vcycle virtual machine lifecycle managers and our experiences in providing production job execution services for ATLAS, CMS, LHCb, and the GridPP VO at sites in the UK, France and at CERN. In both the Vac and Vcycle systems, the virtual machines are created outside of the experiment's job submission and pilot framework. In the case of Vac, a daemon runs on each physical host which manages a pool of virtual machines on that host, and a peer-to-peer UDP protocol is used to achieve the desired target shares between experiments across the site. In the case of Vcycle, a daemon manages a pool of virtual machines on an Infrastructure-as-a-Service cloud system such as OpenStack, and has within itself enough information to create the types of virtual machines to achieve the desired target shares. Both systems allow unused shares for one experiment to temporarily taken up by other experiements with work to be done. The virtual machine lifecycle is managed with a minimum of information, gathered from the virtual machine creation mechanism (such as libvirt or OpenStack) and using the proposed Machine/Job Features API from WLCG. We demonstrate that the same virtual machine designs can be used to run production jobs on Vac and Vcycle/OpenStack sites for ATLAS, CMS, LHCb, and GridPP, and that these technologies allow sites to be operated in a reliable and robust way.

A Dedicated Computational Platform for Cellular Monte Carlo T-CAD Software Tools

DTIC Science & Technology

2015-07-14

computer that establishes an encrypted Virtual Private Network ( OpenVPN [44]) based on the Secure Socket Layer (SSL) paradigm. Each user is given a...security certificate for each device used to connect to the computing nodes. Stable OpenVPN clients are available for Linux, Microsoft Windows, Apple OSX...platform is granted by an encrypted connection base on the Secure Socket Layer (SSL) protocol, and implemented in the OpenVPN Virtual Personal Network

An easy-to-build, low-budget point-of-care ultrasound simulator: from Linux to a web-based solution.

PubMed

Damjanovic, Domagoj; Goebel, Ulrich; Fischer, Benedikt; Huth, Martin; Breger, Hartmut; Buerkle, Hartmut; Schmutz, Axel

2017-12-01

Hands-on training in point-of-care ultrasound (POC-US) should ideally comprise bedside teaching, as well as simulated clinical scenarios. High-fidelity phantoms and portable ultrasound simulation systems are commercially available, however, at considerable costs. This limits their suitability for medical schools. A Linux-based software for Emergency Department Ultrasound Simulation (edus2TM) was developed by Kulyk and Olszynski in 2011. Its feasibility for POC-US education has been well-documented, and shows good acceptance. An important limitation to an even more widespread use of edus2, however, may be due to the need for a virtual machine for WINDOWS ® systems. Our aim was to adapt the original software toward an HTML-based solution, thus making it affordable and applicable in any simulation setting. We created an HTML browser-based ultrasound simulation application, which reads the input of different sensors, triggering an ultrasound video to be displayed on a respective device. RFID tags, NFC tags, and QR Codes™ have been integrated into training phantoms or were attached to standardized patients. The RFID antenna was hidden in a mock ultrasound probe. The application is independent from the respective device. Our application was used successfully with different trigger/scanner combinations and mounted readily into simulated training scenarios. The application runs independently from operating systems or electronic devices. This low-cost, browser-based ultrasound simulator is easy-to-build, very adaptive, and independent from operating systems. It has the potential to facilitate POC-US training throughout the world, especially in resource-limited areas.

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.

LHCb experience with running jobs in virtual machines

NASA Astrophysics Data System (ADS)

McNab, A.; Stagni, F.; Luzzi, C.

2015-12-01

The LHCb experiment has been running production jobs in virtual machines since 2013 as part of its DIRAC-based infrastructure. We describe the architecture of these virtual machines and the steps taken to replicate the WLCG worker node environment expected by user and production jobs. This relies on the uCernVM system for providing root images for virtual machines. We use the CernVM-FS distributed filesystem to supply the root partition files, the LHCb software stack, and the bootstrapping scripts necessary to configure the virtual machines for us. Using this approach, we have been able to minimise the amount of contextualisation which must be provided by the virtual machine managers. We explain the process by which the virtual machine is able to receive payload jobs submitted to DIRAC by users and production managers, and how this differs from payloads executed within conventional DIRAC pilot jobs on batch queue based sites. We describe our operational experiences in running production on VM based sites managed using Vcycle/OpenStack, Vac, and HTCondor Vacuum. Finally we show how our use of these resources is monitored using Ganglia and DIRAC.

A Configuration Framework and Implementation for the Least Privilege Separation Kernel

DTIC Science & Technology

2010-12-01

The Altova Web site states that virtualization software, Parallels for Mac and Wine , is required for running it on MacOS and RedHat Linux...University of Singapore Singapore 28. Tan Lai Poh National University of Singapore Singapore 29. Quek Chee Luan Defence Science & Technology Agency Singapore

Using virtual machine monitors to overcome the challenges of monitoring and managing virtualized cloud infrastructures

NASA Astrophysics Data System (ADS)

Bamiah, Mervat Adib; Brohi, Sarfraz Nawaz; Chuprat, Suriayati

2012-01-01

Virtualization is one of the hottest research topics nowadays. Several academic researchers and developers from IT industry are designing approaches for solving security and manageability issues of Virtual Machines (VMs) residing on virtualized cloud infrastructures. Moving the application from a physical to a virtual platform increases the efficiency, flexibility and reduces management cost as well as effort. Cloud computing is adopting the paradigm of virtualization, using this technique, memory, CPU and computational power is provided to clients' VMs by utilizing the underlying physical hardware. Beside these advantages there are few challenges faced by adopting virtualization such as management of VMs and network traffic, unexpected additional cost and resource allocation. Virtual Machine Monitor (VMM) or hypervisor is the tool used by cloud providers to manage the VMs on cloud. There are several heterogeneous hypervisors provided by various vendors that include VMware, Hyper-V, Xen and Kernel Virtual Machine (KVM). Considering the challenge of VM management, this paper describes several techniques to monitor and manage virtualized cloud infrastructures.

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.

Hardware assisted hypervisor introspection.

PubMed

Shi, Jiangyong; Yang, Yuexiang; Tang, Chuan

2016-01-01

In this paper, we introduce hypervisor introspection, an out-of-box way to monitor the execution of hypervisors. Similar to virtual machine introspection which has been proposed to protect virtual machines in an out-of-box way over the past decade, hypervisor introspection can be used to protect hypervisors which are the basis of cloud security. Virtual machine introspection tools are usually deployed either in hypervisor or in privileged virtual machines, which might also be compromised. By utilizing hardware support including nested virtualization, EPT protection and #BP, we are able to monitor all hypercalls belongs to the virtual machines of one hypervisor, include that of privileged virtual machine and even when the hypervisor is compromised. What's more, hypercall injection method is used to simulate hypercall-based attacks and evaluate the performance of our method. Experiment results show that our method can effectively detect hypercall-based attacks with some performance cost. Lastly, we discuss our furture approaches of reducing the performance cost and preventing the compromised hypervisor from detecting the existence of our introspector, in addition with some new scenarios to apply our hypervisor introspection system.

Agentless Cloud-Wide Monitoring of Virtual Disk State

DTIC Science & Technology

2015-10-01

packages include Apache, MySQL , PHP, Ruby on Rails, Java Application Servers, and many others. Figure 2.12 shows the results of a run of the Software...Linux, Apache, MySQL , PHP (LAMP) set of applications. Thus, many file-level update logs will contain the same versions of files repeated across many

Manipulation of volumetric patient data in a distributed virtual reality environment.

PubMed

Dech, F; Ai, Z; Silverstein, J C

2001-01-01

Due to increases in network speed and bandwidth, distributed exploration of medical data in immersive Virtual Reality (VR) environments is becoming increasingly feasible. The volumetric display of radiological data in such environments presents a unique set of challenges. The shear size and complexity of the datasets involved not only make them difficult to transmit to remote sites, but these datasets also require extensive user interaction in order to make them understandable to the investigator and manageable to the rendering hardware. A sophisticated VR user interface is required in order for the clinician to focus on the aspects of the data that will provide educational and/or diagnostic insight. We will describe a software system of data acquisition, data display, Tele-Immersion, and data manipulation that supports interactive, collaborative investigation of large radiological datasets. The hardware required in this strategy is still at the high-end of the graphics workstation market. Future software ports to Linux and NT, along with the rapid development of PC graphics cards, open the possibility for later work with Linux or NT PCs and PC clusters.

It’s an app. It’s a hypervisor. It’s a hypapp. : Design and Implementation of an eXtensible and Modular Hypervisor Framework

DTIC Science & Technology

2012-06-26

existing commercial-grade virtualization solutions (e.g., Xen, Linux KVM, VMware, or L4 ), but generally do not require such rich functional- ity [9...ports multiprocessor configuration on both AMD and Intel x86 platforms. Xen [8], KVM [27], VMware [39], NOVA [33], Virtual- box‡‡ and L4 are some...popular general purpose (open-source) hypervisors and microkernels which have been used for var- ious hypervisor based research [9,15,26,30,32,34,45

Computer Associates International, CA-ACF2/VM Release 3.1

DTIC Science & Technology

1987-09-09

Associates CA-ACF2/VM Bibliography International Business Machines Corporation, IBM Virtual Machine/Directory Maintenance Program Logic Manual...publication number LY20-0889 International Business Machines International Business Machines Corporation, IBM System/370 Principles of Operation...publication number GA22-7000 International Business Machines Corporation, IBM Virtual Machine/Directory Maintenance Installation and System Administrator’s

An Effective Mechanism for Virtual Machine Placement using Aco in IAAS Cloud

NASA Astrophysics Data System (ADS)

Shenbaga Moorthy, Rajalakshmi; Fareentaj, U.; Divya, T. K.

2017-08-01

Cloud computing provides an effective way to dynamically provide numerous resources to meet customer demands. A major challenging problem for cloud providers is designing efficient mechanisms for optimal virtual machine Placement (OVMP). Such mechanisms enable the cloud providers to effectively utilize their available resources and obtain higher profits. In order to provide appropriate resources to the clients an optimal virtual machine placement algorithm is proposed. Virtual machine placement is NP-Hard problem. Such NP-Hard problem can be solved using heuristic algorithm. In this paper, Ant Colony Optimization based virtual machine placement is proposed. Our proposed system focuses on minimizing the cost spending in each plan for hosting virtual machines in a multiple cloud provider environment and the response time of each cloud provider is monitored periodically, in such a way to minimize delay in providing the resources to the users. The performance of the proposed algorithm is compared with greedy mechanism. The proposed algorithm is simulated in Eclipse IDE. The results clearly show that the proposed algorithm minimizes the cost, response time and also number of migrations.

Red Hat Enterprise Virtualization - KVM-based infrastructure services at BNL

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

Cortijo, D.

2011-06-14

Over the past 18 months, BNL has moved a large percentage of its Linux-based servers and services into a Red Hat Enterprise Virtualization (RHEV) environment. This presentation will address our approach to virtualization, critical decision points, and a discussion of our implementation. Specific topics will include an overview of hardware and software requirements, networking, and storage; discussion of the decision of Red Hat solution over competing products (VMWare, Xen, etc); details on some of the features of RHEV - both current and on their roadmap; Review of performance and reliability gains since deployment completion; path forward for RHEV at BNLmore » and caveats and potential problems.« less

Paging memory from random access memory to backing storage in a parallel computer

DOEpatents

Archer, Charles J; Blocksome, Michael A; Inglett, Todd A; Ratterman, Joseph D; Smith, Brian E

2013-05-21

Paging memory from random access memory (`RAM`) to backing storage in a parallel computer that includes a plurality of compute nodes, including: executing a data processing application on a virtual machine operating system in a virtual machine on a first compute node; providing, by a second compute node, backing storage for the contents of RAM on the first compute node; and swapping, by the virtual machine operating system in the virtual machine on the first compute node, a page of memory from RAM on the first compute node to the backing storage on the second compute node.

LINUX, Virtualization, and the Cloud: A Hands-On Student Introductory Lab

ERIC Educational Resources Information Center

Serapiglia, Anthony

2013-01-01

Many students are entering Computer Science education with limited exposure to operating systems and applications other than those produced by Apple or Microsoft. This gap in familiarity with the Open Source community can quickly be bridged with a simple exercise that can also be used to strengthen two other important current computing concepts,…

Future Cyborgs: Human-Machine Interface for Virtual Reality Applications

DTIC Science & Technology

2007-04-01

FUTURE CYBORGS : HUMAN-MACHINE INTERFACE FOR VIRTUAL REALITY APPLICATIONS Robert R. Powell, Major, USAF April 2007 Blue Horizons...SUBTITLE Future Cyborgs : Human-Machine Interface for Virtual Reality Applications 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...Nicholas Negroponte, Being Digital (New York: Alfred A Knopf, Inc, 1995), 123. 23 Ibid. 24 Andy Clark, Natural-Born Cyborgs (New York: Oxford

An imperialist competitive algorithm for virtual machine placement in cloud computing

NASA Astrophysics Data System (ADS)

Jamali, Shahram; Malektaji, Sepideh; Analoui, Morteza

2017-05-01

Cloud computing, the recently emerged revolution in IT industry, is empowered by virtualisation technology. In this paradigm, the user's applications run over some virtual machines (VMs). The process of selecting proper physical machines to host these virtual machines is called virtual machine placement. It plays an important role on resource utilisation and power efficiency of cloud computing environment. In this paper, we propose an imperialist competitive-based algorithm for the virtual machine placement problem called ICA-VMPLC. The base optimisation algorithm is chosen to be ICA because of its ease in neighbourhood movement, good convergence rate and suitable terminology. The proposed algorithm investigates search space in a unique manner to efficiently obtain optimal placement solution that simultaneously minimises power consumption and total resource wastage. Its final solution performance is compared with several existing methods such as grouping genetic and ant colony-based algorithms as well as bin packing heuristic. The simulation results show that the proposed method is superior to other tested algorithms in terms of power consumption, resource wastage, CPU usage efficiency and memory usage efficiency.

Using Mosix for Wide-Area Compuational Resources

USGS Publications Warehouse

Maddox, Brian G.

2004-01-01

One of the problems with using traditional Beowulf-type distributed processing clusters is that they require an investment in dedicated computer resources. These resources are usually needed in addition to pre-existing ones such as desktop computers and file servers. Mosix is a series of modifications to the Linux kernel that creates a virtual computer, featuring automatic load balancing by migrating processes from heavily loaded nodes to less used ones. An extension of the Beowulf concept is to run a Mosixenabled Linux kernel on a large number of computer resources in an organization. This configuration would provide a very large amount of computational resources based on pre-existing equipment. The advantage of this method is that it provides much more processing power than a traditional Beowulf cluster without the added costs of dedicating resources.

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

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

Exercise environment for Introduction to Cyber Technologies class. This software is essentially a collection of short scripts, configuration files, and small executables that form the exercise component of the Sandia Cyber Technologies Academy's Introduction to Cyber Technologies class. It builds upon other open-source technologies, such as Debian Linux and minimega, to provide comprehensive Linux and networking exercises that make learning these topics exciting and fun. Sample exercises: a pre-built set of home directories the student must navigate through to learn about privilege escalation, the creation of a virtual network playground designed to teach the student about the resiliency of themore » Internet, and a two-hour Capture the Flag challenge for the final lesson. There are approximately thirty (30) exercises included for the students to complete as part of the course.« less

Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries.

PubMed

Ma, Xiao H; Jia, Jia; Zhu, Feng; Xue, Ying; Li, Ze R; Chen, Yu Z

2009-05-01

Machine learning methods have been explored as ligand-based virtual screening tools for facilitating drug lead discovery. These methods predict compounds of specific pharmacodynamic, pharmacokinetic or toxicological properties based on their structure-derived structural and physicochemical properties. Increasing attention has been directed at these methods because of their capability in predicting compounds of diverse structures and complex structure-activity relationships without requiring the knowledge of target 3D structure. This article reviews current progresses in using machine learning methods for virtual screening of pharmacodynamically active compounds from large compound libraries, and analyzes and compares the reported performances of machine learning tools with those of structure-based and other ligand-based (such as pharmacophore and clustering) virtual screening methods. The feasibility to improve the performance of machine learning methods in screening large libraries is discussed.

Integration of the virtual 3D model of a control system with the virtual controller

NASA Astrophysics Data System (ADS)

Herbuś, K.; Ociepka, P.

2015-11-01

Nowadays the design process includes simulation analysis of different components of a constructed object. It involves the need for integration of different virtual object to simulate the whole investigated technical system. The paper presents the issues related to the integration of a virtual 3D model of a chosen control system of with a virtual controller. The goal of integration is to verify the operation of an adopted object of in accordance with the established control program. The object of the simulation work is the drive system of a tunneling machine for trenchless work. In the first stage of work was created an interactive visualization of functioning of the 3D virtual model of a tunneling machine. For this purpose, the software of the VR (Virtual Reality) class was applied. In the elaborated interactive application were created adequate procedures allowing controlling the drive system of a translatory motion, a rotary motion and the drive system of a manipulator. Additionally was created the procedure of turning on and off the output crushing head, mounted on the last element of the manipulator. In the elaborated interactive application have been established procedures for receiving input data from external software, on the basis of the dynamic data exchange (DDE), which allow controlling actuators of particular control systems of the considered machine. In the next stage of work, the program on a virtual driver, in the ladder diagram (LD) language, was created. The control program was developed on the basis of the adopted work cycle of the tunneling machine. The element integrating the virtual model of the tunneling machine for trenchless work with the virtual controller is the application written in a high level language (Visual Basic). In the developed application was created procedures responsible for collecting data from the running, in a simulation mode, virtual controller and transferring them to the interactive application, in which is verified the operation of the adopted research object. The carried out work allowed foot the integration of the virtual model of the control system of the tunneling machine with the virtual controller, enabling the verification of its operation.

Computing with Beowulf

NASA Technical Reports Server (NTRS)

Cohen, Jarrett

1999-01-01

Parallel computers built out of mass-market parts are cost-effectively performing data processing and simulation tasks. The Supercomputing (now known as "SC") series of conferences celebrated its 10th anniversary last November. While vendors have come and gone, the dominant paradigm for tackling big problems still is a shared-resource, commercial supercomputer. Growing numbers of users needing a cheaper or dedicated-access alternative are building their own supercomputers out of mass-market parts. Such machines are generally called Beowulf-class systems after the 11th century epic. This modern-day Beowulf story began in 1994 at NASA's Goddard Space Flight Center. A laboratory for the Earth and space sciences, computing managers there threw down a gauntlet to develop a $50,000 gigaFLOPS workstation for processing satellite data sets. Soon, Thomas Sterling and Don Becker were working on the Beowulf concept at the University Space Research Association (USRA)-run Center of Excellence in Space Data and Information Sciences (CESDIS). Beowulf clusters mix three primary ingredients: commodity personal computers or workstations, low-cost Ethernet networks, and the open-source Linux operating system. One of the larger Beowulfs is Goddard's Highly-parallel Integrated Virtual Environment, or HIVE for short.

VAC: Versatile Advection Code

NASA Astrophysics Data System (ADS)

Tóth, Gábor; Keppens, Rony

2012-07-01

The Versatile Advection Code (VAC) is a freely available general hydrodynamic and magnetohydrodynamic simulation software that works in 1, 2 or 3 dimensions on Cartesian and logically Cartesian grids. VAC runs on any Unix/Linux system with a Fortran 90 (or 77) compiler and Perl interpreter. VAC can run on parallel machines using either the Message Passing Interface (MPI) library or a High Performance Fortran (HPF) compiler.

Hybrid polylingual object model: an efficient and seamless integration of Java and native components on the Dalvik virtual machine.

PubMed

Huang, Yukun; Chen, Rong; Wei, Jingbo; Pei, Xilong; Cao, Jing; Prakash Jayaraman, Prem; Ranjan, Rajiv

2014-01-01

JNI in the Android platform is often observed with low efficiency and high coding complexity. Although many researchers have investigated the JNI mechanism, few of them solve the efficiency and the complexity problems of JNI in the Android platform simultaneously. In this paper, a hybrid polylingual object (HPO) model is proposed to allow a CAR object being accessed as a Java object and as vice in the Dalvik virtual machine. It is an acceptable substitute for JNI to reuse the CAR-compliant components in Android applications in a seamless and efficient way. The metadata injection mechanism is designed to support the automatic mapping and reflection between CAR objects and Java objects. A prototype virtual machine, called HPO-Dalvik, is implemented by extending the Dalvik virtual machine to support the HPO model. Lifespan management, garbage collection, and data type transformation of HPO objects are also handled in the HPO-Dalvik virtual machine automatically. The experimental result shows that the HPO model outweighs the standard JNI in lower overhead on native side, better executing performance with no JNI bridging code being demanded.

The ASSERT Virtual Machine Kernel: Support for Preservation of Temporal Properties

NASA Astrophysics Data System (ADS)

Zamorano, J.; de la Puente, J. A.; Pulido, J. A.; Urueña

2008-08-01

A new approach to building embedded real-time software has been developed in the ASSERT project. One of its key elements is the concept of a virtual machine preserving the non-functional properties of the system, and especially real-time properties, all the way down from high- level design models down to executable code. The paper describes one instance of the virtual machine concept that provides support for the preservation of temporal properties both at the source code level —by accept- ing only "legal" entities, i.e. software components with statically analysable real-tim behaviour— and at run-time —by monitoring the temporal behaviour of the system. The virtual machine has been validated on several pilot projects carried out by aerospace companies in the framework of the ASSERT project.

Means and method of balancing multi-cylinder reciprocating machines

DOEpatents

Corey, John A.; Walsh, Michael M.

1985-01-01

A virtual balancing axis arrangement is described for multi-cylinder reciprocating piston machines for effectively balancing out imbalanced forces and minimizing residual imbalance moments acting on the crankshaft of such machines without requiring the use of additional parallel-arrayed balancing shafts or complex and expensive gear arrangements. The novel virtual balancing axis arrangement is capable of being designed into multi-cylinder reciprocating piston and crankshaft machines for substantially reducing vibrations induced during operation of such machines with only minimal number of additional component parts. Some of the required component parts may be available from parts already required for operation of auxiliary equipment, such as oil and water pumps used in certain types of reciprocating piston and crankshaft machine so that by appropriate location and dimensioning in accordance with the teachings of the invention, the virtual balancing axis arrangement can be built into the machine at little or no additional cost.

Hybrid Cloud Computing Environment for EarthCube and Geoscience Community

NASA Astrophysics Data System (ADS)

Yang, C. P.; Qin, H.

2016-12-01

The NSF EarthCube Integration and Test Environment (ECITE) has built a hybrid cloud computing environment to provides cloud resources from private cloud environments by using cloud system software - OpenStack and Eucalyptus, and also manages public cloud - Amazon Web Service that allow resource synchronizing and bursting between private and public cloud. On ECITE hybrid cloud platform, EarthCube and geoscience community can deploy and manage the applications by using base virtual machine images or customized virtual machines, analyze big datasets by using virtual clusters, and real-time monitor the virtual resource usage on the cloud. Currently, a number of EarthCube projects have deployed or started migrating their projects to this platform, such as CHORDS, BCube, CINERGI, OntoSoft, and some other EarthCube building blocks. To accomplish the deployment or migration, administrator of ECITE hybrid cloud platform prepares the specific needs (e.g. images, port numbers, usable cloud capacity, etc.) of each project in advance base on the communications between ECITE and participant projects, and then the scientists or IT technicians in those projects launch one or multiple virtual machines, access the virtual machine(s) to set up computing environment if need be, and migrate their codes, documents or data without caring about the heterogeneity in structure and operations among different cloud platforms.

Cooperating reduction machines

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

Kluge, W.E.

1983-11-01

This paper presents a concept and a system architecture for the concurrent execution of program expressions of a concrete reduction language based on lamda-expressions. If formulated appropriately, these expressions are well-suited for concurrent execution, following a demand-driven model of computation. In particular, recursive program expressions with nonlinear expansion may, at run time, recursively be partitioned into a hierarchy of independent subexpressions which can be reduced by a corresponding hierarchy of virtual reduction machines. This hierarchy unfolds and collapses dynamically, with virtual machines recursively assuming the role of masters that create and eventually terminate, or synchronize with, slaves. The paper alsomore » proposes a nonhierarchically organized system of reduction machines, each featuring a stack architecture, that effectively supports the allocation of virtual machines to the real machines of the system in compliance with their hierarchical order of creation and termination. 25 references.« less

Complementary Machine Intelligence and Human Intelligence in Virtual Teaching Assistant for Tutoring Program Tracing

ERIC Educational Resources Information Center

Chou, Chih-Yueh; Huang, Bau-Hung; Lin, Chi-Jen

2011-01-01

This study proposes a virtual teaching assistant (VTA) to share teacher tutoring tasks in helping students practice program tracing and proposes two mechanisms of complementing machine intelligence and human intelligence to develop the VTA. The first mechanism applies machine intelligence to extend human intelligence (teacher answers) to evaluate…

"Pack[superscript2]": VM Resource Scheduling for Fine-Grained Application SLAs in Highly Consolidated Environment

ERIC Educational Resources Information Center

Sukwong, Orathai

2013-01-01

Virtualization enables the ability to consolidate multiple servers on a single physical machine, increasing the infrastructure utilization. Maximizing the ratio of server virtual machines (VMs) to physical machines, namely the consolidation ratio, becomes an important goal toward infrastructure cost saving in a cloud. However, the consolidation…

Remotely accessible laboratory for MEMS testing

NASA Astrophysics Data System (ADS)

Sivakumar, Ganapathy; Mulsow, Matthew; Melinger, Aaron; Lacouture, Shelby; Dallas, Tim E.

2010-02-01

We report on the construction of a remotely accessible and interactive laboratory for testing microdevices (aka: MicroElectroMechancial Systems - MEMS). Enabling expanded utilization of microdevices for research, commercial, and educational purposes is very important for driving the creation of future MEMS devices and applications. Unfortunately, the relatively high costs associated with MEMS devices and testing infrastructure makes widespread access to the world of MEMS difficult. The creation of a virtual lab to control and actuate MEMS devices over the internet helps spread knowledge to a larger audience. A host laboratory has been established that contains a digital microscope, microdevices, controllers, and computers that can be logged into through the internet. The overall layout of the tele-operated MEMS laboratory system can be divided into two major parts: the server side and the client side. The server-side is present at Texas Tech University, and hosts a server machine that runs the Linux operating system and is used for interfacing the MEMS lab with the outside world via internet. The controls from the clients are transferred to the lab side through the server interface. The server interacts with the electronics required to drive the MEMS devices using a range of National Instruments hardware and LabView Virtual Instruments. An optical microscope (100 ×) with a CCD video camera is used to capture images of the operating MEMS. The server broadcasts the live video stream over the internet to the clients through the website. When the button is pressed on the website, the MEMS device responds and the video stream shows the movement in close to real time.

Improving Memory Error Handling Using Linux

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

Carlton, Michael Andrew; Blanchard, Sean P.; Debardeleben, Nathan A.

As supercomputers continue to get faster and more powerful in the future, they will also have more nodes. If nothing is done, then the amount of memory in supercomputer clusters will soon grow large enough that memory failures will be unmanageable to deal with by manually replacing memory DIMMs. "Improving Memory Error Handling Using Linux" is a process oriented method to solve this problem by using the Linux kernel to disable (offline) faulty memory pages containing bad addresses, preventing them from being used again by a process. The process of offlining memory pages simplifies error handling and results in reducingmore » both hardware and manpower costs required to run Los Alamos National Laboratory (LANL) clusters. This process will be necessary for the future of supercomputing to allow the development of exascale computers. It will not be feasible without memory error handling to manually replace the number of DIMMs that will fail daily on a machine consisting of 32-128 petabytes of memory. Testing reveals the process of offlining memory pages works and is relatively simple to use. As more and more testing is conducted, the entire process will be automated within the high-performance computing (HPC) monitoring software, Zenoss, at LANL.« less

Elevating Virtual Machine Introspection for Fine-Grained Process Monitoring: Techniques and Applications

ERIC Educational Resources Information Center

Srinivasan, Deepa

2013-01-01

Recent rapid malware growth has exposed the limitations of traditional in-host malware-defense systems and motivated the development of secure virtualization-based solutions. By running vulnerable systems as virtual machines (VMs) and moving security software from inside VMs to the outside, the out-of-VM solutions securely isolate the anti-malware…

Hybrid PolyLingual Object Model: An Efficient and Seamless Integration of Java and Native Components on the Dalvik Virtual Machine

PubMed Central

Huang, Yukun; Chen, Rong; Wei, Jingbo; Pei, Xilong; Cao, Jing; Prakash Jayaraman, Prem; Ranjan, Rajiv

2014-01-01

JNI in the Android platform is often observed with low efficiency and high coding complexity. Although many researchers have investigated the JNI mechanism, few of them solve the efficiency and the complexity problems of JNI in the Android platform simultaneously. In this paper, a hybrid polylingual object (HPO) model is proposed to allow a CAR object being accessed as a Java object and as vice in the Dalvik virtual machine. It is an acceptable substitute for JNI to reuse the CAR-compliant components in Android applications in a seamless and efficient way. The metadata injection mechanism is designed to support the automatic mapping and reflection between CAR objects and Java objects. A prototype virtual machine, called HPO-Dalvik, is implemented by extending the Dalvik virtual machine to support the HPO model. Lifespan management, garbage collection, and data type transformation of HPO objects are also handled in the HPO-Dalvik virtual machine automatically. The experimental result shows that the HPO model outweighs the standard JNI in lower overhead on native side, better executing performance with no JNI bridging code being demanded. PMID:25110745

An incremental anomaly detection model for virtual machines.

PubMed

Zhang, Hancui; Chen, Shuyu; Liu, Jun; Zhou, Zhen; Wu, Tianshu

2017-01-01

Self-Organizing Map (SOM) algorithm as an unsupervised learning method has been applied in anomaly detection due to its capabilities of self-organizing and automatic anomaly prediction. However, because of the algorithm is initialized in random, it takes a long time to train a detection model. Besides, the Cloud platforms with large scale virtual machines are prone to performance anomalies due to their high dynamic and resource sharing characters, which makes the algorithm present a low accuracy and a low scalability. To address these problems, an Improved Incremental Self-Organizing Map (IISOM) model is proposed for anomaly detection of virtual machines. In this model, a heuristic-based initialization algorithm and a Weighted Euclidean Distance (WED) algorithm are introduced into SOM to speed up the training process and improve model quality. Meanwhile, a neighborhood-based searching algorithm is presented to accelerate the detection time by taking into account the large scale and high dynamic features of virtual machines on cloud platform. To demonstrate the effectiveness, experiments on a common benchmark KDD Cup dataset and a real dataset have been performed. Results suggest that IISOM has advantages in accuracy and convergence velocity of anomaly detection for virtual machines on cloud platform.

An incremental anomaly detection model for virtual machines

PubMed Central

Zhang, Hancui; Chen, Shuyu; Liu, Jun; Zhou, Zhen; Wu, Tianshu

2017-01-01

Self-Organizing Map (SOM) algorithm as an unsupervised learning method has been applied in anomaly detection due to its capabilities of self-organizing and automatic anomaly prediction. However, because of the algorithm is initialized in random, it takes a long time to train a detection model. Besides, the Cloud platforms with large scale virtual machines are prone to performance anomalies due to their high dynamic and resource sharing characters, which makes the algorithm present a low accuracy and a low scalability. To address these problems, an Improved Incremental Self-Organizing Map (IISOM) model is proposed for anomaly detection of virtual machines. In this model, a heuristic-based initialization algorithm and a Weighted Euclidean Distance (WED) algorithm are introduced into SOM to speed up the training process and improve model quality. Meanwhile, a neighborhood-based searching algorithm is presented to accelerate the detection time by taking into account the large scale and high dynamic features of virtual machines on cloud platform. To demonstrate the effectiveness, experiments on a common benchmark KDD Cup dataset and a real dataset have been performed. Results suggest that IISOM has advantages in accuracy and convergence velocity of anomaly detection for virtual machines on cloud platform. PMID:29117245

Analysis towards VMEM File of a Suspended Virtual Machine

NASA Astrophysics Data System (ADS)

Song, Zheng; Jin, Bo; Sun, Yongqing

With the popularity of virtual machines, forensic investigators are challenged with more complicated situations, among which discovering the evidences in virtualized environment is of significant importance. This paper mainly analyzes the file suffixed with .vmem in VMware Workstation, which stores all pseudo-physical memory into an image. The internal file structure of .vmem file is studied and disclosed. Key information about processes and threads of a suspended virtual machine is revealed. Further investigation into the Windows XP SP3 heap contents is conducted and a proof-of-concept tool is provided. Different methods to obtain forensic memory images are introduced, with both advantages and limits analyzed. We conclude with an outlook.

The HEPiX Virtualisation Working Group: Towards a Grid of Clouds

NASA Astrophysics Data System (ADS)

Cass, Tony

2012-12-01

The use of virtual machine images, as for example with Cloud services such as Amazon's Elastic Compute Cloud, is attractive for users as they have a guaranteed execution environment, something that cannot today be provided across sites participating in computing grids such as the Worldwide LHC Computing Grid. However, Grid sites often operate within computer security frameworks which preclude the use of remotely generated images. The HEPiX Virtualisation Working Group was setup with the objective to enable use of remotely generated virtual machine images at Grid sites and, to this end, has introduced the idea of trusted virtual machine images which are guaranteed to be secure and configurable by sites such that security policy commitments can be met. This paper describes the requirements and details of these trusted virtual machine images and presents a model for their use to facilitate the integration of Grid- and Cloud-based computing environments for High Energy Physics.

VisIVO: A Tool for the Virtual Observatory and Grid Environment

NASA Astrophysics Data System (ADS)

Becciani, U.; Comparato, M.; Costa, A.; Larsson, B.; Gheller, C.; Pasian, F.; Smareglia, R.

2007-10-01

We present the new features of VisIVO, software for the visualization and analysis of astrophysical data which can be retrieved from the Virtual Observatory framework and used for cosmological simulations running both on Windows and GNU/Linux platforms. VisIVO is VO standards compliant and supports the most important astronomical data formats such as FITS, HDF5 and VOTables. It is free software and can be downloaded from the web site http://visivo.cineca.it. VisIVO can interoperate with other astronomical VO compliant tools through PLASTIC (PLatform for AStronomical Tool InterConnection). This feature allows VisIVO to share data with many other astronomical packages to further analyze the loaded data.

Human Machine Interfaces for Teleoperators and Virtual Environments

NASA Technical Reports Server (NTRS)

Durlach, Nathaniel I. (Compiler); Sheridan, Thomas B. (Compiler); Ellis, Stephen R. (Compiler)

1991-01-01

In Mar. 1990, a meeting organized around the general theme of teleoperation research into virtual environment display technology was conducted. This is a collection of conference-related fragments that will give a glimpse of the potential of the following fields and how they interplay: sensorimotor performance; human-machine interfaces; teleoperation; virtual environments; performance measurement and evaluation methods; and design principles and predictive models.

Virtual C Machine and Integrated Development Environment for ATMS Controllers.

DOT National Transportation Integrated Search

2000-04-01

The overall objective of this project is to develop a prototype virtual machine that fits on current Advanced Traffic Management Systems (ATMS) controllers and provides functionality for complex traffic operations.;Prepared in cooperation with Utah S...

System-Level Virtualization Research at Oak Ridge National Laboratory

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

Scott, Stephen L; Vallee, Geoffroy R; Naughton, III, Thomas J

2010-01-01

System-level virtualization is today enjoying a rebirth as a technique to effectively share what were then considered large computing resources to subsequently fade from the spotlight as individual workstations gained in popularity with a one machine - one user approach. One reason for this resurgence is that the simple workstation has grown in capability to rival that of anything available in the past. Thus, computing centers are again looking at the price/performance benefit of sharing that single computing box via server consolidation. However, industry is only concentrating on the benefits of using virtualization for server consolidation (enterprise computing) whereas ourmore » interest is in leveraging virtualization to advance high-performance computing (HPC). While these two interests may appear to be orthogonal, one consolidating multiple applications and users on a single machine while the other requires all the power from many machines to be dedicated solely to its purpose, we propose that virtualization does provide attractive capabilities that may be exploited to the benefit of HPC interests. This does raise the two fundamental questions of: is the concept of virtualization (a machine sharing technology) really suitable for HPC and if so, how does one go about leveraging these virtualization capabilities for the benefit of HPC. To address these questions, this document presents ongoing studies on the usage of system-level virtualization in a HPC context. These studies include an analysis of the benefits of system-level virtualization for HPC, a presentation of research efforts based on virtualization for system availability, and a presentation of research efforts for the management of virtual systems. The basis for this document was material presented by Stephen L. Scott at the Collaborative and Grid Computing Technologies meeting held in Cancun, Mexico on April 12-14, 2007.« less

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Technical Reports Server (NTRS)

Votava, Petr; Michaelis, Andrew; Spaulding, Ryan; Becker, Jeffrey C.

2016-01-01

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We believe this is an important step towards seamless process deployment in heterogeneous environments that will enhance community access to NASA data and tools in a scalable way, promote software reuse, and improve reproducibility of scientific results.

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Astrophysics Data System (ADS)

Votava, P.; Michaelis, A.; Spaulding, R.; Becker, J. C.

2016-12-01

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We believe this is an important step towards seamless process deployment in heterogeneous environments that will enhance community access to NASA data and tools in a scalable way, promote software reuse, and improve reproducibility of scientific results.

Porting Gravitational Wave Signal Extraction to Parallel Virtual Machine (PVM)

NASA Technical Reports Server (NTRS)

Thirumalainambi, Rajkumar; Thompson, David E.; Redmon, Jeffery

2009-01-01

Laser Interferometer Space Antenna (LISA) is a planned NASA-ESA mission to be launched around 2012. The Gravitational Wave detection is fundamentally the determination of frequency, source parameters, and waveform amplitude derived in a specific order from the interferometric time-series of the rotating LISA spacecrafts. The LISA Science Team has developed a Mock LISA Data Challenge intended to promote the testing of complicated nested search algorithms to detect the 100-1 millihertz frequency signals at amplitudes of 10E-21. However, it has become clear that, sequential search of the parameters is very time consuming and ultra-sensitive; hence, a new strategy has been developed. Parallelization of existing sequential search algorithms of Gravitational Wave signal identification consists of decomposing sequential search loops, beginning with outermost loops and working inward. In this process, the main challenge is to detect interdependencies among loops and partitioning the loops so as to preserve concurrency. Existing parallel programs are based upon either shared memory or distributed memory paradigms. In PVM, master and node programs are used to execute parallelization and process spawning. The PVM can handle process management and process addressing schemes using a virtual machine configuration. The task scheduling and the messaging and signaling can be implemented efficiently for the LISA Gravitational Wave search process using a master and 6 nodes. This approach is accomplished using a server that is available at NASA Ames Research Center, and has been dedicated to the LISA Data Challenge Competition. Historically, gravitational wave and source identification parameters have taken around 7 days in this dedicated single thread Linux based server. Using PVM approach, the parameter extraction problem can be reduced to within a day. The low frequency computation and a proxy signal-to-noise ratio are calculated in separate nodes that are controlled by the master using message and vector of data passing. The message passing among nodes follows a pattern of synchronous and asynchronous send-and-receive protocols. The communication model and the message buffers are allocated dynamically to address rapid search of gravitational wave source information in the Mock LISA data sets.

An element search ant colony technique for solving virtual machine placement problem

NASA Astrophysics Data System (ADS)

Srija, J.; Rani John, Rose; Kanaga, Grace Mary, Dr.

2017-09-01

The data centres in the cloud environment play a key role in providing infrastructure for ubiquitous computing, pervasive computing, mobile computing etc. This computing technique tries to utilize the available resources in order to provide services. Hence maintaining the resource utilization without wastage of power consumption has become a challenging task for the researchers. In this paper we propose the direct guidance ant colony system for effective mapping of virtual machines to the physical machine with maximal resource utilization and minimal power consumption. The proposed algorithm has been compared with the existing ant colony approach which is involved in solving virtual machine placement problem and thus the proposed algorithm proves to provide better result than the existing technique.

Lightweight scheduling of elastic analysis containers in a competitive cloud environment: a Docked Analysis Facility for ALICE

NASA Astrophysics Data System (ADS)

Berzano, D.; Blomer, J.; Buncic, P.; Charalampidis, I.; Ganis, G.; Meusel, R.

2015-12-01

During the last years, several Grid computing centres chose virtualization as a better way to manage diverse use cases with self-consistent environments on the same bare infrastructure. The maturity of control interfaces (such as OpenNebula and OpenStack) opened the possibility to easily change the amount of resources assigned to each use case by simply turning on and off virtual machines. Some of those private clouds use, in production, copies of the Virtual Analysis Facility, a fully virtualized and self-contained batch analysis cluster capable of expanding and shrinking automatically upon need: however, resources starvation occurs frequently as expansion has to compete with other virtual machines running long-living batch jobs. Such batch nodes cannot relinquish their resources in a timely fashion: the more jobs they run, the longer it takes to drain them and shut off, and making one-job virtual machines introduces a non-negligible virtualization overhead. By improving several components of the Virtual Analysis Facility we have realized an experimental “Docked” Analysis Facility for ALICE, which leverages containers instead of virtual machines for providing performance and security isolation. We will present the techniques we have used to address practical problems, such as software provisioning through CVMFS, as well as our considerations on the maturity of containers for High Performance Computing. As the abstraction layer is thinner, our Docked Analysis Facilities may feature a more fine-grained sizing, down to single-job node containers: we will show how this approach will positively impact automatic cluster resizing by deploying lightweight pilot containers instead of replacing central queue polls.

Performance analysis of the Microsoft Kinect sensor for 2D Simultaneous Localization and Mapping (SLAM) techniques.

PubMed

Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

2014-12-05

This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks.

Performance Analysis of the Microsoft Kinect Sensor for 2D Simultaneous Localization and Mapping (SLAM) Techniques

PubMed Central

Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

2014-01-01

This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks. PMID:25490595

Efficient Checkpointing of Virtual Machines using Virtual Machine Introspection

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

Aderholdt, Ferrol; Han, Fang; Scott, Stephen L

Cloud Computing environments rely heavily on system-level virtualization. This is due to the inherent benefits of virtualization including fault tolerance through checkpoint/restart (C/R) mechanisms. Because clouds are the abstraction of large data centers and large data centers have a higher potential for failure, it is imperative that a C/R mechanism for such an environment provide minimal latency as well as a small checkpoint file size. Recently, there has been much research into C/R with respect to virtual machines (VM) providing excellent solutions to reduce either checkpoint latency or checkpoint file size. However, these approaches do not provide both. This papermore » presents a method of checkpointing VMs by utilizing virtual machine introspection (VMI). Through the usage of VMI, we are able to determine which pages of memory within the guest are used or free and are better able to reduce the amount of pages written to disk during a checkpoint. We have validated this work by using various benchmarks to measure the latency along with the checkpoint size. With respect to checkpoint file size, our approach results in file sizes within 24% or less of the actual used memory within the guest. Additionally, the checkpoint latency of our approach is up to 52% faster than KVM s default method.« less

MISR Center Block Time Tool

Atmospheric Science Data Center

2013-04-01

  MISR Center Block Time Tool The misr_time tool calculates the block center times for MISR Level 1B2 files. This is ... version of the IDL package or by using the IDL Virtual Machine application. The IDL Virtual Machine is bundled with IDL and is ...

System-Level Virtualization for High Performance Computing

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

Vallee, Geoffroy R; Naughton, III, Thomas J; Engelmann, Christian

2008-01-01

System-level virtualization has been a research topic since the 70's but regained popularity during the past few years because of the availability of efficient solution such as Xen and the implementation of hardware support in commodity processors (e.g. Intel-VT, AMD-V). However, a majority of system-level virtualization projects is guided by the server consolidation market. As a result, current virtualization solutions appear to not be suitable for high performance computing (HPC) which is typically based on large-scale systems. On another hand there is significant interest in exploiting virtual machines (VMs) within HPC for a number of other reasons. By virtualizing themore » machine, one is able to run a variety of operating systems and environments as needed by the applications. Virtualization allows users to isolate workloads, improving security and reliability. It is also possible to support non-native environments and/or legacy operating environments through virtualization. In addition, it is possible to balance work loads, use migration techniques to relocate applications from failing machines, and isolate fault systems for repair. This document presents the challenges for the implementation of a system-level virtualization solution for HPC. It also presents a brief survey of the different approaches and techniques to address these challenges.« less

The Machine / Job Features Mechanism

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

Alef, M.; Cass, T.; Keijser, J. J.

Within the HEPiX virtualization group and the Worldwide LHC Computing Grid’s Machine/Job Features Task Force, a mechanism has been developed which provides access to detailed information about the current host and the current job to the job itself. This allows user payloads to access meta information, independent of the current batch system or virtual machine model. The information can be accessed either locally via the filesystem on a worker node, or remotely via HTTP(S) from a webserver. This paper describes the final version of the specification from 2016 which was published as an HEP Software Foundation technical note, and themore » design of the implementations of this version for batch and virtual machine platforms. We discuss early experiences with these implementations and how they can be exploited by experiment frameworks.« less

The machine/job features mechanism

NASA Astrophysics Data System (ADS)

Alef, M.; Cass, T.; Keijser, J. J.; McNab, A.; Roiser, S.; Schwickerath, U.; Sfiligoi, I.

2017-10-01

Within the HEPiX virtualization group and the Worldwide LHC Computing Grid’s Machine/Job Features Task Force, a mechanism has been developed which provides access to detailed information about the current host and the current job to the job itself. This allows user payloads to access meta information, independent of the current batch system or virtual machine model. The information can be accessed either locally via the filesystem on a worker node, or remotely via HTTP(S) from a webserver. This paper describes the final version of the specification from 2016 which was published as an HEP Software Foundation technical note, and the design of the implementations of this version for batch and virtual machine platforms. We discuss early experiences with these implementations and how they can be exploited by experiment frameworks.

A three phase optimization method for precopy based VM live migration.

PubMed

Sharma, Sangeeta; Chawla, Meenu

2016-01-01

Virtual machine live migration is a method of moving virtual machine across hosts within a virtualized datacenter. It provides significant benefits for administrator to manage datacenter efficiently. It reduces service interruption by transferring the virtual machine without stopping at source. Transfer of large number of virtual machine memory pages results in long migration time as well as downtime, which also affects the overall system performance. This situation becomes unbearable when migration takes place over slower network or a long distance migration within a cloud. In this paper, precopy based virtual machine live migration method is thoroughly analyzed to trace out the issues responsible for its performance drops. In order to address these issues, this paper proposes three phase optimization (TPO) method. It works in three phases as follows: (i) reduce the transfer of memory pages in first phase, (ii) reduce the transfer of duplicate pages by classifying frequently and non-frequently updated pages, and (iii) reduce the data sent in last iteration of migration by applying the simple RLE compression technique. As a result, each phase significantly reduces total pages transferred, total migration time and downtime respectively. The proposed TPO method is evaluated using different representative workloads on a Xen virtualized environment. Experimental results show that TPO method reduces total pages transferred by 71 %, total migration time by 70 %, downtime by 3 % for higher workload, and it does not impose significant overhead as compared to traditional precopy method. Comparison of TPO method with other methods is also done for supporting and showing its effectiveness. TPO method and precopy methods are also tested at different number of iterations. The TPO method gives better performance even with less number of iterations.

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.

HTTM - Design and Implementation of a Type-2 Hypervisor for MIPS64 Based Systems

NASA Astrophysics Data System (ADS)

Ain, Qurrat ul; Anwar, Usama; Mehmood, Muhammad Amir; Waheed, Abdul

2017-01-01

Virtualization has emerged as an attractive software solution for many problems in server domain. Recently, it has started to enrich embedded systems domain by offering features such as hardware consolidation, security, and isolation. Our objective is to bring virtualization to high-end MIPS64 based systems, such as network routers, switches, wireless base station, etc. For this purpose a Type-2 hypervisor is a viable software solution which is easy to deploy and requires no changes in host system. In this paper we present the internal design HTTM -A Type-2 hypervisor for MIPS64 based systems and demonstrate its functional correctness by using Linux Testing Project (LTP) tests. Finally, we performed LMbench tests for performance evaluation.

Optimizing Virtual Network Functions Placement in Virtual Data Center Infrastructure Using Machine Learning

NASA Astrophysics Data System (ADS)

Bolodurina, I. P.; Parfenov, D. I.

2018-01-01

We have elaborated a neural network model of virtual network flow identification based on the statistical properties of flows circulating in the network of the data center and characteristics that describe the content of packets transmitted through network objects. This enabled us to establish the optimal set of attributes to identify virtual network functions. We have established an algorithm for optimizing the placement of virtual data functions using the data obtained in our research. Our approach uses a hybrid method of visualization using virtual machines and containers, which enables to reduce the infrastructure load and the response time in the network of the virtual data center. The algorithmic solution is based on neural networks, which enables to scale it at any number of the network function copies.

Protection of Mission-Critical Applications from Untrusted Execution Environment: Resource Efficient Replication and Migration of Virtual Machines

DTIC Science & Technology

2015-09-28

the performance of log-and- replay can degrade significantly for VMs configured with multiple virtual CPUs, since the shared memory communication...whether based on checkpoint replication or log-and- replay , existing HA ap- proaches use in- memory backups. The backup VM sits in the memory of a...efficiently. 15. SUBJECT TERMS High-availability virtual machines, live migration, memory and traffic overheads, application suspension, Java

RHE: A JVM Courseware

ERIC Educational Resources Information Center

Liu, S.; Tang, J.; Deng, C.; Li, X.-F.; Gaudiot, J.-L.

2011-01-01

Java Virtual Machine (JVM) education has become essential in training embedded software engineers as well as virtual machine researchers and practitioners. However, due to the lack of suitable instructional tools, it is difficult for students to obtain any kind of hands-on experience and to attain any deep understanding of JVM design. To address…

CFCC: A Covert Flows Confinement Mechanism for Virtual Machine Coalitions

NASA Astrophysics Data System (ADS)

Cheng, Ge; Jin, Hai; Zou, Deqing; Shi, Lei; Ohoussou, Alex K.

Normally, virtualization technology is adopted to construct the infrastructure of cloud computing environment. Resources are managed and organized dynamically through virtual machine (VM) coalitions in accordance with the requirements of applications. Enforcing mandatory access control (MAC) on the VM coalitions will greatly improve the security of VM-based cloud computing. However, the existing MAC models lack the mechanism to confine the covert flows and are hard to eliminate the convert channels. In this paper, we propose a covert flows confinement mechanism for virtual machine coalitions (CFCC), which introduces dynamic conflicts of interest based on the activity history of VMs, each of which is attached with a label. The proposed mechanism can be used to confine the covert flows between VMs in different coalitions. We implement a prototype system, evaluate its performance, and show that our mechanism is practical.

A comparative analysis of dynamic grids vs. virtual grids using the A3pviGrid framework.

PubMed

Shankaranarayanan, Avinas; Amaldas, Christine

2010-11-01

With the proliferation of Quad/Multi-core micro-processors in mainstream platforms such as desktops and workstations; a large number of unused CPU cycles can be utilized for running virtual machines (VMs) as dynamic nodes in distributed environments. Grid services and its service oriented business broker now termed cloud computing could deploy image based virtualization platforms enabling agent based resource management and dynamic fault management. In this paper we present an efficient way of utilizing heterogeneous virtual machines on idle desktops as an environment for consumption of high performance grid services. Spurious and exponential increases in the size of the datasets are constant concerns in medical and pharmaceutical industries due to the constant discovery and publication of large sequence databases. Traditional algorithms are not modeled at handing large data sizes under sudden and dynamic changes in the execution environment as previously discussed. This research was undertaken to compare our previous results with running the same test dataset with that of a virtual Grid platform using virtual machines (Virtualization). The implemented architecture, A3pviGrid utilizes game theoretic optimization and agent based team formation (Coalition) algorithms to improve upon scalability with respect to team formation. Due to the dynamic nature of distributed systems (as discussed in our previous work) all interactions were made local within a team transparently. This paper is a proof of concept of an experimental mini-Grid test-bed compared to running the platform on local virtual machines on a local test cluster. This was done to give every agent its own execution platform enabling anonymity and better control of the dynamic environmental parameters. We also analyze performance and scalability of Blast in a multiple virtual node setup and present our findings. This paper is an extension of our previous research on improving the BLAST application framework using dynamic Grids on virtualization platforms such as the virtual box.

Impact of Machine Virtualization on Timing Precision for Performance-critical Tasks

NASA Astrophysics Data System (ADS)

Karpov, Kirill; Fedotova, Irina; Siemens, Eduard

2017-07-01

In this paper we present a measurement study to characterize the impact of hardware virtualization on basic software timing, as well as on precise sleep operations of an operating system. We investigated how timer hardware is shared among heavily CPU-, I/O- and Network-bound tasks on a virtual machine as well as on the host machine. VMware ESXi and QEMU/KVM have been chosen as commonly used examples of hypervisor- and host-based models. Based on statistical parameters of retrieved distributions, our results provide a very good estimation of timing behavior. It is essential for real-time and performance-critical applications such as image processing or real-time control.

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

Background A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. Results The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. Conclusions With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites. PMID:21266047

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

Nemoto, Kiyotaka; Dan, Ippeita; Rorden, Christopher; Ohnishi, Takashi; Tsuzuki, Daisuke; Okamoto, Masako; Yamashita, Fumio; Asada, Takashi

2011-01-25

A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

Name-Based Address Mapping for Virtual Private Networks

NASA Astrophysics Data System (ADS)

Surányi, Péter; Shinjo, Yasushi; Kato, Kazuhiko

IPv4 private addresses are commonly used in local area networks (LANs). With the increasing popularity of virtual private networks (VPNs), it has become common that a user connects to multiple LANs at the same time. However, private address ranges for LANs frequently overlap. In such cases, existing systems do not allow the user to access the resources on all LANs at the same time. In this paper, we propose name-based address mapping for VPNs, a novel method that allows connecting to hosts through multiple VPNs at the same time, even when the address ranges of the VPNs overlap. In name-based address mapping, rather than using the IP addresses used on the LANs (the real addresses), we assign a unique virtual address to each remote host based on its domain name. The local host uses the virtual addresses to communicate with remote hosts. We have implemented name-based address mapping for layer 3 OpenVPN connections on Linux and measured its performance. The communication overhead of our system is less than 1.5% for throughput and less than 0.2ms for each name resolution.

Software architecture standard for simulation virtual machine, version 2.0

NASA Technical Reports Server (NTRS)

Sturtevant, Robert; Wessale, William

1994-01-01

The Simulation Virtual Machine (SBM) is an Ada architecture which eases the effort involved in the real-time software maintenance and sustaining engineering. The Software Architecture Standard defines the infrastructure which all the simulation models are built from. SVM was developed for and used in the Space Station Verification and Training Facility.

Cloud services for the Fermilab scientific stakeholders

DOE PAGES

Timm, S.; Garzoglio, G.; Mhashilkar, P.; ...

2015-12-23

As part of the Fermilab/KISTI cooperative research project, Fermilab has successfully run an experimental simulation workflow at scale on a federation of Amazon Web Services (AWS), FermiCloud, and local FermiGrid resources. We used the CernVM-FS (CVMFS) file system to deliver the application software. We established Squid caching servers in AWS as well, using the Shoal system to let each individual virtual machine find the closest squid server. We also developed an automatic virtual machine conversion system so that we could transition virtual machines made on FermiCloud to Amazon Web Services. We used this system to successfully run a cosmic raymore » simulation of the NOvA detector at Fermilab, making use of both AWS spot pricing and network bandwidth discounts to minimize the cost. On FermiCloud we also were able to run the workflow at the scale of 1000 virtual machines, using a private network routable inside of Fermilab. As a result, we present in detail the technological improvements that were used to make this work a reality.« less

Cloud services for the Fermilab scientific stakeholders

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

Timm, S.; Garzoglio, G.; Mhashilkar, P.

As part of the Fermilab/KISTI cooperative research project, Fermilab has successfully run an experimental simulation workflow at scale on a federation of Amazon Web Services (AWS), FermiCloud, and local FermiGrid resources. We used the CernVM-FS (CVMFS) file system to deliver the application software. We established Squid caching servers in AWS as well, using the Shoal system to let each individual virtual machine find the closest squid server. We also developed an automatic virtual machine conversion system so that we could transition virtual machines made on FermiCloud to Amazon Web Services. We used this system to successfully run a cosmic raymore » simulation of the NOvA detector at Fermilab, making use of both AWS spot pricing and network bandwidth discounts to minimize the cost. On FermiCloud we also were able to run the workflow at the scale of 1000 virtual machines, using a private network routable inside of Fermilab. As a result, we present in detail the technological improvements that were used to make this work a reality.« less

Runtime Performance and Virtual Network Control Alternatives in VM-Based High-Fidelity Network Simulations

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

Yoginath, Srikanth B; Perumalla, Kalyan S; Henz, Brian J

2012-01-01

In prior work (Yoginath and Perumalla, 2011; Yoginath, Perumalla and Henz, 2012), the motivation, challenges and issues were articulated in favor of virtual time ordering of Virtual Machines (VMs) in network simulations hosted on multi-core machines. Two major components in the overall virtualization challenge are (1) virtual timeline establishment and scheduling of VMs, and (2) virtualization of inter-VM communication. Here, we extend prior work by presenting scaling results for the first component, with experiment results on up to 128 VMs scheduled in virtual time order on a single 12-core host. We also explore the solution space of design alternatives formore » the second component, and present performance results from a multi-threaded, multi-queue implementation of inter-VM network control for synchronized execution with VM scheduling, incorporated in our NetWarp simulation system.« less

Recent advances in PC-Linux systems for electronic structure computations by optimized compilers and numerical libraries.

PubMed

Yu, Jen-Shiang K; Yu, Chin-Hui

2002-01-01

One of the most frequently used packages for electronic structure research, GAUSSIAN 98, is compiled on Linux systems with various hardware configurations, including AMD Athlon (with the "Thunderbird" core), AthlonMP, and AthlonXP (with the "Palomino" core) systems as well as the Intel Pentium 4 (with the "Willamette" core) machines. The default PGI FORTRAN compiler (pgf77) and the Intel FORTRAN compiler (ifc) are respectively employed with different architectural optimization options to compile GAUSSIAN 98 and test the performance improvement. In addition to the BLAS library included in revision A.11 of this package, the Automatically Tuned Linear Algebra Software (ATLAS) library is linked against the binary executables to improve the performance. Various Hartree-Fock, density-functional theories, and the MP2 calculations are done for benchmarking purposes. It is found that the combination of ifc with ATLAS library gives the best performance for GAUSSIAN 98 on all of these PC-Linux computers, including AMD and Intel CPUs. Even on AMD systems, the Intel FORTRAN compiler invariably produces binaries with better performance than pgf77. The enhancement provided by the ATLAS library is more significant for post-Hartree-Fock calculations. The performance on one single CPU is potentially as good as that on an Alpha 21264A workstation or an SGI supercomputer. The floating-point marks by SpecFP2000 have similar trends to the results of GAUSSIAN 98 package.

High speed real-time wavefront processing system for a solid-state laser system

NASA Astrophysics Data System (ADS)

Liu, Yuan; Yang, Ping; Chen, Shanqiu; Ma, Lifang; Xu, Bing

2008-03-01

A high speed real-time wavefront processing system for a solid-state laser beam cleanup system has been built. This system consists of a core2 Industrial PC (IPC) using Linux and real-time Linux (RT-Linux) operation system (OS), a PCI image grabber, a D/A card. More often than not, the phase aberrations of the output beam from solid-state lasers vary fast with intracavity thermal effects and environmental influence. To compensate the phase aberrations of solid-state lasers successfully, a high speed real-time wavefront processing system is presented. Compared to former systems, this system can improve the speed efficiently. In the new system, the acquisition of image data, the output of control voltage data and the implementation of reconstructor control algorithm are treated as real-time tasks in kernel-space, the display of wavefront information and man-machine conversation are treated as non real-time tasks in user-space. The parallel processing of real-time tasks in Symmetric Multi Processors (SMP) mode is the main strategy of improving the speed. In this paper, the performance and efficiency of this wavefront processing system are analyzed. The opened-loop experimental results show that the sampling frequency of this system is up to 3300Hz, and this system can well deal with phase aberrations from solid-state lasers.

Web Service Distributed Management Framework for Autonomic Server Virtualization

NASA Astrophysics Data System (ADS)

Solomon, Bogdan; Ionescu, Dan; Litoiu, Marin; Mihaescu, Mircea

Virtualization for the x86 platform has imposed itself recently as a new technology that can improve the usage of machines in data centers and decrease the cost and energy of running a high number of servers. Similar to virtualization, autonomic computing and more specifically self-optimization, aims to improve server farm usage through provisioning and deprovisioning of instances as needed by the system. Autonomic systems are able to determine the optimal number of server machines - real or virtual - to use at a given time, and add or remove servers from a cluster in order to achieve optimal usage. While provisioning and deprovisioning of servers is very important, the way the autonomic system is built is also very important, as a robust and open framework is needed. One such management framework is the Web Service Distributed Management (WSDM) system, which is an open standard of the Organization for the Advancement of Structured Information Standards (OASIS). This paper presents an open framework built on top of the WSDM specification, which aims to provide self-optimization for applications servers residing on virtual machines.

Virtual Machine Language Controls Remote Devices

NASA Technical Reports Server (NTRS)

2014-01-01

Kennedy Space Center worked with Blue Sun Enterprises, based in Boulder, Colorado, to enhance the company's virtual machine language (VML) to control the instruments on the Regolith and Environment Science and Oxygen and Lunar Volatiles Extraction mission. Now the NASA-improved VML is available for crewed and uncrewed spacecraft, and has potential applications on remote systems such as weather balloons, unmanned aerial vehicles, and submarines.

Human-machine interface for a VR-based medical imaging environment

NASA Astrophysics Data System (ADS)

Krapichler, Christian; Haubner, Michael; Loesch, Andreas; Lang, Manfred K.; Englmeier, Karl-Hans

1997-05-01

Modern 3D scanning techniques like magnetic resonance imaging (MRI) or computed tomography (CT) produce high- quality images of the human anatomy. Virtual environments open new ways to display and to analyze those tomograms. Compared with today's inspection of 2D image sequences, physicians are empowered to recognize spatial coherencies and examine pathological regions more facile, diagnosis and therapy planning can be accelerated. For that purpose a powerful human-machine interface is required, which offers a variety of tools and features to enable both exploration and manipulation of the 3D data. Man-machine communication has to be intuitive and efficacious to avoid long accustoming times and to enhance familiarity with and acceptance of the interface. Hence, interaction capabilities in virtual worlds should be comparable to those in the real work to allow utilization of our natural experiences. In this paper the integration of hand gestures and visual focus, two important aspects in modern human-computer interaction, into a medical imaging environment is shown. With the presented human- machine interface, including virtual reality displaying and interaction techniques, radiologists can be supported in their work. Further, virtual environments can even alleviate communication between specialists from different fields or in educational and training applications.

Dynamically allocated virtual clustering management system

NASA Astrophysics Data System (ADS)

Marcus, Kelvin; Cannata, Jess

2013-05-01

The U.S Army Research Laboratory (ARL) has built a "Wireless Emulation Lab" to support research in wireless mobile networks. In our current experimentation environment, our researchers need the capability to run clusters of heterogeneous nodes to model emulated wireless tactical networks where each node could contain a different operating system, application set, and physical hardware. To complicate matters, most experiments require the researcher to have root privileges. Our previous solution of using a single shared cluster of statically deployed virtual machines did not sufficiently separate each user's experiment due to undesirable network crosstalk, thus only one experiment could be run at a time. In addition, the cluster did not make efficient use of our servers and physical networks. To address these concerns, we created the Dynamically Allocated Virtual Clustering management system (DAVC). This system leverages existing open-source software to create private clusters of nodes that are either virtual or physical machines. These clusters can be utilized for software development, experimentation, and integration with existing hardware and software. The system uses the Grid Engine job scheduler to efficiently allocate virtual machines to idle systems and networks. The system deploys stateless nodes via network booting. The system uses 802.1Q Virtual LANs (VLANs) to prevent experimentation crosstalk and to allow for complex, private networks eliminating the need to map each virtual machine to a specific switch port. The system monitors the health of the clusters and the underlying physical servers and it maintains cluster usage statistics for historical trends. Users can start private clusters of heterogeneous nodes with root privileges for the duration of the experiment. Users also control when to shutdown their clusters.

Open multi-agent control architecture to support virtual-reality-based man-machine interfaces

NASA Astrophysics Data System (ADS)

Freund, Eckhard; Rossmann, Juergen; Brasch, Marcel

2001-10-01

Projective Virtual Reality is a new and promising approach to intuitively operable man machine interfaces for the commanding and supervision of complex automation systems. The user interface part of Projective Virtual Reality heavily builds on latest Virtual Reality techniques, a task deduction component and automatic action planning capabilities. In order to realize man machine interfaces for complex applications, not only the Virtual Reality part has to be considered but also the capabilities of the underlying robot and automation controller are of great importance. This paper presents a control architecture that has proved to be an ideal basis for the realization of complex robotic and automation systems that are controlled by Virtual Reality based man machine interfaces. The architecture does not just provide a well suited framework for the real-time control of a multi robot system but also supports Virtual Reality metaphors and augmentations which facilitate the user's job to command and supervise a complex system. The developed control architecture has already been used for a number of applications. Its capability to integrate sensor information from sensors of different levels of abstraction in real-time helps to make the realized automation system very responsive to real world changes. In this paper, the architecture will be described comprehensively, its main building blocks will be discussed and one realization that is built based on an open source real-time operating system will be presented. The software design and the features of the architecture which make it generally applicable to the distributed control of automation agents in real world applications will be explained. Furthermore its application to the commanding and control of experiments in the Columbus space laboratory, the European contribution to the International Space Station (ISS), is only one example which will be described.

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Terra Harvest software architecture

NASA Astrophysics Data System (ADS)

Humeniuk, Dave; Klawon, Kevin

2012-06-01

Under the Terra Harvest Program, the DIA has the objective of developing a universal Controller for the Unattended Ground Sensor (UGS) community. The mission is to define, implement, and thoroughly document an open architecture that universally supports UGS missions, integrating disparate systems, peripherals, etc. The Controller's inherent interoperability with numerous systems enables the integration of both legacy and future UGS System (UGSS) components, while the design's open architecture supports rapid third-party development to ensure operational readiness. The successful accomplishment of these objectives by the program's Phase 3b contractors is demonstrated via integration of the companies' respective plug-'n'-play contributions that include controllers, various peripherals, such as sensors, cameras, etc., and their associated software drivers. In order to independently validate the Terra Harvest architecture, L-3 Nova Engineering, along with its partner, the University of Dayton Research Institute, is developing the Terra Harvest Open Source Environment (THOSE), a Java Virtual Machine (JVM) running on an embedded Linux Operating System. The Use Cases on which the software is developed support the full range of UGS operational scenarios such as remote sensor triggering, image capture, and data exfiltration. The Team is additionally developing an ARM microprocessor-based evaluation platform that is both energy-efficient and operationally flexible. The paper describes the overall THOSE architecture, as well as the design decisions for some of the key software components. Development process for THOSE is discussed as well.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

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

The Implications of Virtual Machine Introspection for Digital Forensics on Nonquiescent Virtual Machines

DTIC Science & Technology

2011-06-01

metacity [ 2788] gnome-panel [ 2790] nautilus [ 2794] bonobo -activati [ 2797] gnome-vfs-daemo [ 2799] eggcups [ 2800] gnome-volume-ma [ 2809] bt...xrdb [ 2784] metacity [ 2788] gnome-panel [ 2790] nautilus [ 2794] bonobo -activati [ 2797] gnome-vfs-daemo [ 2799] eggcups [ 2800] gnome-volume...gnome-keyring-d [ 2764] gnome-settings- [ 2780] xrdb [ 2784] metacity [ 2788] gnome-panel [ 2790] nautilus [ 2794] bonobo -activati [ 2797] gnome

Slot Machines: Pursuing Responsible Gaming Practices for Virtual Reels and Near Misses

ERIC Educational Resources Information Center

Harrigan, Kevin A.

2009-01-01

Since 1983, slot machines in North America have used a computer and virtual reels to determine the odds. Since at least 1988, a technique called clustering has been used to create a high number of near misses, failures that are close to wins. The result is that what the player sees does not represent the underlying probabilities and randomness,…

Virtual screening by a new Clustering-based Weighted Similarity Extreme Learning Machine approach

PubMed Central

Kudisthalert, Wasu

2018-01-01

Machine learning techniques are becoming popular in virtual screening tasks. One of the powerful machine learning algorithms is Extreme Learning Machine (ELM) which has been applied to many applications and has recently been applied to virtual screening. We propose the Weighted Similarity ELM (WS-ELM) which is based on a single layer feed-forward neural network in a conjunction of 16 different similarity coefficients as activation function in the hidden layer. It is known that the performance of conventional ELM is not robust due to random weight selection in the hidden layer. Thus, we propose a Clustering-based WS-ELM (CWS-ELM) that deterministically assigns weights by utilising clustering algorithms i.e. k-means clustering and support vector clustering. The experiments were conducted on one of the most challenging datasets–Maximum Unbiased Validation Dataset–which contains 17 activity classes carefully selected from PubChem. The proposed algorithms were then compared with other machine learning techniques such as support vector machine, random forest, and similarity searching. The results show that CWS-ELM in conjunction with support vector clustering yields the best performance when utilised together with Sokal/Sneath(1) coefficient. Furthermore, ECFP_6 fingerprint presents the best results in our framework compared to the other types of fingerprints, namely ECFP_4, FCFP_4, and FCFP_6. PMID:29652912

Iris: Constructing and Analyzing Spectral Energy Distributions with the Virtual Observatory

NASA Astrophysics Data System (ADS)

Laurino, O.; Budynkiewicz, J.; Busko, I.; Cresitello-Dittmar, M.; D'Abrusco, R.; Doe, S.; Evans, J.; Pevunova, O.

2014-05-01

We present Iris 2.0, the latest release of the Virtual Astronomical Observatory application for building and analyzing Spectral Energy Distributions (SEDs). With Iris, users may read in and display SEDs inspect and edit any selection of SED data, fit models to SEDs in arbitrary spectral ranges, and calculate confidence limits on best-fit parameters. SED data may be loaded into the application from VOTable and FITS files compliant with the International Virtual Observatoy Alliance interoperable data models, or retrieved directly from NED or the Italian Space Agency Science Data Center; data in non-standard formats may also be converted within the application. Users may seamlessy exchange data between Iris and other Virtual Observatoy tools using the Simple Application Messaging Protocol. Iris 2.0 also provides a tool for redshifting, interpolating, and measuring integratd fluxes, and allows simple aperture corrections for individual points and SED segments. Custom Python functions, template models and template libraries may be imported into Iris for fitting SEDs. Iris may be extended through Java plugins; users can install third-party packages, or develop their own plugin using Iris' Software Development Kit. Iris 2.0 is available for Linux and Mac OS X systems.

An Analysis of Hardware-Assisted Virtual Machine Based Rootkits

DTIC Science & Technology

2014-06-01

certain aspects of TPM implementation just to name a few. HyperWall is an architecture proposed by Szefer and Lee to protect guest VMs from...DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) The use of virtual machine (VM) technology has expanded rapidly since AMD and Intel implemented ...Intel VT-x implementations of Blue Pill to identify commonalities in the respective versions’ attack methodologies from both a functional and technical

Active tactile exploration using a brain-machine-brain interface.

PubMed

O'Doherty, Joseph E; Lebedev, Mikhail A; Ifft, Peter J; Zhuang, Katie Z; Shokur, Solaiman; Bleuler, Hannes; Nicolelis, Miguel A L

2011-10-05

Brain-machine interfaces use neuronal activity recorded from the brain to establish direct communication with external actuators, such as prosthetic arms. It is hoped that brain-machine interfaces can be used to restore the normal sensorimotor functions of the limbs, but so far they have lacked tactile sensation. Here we report the operation of a brain-machine-brain interface (BMBI) that both controls the exploratory reaching movements of an actuator and allows signalling of artificial tactile feedback through intracortical microstimulation (ICMS) of the primary somatosensory cortex. Monkeys performed an active exploration task in which an actuator (a computer cursor or a virtual-reality arm) was moved using a BMBI that derived motor commands from neuronal ensemble activity recorded in the primary motor cortex. ICMS feedback occurred whenever the actuator touched virtual objects. Temporal patterns of ICMS encoded the artificial tactile properties of each object. Neuronal recordings and ICMS epochs were temporally multiplexed to avoid interference. Two monkeys operated this BMBI to search for and distinguish one of three visually identical objects, using the virtual-reality arm to identify the unique artificial texture associated with each. These results suggest that clinical motor neuroprostheses might benefit from the addition of ICMS feedback to generate artificial somatic perceptions associated with mechanical, robotic or even virtual prostheses.

Will Anything Useful Come Out of Virtual Reality? Examination of a Naval Application

DTIC Science & Technology

1993-05-01

The term virtual reality can encompass varying meanings, but some generally accepted attributes of a virtual environment are that it is immersive...technology, but at present there are few practical applications which are utilizing the broad range of virtual reality technology. This paper will discuss an...Operability, operator functions, Virtual reality , Man-machine interface, Decision aids/decision making, Decision support. ASW.

Migrating EO/IR sensors to cloud-based infrastructure as service architectures

NASA Astrophysics Data System (ADS)

Berglie, Stephen T.; Webster, Steven; May, Christopher M.

2014-06-01

The Night Vision Image Generator (NVIG), a product of US Army RDECOM CERDEC NVESD, is a visualization tool used widely throughout Army simulation environments to provide fully attributed synthesized, full motion video using physics-based sensor and environmental effects. The NVIG relies heavily on contemporary hardware-based acceleration and GPU processing techniques, which push the envelope of both enterprise and commodity-level hypervisor support for providing virtual machines with direct access to hardware resources. The NVIG has successfully been integrated into fully virtual environments where system architectures leverage cloudbased technologies to various extents in order to streamline infrastructure and service management. This paper details the challenges presented to engineers seeking to migrate GPU-bound processes, such as the NVIG, to virtual machines and, ultimately, Cloud-Based IAS architectures. In addition, it presents the path that led to success for the NVIG. A brief overview of Cloud-Based infrastructure management tool sets is provided, and several virtual desktop solutions are outlined. A discrimination is made between general purpose virtual desktop technologies compared to technologies that expose GPU-specific capabilities, including direct rendering and hard ware-based video encoding. Candidate hypervisor/virtual machine configurations that nominally satisfy the virtualized hardware-level GPU requirements of the NVIG are presented , and each is subsequently reviewed in light of its implications on higher-level Cloud management techniques. Implementation details are included from the hardware level, through the operating system, to the 3D graphics APls required by the NVIG and similar GPU-bound tools.

A Virtual Sensor for Online Fault Detection of Multitooth-Tools

PubMed Central

Bustillo, Andres; Correa, Maritza; Reñones, Anibal

2011-01-01

The installation of suitable sensors close to the tool tip on milling centres is not possible in industrial environments. It is therefore necessary to design virtual sensors for these machines to perform online fault detection in many industrial tasks. This paper presents a virtual sensor for online fault detection of multitooth tools based on a Bayesian classifier. The device that performs this task applies mathematical models that function in conjunction with physical sensors. Only two experimental variables are collected from the milling centre that performs the machining operations: the electrical power consumption of the feed drive and the time required for machining each workpiece. The task of achieving reliable signals from a milling process is especially complex when multitooth tools are used, because each kind of cutting insert in the milling centre only works on each workpiece during a certain time window. Great effort has gone into designing a robust virtual sensor that can avoid re-calibration due to, e.g., maintenance operations. The virtual sensor developed as a result of this research is successfully validated under real conditions on a milling centre used for the mass production of automobile engine crankshafts. Recognition accuracy, calculated with a k-fold cross validation, had on average 0.957 of true positives and 0.986 of true negatives. Moreover, measured accuracy was 98%, which suggests that the virtual sensor correctly identifies new cases. PMID:22163766

Modeling and Analysis Compute Environments, Utilizing Virtualization Technology in the Climate and Earth Systems Science domain

NASA Astrophysics Data System (ADS)

Michaelis, A.; Nemani, R. R.; Wang, W.; Votava, P.; Hashimoto, H.

2010-12-01

Given the increasing complexity of climate modeling and analysis tools, it is often difficult and expensive to build or recreate an exact replica of the software compute environment used in past experiments. With the recent development of new technologies for hardware virtualization, an opportunity exists to create full modeling, analysis and compute environments that are “archiveable”, transferable and may be easily shared amongst a scientific community or presented to a bureaucratic body if the need arises. By encapsulating and entire modeling and analysis environment in a virtual machine image, others may quickly gain access to the fully built system used in past experiments, potentially easing the task and reducing the costs of reproducing and verify past results produced by other researchers. Moreover, these virtual machine images may be used as a pedagogical tool for others that are interested in performing an academic exercise but don't yet possess the broad expertise required. We built two virtual machine images, one with the Community Earth System Model (CESM) and one with Weather Research Forecast Model (WRF), then ran several small experiments to assess the feasibility, performance overheads costs, reusability, and transferability. We present a list of the pros and cons as well as lessoned learned from utilizing virtualization technology in the climate and earth systems modeling domain.

A virtual sensor for online fault detection of multitooth-tools.

PubMed

Bustillo, Andres; Correa, Maritza; Reñones, Anibal

2011-01-01

The installation of suitable sensors close to the tool tip on milling centres is not possible in industrial environments. It is therefore necessary to design virtual sensors for these machines to perform online fault detection in many industrial tasks. This paper presents a virtual sensor for online fault detection of multitooth tools based on a bayesian classifier. The device that performs this task applies mathematical models that function in conjunction with physical sensors. Only two experimental variables are collected from the milling centre that performs the machining operations: the electrical power consumption of the feed drive and the time required for machining each workpiece. The task of achieving reliable signals from a milling process is especially complex when multitooth tools are used, because each kind of cutting insert in the milling centre only works on each workpiece during a certain time window. Great effort has gone into designing a robust virtual sensor that can avoid re-calibration due to, e.g., maintenance operations. The virtual sensor developed as a result of this research is successfully validated under real conditions on a milling centre used for the mass production of automobile engine crankshafts. Recognition accuracy, calculated with a k-fold cross validation, had on average 0.957 of true positives and 0.986 of true negatives. Moreover, measured accuracy was 98%, which suggests that the virtual sensor correctly identifies new cases.

A Comprehensive Availability Modeling and Analysis of a Virtualized Servers System Using Stochastic Reward Nets

PubMed Central

Kim, Dong Seong; Park, Jong Sou

2014-01-01

It is important to assess availability of virtualized systems in IT business infrastructures. Previous work on availability modeling and analysis of the virtualized systems used a simplified configuration and assumption in which only one virtual machine (VM) runs on a virtual machine monitor (VMM) hosted on a physical server. In this paper, we show a comprehensive availability model using stochastic reward nets (SRN). The model takes into account (i) the detailed failures and recovery behaviors of multiple VMs, (ii) various other failure modes and corresponding recovery behaviors (e.g., hardware faults, failure and recovery due to Mandelbugs and aging-related bugs), and (iii) dependency between different subcomponents (e.g., between physical host failure and VMM, etc.) in a virtualized servers system. We also show numerical analysis on steady state availability, downtime in hours per year, transaction loss, and sensitivity analysis. This model provides a new finding on how to increase system availability by combining both software rejuvenations at VM and VMM in a wise manner. PMID:25165732

Cloud-based opportunities in scientific computing: insights from processing Suomi National Polar-Orbiting Partnership (S-NPP) Direct Broadcast data

NASA Astrophysics Data System (ADS)

Evans, J. D.; Hao, W.; Chettri, S.

2013-12-01

The cloud is proving to be a uniquely promising platform for scientific computing. Our experience with processing satellite data using Amazon Web Services highlights several opportunities for enhanced performance, flexibility, and cost effectiveness in the cloud relative to traditional computing -- for example: - Direct readout from a polar-orbiting satellite such as the Suomi National Polar-Orbiting Partnership (S-NPP) requires bursts of processing a few times a day, separated by quiet periods when the satellite is out of receiving range. In the cloud, by starting and stopping virtual machines in minutes, we can marshal significant computing resources quickly when needed, but not pay for them when not needed. To take advantage of this capability, we are automating a data-driven approach to the management of cloud computing resources, in which new data availability triggers the creation of new virtual machines (of variable size and processing power) which last only until the processing workflow is complete. - 'Spot instances' are virtual machines that run as long as one's asking price is higher than the provider's variable spot price. Spot instances can greatly reduce the cost of computing -- for software systems that are engineered to withstand unpredictable interruptions in service (as occurs when a spot price exceeds the asking price). We are implementing an approach to workflow management that allows data processing workflows to resume with minimal delays after temporary spot price spikes. This will allow systems to take full advantage of variably-priced 'utility computing.' - Thanks to virtual machine images, we can easily launch multiple, identical machines differentiated only by 'user data' containing individualized instructions (e.g., to fetch particular datasets or to perform certain workflows or algorithms) This is particularly useful when (as is the case with S-NPP data) we need to launch many very similar machines to process an unpredictable number of data files concurrently. Our experience shows the viability and flexibility of this approach to workflow management for scientific data processing. - Finally, cloud computing is a promising platform for distributed volunteer ('interstitial') computing, via mechanisms such as the Berkeley Open Infrastructure for Network Computing (BOINC) popularized with the SETI@Home project and others such as ClimatePrediction.net and NASA's Climate@Home. Interstitial computing faces significant challenges as commodity computing shifts from (always on) desktop computers towards smartphones and tablets (untethered and running on scarce battery power); but cloud computing offers significant slack capacity. This capacity includes virtual machines with unused RAM or underused CPUs; virtual storage volumes allocated (& paid for) but not full; and virtual machines that are paid up for the current hour but whose work is complete. We are devising ways to facilitate the reuse of these resources (i.e., cloud-based interstitial computing) for satellite data processing and related analyses. We will present our findings and research directions on these and related topics.

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

A discrete Fourier transform for virtual memory machines

NASA Technical Reports Server (NTRS)

Galant, David C.

1992-01-01

An algebraic theory of the Discrete Fourier Transform is developed in great detail. Examination of the details of the theory leads to a computationally efficient fast Fourier transform for the use on computers with virtual memory. Such an algorithm is of great use on modern desktop machines. A FORTRAN coded version of the algorithm is given for the case when the sequence of numbers to be transformed is a power of two.

Productive High Performance Parallel Programming with Auto-tuned Domain-Specific Embedded Languages

DTIC Science & Technology

2013-01-02

Compilation JVM Java Virtual Machine KB Kilobyte KDT Knowledge Discovery Toolbox LAPACK Linear Algebra Package LLVM Low-Level Virtual Machine LOC Lines...different starting points. Leo Meyerovich also helped solidify some of the ideas here in discussions during Par Lab retreats. I would also like to thank...multi-timestep computations by blocking in both time and space. 88 Implementation Output Approx DSL Type Language Language Parallelism LoC Graphite

Lifelong personal health data and application software via virtual machines in the cloud.

PubMed

Van Gorp, Pieter; Comuzzi, Marco

2014-01-01

Personal Health Records (PHRs) should remain the lifelong property of patients, who should be able to show them conveniently and securely to selected caregivers and institutions. In this paper, we present MyPHRMachines, a cloud-based PHR system taking a radically new architectural solution to health record portability. In MyPHRMachines, health-related data and the application software to view and/or analyze it are separately deployed in the PHR system. After uploading their medical data to MyPHRMachines, patients can access them again from remote virtual machines that contain the right software to visualize and analyze them without any need for conversion. Patients can share their remote virtual machine session with selected caregivers, who will need only a Web browser to access the pre-loaded fragments of their lifelong PHR. We discuss a prototype of MyPHRMachines applied to two use cases, i.e., radiology image sharing and personalized medicine.

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.

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.

An Interactive Web-Based Analysis Framework for Remote Sensing Cloud Computing

NASA Astrophysics Data System (ADS)

Wang, X. Z.; Zhang, H. M.; Zhao, J. H.; Lin, Q. H.; Zhou, Y. C.; Li, J. H.

2015-07-01

Spatiotemporal data, especially remote sensing data, are widely used in ecological, geographical, agriculture, and military research and applications. With the development of remote sensing technology, more and more remote sensing data are accumulated and stored in the cloud. An effective way for cloud users to access and analyse these massive spatiotemporal data in the web clients becomes an urgent issue. In this paper, we proposed a new scalable, interactive and web-based cloud computing solution for massive remote sensing data analysis. We build a spatiotemporal analysis platform to provide the end-user with a safe and convenient way to access massive remote sensing data stored in the cloud. The lightweight cloud storage system used to store public data and users' private data is constructed based on open source distributed file system. In it, massive remote sensing data are stored as public data, while the intermediate and input data are stored as private data. The elastic, scalable, and flexible cloud computing environment is built using Docker, which is a technology of open-source lightweight cloud computing container in the Linux operating system. In the Docker container, open-source software such as IPython, NumPy, GDAL, and Grass GIS etc., are deployed. Users can write scripts in the IPython Notebook web page through the web browser to process data, and the scripts will be submitted to IPython kernel to be executed. By comparing the performance of remote sensing data analysis tasks executed in Docker container, KVM virtual machines and physical machines respectively, we can conclude that the cloud computing environment built by Docker makes the greatest use of the host system resources, and can handle more concurrent spatial-temporal computing tasks. Docker technology provides resource isolation mechanism in aspects of IO, CPU, and memory etc., which offers security guarantee when processing remote sensing data in the IPython Notebook. Users can write complex data processing code on the web directly, so they can design their own data processing algorithm.

Virtualization for Cost-Effective Teaching of Assembly Language Programming

ERIC Educational Resources Information Center

Cadenas, José O.; Sherratt, R. Simon; Howlett, Des; Guy, Chris G.; Lundqvist, Karsten O.

2015-01-01

This paper describes a virtual system that emulates an ARM-based processor machine, created to replace a traditional hardware-based system for teaching assembly language. The virtual system proposed here integrates, in a single environment, all the development tools necessary to deliver introductory or advanced courses on modern assembly language…

Proposal of Modification Strategy of NC Program in the Virtual Manufacturing Environment

NASA Astrophysics Data System (ADS)

Narita, Hirohisa; Chen, Lian-Yi; Fujimoto, Hideo; Shirase, Keiichi; Arai, Eiji

Virtual manufacturing will be a key technology in process planning, because there are no evaluation tools for cutting conditions. Therefore, virtual machining simulator (VMSim), which can predict end milling processes, has been developed. The modification strategy of NC program using VMSim is proposed in this paper.

Active Gaming: Is "Virtual" Reality Right for Your Physical Education Program?

ERIC Educational Resources Information Center

Hansen, Lisa; Sanders, Stephen W.

2012-01-01

Active gaming is growing in popularity and the idea of increasing children's physical activity by using technology is largely accepted by physical educators. Teachers nationwide have been providing active gaming equipment such as virtual bikes, rhythmic dance machines, virtual sporting games, martial arts simulators, balance boards, and other…

Comparative study of state-of-the-art myoelectric controllers for multigrasp prosthetic hands.

PubMed

Segil, Jacob L; Controzzi, Marco; Weir, Richard F ff; Cipriani, Christian

2014-01-01

A myoelectric controller should provide an intuitive and effective human-machine interface that deciphers user intent in real-time and is robust enough to operate in daily life. Many myoelectric control architectures have been developed, including pattern recognition systems, finite state machines, and more recently, postural control schemes. Here, we present a comparative study of two types of finite state machines and a postural control scheme using both virtual and physical assessment procedures with seven nondisabled subjects. The Southampton Hand Assessment Procedure (SHAP) was used in order to compare the effectiveness of the controllers during activities of daily living using a multigrasp artificial hand. Also, a virtual hand posture matching task was used to compare the controllers when reproducing six target postures. The performance when using the postural control scheme was significantly better (p < 0.05) than the finite state machines during the physical assessment when comparing within-subject averages using the SHAP percent difference metric. The virtual assessment results described significantly greater completion rates (97% and 99%) for the finite state machines, but the movement time tended to be faster (2.7 s) for the postural control scheme. Our results substantiate that postural control schemes rival other state-of-the-art myoelectric controllers.

Prospects for Evidence -Based Software Assurance: Models and Analysis

DTIC Science & Technology

2015-09-01

virtual machine is much lighter than the workstation. The virtual machine doesn’t need to run anti- virus , firewalls, intrusion preven- tion systems...34] Maiorca, D., Corona , I., and Giacinto, G. Looking at the bag is not enough to find the bomb: An evasion of structural methods for malicious PDF...CCS ’13, ACM, pp. 119–130. [35] Maiorca, D., Giacinto, G., and Corona , I. A pattern recognition system for malicious PDF files detection. In

Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.

PubMed

Brodie, Ryan; Smith, Alex J; Roper, Rachel L; Tcherepanov, Vasily; Upton, Chris

2004-07-14

With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

Final Report: Enabling Exascale Hardware and Software Design through Scalable System Virtualization

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

Bridges, Patrick G.

2015-02-01

In this grant, we enhanced the Palacios virtual machine monitor to increase its scalability and suitability for addressing exascale system software design issues. This included a wide range of research on core Palacios features, large-scale system emulation, fault injection, perfomrance monitoring, and VMM extensibility. This research resulted in large number of high-impact publications in well-known venues, the support of a number of students, and the graduation of two Ph.D. students and one M.S. student. In addition, our enhanced version of the Palacios virtual machine monitor has been adopted as a core element of the Hobbes operating system under active DOE-fundedmore » research and development.« less

Phenomenology tools on cloud infrastructures using OpenStack

NASA Astrophysics Data System (ADS)

Campos, I.; Fernández-del-Castillo, E.; Heinemeyer, S.; Lopez-Garcia, A.; Pahlen, F.; Borges, G.

2013-04-01

We present a new environment for computations in particle physics phenomenology employing recent developments in cloud computing. On this environment users can create and manage "virtual" machines on which the phenomenology codes/tools can be deployed easily in an automated way. We analyze the performance of this environment based on "virtual" machines versus the utilization of physical hardware. In this way we provide a qualitative result for the influence of the host operating system on the performance of a representative set of applications for phenomenology calculations.

Enhanced networked server management with random remote backups

NASA Astrophysics Data System (ADS)

Kim, Song-Kyoo

2003-08-01

In this paper, the model is focused on available server management in network environments. The (remote) backup servers are hooked up by VPN (Virtual Private Network) and replace broken main severs immediately. A virtual private network (VPN) is a way to use a public network infrastructure and hooks up long-distance servers within a single network infrastructure. The servers can be represent as "machines" and then the system deals with main unreliable and random auxiliary spare (remote backup) machines. When the system performs a mandatory routine maintenance, auxiliary machines are being used for backups during idle periods. Unlike other existing models, the availability of auxiliary machines is changed for each activation in this enhanced model. Analytically tractable results are obtained by using several mathematical techniques and the results are demonstrated in the framework of optimized networked server allocation problems.

Real-Time linux dynamic clamp: a fast and flexible way to construct virtual ion channels in living cells.

PubMed

Dorval, A D; Christini, D J; White, J A

2001-10-01

We describe a system for real-time control of biological and other experiments. This device, based around the Real-Time Linux operating system, was tested specifically in the context of dynamic clamping, a demanding real-time task in which a computational system mimics the effects of nonlinear membrane conductances in living cells. The system is fast enough to represent dozens of nonlinear conductances in real time at clock rates well above 10 kHz. Conductances can be represented in deterministic form, or more accurately as discrete collections of stochastically gating ion channels. Tests were performed using a variety of complex models of nonlinear membrane mechanisms in excitable cells, including simulations of spatially extended excitable structures, and multiple interacting cells. Only in extreme cases does the computational load interfere with high-speed "hard" real-time processing (i.e., real-time processing that never falters). Freely available on the worldwide web, this experimental control system combines good performance. immense flexibility, low cost, and reasonable ease of use. It is easily adapted to any task involving real-time control, and excels in particular for applications requiring complex control algorithms that must operate at speeds over 1 kHz.

A Cooperative Approach to Virtual Machine Based Fault Injection

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

Naughton III, Thomas J; Engelmann, Christian; Vallee, Geoffroy R

Resilience investigations often employ fault injection (FI) tools to study the effects of simulated errors on a target system. It is important to keep the target system under test (SUT) isolated from the controlling environment in order to maintain control of the experiement. Virtual machines (VMs) have been used to aid these investigations due to the strong isolation properties of system-level virtualization. A key challenge in fault injection tools is to gain proper insight and context about the SUT. In VM-based FI tools, this challenge of target con- text is increased due to the separation between host and guest (VM).more » We discuss an approach to VM-based FI that leverages virtual machine introspection (VMI) methods to gain insight into the target s context running within the VM. The key to this environment is the ability to provide basic information to the FI system that can be used to create a map of the target environment. We describe a proof- of-concept implementation and a demonstration of its use to introduce simulated soft errors into an iterative solver benchmark running in user-space of a guest VM.« less

Multiplexing Low and High QoS Workloads in Virtual Environments

NASA Astrophysics Data System (ADS)

Verboven, Sam; Vanmechelen, Kurt; Broeckhove, Jan

Virtualization technology has introduced new ways for managing IT infrastructure. The flexible deployment of applications through self-contained virtual machine images has removed the barriers for multiplexing, suspending and migrating applications with their entire execution environment, allowing for a more efficient use of the infrastructure. These developments have given rise to an important challenge regarding the optimal scheduling of virtual machine workloads. In this paper, we specifically address the VM scheduling problem in which workloads that require guaranteed levels of CPU performance are mixed with workloads that do not require such guarantees. We introduce a framework to analyze this scheduling problem and evaluate to what extent such mixed service delivery is beneficial for a provider of virtualized IT infrastructure. Traditionally providers offer IT resources under a guaranteed and fixed performance profile, which can lead to underutilization. The findings of our simulation study show that through proper tuning of a limited set of parameters, the proposed scheduling algorithm allows for a significant increase in utilization without sacrificing on performance dependability.

Perl Extension to the Bproc Library

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

Grunau, Daryl W.

2004-06-07

The Beowulf Distributed process Space (Bproc) software stack is comprised of UNIX/Linux kernel modifications and a support library by which a cluster of machines, each running their own private kernel, can present itself as a unified process space to the user. A Bproc cluster contains a single front-end machine and many back-end nodes which receive and run processes given to them by the front-end. Any process which is migrated to a back-end node is also visible as a ghost process on the fron-end, and may be controlled there using traditional UNIX semantics (e.g. ps(1), kill(1), etc). This software is amore » Perl extension to the Bproc library which enables the Perl programmer to make direct calls to functions within the Bproc library. See http://www.clustermatic.org, http://bproc.sourceforge.net, and http://www.perl.org« less

A Commodity Computing Cluster

NASA Astrophysics Data System (ADS)

Teuben, P. J.; Wolfire, M. G.; Pound, M. W.; Mundy, L. G.

We have assembled a cluster of Intel-Pentium based PCs running Linux to compute a large set of Photodissociation Region (PDR) and Dust Continuum models. For various reasons the cluster is heterogeneous, currently ranging from a single Pentium-II 333 MHz to dual Pentium-III 450 MHz CPU machines. Although this will be sufficient for our ``embarrassingly parallelizable problem'' it may present some challenges for as yet unplanned future use. In addition the cluster was used to construct a MIRIAD benchmark, and compared to equivalent Ultra-Sparc based workstations. Currently the cluster consists of 8 machines, 14 CPUs, 50GB of disk-space, and a total peak speed of 5.83 GHz, or about 1.5 Gflops. The total cost of this cluster has been about $12,000, including all cabling, networking equipment, rack, and a CD-R backup system. The URL for this project is http://dustem.astro.umd.edu.

PixelLearn

NASA Technical Reports Server (NTRS)

Mazzoni, Dominic; Wagstaff, Kiri; Bornstein, Benjamin; Tang, Nghia; Roden, Joseph

2006-01-01

PixelLearn is an integrated user-interface computer program for classifying pixels in scientific images. Heretofore, training a machine-learning algorithm to classify pixels in images has been tedious and difficult. PixelLearn provides a graphical user interface that makes it faster and more intuitive, leading to more interactive exploration of image data sets. PixelLearn also provides image-enhancement controls to make it easier to see subtle details in images. PixelLearn opens images or sets of images in a variety of common scientific file formats and enables the user to interact with several supervised or unsupervised machine-learning pixel-classifying algorithms while the user continues to browse through the images. The machinelearning algorithms in PixelLearn use advanced clustering and classification methods that enable accuracy much higher than is achievable by most other software previously available for this purpose. PixelLearn is written in portable C++ and runs natively on computers running Linux, Windows, or Mac OS X.

Virtual reality for intelligent and interactive operating, training, and visualization systems

NASA Astrophysics Data System (ADS)

Freund, Eckhard; Rossmann, Juergen; Schluse, Michael

2000-10-01

Virtual Reality Methods allow a new and intuitive way of communication between man and machine. The basic idea of Virtual Reality (VR) is the generation of artificial computer simulated worlds, which the user not only can look at but also can interact with actively using data glove and data helmet. The main emphasis for the use of such techniques at the IRF is the development of a new generation of operator interfaces for the control of robots and other automation components and for intelligent training systems for complex tasks. The basic idea of the methods developed at the IRF for the realization of Projective Virtual Reality is to let the user work in the virtual world as he would act in reality. The user actions are recognized by the Virtual reality System and by means of new and intelligent control software projected onto the automation components like robots which afterwards perform the necessary actions in reality to execute the users task. In this operation mode the user no longer has to be a robot expert to generate tasks for robots or to program them, because intelligent control software recognizes the users intention and generated automatically the commands for nearly every automation component. Now, Virtual Reality Methods are ideally suited for universal man-machine-interfaces for the control and supervision of a big class of automation components, interactive training and visualization systems. The Virtual Reality System of the IRF-COSIMIR/VR- forms the basis for different projects starting with the control of space automation systems in the projects CIROS, VITAL and GETEX, the realization of a comprehensive development tool for the International Space Station and last but not least with the realistic simulation fire extinguishing, forest machines and excavators which will be presented in the final paper in addition to the key ideas of this Virtual Reality System.

Dynamic provisioning of local and remote compute resources with OpenStack

NASA Astrophysics Data System (ADS)

Giffels, M.; Hauth, T.; Polgart, F.; Quast, G.

2015-12-01

Modern high-energy physics experiments rely on the extensive usage of computing resources, both for the reconstruction of measured events as well as for Monte-Carlo simulation. The Institut fur Experimentelle Kernphysik (EKP) at KIT is participating in both the CMS and Belle experiments with computing and storage resources. In the upcoming years, these requirements are expected to increase due to growing amount of recorded data and the rise in complexity of the simulated events. It is therefore essential to increase the available computing capabilities by tapping into all resource pools. At the EKP institute, powerful desktop machines are available to users. Due to the multi-core nature of modern CPUs, vast amounts of CPU time are not utilized by common desktop usage patterns. Other important providers of compute capabilities are classical HPC data centers at universities or national research centers. Due to the shared nature of these installations, the standardized software stack required by HEP applications cannot be installed. A viable way to overcome this constraint and offer a standardized software environment in a transparent manner is the usage of virtualization technologies. The OpenStack project has become a widely adopted solution to virtualize hardware and offer additional services like storage and virtual machine management. This contribution will report on the incorporation of the institute's desktop machines into a private OpenStack Cloud. The additional compute resources provisioned via the virtual machines have been used for Monte-Carlo simulation and data analysis. Furthermore, a concept to integrate shared, remote HPC centers into regular HEP job workflows will be presented. In this approach, local and remote resources are merged to form a uniform, virtual compute cluster with a single point-of-entry for the user. Evaluations of the performance and stability of this setup and operational experiences will be discussed.

Virtualization for the LHCb Online system

NASA Astrophysics Data System (ADS)

Bonaccorsi, Enrico; Brarda, Loic; Moine, Gary; Neufeld, Niko

2011-12-01

Virtualization has long been advertised by the IT-industry as a way to cut down cost, optimise resource usage and manage the complexity in large data-centers. The great number and the huge heterogeneity of hardware, both industrial and custom-made, has up to now led to reluctance in the adoption of virtualization in the IT infrastructure of large experiment installations. Our experience in the LHCb experiment has shown that virtualization improves the availability and the manageability of the whole system. We have done an evaluation of available hypervisors / virtualization solutions and find that the Microsoft HV technology provides a high level of maturity and flexibility for our purpose. We present the results of these comparison tests, describing in detail, the architecture of our virtualization infrastructure with a special emphasis on the security for services visible to the outside world. Security is achieved by a sophisticated combination of VLANs, firewalls and virtual routing - the cost and benefits of this solution are analysed. We have adapted our cluster management tools, notably Quattor, for the needs of virtual machines and this allows us to migrate smoothly services on physical machines to the virtualized infrastructure. The procedures for migration will also be described. In the final part of the document we describe our recent R&D activities aiming to replacing the SAN-backend for the virtualization by a cheaper iSCSI solution - this will allow to move all servers and related services to the virtualized infrastructure, excepting the ones doing hardware control via non-commodity PCI plugin cards.

Evaluating open-source cloud computing solutions for geosciences

NASA Astrophysics Data System (ADS)

Huang, Qunying; Yang, Chaowei; Liu, Kai; Xia, Jizhe; Xu, Chen; Li, Jing; Gui, Zhipeng; Sun, Min; Li, Zhenglong

2013-09-01

Many organizations start to adopt cloud computing for better utilizing computing resources by taking advantage of its scalability, cost reduction, and easy to access characteristics. Many private or community cloud computing platforms are being built using open-source cloud solutions. However, little has been done to systematically compare and evaluate the features and performance of open-source solutions in supporting Geosciences. This paper provides a comprehensive study of three open-source cloud solutions, including OpenNebula, Eucalyptus, and CloudStack. We compared a variety of features, capabilities, technologies and performances including: (1) general features and supported services for cloud resource creation and management, (2) advanced capabilities for networking and security, and (3) the performance of the cloud solutions in provisioning and operating the cloud resources as well as the performance of virtual machines initiated and managed by the cloud solutions in supporting selected geoscience applications. Our study found that: (1) no significant performance differences in central processing unit (CPU), memory and I/O of virtual machines created and managed by different solutions, (2) OpenNebula has the fastest internal network while both Eucalyptus and CloudStack have better virtual machine isolation and security strategies, (3) Cloudstack has the fastest operations in handling virtual machines, images, snapshots, volumes and networking, followed by OpenNebula, and (4) the selected cloud computing solutions are capable for supporting concurrent intensive web applications, computing intensive applications, and small-scale model simulations without intensive data communication.

A performance study of live VM migration technologies: VMotion vs XenMotion

NASA Astrophysics Data System (ADS)

Feng, Xiujie; Tang, Jianxiong; Luo, Xuan; Jin, Yaohui

2011-12-01

Due to the growing demand of flexible resource management for cloud computing services, researches on live virtual machine migration have attained more and more attention. Live migration of virtual machine across different hosts has been a powerful tool to facilitate system maintenance, load balancing, fault tolerance and so on. In this paper, we use a measurement-based approach to compare the performance of two major live migration technologies under certain network conditions, i.e., VMotion and XenMotion. The results show that VMotion generates much less data transferred than XenMotion when migrating identical VMs. However, in network with moderate packet loss and delay, which are typical in a VPN (virtual private network) scenario used to connect the data centers, XenMotion outperforms VMotion in total migration time. We hope that this study can be helpful in choosing suitable virtualization environments for data center administrators and optimizing existing live migration mechanisms.

Charliecloud

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

Priedhorsky, Reid; Randles, Tim

Charliecloud is a set of scripts to let users run a virtual cluster of virtual machines (VMs) on a desktop or supercomputer. Key functions include: 1. Creating (typically by installing an operating system from vendor media) and updating VM images; 2. Running a single VM; 3. Running multiple VMs in a virtual cluster. The virtual machines can talk to one another over the network and (in some cases) the outside world. This is accomplished by calling external programs such as QEMU and the Virtual Distributed Ethernet (VDE) suite. The goal is to let users have a virtual cluster containing nodesmore » where they have privileged access, while isolating that privilege within the virtual cluster so it cannot affect the physical compute resources. Host configuration enforces security; this is not included in Charliecloud, though security guidelines are included in its documentation and Charliecloud is designed to facilitate such configuration. Charliecloud manages passing information from host computers into and out of the virtual machines, such as parameters of the virtual cluster, input data specified by the user, output data from virtual compute jobs, VM console display, and network connections (e.g., SSH or X11). Parameters for the virtual cluster (number of VMs, RAM and disk per VM, etc.) are specified by the user or gathered from the environment (e.g., SLURM environment variables). Example job scripts are included. These include computation examples (such as a "hello world" MPI job) as well as performance tests. They also include a security test script to verify that the virtual cluster is appropriately sandboxed. Tests include: 1. Pinging hosts inside and outside the virtual cluster to explore connectivity; 2. Port scans (again inside and outside) to see what services are available; 3. Sniffing tests to see what traffic is visible to running VMs; 4. IP address spoofing to test network functionality in this case; 5. File access tests to make sure host access permissions are enforced. This test script is not a comprehensive scanner and does not test for specific vulnerabilities. Importantly, no information about physical hosts or network topology is included in this script (or any of Charliecloud); while part of a sensible test, such information is specified by the user when the test is run. That is, one cannot learn anything about the LANL network or computing infrastructure by examining Charliecloud code.« less

VirtualDose: a software for reporting organ doses from CT for adult and pediatric patients.

PubMed

Ding, Aiping; Gao, Yiming; Liu, Haikuan; Caracappa, Peter F; Long, Daniel J; Bolch, Wesley E; Liu, Bob; Xu, X George

2015-07-21

This paper describes the development and testing of VirtualDose--a software for reporting organ doses for adult and pediatric patients who undergo x-ray computed tomography (CT) examinations. The software is based on a comprehensive database of organ doses derived from Monte Carlo (MC) simulations involving a library of 25 anatomically realistic phantoms that represent patients of different ages, body sizes, body masses, and pregnant stages. Models of GE Lightspeed Pro 16 and Siemens SOMATOM Sensation 16 scanners were carefully validated for use in MC dose calculations. The software framework is designed with the 'software as a service (SaaS)' delivery concept under which multiple clients can access the web-based interface simultaneously from any computer without having to install software locally. The RESTful web service API also allows a third-party picture archiving and communication system software package to seamlessly integrate with VirtualDose's functions. Software testing showed that VirtualDose was compatible with numerous operating systems including Windows, Linux, Apple OS X, and mobile and portable devices. The organ doses from VirtualDose were compared against those reported by CT-Expo and ImPACT-two dosimetry tools that were based on the stylized pediatric and adult patient models that were known to be anatomically simple. The organ doses reported by VirtualDose differed from those reported by CT-Expo and ImPACT by as much as 300% in some of the patient models. These results confirm the conclusion from past studies that differences in anatomical realism offered by stylized and voxel phantoms have caused significant discrepancies in CT dose estimations.

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.

Using PVM to host CLIPS in distributed environments

NASA Technical Reports Server (NTRS)

Myers, Leonard; Pohl, Kym

1994-01-01

It is relatively easy to enhance CLIPS (C Language Integrated Production System) to support multiple expert systems running in a distributed environment with heterogeneous machines. The task is minimized by using the PVM (Parallel Virtual Machine) code from Oak Ridge Labs to provide the distributed utility. PVM is a library of C and FORTRAN subprograms that supports distributive computing on many different UNIX platforms. A PVM deamon is easily installed on each CPU that enters the virtual machine environment. Any user with rsh or rexec access to a machine can use the one PVM deamon to obtain a generous set of distributed facilities. The ready availability of both CLIPS and PVM makes the combination of software particularly attractive for budget conscious experimentation of heterogeneous distributive computing with multiple CLIPS executables. This paper presents a design that is sufficient to provide essential message passing functions in CLIPS and enable the full range of PVM facilities.

Virtual Mission Operations of Remote Sensors With Rapid Access To and From Space

NASA Technical Reports Server (NTRS)

Ivancic, William D.; Stewart, Dave; Walke, Jon; Dikeman, Larry; Sage, Steven; Miller, Eric; Northam, James; Jackson, Chris; Taylor, John; Lynch, Scott;

Graphics interfaces and numerical simulations: Mexican Virtual Solar Observatory

NASA Astrophysics Data System (ADS)

Hernández, L.; González, A.; Salas, G.; Santillán, A.

2007-08-01

Preliminary results associated to the computational development and creation of the Mexican Virtual Solar Observatory (MVSO) are presented. Basically, the MVSO prototype consists of two parts: the first, related to observations that have been made during the past ten years at the Solar Observation Station (EOS) and at the Carl Sagan Observatory (OCS) of the Universidad de Sonora in Mexico. The second part is associated to the creation and manipulation of a database produced by numerical simulations related to solar phenomena, we are using the MHD ZEUS-3D code. The development of this prototype was made using mysql, apache, java and VSO 1.2. based GNU and `open source philosophy'. A graphic user interface (GUI) was created in order to make web-based, remote numerical simulations. For this purpose, Mono was used, because it is provides the necessary software to develop and run .NET client and server applications on Linux. Although this project is still under development, we hope to have access, by means of this portal, to other virtual solar observatories and to be able to count on a database created through numerical simulations or, given the case, perform simulations associated to solar phenomena.

A Concept for Optimizing Behavioural Effectiveness & Efficiency

NASA Astrophysics Data System (ADS)

Barca, Jan Carlo; Rumantir, Grace; Li, Raymond

Both humans and machines exhibit strengths and weaknesses that can be enhanced by merging the two entities. This research aims to provide a broader understanding of how closer interactions between these two entities can facilitate more optimal goal-directed performance through the use of artificial extensions of the human body. Such extensions may assist us in adapting to and manipulating our environments in a more effective way than any system known today. To demonstrate this concept, we have developed a simulation where a semi interactive virtual spider can be navigated through an environment consisting of several obstacles and a virtual predator capable of killing the spider. The virtual spider can be navigated through the use of three different control systems that can be used to assist in optimising overall goal directed performance. The first two control systems use, an onscreen button interface and a touch sensor, respectively to facilitate human navigation of the spider. The third control system is an autonomous navigation system through the use of machine intelligence embedded in the spider. This system enables the spider to navigate and react to changes in its local environment. The results of this study indicate that machines should be allowed to override human control in order to maximise the benefits of collaboration between man and machine. This research further indicates that the development of strong machine intelligence, sensor systems that engage all human senses, extra sensory input systems, physical remote manipulators, multiple intelligent extensions of the human body, as well as a tighter symbiosis between man and machine, can support an upgrade of the human form.

The influence of negative training set size on machine learning-based virtual screening.

PubMed

Kurczab, Rafał; Smusz, Sabina; Bojarski, Andrzej J

2014-01-01

The paper presents a thorough analysis of the influence of the number of negative training examples on the performance of machine learning methods. The impact of this rather neglected aspect of machine learning methods application was examined for sets containing a fixed number of positive and a varying number of negative examples randomly selected from the ZINC database. An increase in the ratio of positive to negative training instances was found to greatly influence most of the investigated evaluating parameters of ML methods in simulated virtual screening experiments. In a majority of cases, substantial increases in precision and MCC were observed in conjunction with some decreases in hit recall. The analysis of dynamics of those variations let us recommend an optimal composition of training data. The study was performed on several protein targets, 5 machine learning algorithms (SMO, Naïve Bayes, Ibk, J48 and Random Forest) and 2 types of molecular fingerprints (MACCS and CDK FP). The most effective classification was provided by the combination of CDK FP with SMO or Random Forest algorithms. The Naïve Bayes models appeared to be hardly sensitive to changes in the number of negative instances in the training set. In conclusion, the ratio of positive to negative training instances should be taken into account during the preparation of machine learning experiments, as it might significantly influence the performance of particular classifier. What is more, the optimization of negative training set size can be applied as a boosting-like approach in machine learning-based virtual screening.

The influence of negative training set size on machine learning-based virtual screening

PubMed Central

2014-01-01

Background The paper presents a thorough analysis of the influence of the number of negative training examples on the performance of machine learning methods. Results The impact of this rather neglected aspect of machine learning methods application was examined for sets containing a fixed number of positive and a varying number of negative examples randomly selected from the ZINC database. An increase in the ratio of positive to negative training instances was found to greatly influence most of the investigated evaluating parameters of ML methods in simulated virtual screening experiments. In a majority of cases, substantial increases in precision and MCC were observed in conjunction with some decreases in hit recall. The analysis of dynamics of those variations let us recommend an optimal composition of training data. The study was performed on several protein targets, 5 machine learning algorithms (SMO, Naïve Bayes, Ibk, J48 and Random Forest) and 2 types of molecular fingerprints (MACCS and CDK FP). The most effective classification was provided by the combination of CDK FP with SMO or Random Forest algorithms. The Naïve Bayes models appeared to be hardly sensitive to changes in the number of negative instances in the training set. Conclusions In conclusion, the ratio of positive to negative training instances should be taken into account during the preparation of machine learning experiments, as it might significantly influence the performance of particular classifier. What is more, the optimization of negative training set size can be applied as a boosting-like approach in machine learning-based virtual screening. PMID:24976867

Enterprise Cloud Architecture for Chinese Ministry of Railway

NASA Astrophysics Data System (ADS)

Shan, Xumei; Liu, Hefeng

Enterprise like PRC Ministry of Railways (MOR), is facing various challenges ranging from highly distributed computing environment and low legacy system utilization, Cloud Computing is increasingly regarded as one workable solution to address this. This article describes full scale cloud solution with Intel Tashi as virtual machine infrastructure layer, Hadoop HDFS as computing platform, and self developed SaaS interface, gluing virtual machine and HDFS with Xen hypervisor. As a result, on demand computing task application and deployment have been tackled per MOR real working scenarios at the end of article.

Virtual Reality Enhanced Instructional Learning

ERIC Educational Resources Information Center

Nachimuthu, K.; Vijayakumari, G.

2009-01-01

Virtual Reality (VR) is a creation of virtual 3D world in which one can feel and sense the world as if it is real. It is allowing engineers to design machines and Educationists to design AV [audiovisual] equipment in real time but in 3-dimensional hologram as if the actual material is being made and worked upon. VR allows a least-cost (energy…

Virtual manufacturing work cell for engineering

NASA Astrophysics Data System (ADS)

Watanabe, Hideo; Ohashi, Kazushi; Takahashi, Nobuyuki; Kato, Kiyotaka; Fujita, Satoru

1997-12-01

The life cycles of products have been getting shorter. To meet this rapid turnover, manufacturing systems must be frequently changed as well. In engineering to develop manufacturing systems, there are several tasks such as process planning, layout design, programming, and final testing using actual machines. This development of manufacturing systems takes a long time and is expensive. To aid the above engineering process, we have developed the virtual manufacturing workcell (VMW). This paper describes a concept of VMW and design method through computer aided manufacturing engineering using VMW (CAME-VMW) related to the above engineering tasks. The VMW has all design data, and realizes a behavior of equipment and devices using a simulator. The simulator has logical and physical functionality. The one simulates a sequence control and the other simulates motion control, shape movement in 3D space. The simulator can execute the same control software made for actual machines. Therefore we can verify the behavior precisely before the manufacturing workcell will be constructed. The VMW creates engineering work space for several engineers and offers debugging tools such as virtual equipment and virtual controllers. We applied this VMW to development of a transfer workcell for vaporization machine in actual manufacturing system to produce plasma display panel (PDP) workcell and confirmed its effectiveness.

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.

PubMed

Angiuoli, Samuel V; Matalka, Malcolm; Gussman, Aaron; Galens, Kevin; Vangala, Mahesh; Riley, David R; Arze, Cesar; White, James R; White, Owen; Fricke, W Florian

2011-08-30

Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.

Identification of Program Signatures from Cloud Computing System Telemetry Data

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

Nichols, Nicole M.; Greaves, Mark T.; Smith, William P.

Malicious cloud computing activity can take many forms, including running unauthorized programs in a virtual environment. Detection of these malicious activities while preserving the privacy of the user is an important research challenge. Prior work has shown the potential viability of using cloud service billing metrics as a mechanism for proxy identification of malicious programs. Previously this novel detection method has been evaluated in a synthetic and isolated computational environment. In this paper we demonstrate the ability of billing metrics to identify programs, in an active cloud computing environment, including multiple virtual machines running on the same hypervisor. The openmore » source cloud computing platform OpenStack, is used for private cloud management at Pacific Northwest National Laboratory. OpenStack provides a billing tool (Ceilometer) to collect system telemetry measurements. We identify four different programs running on four virtual machines under the same cloud user account. Programs were identified with up to 95% accuracy. This accuracy is dependent on the distinctiveness of telemetry measurements for the specific programs we tested. Future work will examine the scalability of this approach for a larger selection of programs to better understand the uniqueness needed to identify a program. Additionally, future work should address the separation of signatures when multiple programs are running on the same virtual machine.« less

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.

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

CompactPCI/Linux Platform in FTU Slow Control System

NASA Astrophysics Data System (ADS)

Iannone, F.; Wang, L.; Centioli, C.; Panella, M.; Mazza, G.; Vitale, V.

2004-12-01

In large fusion experiments, such as tokamak devices, there is a common trend for slow control systems. Because of complexity of the plants, the so-called `Standard Model' (SM) in slow control has been adopted on several tokamak machines. This model is based on a three-level hierarchical control: 1) High-Level Control (HLC) with a supervisory function; 2) Medium-Level Control (MLC) to interface and concentrate I/O field equipments; 3) Low-Level Control (LLC) with hard real-time I/O function, often managed by PLCs. FTU control system designed with SM concepts has underwent several stages of developments in its fifteen years duration of runs. The latest evolution was inevitable, due to the obsolescence of the MLC CPUs, based on VME-MOTOROLA 68030 with OS9 operating system. A large amount of C code was developed for that platform to route the data flow from LLC, which is constituted by 24 Westinghouse Numalogic PC-700 PLCs with about 8000 field-points, to HLC, based on a commercial Object-Oriented Real-Time database on Alpha/CompaqTru64 platform. Therefore, we have to look for cost-effective solutions and finally a CompactPCI-Intel x86 platform with Linux operating system was chosen. A software porting has been done, taking into account the differences between OS9 and Linux operating system in terms of Inter/Network Processes Communications and I/O multi-ports serial driver. This paper describes the hardware/software architecture of the new MLC system, emphasizing the reliability and the low costs of the open source solutions. Moreover, a huge amount of software packages available in open source environment will assure a less painful maintenance, and will open the way to further improvements of the system itself.

The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud

PubMed Central

Karimi, Kamran; Vize, Peter D.

2014-01-01

As a model organism database, Xenbase has been providing informatics and genomic data on Xenopus (Silurana) tropicalis and Xenopus laevis frogs for more than a decade. The Xenbase database contains curated, as well as community-contributed and automatically harvested literature, gene and genomic data. A GBrowse genome browser, a BLAST+ server and stock center support are available on the site. When this resource was first built, all software services and components in Xenbase ran on a single physical server, with inherent reliability, scalability and inter-dependence issues. Recent advances in networking and virtualization techniques allowed us to move Xenbase to a virtual environment, and more specifically to a private cloud. To do so we decoupled the different software services and components, such that each would run on a different virtual machine. In the process, we also upgraded many of the components. The resulting system is faster and more reliable. System maintenance is easier, as individual virtual machines can now be updated, backed up and changed independently. We are also experiencing more effective resource allocation and utilization. Database URL: www.xenbase.org PMID:25380782

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

Naval Applications of Virtual Reality,

DTIC Science & Technology

1993-01-01

Expert Virtual Reality Special Report 󈨡, pp. 67- 72. 14. SUBJECT TERMS 15 NUMBER o0 PAGES man-machine interface virtual reality decision support...collective and individual performance. -" Virtual reality projects could help *y by Mark Gembicki Av-t-abilty CodesA Avafllat Idt Iofe and David Rousseau...alt- 67 VIRTUAL . REALITY SPECIAl, REPORT r-OPY avcriaikxb to DD)C qg .- 154,41X~~~~~~~~~~~~j 1411 iI..:41 T a].’ 1,1 4 1111 I 4 1 * .11 ~ 4 l.~w111511 I

BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences

PubMed Central

Dahlö, Martin; Haziza, Frédéric; Kallio, Aleksi; Korpelainen, Eija; Bongcam-Rudloff, Erik; Spjuth, Ola

2015-01-01

Virtualization is becoming increasingly important in bioscience, enabling assembly and provisioning of complete computer setups, including operating system, data, software, and services packaged as virtual machine images (VMIs). We present an open catalog of VMIs for the life sciences, where scientists can share information about images and optionally upload them to a server equipped with a large file system and fast Internet connection. Other scientists can then search for and download images that can be run on the local computer or in a cloud computing environment, providing easy access to bioinformatics environments. We also describe applications where VMIs aid life science research, including distributing tools and data, supporting reproducible analysis, and facilitating education. BioImg.org is freely available at: https://bioimg.org. PMID:26401099

BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences.

PubMed

Dahlö, Martin; Haziza, Frédéric; Kallio, Aleksi; Korpelainen, Eija; Bongcam-Rudloff, Erik; Spjuth, Ola

2015-01-01

Virtualization is becoming increasingly important in bioscience, enabling assembly and provisioning of complete computer setups, including operating system, data, software, and services packaged as virtual machine images (VMIs). We present an open catalog of VMIs for the life sciences, where scientists can share information about images and optionally upload them to a server equipped with a large file system and fast Internet connection. Other scientists can then search for and download images that can be run on the local computer or in a cloud computing environment, providing easy access to bioinformatics environments. We also describe applications where VMIs aid life science research, including distributing tools and data, supporting reproducible analysis, and facilitating education. BioImg.org is freely available at: https://bioimg.org.

Access, Equity, and Opportunity. Women in Machining: A Model Program.

ERIC Educational Resources Information Center

Warner, Heather

The Women in Machining (WIM) program is a Machine Action Project (MAP) initiative that was developed in response to a local skilled metalworking labor shortage, despite a virtual absence of women and people of color from area shops. The project identified post-war stereotypes and other barriers that must be addressed if women are to have an equal…

A genetic algorithm for a bi-objective mathematical model for dynamic virtual cell formation problem

NASA Astrophysics Data System (ADS)

Moradgholi, Mostafa; Paydar, Mohammad Mahdi; Mahdavi, Iraj; Jouzdani, Javid

2016-09-01

Nowadays, with the increasing pressure of the competitive business environment and demand for diverse products, manufacturers are force to seek for solutions that reduce production costs and rise product quality. Cellular manufacturing system (CMS), as a means to this end, has been a point of attraction to both researchers and practitioners. Limitations of cell formation problem (CFP), as one of important topics in CMS, have led to the introduction of virtual CMS (VCMS). This research addresses a bi-objective dynamic virtual cell formation problem (DVCFP) with the objective of finding the optimal formation of cells, considering the material handling costs, fixed machine installation costs and variable production costs of machines and workforce. Furthermore, we consider different skills on different machines in workforce assignment in a multi-period planning horizon. The bi-objective model is transformed to a single-objective fuzzy goal programming model and to show its performance; numerical examples are solved using the LINGO software. In addition, genetic algorithm (GA) is customized to tackle large-scale instances of the problems to show the performance of the solution method.

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

Integration of virtualized worker nodes in standard batch systems

NASA Astrophysics Data System (ADS)

Büge, Volker; Hessling, Hermann; Kemp, Yves; Kunze, Marcel; Oberst, Oliver; Quast, Günter; Scheurer, Armin; Synge, Owen

2010-04-01

Current experiments in HEP only use a limited number of operating system flavours. Their software might only be validated on one single OS platform. Resource providers might have other operating systems of choice for the installation of the batch infrastructure. This is especially the case if a cluster is shared with other communities, or communities that have stricter security requirements. One solution would be to statically divide the cluster into separated sub-clusters. In such a scenario, no opportunistic distribution of the load can be achieved, resulting in a poor overall utilization efficiency. Another approach is to make the batch system aware of virtualization, and to provide each community with its favoured operating system in a virtual machine. Here, the scheduler has full flexibility, resulting in a better overall efficiency of the resources. In our contribution, we present a lightweight concept for the integration of virtual worker nodes into standard batch systems. The virtual machines are started on the worker nodes just before jobs are executed there. No meta-scheduling is introduced. We demonstrate two prototype implementations, one based on the Sun Grid Engine (SGE), the other using Maui/Torque as a batch system. Both solutions support local job as well as Grid job submission. The hypervisors currently used are Xen and KVM, a port to another system is easily envisageable. To better handle different virtual machines on the physical host, the management solution VmImageManager is developed. We will present first experience from running the two prototype implementations. In a last part, we will show the potential future use of this lightweight concept when integrated into high-level (i.e. Grid) work-flows.

Digital Image Correlation Engine

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

Turner, Dan; Crozier, Paul; Reu, Phil

DICe is an open source digital image correlation (DIC) tool intended for use as a module in an external application or as a standalone analysis code. It's primary capability is computing full-field displacements and strains from sequences of digital These images are typically of a material sample undergoing a materials characterization experiment, but DICe is also useful for other applications (for example, trajectory tracking). DICe is machine portable (Windows, Linux and Mac) and can be effectively deployed on a high performance computing platform. Capabilities from DICe can be invoked through a library interface, via source code integration of DICe classesmore » or through a graphical user interface.« less

Grid heterogeneity in in-silico experiments: an exploration of drug screening using DOCK on cloud environments.

PubMed

Yim, Wen-Wai; Chien, Shu; Kusumoto, Yasuyuki; Date, Susumu; Haga, Jason

2010-01-01

Large-scale in-silico screening is a necessary part of drug discovery and Grid computing is one answer to this demand. A disadvantage of using Grid computing is the heterogeneous computational environments characteristic of a Grid. In our study, we have found that for the molecular docking simulation program DOCK, different clusters within a Grid organization can yield inconsistent results. Because DOCK in-silico virtual screening (VS) is currently used to help select chemical compounds to test with in-vitro experiments, such differences have little effect on the validity of using virtual screening before subsequent steps in the drug discovery process. However, it is difficult to predict whether the accumulation of these discrepancies over sequentially repeated VS experiments will significantly alter the results if VS is used as the primary means for identifying potential drugs. Moreover, such discrepancies may be unacceptable for other applications requiring more stringent thresholds. This highlights the need for establishing a more complete solution to provide the best scientific accuracy when executing an application across Grids. One possible solution to platform heterogeneity in DOCK performance explored in our study involved the use of virtual machines as a layer of abstraction. This study investigated the feasibility and practicality of using virtual machine and recent cloud computing technologies in a biological research application. We examined the differences and variations of DOCK VS variables, across a Grid environment composed of different clusters, with and without virtualization. The uniform computer environment provided by virtual machines eliminated inconsistent DOCK VS results caused by heterogeneous clusters, however, the execution time for the DOCK VS increased. In our particular experiments, overhead costs were found to be an average of 41% and 2% in execution time for two different clusters, while the actual magnitudes of the execution time costs were minimal. Despite the increase in overhead, virtual clusters are an ideal solution for Grid heterogeneity. With greater development of virtual cluster technology in Grid environments, the problem of platform heterogeneity may be eliminated through virtualization, allowing greater usage of VS, and will benefit all Grid applications in general.

An Argument for Partial Admissibility of Polygraph Results in Trials by Courts-Martial

DTIC Science & Technology

1990-04-01

FUNDAMENTALS OF THE POLYGRAPH TECHNIQUE 6 A. THE POLYGRAPH MACHINE 7 1. THE CARDIOSPHYMOGRAPH 8 2. THE PNEUMOGRAPH 9 3. THE GALVANOMETER 10 4. THE... Machine Anyone observing a polygraph machine for the first time could easily conclude it is a survivor of the Spanish Inquisition. The lengths of...wire and coils get the immediate attention of the subject. However, the various polygraph machines in use today cause virtually no discomfort. Several

Teaching Cybersecurity Using the Cloud

ERIC Educational Resources Information Center

Salah, Khaled; Hammoud, Mohammad; Zeadally, Sherali

2015-01-01

Cloud computing platforms can be highly attractive to conduct course assignments and empower students with valuable and indispensable hands-on experience. In particular, the cloud can offer teaching staff and students (whether local or remote) on-demand, elastic, dedicated, isolated, (virtually) unlimited, and easily configurable virtual machines.…

Ant-Based Cyber Defense (also known as

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

Glenn Fink, PNNL

2015-09-29

ABCD is a four-level hierarchy with human supervisors at the top, a top-level agent called a Sergeant controlling each enclave, Sentinel agents located at each monitored host, and mobile Sensor agents that swarm through the enclaves to detect cyber malice and misconfigurations. The code comprises four parts: (1) the core agent framework, (2) the user interface and visualization, (3) test-range software to create a network of virtual machines including a simulated Internet and user and host activity emulation scripts, and (4) a test harness to allow the safe running of adversarial code within the framework of monitored virtual machines.

Prototyping Faithful Execution in a Java virtual machine.

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

Tarman, Thomas David; Campbell, Philip LaRoche; Pierson, Lyndon George

2003-09-01

This report presents the implementation of a stateless scheme for Faithful Execution, the design for which is presented in a companion report, ''Principles of Faithful Execution in the Implementation of Trusted Objects'' (SAND 2003-2328). We added a simple cryptographic capability to an already simplified class loader and its associated Java Virtual Machine (JVM) to provide a byte-level implementation of Faithful Execution. The extended class loader and JVM we refer to collectively as the Sandia Faithfully Executing Java architecture (or JavaFE for short). This prototype is intended to enable exploration of more sophisticated techniques which we intend to implement in hardware.

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.

Build and Execute Environment

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

Guan, Qiang

At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will have limited development time at scale and, therefore, must have rich tools to develop, debug, test, and deploy applications. At this scale, successful workflows willmore » compose linked computations from an assortment of reliable, well-defined computation elements, ones that can come and go as required, based on the needs of the workflow over time. We propose a novel framework that utilizes both virtual machines (VMs) and software containers to create a workflow system that establishes a uniform build and execution environment (BEE) beyond the capabilities of current systems. In this environment, applications will run reliably and repeatably across heterogeneous hardware and software. Containers, both commercial (Docker and Rocket) and open-source (LXC and LXD), define a runtime that isolates all software dependencies from the machine operating system. Workflows may contain multiple containers that run different operating systems, different software, and even different versions of the same software. We will run containers in open-source virtual machines (KVM) and emulators (QEMU) so that workflows run on any machine entirely in user-space. On this platform of containers and virtual machines, we will deliver workflow software that provides services, including repeatable execution, provenance, checkpointing, and future proofing. We will capture provenance about how containers were launched and how they interact to annotate workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.« less

Enabling Diverse Software Stacks on Supercomputers using High Performance Virtual Clusters.

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

Younge, Andrew J.; Pedretti, Kevin; Grant, Ryan

While large-scale simulations have been the hallmark of the High Performance Computing (HPC) community for decades, Large Scale Data Analytics (LSDA) workloads are gaining attention within the scientific community not only as a processing component to large HPC simulations, but also as standalone scientific tools for knowledge discovery. With the path towards Exascale, new HPC runtime systems are also emerging in a way that differs from classical distributed com- puting models. However, system software for such capabilities on the latest extreme-scale DOE supercomputing needs to be enhanced to more appropriately support these types of emerging soft- ware ecosystems. In thismore » paper, we propose the use of Virtual Clusters on advanced supercomputing resources to enable systems to support not only HPC workloads, but also emerging big data stacks. Specifi- cally, we have deployed the KVM hypervisor within Cray's Compute Node Linux on a XC-series supercomputer testbed. We also use libvirt and QEMU to manage and provision VMs directly on compute nodes, leveraging Ethernet-over-Aries network emulation. To our knowledge, this is the first known use of KVM on a true MPP supercomputer. We investigate the overhead our solution using HPC benchmarks, both evaluating single-node performance as well as weak scaling of a 32-node virtual cluster. Overall, we find single node performance of our solution using KVM on a Cray is very efficient with near-native performance. However overhead increases by up to 20% as virtual cluster size increases, due to limitations of the Ethernet-over-Aries bridged network. Furthermore, we deploy Apache Spark with large data analysis workloads in a Virtual Cluster, ef- fectively demonstrating how diverse software ecosystems can be supported by High Performance Virtual Clusters.« less

VirtualDose: a software for reporting organ doses from CT for adult and pediatric patients

NASA Astrophysics Data System (ADS)

Ding, Aiping; Gao, Yiming; Liu, Haikuan; Caracappa, Peter F.; Long, Daniel J.; Bolch, Wesley E.; Liu, Bob; Xu, X. George

2015-07-01

This paper describes the development and testing of VirtualDose—a software for reporting organ doses for adult and pediatric patients who undergo x-ray computed tomography (CT) examinations. The software is based on a comprehensive database of organ doses derived from Monte Carlo (MC) simulations involving a library of 25 anatomically realistic phantoms that represent patients of different ages, body sizes, body masses, and pregnant stages. Models of GE Lightspeed Pro 16 and Siemens SOMATOM Sensation 16 scanners were carefully validated for use in MC dose calculations. The software framework is designed with the ‘software as a service (SaaS)’ delivery concept under which multiple clients can access the web-based interface simultaneously from any computer without having to install software locally. The RESTful web service API also allows a third-party picture archiving and communication system software package to seamlessly integrate with VirtualDose’s functions. Software testing showed that VirtualDose was compatible with numerous operating systems including Windows, Linux, Apple OS X, and mobile and portable devices. The organ doses from VirtualDose were compared against those reported by CT-Expo and ImPACT—two dosimetry tools that were based on the stylized pediatric and adult patient models that were known to be anatomically simple. The organ doses reported by VirtualDose differed from those reported by CT-Expo and ImPACT by as much as 300% in some of the patient models. These results confirm the conclusion from past studies that differences in anatomical realism offered by stylized and voxel phantoms have caused significant discrepancies in CT dose estimations.

Prediction based proactive thermal virtual machine scheduling in green clouds.

PubMed

Kinger, Supriya; Kumar, Rajesh; Sharma, Anju

2014-01-01

Cloud computing has rapidly emerged as a widely accepted computing paradigm, but the research on Cloud computing is still at an early stage. Cloud computing provides many advanced features but it still has some shortcomings such as relatively high operating cost and environmental hazards like increasing carbon footprints. These hazards can be reduced up to some extent by efficient scheduling of Cloud resources. Working temperature on which a machine is currently running can be taken as a criterion for Virtual Machine (VM) scheduling. This paper proposes a new proactive technique that considers current and maximum threshold temperature of Server Machines (SMs) before making scheduling decisions with the help of a temperature predictor, so that maximum temperature is never reached. Different workload scenarios have been taken into consideration. The results obtained show that the proposed system is better than existing systems of VM scheduling, which does not consider current temperature of nodes before making scheduling decisions. Thus, a reduction in need of cooling systems for a Cloud environment has been obtained and validated.

Center for Space Telemetering and Telecommunications Systems, New Mexico State University

NASA Technical Reports Server (NTRS)

Horan, Stephen; DeLeon, Phillip; Borah, Deva; Lyman, Ray

2002-01-01

This viewgraph presentation gives an overview of the Center for Space Telemetering and Telecommunications Systems activities at New Mexico State University. Presentations cover the following topics: (1) small satellite communications, including nanosatellite radio and virtual satellite development; (2) modulation and detection studies, including details on smooth phase interpolated keying (SPIK) spectra and highlights of an adaptive turbo multiuser detector; (3) decoupled approaches to nonlinear ISI compensation; (4) space internet testing; (4) optical communication; (5) Linux-based receiver for lightweight optical communications without a laser in space, including software design, performance analysis, and the receiver algorithm; (6) carrier tracking hardware; and (7) subband transforms for adaptive direct sequence spread spectrum receivers.

Workstation-Based Avionics Simulator to Support Mars Science Laboratory Flight Software Development

NASA Technical Reports Server (NTRS)

Henriquez, David; Canham, Timothy; Chang, Johnny T.; McMahon, Elihu

2008-01-01

The Mars Science Laboratory developed the WorkStation TestSet (WSTS) to support flight software development. 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. This provides flight software developers with their own virtual avionics testbed and allows device-level and functional software testing when hardware testbeds are either not yet available or have limited availability. The WSTS has successfully off-loaded many flight software development activities from the project testbeds. At the writing of this paper, the WSTS has averaged an order of magnitude more usage than the project's hardware testbeds.

Research and embedded implementation of Layer 3 switch

NASA Astrophysics Data System (ADS)

Song, Jin; Cheng, Zijing

2009-12-01

In the internetworking world, switches and routers have been deployed for workgroup and enterprise connectivity. In the past, switches mainly operated at Layer 2 (they were extensions of bridges), while routers were clearly Layer3 devices. Recently, the line has blurred and switches operating at Layer 3 are becoming more popular. This paper explains the Linux Bridge, Layer 2 Switches, Virtual LAN (VLAN) and Layer 3 Switches. The flow chart of Layer 3 switches and working routine related to Layer 3 switch technology were investigated in detail. This paper presents a new method to implement layer 3 switching that is entirely accomplished in software and is embedded implemented by code transplanting based on PowerPC 460GT platform.

Virtual Environment Training: Auxiliary Machinery Room (AMR) Watchstation Trainer.

ERIC Educational Resources Information Center

Hriber, Dennis C.; And Others

1993-01-01

Describes a project implemented at Newport News Shipbuilding that used Virtual Environment Training to improve the performance of submarine crewmen. Highlights include development of the Auxiliary Machine Room (AMR) Watchstation Trainer; Digital Video Interactive (DVI); screen layout; test design and evaluation; user reactions; authoring language;…

The virtual machine (VM) scaler: an infrastructure manager supporting environmental modeling on IaaS clouds

USDA-ARS?s Scientific Manuscript database

Infrastructure-as-a-service (IaaS) clouds provide a new medium for deployment of environmental modeling applications. Harnessing advancements in virtualization, IaaS clouds can provide dynamic scalable infrastructure to better support scientific modeling computational demands. Providing scientific m...

Global Detection of Live Virtual Machine Migration Based on Cellular Neural Networks

PubMed Central

Xie, Kang; Yang, Yixian; Zhang, Ling; Jing, Maohua; Xin, Yang; Li, Zhongxian

2014-01-01

In order to meet the demands of operation monitoring of large scale, autoscaling, and heterogeneous virtual resources in the existing cloud computing, a new method of live virtual machine (VM) migration detection algorithm based on the cellular neural networks (CNNs), is presented. Through analyzing the detection process, the parameter relationship of CNN is mapped as an optimization problem, in which improved particle swarm optimization algorithm based on bubble sort is used to solve the problem. Experimental results demonstrate that the proposed method can display the VM migration processing intuitively. Compared with the best fit heuristic algorithm, this approach reduces the processing time, and emerging evidence has indicated that this new approach is affordable to parallelism and analog very large scale integration (VLSI) implementation allowing the VM migration detection to be performed better. PMID:24959631

Global detection of live virtual machine migration based on cellular neural networks.

PubMed

Xie, Kang; Yang, Yixian; Zhang, Ling; Jing, Maohua; Xin, Yang; Li, Zhongxian

2014-01-01

In order to meet the demands of operation monitoring of large scale, autoscaling, and heterogeneous virtual resources in the existing cloud computing, a new method of live virtual machine (VM) migration detection algorithm based on the cellular neural networks (CNNs), is presented. Through analyzing the detection process, the parameter relationship of CNN is mapped as an optimization problem, in which improved particle swarm optimization algorithm based on bubble sort is used to solve the problem. Experimental results demonstrate that the proposed method can display the VM migration processing intuitively. Compared with the best fit heuristic algorithm, this approach reduces the processing time, and emerging evidence has indicated that this new approach is affordable to parallelism and analog very large scale integration (VLSI) implementation allowing the VM migration detection to be performed better.

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

PubMed Central

2011-01-01

Background Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. Results We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. Conclusion The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing. PMID:21878105

Design and fabrication of complete dentures using CAD/CAM technology

PubMed Central

Han, Weili; Li, Yanfeng; Zhang, Yue; lv, Yuan; Zhang, Ying; Hu, Ping; Liu, Huanyue; Ma, Zheng; Shen, Yi

2017-01-01

Abstract The aim of the study was to test the feasibility of using commercially available computer-aided design and computer-aided manufacturing (CAD/CAM) technology including 3Shape Dental System 2013 trial version, WIELAND V2.0.049 and WIELAND ZENOTEC T1 milling machine to design and fabricate complete dentures. The modeling process of full denture available in the trial version of 3Shape Dental System 2013 was used to design virtual complete dentures on the basis of 3-dimensional (3D) digital edentulous models generated from the physical models. The virtual complete dentures designed were exported to CAM software of WIELAND V2.0.049. A WIELAND ZENOTEC T1 milling machine controlled by the CAM software was used to fabricate physical dentitions and baseplates by milling acrylic resin composite plates. The physical dentitions were bonded to the corresponding baseplates to form the maxillary and mandibular complete dentures. Virtual complete dentures were successfully designed using the software through several steps including generation of 3D digital edentulous models, model analysis, arrangement of artificial teeth, trimming relief area, and occlusal adjustment. Physical dentitions and baseplates were successfully fabricated according to the designed virtual complete dentures using milling machine controlled by a CAM software. Bonding physical dentitions to the corresponding baseplates generated the final physical complete dentures. Our study demonstrated that complete dentures could be successfully designed and fabricated by using CAD/CAM. PMID:28072686

Design and implementation of a reliable and cost-effective cloud computing infrastructure: the INFN Napoli experience

NASA Astrophysics Data System (ADS)

Capone, V.; Esposito, R.; Pardi, S.; Taurino, F.; Tortone, G.

2012-12-01

Over the last few years we have seen an increasing number of services and applications needed to manage and maintain cloud computing facilities. This is particularly true for computing in high energy physics, which often requires complex configurations and distributed infrastructures. In this scenario a cost effective rationalization and consolidation strategy is the key to success in terms of scalability and reliability. In this work we describe an IaaS (Infrastructure as a Service) cloud computing system, with high availability and redundancy features, which is currently in production at INFN-Naples and ATLAS Tier-2 data centre. The main goal we intended to achieve was a simplified method to manage our computing resources and deliver reliable user services, reusing existing hardware without incurring heavy costs. A combined usage of virtualization and clustering technologies allowed us to consolidate our services on a small number of physical machines, reducing electric power costs. As a result of our efforts we developed a complete solution for data and computing centres that can be easily replicated using commodity hardware. Our architecture consists of 2 main subsystems: a clustered storage solution, built on top of disk servers running GlusterFS file system, and a virtual machines execution environment. GlusterFS is a network file system able to perform parallel writes on multiple disk servers, providing this way live replication of data. High availability is also achieved via a network configuration using redundant switches and multiple paths between hypervisor hosts and disk servers. We also developed a set of management scripts to easily perform basic system administration tasks such as automatic deployment of new virtual machines, adaptive scheduling of virtual machines on hypervisor hosts, live migration and automated restart in case of hypervisor failures.

The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud.

PubMed

Karimi, Kamran; Vize, Peter D

2014-01-01

As a model organism database, Xenbase has been providing informatics and genomic data on Xenopus (Silurana) tropicalis and Xenopus laevis frogs for more than a decade. The Xenbase database contains curated, as well as community-contributed and automatically harvested literature, gene and genomic data. A GBrowse genome browser, a BLAST+ server and stock center support are available on the site. When this resource was first built, all software services and components in Xenbase ran on a single physical server, with inherent reliability, scalability and inter-dependence issues. Recent advances in networking and virtualization techniques allowed us to move Xenbase to a virtual environment, and more specifically to a private cloud. To do so we decoupled the different software services and components, such that each would run on a different virtual machine. In the process, we also upgraded many of the components. The resulting system is faster and more reliable. System maintenance is easier, as individual virtual machines can now be updated, backed up and changed independently. We are also experiencing more effective resource allocation and utilization. Database URL: www.xenbase.org. © The Author(s) 2014. Published by Oxford University Press.

The Benefits and Complexities of Operating Geographic Information Systems (GIS) in a High Performance Computing (HPC) Environment

NASA Astrophysics Data System (ADS)

Shute, J.; Carriere, L.; Duffy, D.; Hoy, E.; Peters, J.; Shen, Y.; Kirschbaum, D.

2017-12-01

The NASA Center for Climate Simulation (NCCS) at the Goddard Space Flight Center is building and maintaining an Enterprise GIS capability for its stakeholders, to include NASA scientists, industry partners, and the public. This platform is powered by three GIS subsystems operating in a highly-available, virtualized environment: 1) the Spatial Analytics Platform is the primary NCCS GIS and provides users discoverability of the vast DigitalGlobe/NGA raster assets within the NCCS environment; 2) the Disaster Mapping Platform provides mapping and analytics services to NASA's Disaster Response Group; and 3) the internal (Advanced Data Analytics Platform/ADAPT) enterprise GIS provides users with the full suite of Esri and open source GIS software applications and services. All systems benefit from NCCS's cutting edge infrastructure, to include an InfiniBand network for high speed data transfers; a mixed/heterogeneous environment featuring seamless sharing of information between Linux and Windows subsystems; and in-depth system monitoring and warning systems. Due to its co-location with the NCCS Discover High Performance Computing (HPC) environment and the Advanced Data Analytics Platform (ADAPT), the GIS platform has direct access to several large NCCS datasets including DigitalGlobe/NGA, Landsat, MERRA, and MERRA2. Additionally, the NCCS ArcGIS Desktop Windows virtual machines utilize existing NetCDF and OPeNDAP assets for visualization, modelling, and analysis - thus eliminating the need for data duplication. With the advent of this platform, Earth scientists have full access to vast data repositories and the industry-leading tools required for successful management and analysis of these multi-petabyte, global datasets. The full system architecture and integration with scientific datasets will be presented. Additionally, key applications and scientific analyses will be explained, to include the NASA Global Landslide Catalog (GLC) Reporter crowdsourcing application, the NASA GLC Viewer discovery and analysis tool, the DigitalGlobe/NGA Data Discovery Tool, the NASA Disaster Response Group Mapping Platform (https://maps.disasters.nasa.gov), and support for NASA's Arctic - Boreal Vulnerability Experiment (ABoVE).

Research on axisymmetric aspheric surface numerical design and manufacturing technology

NASA Astrophysics Data System (ADS)

Wang, Zhen-zhong; Guo, Yin-biao; Lin, Zheng

2006-02-01

The key technology for aspheric machining offers exact machining path and machining aspheric lens with high accuracy and efficiency, in spite of the development of traditional manual manufacturing into nowadays numerical control (NC) machining. This paper presents a mathematical model between virtual cone and aspheric surface equations, and discusses the technology of uniform wear of grinding wheel and error compensation in aspheric machining. Finally, a software system for high precision aspheric surface manufacturing is designed and realized, based on the mentioned above. This software system can work out grinding wheel path according to input parameters and generate machining NC programs of aspheric surfaces.

2D and 3D virtual interactive laboratories of physics on Unity platform

NASA Astrophysics Data System (ADS)

González, J. D.; Escobar, J. H.; Sánchez, H.; De la Hoz, J.; Beltrán, J. R.

2017-12-01

Using the cross-platform game engine Unity, we develop virtual laboratories for PC, consoles, mobile devices and website as an innovative tool to study physics. There is extensive uptake of ICT in the teaching of science and its impact on the learning, and considering the limited availability of laboratories for physics teaching and the difficulties this causes in the learning of school students, we design the virtual laboratories to enhance studentâĂŹs knowledge of concepts in physics. To achieve this goal, we use Unity due to provide support bump mapping, reflection mapping, parallax mapping, dynamics shadows using shadows maps, full-screen post-processing effects and render-to-texture. Unity can use the best variant for the current video hardware and, if none are compatible, to use an alternative shader that may sacrifice features for performance. The control over delivery to mobile devices, web browsers, consoles and desktops is the main reason Unity is the best option among the same kind cross-platform. Supported platforms include Android, Apple TV, Linux, iOS, Nintendo 3DS line, macOS, PlayStation 4, Windows Phone 8, Wii but also an asset server and Nvidia’s PhysX physics engine which is the most relevant tool on Unity for our PhysLab.

Virtual Planning, Control, and Machining for a Modular-Based Automated Factory Operation in an Augmented Reality Environment

PubMed Central

Pai, Yun Suen; Yap, Hwa Jen; Md Dawal, Siti Zawiah; Ramesh, S.; Phoon, Sin Ye

2016-01-01

This study presents a modular-based implementation of augmented reality to provide an immersive experience in learning or teaching the planning phase, control system, and machining parameters of a fully automated work cell. The architecture of the system consists of three code modules that can operate independently or combined to create a complete system that is able to guide engineers from the layout planning phase to the prototyping of the final product. The layout planning module determines the best possible arrangement in a layout for the placement of various machines, in this case a conveyor belt for transportation, a robot arm for pick-and-place operations, and a computer numerical control milling machine to generate the final prototype. The robotic arm module simulates the pick-and-place operation offline from the conveyor belt to a computer numerical control (CNC) machine utilising collision detection and inverse kinematics. Finally, the CNC module performs virtual machining based on the Uniform Space Decomposition method and axis aligned bounding box collision detection. The conducted case study revealed that given the situation, a semi-circle shaped arrangement is desirable, whereas the pick-and-place system and the final generated G-code produced the highest deviation of 3.83 mm and 5.8 mm respectively. PMID:27271840

Virtual Planning, Control, and Machining for a Modular-Based Automated Factory Operation in an Augmented Reality Environment.

PubMed

Pai, Yun Suen; Yap, Hwa Jen; Md Dawal, Siti Zawiah; Ramesh, S; Phoon, Sin Ye

2016-06-07

This study presents a modular-based implementation of augmented reality to provide an immersive experience in learning or teaching the planning phase, control system, and machining parameters of a fully automated work cell. The architecture of the system consists of three code modules that can operate independently or combined to create a complete system that is able to guide engineers from the layout planning phase to the prototyping of the final product. The layout planning module determines the best possible arrangement in a layout for the placement of various machines, in this case a conveyor belt for transportation, a robot arm for pick-and-place operations, and a computer numerical control milling machine to generate the final prototype. The robotic arm module simulates the pick-and-place operation offline from the conveyor belt to a computer numerical control (CNC) machine utilising collision detection and inverse kinematics. Finally, the CNC module performs virtual machining based on the Uniform Space Decomposition method and axis aligned bounding box collision detection. The conducted case study revealed that given the situation, a semi-circle shaped arrangement is desirable, whereas the pick-and-place system and the final generated G-code produced the highest deviation of 3.83 mm and 5.8 mm respectively.

Virtual Planning, Control, and Machining for a Modular-Based Automated Factory Operation in an Augmented Reality Environment

NASA Astrophysics Data System (ADS)

Pai, Yun Suen; Yap, Hwa Jen; Md Dawal, Siti Zawiah; Ramesh, S.; Phoon, Sin Ye

2016-06-01

This study presents a modular-based implementation of augmented reality to provide an immersive experience in learning or teaching the planning phase, control system, and machining parameters of a fully automated work cell. The architecture of the system consists of three code modules that can operate independently or combined to create a complete system that is able to guide engineers from the layout planning phase to the prototyping of the final product. The layout planning module determines the best possible arrangement in a layout for the placement of various machines, in this case a conveyor belt for transportation, a robot arm for pick-and-place operations, and a computer numerical control milling machine to generate the final prototype. The robotic arm module simulates the pick-and-place operation offline from the conveyor belt to a computer numerical control (CNC) machine utilising collision detection and inverse kinematics. Finally, the CNC module performs virtual machining based on the Uniform Space Decomposition method and axis aligned bounding box collision detection. The conducted case study revealed that given the situation, a semi-circle shaped arrangement is desirable, whereas the pick-and-place system and the final generated G-code produced the highest deviation of 3.83 mm and 5.8 mm respectively.

Research on numerical control system based on S3C2410 and MCX314AL

NASA Astrophysics Data System (ADS)

Ren, Qiang; Jiang, Tingbiao

2008-10-01

With the rapid development of micro-computer technology, embedded system, CNC technology and integrated circuits, numerical control system with powerful functions can be realized by several high-speed CPU chips and RISC (Reduced Instruction Set Computing) chips which have small size and strong stability. In addition, the real-time operating system also makes the attainment of embedded system possible. Developing the NC system based on embedded technology can overcome some shortcomings of common PC-based CNC system, such as the waste of resources, low control precision, low frequency and low integration. This paper discusses a hardware platform of ENC (Embedded Numerical Control) system based on embedded processor chip ARM (Advanced RISC Machines)-S3C2410 and DSP (Digital Signal Processor)-MCX314AL and introduces the process of developing ENC system software. Finally write the MCX314AL's driver under the embedded Linux operating system. The embedded Linux operating system can deal with multitask well moreover satisfy the real-time and reliability of movement control. NC system has the advantages of best using resources and compact system with embedded technology. It provides a wealth of functions and superior performance with a lower cost. It can be sure that ENC is the direction of the future development.

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

Virtual reality in surgical training.

PubMed

Lange, T; Indelicato, D J; Rosen, J M

2000-01-01

Virtual reality in surgery and, more specifically, in surgical training, faces a number of challenges in the future. These challenges are building realistic models of the human body, creating interface tools to view, hear, touch, feel, and manipulate these human body models, and integrating virtual reality systems into medical education and treatment. A final system would encompass simulators specifically for surgery, performance machines, telemedicine, and telesurgery. Each of these areas will need significant improvement for virtual reality to impact medicine successfully in the next century. This article gives an overview of, and the challenges faced by, current systems in the fast-changing field of virtual reality technology, and provides a set of specific milestones for a truly realistic virtual human body.

Cloud flexibility using DIRAC interware

NASA Astrophysics Data System (ADS)

Fernandez Albor, Víctor; Seco Miguelez, Marcos; Fernandez Pena, Tomas; Mendez Muñoz, Victor; Saborido Silva, Juan Jose; Graciani Diaz, Ricardo

2014-06-01

Communities of different locations are running their computing jobs on dedicated infrastructures without the need to worry about software, hardware or even the site where their programs are going to be executed. Nevertheless, this usually implies that they are restricted to use certain types or versions of an Operating System because either their software needs an definite version of a system library or a specific platform is required by the collaboration to which they belong. On this scenario, if a data center wants to service software to incompatible communities, it has to split its physical resources among those communities. This splitting will inevitably lead to an underuse of resources because the data centers are bound to have periods where one or more of its subclusters are idle. It is, in this situation, where Cloud Computing provides the flexibility and reduction in computational cost that data centers are searching for. This paper describes a set of realistic tests that we ran on one of such implementations. The test comprise software from three different HEP communities (Auger, LHCb and QCD phenomelogists) and the Parsec Benchmark Suite running on one or more of three Linux flavors (SL5, Ubuntu 10.04 and Fedora 13). The implemented infrastructure has, at the cloud level, CloudStack that manages the virtual machines (VM) and the hosts on which they run, and, at the user level, the DIRAC framework along with a VM extension that will submit, monitorize and keep track of the user jobs and also requests CloudStack to start or stop the necessary VM's. In this infrastructure, the community software is distributed via the CernVM-FS, which has been proven to be a reliable and scalable software distribution system. With the resulting infrastructure, users are allowed to send their jobs transparently to the Data Center. The main purpose of this system is the creation of flexible cluster, multiplatform with an scalable method for software distribution for several VOs. Users from different communities do not need to care about the installation of the standard software that is available at the nodes, nor the operating system of the host machine, which is transparent to the user.

AstroCloud, a Cyber-Infrastructure for Astronomy Research: Data Access and Interoperability

NASA Astrophysics Data System (ADS)

Fan, D.; He, B.; Xiao, J.; Li, S.; Li, C.; Cui, C.; Yu, C.; Hong, Z.; Yin, S.; Wang, C.; Cao, Z.; Fan, Y.; Mi, L.; Wan, W.; Wang, J.

2015-09-01

Data access and interoperability module connects the observation proposals, data, virtual machines and software. According to the unique identifier of PI (principal investigator), an email address or an internal ID, data can be collected by PI's proposals, or by the search interfaces, e.g. conesearch. Files associated with the searched results could be easily transported to cloud storages, including the storage with virtual machines, or several commercial platforms like Dropbox. Benefitted from the standards of IVOA (International Observatories Alliance), VOTable formatted searching result could be sent to kinds of VO software. Latter endeavor will try to integrate more data and connect archives and some other astronomical resources.

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

An efficient approach for improving virtual machine placement in cloud computing environment

NASA Astrophysics Data System (ADS)

Ghobaei-Arani, Mostafa; Shamsi, Mahboubeh; Rahmanian, Ali A.

2017-11-01

The ever increasing demand for the cloud services requires more data centres. The power consumption in the data centres is a challenging problem for cloud computing, which has not been considered properly by the data centre developer companies. Especially, large data centres struggle with the power cost and the Greenhouse gases production. Hence, employing the power efficient mechanisms are necessary to optimise the mentioned effects. Moreover, virtual machine (VM) placement can be used as an effective method to reduce the power consumption in data centres. In this paper by grouping both virtual and physical machines, and taking into account the maximum absolute deviation during the VM placement, the power consumption as well as the service level agreement (SLA) deviation in data centres are reduced. To this end, the best-fit decreasing algorithm is utilised in the simulation to reduce the power consumption by about 5% compared to the modified best-fit decreasing algorithm, and at the same time, the SLA violation is improved by 6%. Finally, the learning automata are used to a trade-off between power consumption reduction from one side, and SLA violation percentage from the other side.

Specifications and implementation of the RT MHD control system for the EC launcher of FTU

NASA Astrophysics Data System (ADS)

Galperti, C.; Alessi, E.; Boncagni, L.; Bruschi, A.; Granucci, G.; Grosso, A.; Iannone, F.; Marchetto, C.; Nowak, S.; Panella, M.; Sozzi, C.; Tilia, B.

2012-09-01

To perform real time plasma control experiments using EC heating waves by using the new fast launcher installed on FTU a dedicated data acquisition and elaboration system has been designed recently. A prototypical version of the acquisition/control system has been recently developed and will be tested on FTU machine in its next experimental campaign. The open-source framework MARTe (Multi-threaded Application Real-Time executor) on Linux/RTAI real-time operating system has been chosen as software platform to realize the control system. Standard open-architecture industrial PCs, based either on VME bus and CompactPCI bus equipped with standard input/output cards are the chosen hardware platform.

Tablet—next generation sequence assembly visualization

PubMed Central

Milne, Iain; Bayer, Micha; Cardle, Linda; Shaw, Paul; Stephen, Gordon; Wright, Frank; Marshall, David

2010-01-01

Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions. Contact: tablet@scri.ac.uk PMID:19965881

CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping.

PubMed

de Givry, Simon; Bouchez, Martin; Chabrier, Patrick; Milan, Denis; Schiex, Thomas

2005-04-15

CAR(H)(T)A GENE: is an integrated genetic and radiation hybrid (RH) mapping tool which can deal with multiple populations, including mixtures of genetic and RH data. CAR(H)(T)A GENE: performs multipoint maximum likelihood estimations with accelerated expectation-maximization algorithms for some pedigrees and has sophisticated algorithms for marker ordering. Dedicated heuristics for framework mapping are also included. CAR(H)(T)A GENE: can be used as a C++ library, through a shell command and a graphical interface. The XML output for companion tools is integrated. The program is available free of charge from www.inra.fr/bia/T/CarthaGene for Linux, Windows and Solaris machines (with Open Source). tschiex@toulouse.inra.fr.

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

Self-replicating machines in continuous space with virtual physics.

PubMed

Smith, Arnold; Turney, Peter; Ewaschuk, Robert

2003-01-01

JohnnyVon is an implementation of self-replicating machines in continuous two-dimensional space. Two types of particles drift about in a virtual liquid. The particles are automata with discrete internal states but continuous external relationships. Their internal states are governed by finite state machines, but their external relationships are governed by a simulated physics that includes Brownian motion, viscosity, and springlike attractive and repulsive forces. The particles can be assembled into patterns that can encode arbitrary strings of bits. We demonstrate that, if an arbitrary seed pattern is put in a soup of separate individual particles, the pattern will replicate by assembling the individual particles into copies of itself. We also show that, given sufficient time, a soup of separate individual particles will eventually spontaneously form self-replicating patterns. We discuss the implications of JohnnyVon for research in nanotechnology, theoretical biology, and artificial life.

Noise and Vibration Risk Prevention Virtual Web for Ubiquitous Training

ERIC Educational Resources Information Center

Redel-Macías, María Dolores; Cubero-Atienza, Antonio J.; Martínez-Valle, José Miguel; Pedrós-Pérez, Gerardo; del Pilar Martínez-Jiménez, María

2015-01-01

This paper describes a new Web portal offering experimental labs for ubiquitous training of university engineering students in work-related risk prevention. The Web-accessible computer program simulates the noise and machine vibrations met in the work environment, in a series of virtual laboratories that mimic an actual laboratory and provide the…

Using shadow page cache to improve isolated drivers performance.

PubMed

Zheng, Hao; Dong, Xiaoshe; Wang, Endong; Chen, Baoke; Zhu, Zhengdong; Liu, Chengzhe

2015-01-01

With the advantage of the reusability property of the virtualization technology, users can reuse various types and versions of existing operating systems and drivers in a virtual machine, so as to customize their application environment. In order to prevent users' virtualization environments being impacted by driver faults in virtual machine, Chariot examines the correctness of driver's write operations by the method of combining a driver's write operation capture and a driver's private access control table. However, this method needs to keep the write permission of shadow page table as read-only, so as to capture isolated driver's write operations through page faults, which adversely affect the performance of the driver. Based on delaying setting frequently used shadow pages' write permissions to read-only, this paper proposes an algorithm using shadow page cache to improve the performance of isolated drivers and carefully study the relationship between the performance of drivers and the size of shadow page cache. Experimental results show that, through the shadow page cache, the performance of isolated drivers can be greatly improved without impacting Chariot's reliability too much.

Using Shadow Page Cache to Improve Isolated Drivers Performance

PubMed Central

Dong, Xiaoshe; Wang, Endong; Chen, Baoke; Zhu, Zhengdong; Liu, Chengzhe

2015-01-01

With the advantage of the reusability property of the virtualization technology, users can reuse various types and versions of existing operating systems and drivers in a virtual machine, so as to customize their application environment. In order to prevent users' virtualization environments being impacted by driver faults in virtual machine, Chariot examines the correctness of driver's write operations by the method of combining a driver's write operation capture and a driver's private access control table. However, this method needs to keep the write permission of shadow page table as read-only, so as to capture isolated driver's write operations through page faults, which adversely affect the performance of the driver. Based on delaying setting frequently used shadow pages' write permissions to read-only, this paper proposes an algorithm using shadow page cache to improve the performance of isolated drivers and carefully study the relationship between the performance of drivers and the size of shadow page cache. Experimental results show that, through the shadow page cache, the performance of isolated drivers can be greatly improved without impacting Chariot's reliability too much. PMID:25815373

VirtualSpace: A vision of a machine-learned virtual space environment

NASA Astrophysics Data System (ADS)

Bortnik, J.; Sarno-Smith, L. K.; Chu, X.; Li, W.; Ma, Q.; Angelopoulos, V.; Thorne, R. M.

2017-12-01

Space borne instrumentation tends to come and go. A typical instrument will go through a phase of design and construction, be deployed on a spacecraft for several years while it collects data, and then be decommissioned and fade into obscurity. The data collected from that instrument will typically receive much attention while it is being collected, perhaps in the form of event studies, conjunctions with other instruments, or a few statistical surveys, but once the instrument or spacecraft is decommissioned, the data will be archived and receive progressively less attention with every passing year. This is the fate of all historical data, and will be the fate of data being collected by instruments even at the present time. But what if those instruments could come alive, and all be simultaneously present at any and every point in time and space? Imagine the scientific insights, and societal gains that could be achieved with a grand (virtual) heliophysical observatory that consists of every current and historical mission ever deployed? We propose that this is not just fantasy but is imminently doable with the data currently available, with the present computational resources, and with currently available algorithms. This project revitalizes existing data resources and lays the groundwork for incorporating data from every future mission to expand the scope and refine the resolution of the virtual observatory. We call this project VirtualSpace: a machine-learned virtual space environment.

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

Hart, William Eugene

These slides describe different strategies for installing Python software. Although I am a big fan of Python software development, robust strategies for software installation remains a challenge. This talk describes several different installation scenarios. The Good: the user has administrative privileges - Installing on Windows with an installer executable, Installing with Linux application utility, Installing a Python package from the PyPI repository, and Installing a Python package from source. The Bad: the user does not have administrative privileges - Using a virtual environment to isolate package installations, and Using an installer executable on Windows with a virtual environment. The Ugly:more » the user needs to install an extension package from source - Installing a Python extension package from source, and PyCoinInstall - Managing builds for Python extension packages. The last item referring to PyCoinInstall describes a utility being developed for the COIN-OR software, which is used within the operations research community. COIN-OR includes a variety of Python and C++ software packages, and this script uses a simple plug-in system to support the management of package builds and installation.« less

Virtual pools for interactive analysis and software development through an integrated Cloud environment

NASA Astrophysics Data System (ADS)

Grandi, C.; Italiano, A.; Salomoni, D.; Calabrese Melcarne, A. K.

2011-12-01

WNoDeS, an acronym for Worker Nodes on Demand Service, is software developed at CNAF-Tier1, the National Computing Centre of the Italian Institute for Nuclear Physics (INFN) located in Bologna. WNoDeS provides on demand, integrated access to both Grid and Cloud resources through virtualization technologies. Besides the traditional use of computing resources in batch mode, users need to have interactive and local access to a number of systems. WNoDeS can dynamically select these computers instantiating Virtual Machines, according to the requirements (computing, storage and network resources) of users through either the Open Cloud Computing Interface API, or through a web console. An interactive use is usually limited to activities in user space, i.e. where the machine configuration is not modified. In some other instances the activity concerns development and testing of services and thus implies the modification of the system configuration (and, therefore, root-access to the resource). The former use case is a simple extension of the WNoDeS approach, where the resource is provided in interactive mode. The latter implies saving the virtual image at the end of each user session so that it can be presented to the user at subsequent requests. This work describes how the LHC experiments at INFN-Bologna are testing and making use of these dynamically created ad-hoc machines via WNoDeS to support flexible, interactive analysis and software development at the INFN Tier-1 Computing Centre.

OpenStereo: Open Source, Cross-Platform Software for Structural Geology Analysis

NASA Astrophysics Data System (ADS)

Grohmann, C. H.; Campanha, G. A.

2010-12-01

Free and open source software (FOSS) are increasingly seen as synonyms of innovation and progress. Freedom to run, copy, distribute, study, change and improve the software (through access to the source code) assure a high level of positive feedback between users and developers, which results in stable, secure and constantly updated systems. Several software packages for structural geology analysis are available to the user, with commercial licenses or that can be downloaded at no cost from the Internet. Some provide basic tools of stereographic projections such as plotting poles, great circles, density contouring, eigenvector analysis, data rotation etc, while others perform more specific tasks, such as paleostress or geotechnical/rock stability analysis. This variety also means a wide range of data formating for input, Graphical User Interface (GUI) design and graphic export format. The majority of packages is built for MS-Windows and even though there are packages for the UNIX-based MacOS, there aren't native packages for *nix (UNIX, Linux, BSD etc) Operating Systems (OS), forcing the users to run these programs with emulators or virtual machines. Those limitations lead us to develop OpenStereo, an open source, cross-platform software for stereographic projections and structural geology. The software is written in Python, a high-level, cross-platform programming language and the GUI is designed with wxPython, which provide a consistent look regardless the OS. Numeric operations (like matrix and linear algebra) are performed with the Numpy module and all graphic capabilities are provided by the Matplolib library, including on-screen plotting and graphic exporting to common desktop formats (emf, eps, ps, pdf, png, svg). Data input is done with simple ASCII text files, with values of dip direction and dip/plunge separated by spaces, tabs or commas. The user can open multiple file at the same time (or the same file more than once), and overlay different elements of each dataset (poles, great circles etc). The GUI shows the opened files in a tree structure, similar to “layers” of many illustration software, where the vertical order of the files in the tree reflects the drawing order of the selected elements. At this stage, the software performs plotting operations of poles to planes, lineations, great circles, density contours and rose diagrams. A set of statistics is calculated for each file and its eigenvalues and eigenvectors are used to suggest if the data is clustered about a mean value or distributed along a girdle. Modified Flinn, Triangular and histograms plots are also available. Next step of development will focus on tools as merging and rotation of datasets, possibility to save 'projects' and paleostress analysis. In its current state, OpenStereo requires Python, wxPython, Numpy and Matplotlib installed in the system. We recommend installing PythonXY or the Enthought Python Distribution on MS-Windows and MacOS machines, since all dependencies are provided. Most Linux distributions provide an easy way to install all dependencies through software repositories. OpenStereo is released under the GNU General Public License. Programmers willing to contribute are encouraged to contact the authors directly. FAPESP Grant #09/17675-5

Electrical Machines Laminations Magnetic Properties: A Virtual Instrument Laboratory

ERIC Educational Resources Information Center

Martinez-Roman, Javier; Perez-Cruz, Juan; Pineda-Sanchez, Manuel; Puche-Panadero, Ruben; Roger-Folch, Jose; Riera-Guasp, Martin; Sapena-Baño, Angel

2015-01-01

Undergraduate courses in electrical machines often include an introduction to their magnetic circuits and to the various magnetic materials used in their construction and their properties. The students must learn to be able to recognize and compare the permeability, saturation, and losses of these magnetic materials, relate each material to its…

MLViS: A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development

PubMed Central

Korkmaz, Selcuk; Zararsiz, Gokmen; Goksuluk, Dincer

2015-01-01

Virtual screening is an important step in early-phase of drug discovery process. Since there are thousands of compounds, this step should be both fast and effective in order to distinguish drug-like and nondrug-like molecules. Statistical machine learning methods are widely used in drug discovery studies for classification purpose. Here, we aim to develop a new tool, which can classify molecules as drug-like and nondrug-like based on various machine learning methods, including discriminant, tree-based, kernel-based, ensemble and other algorithms. To construct this tool, first, performances of twenty-three different machine learning algorithms are compared by ten different measures, then, ten best performing algorithms have been selected based on principal component and hierarchical cluster analysis results. Besides classification, this application has also ability to create heat map and dendrogram for visual inspection of the molecules through hierarchical cluster analysis. Moreover, users can connect the PubChem database to download molecular information and to create two-dimensional structures of compounds. This application is freely available through www.biosoft.hacettepe.edu.tr/MLViS/. PMID:25928885

Prediction Based Proactive Thermal Virtual Machine Scheduling in Green Clouds

PubMed Central

Kinger, Supriya; Kumar, Rajesh; Sharma, Anju

2014-01-01

Cloud computing has rapidly emerged as a widely accepted computing paradigm, but the research on Cloud computing is still at an early stage. Cloud computing provides many advanced features but it still has some shortcomings such as relatively high operating cost and environmental hazards like increasing carbon footprints. These hazards can be reduced up to some extent by efficient scheduling of Cloud resources. Working temperature on which a machine is currently running can be taken as a criterion for Virtual Machine (VM) scheduling. This paper proposes a new proactive technique that considers current and maximum threshold temperature of Server Machines (SMs) before making scheduling decisions with the help of a temperature predictor, so that maximum temperature is never reached. Different workload scenarios have been taken into consideration. The results obtained show that the proposed system is better than existing systems of VM scheduling, which does not consider current temperature of nodes before making scheduling decisions. Thus, a reduction in need of cooling systems for a Cloud environment has been obtained and validated. PMID:24737962

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.

VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development.

PubMed

Merks, Roeland M H; Guravage, Michael; Inzé, Dirk; Beemster, Gerrit T S

2011-02-01

Plant organs, including leaves and roots, develop by means of a multilevel cross talk between gene regulation, patterned cell division and cell expansion, and tissue mechanics. The multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies implicitly assume a direct relation between genes and traits at the level of the whole plant or organ. Instead, understanding gene function requires insight into the roles of gene products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible to understand intuitively. Mathematical and computer modeling allows researchers to design new hypotheses and produce experimentally testable insights. However, the required mathematics and programming experience makes modeling poorly accessible to experimental biologists. Problem-solving environments provide biologically intuitive in silico objects ("cells", "regulation networks") required for setting up a simulation and present those to the user in terms of familiar, biological terminology. Here, we introduce the cell-based computer modeling framework VirtualLeaf for plant tissue morphogenesis. The current version defines a set of biologically intuitive C++ objects, including cells, cell walls, and diffusing and reacting chemicals, that provide useful abstractions for building biological simulations of developmental processes. We present a step-by-step introduction to building models with VirtualLeaf, providing basic example models of leaf venation and meristem development. VirtualLeaf-based models provide a means for plant researchers to analyze the function of developmental genes in the context of the biophysics of growth and patterning. VirtualLeaf is an ongoing open-source software project (http://virtualleaf.googlecode.com) that runs on Windows, Mac, and Linux.

1001 Ways to run AutoDock Vina for virtual screening

NASA Astrophysics Data System (ADS)

Jaghoori, Mohammad Mahdi; Bleijlevens, Boris; Olabarriaga, Silvia D.

2016-03-01

Large-scale computing technologies have enabled high-throughput virtual screening involving thousands to millions of drug candidates. It is not trivial, however, for biochemical scientists to evaluate the technical alternatives and their implications for running such large experiments. Besides experience with the molecular docking tool itself, the scientist needs to learn how to run it on high-performance computing (HPC) infrastructures, and understand the impact of the choices made. Here, we review such considerations for a specific tool, AutoDock Vina, and use experimental data to illustrate the following points: (1) an additional level of parallelization increases virtual screening throughput on a multi-core machine; (2) capturing of the random seed is not enough (though necessary) for reproducibility on heterogeneous distributed computing systems; (3) the overall time spent on the screening of a ligand library can be improved by analysis of factors affecting execution time per ligand, including number of active torsions, heavy atoms and exhaustiveness. We also illustrate differences among four common HPC infrastructures: grid, Hadoop, small cluster and multi-core (virtual machine on the cloud). Our analysis shows that these platforms are suitable for screening experiments of different sizes. These considerations can guide scientists when choosing the best computing platform and set-up for their future large virtual screening experiments.

1001 Ways to run AutoDock Vina for virtual screening.

PubMed

Jaghoori, Mohammad Mahdi; Bleijlevens, Boris; Olabarriaga, Silvia D

2016-03-01

Large-scale computing technologies have enabled high-throughput virtual screening involving thousands to millions of drug candidates. It is not trivial, however, for biochemical scientists to evaluate the technical alternatives and their implications for running such large experiments. Besides experience with the molecular docking tool itself, the scientist needs to learn how to run it on high-performance computing (HPC) infrastructures, and understand the impact of the choices made. Here, we review such considerations for a specific tool, AutoDock Vina, and use experimental data to illustrate the following points: (1) an additional level of parallelization increases virtual screening throughput on a multi-core machine; (2) capturing of the random seed is not enough (though necessary) for reproducibility on heterogeneous distributed computing systems; (3) the overall time spent on the screening of a ligand library can be improved by analysis of factors affecting execution time per ligand, including number of active torsions, heavy atoms and exhaustiveness. We also illustrate differences among four common HPC infrastructures: grid, Hadoop, small cluster and multi-core (virtual machine on the cloud). Our analysis shows that these platforms are suitable for screening experiments of different sizes. These considerations can guide scientists when choosing the best computing platform and set-up for their future large virtual screening experiments.

Virtual reality hardware and graphic display options for brain-machine interfaces

PubMed Central

Marathe, Amar R.; Carey, Holle L.; Taylor, Dawn M.

2009-01-01

Virtual reality hardware and graphic displays are reviewed here as a development environment for brain-machine interfaces (BMIs). Two desktop stereoscopic monitors and one 2D monitor were compared in a visual depth discrimination task and in a 3D target-matching task where able-bodied individuals used actual hand movements to match a virtual hand to different target hands. Three graphic representations of the hand were compared: a plain sphere, a sphere attached to the fingertip of a realistic hand and arm, and a stylized pacman-like hand. Several subjects had great difficulty using either stereo monitor for depth perception when perspective size cues were removed. A mismatch in stereo and size cues generated inappropriate depth illusions. This phenomenon has implications for choosing target and virtual hand sizes in BMI experiments. Target matching accuracy was about as good with the 2D monitor as with either 3D monitor. However, users achieved this accuracy by exploring the boundaries of the hand in the target with carefully controlled movements. This method of determining relative depth may not be possible in BMI experiments if movement control is more limited. Intuitive depth cues, such as including a virtual arm, can significantly improve depth perception accuracy with or without stereo viewing. PMID:18006069

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

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

A Framework for Adaptable Operating and Runtime Systems

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

Sterling, Thomas

The emergence of new classes of HPC systems where performance improvement is enabled by Moore’s Law for technology is manifest through multi-core-based architectures including specialized GPU structures. Operating systems were originally designed for control of uniprocessor systems. By the 1980s multiprogramming, virtual memory, and network interconnection were integral services incorporated as part of most modern computers. HPC operating systems were primarily derivatives of the Unix model with Linux dominating the Top-500 list. The use of Linux for commodity clusters was first pioneered by the NASA Beowulf Project. However, the rapid increase in number of cores to achieve performance gain throughmore » technology advances has exposed the limitations of POSIX general-purpose operating systems in scaling and efficiency. This project was undertaken through the leadership of Sandia National Laboratories and in partnership of the University of New Mexico to investigate the alternative of composable lightweight kernels on scalable HPC architectures to achieve superior performance for a wide range of applications. The use of composable operating systems is intended to provide a minimalist set of services specifically required by a given application to preclude overheads and operational uncertainties (“OS noise”) that have been demonstrated to degrade efficiency and operational consistency. This project was undertaken as an exploration to investigate possible strategies and methods for composable lightweight kernel operating systems towards support for extreme scale systems.« less

General-Purpose Front End for Real-Time Data Processing

NASA Technical Reports Server (NTRS)

James, Mark

2007-01-01

FRONTIER is a computer program that functions as a front end for any of a variety of other software of both the artificial intelligence (AI) and conventional data-processing types. As used here, front end signifies interface software needed for acquiring and preprocessing data and making the data available for analysis by the other software. FRONTIER is reusable in that it can be rapidly tailored to any such other software with minimum effort. Each component of FRONTIER is programmable and is executed in an embedded virtual machine. Each component can be reconfigured during execution. The virtual-machine implementation making FRONTIER independent of the type of computing hardware on which it is executed.

Examining Effects of Virtual Machine Settings on Voice over Internet Protocol in a Private Cloud Environment

ERIC Educational Resources Information Center

Liao, Yuan

2011-01-01

The virtualization of computing resources, as represented by the sustained growth of cloud computing, continues to thrive. Information Technology departments are building their private clouds due to the perception of significant cost savings by managing all physical computing resources from a single point and assigning them to applications or…

New Virtual Field Trips. Revised Edition.

ERIC Educational Resources Information Center

Cooper, Gail; Cooper, Garry

This book is an annotated guidebook, arranged by subject matter, of World Wide Web sites for K-12 students. The following chapters are included: (1) Virtual Time Machine (i.e., sites that cover topics in world history); (2) Tour the World (i.e., sites that include information about countries); (3) Outer Space; (4) The Great Outdoors; (5) Aquatic…

Virtual Factory Framework for Supporting Production Planning and Control.

PubMed

Kibira, Deogratias; Shao, Guodong

2017-01-01

Developing optimal production plans for smart manufacturing systems is challenging because shop floor events change dynamically. A virtual factory incorporating engineering tools, simulation, and optimization generates and communicates performance data to guide wise decision making for different control levels. This paper describes such a platform specifically for production planning. We also discuss verification and validation of the constituent models. A case study of a machine shop is used to demonstrate data generation for production planning in a virtual factory.

Performance comparison analysis library communication cluster system using merge sort

NASA Astrophysics Data System (ADS)

Wulandari, D. A. R.; Ramadhan, M. E.

2018-04-01

Begins by using a single processor, to increase the speed of computing time, the use of multi-processor was introduced. The second paradigm is known as parallel computing, example cluster. The cluster must have the communication potocol for processing, one of it is message passing Interface (MPI). MPI have many library, both of them OPENMPI and MPICH2. Performance of the cluster machine depend on suitable between performance characters of library communication and characters of the problem so this study aims to analyze the comparative performances libraries in handling parallel computing process. The case study in this research are MPICH2 and OpenMPI. This case research execute sorting’s problem to know the performance of cluster system. The sorting problem use mergesort method. The research method is by implementing OpenMPI and MPICH2 on a Linux-based cluster by using five computer virtual then analyze the performance of the system by different scenario tests and three parameters for to know the performance of MPICH2 and OpenMPI. These performances are execution time, speedup and efficiency. The results of this study showed that the addition of each data size makes OpenMPI and MPICH2 have an average speed-up and efficiency tend to increase but at a large data size decreases. increased data size doesn’t necessarily increased speed up and efficiency but only execution time example in 100000 data size. OpenMPI has a execution time greater than MPICH2 example in 1000 data size average execution time with MPICH2 is 0,009721 and OpenMPI is 0,003895 OpenMPI can customize communication needs.

Training the next generation of scientists in Weather Forecasting: new approaches with real models

NASA Astrophysics Data System (ADS)

Carver, Glenn; Váňa, Filip; Siemen, Stephan; Kertesz, Sandor; Keeley, Sarah

2014-05-01

The European Centre for Medium Range Weather Forecasts operationally produce medium range forecasts using what is internationally acknowledged as the world leading global weather forecast model. Future development of this scientifically advanced model relies on a continued availability of experts in the field of meteorological science and with high-level software skills. ECMWF therefore has a vested interest in young scientists and University graduates developing the necessary skills in numerical weather prediction including both scientific and technical aspects. The OpenIFS project at ECMWF maintains a portable version of the ECMWF forecast model (known as IFS) for use in education and research at Universities, National Meteorological Services and other research and education organisations. OpenIFS models can be run on desktop or high performance computers to produce weather forecasts in a similar way to the operational forecasts at ECMWF. ECMWF also provide the Metview desktop application, a modern, graphical, and easy to use tool for analysing and visualising forecasts that is routinely used by scientists and forecasters at ECMWF and other institutions. The combination of Metview with the OpenIFS models has the potential to deliver classroom-friendly tools allowing students to apply their theoretical knowledge to real-world examples using a world-leading weather forecasting model. In this paper we will describe how the OpenIFS model has been used for teaching. We describe the use of Linux based 'virtual machines' pre-packaged on USB sticks that support a technically easy and safe way of providing 'classroom-on-a-stick' learning environments for advanced training in numerical weather prediction. We welcome discussions with interested parties.

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.

Performance of an MPI-only semiconductor device simulator on a quad socket/quad core InfiniBand platform.

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

Shadid, John Nicolas; Lin, Paul Tinphone

2009-01-01

This preliminary study considers the scaling and performance of a finite element (FE) semiconductor device simulator on a capacity cluster with 272 compute nodes based on a homogeneous multicore node architecture utilizing 16 cores. The inter-node communication backbone for this Tri-Lab Linux Capacity Cluster (TLCC) machine is comprised of an InfiniBand interconnect. The nonuniform memory access (NUMA) nodes consist of 2.2 GHz quad socket/quad core AMD Opteron processors. The performance results for this study are obtained with a FE semiconductor device simulation code (Charon) that is based on a fully-coupled Newton-Krylov solver with domain decomposition and multilevel preconditioners. Scaling andmore » multicore performance results are presented for large-scale problems of 100+ million unknowns on up to 4096 cores. A parallel scaling comparison is also presented with the Cray XT3/4 Red Storm capability platform. The results indicate that an MPI-only programming model for utilizing the multicore nodes is reasonably efficient on all 16 cores per compute node. However, the results also indicated that the multilevel preconditioner, which is critical for large-scale capability type simulations, scales better on the Red Storm machine than the TLCC machine.« less

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

Exploring Infiniband Hardware Virtualization in OpenNebula towards Efficient High-Performance Computing

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

Pais Pitta de Lacerda Ruivo, Tiago; Bernabeu Altayo, Gerard; Garzoglio, Gabriele

2014-11-11

has been widely accepted that software virtualization has a big negative impact on high-performance computing (HPC) application performance. This work explores the potential use of Infiniband hardware virtualization in an OpenNebula cloud towards the efficient support of MPI-based workloads. We have implemented, deployed, and tested an Infiniband network on the FermiCloud private Infrastructure-as-a-Service (IaaS) cloud. To avoid software virtualization towards minimizing the virtualization overhead, we employed a technique called Single Root Input/Output Virtualization (SRIOV). Our solution spanned modifications to the Linux’s Hypervisor as well as the OpenNebula manager. We evaluated the performance of the hardware virtualization on up to 56more » virtual machines connected by up to 8 DDR Infiniband network links, with micro-benchmarks (latency and bandwidth) as well as w a MPI-intensive application (the HPL Linpack benchmark).« less

Virtual Network Configuration Management System for Data Center Operations and Management

NASA Astrophysics Data System (ADS)

Okita, Hideki; Yoshizawa, Masahiro; Uehara, Keitaro; Mizuno, Kazuhiko; Tarui, Toshiaki; Naono, Ken

Virtualization technologies are widely deployed in data centers to improve system utilization. However, they increase the workload for operators, who have to manage the structure of virtual networks in data centers. A virtual-network management system which automates the integration of the configurations of the virtual networks is provided. The proposed system collects the configurations from server virtualization platforms and VLAN-supported switches, and integrates these configurations according to a newly developed XML-based management information model for virtual-network configurations. Preliminary evaluations show that the proposed system helps operators by reducing the time to acquire the configurations from devices and correct the inconsistency of operators' configuration management database by about 40 percent. Further, they also show that the proposed system has excellent scalability; the system takes less than 20 minutes to acquire the virtual-network configurations from a large scale network that includes 300 virtual machines. These results imply that the proposed system is effective for improving the configuration management process for virtual networks in data centers.

Efficient operating system level virtualization techniques for cloud resources

NASA Astrophysics Data System (ADS)

Ansu, R.; Samiksha; Anju, S.; Singh, K. John

2017-11-01

Cloud computing is an advancing technology which provides the servcies of Infrastructure, Platform and Software. Virtualization and Computer utility are the keys of Cloud computing. The numbers of cloud users are increasing day by day. So it is the need of the hour to make resources available on demand to satisfy user requirements. The technique in which resources namely storage, processing power, memory and network or I/O are abstracted is known as Virtualization. For executing the operating systems various virtualization techniques are available. They are: Full System Virtualization and Para Virtualization. In Full Virtualization, the whole architecture of hardware is duplicated virtually. No modifications are required in Guest OS as the OS deals with the VM hypervisor directly. In Para Virtualization, modifications of OS is required to run in parallel with other OS. For the Guest OS to access the hardware, the host OS must provide a Virtual Machine Interface. OS virtualization has many advantages such as migrating applications transparently, consolidation of server, online maintenance of OS and providing security. This paper briefs both the virtualization techniques and discusses the issues in OS level virtualization.

Virtual Employment Test Bed Operational Research and Systems Analysis to Test Armaments Designs Early in the Life Cycle

DTIC Science & Technology

2014-06-01

motion capture data used to determine position and orientation of a Soldier’s head, turret and the M2 machine gun • Controlling and acquiring user/weapon...data from the M2 simulation machine gun • Controlling paintball guns used to fire at the GPK during an experimental run • Sending and receiving TCP...Mounted, Armor/Cavalry, Combat Engineers, Field Artillery Cannon Crewmember, or MP duty assignment – Currently M2 .50 Caliber Machine Gun qualified

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

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.

An Introduction to 3-D Sound

NASA Technical Reports Server (NTRS)

Begault, Durand R.; Null, Cynthia H. (Technical Monitor)

1997-01-01

This talk will overview the basic technologies related to the creation of virtual acoustic images, and the potential of including spatial auditory displays in human-machine interfaces. Research into the perceptual error inherent in both natural and virtual spatial hearing is reviewed, since the formation of improved technologies is tied to psychoacoustic research. This includes a discussion of Head Related Transfer Function (HRTF) measurement techniques (the HRTF provides important perceptual cues within a virtual acoustic display). Many commercial applications of virtual acoustics have so far focused on games and entertainment ; in this review, other types of applications are examined, including aeronautic safety, voice communications, virtual reality, and room acoustic simulation. In particular, the notion that realistic simulation is optimized within a virtual acoustic display when head motion and reverberation cues are included within a perceptual model.

Efficiently Scheduling Multi-core Guest Virtual Machines on Multi-core Hosts in Network Simulation

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

Yoginath, Srikanth B; Perumalla, Kalyan S

2011-01-01

Virtual machine (VM)-based simulation is a method used by network simulators to incorporate realistic application behaviors by executing actual VMs as high-fidelity surrogates for simulated end-hosts. A critical requirement in such a method is the simulation time-ordered scheduling and execution of the VMs. Prior approaches such as time dilation are less efficient due to the high degree of multiplexing possible when multiple multi-core VMs are simulated on multi-core host systems. We present a new simulation time-ordered scheduler to efficiently schedule multi-core VMs on multi-core real hosts, with a virtual clock realized on each virtual core. The distinguishing features of ourmore » approach are: (1) customizable granularity of the VM scheduling time unit on the simulation time axis, (2) ability to take arbitrary leaps in virtual time by VMs to maximize the utilization of host (real) cores when guest virtual cores idle, and (3) empirically determinable optimality in the tradeoff between total execution (real) time and time-ordering accuracy levels. Experiments show that it is possible to get nearly perfect time-ordered execution, with a slight cost in total run time, relative to optimized non-simulation VM schedulers. Interestingly, with our time-ordered scheduler, it is also possible to reduce the time-ordering error from over 50% of non-simulation scheduler to less than 1% realized by our scheduler, with almost the same run time efficiency as that of the highly efficient non-simulation VM schedulers.« less

Open access for ALICE analysis based on virtualization technology

NASA Astrophysics Data System (ADS)

Buncic, P.; Gheata, M.; Schutz, Y.

2015-12-01

Open access is one of the important leverages for long-term data preservation for a HEP experiment. To guarantee the usability of data analysis tools beyond the experiment lifetime it is crucial that third party users from the scientific community have access to the data and associated software. The ALICE Collaboration has developed a layer of lightweight components built on top of virtualization technology to hide the complexity and details of the experiment-specific software. Users can perform basic analysis tasks within CernVM, a lightweight generic virtual machine, paired with an ALICE specific contextualization. Once the virtual machine is launched, a graphical user interface is automatically started without any additional configuration. This interface allows downloading the base ALICE analysis software and running a set of ALICE analysis modules. Currently the available tools include fully documented tutorials for ALICE analysis, such as the measurement of strange particle production or the nuclear modification factor in Pb-Pb collisions. The interface can be easily extended to include an arbitrary number of additional analysis modules. We present the current status of the tools used by ALICE through the CERN open access portal, and the plans for future extensions of this system.

Performance Comparison of EPICS IOC and MARTe in a Hard Real-Time Control Application

NASA Astrophysics Data System (ADS)

Barbalace, Antonio; Manduchi, Gabriele; Neto, A.; De Tommasi, G.; Sartori, F.; Valcarcel, D. F.

2011-12-01

EPICS is used worldwide mostly for controlling accelerators and large experimental physics facilities. Although EPICS is well fit for the design and development of automation systems, which are typically VME or PLC-based systems, and for soft real-time systems, it may present several drawbacks when used to develop hard real-time systems/applications especially when general purpose operating systems as plain Linux are chosen. This is in particular true in fusion research devices typically employing several hard real-time systems, such as the magnetic control systems, that may require strict determinism, and high performance in terms of jitter and latency. Serious deterioration of important plasma parameters may happen otherwise, possibly leading to an abrupt termination of the plasma discharge. The MARTe framework has been recently developed to fulfill the demanding requirements for such real-time systems that are alike to run on general purpose operating systems, possibly integrated with the low-latency real-time preemption patches. MARTe has been adopted to develop a number of real-time systems in different Tokamaks. In this paper, we first summarize differences and similarities between EPICS IOC and MARTe. Then we report on a set of performance measurements executed on an x86 64 bit multicore machine running Linux with an IO control algorithm implemented in an EPICS IOC and in MARTe.

Enhanced emotional responses during social coordination with a virtual partner

PubMed Central

Dumas, Guillaume; Kelso, J.A. Scott; Tognoli, Emmanuelle

2016-01-01

Emotion and motion, though seldom studied in tandem, are complementary aspects of social experience. This study investigates variations in emotional responses during movement coordination between a human and a Virtual Partner (VP), an agent whose virtual finger movements are driven by the Haken-Kelso-Bunz (HKB) equations of Coordination Dynamics. Twenty-one subjects were instructed to coordinate finger movements with the VP in either inphase or antiphase patterns. By adjusting model parameters, we manipulated the ‘intention’ of VP as cooperative or competitive with the human's instructed goal. Skin potential responses (SPR) were recorded to quantify the intensity of emotional response. At the end of each trial, subjects rated the VP's intention and whether they thought their partner was another human being or a machine. We found greater emotional responses when subjects reported that their partner was human and when coordination was stable. That emotional responses are strongly influenced by dynamic features of the VP's behavior, has implications for mental health, brain disorders and the design of socially cooperative machines. PMID:27094374

Introduction of Virtualization Technology to Multi-Process Model Checking

NASA Technical Reports Server (NTRS)

Leungwattanakit, Watcharin; Artho, Cyrille; Hagiya, Masami; Tanabe, Yoshinori; Yamamoto, Mitsuharu

2009-01-01

Model checkers find failures in software by exploring every possible execution schedule. Java PathFinder (JPF), a Java model checker, has been extended recently to cover networked applications by caching data transferred in a communication channel. A target process is executed by JPF, whereas its peer process runs on a regular virtual machine outside. However, non-deterministic target programs may produce different output data in each schedule, causing the cache to restart the peer process to handle the different set of data. Virtualization tools could help us restore previous states of peers, eliminating peer restart. This paper proposes the application of virtualization technology to networked model checking, concentrating on JPF.

Achieving High Resolution Timer Events in Virtualized Environment.

PubMed

Adamczyk, Blazej; Chydzinski, Andrzej

2015-01-01

Virtual Machine Monitors (VMM) have become popular in different application areas. Some applications may require to generate the timer events with high resolution and precision. This however may be challenging due to the complexity of VMMs. In this paper we focus on the timer functionality provided by five different VMMs-Xen, KVM, Qemu, VirtualBox and VMWare. Firstly, we evaluate resolutions and precisions of their timer events. Apparently, provided resolutions and precisions are far too low for some applications (e.g. networking applications with the quality of service). Then, using Xen virtualization we demonstrate the improved timer design that greatly enhances both the resolution and precision of achieved timer events.

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...

A video, text, and speech-driven realistic 3-d virtual head for human-machine interface.

PubMed

Yu, Jun; Wang, Zeng-Fu

2015-05-01

A multiple inputs-driven realistic facial animation system based on 3-D virtual head for human-machine interface is proposed. The system can be driven independently by video, text, and speech, thus can interact with humans through diverse interfaces. The combination of parameterized model and muscular model is used to obtain a tradeoff between computational efficiency and high realism of 3-D facial animation. The online appearance model is used to track 3-D facial motion from video in the framework of particle filtering, and multiple measurements, i.e., pixel color value of input image and Gabor wavelet coefficient of illumination ratio image, are infused to reduce the influence of lighting and person dependence for the construction of online appearance model. The tri-phone model is used to reduce the computational consumption of visual co-articulation in speech synchronized viseme synthesis without sacrificing any performance. The objective and subjective experiments show that the system is suitable for human-machine interaction.

Strength computation of forged parts taking into account strain hardening and damage

NASA Astrophysics Data System (ADS)

Cristescu, Michel L.

2004-06-01

Modern non-linear simulation software, such as FORGE 3 (registered trade mark of TRANSVALOR), are able to compute the residual stresses, the strain hardening and the damage during the forging process. A thermally dependent elasto-visco-plastic law is used to simulate the behavior of the material of the hot forged piece. A modified Lemaitre law coupled with elasticiy, plasticity and thermic is used to simulate the damage. After the simulation of the different steps of the forging process, the part is cooled and then virtually machined, in order to obtain the finished part. An elastic computation is then performed to equilibrate the residual stresses, so that we obtain the true geometry of the finished part after machining. The response of the part to the loadings it will sustain during it's life is then computed, taking into account the residual stresses, the strain hardening and the damage that occur during forging. This process is illustrated by the forging, virtual machining and stress analysis of an aluminium wheel hub.

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

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

Dynamically programmable cache

NASA Astrophysics Data System (ADS)

Nakkar, Mouna; Harding, John A.; Schwartz, David A.; Franzon, Paul D.; Conte, Thomas

1998-10-01

Reconfigurable machines have recently been used as co- processors to accelerate the execution of certain algorithms or program subroutines. The problems with the above approach include high reconfiguration time and limited partial reconfiguration. By far the most critical problems are: (1) the small on-chip memory which results in slower execution time, and (2) small FPGA areas that cannot implement large subroutines. Dynamically Programmable Cache (DPC) is a novel architecture for embedded processors which offers solutions to the above problems. To solve memory access problems, DPC processors merge reconfigurable arrays with the data cache at various cache levels to create a multi-level reconfigurable machines. As a result DPC machines have both higher data accessibility and FPGA memory bandwidth. To solve the limited FPGA resource problem, DPC processors implemented multi-context switching (Virtualization) concept. Virtualization allows implementation of large subroutines with fewer FPGA cells. Additionally, DPC processors can parallelize the execution of several operations resulting in faster execution time. In this paper, the speedup improvement for DPC machines are shown to be 5X faster than an Altera FLEX10K FPGA chip and 2X faster than a Sun Ultral SPARC station for two different algorithms (convolution and motion estimation).

Agreements in Virtual Organizations

NASA Astrophysics Data System (ADS)

Pankowska, Malgorzata

This chapter is an attempt to explain the important impact that contract theory delivers with respect to the concept of virtual organization. The author believes that not enough research has been conducted in order to transfer theoretical foundations for networking to the phenomena of virtual organizations and open autonomic computing environment to ensure the controllability and management of them. The main research problem of this chapter is to explain the significance of agreements for virtual organizations governance. The first part of this chapter comprises explanations of differences among virtual machines and virtual organizations for further descriptions of the significance of the first ones to the development of the second. Next, the virtual organization development tendencies are presented and problems of IT governance in highly distributed organizational environment are discussed. The last part of this chapter covers analysis of contracts and agreements management for governance in open computing environments.

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.

PiCO QL: A software library for runtime interactive queries on program data

NASA Astrophysics Data System (ADS)

Fragkoulis, Marios; Spinellis, Diomidis; Louridas, Panos

PiCO QL is an open source C/C++ software whose scientific scope is real-time interactive analysis of in-memory data through SQL queries. It exposes a relational view of a system's or application's data structures, which is queryable through SQL. While the application or system is executing, users can input queries through a web-based interface or issue web service requests. Queries execute on the live data structures through the respective relational views. PiCO QL makes a good candidate for ad-hoc data analysis in applications and for diagnostics in systems settings. Applications of PiCO QL include the Linux kernel, the Valgrind instrumentation framework, a GIS application, a virtual real-time observatory of stellar objects, and a source code analyser.

An efficient approach to the deployment of complex open source information systems

PubMed Central

Cong, Truong Van Chi; Groeneveld, Eildert

2011-01-01

Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information system in molecular genetics labs. It is a low-cost solution to benefit both software developers and end-users. PMID:22102770

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

McCaskey, Alexander J.

There is a lack of state-of-the-art HPC simulation tools for simulating general quantum computing. Furthermore, there are no real software tools that integrate current quantum computers into existing classical HPC workflows. This product, the Quantum Virtual Machine (QVM), solves this problem by providing an extensible framework for pluggable virtual, or physical, quantum processing units (QPUs). It enables the execution of low level quantum assembly codes and returns the results of such executions.

The Fluke Security Project

DTIC Science & Technology

2000-04-01

be an extension of Utah’s nascent Quarks system, oriented to closely coupled cluster environments. However, the grant did not actually begin until... Intel x86, implemented ten virtual machine monitors and servers, including a virtual memory manager, a checkpointer, a process manager, a file server...Fluke, we developed a novel hierarchical processor scheduling frame- work called CPU inheritance scheduling [5]. This is a framework for scheduling

The Integration of CloudStack and OCCI/OpenNebula with DIRAC

NASA Astrophysics Data System (ADS)

Méndez Muñoz, Víctor; Fernández Albor, Víctor; Graciani Diaz, Ricardo; Casajús Ramo, Adriàn; Fernández Pena, Tomás; Merino Arévalo, Gonzalo; José Saborido Silva, Juan

2012-12-01

The increasing availability of Cloud resources is arising as a realistic alternative to the Grid as a paradigm for enabling scientific communities to access large distributed computing resources. The DIRAC framework for distributed computing is an easy way to efficiently access to resources from both systems. This paper explains the integration of DIRAC with two open-source Cloud Managers: OpenNebula (taking advantage of the OCCI standard) and CloudStack. These are computing tools to manage the complexity and heterogeneity of distributed data center infrastructures, allowing to create virtual clusters on demand, including public, private and hybrid clouds. This approach has required to develop an extension to the previous DIRAC Virtual Machine engine, which was developed for Amazon EC2, allowing the connection with these new cloud managers. In the OpenNebula case, the development has been based on the CernVM Virtual Software Appliance with appropriate contextualization, while in the case of CloudStack, the infrastructure has been kept more general, which permits other Virtual Machine sources and operating systems being used. In both cases, CernVM File System has been used to facilitate software distribution to the computing nodes. With the resulting infrastructure, the cloud resources are transparent to the users through a friendly interface, like the DIRAC Web Portal. The main purpose of this integration is to get a system that can manage cloud and grid resources at the same time. This particular feature pushes DIRAC to a new conceptual denomination as interware, integrating different middleware. Users from different communities do not need to care about the installation of the standard software that is available at the nodes, nor the operating system of the host machine which is transparent to the user. This paper presents an analysis of the overhead of the virtual layer, doing some tests to compare the proposed approach with the existing Grid solution. License Notice: Published under licence in Journal of Physics: Conference Series by IOP Publishing Ltd.

Generating Contextual Descriptions of Virtual Reality (VR) Spaces

NASA Astrophysics Data System (ADS)

Olson, D. M.; Zaman, C. H.; Sutherland, A.

2017-12-01

Virtual reality holds great potential for science communication, education, and research. However, interfaces for manipulating data and environments in virtual worlds are limited and idiosyncratic. Furthermore, speech and vision are the primary modalities by which humans collect information about the world, but the linking of visual and natural language domains is a relatively new pursuit in computer vision. Machine learning techniques have been shown to be effective at image and speech classification, as well as at describing images with language (Karpathy 2016), but have not yet been used to describe potential actions. We propose a technique for creating a library of possible context-specific actions associated with 3D objects in immersive virtual worlds based on a novel dataset generated natively in virtual reality containing speech, image, gaze, and acceleration data. We will discuss the design and execution of a user study in virtual reality that enabled the collection and the development of this dataset. We will also discuss the development of a hybrid machine learning algorithm linking vision data with environmental affordances in natural language. Our findings demonstrate that it is possible to develop a model which can generate interpretable verbal descriptions of possible actions associated with recognized 3D objects within immersive VR environments. This suggests promising applications for more intuitive user interfaces through voice interaction within 3D environments. It also demonstrates the potential to apply vast bodies of embodied and semantic knowledge to enrich user interaction within VR environments. This technology would allow for applications such as expert knowledge annotation of 3D environments, complex verbal data querying and object manipulation in virtual spaces, and computer-generated, dynamic 3D object affordances and functionality during simulations.

The perception of spatial layout in real and virtual worlds.

PubMed

Arthur, E J; Hancock, P A; Chrysler, S T

1997-01-01

As human-machine interfaces grow more immersive and graphically-oriented, virtual environment systems become more prominent as the medium for human-machine communication. Often, virtual environments (VE) are built to provide exact metrical representations of existing or proposed physical spaces. However, it is not known how individuals develop representational models of these spaces in which they are immersed and how those models may be distorted with respect to both the virtual and real-world equivalents. To evaluate the process of model development, the present experiment examined participant's ability to reproduce a complex spatial layout of objects having experienced them previously under different viewing conditions. The layout consisted of nine common objects arranged on a flat plane. These objects could be viewed in a free binocular virtual condition, a free binocular real-world condition, and in a static monocular view of the real world. The first two allowed active exploration of the environment while the latter condition allowed the participant only a passive opportunity to observe from a single viewpoint. Viewing conditions were a between-subject variable with 10 participants randomly assigned to each condition. Performance was assessed using mapping accuracy and triadic comparisons of relative inter-object distances. Mapping results showed a significant effect of viewing condition where, interestingly, the static monocular condition was superior to both the active virtual and real binocular conditions. Results for the triadic comparisons showed a significant interaction for gender by viewing condition in which males were more accurate than females. These results suggest that the situation model resulting from interaction with a virtual environment was indistinguishable from interaction with real objects at least within the constraints of the present procedure.

Real-time data collection in Linux: a case study.

PubMed

Finney, S A

2001-05-01

Multiuser UNIX-like operating systems such as Linux are often considered unsuitable for real-time data collection because of the potential for indeterminate timing latencies resulting from preemptive scheduling. In this paper, Linux is shown to be fully adequate for precisely controlled programming with millisecond resolution or better. The Linux system calls that subserve such timing control are described and tested and then utilized in a MIDI-based program for tapping and music performance experiments. The timing of this program, including data input and output, is shown to be accurate at the millisecond level. This demonstrates that Linux, with proper programming, is suitable for real-time experiment software. In addition, the detailed description and test of both the operating system facilities and the application program itself may serve as a model for publicly documenting programming methods and software performance on other operating systems.

Performance of machine-learning scoring functions in structure-based virtual screening.

PubMed

Wójcikowski, Maciej; Ballester, Pedro J; Siedlecki, Pawel

2017-04-25

Classical scoring functions have reached a plateau in their performance in virtual screening and binding affinity prediction. Recently, machine-learning scoring functions trained on protein-ligand complexes have shown great promise in small tailored studies. They have also raised controversy, specifically concerning model overfitting and applicability to novel targets. Here we provide a new ready-to-use scoring function (RF-Score-VS) trained on 15 426 active and 893 897 inactive molecules docked to a set of 102 targets. We use the full DUD-E data sets along with three docking tools, five classical and three machine-learning scoring functions for model building and performance assessment. Our results show RF-Score-VS can substantially improve virtual screening performance: RF-Score-VS top 1% provides 55.6% hit rate, whereas that of Vina only 16.2% (for smaller percent the difference is even more encouraging: RF-Score-VS top 0.1% achieves 88.6% hit rate for 27.5% using Vina). In addition, RF-Score-VS provides much better prediction of measured binding affinity than Vina (Pearson correlation of 0.56 and -0.18, respectively). Lastly, we test RF-Score-VS on an independent test set from the DEKOIS benchmark and observed comparable results. We provide full data sets to facilitate further research in this area (http://github.com/oddt/rfscorevs) as well as ready-to-use RF-Score-VS (http://github.com/oddt/rfscorevs_binary).

Bridging Realty to Virtual Reality: Investigating Gender Effect and Student Engagement on Learning through Video Game Play in an Elementary School Classroom

ERIC Educational Resources Information Center

Annetta, Leonard; Mangrum, Jennifer; Holmes, Shawn; Collazo, Kimberly; Cheng, Meng-Tzu

2009-01-01

The purpose of this study was to examine students' learning of simple machines, a fifth-grade (ages 10-11) forces and motion unit, and student engagement using a teacher-created Multiplayer Educational Gaming Application. This mixed-method study collected pre-test/post-test results to determine student knowledge about simple machines. A survey…

Metronome LKM: An open source virtual keyboard driver to measure experiment software latencies.

PubMed

Garaizar, Pablo; Vadillo, Miguel A

2017-10-01

Experiment software is often used to measure reaction times gathered with keyboards or other input devices. In previous studies, the accuracy and precision of time stamps has been assessed through several means: (a) generating accurate square wave signals from an external device connected to the parallel port of the computer running the experiment software, (b) triggering the typematic repeat feature of some keyboards to get an evenly separated series of keypress events, or (c) using a solenoid handled by a microcontroller to press the input device (keyboard, mouse button, touch screen) that will be used in the experimental setup. Despite the advantages of these approaches in some contexts, none of them can isolate the measurement error caused by the experiment software itself. Metronome LKM provides a virtual keyboard to assess an experiment's software. Using this open source driver, researchers can generate keypress events using high-resolution timers and compare the time stamps collected by the experiment software with those gathered by Metronome LKM (with nanosecond resolution). Our software is highly configurable (in terms of keys pressed, intervals, SysRq activation) and runs on 2.6-4.8 Linux kernels.

Managing a tier-2 computer centre with a private cloud infrastructure

NASA Astrophysics Data System (ADS)

Bagnasco, Stefano; Berzano, Dario; Brunetti, Riccardo; Lusso, Stefano; Vallero, Sara

2014-06-01

In a typical scientific computing centre, several applications coexist and share a single physical infrastructure. An underlying Private Cloud infrastructure eases the management and maintenance of such heterogeneous applications (such as multipurpose or application-specific batch farms, Grid sites, interactive data analysis facilities and others), allowing dynamic allocation resources to any application. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques. Such infrastructures are being deployed in some large centres (see e.g. the CERN Agile Infrastructure project), but with several open-source tools reaching maturity this is becoming viable also for smaller sites. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 centre, an Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The private cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem and the OpenWRT Linux distribution (used for network virtualization); a future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and OCCI.

Architecture and Key Techniques of Augmented Reality Maintenance Guiding System for Civil Aircrafts

NASA Astrophysics Data System (ADS)

hong, Zhou; Wenhua, Lu

2017-01-01

Augmented reality technology is introduced into the maintenance related field for strengthened information in real-world scenarios through integration of virtual assistant maintenance information with real-world scenarios. This can lower the difficulty of maintenance, reduce maintenance errors, and improve the maintenance efficiency and quality of civil aviation crews. Architecture of augmented reality virtual maintenance guiding system is proposed on the basis of introducing the definition of augmented reality and analyzing the characteristics of augmented reality virtual maintenance. Key techniques involved, such as standardization and organization of maintenance data, 3D registration, modeling of maintenance guidance information and virtual maintenance man-machine interaction, are elaborated emphatically, and solutions are given.

Achieving High Resolution Timer Events in Virtualized Environment

PubMed Central

Adamczyk, Blazej; Chydzinski, Andrzej

2015-01-01

Virtual Machine Monitors (VMM) have become popular in different application areas. Some applications may require to generate the timer events with high resolution and precision. This however may be challenging due to the complexity of VMMs. In this paper we focus on the timer functionality provided by five different VMMs—Xen, KVM, Qemu, VirtualBox and VMWare. Firstly, we evaluate resolutions and precisions of their timer events. Apparently, provided resolutions and precisions are far too low for some applications (e.g. networking applications with the quality of service). Then, using Xen virtualization we demonstrate the improved timer design that greatly enhances both the resolution and precision of achieved timer events. PMID:26177366

A computer-based training system combining virtual reality and multimedia

NASA Technical Reports Server (NTRS)

Stansfield, Sharon A.

1993-01-01

Training new users of complex machines is often an expensive and time-consuming process. This is particularly true for special purpose systems, such as those frequently encountered in DOE applications. This paper presents a computer-based training system intended as a partial solution to this problem. The system extends the basic virtual reality (VR) training paradigm by adding a multimedia component which may be accessed during interaction with the virtual environment. The 3D model used to create the virtual reality is also used as the primary navigation tool through the associated multimedia. This method exploits the natural mapping between a virtual world and the real world that it represents to provide a more intuitive way for the student to interact with all forms of information about the system.

DIRAC universal pilots

NASA Astrophysics Data System (ADS)

Stagni, F.; McNab, A.; Luzzi, C.; Krzemien, W.; Consortium, DIRAC

2017-10-01

In the last few years, new types of computing models, such as IAAS (Infrastructure as a Service) and IAAC (Infrastructure as a Client), gained popularity. New resources may come as part of pledged resources, while others are in the form of opportunistic ones. Most but not all of these new infrastructures are based on virtualization techniques. In addition, some of them, present opportunities for multi-processor computing slots to the users. Virtual Organizations are therefore facing heterogeneity of the available resources and the use of an Interware software like DIRAC to provide the transparent, uniform interface has become essential. The transparent access to the underlying resources is realized by implementing the pilot model. DIRAC’s newest generation of generic pilots (the so-called Pilots 2.0) are the “pilots for all the skies”, and have been successfully released in production more than a year ago. They use a plugin mechanism that makes them easily adaptable. Pilots 2.0 have been used for fetching and running jobs on every type of resource, being it a Worker Node (WN) behind a CREAM/ARC/HTCondor/DIRAC Computing element, a Virtual Machine running on IaaC infrastructures like Vac or BOINC, on IaaS cloud resources managed by Vcycle, the LHCb High Level Trigger farm nodes, and any type of opportunistic computing resource. Make a machine a “Pilot Machine”, and all diversities between them will disappear. This contribution describes how pilots are made suitable for different resources, and the recent steps taken towards a fully unified framework, including monitoring. Also, the cases of multi-processor computing slots either on real or virtual machines, with the whole node or a partition of it, is discussed.

A virtual simulator designed for collision prevention in proton therapy.

PubMed

Jung, Hyunuk; Kum, Oyeon; Han, Youngyih; Park, Hee Chul; Kim, Jin Sung; Choi, Doo Ho

2015-10-01

In proton therapy, collisions between the patient and nozzle potentially occur because of the large nozzle structure and efforts to minimize the air gap. Thus, software was developed to predict such collisions between the nozzle and patient using treatment virtual simulation. Three-dimensional (3D) modeling of a gantry inner-floor, nozzle, and robotic-couch was performed using SolidWorks based on the manufacturer's machine data. To obtain patient body information, a 3D-scanner was utilized right before CT scanning. Using the acquired images, a 3D-image of the patient's body contour was reconstructed. The accuracy of the image was confirmed against the CT image of a humanoid phantom. The machine components and the virtual patient were combined on the treatment-room coordinate system, resulting in a virtual simulator. The simulator simulated the motion of its components such as rotation and translation of the gantry, nozzle, and couch in real scale. A collision, if any, was examined both in static and dynamic modes. The static mode assessed collisions only at fixed positions of the machine's components, while the dynamic mode operated any time a component was in motion. A collision was identified if any voxels of two components, e.g., the nozzle and the patient or couch, overlapped when calculating volume locations. The event and collision point were visualized, and collision volumes were reported. All components were successfully assembled, and the motions were accurately controlled. The 3D-shape of the phantom agreed with CT images within a deviation of 2 mm. Collision situations were simulated within minutes, and the results were displayed and reported. The developed software will be useful in improving patient safety and clinical efficiency of proton therapy.

How can machine-learning methods assist in virtual screening for hyperuricemia? A healthcare machine-learning approach.

PubMed

Ichikawa, Daisuke; Saito, Toki; Ujita, Waka; Oyama, Hiroshi

2016-12-01

Our purpose was to develop a new machine-learning approach (a virtual health check-up) toward identification of those at high risk of hyperuricemia. Applying the system to general health check-ups is expected to reduce medical costs compared with administering an additional test. Data were collected during annual health check-ups performed in Japan between 2011 and 2013 (inclusive). We prepared training and test datasets from the health check-up data to build prediction models; these were composed of 43,524 and 17,789 persons, respectively. Gradient-boosting decision tree (GBDT), random forest (RF), and logistic regression (LR) approaches were trained using the training dataset and were then used to predict hyperuricemia in the test dataset. Undersampling was applied to build the prediction models to deal with the imbalanced class dataset. The results showed that the RF and GBDT approaches afforded the best performances in terms of sensitivity and specificity, respectively. The area under the curve (AUC) values of the models, which reflected the total discriminative ability of the classification, were 0.796 [95% confidence interval (CI): 0.766-0.825] for the GBDT, 0.784 [95% CI: 0.752-0.815] for the RF, and 0.785 [95% CI: 0.752-0.819] for the LR approaches. No significant differences were observed between pairs of each approach. Small changes occurred in the AUCs after applying undersampling to build the models. We developed a virtual health check-up that predicted the development of hyperuricemia using machine-learning methods. The GBDT, RF, and LR methods had similar predictive capability. Undersampling did not remarkably improve predictive power. Copyright © 2016 Elsevier Inc. All rights reserved.

The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms

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

Sunderam, Vaidy S.

2012-03-20

The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept ofmore » a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds.« less

Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach.

PubMed

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D; Duvenaud, David; Maclaurin, Dougal; Blood-Forsythe, Martin A; Chae, Hyun Sik; Einzinger, Markus; Ha, Dong-Gwang; Wu, Tony; Markopoulos, Georgios; Jeon, Soonok; Kang, Hosuk; Miyazaki, Hiroshi; Numata, Masaki; Kim, Sunghan; Huang, Wenliang; Hong, Seong Ik; Baldo, Marc; Adams, Ryan P; Aspuru-Guzik, Alán

2016-10-01

Virtual screening is becoming a ground-breaking tool for molecular discovery due to the exponential growth of available computer time and constant improvement of simulation and machine learning techniques. We report an integrated organic functional material design process that incorporates theoretical insight, quantum chemistry, cheminformatics, machine learning, industrial expertise, organic synthesis, molecular characterization, device fabrication and optoelectronic testing. After exploring a search space of 1.6 million molecules and screening over 400,000 of them using time-dependent density functional theory, we identified thousands of promising novel organic light-emitting diode molecules across the visible spectrum. Our team collaboratively selected the best candidates from this set. The experimentally determined external quantum efficiencies for these synthesized candidates were as large as 22%.

Using a Virtual Tablet Machine to Improve Student Understanding of the Complex Processes Involved in Tablet Manufacturing.

PubMed

Mattsson, Sofia; Sjöström, Hans-Erik; Englund, Claire

2016-06-25

Objective. To develop and implement a virtual tablet machine simulation to aid distance students' understanding of the processes involved in tablet production. Design. A tablet simulation was created enabling students to study the effects different parameters have on the properties of the tablet. Once results were generated, students interpreted and explained them on the basis of current theory. Assessment. The simulation was evaluated using written questionnaires and focus group interviews. Students appreciated the exercise and considered it to be motivational. Students commented that they found the simulation, together with the online seminar and the writing of the report, was beneficial for their learning process. Conclusion. According to students' perceptions, the use of the tablet simulation contributed to their understanding of the compaction process.

Using a Virtual Tablet Machine to Improve Student Understanding of the Complex Processes Involved in Tablet Manufacturing

PubMed Central

Sjöström, Hans-Erik; Englund, Claire

2016-01-01

Objective. To develop and implement a virtual tablet machine simulation to aid distance students’ understanding of the processes involved in tablet production. Design. A tablet simulation was created enabling students to study the effects different parameters have on the properties of the tablet. Once results were generated, students interpreted and explained them on the basis of current theory. Assessment. The simulation was evaluated using written questionnaires and focus group interviews. Students appreciated the exercise and considered it to be motivational. Students commented that they found the simulation, together with the online seminar and the writing of the report, was beneficial for their learning process. Conclusion. According to students’ perceptions, the use of the tablet simulation contributed to their understanding of the compaction process. PMID:27402990

Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Duvenaud, David; MacLaurin, Dougal; Blood-Forsythe, Martin A.; Chae, Hyun Sik; Einzinger, Markus; Ha, Dong-Gwang; Wu, Tony; Markopoulos, Georgios; Jeon, Soonok; Kang, Hosuk; Miyazaki, Hiroshi; Numata, Masaki; Kim, Sunghan; Huang, Wenliang; Hong, Seong Ik; Baldo, Marc; Adams, Ryan P.; Aspuru-Guzik, Alán

2016-10-01

Virtual screening is becoming a ground-breaking tool for molecular discovery due to the exponential growth of available computer time and constant improvement of simulation and machine learning techniques. We report an integrated organic functional material design process that incorporates theoretical insight, quantum chemistry, cheminformatics, machine learning, industrial expertise, organic synthesis, molecular characterization, device fabrication and optoelectronic testing. After exploring a search space of 1.6 million molecules and screening over 400,000 of them using time-dependent density functional theory, we identified thousands of promising novel organic light-emitting diode molecules across the visible spectrum. Our team collaboratively selected the best candidates from this set. The experimentally determined external quantum efficiencies for these synthesized candidates were as large as 22%.

Making extreme computations possible with virtual machines

NASA Astrophysics Data System (ADS)

Reuter, J.; Chokoufe Nejad, B.; Ohl, T.

2016-10-01

State-of-the-art algorithms generate scattering amplitudes for high-energy physics at leading order for high-multiplicity processes as compiled code (in Fortran, C or C++). For complicated processes the size of these libraries can become tremendous (many GiB). We show that amplitudes can be translated to byte-code instructions, which even reduce the size by one order of magnitude. The byte-code is interpreted by a Virtual Machine with runtimes comparable to compiled code and a better scaling with additional legs. We study the properties of this algorithm, as an extension of the Optimizing Matrix Element Generator (O'Mega). The bytecode matrix elements are available as alternative input for the event generator WHIZARD. The bytecode interpreter can be implemented very compactly, which will help with a future implementation on massively parallel GPUs.

A One-Year Case Study: Understanding the Rich Potential of Project-Based Learning in a Virtual Reality Class for High School Students

ERIC Educational Resources Information Center

Morales, Teresa M.; Bang, EunJin; Andre, Thomas

2013-01-01

This paper presents a qualitative case analysis of a new and unique, high school, student-directed, project-based learning (PBL), virtual reality (VR) class. In order to create projects, students learned, on an independent basis, how to program an industrial-level VR machine. A constraint was that students were required to produce at least one…

Can Science Education Research Give an Answer to Questions Posed by History of Science and Technology? The Case of Steam Engine's Measurement

ERIC Educational Resources Information Center

Kanderakis, Nikos E.

2009-01-01

According to the principle of virtual velocities, if on a simple machine in equilibrium we suppose a slight virtual movement, then the ratio of weights or forces equals the inverse ratio of velocities or displacements. The product of the weight raised or force applied multiplied by the height or displacement plays a central role there. British…

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.

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

PubMed

Cole, Charles; Krampis, Konstantinos; Karagiannis, Konstantinos; Almeida, Jonas S; Faison, William J; Motwani, Mona; Wan, Quan; Golikov, Anton; Pan, Yang; Simonyan, Vahan; Mazumder, Raja

2014-01-27

Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides.

Semantic Web-based Vocabulary Broker for Open Science

NASA Astrophysics Data System (ADS)

Ritschel, B.; Neher, G.; Iyemori, T.; Murayama, Y.; Kondo, Y.; Koyama, Y.; King, T. A.; Galkin, I. A.; Fung, S. F.; Wharton, S.; Cecconi, B.

2016-12-01

Keyword vocabularies are used to tag and to identify data of science data repositories. Such vocabularies consist of controlled terms and the appropriate concepts, such as GCMD1 keywords or the ESPAS2 keyword ontology. The Semantic Web-based mash-up of domain-specific, cross- or even trans-domain vocabularies provides unique capabilities in the network of appropriate data resources. Based on a collaboration between GFZ3, the FHP4, the WDC for Geomagnetism5 and the NICT6 we developed the concept of a vocabulary broker for inter- and trans-disciplinary data detection and integration. Our prototype of the Semantic Web-based vocabulary broker uses OSF7 for the mash-up of geo and space research vocabularies, such as GCMD keywords, ESPAS keyword ontology and SPASE8 keyword vocabulary. The vocabulary broker starts the search with "free" keywords or terms of a specific vocabulary scheme. The vocabulary broker almost automatically connects the different science data repositories which are tagged by terms of the aforementioned vocabularies. Therefore the mash-up of the SKOS9 based vocabularies with appropriate metadata from different domains can be realized by addressing LOD10 resources or virtual SPARQL11 endpoints which maps relational structures into the RDF format12. In order to demonstrate such a mash-up approach in real life, we installed and use a D2RQ13 server for the integration of IUGONET14 data which are managed by a relational database. The OSF based vocabulary broker and the D2RQ platform are installed at virtual LINUX machines at the Kyoto University. The vocabulary broker meets the standard of a main component of the WDS15 knowledge network. The Web address of the vocabulary broker is http://wdcosf.kugi.kyoto-u.ac.jp 1 Global Change Master Directory2 Near earth space data infrastructure for e-science3 German Research Centre for Geosciences4 University of Applied Sciences Potsdam5 World Data Center for Geomagnetism Kyoto6 National Institute of Information and Communications Technology Tokyo7 Open Semantic Framework8 Space Physics Archive Search and Extract9 Simple Knowledge Organization System10 Linked Open Data11 SPARQL Protocol And RDF Query12 Resource Description Framework13 Database to RDF Query14 Inter-university Upper atmosphere Global Observation NETwork15 World Data System

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

PubMed Central

2014-01-01

Background Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. Results To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). Conclusions Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides. PMID:24467687

Methods For Self-Organizing Software

DOEpatents

Bouchard, Ann M.; Osbourn, Gordon C.

2005-10-18

A method for dynamically self-assembling and executing software is provided, containing machines that self-assemble execution sequences and data structures. In addition to ordered functions calls (found commonly in other software methods), mutual selective bonding between bonding sites of machines actuates one or more of the bonding machines. Two or more machines can be virtually isolated by a construct, called an encapsulant, containing a population of machines and potentially other encapsulants that can only bond with each other. A hierarchical software structure can be created using nested encapsulants. Multi-threading is implemented by populations of machines in different encapsulants that are interacting concurrently. Machines and encapsulants can move in and out of other encapsulants, thereby changing the functionality. Bonding between machines' sites can be deterministic or stochastic with bonding triggering a sequence of actions that can be implemented by each machine. A self-assembled execution sequence occurs as a sequence of stochastic binding between machines followed by their deterministic actuation. It is the sequence of bonding of machines that determines the execution sequence, so that the sequence of instructions need not be contiguous in memory.

Technological choices for mobile clinical applications.

PubMed

Ehrler, Frederic; Issom, David; Lovis, Christian

2011-01-01

The rise of cheaper and more powerful mobile devices make them a new and attractive platform for clinical applications. The interaction paradigm and portability of the device facilitates bedside human-machine interactions. The better accessibility to information and decision-support anywhere in the hospital improves the efficiency and the safety of care processes. In this study, we attempt to find out what are the most appropriate Operating System (OS) and Software Development Kit (SDK) to support the development of clinical applications on mobile devices. The Android platform is a Linux-based, open source platform that has many advantages. Two main SDKs are available on this platform: the native Android and the Adobe Flex SDK. Both of them have interesting features, but the latter has been preferred due its portability at comparable performance and ease of development.

BigView Image Viewing on Tiled Displays

NASA Technical Reports Server (NTRS)

Sandstrom, Timothy

2007-01-01

BigView allows for interactive panning and zooming of images of arbitrary size on desktop PCs running Linux. Additionally, it can work in a multi-screen environment where multiple PCs cooperate to view a single, large image. Using this software, one can explore on relatively modest machines images such as the Mars Orbiter Camera mosaic [92,160 33,280 pixels]. The images must be first converted into paged format, where the image is stored in 256 256 pages to allow rapid movement of pixels into texture memory. The format contains an image pyramid : a set of scaled versions of the original image. Each scaled image is 1/2 the size of the previous, starting with the original down to the smallest, which fits into a single 256 x 256 page.

A Novel Artificial Bee Colony Approach of Live Virtual Machine Migration Policy Using Bayes Theorem

PubMed Central

Xu, Gaochao; Hu, Liang; Fu, Xiaodong

2013-01-01

Green cloud data center has become a research hotspot of virtualized cloud computing architecture. Since live virtual machine (VM) migration technology is widely used and studied in cloud computing, we have focused on the VM placement selection of live migration for power saving. We present a novel heuristic approach which is called PS-ABC. Its algorithm includes two parts. One is that it combines the artificial bee colony (ABC) idea with the uniform random initialization idea, the binary search idea, and Boltzmann selection policy to achieve an improved ABC-based approach with better global exploration's ability and local exploitation's ability. The other one is that it uses the Bayes theorem to further optimize the improved ABC-based process to faster get the final optimal solution. As a result, the whole approach achieves a longer-term efficient optimization for power saving. The experimental results demonstrate that PS-ABC evidently reduces the total incremental power consumption and better protects the performance of VM running and migrating compared with the existing research. It makes the result of live VM migration more high-effective and meaningful. PMID:24385877

A novel artificial bee colony approach of live virtual machine migration policy using Bayes theorem.

PubMed

Xu, Gaochao; Ding, Yan; Zhao, Jia; Hu, Liang; Fu, Xiaodong

2013-01-01

Green cloud data center has become a research hotspot of virtualized cloud computing architecture. Since live virtual machine (VM) migration technology is widely used and studied in cloud computing, we have focused on the VM placement selection of live migration for power saving. We present a novel heuristic approach which is called PS-ABC. Its algorithm includes two parts. One is that it combines the artificial bee colony (ABC) idea with the uniform random initialization idea, the binary search idea, and Boltzmann selection policy to achieve an improved ABC-based approach with better global exploration's ability and local exploitation's ability. The other one is that it uses the Bayes theorem to further optimize the improved ABC-based process to faster get the final optimal solution. As a result, the whole approach achieves a longer-term efficient optimization for power saving. The experimental results demonstrate that PS-ABC evidently reduces the total incremental power consumption and better protects the performance of VM running and migrating compared with the existing research. It makes the result of live VM migration more high-effective and meaningful.

Human Machine Interfaces for Teleoperators and Virtual Environments Conference

NASA Technical Reports Server (NTRS)

1990-01-01

In a teleoperator system the human operator senses, moves within, and operates upon a remote or hazardous environment by means of a slave mechanism (a mechanism often referred to as a teleoperator). In a virtual environment system the interactive human machine interface is retained but the slave mechanism and its environment are replaced by a computer simulation. Video is replaced by computer graphics. The auditory and force sensations imparted to the human operator are similarly computer generated. In contrast to a teleoperator system, where the purpose is to extend the operator's sensorimotor system in a manner that facilitates exploration and manipulation of the physical environment, in a virtual environment system, the purpose is to train, inform, alter, or study the human operator to modify the state of the computer and the information environment. A major application in which the human operator is the target is that of flight simulation. Although flight simulators have been around for more than a decade, they had little impact outside aviation presumably because the application was so specialized and so expensive.

Mathematical defense method of networked servers with controlled remote backups

NASA Astrophysics Data System (ADS)

Kim, Song-Kyoo

2006-05-01

The networked server defense model is focused on reliability and availability in security respects. The (remote) backup servers are hooked up by VPN (Virtual Private Network) with high-speed optical network and replace broken main severs immediately. The networked server can be represent as "machines" and then the system deals with main unreliable, spare, and auxiliary spare machine. During vacation periods, when the system performs a mandatory routine maintenance, auxiliary machines are being used for back-ups; the information on the system is naturally delayed. Analog of the N-policy to restrict the usage of auxiliary machines to some reasonable quantity. The results are demonstrated in the network architecture by using the stochastic optimization techniques.

OpenVirtualToxLab--a platform for generating and exchanging in silico toxicity data.

PubMed

Vedani, Angelo; Dobler, Max; Hu, Zhenquan; Smieško, Martin

2015-01-22

The VirtualToxLab is an in silico technology for estimating the toxic potential--endocrine and metabolic disruption, some aspects of carcinogenicity and cardiotoxicity--of drugs, chemicals and natural products. The technology is based on an automated protocol that simulates and quantifies the binding of small molecules towards a series of currently 16 proteins, known or suspected to trigger adverse effects: 10 nuclear receptors (androgen, estrogen α, estrogen β, glucocorticoid, liver X, mineralocorticoid, peroxisome proliferator-activated receptor γ, progesterone, thyroid α, thyroid β), four members of the cytochrome P450 enzyme family (1A2, 2C9, 2D6, 3A4), a cytosolic transcription factor (aryl hydrocarbon receptor) and a potassium ion channel (hERG). The toxic potential of a compound--its ability to trigger adverse effects--is derived from its computed binding affinities toward these very proteins: the computationally demanding simulations are executed in client-server model on a Linux cluster of the University of Basel. The graphical-user interface supports all computer platforms, allows building and uploading molecular structures, inspecting and downloading the results and, most important, rationalizing any prediction at the atomic level by interactively analyzing the binding mode of a compound with its target protein(s) in real-time 3D. Access to the VirtualToxLab is available free of charge for universities, governmental agencies, regulatory bodies and non-profit organizations. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

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

On Why It Is Impossible to Prove that the BDX90 Dispatcher Implements a Time-sharing System

NASA Technical Reports Server (NTRS)

Boyer, R. S.; Moore, J. S.

1983-01-01

The Software Implemented Fault Tolerance SIFT system, is written in PASCAL except for about a page of machine code. The SIFT system implements a small time sharing system in which PASCAL programs for separate application tasks are executed according to a schedule with real time constraints. The PASCAL language has no provision for handling the notion of an interrupt such as the B930 clock interrupt. The PASCAL language also lacks the notion of running a PASCAL subroutine for a given amount of time, suspending it, saving away the suspension, and later activating the suspension. Machine code was used to overcome these inadequacies of PASCAL. Code which handles clock interrupts and suspends processes is called a dispatcher. The time sharing/virtual machine idea is completely destroyed by the reconfiguration task. After termination of the reconfiguration task, the tasks run by the dispatcher have no relation to those run before reconfiguration. It is impossible to view the dispatcher as a time-sharing system implementing virtual BDX930s running concurrently when one process can wipe out the others.

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

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.

Broadband network on-line data acquisition system with web based interface for control and basic analysis

NASA Astrophysics Data System (ADS)

Polkowski, Marcin; Grad, Marek

2016-04-01

Passive seismic experiment "13BB Star" is operated since mid 2013 in northern Poland and consists of 13 broadband seismic stations. One of the elements of this experiment is dedicated on-line data acquisition system comprised of both client (station) side and server side modules with web based interface that allows monitoring of network status and provides tools for preliminary data analysis. Station side is controlled by ARM Linux board that is programmed to maintain 3G/EDGE internet connection, receive data from digitizer, send data do central server among with additional auxiliary parameters like temperatures, voltages and electric current measurements. Station side is controlled by set of easy to install PHP scripts. Data is transmitted securely over SSH protocol to central server. Central server is a dedicated Linux based machine. Its duty is receiving and processing all data from all stations including auxiliary parameters. Server side software is written in PHP and Python. Additionally, it allows remote station configuration and provides web based interface for user friendly interaction. All collected data can be displayed for each day and station. It also allows manual creation of event oriented plots with different filtering abilities and provides numerous status and statistic information. Our solution is very flexible and easy to modify. In this presentation we would like to share our solution and experience. National Science Centre Poland provided financial support for this work via NCN grant DEC-2011/02/A/ST10/00284.

Simplified Deployment of Health Informatics Applications by Providing Docker Images.

PubMed

Löbe, Matthias; Ganslandt, Thomas; Lotzmann, Lydia; Mate, Sebastian; Christoph, Jan; Baum, Benjamin; Sariyar, Murat; Wu, Jie; Stäubert, Sebastian

2016-01-01

Due to the specific needs of biomedical researchers, in-house development of software is widespread. A common problem is to maintain and enhance software after the funded project has ended. Even if many tools are made open source, only a couple of projects manage to attract a user basis large enough to ensure sustainability. Reasons for this include complex installation and configuration of biomedical software as well as an ambiguous terminology of the features provided; all of which make evaluation of software laborious. Docker is a para-virtualization technology based on Linux containers that eases deployment of applications and facilitates evaluation. We investigated a suite of software developments funded by a large umbrella organization for networked medical research within the last 10 years and created Docker containers for a number of applications to support utilization and dissemination.

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network

PubMed Central

Sward, Katherine A; Newth, Christopher JL; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-01-01

Objectives To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Material and Methods Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Results Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Conclusions Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. PMID:25796596

Liberating Virtual Machines from Physical Boundaries through Execution Knowledge

DTIC Science & Technology

2015-12-01

trivial infrastructures such as VM distribution networks, clients need to wait for an extended period of time before launching a VM. In cloud settings...hardware support. MobiDesk [28] efficiently supports virtual desktops in mobile environments by decou- pling the user’s workload from host systems and...experiment set-up. VMs are migrated between a pair of source and destination hosts, which are connected through a backend 10 Gbps network for

Humans and machines in space: The vision, the challenge, the payoff; Proceedings of the 29th Goddard Memorial Symposium, Washington, Mar. 14, 15, 1991

NASA Astrophysics Data System (ADS)

Johnson, Bradley; May, Gayle L.; Korn, Paula

The present conference discusses the currently envisioned goals of human-machine systems in spacecraft environments, prospects for human exploration of the solar system, and plausible methods for meeting human needs in space. Also discussed are the problems of human-machine interaction in long-duration space flights, remote medical systems for space exploration, the use of virtual reality for planetary exploration, the alliance between U.S. Antarctic and space programs, and the economic and educational impacts of the U.S. space program.

Fundamental Study about the Landscape Estimation and Analysis by CG

NASA Astrophysics Data System (ADS)

Nakashima, Yoshio; Miyagoshi, Takashi; Takamatsu, Mamoru; Sassa, Kazuhiro

In recent years, the color of advertising signboards or vending machines on the streets should be harmonized with the surrounding landscape. In this study, we investigated how the colors (red and white) of the vending machines virtually installed by CG would affect the traditional landscape. 20 subjects estimated landscape samples in Hida-Furukawa by the SD technique. The result of our experiment shows that the vending machines have great influence on the surrounding landscape. On the other hand, we have confirmed that they can harmonize with the circumference landscape by the color to use.

A Framework for Analyzing the Whole Body Surface Area from a Single View

PubMed Central

Doretto, Gianfranco; Adjeroh, Donald

2017-01-01

We present a virtual reality (VR) framework for the analysis of whole human body surface area. Usual methods for determining the whole body surface area (WBSA) are based on well known formulae, characterized by large errors when the subject is obese, or belongs to certain subgroups. For these situations, we believe that a computer vision approach can overcome these problems and provide a better estimate of this important body indicator. Unfortunately, using machine learning techniques to design a computer vision system able to provide a new body indicator that goes beyond the use of only body weight and height, entails a long and expensive data acquisition process. A more viable solution is to use a dataset composed of virtual subjects. Generating a virtual dataset allowed us to build a population with different characteristics (obese, underweight, age, gender). However, synthetic data might differ from a real scenario, typical of the physician’s clinic. For this reason we develop a new virtual environment to facilitate the analysis of human subjects in 3D. This framework can simulate the acquisition process of a real camera, making it easy to analyze and to create training data for machine learning algorithms. With this virtual environment, we can easily simulate the real setup of a clinic, where a subject is standing in front of a camera, or may assume a different pose with respect to the camera. We use this newly designated environment to analyze the whole body surface area (WBSA). In particular, we show that we can obtain accurate WBSA estimations with just one view, virtually enabling the possibility to use inexpensive depth sensors (e.g., the Kinect) for large scale quantification of the WBSA from a single view 3D map. PMID:28045895

Virtual Machine Language 2.1

NASA Technical Reports Server (NTRS)

Riedel, Joseph E.; Grasso, Christopher A.

2012-01-01

VML (Virtual Machine Language) is an advanced computing environment that allows spacecraft to operate using mechanisms ranging from simple, time-oriented sequencing to advanced, multicomponent reactive systems. VML has developed in four evolutionary stages. VML 0 is a core execution capability providing multi-threaded command execution, integer data types, and rudimentary branching. VML 1 added named parameterized procedures, extensive polymorphism, data typing, branching, looping issuance of commands using run-time parameters, and named global variables. VML 2 added for loops, data verification, telemetry reaction, and an open flight adaptation architecture. VML 2.1 contains major advances in control flow capabilities for executable state machines. On the resource requirements front, VML 2.1 features a reduced memory footprint in order to fit more capability into modestly sized flight processors, and endian-neutral data access for compatibility with Intel little-endian processors. Sequence packaging has been improved with object-oriented programming constructs and the use of implicit (rather than explicit) time tags on statements. Sequence event detection has been significantly enhanced with multi-variable waiting, which allows a sequence to detect and react to conditions defined by complex expressions with multiple global variables. This multi-variable waiting serves as the basis for implementing parallel rule checking, which in turn, makes possible executable state machines. The new state machine feature in VML 2.1 allows the creation of sophisticated autonomous reactive systems without the need to develop expensive flight software. Users specify named states and transitions, along with the truth conditions required, before taking transitions. Transitions with the same signal name allow separate state machines to coordinate actions: the conditions distributed across all state machines necessary to arm a particular signal are evaluated, and once found true, that signal is raised. The selected signal then causes all identically named transitions in all present state machines to be taken simultaneously. VML 2.1 has relevance to all potential space missions, both manned and unmanned. It was under consideration for use on Orion.

Distributed computing methodology for training neural networks in an image-guided diagnostic application.

PubMed

Plagianakos, V P; Magoulas, G D; Vrahatis, M N

2006-03-01

Distributed computing is a process through which a set of computers connected by a network is used collectively to solve a single problem. In this paper, we propose a distributed computing methodology for training neural networks for the detection of lesions in colonoscopy. Our approach is based on partitioning the training set across multiple processors using a parallel virtual machine. In this way, interconnected computers of varied architectures can be used for the distributed evaluation of the error function and gradient values, and, thus, training neural networks utilizing various learning methods. The proposed methodology has large granularity and low synchronization, and has been implemented and tested. Our results indicate that the parallel virtual machine implementation of the training algorithms developed leads to considerable speedup, especially when large network architectures and training sets are used.

Performance of machine-learning scoring functions in structure-based virtual screening

PubMed Central

Wójcikowski, Maciej; Ballester, Pedro J.; Siedlecki, Pawel

2017-01-01

Classical scoring functions have reached a plateau in their performance in virtual screening and binding affinity prediction. Recently, machine-learning scoring functions trained on protein-ligand complexes have shown great promise in small tailored studies. They have also raised controversy, specifically concerning model overfitting and applicability to novel targets. Here we provide a new ready-to-use scoring function (RF-Score-VS) trained on 15 426 active and 893 897 inactive molecules docked to a set of 102 targets. We use the full DUD-E data sets along with three docking tools, five classical and three machine-learning scoring functions for model building and performance assessment. Our results show RF-Score-VS can substantially improve virtual screening performance: RF-Score-VS top 1% provides 55.6% hit rate, whereas that of Vina only 16.2% (for smaller percent the difference is even more encouraging: RF-Score-VS top 0.1% achieves 88.6% hit rate for 27.5% using Vina). In addition, RF-Score-VS provides much better prediction of measured binding affinity than Vina (Pearson correlation of 0.56 and −0.18, respectively). Lastly, we test RF-Score-VS on an independent test set from the DEKOIS benchmark and observed comparable results. We provide full data sets to facilitate further research in this area (http://github.com/oddt/rfscorevs) as well as ready-to-use RF-Score-VS (http://github.com/oddt/rfscorevs_binary). PMID:28440302

Decentralized real-time simulation of forest machines

NASA Astrophysics Data System (ADS)

Freund, Eckhard; Adam, Frank; Hoffmann, Katharina; Rossmann, Juergen; Kraemer, Michael; Schluse, Michael

2000-10-01

To develop realistic forest machine simulators is a demanding task. A useful simulator has to provide a close- to-reality simulation of the forest environment as well as the simulation of the physics of the vehicle. Customers demand a highly realistic three dimensional forestry landscape and the realistic simulation of the complex motion of the vehicle even in rough terrain in order to be able to use the simulator for operator training under close-to- reality conditions. The realistic simulation of the vehicle, especially with the driver's seat mounted on a motion platform, greatly improves the effect of immersion into the virtual reality of a simulated forest and the achievable level of education of the driver. Thus, the connection of the real control devices of forest machines to the simulation system has to be supported, i.e. the real control devices like the joysticks or the board computer system to control the crane, the aggregate etc. Beyond, the fusion of the board computer system and the simulation system is realized by means of sensors, i.e. digital and analog signals. The decentralized system structure allows several virtual reality systems to evaluate and visualize the information of the control devices and the sensors. So, while the driver is practicing, the instructor can immerse into the same virtual forest to monitor the session from his own viewpoint. In this paper, we are describing the realized structure as well as the necessary software and hardware components and application experiences.

Embedded Real-Time Linux for Instrument Control and Data Logging

NASA Technical Reports Server (NTRS)

Clanton, Sam; Gore, Warren J. (Technical Monitor)

2002-01-01

When I moved to the west. coast to take a job at NASA's Ames Research Center in Mountain View, CA, I was impressed with the variety of equipment and software which scientists at the center use to conduct their research. was happy to find that I was just as likely to see a machine running Lenox as one running Windows in the offices and laboratories of NASA Ames (although many people seem to use Moos around here). I was especially happy to find that the particular group with whom I was going to work, the Atmospheric Physics Branch at Ames, relied almost entirely on Lenox machines for their day-to-day work. So it was no surprise that when it was time to construct a new control system for one of their most important pieces of hardware, a switch from an unpredictable DOS-based platform to an Embedded Linux-based one was a decision easily made. The system I am working on is called the Solar Spectral Flux Radiometer (SSFR), a PC-104 based system custom-built by Dr. Warren Gore at Ames. Dr. Gore, Dr. Peter Pilewskie, Dr. Maura Robberies and Larry Pezzolo use the SSFR in their research. The team working on the controller project consists of Dr. Gore, John Pommier, and myself. The SSFR is used by the ,cities Atmospheric Radiation Group to measure solar spectral irradiance at moderate resolution to determine the radiative effect of clouds, aerosols, and gases on climate, and also to infer the physical properties of aerosols and clouds. Two identical SSFR's have been built and successfully deployed in three field missions: 1) the Department of Energy Atmospheric Radiation Measurement (ARM) Enhanced Shortwave Experiment (ARESE) II in February/March, 2000; 2) the Puerto Rico Dust Experiment (PRIDE) in July, 2000; and 3) the South African Regional Science Initiative (SAFARI) in August/September, 2000. Additionally, the SSFR was used to acquire water vapor spectra using the Ames Diameter base-path multiple-reflection absorption cell in a laboratory experiment.

Virtual terrain: a security-based representation of a computer network

NASA Astrophysics Data System (ADS)

Holsopple, Jared; Yang, Shanchieh; Argauer, Brian

2008-03-01

Much research has been put forth towards detection, correlating, and prediction of cyber attacks in recent years. As this set of research progresses, there is an increasing need for contextual information of a computer network to provide an accurate situational assessment. Typical approaches adopt contextual information as needed; yet such ad hoc effort may lead to unnecessary or even conflicting features. The concept of virtual terrain is, therefore, developed and investigated in this work. Virtual terrain is a common representation of crucial information about network vulnerabilities, accessibilities, and criticalities. A virtual terrain model encompasses operating systems, firewall rules, running services, missions, user accounts, and network connectivity. It is defined as connected graphs with arc attributes defining dynamic relationships among vertices modeling network entities, such as services, users, and machines. The virtual terrain representation is designed to allow feasible development and maintenance of the model, as well as efficacy in terms of the use of the model. This paper will describe the considerations in developing the virtual terrain schema, exemplary virtual terrain models, and algorithms utilizing the virtual terrain model for situation and threat assessment.

Humans and machines in space: The vision, the challenge, the payoff; AAS Goddard Memorial Symposium, 29th, Washington, DC, March 14-15, 1991

NASA Astrophysics Data System (ADS)

Johnson, Bradley; May, Gayle L.; Korn, Paula

A recent symposium produced papers in the areas of solar system exploration, man machine interfaces, cybernetics, virtual reality, telerobotics, life support systems and the scientific and technology spinoff from the NASA space program. A number of papers also addressed the social and economic impacts of the space program. For individual titles, see A95-87468 through A95-87479.

Software Support Measurement and Estimating for Oracle Database Applications Using Mark II Function Points

DTIC Science & Technology

1992-12-01

36 V.33. Coe ncint of De minstioi ........................ 37 V3A. F-Raio .................................... 37 V3.5... de ations. Instructions ae defined as lines of code or card images. Thus, a line containin two or mome souce statements counts as one instruction; a...understand the productivity paradox, recall de concept of virtual machines. When a higher level machine groups ogether many instructm of a lower level

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.

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

Information integration and diagnosis analysis of equipment status and production quality for machining process

NASA Astrophysics Data System (ADS)

Zan, Tao; Wang, Min; Hu, Jianzhong

2010-12-01

Machining status monitoring technique by multi-sensors can acquire and analyze the machining process information to implement abnormity diagnosis and fault warning. Statistical quality control technique is normally used to distinguish abnormal fluctuations from normal fluctuations through statistical method. In this paper by comparing the advantages and disadvantages of the two methods, the necessity and feasibility of integration and fusion is introduced. Then an approach that integrates multi-sensors status monitoring and statistical process control based on artificial intelligent technique, internet technique and database technique is brought forward. Based on virtual instrument technique the author developed the machining quality assurance system - MoniSysOnline, which has been used to monitoring the grinding machining process. By analyzing the quality data and AE signal information of wheel dressing process the reason of machining quality fluctuation has been obtained. The experiment result indicates that the approach is suitable for the status monitoring and analyzing of machining process.

Implementation of NASTRAN on the IBM/370 CMS operating system

NASA Technical Reports Server (NTRS)

Britten, S. S.; Schumacker, B.

1980-01-01

The NASA Structural Analysis (NASTRAN) computer program is operational on the IBM 360/370 series computers. While execution of NASTRAN has been described and implemented under the virtual storage operating systems of the IBM 370 models, the IBM 370/168 computer can also operate in a time-sharing mode under the virtual machine operating system using the Conversational Monitor System (CMS) subset. The changes required to make NASTRAN operational under the CMS operating system are described.

Virtual reality hardware for use in interactive 3D data fusion and visualization

NASA Astrophysics Data System (ADS)

Gourley, Christopher S.; Abidi, Mongi A.

1997-09-01

Virtual reality has become a tool for use in many areas of research. We have designed and built a VR system for use in range data fusion and visualization. One major VR tool is the CAVE. This is the ultimate visualization tool, but comes with a large price tag. Our design uses a unique CAVE whose graphics are powered by a desktop computer instead of a larger rack machine making it much less costly. The system consists of a screen eight feet tall by twenty-seven feet wide giving a variable field-of-view currently set at 160 degrees. A silicon graphics Indigo2 MaxImpact with the impact channel option is used for display. This gives the capability to drive three projectors at a resolution of 640 by 480 for use in displaying the virtual environment and one 640 by 480 display for a user control interface. This machine is also the first desktop package which has built-in hardware texture mapping. This feature allows us to quickly fuse the range and intensity data and other multi-sensory data. The final goal is a complete 3D texture mapped model of the environment. A dataglove, magnetic tracker, and spaceball are to be used for manipulation of the data and navigation through the virtual environment. This system gives several users the ability to interactively create 3D models from multiple range images.

An adaptive process-based cloud infrastructure for space situational awareness applications

NASA Astrophysics Data System (ADS)

Liu, Bingwei; Chen, Yu; Shen, Dan; Chen, Genshe; Pham, Khanh; Blasch, Erik; Rubin, Bruce

2014-06-01

Space situational awareness (SSA) and defense space control capabilities are top priorities for groups that own or operate man-made spacecraft. Also, with the growing amount of space debris, there is an increase in demand for contextual understanding that necessitates the capability of collecting and processing a vast amount sensor data. Cloud computing, which features scalable and flexible storage and computing services, has been recognized as an ideal candidate that can meet the large data contextual challenges as needed by SSA. Cloud computing consists of physical service providers and middleware virtual machines together with infrastructure, platform, and software as service (IaaS, PaaS, SaaS) models. However, the typical Virtual Machine (VM) abstraction is on a per operating systems basis, which is at too low-level and limits the flexibility of a mission application architecture. In responding to this technical challenge, a novel adaptive process based cloud infrastructure for SSA applications is proposed in this paper. In addition, the details for the design rationale and a prototype is further examined. The SSA Cloud (SSAC) conceptual capability will potentially support space situation monitoring and tracking, object identification, and threat assessment. Lastly, the benefits of a more granular and flexible cloud computing resources allocation are illustrated for data processing and implementation considerations within a representative SSA system environment. We show that the container-based virtualization performs better than hypervisor-based virtualization technology in an SSA scenario.

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).

Network Hardware Virtualization for Application Provisioning in Core Networks

DOE PAGES

Gumaste, Ashwin; Das, Tamal; Khandwala, Kandarp; ...

2017-02-03

We present that service providers and vendors are moving toward a network virtualized core, whereby multiple applications would be treated on their own merit in programmable hardware. Such a network would have the advantage of being customized for user requirements and allow provisioning of next generation services that are built specifically to meet user needs. In this article, we articulate the impact of network virtualization on networks that provide customized services and how a provider's business can grow with network virtualization. We outline a decision map that allows mapping of applications with technology that is supported in network-virtualization - orientedmore » equipment. Analogies to the world of virtual machines and generic virtualization show that hardware supporting network virtualization will facilitate new customer needs while optimizing the provider network from the cost and performance perspectives. A key conclusion of the article is that growth would yield sizable revenue when providers plan ahead in terms of supporting network-virtualization-oriented technology in their networks. To be precise, providers have to incorporate into their growth plans network elements capable of new service deployments while protecting network neutrality. Finally, a simulation study validates our NV-induced model.« less

Network Hardware Virtualization for Application Provisioning in Core Networks

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

Gumaste, Ashwin; Das, Tamal; Khandwala, Kandarp

We present that service providers and vendors are moving toward a network virtualized core, whereby multiple applications would be treated on their own merit in programmable hardware. Such a network would have the advantage of being customized for user requirements and allow provisioning of next generation services that are built specifically to meet user needs. In this article, we articulate the impact of network virtualization on networks that provide customized services and how a provider's business can grow with network virtualization. We outline a decision map that allows mapping of applications with technology that is supported in network-virtualization - orientedmore » equipment. Analogies to the world of virtual machines and generic virtualization show that hardware supporting network virtualization will facilitate new customer needs while optimizing the provider network from the cost and performance perspectives. A key conclusion of the article is that growth would yield sizable revenue when providers plan ahead in terms of supporting network-virtualization-oriented technology in their networks. To be precise, providers have to incorporate into their growth plans network elements capable of new service deployments while protecting network neutrality. Finally, a simulation study validates our NV-induced model.« less

Suitability of virtual prototypes to support human factors/ergonomics evaluation during the design.

PubMed

Aromaa, Susanna; Väänänen, Kaisa

2016-09-01

In recent years, the use of virtual prototyping has increased in product development processes, especially in the assessment of complex systems targeted at end-users. The purpose of this study was to evaluate the suitability of virtual prototyping to support human factors/ergonomics evaluation (HFE) during the design phase. Two different virtual prototypes were used: augmented reality (AR) and virtual environment (VE) prototypes of a maintenance platform of a rock crushing machine. Nineteen designers and other stakeholders were asked to assess the suitability of the prototype for HFE evaluation. Results indicate that the system model characteristics and user interface affect the experienced suitability. The VE system was valued as being more suitable to support the assessment of visibility, reach, and the use of tools than the AR system. The findings of this study can be used as a guidance for the implementing virtual prototypes in the product development process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Design of virtual SCADA simulation system for pressurized water reactor

NASA Astrophysics Data System (ADS)

Wijaksono, Umar; Abdullah, Ade Gafar; Hakim, Dadang Lukman

2016-02-01

The Virtual SCADA system is a software-based Human-Machine Interface that can visualize the process of a plant. This paper described the results of the virtual SCADA system design that aims to recognize the principle of the Nuclear Power Plant type Pressurized Water Reactor. This simulation uses technical data of the Nuclear Power Plant Unit Olkiluoto 3 in Finland. This device was developed using Wonderware Intouch, which is equipped with manual books for each component, animation links, alarm systems, real time and historical trending, and security system. The results showed that in general this device can demonstrate clearly the principles of energy flow and energy conversion processes in Pressurized Water Reactors. This virtual SCADA simulation system can be used as instructional media to recognize the principle of Pressurized Water Reactor.

Eternal Sunshine of the Spotless Machine: Protecting Privacy with Ephemeral Channels

PubMed Central

Dunn, Alan M.; Lee, Michael Z.; Jana, Suman; Kim, Sangman; Silberstein, Mark; Xu, Yuanzhong; Shmatikov, Vitaly; Witchel, Emmett

2014-01-01

Modern systems keep long memories. As we show in this paper, an adversary who gains access to a Linux system, even one that implements secure deallocation, can recover the contents of applications’ windows, audio buffers, and data remaining in device drivers—long after the applications have terminated. We design and implement Lacuna, a system that allows users to run programs in “private sessions.” After the session is over, all memories of its execution are erased. The key abstraction in Lacuna is an ephemeral channel, which allows the protected program to talk to peripheral devices while making it possible to delete the memories of this communication from the host. Lacuna can run unmodified applications that use graphics, sound, USB input devices, and the network, with only 20 percentage points of additional CPU utilization. PMID:24755709

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.

Realizing a partial general quantum cloning machine with superconducting quantum-interference devices in a cavity QED

NASA Astrophysics Data System (ADS)

Fang, Bao-Long; Yang, Zhen; Ye, Liu

2009-05-01

We propose a scheme for implementing a partial general quantum cloning machine with superconducting quantum-interference devices coupled to a nonresonant cavity. By regulating the time parameters, our system can perform optimal symmetric (asymmetric) universal quantum cloning, optimal symmetric (asymmetric) phase-covariant cloning, and optimal symmetric economical phase-covariant cloning. In the scheme the cavity is only virtually excited, thus, the cavity decay is suppressed during the cloning operations.

A Unified Access Model for Interconnecting Heterogeneous Wireless Networks

DTIC Science & Technology

2015-05-01

Defined Networking, OpenFlow, WiFi, LTE 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 18 19a. NAME OF...Machine Configurations with WiFi and LTE 4 2.3 Three Virtual Machine Configurations with WiFi and LTE 5 3. Results and Discussion 5 4. Summary and...WiFi and long-term evolution ( LTE ), and created a communication pathway between them via a central controller node. Our simulation serves as a

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

Garzoglio, Gabriele

The Fermilab Grid and Cloud Computing Department and the KISTI Global Science experimental Data hub Center are working on a multi-year Collaborative Research and Development Agreement.With the knowledge developed in the first year on how to provision and manage a federation of virtual machines through Cloud management systems. In this second year, we expanded the work on provisioning and federation, increasing both scale and diversity of solutions, and we started to build on-demand services on the established fabric, introducing the paradigm of Platform as a Service to assist with the execution of scientific workflows. We have enabled scientific workflows ofmore » stakeholders to run on multiple cloud resources at the scale of 1,000 concurrent machines. The demonstrations have been in the areas of (a) Virtual Infrastructure Automation and Provisioning, (b) Interoperability and Federation of Cloud Resources, and (c) On-demand Services for ScientificWorkflows.« less

Learning Motion Features for Example-Based Finger Motion Estimation for Virtual Characters

NASA Astrophysics Data System (ADS)

Mousas, Christos; Anagnostopoulos, Christos-Nikolaos

2017-09-01

This paper presents a methodology for estimating the motion of a character's fingers based on the use of motion features provided by a virtual character's hand. In the presented methodology, firstly, the motion data is segmented into discrete phases. Then, a number of motion features are computed for each motion segment of a character's hand. The motion features are pre-processed using restricted Boltzmann machines, and by using the different variations of semantically similar finger gestures in a support vector machine learning mechanism, the optimal weights for each feature assigned to a metric are computed. The advantages of the presented methodology in comparison to previous solutions are the following: First, we automate the computation of optimal weights that are assigned to each motion feature counted in our metric. Second, the presented methodology achieves an increase (about 17%) in correctly estimated finger gestures in comparison to a previous method.

A Cloud-based Approach to Medical NLP

PubMed Central

Chard, Kyle; Russell, Michael; Lussier, Yves A.; Mendonça, Eneida A; Silverstein, Jonathan C.

2011-01-01

Natural Language Processing (NLP) enables access to deep content embedded in medical texts. To date, NLP has not fulfilled its promise of enabling robust clinical encoding, clinical use, quality improvement, and research. We submit that this is in part due to poor accessibility, scalability, and flexibility of NLP systems. We describe here an approach and system which leverages cloud-based approaches such as virtual machines and Representational State Transfer (REST) to extract, process, synthesize, mine, compare/contrast, explore, and manage medical text data in a flexibly secure and scalable architecture. Available architectures in which our Smntx (pronounced as semantics) system can be deployed include: virtual machines in a HIPAA-protected hospital environment, brought up to run analysis over bulk data and destroyed in a local cloud; a commercial cloud for a large complex multi-institutional trial; and within other architectures such as caGrid, i2b2, or NHIN. PMID:22195072

A cloud-based approach to medical NLP.

PubMed

Chard, Kyle; Russell, Michael; Lussier, Yves A; Mendonça, Eneida A; Silverstein, Jonathan C

2011-01-01

Natural Language Processing (NLP) enables access to deep content embedded in medical texts. To date, NLP has not fulfilled its promise of enabling robust clinical encoding, clinical use, quality improvement, and research. We submit that this is in part due to poor accessibility, scalability, and flexibility of NLP systems. We describe here an approach and system which leverages cloud-based approaches such as virtual machines and Representational State Transfer (REST) to extract, process, synthesize, mine, compare/contrast, explore, and manage medical text data in a flexibly secure and scalable architecture. Available architectures in which our Smntx (pronounced as semantics) system can be deployed include: virtual machines in a HIPAA-protected hospital environment, brought up to run analysis over bulk data and destroyed in a local cloud; a commercial cloud for a large complex multi-institutional trial; and within other architectures such as caGrid, i2b2, or NHIN.

Hardware/software codesign for embedded RISC core

NASA Astrophysics Data System (ADS)

Liu, Peng

2001-12-01

This paper describes hardware/software codesign method of the extendible embedded RISC core VIRGO, which based on MIPS-I instruction set architecture. VIRGO is described by Verilog hardware description language that has five-stage pipeline with shared 32-bit cache/memory interface, and it is controlled by distributed control scheme. Every pipeline stage has one small controller, which controls the pipeline stage status and cooperation among the pipeline phase. Since description use high level language and structure is distributed, VIRGO core has highly extension that can meet the requirements of application. We take look at the high-definition television MPEG2 MPHL decoder chip, constructed the hardware/software codesign virtual prototyping machine that can research on VIRGO core instruction set architecture, and system on chip memory size requirements, and system on chip software, etc. We also can evaluate the system on chip design and RISC instruction set based on the virtual prototyping machine platform.

Human intestinal transporter database: QSAR modeling and virtual profiling of drug uptake, efflux and interactions.

PubMed

Sedykh, Alexander; Fourches, Denis; Duan, Jianmin; Hucke, Oliver; Garneau, Michel; Zhu, Hao; Bonneau, Pierre; Tropsha, Alexander

2013-04-01

Membrane transporters mediate many biological effects of chemicals and play a major role in pharmacokinetics and drug resistance. The selection of viable drug candidates among biologically active compounds requires the assessment of their transporter interaction profiles. Using public sources, we have assembled and curated the largest, to our knowledge, human intestinal transporter database (>5,000 interaction entries for >3,700 molecules). This data was used to develop thoroughly validated classification Quantitative Structure-Activity Relationship (QSAR) models of transport and/or inhibition of several major transporters including MDR1, BCRP, MRP1-4, PEPT1, ASBT, OATP2B1, OCT1, and MCT1. QSAR models have been developed with advanced machine learning techniques such as Support Vector Machines, Random Forest, and k Nearest Neighbors using Dragon and MOE chemical descriptors. These models afforded high external prediction accuracies of 71-100% estimated by 5-fold external validation, and showed hit retrieval rates with up to 20-fold enrichment in the virtual screening of DrugBank compounds. The compendium of predictive QSAR models developed in this study can be used for virtual profiling of drug candidates and/or environmental agents with the optimal transporter profiles.

A Distributed Parallel Genetic Algorithm of Placement Strategy for Virtual Machines Deployment on Cloud Platform

PubMed Central

Dong, Yu-Shuang; Xu, Gao-Chao; Fu, Xiao-Dong

2014-01-01

The cloud platform provides various services to users. More and more cloud centers provide infrastructure as the main way of operating. To improve the utilization rate of the cloud center and to decrease the operating cost, the cloud center provides services according to requirements of users by sharding the resources with virtualization. Considering both QoS for users and cost saving for cloud computing providers, we try to maximize performance and minimize energy cost as well. In this paper, we propose a distributed parallel genetic algorithm (DPGA) of placement strategy for virtual machines deployment on cloud platform. It executes the genetic algorithm parallelly and distributedly on several selected physical hosts in the first stage. Then it continues to execute the genetic algorithm of the second stage with solutions obtained from the first stage as the initial population. The solution calculated by the genetic algorithm of the second stage is the optimal one of the proposed approach. The experimental results show that the proposed placement strategy of VM deployment can ensure QoS for users and it is more effective and more energy efficient than other placement strategies on the cloud platform. PMID:25097872

A distributed parallel genetic algorithm of placement strategy for virtual machines deployment on cloud platform.

PubMed

Dong, Yu-Shuang; Xu, Gao-Chao; Fu, Xiao-Dong

2014-01-01

The cloud platform provides various services to users. More and more cloud centers provide infrastructure as the main way of operating. To improve the utilization rate of the cloud center and to decrease the operating cost, the cloud center provides services according to requirements of users by sharding the resources with virtualization. Considering both QoS for users and cost saving for cloud computing providers, we try to maximize performance and minimize energy cost as well. In this paper, we propose a distributed parallel genetic algorithm (DPGA) of placement strategy for virtual machines deployment on cloud platform. It executes the genetic algorithm parallelly and distributedly on several selected physical hosts in the first stage. Then it continues to execute the genetic algorithm of the second stage with solutions obtained from the first stage as the initial population. The solution calculated by the genetic algorithm of the second stage is the optimal one of the proposed approach. The experimental results show that the proposed placement strategy of VM deployment can ensure QoS for users and it is more effective and more energy efficient than other placement strategies on the cloud platform.

Virtual reality and neuropsychological assessment: The reliability of a virtual kitchen to assess daily-life activities in victims of traumatic brain injury.

PubMed

Besnard, Jeremy; Richard, Paul; Banville, Frederic; Nolin, Pierre; Aubin, Ghislaine; Le Gall, Didier; Richard, Isabelle; Allain, Phillippe

2016-01-01

Traumatic brain injury (TBI) causes impairments affecting instrumental activities of daily living (IADL). However, few studies have considered virtual reality as an ecologically valid tool for the assessment of IADL in patients who have sustained a TBI. The main objective of the present study was to examine the use of the Nonimmersive Virtual Coffee Task (NI-VCT) for IADL assessment in patients with TBI. We analyzed the performance of 19 adults suffering from TBI and 19 healthy controls (HCs) in the real and virtual tasks of making coffee with a coffee machine, as well as in global IQ and executive functions. Patients performed worse than HCs on both real and virtual tasks and on all tests of executive functions. Correlation analyses revealed that NI-VCT scores were related to scores on the real task. Moreover, regression analyses demonstrated that performance on NI-VCT matched real-task performance. Our results support the idea that the virtual kitchen is a valid tool for IADL assessment in patients who have sustained a TBI.

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.

Virtualization - A Key Cost Saver in NASA Multi-Mission Ground System Architecture

NASA Technical Reports Server (NTRS)

Swenson, Paul; Kreisler, Stephen; Sager, Jennifer A.; Smith, Dan

2014-01-01

With science team budgets being slashed, and a lack of adequate facilities for science payload teams to operate their instruments, there is a strong need for innovative new ground systems that are able to provide necessary levels of capability processing power, system availability and redundancy while maintaining a small footprint in terms of physical space, power utilization and cooling.The ground system architecture being presented is based off of heritage from several other projects currently in development or operations at Goddard, but was designed and built specifically to meet the needs of the Science and Planetary Operations Control Center (SPOCC) as a low-cost payload command, control, planning and analysis operations center. However, this SPOCC architecture was designed to be generic enough to be re-used partially or in whole by other labs and missions (since its inception that has already happened in several cases!)The SPOCC architecture leverages a highly available VMware-based virtualization cluster with shared SAS Direct-Attached Storage (DAS) to provide an extremely high-performing, low-power-utilization and small-footprint compute environment that provides Virtual Machine resources shared among the various tenant missions in the SPOCC. The storage is also expandable, allowing future missions to chain up to 7 additional 2U chassis of storage at an extremely competitive cost if they require additional archive or virtual machine storage space.The software architecture provides a fully-redundant GMSEC-based message bus architecture based on the ActiveMQ middleware to track all health and safety status within the SPOCC ground system. All virtual machines utilize the GMSEC system agents to report system host health over the GMSEC bus, and spacecraft payload health is monitored using the Hammers Integrated Test and Operations System (ITOS) Galaxy Telemetry and Command (TC) system, which performs near-real-time limit checking and data processing on the downlinked data stream and injects messages into the GMSEC bus that are monitored to automatically page the on-call operator or Systems Administrator (SA) when an off-nominal condition is detected. This architecture, like the LTSP thin clients, are shared across all tenant missions.Other required IT security controls are implemented at the ground system level, including physical access controls, logical system-level authentication authorization management, auditing and reporting, network management and a NIST 800-53 FISMA-Moderate IT Security plan Risk Assessment Contingency Plan, helping multiple missions share the cost of compliance with agency-mandated directives.The SPOCC architecture provides science payload control centers and backup mission operations centers with a cost-effective, standardized approach to virtualizing and monitoring resources that were traditionally multiple racks full of physical machines. The increased agility in deploying new virtual systems and thin client workstations can provide significant savings in personnel costs for maintaining the ground system. The cost savings in procurement, power, rack footprint and cooling as well as the shared multi-mission design greatly reduces upfront cost for missions moving into the facility. Overall, the authors hope that this architecture will become a model for how future NASA operations centers are constructed!

Media-Augmented Exercise Machines

NASA Astrophysics Data System (ADS)

Krueger, T.

2002-01-01

Cardio-vascular exercise has been used to mitigate the muscle and cardiac atrophy associated with adaptation to micro-gravity environments. Several hours per day may be required. In confined spaces and long duration missions this kind of exercise is inevitably repetitive and rapidly becomes uninteresting. At the same time, there are pressures to accomplish as much as possible given the cost- per-hour for humans occupying orbiting or interplanetary. Media augmentation provides a the means to overlap activities in time by supplementing the exercise with social, recreational, training or collaborative activities and thereby reducing time pressures. In addition, the machine functions as an interface to a wide range of digital environments allowing for spatial variety in an otherwise confined environment. We hypothesize that the adoption of media augmented exercise machines will have a positive effect on psycho-social well-being on long duration missions. By organizing and supplementing exercise machines, data acquisition hardware, computers and displays into an interacting system this proposal increases functionality with limited additional mass. This paper reviews preliminary work on a project to augment exercise equipment in a manner that addresses these issues and at the same time opens possibilities for additional benefits. A testbed augmented exercise machine uses a specialty built cycle trainer as both input to a virtual environment and as an output device from it using spatialized sound, and visual displays, vibration transducers and variable resistance. The resulting interactivity increases a sense of engagement in the exercise, provides a rich experience of the digital environments. Activities in the virtual environment and accompanying physiological and psychological indicators may be correlated to track and evaluate the health of the crew.

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.

MO-FG-202-09: Virtual IMRT QA Using Machine Learning: A Multi-Institutional Validation

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

Valdes, G; Scheuermann, R; Solberg, T

Purpose: To validate a machine learning approach to Virtual IMRT QA for accurately predicting gamma passing rates using different QA devices at different institutions. Methods: A Virtual IMRT QA was constructed using a machine learning algorithm based on 416 IMRT plans, in which QA measurements were performed using diode-array detectors and a 3%local/3mm with 10% threshold. An independent set of 139 IMRT measurements from a different institution, with QA data based on portal dosimetry using the same gamma index and 10% threshold, was used to further test the algorithm. Plans were characterized by 90 different complexity metrics. A weighted poisonmore » regression with Lasso regularization was trained to predict passing rates using the complexity metrics as input. Results: In addition to predicting passing rates with 3% accuracy for all composite plans using diode-array detectors, passing rates for portal dosimetry on per-beam basis were predicted with an error <3.5% for 120 IMRT measurements. The remaining measurements (19) had large areas of low CU, where portal dosimetry has larger disagreement with the calculated dose and, as such, large errors were expected. These beams need to be further modeled to correct the under-response in low dose regions. Important features selected by Lasso to predict gamma passing rates were: complete irradiated area outline (CIAO) area, jaw position, fraction of MLC leafs with gaps smaller than 20 mm or 5mm, fraction of area receiving less than 50% of the total CU, fraction of the area receiving dose from penumbra, weighted Average Irregularity Factor, duty cycle among others. Conclusion: We have demonstrated that the Virtual IMRT QA can predict passing rates using different QA devices and across multiple institutions. Prediction of QA passing rates could have profound implications on the current IMRT process.« less

Virtualization and cloud computing in dentistry.

PubMed

Chow, Frank; Muftu, Ali; Shorter, Richard

2014-01-01

The use of virtualization and cloud computing has changed the way we use computers. Virtualization is a method of placing software called a hypervisor on the hardware of a computer or a host operating system. It allows a guest operating system to run on top of the physical computer with a virtual machine (i.e., virtual computer). Virtualization allows multiple virtual computers to run on top of one physical computer and to share its hardware resources, such as printers, scanners, and modems. This increases the efficient use of the computer by decreasing costs (e.g., hardware, electricity administration, and management) since only one physical computer is needed and running. This virtualization platform is the basis for cloud computing. It has expanded into areas of server and storage virtualization. One of the commonly used dental storage systems is cloud storage. Patient information is encrypted as required by the Health Insurance Portability and Accountability Act (HIPAA) and stored on off-site private cloud services for a monthly service fee. As computer costs continue to increase, so too will the need for more storage and processing power. Virtual and cloud computing will be a method for dentists to minimize costs and maximize computer efficiency in the near future. This article will provide some useful information on current uses of cloud computing.

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.

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.

RTS2: a powerful robotic observatory manager

NASA Astrophysics Data System (ADS)

Kubánek, Petr; Jelínek, Martin; Vítek, Stanislav; de Ugarte Postigo, Antonio; Nekola, Martin; French, John

2006-06-01

RTS2, or Remote Telescope System, 2nd Version, is an integrated package for remote telescope control under the Linux operating system. It is designed to run in fully autonomous mode, picking targets from a database table, storing image meta data to the database, processing images and storing their WCS coordinates in the database and offering Virtual-Observatory enabled access to them. It is currently running on various telescope setups world-wide. For control of devices from various manufacturers we developed an abstract device layer, enabling control of all possible combinations of mounts, CCDs, photometers, roof and cupola controllers. We describe the evolution of RTS2 from Python-based RTS to C and later C++ based RTS2, focusing on the problems we faced during development. The internal structure of RTS2, focusing on object layering, which is used to uniformly control various devices and provides uniform reporting layer, is also discussed.

An Analysis Platform for Mobile Ad Hoc Network (MANET) Scenario Execution Log Data

DTIC Science & Technology

2016-01-01

these technologies. 4.1 Backend Technologies • Java 1.8 • my-sql-connector- java -5.0.8.jar • Tomcat • VirtualBox • Kali MANET Virtual Machine 4.2...Frontend Technologies • LAMPP 4.3 Database • MySQL Server 5. Database The SEDAP database settings and structure are described in this section...contains all the backend java functionality including the web services, should be placed in the webapps directory inside the Tomcat installation

Virtual reality and planetary exploration

NASA Technical Reports Server (NTRS)

Mcgreevy, Michael W.

1992-01-01

NASA-Ames is intensively developing virtual-reality (VR) capabilities that can extend and augment computer-generated and remote spatial environments. VR is envisioned not only as a basis for improving human/machine interactions involved in planetary exploration, but also as a medium for the more widespread sharing of the experience of exploration, thereby broadening the support-base for the lunar and planetary-exploration endeavors. Imagery representative of Mars are being gathered for VR presentation at such terrestrial sites as Antarctica and Death Valley.

A Lightweight Intelligent Virtual Cinematography System for Machinima Production

DTIC Science & Technology

2007-01-01

portmanteau of machine and cinema , machinima refers to the innovation of leveraging video game technology to greatly ease the creation of computer...selecting camera angles to capture the action of an a priori unknown script as aesthetically appropriate cinema . There are a number of challenges therein...Proc. of the 4th International Conf. on Autonomous Agents. Young, R.M. and Riedl, M.O. 2003. Towards an Architecture for Intelligent Control of Narrative in Interactive Virtual Worlds. In Proc. of IUI 2003.

The use of physical and virtual manipulatives in an undergraduate mechanical engineering (Dynamics) course

NASA Astrophysics Data System (ADS)

Pan, Edward A.

Science, technology, engineering, and mathematics (STEM) education is a national focus. Engineering education, as part of STEM education, needs to adapt to meet the needs of the nation in a rapidly changing world. Using computer-based visualization tools and corresponding 3D printed physical objects may help nontraditional students succeed in engineering classes. This dissertation investigated how adding physical or virtual learning objects (called manipulatives) to courses that require mental visualization of mechanical systems can aid student performance. Dynamics is one such course, and tends to be taught using lecture and textbooks with static diagrams of moving systems. Students often fail to solve the problems correctly and an inability to mentally visualize the system can contribute to student difficulties. This study found no differences between treatment groups on quantitative measures of spatial ability and conceptual knowledge. There were differences between treatments on measures of mechanical reasoning ability, in favor of the use of physical and virtual manipulatives over static diagrams alone. There were no major differences in student performance between the use of physical and virtual manipulatives. Students used the physical and virtual manipulatives to test their theories about how the machines worked, however their actual time handling the manipulatives was extremely limited relative to the amount of time they spent working on the problems. Students used the physical and virtual manipulatives as visual aids when communicating about the problem with their partners, and this behavior was also seen with Traditional group students who had to use the static diagrams and gesture instead. The explanations students gave for how the machines worked provided evidence of mental simulation; however, their causal chain analyses were often flawed, probably due to attempts to decrease cognitive load. Student opinions about the static diagrams and dynamic models varied by type of model (static, physical, virtual), but were generally favorable. The Traditional group students, however, indicated that the lack of adequate representation of motion in the static diagrams was a problem, and wished they had access to the physical and virtual models.

Ligand-based virtual screening under partial shape constraints.

PubMed

von Behren, Mathias M; Rarey, Matthias

2017-04-01

Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).

Ligand-based virtual screening under partial shape constraints

NASA Astrophysics Data System (ADS)

von Behren, Mathias M.; Rarey, Matthias

2017-04-01

Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise).

Automated Inference of Chemical Discriminants of Biological Activity.

PubMed

Raschka, Sebastian; Scott, Anne M; Huertas, Mar; Li, Weiming; Kuhn, Leslie A

2018-01-01

Ligand-based virtual screening has become a standard technique for the efficient discovery of bioactive small molecules. Following assays to determine the activity of compounds selected by virtual screening, or other approaches in which dozens to thousands of molecules have been tested, machine learning techniques make it straightforward to discover the patterns of chemical groups that correlate with the desired biological activity. Defining the chemical features that generate activity can be used to guide the selection of molecules for subsequent rounds of screening and assaying, as well as help design new, more active molecules for organic synthesis.The quantitative structure-activity relationship machine learning protocols we describe here, using decision trees, random forests, and sequential feature selection, take as input the chemical structure of a single, known active small molecule (e.g., an inhibitor, agonist, or substrate) for comparison with the structure of each tested molecule. Knowledge of the atomic structure of the protein target and its interactions with the active compound are not required. These protocols can be modified and applied to any data set that consists of a series of measured structural, chemical, or other features for each tested molecule, along with the experimentally measured value of the response variable you would like to predict or optimize for your project, for instance, inhibitory activity in a biological assay or ΔG binding . To illustrate the use of different machine learning algorithms, we step through the analysis of a dataset of inhibitor candidates from virtual screening that were tested recently for their ability to inhibit GPCR-mediated signaling in a vertebrate.

Electro-chemical grinding

NASA Technical Reports Server (NTRS)

Feagans, P. L.

1972-01-01

Electro-chemical grinding technique has rotation speed control, constant feed rates, and contour control. Hypersonic engine parts of nickel alloys can be almost 100% machined, keeping tool pressure at virtual zero. Technique eliminates galling and permits constant surface finish and burr-free interrupted cutting.

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

Simpson, Wayne; Borders, Tammie

INL successfully developed a proof of concept for "Software Defined Anything" by emulating the laboratory's business applications that run on Virtual Machines. The work INL conducted demonstrates to industry on how this methodology can be used to improve security, automate and repeat processes, and improve consistency.

Alchemy: A Web 2.0 Real-time Quality Assurance Platform for Human Immunodeficiency Virus, Hepatitis C Virus, and BK Virus Quantitation Assays.

PubMed

Agosto-Arroyo, Emmanuel; Coshatt, Gina M; Winokur, Thomas S; Harada, Shuko; Park, Seung L

2017-01-01

The molecular diagnostics laboratory faces the challenge of improving test turnaround time (TAT). Low and consistent TATs are of great clinical and regulatory importance, especially for molecular virology tests. Laboratory information systems (LISs) contain all the data elements necessary to do accurate quality assurance (QA) reporting of TAT and other measures, but these reports are in most cases still performed manually: a time-consuming and error-prone task. The aim of this study was to develop a web-based real-time QA platform that would automate QA reporting in the molecular diagnostics laboratory at our institution, and minimize the time expended in preparing these reports. Using a standard Linux, Nginx, MariaDB, PHP stack virtual machine running atop a Dell Precision 5810, we designed and built a web-based QA platform, code-named Alchemy. Data files pulled periodically from the LIS in comma-separated value format were used to autogenerate QA reports for the human immunodeficiency virus (HIV) quantitation, hepatitis C virus (HCV) quantitation, and BK virus (BKV) quantitation. Alchemy allowed the user to select a specific timeframe to be analyzed and calculated key QA statistics in real-time, including the average TAT in days, tests falling outside the expected TAT ranges, and test result ranges. Before implementing Alchemy, reporting QA for the HIV, HCV, and BKV quantitation assays took 45-60 min of personnel time per test every month. With Alchemy, that time has decreased to 15 min total per month. Alchemy allowed the user to select specific periods of time and analyzed the TAT data in-depth without the need of extensive manual calculations. Alchemy has significantly decreased the time and the human error associated with QA report generation in our molecular diagnostics laboratory. Other tests will be added to this web-based platform in future updates. This effort shows the utility of informatician-supervised resident/fellow programming projects as learning opportunities and workflow improvements in the molecular laboratory.

Cloud-enabled large-scale land surface model simulations with the NASA Land Information System

NASA Astrophysics Data System (ADS)

Duffy, D.; Vaughan, G.; Clark, M. P.; Peters-Lidard, C. D.; Nijssen, B.; Nearing, G. S.; Rheingrover, S.; Kumar, S.; Geiger, J. V.

2017-12-01

Developed by the Hydrological Sciences Laboratory at NASA Goddard Space Flight Center (GSFC), the Land Information System (LIS) is a high-performance software framework for terrestrial hydrology modeling and data assimilation. LIS provides the ability to integrate satellite and ground-based observational products and advanced modeling algorithms to extract land surface states and fluxes. Through a partnership with the National Center for Atmospheric Research (NCAR) and the University of Washington, the LIS model is currently being extended to include the Structure for Unifying Multiple Modeling Alternatives (SUMMA). With the addition of SUMMA in LIS, meaningful simulations containing a large multi-model ensemble will be enabled and can provide advanced probabilistic continental-domain modeling capabilities at spatial scales relevant for water managers. The resulting LIS/SUMMA application framework is difficult for non-experts to install due to the large amount of dependencies on specific versions of operating systems, libraries, and compilers. This has created a significant barrier to entry for domain scientists that are interested in using the software on their own systems or in the cloud. In addition, the requirement to support multiple run time environments across the LIS community has created a significant burden on the NASA team. To overcome these challenges, LIS/SUMMA has been deployed using Linux containers, which allows for an entire software package along with all dependences to be installed within a working runtime environment, and Kubernetes, which orchestrates the deployment of a cluster of containers. Within a cloud environment, users can now easily create a cluster of virtual machines and run large-scale LIS/SUMMA simulations. Installations that have taken weeks and months can now be performed in minutes of time. This presentation will discuss the steps required to create a cloud-enabled large-scale simulation, present examples of its use, and describe the potential deployment of this information technology with other NASA applications.

SG2PS (structural geology to postscript converter) - A graphical solution for brittle structural data evaluation and paleostress calculation

NASA Astrophysics Data System (ADS)

Sasvári, Ágoston; Baharev, Ali

2014-05-01

The aim of this work was to create an open source cross platform application to process brittle structural geological data with seven paleostress inversion algorithms published by different authors and formerly not available within a single desktop application. The tool facilitates separate processing and plotting of different localities, data types and user made groups, using the same single input file. Simplified data input is supported, requiring as small amount of data as possible. Data rotation to correct for bedding tilting, rotation with paleomagnetic declination and k-means clustering are available. RUP and ANG stress estimators calculation and visualization, resolved shear direction display and Mohr circle stress visualization are available. RGB-colored vector graphical outputs are automatically generated in Encapsulated PostScript and Portable Document Format. Stereographical displays on great circle or pole point plot, equal area or equal angle net and upper or lower hemisphere projections are implemented. Rose plots displaying dip direction or strike, with dip angle distribution of the input data set are available. This tool is ideal for preliminary data interpretation on the field (quick processing and visualization in seconds); the implemented methods can be regularly used in the daily academic and industrial work as well. The authors' goal was to create an open source and self-contained desktop application that does not require any additional third party framework (such as .NET) or the Java Virtual Machine. The software has a clear and highly modular structure enabling good code portability, easy maintainability, reusability and extensibility. A Windows installer is publicly available and the program is also fully functional on Linux. The Mac OS X port should be feasible with minimal effort. The install file with test and demo data sets, detailed manual, and links to the GitHub repositories are available on the regularly updated website www.sg2ps.eu.

Increasing Realism in Virtual Marksmanship Simulators

DTIC Science & Technology

2012-12-01

M16 5.56 mm service rifle M2 .50-caliber machine gun M240 7.62 mm machine gun M9 9 mm Berretta MPI Mean Point of Impact NHQC Navy Handgun...Corps 14 Concepts in Programs, 2008, p. 214). ISMT has the capability to use a wide variety of weapons, including the .50cal. machinegun ( M2 ), 9...a time. ISMT has the unique capability to “provide immediate feedback to the instructor and trainee on weapon trigger pull, cant position, barrel

Mega-Amp Opening Switch with Nested Electrodes/Pulsed Generator of Ion and Ion Cluster Beams

DTIC Science & Technology

1987-07-30

The use of a plasma focus as a mega-amp opening switch has been demonstrated by two modes of operation: (a) Single shot mode; (b) Repetitive Mode...energy level and under the same voltage and filling-pressure conditions but without field distortion elements. Misfirings of the plasma focus machine...are also virtually eliminated by using FDE at the coaxial electrode breech. The tests (based on about 10000 shots and five plasma focus machines

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.

Handling knowledge via Concept Maps: a space weather use case

NASA Astrophysics Data System (ADS)

Messerotti, Mauro; Fox, Peter

Concept Maps (Cmaps) are powerful means for knowledge coding in graphical form. As flexible software tools exist to manipulate the knowledge embedded in Cmaps in machine-readable form, such complex entities are suitable candidates not only for the representation of ontologies and semantics in Virtual Observatory (VO) architectures, but also for knowledge handling and knowledge discovery. In this work, we present a use case relevant to space weather applications and we elaborate on its possible implementation and adavanced use in Semantic Virtual Observatories dedicated to Sun-Earth Connections. This analysis was carried out in the framework of the Electronic Geophysical Year (eGY) and represents an achievement synergized by the eGY Virtual Observatories Working Group.

Design of virtual SCADA simulation system for pressurized water reactor

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

Wijaksono, Umar, E-mail: umar.wijaksono@student.upi.edu; Abdullah, Ade Gafar; Hakim, Dadang Lukman

The Virtual SCADA system is a software-based Human-Machine Interface that can visualize the process of a plant. This paper described the results of the virtual SCADA system design that aims to recognize the principle of the Nuclear Power Plant type Pressurized Water Reactor. This simulation uses technical data of the Nuclear Power Plant Unit Olkiluoto 3 in Finland. This device was developed using Wonderware Intouch, which is equipped with manual books for each component, animation links, alarm systems, real time and historical trending, and security system. The results showed that in general this device can demonstrate clearly the principles ofmore » energy flow and energy conversion processes in Pressurized Water Reactors. This virtual SCADA simulation system can be used as instructional media to recognize the principle of Pressurized Water Reactor.« less

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

The fully programmable spacecraft: procedural sequencing for JPL deep space missions using VML (Virtual Machine Language)

NASA Technical Reports Server (NTRS)

Grasso, C. A.

2002-01-01

This paper lays out language constructs and capabilities, code features, and VML operations development concepts. The ability to migrate to the spacecraft functionality which is more traditionally implemented on the ground is examined.

IPCS user's manual

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

McGoldrick, P.R.

1980-12-11

The Interprocess Communications System (IPCS) was written to provide a virtual machine upon which the Supervisory Control and Diagnostic System (SCDS) for the Mirror Fusion Test Facility (MFTF) could be built. The hardware upon which the IPCS runs consists of nine minicomputers sharing some common memory.

[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.

Virtual machine-based simulation platform for mobile ad-hoc network-based cyber infrastructure

DOE PAGES

Yoginath, Srikanth B.; Perumalla, Kayla S.; Henz, Brian J.

2015-09-29

In modeling and simulating complex systems such as mobile ad-hoc networks (MANETs) in de-fense communications, it is a major challenge to reconcile multiple important considerations: the rapidity of unavoidable changes to the software (network layers and applications), the difficulty of modeling the critical, implementation-dependent behavioral effects, the need to sustain larger scale scenarios, and the desire for faster simulations. Here we present our approach in success-fully reconciling them using a virtual time-synchronized virtual machine(VM)-based parallel ex-ecution framework that accurately lifts both the devices as well as the network communications to a virtual time plane while retaining full fidelity. At themore » core of our framework is a scheduling engine that operates at the level of a hypervisor scheduler, offering a unique ability to execute multi-core guest nodes over multi-core host nodes in an accurate, virtual time-synchronized manner. In contrast to other related approaches that suffer from either speed or accuracy issues, our framework provides MANET node-wise scalability, high fidelity of software behaviors, and time-ordering accuracy. The design and development of this framework is presented, and an ac-tual implementation based on the widely used Xen hypervisor system is described. Benchmarks with synthetic and actual applications are used to identify the benefits of our approach. The time inaccuracy of traditional emulation methods is demonstrated, in comparison with the accurate execution of our framework verified by theoretically correct results expected from analytical models of the same scenarios. In the largest high fidelity tests, we are able to perform virtual time-synchronized simulation of 64-node VM-based full-stack, actual software behaviors of MANETs containing a mix of static and mobile (unmanned airborne vehicle) nodes, hosted on a 32-core host, with full fidelity of unmodified ad-hoc routing protocols, unmodified application executables, and user-controllable physical layer effects including inter-device wireless signal strength, reachability, and connectivity.« less

Virtual machine-based simulation platform for mobile ad-hoc network-based cyber infrastructure

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

Yoginath, Srikanth B.; Perumalla, Kayla S.; Henz, Brian J.

In modeling and simulating complex systems such as mobile ad-hoc networks (MANETs) in de-fense communications, it is a major challenge to reconcile multiple important considerations: the rapidity of unavoidable changes to the software (network layers and applications), the difficulty of modeling the critical, implementation-dependent behavioral effects, the need to sustain larger scale scenarios, and the desire for faster simulations. Here we present our approach in success-fully reconciling them using a virtual time-synchronized virtual machine(VM)-based parallel ex-ecution framework that accurately lifts both the devices as well as the network communications to a virtual time plane while retaining full fidelity. At themore » core of our framework is a scheduling engine that operates at the level of a hypervisor scheduler, offering a unique ability to execute multi-core guest nodes over multi-core host nodes in an accurate, virtual time-synchronized manner. In contrast to other related approaches that suffer from either speed or accuracy issues, our framework provides MANET node-wise scalability, high fidelity of software behaviors, and time-ordering accuracy. The design and development of this framework is presented, and an ac-tual implementation based on the widely used Xen hypervisor system is described. Benchmarks with synthetic and actual applications are used to identify the benefits of our approach. The time inaccuracy of traditional emulation methods is demonstrated, in comparison with the accurate execution of our framework verified by theoretically correct results expected from analytical models of the same scenarios. In the largest high fidelity tests, we are able to perform virtual time-synchronized simulation of 64-node VM-based full-stack, actual software behaviors of MANETs containing a mix of static and mobile (unmanned airborne vehicle) nodes, hosted on a 32-core host, with full fidelity of unmodified ad-hoc routing protocols, unmodified application executables, and user-controllable physical layer effects including inter-device wireless signal strength, reachability, and connectivity.« less

Virtual Distances Methodology as Verification Technique for AACMMs with a Capacitive Sensor Based Indexed Metrology Platform

PubMed Central

Acero, Raquel; Santolaria, Jorge; Brau, Agustin; Pueo, Marcos

2016-01-01

This paper presents a new verification procedure for articulated arm coordinate measuring machines (AACMMs) together with a capacitive sensor-based indexed metrology platform (IMP) based on the generation of virtual reference distances. The novelty of this procedure lays on the possibility of creating virtual points, virtual gauges and virtual distances through the indexed metrology platform’s mathematical model taking as a reference the measurements of a ball bar gauge located in a fixed position of the instrument’s working volume. The measurements are carried out with the AACMM assembled on the IMP from the six rotating positions of the platform. In this way, an unlimited number and types of reference distances could be created without the need of using a physical gauge, therefore optimizing the testing time, the number of gauge positions and the space needed in the calibration and verification procedures. Four evaluation methods are presented to assess the volumetric performance of the AACMM. The results obtained proved the suitability of the virtual distances methodology as an alternative procedure for verification of AACMMs using the indexed metrology platform. PMID:27869722

Simulation of Physical Experiments in Immersive Virtual Environments

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Wasfy, Tamer M.

2001-01-01

An object-oriented event-driven immersive Virtual environment is described for the creation of virtual labs (VLs) for simulating physical experiments. Discussion focuses on a number of aspects of the VLs, including interface devices, software objects, and various applications. The VLs interface with output devices, including immersive stereoscopic screed(s) and stereo speakers; and a variety of input devices, including body tracking (head and hands), haptic gloves, wand, joystick, mouse, microphone, and keyboard. The VL incorporates the following types of primitive software objects: interface objects, support objects, geometric entities, and finite elements. Each object encapsulates a set of properties, methods, and events that define its behavior, appearance, and functions. A container object allows grouping of several objects. Applications of the VLs include viewing the results of the physical experiment, viewing a computer simulation of the physical experiment, simulation of the experiments procedure, computational steering, and remote control of the physical experiment. In addition, the VL can be used as a risk-free (safe) environment for training. The implementation of virtual structures testing machines, virtual wind tunnels, and a virtual acoustic testing facility is described.

Virtual Distances Methodology as Verification Technique for AACMMs with a Capacitive Sensor Based Indexed Metrology Platform.

PubMed

Acero, Raquel; Santolaria, Jorge; Brau, Agustin; Pueo, Marcos

2016-11-18

This paper presents a new verification procedure for articulated arm coordinate measuring machines (AACMMs) together with a capacitive sensor-based indexed metrology platform (IMP) based on the generation of virtual reference distances. The novelty of this procedure lays on the possibility of creating virtual points, virtual gauges and virtual distances through the indexed metrology platform's mathematical model taking as a reference the measurements of a ball bar gauge located in a fixed position of the instrument's working volume. The measurements are carried out with the AACMM assembled on the IMP from the six rotating positions of the platform. In this way, an unlimited number and types of reference distances could be created without the need of using a physical gauge, therefore optimizing the testing time, the number of gauge positions and the space needed in the calibration and verification procedures. Four evaluation methods are presented to assess the volumetric performance of the AACMM. The results obtained proved the suitability of the virtual distances methodology as an alternative procedure for verification of AACMMs using the indexed metrology platform.

Game controller modification for fMRI hyperscanning experiments in a cooperative virtual reality environment.

PubMed

Trees, Jason; Snider, Joseph; Falahpour, Maryam; Guo, Nick; Lu, Kun; Johnson, Douglas C; Poizner, Howard; Liu, Thomas T

2014-01-01

Hyperscanning, an emerging technique in which data from multiple interacting subjects' brains are simultaneously recorded, has become an increasingly popular way to address complex topics, such as "theory of mind." However, most previous fMRI hyperscanning experiments have been limited to abstract social interactions (e.g. phone conversations). Our new method utilizes a virtual reality (VR) environment used for military training, Virtual Battlespace 2 (VBS2), to create realistic avatar-avatar interactions and cooperative tasks. To control the virtual avatar, subjects use a MRI compatible Playstation 3 game controller, modified by removing all extraneous metal components and replacing any necessary ones with 3D printed plastic models. Control of both scanners' operation is initiated by a VBS2 plugin to sync scanner time to the known time within the VR environment. Our modifications include:•Modification of game controller to be MRI compatible.•Design of VBS2 virtual environment for cooperative interactions.•Syncing two MRI machines for simultaneous recording.

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network.

PubMed

Frey, Lewis J; Sward, Katherine A; Newth, Christopher J L; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-11-01

To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Virtual reality and planetary exploration

NASA Technical Reports Server (NTRS)

Mcgreevy, Michael W.

1992-01-01

Exploring planetary environments is central to NASA's missions and goals. A new computing technology called Virtual Reality has much to offer in support of planetary exploration. This technology augments and extends human presence within computer-generated and remote spatial environments. Historically, NASA has been a leader in many of the fundamental concepts and technologies that comprise Virtual Reality. Indeed, Ames Research Center has a central role in the development of this rapidly emerging approach to using computers. This ground breaking work has inspired researchers in academia, industry, and the military. Further, NASA's leadership in this technology has spun off new businesses, has caught the attention of the international business community, and has generated several years of positive international media coverage. In the future, Virtual Reality technology will enable greatly improved human-machine interactions for more productive planetary surface exploration. Perhaps more importantly, Virtual Reality technology will democratize the experience of planetary exploration and thereby broaden understanding of, and support for, this historic enterprise.

Virtual reality and planetary exploration

NASA Astrophysics Data System (ADS)

McGreevy, Michael W.

Exploring planetary environments is central to NASA's missions and goals. A new computing technology called Virtual Reality has much to offer in support of planetary exploration. This technology augments and extends human presence within computer-generated and remote spatial environments. Historically, NASA has been a leader in many of the fundamental concepts and technologies that comprise Virtual Reality. Indeed, Ames Research Center has a central role in the development of this rapidly emerging approach to using computers. This ground breaking work has inspired researchers in academia, industry, and the military. Further, NASA's leadership in this technology has spun off new businesses, has caught the attention of the international business community, and has generated several years of positive international media coverage. In the future, Virtual Reality technology will enable greatly improved human-machine interactions for more productive planetary surface exploration. Perhaps more importantly, Virtual Reality technology will democratize the experience of planetary exploration and thereby broaden understanding of, and support for, this historic enterprise.

Game controller modification for fMRI hyperscanning experiments in a cooperative virtual reality environment

PubMed Central

Trees, Jason; Snider, Joseph; Falahpour, Maryam; Guo, Nick; Lu, Kun; Johnson, Douglas C.; Poizner, Howard; Liu, Thomas T.

2014-01-01

Hyperscanning, an emerging technique in which data from multiple interacting subjects’ brains are simultaneously recorded, has become an increasingly popular way to address complex topics, such as “theory of mind.” However, most previous fMRI hyperscanning experiments have been limited to abstract social interactions (e.g. phone conversations). Our new method utilizes a virtual reality (VR) environment used for military training, Virtual Battlespace 2 (VBS2), to create realistic avatar-avatar interactions and cooperative tasks. To control the virtual avatar, subjects use a MRI compatible Playstation 3 game controller, modified by removing all extraneous metal components and replacing any necessary ones with 3D printed plastic models. Control of both scanners’ operation is initiated by a VBS2 plugin to sync scanner time to the known time within the VR environment. Our modifications include:•Modification of game controller to be MRI compatible.•Design of VBS2 virtual environment for cooperative interactions.•Syncing two MRI machines for simultaneous recording. PMID:26150964

PMICALC: an R code-based software for estimating post-mortem interval (PMI) compatible with Windows, Mac and Linux operating systems.

PubMed

Muñoz-Barús, José I; Rodríguez-Calvo, María Sol; Suárez-Peñaranda, José M; Vieira, Duarte N; Cadarso-Suárez, Carmen; Febrero-Bande, Manuel

2010-01-30

In legal medicine the correct determination of the time of death is of utmost importance. Recent advances in estimating post-mortem interval (PMI) have made use of vitreous humour chemistry in conjunction with Linear Regression, but the results are questionable. In this paper we present PMICALC, an R code-based freeware package which estimates PMI in cadavers of recent death by measuring the concentrations of potassium ([K+]), hypoxanthine ([Hx]) and urea ([U]) in the vitreous humor using two different regression models: Additive Models (AM) and Support Vector Machine (SVM), which offer more flexibility than the previously used Linear Regression. The results from both models are better than those published to date and can give numerical expression of PMI with confidence intervals and graphic support within 20 min. The program also takes into account the cause of death. 2009 Elsevier Ireland Ltd. All rights reserved.

Centralized Authentication with Kerberos 5, Part I

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

Wachsmann, A

Account administration in a distributed Unix/Linux environment can become very complicated and messy if done by hand. Large sites use special tools to deal with this problem. I will describe how even very small installations like your three computer network at home can take advantage of the very same tools. The problem in a distributed environment is that password and shadow files need to be changed individually on each machine if an account change occurs. Account changes include: password change, addition/removal of accounts, name change of an account (UID/GID changes are a big problem in any case), additional or removedmore » login privileges to a (group of) computer(s), etc. In this article, I will show how Kerberos 5 solves the authentication problem in a distributed computing environment. A second article will describe a solution for the authorization problem.« less

Performance of the dot product function in radiative transfer code SORD

NASA Astrophysics Data System (ADS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Aliaksandr; Holben, Brent

2016-10-01

The successive orders of scattering radiative transfer (RT) codes frequently call the scalar (dot) product function. In this paper, we study performance of some implementations of the dot product in the RT code SORD using 50 scenarios for light scattering in the atmosphere-surface system. In the dot product function, we use the unrolled loops technique with different unrolling factor. We also considered the intrinsic Fortran functions. We show results for two machines: ifort compiler under Windows, and pgf90 under Linux. Intrinsic DOT_PRODUCT function showed best performance for the ifort. For the pgf90, the dot product implemented with unrolling factor 4 was the fastest. The RT code SORD together with the interface that runs all the mentioned tests are publicly available from ftp://maiac.gsfc.nasa.gov/pub/skorkin/SORD_IP_16B (current release) or by email request from the corresponding (first) author.

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

Man, mind, and machine: the past and future of virtual reality simulation in neurologic surgery.

PubMed

Robison, R Aaron; Liu, Charles Y; Apuzzo, Michael L J

2011-11-01

To review virtual reality in neurosurgery, including the history of simulation and virtual reality and some of the current implementations; to examine some of the technical challenges involved; and to propose a potential paradigm for the development of virtual reality in neurosurgery going forward. A search was made on PubMed using key words surgical simulation, virtual reality, haptics, collision detection, and volumetric modeling to assess the current status of virtual reality in neurosurgery. Based on previous results, investigators extrapolated the possible integration of existing efforts and potential future directions. Simulation has a rich history in surgical training, and there are numerous currently existing applications and systems that involve virtual reality. All existing applications are limited to specific task-oriented functions and typically sacrifice visual realism for real-time interactivity or vice versa, owing to numerous technical challenges in rendering a virtual space in real time, including graphic and tissue modeling, collision detection, and direction of the haptic interface. With ongoing technical advancements in computer hardware and graphic and physical rendering, incremental or modular development of a fully immersive, multipurpose virtual reality neurosurgical simulator is feasible. The use of virtual reality in neurosurgery is predicted to change the nature of neurosurgical education, and to play an increased role in surgical rehearsal and the continuing education and credentialing of surgical practitioners. Copyright © 2011 Elsevier Inc. All rights reserved.

ATLAS@AWS

NASA Astrophysics Data System (ADS)

Gehrcke, Jan-Philip; Kluth, Stefan; Stonjek, Stefan

2010-04-01

We show how the ATLAS offline software is ported on the Amazon Elastic Compute Cloud (EC2). We prepare an Amazon Machine Image (AMI) on the basis of the standard ATLAS platform Scientific Linux 4 (SL4). Then an instance of the SLC4 AMI is started on EC2 and we install and validate a recent release of the ATLAS offline software distribution kit. The installed software is archived as an image on the Amazon Simple Storage Service (S3) and can be quickly retrieved and connected to new SL4 AMI instances using the Amazon Elastic Block Store (EBS). ATLAS jobs can then configure against the release kit using the ATLAS configuration management tool (cmt) in the standard way. The output of jobs is exported to S3 before the SL4 AMI is terminated. Job status information is transferred to the Amazon SimpleDB service. The whole process of launching instances of our AMI, starting, monitoring and stopping jobs and retrieving job output from S3 is controlled from a client machine using python scripts implementing the Amazon EC2/S3 API via the boto library working together with small scripts embedded in the SL4 AMI. We report our experience with setting up and operating the system using standard ATLAS job transforms.

MEMS deformable mirror embedded wavefront sensing and control system

NASA Astrophysics Data System (ADS)

Owens, Donald; Schoen, Michael; Bush, Keith

2006-01-01

Electrostatic Membrane Deformable Mirror (MDM) technology developed using silicon bulk micro-machining techniques offers the potential of providing low-cost, compact wavefront control systems for diverse optical system applications. Electrostatic mirror construction using bulk micro-machining allows for custom designs to satisfy wavefront control requirements for most optical systems. An electrostatic MDM consists of a thin membrane, generally with a thin metal or multi-layer high-reflectivity coating, suspended over an actuator pad array that is connected to a high-voltage driver. Voltages applied to the array elements deflect the membrane to provide an optical surface capable of correcting for measured optical aberrations in a given system. Electrostatic membrane DM designs are derived from well-known principles of membrane mechanics and electrostatics, the desired optical wavefront control requirements, and the current limitations of mirror fabrication and actuator drive electronics. MDM performance is strongly dependent on mirror diameter and air damping in meeting desired spatial and temporal frequency requirements. In this paper, we present wavefront control results from an embedded wavefront control system developed around a commercially available high-speed camera and an AgilOptics Unifi MDM driver using USB 2.0 communications and the Linux development environment. This new product, ClariFast TM, combines our previous Clarifi TM product offering into a faster more streamlined version dedicated strictly to Hartmann Wavefront sensing.

Third generation of correlators for six antennas

NASA Astrophysics Data System (ADS)

Torres, Marc

2000-07-01

The technical evolution of the correlators of the Plateau de Bure interferometer since the first fringes, 14 years ago, is shortly presented. The progressive addition of antennas over this period has allowed the Grenoble correlator group to undertake several 'start-from-scratch' designs, which have replaced on-site equipment as it came obsolete. The tradeoff between design cycle time and lifetime of such equipment is discussed. The latest design is described in detail. The new correlator can be set to analyze up to eight simultaneous windows, adjustable in size and center frequency, thanks to a 2 X 220 MHz image rejection mixer. Advantages of analog IF processing are presented. The frequency plan of the IF processor has been designed to be fully compatible with MarkIV VLBI recording. The correlator is then used to sum up the signals of the 6 antennas over 256 MHz. The digital section mainly uses an IRAM-designed low-power, low-cost ASIC. Delay lines use FPGA's and phase rotators use DDS's. Surface-mount technology is used everywhere. A commercial CPU module runs the real-time software under Linux. A 21-slot VME chassis hosts the hardware. Test results and measurements of performance on the full-size machine are presented. The difficulties encountered in achieving this kind of machine within schedule in today's industrial environment are retrospectively analyzed.

Secure Autonomous Automated Scheduling (SAAS). Rev. 1.1

NASA Technical Reports Server (NTRS)

Walke, Jon G.; Dikeman, Larry; Sage, Stephen P.; Miller, Eric M.

2010-01-01

This report describes network-centric operations, where a virtual mission operations center autonomously receives sensor triggers, and schedules space and ground assets using Internet-based technologies and service-oriented architectures. For proof-of-concept purposes, sensor triggers are received from the United States Geological Survey (USGS) to determine targets for space-based sensors. The Surrey Satellite Technology Limited (SSTL) Disaster Monitoring Constellation satellite, the UK-DMC, is used as the space-based sensor. The UK-DMC's availability is determined via machine-to-machine communications using SSTL's mission planning system. Access to/from the UK-DMC for tasking and sensor data is via SSTL's and Universal Space Network's (USN) ground assets. The availability and scheduling of USN's assets can also be performed autonomously via machine-to-machine communications. All communication, both on the ground and between ground and space, uses open Internet standards

Performance prediction: A case study using a multi-ring KSR-1 machine

NASA Technical Reports Server (NTRS)

Sun, Xian-He; Zhu, Jianping

1995-01-01

While computers with tens of thousands of processors have successfully delivered high performance power for solving some of the so-called 'grand-challenge' applications, the notion of scalability is becoming an important metric in the evaluation of parallel machine architectures and algorithms. In this study, the prediction of scalability and its application are carefully investigated. A simple formula is presented to show the relation between scalability, single processor computing power, and degradation of parallelism. A case study is conducted on a multi-ring KSR1 shared virtual memory machine. Experimental and theoretical results show that the influence of topology variation of an architecture is predictable. Therefore, the performance of an algorithm on a sophisticated, heirarchical architecture can be predicted and the best algorithm-machine combination can be selected for a given application.

Grids, virtualization, and clouds at Fermilab

DOE PAGES

Timm, S.; Chadwick, K.; Garzoglio, G.; ...

2014-06-11

Fermilab supports a scientific program that includes experiments and scientists located across the globe. To better serve this community, in 2004, the (then) Computing Division undertook the strategy of placing all of the High Throughput Computing (HTC) resources in a Campus Grid known as FermiGrid, supported by common shared services. In 2007, the FermiGrid Services group deployed a service infrastructure that utilized Xen virtualization, LVS network routing and MySQL circular replication to deliver highly available services that offered significant performance, reliability and serviceability improvements. This deployment was further enhanced through the deployment of a distributed redundant network core architecture andmore » the physical distribution of the systems that host the virtual machines across multiple buildings on the Fermilab Campus. In 2010, building on the experience pioneered by FermiGrid in delivering production services in a virtual infrastructure, the Computing Sector commissioned the FermiCloud, General Physics Computing Facility and Virtual Services projects to serve as platforms for support of scientific computing (FermiCloud 6 GPCF) and core computing (Virtual Services). Lastly, this work will present the evolution of the Fermilab Campus Grid, Virtualization and Cloud Computing infrastructure together with plans for the future.« less

Grids, virtualization, and clouds at Fermilab

NASA Astrophysics Data System (ADS)

Timm, S.; Chadwick, K.; Garzoglio, G.; Noh, S.

2014-06-01

Fermilab supports a scientific program that includes experiments and scientists located across the globe. To better serve this community, in 2004, the (then) Computing Division undertook the strategy of placing all of the High Throughput Computing (HTC) resources in a Campus Grid known as FermiGrid, supported by common shared services. In 2007, the FermiGrid Services group deployed a service infrastructure that utilized Xen virtualization, LVS network routing and MySQL circular replication to deliver highly available services that offered significant performance, reliability and serviceability improvements. This deployment was further enhanced through the deployment of a distributed redundant network core architecture and the physical distribution of the systems that host the virtual machines across multiple buildings on the Fermilab Campus. In 2010, building on the experience pioneered by FermiGrid in delivering production services in a virtual infrastructure, the Computing Sector commissioned the FermiCloud, General Physics Computing Facility and Virtual Services projects to serve as platforms for support of scientific computing (FermiCloud 6 GPCF) and core computing (Virtual Services). This work will present the evolution of the Fermilab Campus Grid, Virtualization and Cloud Computing infrastructure together with plans for the future.

The Virtual Climate Data Server (vCDS): An iRODS-Based Data Management Software Appliance Supporting Climate Data Services and Virtualization-as-a-Service in the NASA Center for Climate Simulation

NASA Technical Reports Server (NTRS)

Schnase, John L.; Tamkin, Glenn S.; Ripley, W. David III; Stong, Savannah; Gill, Roger; Duffy, Daniel Q.

2012-01-01

Scientific data services are becoming an important part of the NASA Center for Climate Simulation's mission. Our technological response to this expanding role is built around the concept of a Virtual Climate Data Server (vCDS), repetitive provisioning, image-based deployment and distribution, and virtualization-as-a-service. The vCDS is an iRODS-based data server specialized to the needs of a particular data-centric application. We use RPM scripts to build vCDS images in our local computing environment, our local Virtual Machine Environment, NASA s Nebula Cloud Services, and Amazon's Elastic Compute Cloud. Once provisioned into one or more of these virtualized resource classes, vCDSs can use iRODS s federation capabilities to create an integrated ecosystem of managed collections that is scalable and adaptable to changing resource requirements. This approach enables platform- or software-asa- service deployment of vCDS and allows the NCCS to offer virtualization-as-a-service: a capacity to respond in an agile way to new customer requests for data services.

Integration of Openstack cloud resources in BES III computing cluster

NASA Astrophysics Data System (ADS)

Li, Haibo; Cheng, Yaodong; Huang, Qiulan; Cheng, Zhenjing; Shi, Jingyan

2017-10-01

Cloud computing provides a new technical means for data processing of high energy physics experiment. However, the resource of each queue is fixed and the usage of the resource is static in traditional job management system. In order to make it simple and transparent for physicist to use, we developed a virtual cluster system (vpmanager) to integrate IHEPCloud and different batch systems such as Torque and HTCondor. Vpmanager provides dynamic virtual machines scheduling according to the job queue. The BES III use case results show that resource efficiency is greatly improved.

A location selection policy of live virtual machine migration for power saving and load balancing.

PubMed

Zhao, Jia; Ding, Yan; Xu, Gaochao; Hu, Liang; Dong, Yushuang; Fu, Xiaodong

2013-01-01

Green cloud data center has become a research hotspot of virtualized cloud computing architecture. And load balancing has also been one of the most important goals in cloud data centers. Since live virtual machine (VM) migration technology is widely used and studied in cloud computing, we have focused on location selection (migration policy) of live VM migration for power saving and load balancing. We propose a novel approach MOGA-LS, which is a heuristic and self-adaptive multiobjective optimization algorithm based on the improved genetic algorithm (GA). This paper has presented the specific design and implementation of MOGA-LS such as the design of the genetic operators, fitness values, and elitism. We have introduced the Pareto dominance theory and the simulated annealing (SA) idea into MOGA-LS and have presented the specific process to get the final solution, and thus, the whole approach achieves a long-term efficient optimization for power saving and load balancing. The experimental results demonstrate that MOGA-LS evidently reduces the total incremental power consumption and better protects the performance of VM migration and achieves the balancing of system load compared with the existing research. It makes the result of live VM migration more high-effective and meaningful.

A Location Selection Policy of Live Virtual Machine Migration for Power Saving and Load Balancing

PubMed Central

Xu, Gaochao; Hu, Liang; Dong, Yushuang; Fu, Xiaodong

2013-01-01

Green cloud data center has become a research hotspot of virtualized cloud computing architecture. And load balancing has also been one of the most important goals in cloud data centers. Since live virtual machine (VM) migration technology is widely used and studied in cloud computing, we have focused on location selection (migration policy) of live VM migration for power saving and load balancing. We propose a novel approach MOGA-LS, which is a heuristic and self-adaptive multiobjective optimization algorithm based on the improved genetic algorithm (GA). This paper has presented the specific design and implementation of MOGA-LS such as the design of the genetic operators, fitness values, and elitism. We have introduced the Pareto dominance theory and the simulated annealing (SA) idea into MOGA-LS and have presented the specific process to get the final solution, and thus, the whole approach achieves a long-term efficient optimization for power saving and load balancing. The experimental results demonstrate that MOGA-LS evidently reduces the total incremental power consumption and better protects the performance of VM migration and achieves the balancing of system load compared with the existing research. It makes the result of live VM migration more high-effective and meaningful. PMID:24348165

Dynamic virtual machine allocation policy in cloud computing complying with service level agreement using CloudSim

NASA Astrophysics Data System (ADS)

Aneri, Parikh; Sumathy, S.

2017-11-01

Cloud computing provides services over the internet and provides application resources and data to the users based on their demand. Base of the Cloud Computing is consumer provider model. Cloud provider provides resources which consumer can access using cloud computing model in order to build their application based on their demand. Cloud data center is a bulk of resources on shared pool architecture for cloud user to access. Virtualization is the heart of the Cloud computing model, it provides virtual machine as per application specific configuration and those applications are free to choose their own configuration. On one hand, there is huge number of resources and on other hand it has to serve huge number of requests effectively. Therefore, resource allocation policy and scheduling policy play very important role in allocation and managing resources in this cloud computing model. This paper proposes the load balancing policy using Hungarian algorithm. Hungarian Algorithm provides dynamic load balancing policy with a monitor component. Monitor component helps to increase cloud resource utilization by managing the Hungarian algorithm by monitoring its state and altering its state based on artificial intelligent. CloudSim used in this proposal is an extensible toolkit and it simulates cloud computing environment.

Synthetic hardware performance analysis in virtualized cloud environment for healthcare organization.

PubMed

Tan, Chee-Heng; Teh, Ying-Wah

2013-08-01

The main obstacles in mass adoption of cloud computing for database operations in healthcare organization are the data security and privacy issues. In this paper, it is shown that IT services particularly in hardware performance evaluation in virtual machine can be accomplished effectively without IT personnel gaining access to actual data for diagnostic and remediation purposes. The proposed mechanisms utilized the hypothetical data from TPC-H benchmark, to achieve 2 objectives. First, the underlying hardware performance and consistency is monitored via a control system, which is constructed using TPC-H queries. Second, the mechanism to construct stress-testing scenario is envisaged in the host, using a single or combination of TPC-H queries, so that the resource threshold point can be verified, if the virtual machine is still capable of serving critical transactions at this constraining juncture. This threshold point uses server run queue size as input parameter, and it serves 2 purposes: It provides the boundary threshold to the control system, so that periodic learning of the synthetic data sets for performance evaluation does not reach the host's constraint level. Secondly, when the host undergoes hardware change, stress-testing scenarios are simulated in the host by loading up to this resource threshold level, for subsequent response time verification from real and critical transactions.

A 3-D mixed-reality system for stereoscopic visualization of medical dataset.

PubMed

Ferrari, Vincenzo; Megali, Giuseppe; Troia, Elena; Pietrabissa, Andrea; Mosca, Franco

2009-11-01

We developed a simple, light, and cheap 3-D visualization device based on mixed reality that can be used by physicians to see preoperative radiological exams in a natural way. The system allows the user to see stereoscopic "augmented images," which are created by mixing 3-D virtual models of anatomies obtained by processing preoperative volumetric radiological images (computed tomography or MRI) with real patient live images, grabbed by means of cameras. The interface of the system consists of a head-mounted display equipped with two high-definition cameras. Cameras are mounted in correspondence of the user's eyes and allow one to grab live images of the patient with the same point of view of the user. The system does not use any external tracker to detect movements of the user or the patient. The movements of the user's head and the alignment of virtual patient with the real one are done using machine vision methods applied on pairs of live images. Experimental results, concerning frame rate and alignment precision between virtual and real patient, demonstrate that machine vision methods used for localization are appropriate for the specific application and that systems based on stereoscopic mixed reality are feasible and can be proficiently adopted in clinical practice.

PISCES: An environment for parallel scientific computation

NASA Technical Reports Server (NTRS)

Pratt, T. W.

1985-01-01

The parallel implementation of scientific computing environment (PISCES) is a project to provide high-level programming environments for parallel MIMD computers. Pisces 1, the first of these environments, is a FORTRAN 77 based environment which runs under the UNIX operating system. The Pisces 1 user programs in Pisces FORTRAN, an extension of FORTRAN 77 for parallel processing. The major emphasis in the Pisces 1 design is in providing a carefully specified virtual machine that defines the run-time environment within which Pisces FORTRAN programs are executed. Each implementation then provides the same virtual machine, regardless of differences in the underlying architecture. The design is intended to be portable to a variety of architectures. Currently Pisces 1 is implemented on a network of Apollo workstations and on a DEC VAX uniprocessor via simulation of the task level parallelism. An implementation for the Flexible Computing Corp. FLEX/32 is under construction. An introduction to the Pisces 1 virtual computer and the FORTRAN 77 extensions is presented. An example of an algorithm for the iterative solution of a system of equations is given. The most notable features of the design are the provision for several granularities of parallelism in programs and the provision of a window mechanism for distributed access to large arrays of data.

Suitability of digital camcorders for virtual reality image data capture

NASA Astrophysics Data System (ADS)

D'Apuzzo, Nicola; Maas, Hans-Gerd

1998-12-01

Today's consumer market digital camcorders offer features which make them appear quite interesting devices for virtual reality data capture. The paper compares a digital camcorder with an analogue camcorder and a machine vision type CCD camera and discusses the suitability of these three cameras for virtual reality applications. Besides the discussion of technical features of the cameras, this includes a detailed accuracy test in order to define the range of applications. In combination with the cameras, three different framegrabbers are tested. The geometric accuracy potential of all three cameras turned out to be surprisingly large, and no problems were noticed in the radiometric performance. On the other hand, some disadvantages have to be reported: from the photogrammetrists point of view, the major disadvantage of most camcorders is the missing possibility to synchronize multiple devices, limiting the suitability for 3-D motion data capture. Moreover, the standard video format contains interlacing, which is also undesirable for all applications dealing with moving objects or moving cameras. Further disadvantages are computer interfaces with functionality, which is still suboptimal. While custom-made solutions to these problems are probably rather expensive (and will make potential users turn back to machine vision like equipment), this functionality could probably be included by the manufacturers at almost zero cost.

Cloud Computing Applications in Support of Earth Science Activities at Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

Molthan, Andrew L.; Limaye, Ashutosh S.; Srikishen, Jayanthi

2011-01-01

Currently, the NASA Nebula Cloud Computing Platform is available to Agency personnel in a pre-release status as the system undergoes a formal operational readiness review. Over the past year, two projects within the Earth Science Office at NASA Marshall Space Flight Center have been investigating the performance and value of Nebula s "Infrastructure as a Service", or "IaaS" concept and applying cloud computing concepts to advance their respective mission goals. The Short-term Prediction Research and Transition (SPoRT) Center focuses on the transition of unique NASA satellite observations and weather forecasting capabilities for use within the operational forecasting community through partnerships with NOAA s National Weather Service (NWS). SPoRT has evaluated the performance of the Weather Research and Forecasting (WRF) model on virtual machines deployed within Nebula and used Nebula instances to simulate local forecasts in support of regional forecast studies of interest to select NWS forecast offices. In addition to weather forecasting applications, rapidly deployable Nebula virtual machines have supported the processing of high resolution NASA satellite imagery to support disaster assessment following the historic severe weather and tornado outbreak of April 27, 2011. Other modeling and satellite analysis activities are underway in support of NASA s SERVIR program, which integrates satellite observations, ground-based data and forecast models to monitor environmental change and improve disaster response in Central America, the Caribbean, Africa, and the Himalayas. Leveraging SPoRT s experience, SERVIR is working to establish a real-time weather forecasting model for Central America. Other modeling efforts include hydrologic forecasts for Kenya, driven by NASA satellite observations and reanalysis data sets provided by the broader meteorological community. Forecast modeling efforts are supplemented by short-term forecasts of convective initiation, determined by geostationary satellite observations processed on virtual machines powered by Nebula.

Development and experimental test of support vector machines virtual screening method for searching Src inhibitors from large compound libraries.

PubMed

Han, Bucong; Ma, Xiaohua; Zhao, Ruiying; Zhang, Jingxian; Wei, Xiaona; Liu, Xianghui; Liu, Xin; Zhang, Cunlong; Tan, Chunyan; Jiang, Yuyang; Chen, Yuzong

2012-11-23

Src plays various roles in tumour progression, invasion, metastasis, angiogenesis and survival. It is one of the multiple targets of multi-target kinase inhibitors in clinical uses and trials for the treatment of leukemia and other cancers. These successes and appearances of drug resistance in some patients have raised significant interest and efforts in discovering new Src inhibitors. Various in-silico methods have been used in some of these efforts. It is desirable to explore additional in-silico methods, particularly those capable of searching large compound libraries at high yields and reduced false-hit rates. We evaluated support vector machines (SVM) as virtual screening tools for searching Src inhibitors from large compound libraries. SVM trained and tested by 1,703 inhibitors and 63,318 putative non-inhibitors correctly identified 93.53%~ 95.01% inhibitors and 99.81%~ 99.90% non-inhibitors in 5-fold cross validation studies. SVM trained by 1,703 inhibitors reported before 2011 and 63,318 putative non-inhibitors correctly identified 70.45% of the 44 inhibitors reported since 2011, and predicted as inhibitors 44,843 (0.33%) of 13.56M PubChem, 1,496 (0.89%) of 168 K MDDR, and 719 (7.73%) of 9,305 MDDR compounds similar to the known inhibitors. SVM showed comparable yield and reduced false hit rates in searching large compound libraries compared to the similarity-based and other machine-learning VS methods developed from the same set of training compounds and molecular descriptors. We tested three virtual hits of the same novel scaffold from in-house chemical libraries not reported as Src inhibitor, one of which showed moderate activity. SVM may be potentially explored for searching Src inhibitors from large compound libraries at low false-hit rates.

Optimized Hypervisor Scheduler for Parallel Discrete Event Simulations on Virtual Machine Platforms

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

Yoginath, Srikanth B; Perumalla, Kalyan S

2013-01-01

With the advent of virtual machine (VM)-based platforms for parallel computing, it is now possible to execute parallel discrete event simulations (PDES) over multiple virtual machines, in contrast to executing in native mode directly over hardware as is traditionally done over the past decades. While mature VM-based parallel systems now offer new, compelling benefits such as serviceability, dynamic reconfigurability and overall cost effectiveness, the runtime performance of parallel applications can be significantly affected. In particular, most VM-based platforms are optimized for general workloads, but PDES execution exhibits unique dynamics significantly different from other workloads. Here we first present results frommore » experiments that highlight the gross deterioration of the runtime performance of VM-based PDES simulations when executed using traditional VM schedulers, quantitatively showing the bad scaling properties of the scheduler as the number of VMs is increased. The mismatch is fundamental in nature in the sense that any fairness-based VM scheduler implementation would exhibit this mismatch with PDES runs. We also present a new scheduler optimized specifically for PDES applications, and describe its design and implementation. Experimental results obtained from running PDES benchmarks (PHOLD and vehicular traffic simulations) over VMs show over an order of magnitude improvement in the run time of the PDES-optimized scheduler relative to the regular VM scheduler, with over 20 reduction in run time of simulations using up to 64 VMs. The observations and results are timely in the context of emerging systems such as cloud platforms and VM-based high performance computing installations, highlighting to the community the need for PDES-specific support, and the feasibility of significantly reducing the runtime overhead for scalable PDES on VM platforms.« less

Security model for VM in cloud

NASA Astrophysics Data System (ADS)

Kanaparti, Venkataramana; Naveen K., R.; Rajani, S.; Padmvathamma, M.; Anitha, C.

2013-03-01

Cloud computing is a new approach emerged to meet ever-increasing demand for computing resources and to reduce operational costs and Capital Expenditure for IT services. As this new way of computation allows data and applications to be stored away from own corporate server, it brings more issues in security such as virtualization security, distributed computing, application security, identity management, access control and authentication. Even though Virtualization forms the basis for cloud computing it poses many threats in securing cloud. As most of Security threats lies at Virtualization layer in cloud we proposed this new Security Model for Virtual Machine in Cloud (SMVC) in which every process is authenticated by Trusted-Agent (TA) in Hypervisor as well as in VM. Our proposed model is designed to with-stand attacks by unauthorized process that pose threat to applications related to Data Mining, OLAP systems, Image processing which requires huge resources in cloud deployed on one or more VM's.

The effective use of virtualization for selection of data centers in a cloud computing environment

NASA Astrophysics Data System (ADS)

Kumar, B. Santhosh; Parthiban, Latha

2018-04-01

Data centers are the places which consist of network of remote servers to store, access and process the data. Cloud computing is a technology where users worldwide will submit the tasks and the service providers will direct the requests to the data centers which are responsible for execution of tasks. The servers in the data centers need to employ the virtualization concept so that multiple tasks can be executed simultaneously. In this paper we proposed an algorithm for data center selection based on energy of virtual machines created in server. The virtualization energy in each of the server is calculated and total energy of the data center is obtained by the summation of individual server energy. The tasks submitted are routed to the data center with least energy consumption which will result in minimizing the operational expenses of a service provider.

Using virtualization to protect the proprietary material science applications in volunteer computing

NASA Astrophysics Data System (ADS)

Khrapov, Nikolay P.; Rozen, Valery V.; Samtsevich, Artem I.; Posypkin, Mikhail A.; Sukhomlin, Vladimir A.; Oganov, Artem R.

2018-04-01

USPEX is a world-leading software for computational material design. In essence, USPEX splits simulation into a large number of workunits that can be processed independently. This scheme ideally fits the desktop grid architecture. Workunit processing is done by a simulation package aimed at energy minimization. Many of such packages are proprietary and should be protected from unauthorized access when running on a volunteer PC. In this paper we present an original approach based on virtualization. In a nutshell, the proprietary code and input files are stored in an encrypted folder and run inside a virtual machine image that is also password protected. The paper describes this approach in detail and discusses its application in USPEX@home volunteer project.

A nested virtualization tool for information technology practical education.

PubMed

Pérez, Carlos; Orduña, Juan M; Soriano, Francisco R

2016-01-01

A common problem of some information technology courses is the difficulty of providing practical exercises. Although different approaches have been followed to solve this problem, it is still an open issue, specially in security and computer network courses. This paper proposes NETinVM, a tool based on nested virtualization that includes a fully functional lab, comprising several computers and networks, in a single virtual machine. It also analyzes and evaluates how it has been used in different teaching environments. The results show that this tool makes it possible to perform demos, labs and practical exercises, greatly appreciated by the students, that would otherwise be unfeasible. Also, its portability allows to reproduce classroom activities, as well as the students' autonomous work.

Virtual hospital--a computer-aided platform to evaluate the sense of direction.

PubMed

Jiang, Ching-Fen; Li, Yuan-Shyi

2007-01-01

This paper presents a computer-aided platform, named Virtual Hospital (VH), to evaluate the wayfinding ability that is found impaired in senile people with early dementia. The development of the VH takes the advantage of virtual reality technology to make the evaluation of the sense of direction more convenient and accurate then the conventional way. A pilot study was carried out to test its feasibility in differentiating the sense of direction between different genders. The results with significant differences in the response time (p<0.05) and the pointing error (p<0.01) between genders suggest the potential of the VH for clinical uses. Further improvement on the human-machine interface is necessary to make it easy for geriatric people to use.

Human Factors Consideration for the Design of Collaborative Machine Assistants

NASA Astrophysics Data System (ADS)

Park, Sung; Fisk, Arthur D.; Rogers, Wendy A.

Recent improvements in technology have facilitated the use of robots and virtual humans not only in entertainment and engineering but also in the military (Hill et al., 2003), healthcare (Pollack et al., 2002), and education domains (Johnson, Rickel, & Lester, 2000). As active partners of humans, such machine assistants can take the form of a robot or a graphical representation and serve the role of a financial assistant, a health manager, or even a social partner. As a result, interactive technologies are becoming an integral component of people's everyday lives.

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

McCaskey, Alexander J.

There is a lack of state-of-the-art quantum computing simulation software that scales on heterogeneous systems like Titan. Tensor Network Quantum Virtual Machine (TNQVM) provides a quantum simulator that leverages a distributed network of GPUs to simulate quantum circuits in a manner that leverages recent results from tensor network theory.

Hardware Support for Malware Defense and End-to-End Trust

DTIC Science & Technology

2017-02-01

IoT) sensors and actuators, mobile devices and servers; cloud based, stand alone, and traditional mainframes. The prototype developed demonstrated...virtual machines. For mobile platforms we developed and prototyped an architecture supporting separation of personalities on the same platform...4 3.1. MOBILE

Request queues for interactive clients in a shared file system of a parallel computing system

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

Bent, John M.; Faibish, Sorin

Interactive requests are processed from users of log-in nodes. A metadata server node is provided for use in a file system shared by one or more interactive nodes and one or more batch nodes. The interactive nodes comprise interactive clients to execute interactive tasks and the batch nodes execute batch jobs for one or more batch clients. The metadata server node comprises a virtual machine monitor; an interactive client proxy to store metadata requests from the interactive clients in an interactive client queue; a batch client proxy to store metadata requests from the batch clients in a batch client queue;more » and a metadata server to store the metadata requests from the interactive client queue and the batch client queue in a metadata queue based on an allocation of resources by the virtual machine monitor. The metadata requests can be prioritized, for example, based on one or more of a predefined policy and predefined rules.« less

Geometric dimension model of virtual astronaut body for ergonomic analysis of man-machine space system

NASA Astrophysics Data System (ADS)

Qianxiang, Zhou

2012-07-01

It is very important to clarify the geometric characteristic of human body segment and constitute analysis model for ergonomic design and the application of ergonomic virtual human. The typical anthropometric data of 1122 Chinese men aged 20-35 years were collected using three-dimensional laser scanner for human body. According to the correlation between different parameters, curve fitting were made between seven trunk parameters and ten body parameters with the SPSS 16.0 software. It can be concluded that hip circumference and shoulder breadth are the most important parameters in the models and the two parameters have high correlation with the others parameters of human body. By comparison with the conventional regressive curves, the present regression equation with the seven trunk parameters is more accurate to forecast the geometric dimensions of head, neck, height and the four limbs with high precision. Therefore, it is greatly valuable for ergonomic design and analysis of man-machine system.This result will be very useful to astronaut body model analysis and application.

A Virtual Geant4 Environment

NASA Astrophysics Data System (ADS)

Iwai, Go

2015-12-01

We describe the development of an environment for Geant4 consisting of an application and data that provide users with a more efficient way to access Geant4 applications without having to download and build the software locally. The environment is platform neutral and offers the users near-real time performance. In addition, the environment consists of data and Geant4 libraries built using low-level virtual machine (LLVM) tools which can produce bitcode that can be embedded in HTML and accessed via a browser. The bitcode is downloaded to the local machine via the browser and can then be configured by the user. This approach provides a way of minimising the risk of leaking potentially sensitive data used to construct the Geant4 model and application in the medical domain for treatment planning. We describe several applications that have used this approach and compare their performance with that of native applications. We also describe potential user communities that could benefit from this approach.

The core legion object model

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

Lewis, M.; Grimshaw, A.

1996-12-31

The Legion project at the University of Virginia is an architecture for designing and building system services that provide the illusion of a single virtual machine to users, a virtual machine that provides secure shared object and shared name spaces, application adjustable fault-tolerance, improved response time, and greater throughput. Legion targets wide area assemblies of workstations, supercomputers, and parallel supercomputers, Legion tackles problems not solved by existing workstation based parallel processing tools; the system will enable fault-tolerance, wide area parallel processing, inter-operability, heterogeneity, a single global name space, protection, security, efficient scheduling, and comprehensive resource management. This paper describes themore » core Legion object model, which specifies the composition and functionality of Legion`s core objects-those objects that cooperate to create, locate, manage, and remove objects in the Legion system. The object model facilitates a flexible extensible implementation, provides a single global name space, grants site autonomy to participating organizations, and scales to millions of sites and trillions of objects.« less

An Extended Proof-Carrying Code Framework for Security Enforcement

NASA Astrophysics Data System (ADS)

Pirzadeh, Heidar; Dubé, Danny; Hamou-Lhadj, Abdelwahab

The rapid growth of the Internet has resulted in increased attention to security to protect users from being victims of security threats. In this paper, we focus on security mechanisms that are based on Proof-Carrying Code (PCC) techniques. In a PCC system, a code producer sends a code along with its safety proof to the consumer. The consumer executes the code only if the proof is valid. Although PCC has been shown to be a useful security framework, it suffers from the sheer size of typical proofs -proofs of even small programs can be considerably large. In this paper, we propose an extended PCC framework (EPCC) in which, instead of the proof, a proof generator for the program in question is transmitted. This framework enables the execution of the proof generator and the recovery of the proof on the consumer's side in a secure manner using a newly created virtual machine called the VEP (Virtual Machine for Extended PCC).

Development of a HIPAA-compliant environment for translational research data and analytics.

PubMed

Bradford, Wayne; Hurdle, John F; LaSalle, Bernie; Facelli, Julio C

2014-01-01

High-performance computing centers (HPC) traditionally have far less restrictive privacy management policies than those encountered in healthcare. We show how an HPC can be re-engineered to accommodate clinical data while retaining its utility in computationally intensive tasks such as data mining, machine learning, and statistics. We also discuss deploying protected virtual machines. A critical planning step was to engage the university's information security operations and the information security and privacy office. Access to the environment requires a double authentication mechanism. The first level of authentication requires access to the university's virtual private network and the second requires that the users be listed in the HPC network information service directory. The physical hardware resides in a data center with controlled room access. All employees of the HPC and its users take the university's local Health Insurance Portability and Accountability Act training series. In the first 3 years, researcher count has increased from 6 to 58.

New Web Server - the Java Version of Tempest - Produced

NASA Technical Reports Server (NTRS)

York, David W.; Ponyik, Joseph G.

2000-01-01

A new software design and development effort has produced a Java (Sun Microsystems, Inc.) version of the award-winning Tempest software (refs. 1 and 2). In 1999, the Embedded Web Technology (EWT) team received a prestigious R&D 100 Award for Tempest, Java Version. In this article, "Tempest" will refer to the Java version of Tempest, a World Wide Web server for desktop or embedded systems. Tempest was designed at the NASA Glenn Research Center at Lewis Field to run on any platform for which a Java Virtual Machine (JVM, Sun Microsystems, Inc.) exists. The JVM acts as a translator between the native code of the platform and the byte code of Tempest, which is compiled in Java. These byte code files are Java executables with a ".class" extension. Multiple byte code files can be zipped together as a "*.jar" file for more efficient transmission over the Internet. Today's popular browsers, such as Netscape (Netscape Communications Corporation) and Internet Explorer (Microsoft Corporation) have built-in Virtual Machines to display Java applets.

Machine learning-based assessment tool for imbalance and vestibular dysfunction with virtual reality rehabilitation system.

PubMed

Yeh, Shih-Ching; Huang, Ming-Chun; Wang, Pa-Chun; Fang, Te-Yung; Su, Mu-Chun; Tsai, Po-Yi; Rizzo, Albert

2014-10-01

Dizziness is a major consequence of imbalance and vestibular dysfunction. Compared to surgery and drug treatments, balance training is non-invasive and more desired. However, training exercises are usually tedious and the assessment tool is insufficient to diagnose patient's severity rapidly. An interactive virtual reality (VR) game-based rehabilitation program that adopted Cawthorne-Cooksey exercises, and a sensor-based measuring system were introduced. To verify the therapeutic effect, a clinical experiment with 48 patients and 36 normal subjects was conducted. Quantified balance indices were measured and analyzed by statistical tools and a Support Vector Machine (SVM) classifier. In terms of balance indices, patients who completed the training process are progressed and the difference between normal subjects and patients is obvious. Further analysis by SVM classifier show that the accuracy of recognizing the differences between patients and normal subject is feasible, and these results can be used to evaluate patients' severity and make rapid assessment. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0.

PubMed

Jiang, Xiaohui; Kumar, Kamal; Hu, Xin; Wallqvist, Anders; Reifman, Jaques

2008-09-08

Small-molecule docking is an important tool in studying receptor-ligand interactions and in identifying potential drug candidates. Previously, we developed a software tool (DOVIS) to perform large-scale virtual screening of small molecules in parallel on Linux clusters, using AutoDock 3.05 as the docking engine. DOVIS enables the seamless screening of millions of compounds on high-performance computing platforms. In this paper, we report significant advances in the software implementation of DOVIS 2.0, including enhanced screening capability, improved file system efficiency, and extended usability. To keep DOVIS up-to-date, we upgraded the software's docking engine to the more accurate AutoDock 4.0 code. We developed a new parallelization scheme to improve runtime efficiency and modified the AutoDock code to reduce excessive file operations during large-scale virtual screening jobs. We also implemented an algorithm to output docked ligands in an industry standard format, sd-file format, which can be easily interfaced with other modeling programs. Finally, we constructed a wrapper-script interface to enable automatic rescoring of docked ligands by arbitrarily selected third-party scoring programs. The significance of the new DOVIS 2.0 software compared with the previous version lies in its improved performance and usability. The new version makes the computation highly efficient by automating load balancing, significantly reducing excessive file operations by more than 95%, providing outputs that conform to industry standard sd-file format, and providing a general wrapper-script interface for rescoring of docked ligands. The new DOVIS 2.0 package is freely available to the public under the GNU General Public License.

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

PubMed

Nadkarni, P M; Miller, P L

1991-01-01

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations.

"Tactic": Traffic Aware Cloud for Tiered Infrastructure Consolidation

ERIC Educational Resources Information Center

Sangpetch, Akkarit

2013-01-01

Large-scale enterprise applications are deployed as distributed applications. These applications consist of many inter-connected components with heterogeneous roles and complex dependencies. Each component typically consumes 5-15% of the server capacity. Deploying each component as a separate virtual machine (VM) allows us to consolidate the…

Airlift Operation Modeling Using Discrete Event Simulation (DES)

DTIC Science & Technology

2009-12-01

Java ......................................................................................................20 2. Simkit...JRE Java Runtime Environment JVM Java Virtual Machine lbs Pounds LAM Load Allocation Mode LRM Landing Spot Reassignment Mode LEGO Listener Event...SOFTWARE DEVELOPMENT ENVIRONMENT The following are the software tools and development environment used for constructing the models. 1. Java Java

The Warsaw Ghetto: A Shattered Window on the Holocaust.

ERIC Educational Resources Information Center

Burstin, Barbara Stern

1980-01-01

Reviews literature about the Warsaw ghetto uprising in April, 1943, in which Jewish resistance fighters fought to the last against the Nazi war machine. The author notes that history textbooks at both high school and college levels give virtually no mention of the revolt. (Author/KC)

Networked Resources.

ERIC Educational Resources Information Center

Nickerson, Gord

1991-01-01

Describes the use and applications of the communications program Telenet for remote log-in, a basic interactive resource sharing service that enables users to connect to any machine on the Internet and conduct a session. The Virtual Terminal--the central component of Telenet--is also described, as well as problems with terminals, services…

Lean Green Machines

ERIC Educational Resources Information Center

Villano, Matt

2011-01-01

Colleges and universities have been among the leaders nationwide in adopting green initiatives, partly due to their demographics, but also because they are facing their own budget pressures. Virtualization has become the poster child of many schools' efforts, because it provides significant bang for the buck. However, more and more higher…

A package of Linux scripts for the parallelization of Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Badal, Andreu; Sempau, Josep

2006-09-01

Despite the fact that fast computers are nowadays available at low cost, there are many situations where obtaining a reasonably low statistical uncertainty in a Monte Carlo (MC) simulation involves a prohibitively large amount of time. This limitation can be overcome by having recourse to parallel computing. Most tools designed to facilitate this approach require modification of the source code and the installation of additional software, which may be inconvenient for some users. We present a set of tools, named clonEasy, that implement a parallelization scheme of a MC simulation that is free from these drawbacks. In clonEasy, which is designed to run under Linux, a set of "clone" CPUs is governed by a "master" computer by taking advantage of the capabilities of the Secure Shell (ssh) protocol. Any Linux computer on the Internet that can be ssh-accessed by the user can be used as a clone. A key ingredient for the parallel calculation to be reliable is the availability of an independent string of random numbers for each CPU. Many generators—such as RANLUX, RANECU or the Mersenne Twister—can readily produce these strings by initializing them appropriately and, hence, they are suitable to be used with clonEasy. This work was primarily motivated by the need to find a straightforward way to parallelize PENELOPE, a code for MC simulation of radiation transport that (in its current 2005 version) employs the generator RANECU, which uses a combination of two multiplicative linear congruential generators (MLCGs). Thus, this paper is focused on this class of generators and, in particular, we briefly present an extension of RANECU that increases its period up to ˜5×10 and we introduce seedsMLCG, a tool that provides the information necessary to initialize disjoint sequences of an MLCG to feed different CPUs. This program, in combination with clonEasy, allows to run PENELOPE in parallel easily, without requiring specific libraries or significant alterations of the sequential code. Program summary 1Title of program:clonEasy Catalogue identifier:ADYD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYD_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a Unix style shell (bash), support for the Secure Shell protocol and a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1) Compilers:GNU FORTRAN g77 (Linux); g95 (Linux); Intel Fortran Compiler 7.1 (Linux) Programming language used:Linux shell (bash) script, FORTRAN 77 No. of bits in a word:32 No. of lines in distributed program, including test data, etc.:1916 No. of bytes in distributed program, including test data, etc.:18 202 Distribution format:tar.gz Nature of the physical problem:There are many situations where a Monte Carlo simulation involves a huge amount of CPU time. The parallelization of such calculations is a simple way of obtaining a relatively low statistical uncertainty using a reasonable amount of time. Method of solution:The presented collection of Linux scripts and auxiliary FORTRAN programs implement Secure Shell-based communication between a "master" computer and a set of "clones". The aim of this communication is to execute a code that performs a Monte Carlo simulation on all the clones simultaneously. The code is unique, but each clone is fed with a different set of random seeds. Hence, clonEasy effectively permits the parallelization of the calculation. Restrictions on the complexity of the program:clonEasy can only be used with programs that produce statistically independent results using the same code, but with a different sequence of random numbers. Users must choose the initialization values for the random number generator on each computer and combine the output from the different executions. A FORTRAN program to combine the final results is also provided. Typical running time:The execution time of each script largely depends on the number of computers that are used, the actions that are to be performed and, to a lesser extent, on the network connexion bandwidth. Unusual features of the program:Any computer on the Internet with a Secure Shell client/server program installed can be used as a node of a virtual computer cluster for parallel calculations with the sequential source code. The simplicity of the parallelization scheme makes the use of this package a straightforward task, which does not require installing any additional libraries. Program summary 2Title of program:seedsMLCG Catalogue identifier:ADYE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYE_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1), MS Windows (2000, XP) Compilers:GNU FORTRAN g77 (Linux and Windows); g95 (Linux); Intel Fortran Compiler 7.1 (Linux); Compaq Visual Fortran 6.1 (Windows) Programming language used:FORTRAN 77 No. of bits in a word:32 Memory required to execute with typical data:500 kilobytes No. of lines in distributed program, including test data, etc.:492 No. of bytes in distributed program, including test data, etc.:5582 Distribution format:tar.gz Nature of the physical problem:Statistically independent results from different runs of a Monte Carlo code can be obtained using uncorrelated sequences of random numbers on each execution. Multiplicative linear congruential generators (MLCG), or other generators that are based on them such as RANECU, can be adapted to produce these sequences. Method of solution:For a given MLCG, the presented program calculates initialization values that produce disjoint, consecutive sequences of pseudo-random numbers. The calculated values initiate the generator in distant positions of the random number cycle and can be used, for instance, on a parallel simulation. The values are found using the formula S=(aS)MODm, which gives the random value that will be generated after J iterations of the MLCG. Restrictions on the complexity of the program:The 32-bit length restriction for the integer variables in standard FORTRAN 77 limits the produced seeds to be separated a distance smaller than 2 31, when the distance J is expressed as an integer value. The program allows the user to input the distance as a power of 10 for the purpose of efficiently splitting the sequence of generators with a very long period. Typical running time:The execution time depends on the parameters of the used MLCG and the distance between the generated seeds. The generation of 10 6 seeds separated 10 12 units in the sequential cycle, for one of the MLCGs found in the RANECU generator, takes 3 s on a 2.4 GHz Intel Pentium 4 using the g77 compiler.

GREEN SUPERCOMPUTING IN A DESKTOP BOX

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

HSU, CHUNG-HSING; FENG, WU-CHUN; CHING, AVERY

2007-01-17

The computer workstation, introduced by Sun Microsystems in 1982, was the tool of choice for scientists and engineers as an interactive computing environment for the development of scientific codes. However, by the mid-1990s, the performance of workstations began to lag behind high-end commodity PCs. This, coupled with the disappearance of BSD-based operating systems in workstations and the emergence of Linux as an open-source operating system for PCs, arguably led to the demise of the workstation as we knew it. Around the same time, computational scientists started to leverage PCs running Linux to create a commodity-based (Beowulf) cluster that provided dedicatedmore » computer cycles, i.e., supercomputing for the rest of us, as a cost-effective alternative to large supercomputers, i.e., supercomputing for the few. However, as the cluster movement has matured, with respect to cluster hardware and open-source software, these clusters have become much more like their large-scale supercomputing brethren - a shared (and power-hungry) datacenter resource that must reside in a machine-cooled room in order to operate properly. Consequently, the above observations, when coupled with the ever-increasing performance gap between the PC and cluster supercomputer, provide the motivation for a 'green' desktop supercomputer - a turnkey solution that provides an interactive and parallel computing environment with the approximate form factor of a Sun SPARCstation 1 'pizza box' workstation. In this paper, they present the hardware and software architecture of such a solution as well as its prowess as a developmental platform for parallel codes. In short, imagine a 12-node personal desktop supercomputer that achieves 14 Gflops on Linpack but sips only 185 watts of power at load, resulting in a performance-power ratio that is over 300% better than their reference SMP platform.« less

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.

Manufacturing data analytics using a virtual factory representation.

PubMed

Jain, Sanjay; Shao, Guodong; Shin, Seung-Jun

2017-01-01

Large manufacturers have been using simulation to support decision-making for design and production. However, with the advancement of technologies and the emergence of big data, simulation can be utilised to perform and support data analytics for associated performance gains. This requires not only significant model development expertise, but also huge data collection and analysis efforts. This paper presents an approach within the frameworks of Design Science Research Methodology and prototyping to address the challenge of increasing the use of modelling, simulation and data analytics in manufacturing via reduction of the development effort. The use of manufacturing simulation models is presented as data analytics applications themselves and for supporting other data analytics applications by serving as data generators and as a tool for validation. The virtual factory concept is presented as the vehicle for manufacturing modelling and simulation. Virtual factory goes beyond traditional simulation models of factories to include multi-resolution modelling capabilities and thus allowing analysis at varying levels of detail. A path is proposed for implementation of the virtual factory concept that builds on developments in technologies and standards. A virtual machine prototype is provided as a demonstration of the use of a virtual representation for manufacturing data analytics.

Virtual Proprioception for eccentric training.

PubMed

LeMoyne, Robert; Mastroianni, Timothy

2017-07-01

Wireless inertial sensors enable quantified feedback, which can be applied to evaluate the efficacy of therapy and rehabilitation. In particular eccentric training promotes a beneficial rehabilitation and strength training strategy. Virtual Proprioception for eccentric training applies real-time feedback from a wireless gyroscope platform enabled through a software application for a smartphone. Virtual Proprioception for eccentric training is applied to the eccentric phase of a biceps brachii strength training and contrasted to a biceps brachii strength training scenario without feedback. During the operation of Virtual Proprioception for eccentric training the intent is to not exceed a prescribed gyroscope signal threshold based on the real-time presentation of the gyroscope signal, in order to promote the eccentric aspect of the strength training endeavor. The experimental trial data is transmitted wireless through connectivity to the Internet as an email attachment for remote post-processing. A feature set is derived from the gyroscope signal for machine learning classification of the two scenarios of Virtual Proprioception real-time feedback for eccentric training and eccentric training without feedback. Considerable classification accuracy is achieved through the application of a multilayer perceptron neural network for distinguishing between the Virtual Proprioception real-time feedback for eccentric training and eccentric training without feedback.

The Multimission Image Processing Laboratory's virtual frame buffer interface

NASA Technical Reports Server (NTRS)

Wolfe, T.

1984-01-01

Large image processing systems use multiple frame buffers with differing architectures and vendor supplied interfaces. This variety of architectures and interfaces creates software development, maintenance and portability problems for application programs. Several machine-dependent graphics standards such as ANSI Core and GKS are available, but none of them are adequate for image processing. Therefore, the Multimission Image Processing laboratory project has implemented a programmer level virtual frame buffer interface. This interface makes all frame buffers appear as a generic frame buffer with a specified set of characteristics. This document defines the virtual frame uffer interface and provides information such as FORTRAN subroutine definitions, frame buffer characteristics, sample programs, etc. It is intended to be used by application programmers and system programmers who are adding new frame buffers to a system.

Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Cancer Genomics Browser | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The Cancer Analysis Virtual Machine (CAVM) project will leverage cloud technology, the UCSC Cancer Genomics Browser, and the Galaxy analysis workflow system to provide investigators with a flexible, scalable platform for hosting, visualizing and analyzing their own genomic data.

Performance Analysis of Saturated Induction Motors by Virtual Tests

ERIC Educational Resources Information Center

Ojaghi, M.; Faiz, J.; Kazemi, M.; Rezaei, M.

2012-01-01

Many undergraduate-level electrical machines textbooks give detailed treatments of the performance of induction motors. Students can deepen this understanding of motor performance by performing the appropriate practical work in laboratories or in simulation using proper software packages. This paper considers various common and less-common tests…

Untangling the Tangled Webs We Weave: A Team Approach to Cyberspace.

ERIC Educational Resources Information Center

Broidy, Ellen; And Others

Working in a cooperative team environment across libraries and job classifications, librarians and support staff at the University of California at Irvine (UCI) have mounted several successful web projects, including two versions of the Libraries' home page, a virtual reference collection, and Science Library "ANTswer Machine." UCI's…

Computer Security Primer: Systems Architecture, Special Ontology and Cloud Virtual Machines

ERIC Educational Resources Information Center

Waguespack, Leslie J.

2014-01-01

With the increasing proliferation of multitasking and Internet-connected devices, security has reemerged as a fundamental design concern in information systems. The shift of IS curricula toward a largely organizational perspective of security leaves little room for focus on its foundation in systems architecture, the computational underpinnings of…

Identification and Triage of Compromised Virtual Machines

DTIC Science & Technology

2014-09-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA APPLIED CYBER OPERATIONS CAPSTONE PROJECT REPORT Approved for public release...ADDRESS(ES) Naval Postgraduate School Monterey, CA 93943-5000 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING /MONITORING AGENCY NAME(S...IN APPLIED CYBER OPERATIONS from the NAVAL POSTGRADUATE SCHOOL September 2014 Authors: John Paulenich Chukwuemeka Agbedo

Parallel Compilation on Virtual Machines in a Development Cloud Environment

DTIC Science & Technology

2013-09-01

the potential impact of a possible course of action. 1-2 2. Approach We performed a simple experiment to determine whether the multiple CPUs...PERFORMING ORGANIZATION NAME(S) AND ADDRESSES 8. PERFORMING ORGANIZATION REPORT NUMBER D-4996 H13 -001206 Institute for Defense Analyses 4850 Mark