Computation of Coupled Thermal-Fluid Problems in Distributed Memory Environment

NASA Technical Reports Server (NTRS)

Wei, H.; Shang, H. M.; Chen, Y. S.

2001-01-01

The thermal-fluid coupling problems are very important to aerospace and engineering applications. Instead of analyzing heat transfer and fluid flow separately, this study merged two well-accepted engineering solution methods, SINDA for thermal analysis and FDNS for fluid flow simulation, into a unified multi-disciplinary thermal fluid prediction method. A fully conservative patched grid interface algorithm for arbitrary two-dimensional and three-dimensional geometry has been developed. The state-of-the-art parallel computing concept was used to couple SINDA and FDNS for the communication of boundary conditions through PVM (Parallel Virtual Machine) libraries. Therefore, the thermal analysis performed by SINDA and the fluid flow calculated by FDNS are fully coupled to obtain steady state or transient solutions. The natural convection between two thick-walled eccentric tubes was calculated and the predicted results match the experiment data perfectly. A 3-D rocket engine model and a real 3-D SSME geometry were used to test the current model, and the reasonable temperature field was obtained.

A heterogeneous computing environment for simulating astrophysical fluid flows

NASA Technical Reports Server (NTRS)

Cazes, J.

1994-01-01

In the Concurrent Computing Laboratory in the Department of Physics and Astronomy at Louisiana State University we have constructed a heterogeneous computing environment that permits us to routinely simulate complicated three-dimensional fluid flows and to readily visualize the results of each simulation via three-dimensional animation sequences. An 8192-node MasPar MP-1 computer with 0.5 GBytes of RAM provides 250 MFlops of execution speed for our fluid flow simulations. Utilizing the parallel virtual machine (PVM) language, at periodic intervals data is automatically transferred from the MP-1 to a cluster of workstations where individual three-dimensional images are rendered for inclusion in a single animation sequence. Work is underway to replace executions on the MP-1 with simulations performed on the 512-node CM-5 at NCSA and to simultaneously gain access to more potent volume rendering workstations.

Users manual for the Chameleon parallel programming tools

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

Gropp, W.; Smith, B.

1993-06-01

Message passing is a common method for writing programs for distributed-memory parallel computers. Unfortunately, the lack of a standard for message passing has hampered the construction of portable and efficient parallel programs. In an attempt to remedy this problem, a number of groups have developed their own message-passing systems, each with its own strengths and weaknesses. Chameleon is a second-generation system of this type. Rather than replacing these existing systems, Chameleon is meant to supplement them by providing a uniform way to access many of these systems. Chameleon`s goals are to (a) be very lightweight (low over-head), (b) be highlymore » portable, and (c) help standardize program startup and the use of emerging message-passing operations such as collective operations on subsets of processors. Chameleon also provides a way to port programs written using PICL or Intel NX message passing to other systems, including collections of workstations. Chameleon is tracking the Message-Passing Interface (MPI) draft standard and will provide both an MPI implementation and an MPI transport layer. Chameleon provides support for heterogeneous computing by using p4 and PVM. Chameleon`s support for homogeneous computing includes the portable libraries p4, PICL, and PVM and vendor-specific implementation for Intel NX, IBM EUI (SP-1), and Thinking Machines CMMD (CM-5). Support for Ncube and PVM 3.x is also under development.« less

Demonstration of a full volume 3D pre-stack depth migration in the Garden Banks area using massively parallel processor (MPP) technology

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

Solano, M.; Chang, H.; VanDyke, J.

1996-12-31

This paper describes the implementation and results of portable, production-scale 3D Pre-stack Kirchhoff depth migration software. Full volume pre-stack imaging was applied to a six million trace (46.9 Gigabyte) data set from a subsalt play in the Garden Banks area in the Gulf of Mexico. The velocity model building and updating, were derived using image depth gathers and an image-driven strategy. After three velocity iterations, depth migrated sections revealed drilling targets that were not visible in the conventional 3D post-stack time migrated data set. As expected from the implementation of the migration algorithm, it was found that amplitudes are wellmore » preserved and anomalies associated with known reservoirs, conform to petrophysical predictions. Image gathers for velocity analysis and the final depth migrated volume, were generated on an 1824 node Intel Paragon at Sandia National Laboratories. The code has been successfully ported to a CRAY (T3D) and Unix workstation Parallel Virtual Machine environments (PVM).« less

High Performance Programming Using Explicit Shared Memory Model on Cray T3D1

NASA Technical Reports Server (NTRS)

Simon, Horst D.; Saini, Subhash; Grassi, Charles

1994-01-01

The Cray T3D system is the first-phase system in Cray Research, Inc.'s (CRI) three-phase massively parallel processing (MPP) program. This system features a heterogeneous architecture that closely couples DEC's Alpha microprocessors and CRI's parallel-vector technology, i.e., the Cray Y-MP and Cray C90. An overview of the Cray T3D hardware and available programming models is presented. Under Cray Research adaptive Fortran (CRAFT) model four programming methods (data parallel, work sharing, message-passing using PVM, and explicit shared memory model) are available to the users. However, at this time data parallel and work sharing programming models are not available to the user community. The differences between standard PVM and CRI's PVM are highlighted with performance measurements such as latencies and communication bandwidths. We have found that the performance of neither standard PVM nor CRI s PVM exploits the hardware capabilities of the T3D. The reasons for the bad performance of PVM as a native message-passing library are presented. This is illustrated by the performance of NAS Parallel Benchmarks (NPB) programmed in explicit shared memory model on Cray T3D. In general, the performance of standard PVM is about 4 to 5 times less than obtained by using explicit shared memory model. This degradation in performance is also seen on CM-5 where the performance of applications using native message-passing library CMMD on CM-5 is also about 4 to 5 times less than using data parallel methods. The issues involved (such as barriers, synchronization, invalidating data cache, aligning data cache etc.) while programming in explicit shared memory model are discussed. Comparative performance of NPB using explicit shared memory programming model on the Cray T3D and other highly parallel systems such as the TMC CM-5, Intel Paragon, Cray C90, IBM-SP1, etc. is presented.

The Pedagogical Variation Model (PVM) for Work-Based Training in Virtual Classrooms: Evaluation at Kuwait University

ERIC Educational Resources Information Center

Rogers, Maria Susy; Aldhafeeri, Fayiz Mensher

2015-01-01

A collaborative research initiative was undertaken to evaluate the pedagogical variation model (PVM) for online learning and teaching at Kuwait University. Outcomes from sample populations of students--both postgraduates and undergraduates--from the Faculty of Education were analyzed for comparison. As predicted in the PVM, the findings indicate…

Searching for patterns in remote sensing image databases using neural networks

NASA Technical Reports Server (NTRS)

Paola, Justin D.; Schowengerdt, Robert A.

1995-01-01

We have investigated a method, based on a successful neural network multispectral image classification system, of searching for single patterns in remote sensing databases. While defining the pattern to search for and the feature to be used for that search (spectral, spatial, temporal, etc.) is challenging, a more difficult task is selecting competing patterns to train against the desired pattern. Schemes for competing pattern selection, including random selection and human interpreted selection, are discussed in the context of an example detection of dense urban areas in Landsat Thematic Mapper imagery. When applying the search to multiple images, a simple normalization method can alleviate the problem of inconsistent image calibration. Another potential problem, that of highly compressed data, was found to have a minimal effect on the ability to detect the desired pattern. The neural network algorithm has been implemented using the PVM (Parallel Virtual Machine) library and nearly-optimal speedups have been obtained that help alleviate the long process of searching through imagery.

Visual Computing Environment

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Putt, Charles W.

1997-01-01

The Visual Computing Environment (VCE) is a NASA Lewis Research Center project to develop a framework for intercomponent and multidisciplinary computational simulations. Many current engineering analysis codes simulate various aspects of aircraft engine operation. For example, existing computational fluid dynamics (CFD) codes can model the airflow through individual engine components such as the inlet, compressor, combustor, turbine, or nozzle. Currently, these codes are run in isolation, making intercomponent and complete system simulations very difficult to perform. In addition, management and utilization of these engineering codes for coupled component simulations is a complex, laborious task, requiring substantial experience and effort. To facilitate multicomponent aircraft engine analysis, the CFD Research Corporation (CFDRC) is developing the VCE system. This system, which is part of NASA's Numerical Propulsion Simulation System (NPSS) program, can couple various engineering disciplines, such as CFD, structural analysis, and thermal analysis. The objectives of VCE are to (1) develop a visual computing environment for controlling the execution of individual simulation codes that are running in parallel and are distributed on heterogeneous host machines in a networked environment, (2) develop numerical coupling algorithms for interchanging boundary conditions between codes with arbitrary grid matching and different levels of dimensionality, (3) provide a graphical interface for simulation setup and control, and (4) provide tools for online visualization and plotting. VCE was designed to provide a distributed, object-oriented environment. Mechanisms are provided for creating and manipulating objects, such as grids, boundary conditions, and solution data. This environment includes parallel virtual machine (PVM) for distributed processing. Users can interactively select and couple any set of codes that have been modified to run in a parallel distributed fashion on a cluster of heterogeneous workstations. A scripting facility allows users to dictate the sequence of events that make up the particular simulation.

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.

Automated Concurrent Blackboard System Generation in C++

NASA Technical Reports Server (NTRS)

Kaplan, J. A.; McManus, J. W.; Bynum, W. L.

1999-01-01

In his 1992 Ph.D. thesis, "Design and Analysis Techniques for Concurrent Blackboard Systems", John McManus defined several performance metrics for concurrent blackboard systems and developed a suite of tools for creating and analyzing such systems. These tools allow a user to analyze a concurrent blackboard system design and predict the performance of the system before any code is written. The design can be modified until simulated performance is satisfactory. Then, the code generator can be invoked to generate automatically all of the code required for the concurrent blackboard system except for the code implementing the functionality of each knowledge source. We have completed the port of the source code generator and a simulator for a concurrent blackboard system. The source code generator generates the necessary C++ source code to implement the concurrent blackboard system using Parallel Virtual Machine (PVM) running on a heterogeneous network of UNIX(trademark) workstations. The concurrent blackboard simulator uses the blackboard specification file to predict the performance of the concurrent blackboard design. The only part of the source code for the concurrent blackboard system that the user must supply is the code implementing the functionality of the knowledge sources.

Efficient Process Migration for Parallel Processing on Non-Dedicated Networks of Workstations

NASA Technical Reports Server (NTRS)

Chanchio, Kasidit; Sun, Xian-He

1996-01-01

This paper presents the design and preliminary implementation of MpPVM, a software system that supports process migration for PVM application programs in a non-dedicated heterogeneous computing environment. New concepts of migration point as well as migration point analysis and necessary data analysis are introduced. In MpPVM, process migrations occur only at previously inserted migration points. Migration point analysis determines appropriate locations to insert migration points; whereas, necessary data analysis provides a minimum set of variables to be transferred at each migration pint. A new methodology to perform reliable point-to-point data communications in a migration environment is also discussed. Finally, a preliminary implementation of MpPVM and its experimental results are presented, showing the correctness and promising performance of our process migration mechanism in a scalable non-dedicated heterogeneous computing environment. While MpPVM is developed on top of PVM, the process migration methodology introduced in this study is general and can be applied to any distributed software environment.

Implementation of Helioseismic Data Reduction and Diagnostic Techniques on Massively Parallel Architectures

NASA Technical Reports Server (NTRS)

Korzennik, Sylvain

1997-01-01

Under the direction of Dr. Rhodes, and the technical supervision of Dr. Korzennik, the data assimilation of high spatial resolution solar dopplergrams has been carried out throughout the program on the Intel Delta Touchstone supercomputer. With the help of a research assistant, partially supported by this grant, and under the supervision of Dr. Korzennik, code development was carried out at SAO, using various available resources. To ensure cross-platform portability, PVM was selected as the message passing library. A parallel implementation of power spectra computation for helioseismology data reduction, using PVM was successfully completed. It was successfully ported to SMP architectures (i.e. SUN), and to some MPP architectures (i.e. the CM5). Due to limitation of the implementation of PVM on the Cray T3D, the port to that architecture was not completed at the time.

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

Portable parallel stochastic optimization for the design of aeropropulsion components

NASA Technical Reports Server (NTRS)

Sues, Robert H.; Rhodes, G. S.

1994-01-01

This report presents the results of Phase 1 research to develop a methodology for performing large-scale Multi-disciplinary Stochastic Optimization (MSO) for the design of aerospace systems ranging from aeropropulsion components to complete aircraft configurations. The current research recognizes that such design optimization problems are computationally expensive, and require the use of either massively parallel or multiple-processor computers. The methodology also recognizes that many operational and performance parameters are uncertain, and that uncertainty must be considered explicitly to achieve optimum performance and cost. The objective of this Phase 1 research was to initialize the development of an MSO methodology that is portable to a wide variety of hardware platforms, while achieving efficient, large-scale parallelism when multiple processors are available. The first effort in the project was a literature review of available computer hardware, as well as review of portable, parallel programming environments. The first effort was to implement the MSO methodology for a problem using the portable parallel programming language, Parallel Virtual Machine (PVM). The third and final effort was to demonstrate the example on a variety of computers, including a distributed-memory multiprocessor, a distributed-memory network of workstations, and a single-processor workstation. Results indicate the MSO methodology can be well-applied towards large-scale aerospace design problems. Nearly perfect linear speedup was demonstrated for computation of optimization sensitivity coefficients on both a 128-node distributed-memory multiprocessor (the Intel iPSC/860) and a network of workstations (speedups of almost 19 times achieved for 20 workstations). Very high parallel efficiencies (75 percent for 31 processors and 60 percent for 50 processors) were also achieved for computation of aerodynamic influence coefficients on the Intel. Finally, the multi-level parallelization strategy that will be needed for large-scale MSO problems was demonstrated to be highly efficient. The same parallel code instructions were used on both platforms, demonstrating portability. There are many applications for which MSO can be applied, including NASA's High-Speed-Civil Transport, and advanced propulsion systems. The use of MSO will reduce design and development time and testing costs dramatically.

Prototype Vector Machine for Large Scale Semi-Supervised Learning

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

Zhang, Kai; Kwok, James T.; Parvin, Bahram

2009-04-29

Practicaldataminingrarelyfalls exactlyinto the supervisedlearning scenario. Rather, the growing amount of unlabeled data poses a big challenge to large-scale semi-supervised learning (SSL). We note that the computationalintensivenessofgraph-based SSLarises largely from the manifold or graph regularization, which in turn lead to large models that are dificult to handle. To alleviate this, we proposed the prototype vector machine (PVM), a highlyscalable,graph-based algorithm for large-scale SSL. Our key innovation is the use of"prototypes vectors" for effcient approximation on both the graph-based regularizer and model representation. The choice of prototypes are grounded upon two important criteria: they not only perform effective low-rank approximation of themore » kernel matrix, but also span a model suffering the minimum information loss compared with the complete model. We demonstrate encouraging performance and appealing scaling properties of the PVM on a number of machine learning benchmark data sets.« less

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

Painter, J.; McCormick, P.; Krogh, M.

This paper presents the ACL (Advanced Computing Lab) Message Passing Library. It is a high throughput, low latency communications library, based on Thinking Machines Corp.`s CMMD, upon which message passing applications can be built. The library has been implemented on the Cray T3D, Thinking Machines CM-5, SGI workstations, and on top of PVM.

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.

Monitoring Data-Structure Evolution in Distributed Message-Passing Programs

NASA Technical Reports Server (NTRS)

Sarukkai, Sekhar R.; Beers, Andrew; Woodrow, Thomas S. (Technical Monitor)

1996-01-01

Monitoring the evolution of data structures in parallel and distributed programs, is critical for debugging its semantics and performance. However, the current state-of-art in tracking and presenting data-structure information on parallel and distributed environments is cumbersome and does not scale. In this paper we present a methodology that automatically tracks memory bindings (not the actual contents) of static and dynamic data-structures of message-passing C programs, using PVM. With the help of a number of examples we show that in addition to determining the impact of memory allocation overheads on program performance, graphical views can help in debugging the semantics of program execution. Scalable animations of virtual address bindings of source-level data-structures are used for debugging the semantics of parallel programs across all processors. In conjunction with light-weight core-files, this technique can be used to complement traditional debuggers on single processors. Detailed information (such as data-structure contents), on specific nodes, can be determined using traditional debuggers after the data structure evolution leading to the semantic error is observed graphically.

Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method.

PubMed

Vareková, R Svobodová; Koca, J

2006-02-01

The most common way to calculate charge distribution in a molecule is ab initio quantum mechanics (QM). Some faster alternatives to QM have also been developed, the so-called "equalization methods" EEM and ABEEM, which are based on DFT. We have implemented and optimized the EEM and ABEEM methods and created the EEM SOLVER and ABEEM SOLVER programs. It has been found that the most time-consuming part of equalization methods is the reduction of the matrix belonging to the equation system generated by the method. Therefore, for both methods this part was replaced by the parallel algorithm WIRS and implemented within the PVM environment. The parallelized versions of the programs EEM SOLVER and ABEEM SOLVER showed promising results, especially on a single computer with several processors (compact PVM). The implemented programs are available through the Web page http://ncbr.chemi.muni.cz/~n19n/eem_abeem.

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.

Development and Application of a Parallel LCAO Cluster Method

NASA Astrophysics Data System (ADS)

Patton, David C.

1997-08-01

CPU intensive steps in the SCF electronic structure calculations of clusters and molecules with a first-principles LCAO method have been fully parallelized via a message passing paradigm. Identification of the parts of the code that are composed of many independent compute-intensive steps is discussed in detail as they are the most readily parallelized. Most of the parallelization involves spatially decomposing numerical operations on a mesh. One exception is the solution of Poisson's equation which relies on distribution of the charge density and multipole methods. The method we use to parallelize this part of the calculation is quite novel and is covered in detail. We present a general method for dynamically load-balancing a parallel calculation and discuss how we use this method in our code. The results of benchmark calculations of the IR and Raman spectra of PAH molecules such as anthracene (C_14H_10) and tetracene (C_18H_12) are presented. These benchmark calculations were performed on an IBM SP2 and a SUN Ultra HPC server with both MPI and PVM. Scalability and speedup for these calculations is analyzed to determine the efficiency of the code. In addition, performance and usage issues for MPI and PVM are presented.

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

PubMed Central

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. PMID:1807632

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.

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.

Parallel Event Analysis Under Unix

NASA Astrophysics Data System (ADS)

Looney, S.; Nilsson, B. S.; Oest, T.; Pettersson, T.; Ranjard, F.; Thibonnier, J.-P.

The ALEPH experiment at LEP, the CERN CN division and Digital Equipment Corp. have, in a joint project, developed a parallel event analysis system. The parallel physics code is identical to ALEPH's standard analysis code, ALPHA, only the organisation of input/output is changed. The user may switch between sequential and parallel processing by simply changing one input "card". The initial implementation runs on an 8-node DEC 3000/400 farm, using the PVM software, and exhibits a near-perfect speed-up linearity, reducing the turn-around time by a factor of 8.

High-energy physics software parallelization using database techniques

NASA Astrophysics Data System (ADS)

Argante, E.; van der Stok, P. D. V.; Willers, I.

1997-02-01

A programming model for software parallelization, called CoCa, is introduced that copes with problems caused by typical features of high-energy physics software. By basing CoCa on the database transaction paradimg, the complexity induced by the parallelization is for a large part transparent to the programmer, resulting in a higher level of abstraction than the native message passing software. CoCa is implemented on a Meiko CS-2 and on a SUN SPARCcenter 2000 parallel computer. On the CS-2, the performance is comparable with the performance of native PVM and MPI.

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

Air Traffic Complexity Measurement Environment (ACME): Software User's Guide

NASA Technical Reports Server (NTRS)

1996-01-01

A user's guide for the Air Traffic Complexity Measurement Environment (ACME) software is presented. The ACME consists of two major components, a complexity analysis tool and user interface. The Complexity Analysis Tool (CAT) analyzes complexity off-line, producing data files which may be examined interactively via the Complexity Data Analysis Tool (CDAT). The Complexity Analysis Tool is composed of three independently executing processes that communicate via PVM (Parallel Virtual Machine) and Unix sockets. The Runtime Data Management and Control process (RUNDMC) extracts flight plan and track information from a SAR input file, and sends the information to GARP (Generate Aircraft Routes Process) and CAT (Complexity Analysis Task). GARP in turn generates aircraft trajectories, which are utilized by CAT to calculate sector complexity. CAT writes flight plan, track and complexity data to an output file, which can be examined interactively. The Complexity Data Analysis Tool (CDAT) provides an interactive graphic environment for examining the complexity data produced by the Complexity Analysis Tool (CAT). CDAT can also play back track data extracted from System Analysis Recording (SAR) tapes. The CDAT user interface consists of a primary window, a controls window, and miscellaneous pop-ups. Aircraft track and position data is displayed in the main viewing area of the primary window. The controls window contains miscellaneous control and display items. Complexity data is displayed in pop-up windows. CDAT plays back sector complexity and aircraft track and position data as a function of time. Controls are provided to start and stop playback, adjust the playback rate, and reposition the display to a specified time.

By Hand or Not By-Hand: A Case Study of Alternative Approaches to Parallelize CFD Applications

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Bailey, David (Technical Monitor)

1997-01-01

While parallel processing promises to speed up applications by several orders of magnitude, the performance achieved still depends upon several factors, including the multiprocessor architecture, system software, data distribution and alignment, as well as the methods used for partitioning the application and mapping its components onto the architecture. The existence of the Gorden Bell Prize given out at Supercomputing every year suggests that while good performance can be attained for real applications on general purpose multiprocessors, the large investment in man-power and time still has to be repeated for each application-machine combination. As applications and machine architectures become more complex, the cost and time-delays for obtaining performance by hand will become prohibitive. Computer users today can turn to three possible avenues for help: parallel libraries, parallel languages and compilers, interactive parallelization tools. The success of these methodologies, in turn, depends on proper application of data dependency analysis, program structure recognition and transformation, performance prediction as well as exploitation of user supplied knowledge. NASA has been developing multidisciplinary applications on highly parallel architectures under the High Performance Computing and Communications Program. Over the past six years, the transition of underlying hardware and system software have forced the scientists to spend a large effort to migrate and recede their applications. Various attempts to exploit software tools to automate the parallelization process have not produced favorable results. In this paper, we report our most recent experience with CAPTOOL, a package developed at Greenwich University. We have chosen CAPTOOL for three reasons: 1. CAPTOOL accepts a FORTRAN 77 program as input. This suggests its potential applicability to a large collection of legacy codes currently in use. 2. CAPTOOL employs domain decomposition to obtain parallelism. Although the fact that not all kinds of parallelism are handled may seem unappealing, many NASA applications in computational aerosciences as well as earth and space sciences are amenable to domain decomposition. 3. CAPTOOL generates code for a large variety of environments employed across NASA centers: MPI/PVM on network of workstations to the IBS/SP2 and CRAY/T3D.

RISC Processors and High Performance Computing

NASA Technical Reports Server (NTRS)

Saini, Subhash; Bailey, David H.; Lasinski, T. A. (Technical Monitor)

1995-01-01

In this tutorial, we will discuss top five current RISC microprocessors: The IBM Power2, which is used in the IBM RS6000/590 workstation and in the IBM SP2 parallel supercomputer, the DEC Alpha, which is in the DEC Alpha workstation and in the Cray T3D; the MIPS R8000, which is used in the SGI Power Challenge; the HP PA-RISC 7100, which is used in the HP 700 series workstations and in the Convex Exemplar; and the Cray proprietary processor, which is used in the new Cray J916. The architecture of these microprocessors will first be presented. The effective performance of these processors will then be compared, both by citing standard benchmarks and also in the context of implementing a real applications. In the process, different programming models such as data parallel (CM Fortran and HPF) and message passing (PVM and MPI) will be introduced and compared. The latest NAS Parallel Benchmark (NPB) absolute performance and performance per dollar figures will be presented. The next generation of the NP13 will also be described. The tutorial will conclude with a discussion of general trends in the field of high performance computing, including likely future developments in hardware and software technology, and the relative roles of vector supercomputers tightly coupled parallel computers, and clusters of workstations. This tutorial will provide a unique cross-machine comparison not available elsewhere.

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

Performance Measurement, Visualization and Modeling of Parallel and Distributed Programs

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Sarukkai, Sekhar R.; Mehra, Pankaj; Lum, Henry, Jr. (Technical Monitor)

1994-01-01

This paper presents a methodology for debugging the performance of message-passing programs on both tightly coupled and loosely coupled distributed-memory machines. The AIMS (Automated Instrumentation and Monitoring System) toolkit, a suite of software tools for measurement and analysis of performance, is introduced and its application illustrated using several benchmark programs drawn from the field of computational fluid dynamics. AIMS includes (i) Xinstrument, a powerful source-code instrumentor, which supports both Fortran77 and C as well as a number of different message-passing libraries including Intel's NX Thinking Machines' CMMD, and PVM; (ii) Monitor, a library of timestamping and trace -collection routines that run on supercomputers (such as Intel's iPSC/860, Delta, and Paragon and Thinking Machines' CM5) as well as on networks of workstations (including Convex Cluster and SparcStations connected by a LAN); (iii) Visualization Kernel, a trace-animation facility that supports source-code clickback, simultaneous visualization of computation and communication patterns, as well as analysis of data movements; (iv) Statistics Kernel, an advanced profiling facility, that associates a variety of performance data with various syntactic components of a parallel program; (v) Index Kernel, a diagnostic tool that helps pinpoint performance bottlenecks through the use of abstract indices; (vi) Modeling Kernel, a facility for automated modeling of message-passing programs that supports both simulation -based and analytical approaches to performance prediction and scalability analysis; (vii) Intrusion Compensator, a utility for recovering true performance from observed performance by removing the overheads of monitoring and their effects on the communication pattern of the program; and (viii) Compatibility Tools, that convert AIMS-generated traces into formats used by other performance-visualization tools, such as ParaGraph, Pablo, and certain AVS/Explorer modules.

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.

Highly parallel sparse Cholesky factorization

NASA Technical Reports Server (NTRS)

Gilbert, John R.; Schreiber, Robert

1990-01-01

Several fine grained parallel algorithms were developed and compared to compute the Cholesky factorization of a sparse matrix. The experimental implementations are on the Connection Machine, a distributed memory SIMD machine whose programming model conceptually supplies one processor per data element. In contrast to special purpose algorithms in which the matrix structure conforms to the connection structure of the machine, the focus is on matrices with arbitrary sparsity structure. The most promising algorithm is one whose inner loop performs several dense factorizations simultaneously on a 2-D grid of processors. Virtually any massively parallel dense factorization algorithm can be used as the key subroutine. The sparse code attains execution rates comparable to those of the dense subroutine. Although at present architectural limitations prevent the dense factorization from realizing its potential efficiency, it is concluded that a regular data parallel architecture can be used efficiently to solve arbitrarily structured sparse problems. A performance model is also presented and it is used to analyze the algorithms.

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.

Evaluation of Pneumonia Virus of Mice as a Possible Human Pathogen

PubMed Central

Brock, Linda G.; Karron, Ruth A.; Krempl, Christine D.; Collins, Peter L.

2012-01-01

Pneumonia virus of mice (PVM), a relative of human respiratory syncytial virus (RSV), causes respiratory disease in mice. There is serologic evidence suggesting widespread exposure of humans to PVM. To investigate replication in primates, African green monkeys (AGM) and rhesus macaques (n = 4) were inoculated with PVM by the respiratory route. Virus was shed intermittently at low levels by a subset of animals, suggesting poor permissiveness. PVM efficiently replicated in cultured human cells and inhibited the type I interferon (IFN) response in these cells. This suggests that poor replication in nonhuman primates was not due to a general nonpermissiveness of primate cells or poor control of the IFN response. Seroprevalence in humans was examined by screening sera from 30 adults and 17 young children for PVM-neutralizing activity. Sera from a single child (6%) and 40% of adults had low neutralizing activity against PVM, which could be consistent with increasing incidence of exposure following early childhood. There was no cross-reaction of human or AGM sera between RSV and PVM and no cross-protection in the mouse model. In native Western blots, human sera reacted with RSV but not PVM proteins under conditions in which AGM immune sera reacted strongly. Serum reactivity was further evaluated by flow cytometry using unfixed Vero cells infected with PVM or RSV expressing green fluorescent protein (GFP) as a measure of viral gene expression. The reactivity of human sera against RSV-infected cells correlated with GFP expression, whereas reactivity against PVM-infected cells was low and uncorrelated with GFP expression. Thus, PVM specificity was not evident. Our results indicate that the PVM-neutralizing activity of human sera is not due to RSV- or PVM-specific antibodies but may be due to low-affinity, polyreactive natural antibodies of the IgG subclass. The absence of PVM-specific antibodies and restriction in nonhuman primates makes PVM unlikely to be a human pathogen. PMID:22438539

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.

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.

High Performance Programming Using Explicit Shared Memory Model on the Cray T3D

NASA Technical Reports Server (NTRS)

Saini, Subhash; Simon, Horst D.; Lasinski, T. A. (Technical Monitor)

1994-01-01

The Cray T3D is the first-phase system in Cray Research Inc.'s (CRI) three-phase massively parallel processing program. In this report we describe the architecture of the T3D, as well as the CRAFT (Cray Research Adaptive Fortran) programming model, and contrast it with PVM, which is also supported on the T3D We present some performance data based on the NAS Parallel Benchmarks to illustrate both architectural and software features of the T3D.

Unique nonstructural proteins of Pneumonia Virus of Mice (PVM) promote degradation of interferon (IFN) pathway components and IFN-stimulated gene proteins.

PubMed

Dhar, Jayeeta; Barik, Sailen

2016-12-01

Pneumonia Virus of Mice (PVM) is the only virus that shares the Pneumovirus genus of the Paramyxoviridae family with Respiratory Syncytial Virus (RSV). A deadly mouse pathogen, PVM has the potential to serve as a robust animal model of RSV infection, since human RSV does not fully replicate the human pathology in mice. Like RSV, PVM also encodes two nonstructural proteins that have been implicated to suppress the IFN pathway, but surprisingly, they exhibit no sequence similarity with their RSV equivalents. The molecular mechanism of PVM NS function, therefore, remains unknown. Here, we show that recombinant PVM NS proteins degrade the mouse counterparts of the IFN pathway components. Proteasomal degradation appears to be mediated by ubiquitination promoted by PVM NS proteins. Interestingly, NS proteins of PVM lowered the levels of several ISG (IFN-stimulated gene) proteins as well. These results provide a molecular foundation for the mechanisms by which PVM efficiently subverts the IFN response of the murine cell. They also reveal that in spite of their high sequence dissimilarity, the two pneumoviral NS proteins are functionally and mechanistically similar.

21 CFR 872.3500 - Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium...

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Polyvinylmethylether maleic anhydride (PVM-MA...) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3500 Polyvinylmethylether maleic anhydride (PVM-MA.... Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium (NACMC) denture...

21 CFR 872.3500 - Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium...

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Polyvinylmethylether maleic anhydride (PVM-MA...) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3500 Polyvinylmethylether maleic anhydride (PVM-MA.... Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium (NACMC) denture...

21 CFR 872.3500 - Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium...

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Polyvinylmethylether maleic anhydride (PVM-MA...) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3500 Polyvinylmethylether maleic anhydride (PVM-MA.... Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium (NACMC) denture...

21 CFR 872.3500 - Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium...

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Polyvinylmethylether maleic anhydride (PVM-MA...) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3500 Polyvinylmethylether maleic anhydride (PVM-MA.... Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium (NACMC) denture...

21 CFR 872.3500 - Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium...

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Polyvinylmethylether maleic anhydride (PVM-MA...) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3500 Polyvinylmethylether maleic anhydride (PVM-MA.... Polyvinylmethylether maleic anhydride (PVM-MA), acid copolymer, and carboxymethylcellulose sodium (NACMC) denture...

Shared virtual memory and generalized speedup

NASA Technical Reports Server (NTRS)

Sun, Xian-He; Zhu, Jianping

1994-01-01

Generalized speedup is defined as parallel speed over sequential speed. The generalized speedup and its relation with other existing performance metrics, such as traditional speedup, efficiency, scalability, etc., are carefully studied. In terms of the introduced asymptotic speed, it was shown that the difference between the generalized speedup and the traditional speedup lies in the definition of the efficiency of uniprocessor processing, which is a very important issue in shared virtual memory machines. A scientific application was implemented on a KSR-1 parallel computer. Experimental and theoretical results show that the generalized speedup is distinct from the traditional speedup and provides a more reasonable measurement. In the study of different speedups, various causes of superlinear speedup are also presented.

A distributed version of the NASA Engine Performance Program

NASA Technical Reports Server (NTRS)

Cours, Jeffrey T.; Curlett, Brian P.

1993-01-01

Distributed NEPP, a version of the NASA Engine Performance Program, uses the original NEPP code but executes it in a distributed computer environment. Multiple workstations connected by a network increase the program's speed and, more importantly, the complexity of the cases it can handle in a reasonable time. Distributed NEPP uses the public domain software package, called Parallel Virtual Machine, allowing it to execute on clusters of machines containing many different architectures. It includes the capability to link with other computers, allowing them to process NEPP jobs in parallel. This paper discusses the design issues and granularity considerations that entered into programming Distributed NEPP and presents the results of timing runs.

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

Detection of a pneumonia virus of mice (PVM) in an African hedgehog (Atelerix arbiventris) with suspected wobbly hedgehog syndrome (WHS).

PubMed

Madarame, Hiroo; Ogihara, Kikumi; Kimura, Moe; Nagai, Makoto; Omatsu, Tsutomu; Ochiai, Hideharu; Mizutani, Tetsyuya

2014-09-17

A pneumonia virus of mice (PVM) from an African hedgehog (Atelerix arbiventris) with suspected wobbly hedgehog syndrome (WHS) was detected and genetically characterized. The affected hedgehog had a nonsuppurative encephalitis with vacuolization of the white matter, and the brain samples yielded RNA reads highly homogeneous to PVM strain 15 (96.5% of full genomic sequence homology by analysis of next generation sequencing). PVM antigen was also detected in the brain and the lungs immunohistochemically. A PVM was strongly suggested as a causative agent of encephalitis of a hedgehog with suspected WHS. This is a first report of PVM infection in hedgehogs. Copyright © 2014 Elsevier B.V. All rights reserved.

A Parallel Vector Machine for the PM Programming Language

NASA Astrophysics Data System (ADS)

Bellerby, Tim

2016-04-01

PM is a new programming language which aims to make the writing of computational geoscience models on parallel hardware accessible to scientists who are not themselves expert parallel programmers. It is based around the concept of communicating operators: language constructs that enable variables local to a single invocation of a parallelised loop to be viewed as if they were arrays spanning the entire loop domain. This mechanism enables different loop invocations (which may or may not be executing on different processors) to exchange information in a manner that extends the successful Communicating Sequential Processes idiom from single messages to collective communication. Communicating operators avoid the additional synchronisation mechanisms, such as atomic variables, required when programming using the Partitioned Global Address Space (PGAS) paradigm. Using a single loop invocation as the fundamental unit of concurrency enables PM to uniformly represent different levels of parallelism from vector operations through shared memory systems to distributed grids. This paper describes an implementation of PM based on a vectorised virtual machine. On a single processor node, concurrent operations are implemented using masked vector operations. Virtual machine instructions operate on vectors of values and may be unmasked, masked using a Boolean field, or masked using an array of active vector cell locations. Conditional structures (such as if-then-else or while statement implementations) calculate and apply masks to the operations they control. A shift in mask representation from Boolean to location-list occurs when active locations become sufficiently sparse. Parallel loops unfold data structures (or vectors of data structures for nested loops) into vectors of values that may additionally be distributed over multiple computational nodes and then split into micro-threads compatible with the size of the local cache. Inter-node communication is accomplished using standard OpenMP and MPI. Performance analyses of the PM vector machine, demonstrating its scaling properties with respect to domain size and the number of processor nodes will be presented for a range of hardware configurations. The PM software and language definition are being made available under unrestrictive MIT and Creative Commons Attribution licenses respectively: www.pm-lang.org.

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.

Methodologies and systems for heterogeneous concurrent computing

NASA Technical Reports Server (NTRS)

Sunderam, V. S.

1994-01-01

Heterogeneous concurrent computing is gaining increasing acceptance as an alternative or complementary paradigm to multiprocessor-based parallel processing as well as to conventional supercomputing. While algorithmic and programming aspects of heterogeneous concurrent computing are similar to their parallel processing counterparts, system issues, partitioning and scheduling, and performance aspects are significantly different. In this paper, we discuss critical design and implementation issues in heterogeneous concurrent computing, and describe techniques for enhancing its effectiveness. In particular, we highlight the system level infrastructures that are required, aspects of parallel algorithm development that most affect performance, system capabilities and limitations, and tools and methodologies for effective computing in heterogeneous networked environments. We also present recent developments and experiences in the context of the PVM system and comment on ongoing and future work.

A framework for grand scale parallelization of the combined finite discrete element method in 2d

NASA Astrophysics Data System (ADS)

Lei, Z.; Rougier, E.; Knight, E. E.; Munjiza, A.

2014-09-01

Within the context of rock mechanics, the Combined Finite-Discrete Element Method (FDEM) has been applied to many complex industrial problems such as block caving, deep mining techniques (tunneling, pillar strength, etc.), rock blasting, seismic wave propagation, packing problems, dam stability, rock slope stability, rock mass strength characterization problems, etc. The reality is that most of these were accomplished in a 2D and/or single processor realm. In this work a hardware independent FDEM parallelization framework has been developed using the Virtual Parallel Machine for FDEM, (V-FDEM). With V-FDEM, a parallel FDEM software can be adapted to different parallel architecture systems ranging from just a few to thousands of cores.

Sensory Neuron Fates Are Distinguished by a Transcriptional Switch that Regulates Dendrite Branch Stabilization

PubMed Central

Smith, Cody J.; O’Brien, Timothy; Chatzigeorgiou, Marios; Spencer, W. Clay; Feingold-Link, Elana; Husson, Steven J.; Hori, Sayaka; Mitani, Shohei; Gottschalk, Alexander; Schafer, William R.; Miller, David M.

2013-01-01

SUMMARY Sensory neurons adopt distinct morphologies and functional modalities to mediate responses to specific stimuli. Transcription factors and their downstream effectors orchestrate this outcome but are incompletely defined. Here, we show that different classes of mechanosensory neurons in C. elegans are distinguished by the combined action of the transcription factors MEC-3, AHR-1, and ZAG-1. Low levels of MEC-3 specify the elaborate branching pattern of PVD nociceptors, whereas high MEC-3 is correlated with the simple morphology of AVM and PVM touch neurons. AHR-1 specifies AVM touch neuron fate by elevating MEC-3 while simultaneously blocking expression of nociceptive genes such as the MEC-3 target, the claudin-like membrane protein HPO-30, that promotes the complex dendritic branching pattern of PVD. ZAG-1 exercises a parallel role to prevent PVM from adopting the PVD fate. The conserved dendritic branching function of the Drosophila AHR-1 homolog, Spineless, argues for similar pathways in mammals. PMID:23889932

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

Brain perivascular macrophages: characterization and functional roles in health and disease.

PubMed

Faraco, Giuseppe; Park, Laibaik; Anrather, Josef; Iadecola, Costantino

2017-11-01

Perivascular macrophages (PVM) are a distinct population of resident brain macrophages characterized by a close association with the cerebral vasculature. PVM migrate from the yolk sac into the brain early in development and, like microglia, are likely to be a self-renewing cell population that, in the normal state, is not replenished by circulating monocytes. Increasing evidence implicates PVM in several disease processes, ranging from brain infections and immune activation to regulation of the hypothalamic-adrenal axis and neurovascular-neurocognitive dysfunction in the setting of hypertension, Alzheimer disease pathology, or obesity. These effects involve crosstalk between PVM and cerebral endothelial cells, interaction with circulating immune cells, and/or production of reactive oxygen species. Overall, the available evidence supports the idea that PVM are a key component of the brain-resident immune system with broad implications for the pathogenesis of major brain diseases. A better understanding of the biology and pathobiology of PVM may lead to new insights and therapeutic strategies for a wide variety of brain diseases.

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.

Thermal control system for Space Station Freedom photovoltaic power module

NASA Technical Reports Server (NTRS)

Hacha, Thomas H.; Howard, Laura

1994-01-01

The electric power for Space Station Freedom (SSF) is generated by the solar arrays of the photovoltaic power modules (PVM's) and conditioned, controlled, and distributed by a power management and distribution system. The PVM's are located outboard of the alpha gimbals of SSF. A single-phase thermal control system is being developed to provide thermal control of PVM electrical equipment and energy storage batteries. This system uses ammonia as the coolant and a direct-flow deployable radiator. The description and development status of the PVM thermal control system is presented.

Thermal control system for Space Station Freedom photovoltaic power module

NASA Technical Reports Server (NTRS)

Hacha, Thomas H.; Howard, Laura S.

1992-01-01

The electric power for Space Station Freedom (SSF) is generated by the solar arrays of the photovoltaic power modules (PVM's) and conditioned, controlled, and distributed by a power management and distribution system. The PVM's are located outboard of the alpha gimbals of SSF. A single-phase thermal control system is being developed to provide thermal control of PVM electrical equipment and energy storage batteries. This system uses ammonia as the coolant and a direct-flow deployable radiator. This paper presents the description and development status of the PVM thermal control system.

Parallel algorithms for modeling flow in permeable media. Annual report, February 15, 1995 - February 14, 1996

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

G.A. Pope; K. Sephernoori; D.C. McKinney

1996-03-15

This report describes the application of distributed-memory parallel programming techniques to a compositional simulator called UTCHEM. The University of Texas Chemical Flooding reservoir simulator (UTCHEM) is a general-purpose vectorized chemical flooding simulator that models the transport of chemical species in three-dimensional, multiphase flow through permeable media. The parallel version of UTCHEM addresses solving large-scale problems by reducing the amount of time that is required to obtain the solution as well as providing a flexible and portable programming environment. In this work, the original parallel version of UTCHEM was modified and ported to CRAY T3D and CRAY T3E, distributed-memory, multiprocessor computersmore » using CRAY-PVM as the interprocessor communication library. Also, the data communication routines were modified such that the portability of the original code across different computer architectures was mad possible.« less

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.

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.

Laboratory Investigation of Direct Measurement of Ice Water Content, Ice Surface Area, and Effective Radius of Ice Crystals Using a Laser-Diffraction Instrument

NASA Technical Reports Server (NTRS)

Gerber, H.; DeMott, P. J.; Rogers, D. C.

1995-01-01

The aircraft microphysics probe, PVM-100A, was tested in the Colorado State University dynamic cloud chamber to establish its ability to measure ice water content (IWC), PSA, and Re in ice clouds. Its response was compared to other means of measuring those ice-cloud parameters that included using FSSP-100 and 230-X 1-D optical probes for ice-crystal concentrations, a film-loop microscope for ice-crystal habits and dimensions, and an in-situ microscope for determining ice-crystal orientation. Intercomparisons were made in ice clouds containing ice crystals ranging in size from about 10 microns to 150 microns diameter, and ice crystals with plate, columnar, dendritic, and spherical shapes. It was not possible to determine conclusively that the PVM accurately measures IWC, PSA, and Re of ice crystals, because heat from the PVM evaporated in part the crystals in its vicinity in the chamber thus affecting its measurements. Similarities in the operating principle of the FSSP and PVM, and a comparison between Re measured by both instruments, suggest, however, that the PVM can make those measurements. The resolution limit of the PVM for IWC measurements was found to be on the order of 0.001 g/cubic m. Algorithms for correcting IWC measured by FSSP and PVM were developed.

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).

Computational strategies for three-dimensional flow simulations on distributed computer systems. Ph.D. Thesis Semiannual Status Report, 15 Aug. 1993 - 15 Feb. 1994

NASA Technical Reports Server (NTRS)

Weed, Richard Allen; Sankar, L. N.

1994-01-01

An increasing amount of research activity in computational fluid dynamics has been devoted to the development of efficient algorithms for parallel computing systems. The increasing performance to price ratio of engineering workstations has led to research to development procedures for implementing a parallel computing system composed of distributed workstations. This thesis proposal outlines an ongoing research program to develop efficient strategies for performing three-dimensional flow analysis on distributed computing systems. The PVM parallel programming interface was used to modify an existing three-dimensional flow solver, the TEAM code developed by Lockheed for the Air Force, to function as a parallel flow solver on clusters of workstations. Steady flow solutions were generated for three different wing and body geometries to validate the code and evaluate code performance. The proposed research will extend the parallel code development to determine the most efficient strategies for unsteady flow simulations.

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.

Preparation of Poly-(Methyl vinyl ether-co-maleic Anhydride) Nanoparticles by Solution-Enhanced Dispersion by Supercritical CO2

PubMed Central

Chen, Ai-Zheng; Wang, Guang-Ya; Wang, Shi-Bin; Feng, Jian-Gang; Liu, Yuan-Gang; Kang, Yong-Qiang

2012-01-01

The supercritical CO2-based technologies have been widely used in the formation of drug and/or polymer particles for biomedical applications. In this study, nanoparticles of poly-(methyl vinyl ether-co-maleic anhydride) (PVM/MA) were successfully fabricated by a process of solution-enhanced dispersion by supercritical CO2 (SEDS). A 23 factorial experiment was designed to investigate and identify the significance of the processing parameters (concentration, flow and solvent/nonsolvent) for the surface morphology, particle size, and particle size distribution of the products. The effect of the concentration of PVM/MA was found to be dominant in the results regarding particle size. Decreasing the initial solution concentration of PVM/MA decreased the particle size significantly. After optimization, the resulting PVM/MA nanoparticles exhibited a good spherical shape, a smooth surface, and a narrow particle size distribution. Fourier transform infrared spectroscopy (FTIR) spectra demonstrated that the chemical composition of PVM/MA was not altered during the SEDS process and that the SEDS process was therefore a typical physical process. The absolute value of zeta potential of the obtained PVM/MA nanoparticles was larger than 40 mV, indicating the samples’ stability in aqueous suspension. Analysis of thermogravimetry-differential scanning calorimetry (TG-DSC) revealed that the effect of the SEDS process on the thermostability of PVM/MA was negligible. The results of gas chromatography (GC) analysis confirmed that the SEDS process could efficiently remove the organic residue.

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.

The use of portable video media vs standard verbal communication in the urological consent process: a multicentre, randomised controlled, crossover trial.

PubMed

Winter, Matthew; Kam, Jonathan; Nalavenkata, Sunny; Hardy, Ellen; Handmer, Marcus; Ainsworth, Hannah; Lee, Wai Gin; Louie-Johnsun, Mark

2016-11-01

To determine if portable video media (PVM) improves patient's knowledge and satisfaction acquired during the consent process for cystoscopy and insertion of a ureteric stent compared to standard verbal communication (SVC), as informed consent is a crucial component of patient care and PVM is an emerging technology that may help improve the consent process. In this multi-centre randomised controlled crossover trial, patients requiring cystoscopy and stent insertion were recruited from two major teaching hospitals in Australia over a 15-month period (July 2014-December 2015). Patient information delivery was via PVM and SVC. The PVM consisted of an audio-visual presentation with cartoon animation presented on an iPad. Patient satisfaction was assessed using the validated Client Satisfaction Questionnaire 8 (CSQ-8; maximum score 32) and knowledge was tested using a true/false questionnaire (maximum score 28). Questionnaires were completed after first intervention and after crossover. Scores were analysed using the independent samples t-test and Wilcoxon signed-rank test for the crossover analysis. In all, 88 patients were recruited. A significant 3.1 point (15.5%) increase in understanding was demonstrable favouring the use of PVM (P < 0.001). There was no difference in patient satisfaction between the groups as judged by the CSQ-8. A significant 3.6 point (17.8%) increase in knowledge score was seen when the SVC group were crossed over to the PVM arm. A total of 80.7% of patients preferred PVM and 19.3% preferred SVC. Limitations include the lack of a validated questionnaire to test knowledge acquired from the interventions. This study demonstrates patients' preference towards PVM in the urological consent process of cystoscopy and ureteric stent insertion. PVM improves patient's understanding compared with SVC and is a more effective means of content delivery to patients in terms of overall preference and knowledge gained during the consent process. © 2016 The Authors BJU International © 2016 BJU International Published by John Wiley & Sons Ltd.

Development of a Big Data Application Architecture for Navy Manpower, Personnel, Training, and Education

DTIC Science & Technology

2016-03-01

science IT information technology JBOD just a bunch of disks JDBC java database connectivity xviii JPME Joint Professional Military Education JSO...Joint Service Officer JVM java virtual machine MPP massively parallel processing MPTE Manpower, Personnel, Training, and Education NAVMAC Navy...27 external database, whether it is MySQL , Oracle, DB2, or SQL Server (Teller, 2015). Connectors optimize the data transfer by obtaining metadata

Professional Veterinary Programs' Perceptions and Experiences Pertaining to Emotional Support Animals and Service Animals, and Recommendations for Policy Development.

PubMed

Schoenfeld-Tacher, Regina M; Kogan, Lori R

Given the unique nature of programs in professional veterinary medicine (PVM), the increasing numbers of students requesting accommodations for emotional support animals (ESAs) in higher education settings is of growing interest to student affairs and administrative staff in PVM settings. Since the legislation pertaining to this type of support animal differs from the laws governing disability service animals, colleges and universities now need to develop new policies and guidelines. Representatives from a sample of 28 PVM programs completed a survey about the prevalence of student requests for ESAs and service animals. PVM associate deans for academic affairs also reported their perceptions of this issue and the challenges these requests might pose within veterinary teaching laboratories and patient treatment areas. Responses indicated that approximately one third of PVM programs have received requests for ESAs (32.1%) in the last 2 years, 17.9% have had requests for psychiatric service animals, and 17.9% for other types of service animals. Despite this, most associate deans reported not having or not being aware of university or college policies pertaining to these issues. Most associate deans are interested in learning more about this topic. This paper provides general recommendations for establishing university or PVM program policies.

Trajectory Tracking of a Planer Parallel Manipulator by Using Computed Force Control Method

NASA Astrophysics Data System (ADS)

Bayram, Atilla

2017-03-01

Despite small workspace, parallel manipulators have some advantages over their serial counterparts in terms of higher speed, acceleration, rigidity, accuracy, manufacturing cost and payload. Accordingly, this type of manipulators can be used in many applications such as in high-speed machine tools, tuning machine for feeding, sensitive cutting, assembly and packaging. This paper presents a special type of planar parallel manipulator with three degrees of freedom. It is constructed as a variable geometry truss generally known planar Stewart platform. The reachable and orientation workspaces are obtained for this manipulator. The inverse kinematic analysis is solved for the trajectory tracking according to the redundancy and joint limit avoidance. Then, the dynamics model of the manipulator is established by using Virtual Work method. The simulations are performed to follow the given planar trajectories by using the dynamic equations of the variable geometry truss manipulator and computed force control method. In computed force control method, the feedback gain matrices for PD control are tuned with fixed matrices by trail end error and variable ones by means of optimization with genetic algorithm.

Efficiently modeling neural networks on massively parallel computers

NASA Technical Reports Server (NTRS)

Farber, Robert M.

1993-01-01

Neural networks are a very useful tool for analyzing and modeling complex real world systems. Applying neural network simulations to real world problems generally involves large amounts of data and massive amounts of computation. To efficiently handle the computational requirements of large problems, we have implemented at Los Alamos a highly efficient neural network compiler for serial computers, vector computers, vector parallel computers, and fine grain SIMD computers such as the CM-2 connection machine. This paper describes the mapping used by the compiler to implement feed-forward backpropagation neural networks for a SIMD (Single Instruction Multiple Data) architecture parallel computer. Thinking Machines Corporation has benchmarked our code at 1.3 billion interconnects per second (approximately 3 gigaflops) on a 64,000 processor CM-2 connection machine (Singer 1990). This mapping is applicable to other SIMD computers and can be implemented on MIMD computers such as the CM-5 connection machine. Our mapping has virtually no communications overhead with the exception of the communications required for a global summation across the processors (which has a sub-linear runtime growth on the order of O(log(number of processors)). We can efficiently model very large neural networks which have many neurons and interconnects and our mapping can extend to arbitrarily large networks (within memory limitations) by merging the memory space of separate processors with fast adjacent processor interprocessor communications. This paper will consider the simulation of only feed forward neural network although this method is extendable to recurrent networks.

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

A Spectral Element Ocean Model on the Cray T3D: the interannual variability of the Mediterranean Sea general circulation

NASA Astrophysics Data System (ADS)

Molcard, A. J.; Pinardi, N.; Ansaloni, R.

A new numerical model, SEOM (Spectral Element Ocean Model, (Iskandarani et al, 1994)), has been implemented in the Mediterranean Sea. Spectral element methods combine the geometric flexibility of finite element techniques with the rapid convergence rate of spectral schemes. The current version solves the shallow water equations with a fifth (or sixth) order accuracy spectral scheme and about 50.000 nodes. The domain decomposition philosophy makes it possible to exploit the power of parallel machines. The original MIMD master/slave version of SEOM, written in F90 and PVM, has been ported to the Cray T3D. When critical for performance, Cray specific high-performance one-sided communication routines (SHMEM) have been adopted to fully exploit the Cray T3D interprocessor network. Tests performed with highly unstructured and irregular grid, on up to 128 processors, show an almost linear scalability even with unoptimized domain decomposition techniques. Results from various case studies on the Mediterranean Sea are shown, involving realistic coastline geometry, and monthly mean 1000mb winds from the ECMWF's atmospheric model operational analysis from the period January 1987 to December 1994. The simulation results show that variability in the wind forcing considerably affect the circulation dynamics of the Mediterranean Sea.

LAVA web-based remote simulation: enhancements for education and technology innovation

NASA Astrophysics Data System (ADS)

Lee, Sang Il; Ng, Ka Chun; Orimoto, Takashi; Pittenger, Jason; Horie, Toshi; Adam, Konstantinos; Cheng, Mosong; Croffie, Ebo H.; Deng, Yunfei; Gennari, Frank E.; Pistor, Thomas V.; Robins, Garth; Williamson, Mike V.; Wu, Bo; Yuan, Lei; Neureuther, Andrew R.

2001-09-01

The Lithography Analysis using Virtual Access (LAVA) web site at http://cuervo.eecs.berkeley.edu/Volcano/ has been enhanced with new optical and deposition applets, graphical infrastructure and linkage to parallel execution on networks of workstations. More than ten new graphical user interface applets have been designed to support education, illustrate novel concepts from research, and explore usage of parallel machines. These applets have been improved through feedback and classroom use. Over the last year LAVA provided industry and other academic communities 1,300 session and 700 rigorous simulations per month among the SPLAT, SAMPLE2D, SAMPLE3D, TEMPEST, STORM, and BEBS simulators.

: A Scalable and Transparent System for Simulating MPI Programs

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

Perumalla, Kalyan S

2010-01-01

is a scalable, transparent system for experimenting with the execution of parallel programs on simulated computing platforms. The level of simulated detail can be varied for application behavior as well as for machine characteristics. Unique features of are repeatability of execution, scalability to millions of simulated (virtual) MPI ranks, scalability to hundreds of thousands of host (real) MPI ranks, portability of the system to a variety of host supercomputing platforms, and the ability to experiment with scientific applications whose source-code is available. The set of source-code interfaces supported by is being expanded to support a wider set of applications, andmore » MPI-based scientific computing benchmarks are being ported. In proof-of-concept experiments, has been successfully exercised to spawn and sustain very large-scale executions of an MPI test program given in source code form. Low slowdowns are observed, due to its use of purely discrete event style of execution, and due to the scalability and efficiency of the underlying parallel discrete event simulation engine, sik. In the largest runs, has been executed on up to 216,000 cores of a Cray XT5 supercomputer, successfully simulating over 27 million virtual MPI ranks, each virtual rank containing its own thread context, and all ranks fully synchronized by virtual time.« less

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

STUDIES ON PNEUMONIA VIRUS OF MICE (PVM) IN CELL CULTURE

PubMed Central

Harter, Donald H.; Choppin, Purnell W.

1967-01-01

Pneumonia virus of mice (PVM) has been serially propagated in a line of baby hamster kidney (BHK21) cells. A maximum titer of 6.3 x 106 TCID50 per ml was obtained, and there was little variation in yield on serial passage. PVM grown in BHK21 cells was antigenically similar to virus obtained from the mouse lung, but was somewhat less virulent for the mouse after 10 serial passages in these cells. Virus produced by BHK21 cells agglutinated mouse erythrocytes without prior heating or other treatment. Sedimentation of PVM in the ultracentrifuge or precipitation by ammonium sulfate resulted in a loss in infectivity but an increase in hemagglutinating activity, presumably due to disruption of the virus particle. In a potassium tartrate density gradient, the major portion of infective virus sedimented at a density of approximately 1.15, and noninfective hemagglutinin, at a density of approximately 1.13. Stock virus preparations appear to contain a large amount of noninfective hemagglutinin. The replication of PVM was not inhibited by 5-fluoro-2'-deoxyuridine, 5-bromo-2'-deoxyuridine, or 5-iodo-2'-deoxyuridine. Infected cells contained eosinophilic cytoplasmic inclusions which showed the acridine orange staining characteristic of single-stranded RNA. Foci of viral antigen were observed in the cytoplasm of infected cells by fluorescent antibody staining. The results suggest that PVM is an RNA virus that replicates in the cytoplasm. PMID:4165740

Molecular make-up of the Plasmodium parasitophorous vacuolar membrane.

PubMed

Spielmann, Tobias; Montagna, Georgina N; Hecht, Leonie; Matuschewski, Kai

2012-10-01

Plasmodium, the causative agent of malaria, is an obligate, intracellular, eukaryotic cell that invades, replicates, and differentiates within hepatocytes and erythrocytes. Inside a host cell, a second membrane delineates the developing pathogen in addition to the parasite plasma membrane, resulting in a distinct cellular compartment, termed parasitophorous vacuole (PV). The PV membrane (PVM) constitutes the parasite-host cell interface and is likely central to nutrient acquisition, host cell remodeling, waste disposal, environmental sensing, and protection from innate defense. Over the past two decades, a number of parasite-encoded PVM proteins have been identified. They include multigene families and protein complexes, such as early-transcribed membrane proteins (ETRAMPs) and the Plasmodium translocon for exported proteins (PTEX). Nearly all Plasmodium PVM proteins are restricted to this genus and display transient and stage-specific expression. Here, we provide an overview of the PVM proteins of Plasmodium blood and liver stages. Biochemical and experimental genetics data suggest that some PVM proteins are ideal targets for novel anti-malarial intervention strategies. Copyright © 2012 Elsevier GmbH. All rights reserved.

Virtual Microscopy: A Useful Tool for Meeting Evolving Challenges in the Veterinary Medical Curriculum

NASA Astrophysics Data System (ADS)

Kogan, Lori R.; Dowers, Kristy L.; Cerda, Jacey R.; Schoenfeld-Tacher, Regina M.; Stewart, Sherry M.

2014-12-01

Veterinary schools, similar to many professional health programs, face a myriad of evolving challenges in delivering their professional curricula including expansion of class size, costs to maintain expensive laboratories, and increased demands on veterinary educators to use curricular time efficiently and creatively. Additionally, exponential expansion of the knowledge base through ongoing biomedical research, educational goals to increase student engagement and clinical reasoning earlier in the curriculum, and students' desire to access course materials and enhance their educational experience through the use of technology all support the need to reassess traditional microscope laboratories within Professional Veterinary Medical (PVM) educational programs. While there is clear justification for teaching veterinary students how to use a microscope for clinical evaluation of cytological preparations (i.e., complete blood count, urinalysis, fecal analysis, fine needle aspirates, etc.), virtual microscopy may be a viable alternative to using light microscopy for teaching and learning fundamental histological concepts. This article discusses results of a survey given to assess Professional Veterinary Medical students' perceptions of using virtual microscope for learning basic histology/microscopic anatomy and implications of these results for using virtual microscopy as a pedagogical tool in teaching first-year Professional Veterinary Medical students' basic histology.

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

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.

Environmental concept for engineering software on MIMD computers

NASA Technical Reports Server (NTRS)

Lopez, L. A.; Valimohamed, K.

1989-01-01

The issues related to developing an environment in which engineering systems can be implemented on MIMD machines are discussed. The problem is presented in terms of implementing the finite element method under such an environment. However, neither the concepts nor the prototype implementation environment are limited to this application. The topics discussed include: the ability to schedule and synchronize tasks efficiently; granularity of tasks; load balancing; and the use of a high level language to specify parallel constructs, manage data, and achieve portability. The objective of developing a virtual machine concept which incorporates solutions to the above issues leads to a design that can be mapped onto loosely coupled, tightly coupled, and hybrid systems.

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

Glineur, Stephanie F.; Renshaw, Randall W.; Percopo, Caroline M.

A previous report of a novel pneumovirus (PnV) isolated from the respiratory tract of a dog described its significant homology to the rodent pathogen, pneumonia virus of mice (PVM). The original PnV–Ane4 pathogen replicated in and could be re-isolated in infectious state from mouse lung but elicited minimal mortality compared to PVM strain J3666. Here we assess phylogeny and physiologic responses to 10 new PnV isolates. The G/glycoprotein sequences of all PnVs include elongated amino-termini when compared to the characterized PVMs, and suggest division into groups A and B. While we observed significant differences in cytokine production and neutrophil recruitmentmore » to the lungs of BALB/c mice in response to survival doses (50 TCID{sub 50} units) of representative group A (114378-10-29-KY-F) and group B (7968-11-OK) PnVs, we observed no evidence for positive selection (dN>dS) among the PnV/PnV, PVM/PnV or PVM/PVM G/glycoprotein or F/fusion protein sequence pairs. - Highlights: • We consider ten novel isolates of the pneumovirus (PnV) first described by Renshaw and colleagues. • The G/glycoprotein sequences of all PnVs include elongated amino-termini when compared to PVM. • We detect cytokine production and neutrophil recruitment to the lungs of mice in response to PnV. • We observed no evidence for positive selection (dN>dS) among the gene sequence pairs.« less

Interactions between Multiple Genetic Determinants in the 5′ UTR and VP1 Capsid Control Pathogenesis of Chronic Post-Viral Myopathy caused by Coxsackievirus B1

PubMed Central

Sandager, Maribeth M.; Nugent, Jaime L.; Schulz, Wade L.; Messner, Ronald P.; Tam, Patricia E.

2008-01-01

Mice infected with coxsackievirus B1 Tucson (CVB1T) develop chronic, post-viral myopathy (PVM) with clinical manifestations of hind limb muscle weakness and myositis. The objective of the current study was to establish the genetic basis of myopathogenicity in CVB1T. Using a reverse genetics approach, full attenuation of PVM could only be achieved by simultaneously mutating four sites located at C706U in the 5′ untranslated region (5′ UTR) and at Y87F, V136A, and T276A in the VP1 capsid. Engineering these four myopathic determinants into an amyopathic CVB1T variant restored the ability to cause PVM. Moreover, these same four determinants controlled PVM expression in a second strain of mice, indicating that the underlying mechanism is operational in mice of different genetic backgrounds. Modeling studies predict that C706U alters both local and long-range pairing in the 5′ UTR, and that VP1 determinants are located on the capsid surface. However, these differences did not affect viral titers, temperature stability, pH stability, or the antibody response to virus. These studies demonstrate that PVM develops from a complex interplay between viral determinants in the 5′ UTR and VP1 capsid and have uncovered intriguing similarities between genetic determinants that cause PVM and those involved in pathogenesis of other enteroviruses. PMID:18029287

Pneumonia Virus of Mice Severe Respiratory Virus Infection in a Natural Host

PubMed Central

Rosenberg, Helene F.; Domachowske, Joseph B.

2008-01-01

Pneumonia virus of mice (PVM; family Paramyxoviridae, genus Pneumovirus) is a natural mouse pathogen that is closely related to the human and bovine respiratory syncytial viruses. Among the prominent features of this infection, robust replication of PVM takes place in bronchial epithelial cells in response to a minimal virus inoculum. Virus replication in situ results in local production of proinflammatory cytokines (MIP-1α, MIP-2, MCP-1 and IFNγ) and granulocyte recruitment to the lung. If left unchecked, PVM infection and the ensuing inflammatory response ultimately lead to pulmonary edema, respiratory compromise and death. In this review, we consider the recent studies using the PVM model that have provided important insights into the role of the inflammatory response in the pathogenesis of severe respiratory virus infection. We also highlight several works that have elucidated acquired immune responses to this pathogen, including T cell responses and the development of humoral immunity. Finally, we consider several immunomodulatory strategies that have been used successfully to reduce morbidity and mortality when administered to PVM infected, symptomatic mice, and thus hold promise as realistic therapeutic strategies for severe respiratory virus infections in human subjects. PMID:18471897

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.

Software platform virtualization in chemistry research and university teaching

PubMed Central

2009-01-01

Background Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Results Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Conclusion Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide. PMID:20150997

Software platform virtualization in chemistry research and university teaching.

PubMed

Kind, Tobias; Leamy, Tim; Leary, Julie A; Fiehn, Oliver

2009-11-16

Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.

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.

Parallel Navier-Stokes computations on shared and distributed memory architectures

NASA Technical Reports Server (NTRS)

Hayder, M. Ehtesham; Jayasimha, D. N.; Pillay, Sasi Kumar

1995-01-01

We study a high order finite difference scheme to solve the time accurate flow field of a jet using the compressible Navier-Stokes equations. As part of our ongoing efforts, we have implemented our numerical model on three parallel computing platforms to study the computational, communication, and scalability characteristics. The platforms chosen for this study are a cluster of workstations connected through fast networks (the LACE experimental testbed at NASA Lewis), a shared memory multiprocessor (the Cray YMP), and a distributed memory multiprocessor (the IBM SPI). Our focus in this study is on the LACE testbed. We present some results for the Cray YMP and the IBM SP1 mainly for comparison purposes. On the LACE testbed, we study: (1) the communication characteristics of Ethernet, FDDI, and the ALLNODE networks and (2) the overheads induced by the PVM message passing library used for parallelizing the application. We demonstrate that clustering of workstations is effective and has the potential to be computationally competitive with supercomputers at a fraction of the cost.

Final report of PVM-6 and PVM-7 Weather Documentation, AFCRL/Minuteman Report Number 6

DTIC Science & Technology

1975-09-11

Research Laboratories, Hanscon AFB, MA 01731. USAFGL ltr, 1 Aug 1983 TH!3 R~PORT HAS BEEN DELIMI~ED AND CLtARED FOR PUBLIC REL~5E UNDER DOP DiRECTIVE...5200.20 AND NO RESTniCTIONS ARE IMPDSED UPON r rs usE P.ND n 1 scu1sURI:. DISTRIBUTION STATE~ENT A APPROVED FQR PUBLIC RELEASE; DISTRIBUTION...NO AFCRL -TR-75 -04817^ F C ^ I - 1 ^T" 1 . » " 3^ 3 / *■ TlTUSfltf fidUtUlt- JINAL REPORT OFPyM-6 AND PVM-7 WEATHER DOCUMENTATION^ | AFCRl

Non-Traumatic Myositis Ossificans in the Lumbosacral Paravertebral Muscle

PubMed Central

Jung, DaeYoung; Roh, Ji Hyeon

2013-01-01

Myositis ossificans (MO) is a benign condition of non-neoplastic heterotopic bone formation in the muscle or soft tissue. Trauma plays a role in the development of MO, thus, non-traumatic MO is very rare. Although MO may occur anywhere in the body, it is rarely seen in the lumbosacral paravertebral muscle (PVM). Herein, we report a case of non-traumatic MO in the lumbosacral PVM. A 42-year-old man with no history of trauma was referred to our hospital for pain in the low back, left buttock, and left thigh. On physical examination, a slightly tender, hard, and fixed mass was palpated in the left lumbosacral PVM. Computed tomography showed a calcified mass within the left lumbosacral PVM. Magnetic resonance imaging (MRI) showed heterogeneous high signal intensity in T1- and T2-weighted image, and no enhancement of the mass was found in the postcontrast T1-weighted MRI. The lack of typical imaging features required an open biopsy, and MO was confirmed. MO should be considered in the differential diagnosis when the imaging findings show a mass involving PVM. When it is difficult to distinguish MO from soft tissue or bone malignancy by radiology, it is necessary to perform a biopsy to confirm the diagnosis. PMID:23908707

Test of prototype liquid-water-content meter for aircraft use

NASA Technical Reports Server (NTRS)

Gerber, Hermann E.

1993-01-01

This report describes the effort undertaken to meet the objectives of National Science Foundation Grant ATM-9207345 titled 'Test of Prototype Liquid-Water-Content Meter for Aircraft Use.' Three activities were proposed for testing the new aircraft instrument, PVM-100A: (1) Calibrate the PVM-100A in a facility where the liquid-water-content (LWC) channel, and the integrated surface area channel (PSA) could be compared to standard means for LWC and PSA measurements. Scaling constant for the channels were to be determined in this facility. The fog/wind tunnel at ECN, Petten, The Netherlands was judged the most suitable facility for this effort. (2) Expose the PVM-100A to high wind speeds similar to those expected on research aircraft, and test the anti-icing heaters on the PVM-100A under typical icing conditions expected in atmospheric clouds. The high-speed icing tunnel at NRC, Ottawa, Canada was to be utilized. (3) Operate the PVM-100A on an aircraft during cloud penetrations to determine its stability and practicality for such measurements. The C-131A aircraft of the University of Washington was the aircraft of opportunity for these-tests, which were to be conducted during the 4-week Atlantic Stratocumulus Transition Experiment (ASTEX) in June of 1992.

On the anatomy and histology of the pubovisceral muscle enthesis in women.

PubMed

Kim, Jinyong; Ramanah, Rajeev; DeLancey, John O L; Ashton-Miller, James A

2011-09-01

The origin of the pubovisceral muscle (PVM) from the pubic bone is known to be at elevated risk for injury during difficult vaginal births. We examined the anatomy and histology of its enthesial origin to classify its type and see if it differs from appendicular entheses. Parasagittal sections of the pubic bone, PVM enthesis, myotendinous junction, and muscle proper were harvested from five female cadavers (51-98 years). Histological sections were prepared with hematoxylin and eosin, Masson's trichrome, and Verhoeff-Van Gieson stains. The type of enthesis was identified according to a published enthesial classification scheme. Quantitative imaging analysis was performed in sampling bands 2 mm apart along the enthesis to determine its cross-sectional area and composition. The PVM enthesis can be classified as a fibrous enthesis. The PVM muscle fibers terminated in collagenous fibers that insert tangentially onto the periosteum of the pubic bone for the most part. Sharpey's fibers were not observed. In a longitudinal cross-section, the area of the connective tissue and muscle becomes equal approximately 8 mm from the pubic bone. The PVM originates bilaterally from the pubic bone via fibrous entheses whose collagen fibers arise tangentially from the periosteum of the pubic bone. Copyright © 2010 Wiley-Liss, Inc.

On the Anatomy and Histology of the Pubovisceral Muscle Enthesis in Women

PubMed Central

Kim, Jinyong; Ramanah, Rajeev; DeLancey, John O. L.; Ashton-Miller, James A.

2012-01-01

Aims The origin of the pubovisceral muscle (PVM) from the pubic bone is known to be at elevated risk for injury during difficult vaginal births. We examined the anatomy and histology of its enthesial origin to classify its type and see if it differs from appendicular entheses. Methods Parasagittal sections of the pubic bone, PVM enthesis, myotendinous junction and muscle proper were harvested from five female cadavers (51 - 98 years). Histological sections were prepared with hematoxylin and eosin, Masson’s trichrome, and Verhoeff-Van Gieson stains. The type of enthesis was identified according to a published enthesial classification scheme. Quantitative imaging analysis was performed in sampling bands 2 mm apart along the enthesis to determine its cross-sectional area and composition. Results The PVM enthesis can be classified as a fibrous enthesis. The PVM muscle fibers terminated in collagenous fibers that insert tangentially onto the periosteum of the pubic bone for the most part. Sharpey’s fibers were not observed. In a longitudinal cross-section, the area of the connective tissue and muscle becomes equal approximately 8 mm from the pubic bone. Conclusion The PVM originates bilaterally from the pubic bone via fibrous entheses whose collagen fibers arise tangentially from the periosteum of the pubic bone. PMID:21567449

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.

Portable Video Media Versus Standard Verbal Communication in Surgical Information Delivery to Nurses: A Prospective Multicenter, Randomized Controlled Crossover Trial.

PubMed

Kam, Jonathan; Ainsworth, Hannah; Handmer, Marcus; Louie-Johnsun, Mark; Winter, Matthew

2016-10-01

Continuing education of health professionals is important for delivery of quality health care. Surgical nurses are often required to understand surgical procedures. Nurses need to be aware of the expected outcomes and recognize potential complications of such procedures during their daily work. Traditional educational methods, such as conferences and tutorials or informal education at the bedside, have many drawbacks for delivery of this information in a universal, standardized, and timely manner. The rapid uptake of portable media devices makes portable video media (PVM) a potential alternative to current educational methods. To compare PVM to standard verbal communication (SVC) for surgical information delivery and educational training for nurses and evaluate its impact on knowledge acquisition and participant satisfaction. Prospective, multicenter, randomized controlled crossover trial. Two hospitals: Gosford District Hospital and Wyong Hospital. Seventy-two nursing staff (36 at each site). Information delivery via PVM--7-minute video compared to information delivered via SVC. Knowledge acquisition was measured by a 32-point questionnaire, and satisfaction with the method of education delivery was measured using the validated Client Satisfaction Questionnaire (CSQ-8). Knowledge acquisition was higher via PVM compared to SVC 25.9 (95% confidence interval [CI] 25.2-26.6) versus 24.3 (95% CI 23.5-25.1), p = .004. Participant satisfaction was higher with PVM 29.5 (95% CI 28.3-30.7) versus 26.5 (95% CI 25.1-27.9), p = .003. Following information delivery via SVC, participants had a 6% increase in knowledge scores, 24.3 (95% CI 23.5-25.1) versus 25.7 (95% CI 24.9-26.5) p = .001, and a 13% increase in satisfaction scores, 26.5 (95% CI 25.1-27.9) versus 29.9 (95% CI 28.8-31.0) p < .001, when they crossed-over to information delivery via PVM. PVM provides a novel method for providing education to nurses that improves knowledge retention and satisfaction with the educational process. © 2016 Sigma Theta Tau International.

Kinematics and dynamics of robotic systems with multiple closed loops

NASA Astrophysics Data System (ADS)

Zhang, Chang-De

The kinematics and dynamics of robotic systems with multiple closed loops, such as Stewart platforms, walking machines, and hybrid manipulators, are studied. In the study of kinematics, focus is on the closed-form solutions of the forward position analysis of different parallel systems. A closed-form solution means that the solution is expressed as a polynomial in one variable. If the order of the polynomial is less than or equal to four, the solution has analytical closed-form. First, the conditions of obtaining analytical closed-form solutions are studied. For a Stewart platform, the condition is found to be that one rotational degree of freedom of the output link is decoupled from the other five. Based on this condition, a class of Stewart platforms which has analytical closed-form solution is formulated. Conditions of analytical closed-form solution for other parallel systems are also studied. Closed-form solutions of forward kinematics for walking machines and multi-fingered grippers are then studied. For a parallel system with three three-degree-of-freedom subchains, there are 84 possible ways to select six independent joints among nine joints. These 84 ways can be classified into three categories: Category 3:3:0, Category 3:2:1, and Category 2:2:2. It is shown that the first category has no solutions; the solutions of the second category have analytical closed-form; and the solutions of the last category are higher order polynomials. The study is then extended to a nearly general Stewart platform. The solution is a 20th order polynomial and the Stewart platform has a maximum of 40 possible configurations. Also, the study is extended to a new class of hybrid manipulators which consists of two serially connected parallel mechanisms. In the study of dynamics, a computationally efficient method for inverse dynamics of manipulators based on the virtual work principle is developed. Although this method is comparable with the recursive Newton-Euler method for serial manipulators, its advantage is more noteworthy when applied to parallel systems. An approach of inverse dynamics of a walking machine is also developed, which includes inverse dynamic modeling, foot force distribution, and joint force/torque allocation.

Model institutional infrastructures for recycling of photovoltaic modules

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

Reaven, S.J.; Moskowitz, P.D.; Fthenakis, V.

1996-01-01

How will photovoltaic modules (PVMS) be recycled at the end of their service lives? This question has technological and institutional components (Reaven, 1994a). The technological aspect concerns the physical means of recycling: what advantages and disadvantages of the several existing and emerging mechanical, thermal, and chemical recycling processes and facilities merit consideration? The institutional dimension refers to the arrangements for recycling: what are the operational and financial roles of the parties with an interest in PVM recycling? These parties include PVM manufacturers, trade organizations; distributors, and retailers; residential, commercial, and utility PVM users; waste collectors, transporters, reclaimers, and reclaimers; andmore » governments.« less

Intranasal treatment with a novel immunomodulator mediates innate immune protection against lethal pneumonia virus of mice.

PubMed

Martinez, Elisa C; Garg, Ravendra; Shrivastava, Pratima; Gomis, Susantha; van Drunen Littel-van den Hurk, Sylvia

2016-11-01

Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections in infants and young children. There are no licensed RSV vaccines available, and the few treatment options for high-risk individuals are either extremely costly or cause severe side effects and toxicity. Immunomodulation mediated by a novel formulation consisting of the toll-like receptor 3 agonist poly(I:C), an innate defense regulator peptide and a polyphosphazene (P-I-P) was evaluated in the context of lethal infection with pneumonia virus of mice (PVM). Intranasal delivery of a single dose of P-I-P protected adult mice against PVM when given 24 h prior to challenge. These animals experienced minimal weight loss, no clinical disease, 100% survival, and reduced lung pathology. Similar clinical outcomes were observed in mice treated up to 3 days prior to infection. P-I-P pre-treatment induced early mRNA and protein expression of key chemokine and cytokine genes, reduced the recruitment of neutrophils and eosinophils, decreased virus titers in the lungs, and modulated the delayed exacerbated nature of PVM disease without any short-term side effects. On day 14 post-infection, P-I-P-treated mice were confirmed to be PVM-free. These results demonstrate the capacity of this formulation to prevent PVM and possibly other viral respiratory infections. Copyright © 2016 Elsevier B.V. All rights reserved.

A robot arm simulation with a shared memory multiprocessor machine

NASA Technical Reports Server (NTRS)

Kim, Sung-Soo; Chuang, Li-Ping

1989-01-01

A parallel processing scheme for a single chain robot arm is presented for high speed computation on a shared memory multiprocessor. A recursive formulation that is derived from a virtual work form of the d'Alembert equations of motion is utilized for robot arm dynamics. A joint drive system that consists of a motor rotor and gears is included in the arm dynamics model, in order to take into account gyroscopic effects due to the spinning of the rotor. The fine grain parallelism of mechanical and control subsystem models is exploited, based on independent computation associated with bodies, joint drive systems, and controllers. Efficiency and effectiveness of the parallel scheme are demonstrated through simulations of a telerobotic manipulator arm. Two different mechanical subsystem models, i.e., with and without gyroscopic effects, are compared, to show the trade-off between efficiency and accuracy.

Parallel computing on Unix workstation arrays

NASA Astrophysics Data System (ADS)

Reale, F.; Bocchino, F.; Sciortino, S.

1994-12-01

We have tested arrays of general-purpose Unix workstations used as MIMD systems for massive parallel computations. In particular we have solved numerically a demanding test problem with a 2D hydrodynamic code, generally developed to study astrophysical flows, by exucuting it on arrays either of DECstations 5000/200 on Ethernet LAN, or of DECstations 3000/400, equipped with powerful Alpha processors, on FDDI LAN. The code is appropriate for data-domain decomposition, and we have used a library for parallelization previously developed in our Institute, and easily extended to work on Unix workstation arrays by using the PVM software toolset. We have compared the parallel efficiencies obtained on arrays of several processors to those obtained on a dedicated MIMD parallel system, namely a Meiko Computing Surface (CS-1), equipped with Intel i860 processors. We discuss the feasibility of using non-dedicated parallel systems and conclude that the convenience depends essentially on the size of the computational domain as compared to the relative processor power and network bandwidth. We point out that for future perspectives a parallel development of processor and network technology is important, and that the software still offers great opportunities of improvement, especially in terms of latency times in the message-passing protocols. In conditions of significant gain in terms of speedup, such workstation arrays represent a cost-effective approach to massive parallel computations.

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.

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.

Role of Open Source Tools and Resources in Virtual Screening for Drug Discovery.

PubMed

Karthikeyan, Muthukumarasamy; Vyas, Renu

2015-01-01

Advancement in chemoinformatics research in parallel with availability of high performance computing platform has made handling of large scale multi-dimensional scientific data for high throughput drug discovery easier. In this study we have explored publicly available molecular databases with the help of open-source based integrated in-house molecular informatics tools for virtual screening. The virtual screening literature for past decade has been extensively investigated and thoroughly analyzed to reveal interesting patterns with respect to the drug, target, scaffold and disease space. The review also focuses on the integrated chemoinformatics tools that are capable of harvesting chemical data from textual literature information and transform them into truly computable chemical structures, identification of unique fragments and scaffolds from a class of compounds, automatic generation of focused virtual libraries, computation of molecular descriptors for structure-activity relationship studies, application of conventional filters used in lead discovery along with in-house developed exhaustive PTC (Pharmacophore, Toxicophores and Chemophores) filters and machine learning tools for the design of potential disease specific inhibitors. A case study on kinase inhibitors is provided as an example.

Shared elements of host-targeting pathways among apicomplexan parasites of differing lifestyles.

PubMed

Pellé, Karell G; Jiang, Rays H Y; Mantel, Pierre-Yves; Xiao, Yu-Ping; Hjelmqvist, Daisy; Gallego-Lopez, Gina M; O T Lau, Audrey; Kang, Byung-Ho; Allred, David R; Marti, Matthias

2015-11-01

Apicomplexans are a diverse group of obligate parasites occupying different intracellular niches that require modification to meet the needs of the parasite. To efficiently manipulate their environment, apicomplexans translocate numerous parasite proteins into the host cell. Whereas some parasites remain contained within a parasitophorous vacuole membrane (PVM) throughout their developmental cycle, others do not, a difference that affects the machinery needed for protein export. A signal-mediated pathway for protein export into the host cell has been characterized in Plasmodium parasites, which maintain the PVM. Here, we functionally demonstrate an analogous host-targeting pathway involving organellar staging prior to secretion in the related bovine parasite, Babesia bovis, a parasite that destroys the PVM shortly after invasion. Taking into account recent identification of a similar signal-mediated pathway in the coccidian parasite Toxoplasma gondii, we suggest a model in which this conserved pathway has evolved in multiple steps from signal-mediated trafficking to specific secretory organelles for controlled secretion to a complex protein translocation process across the PVM. © 2015 John Wiley & Sons Ltd.

Generalization of soft phonon modes

NASA Astrophysics Data System (ADS)

Rudin, Sven P.

2018-04-01

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. Here, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system with N atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, PVM0, represents the 3 N -dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, PVM0 serves as a generalization of soft phonon modes. At low temperatures, PVM0 reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case PVM0 culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, PVM0 can be equally well calculated on either side of the structural phase transition. Two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the β phase of uranium, the higher-symmetry structure of which stabilizes with temperature.

Preparation of Chitosan-Based Hemostatic Sponges by Supercritical Fluid Technology

PubMed Central

Song, Hu-Fan; Chen, Ai-Zheng; Wang, Shi-Bin; Kang, Yong-Qiang; Ye, Shi-Fu; Liu, Yuan-Gang; Wu, Wen-Guo

2014-01-01

Using ammonium bicarbonate (AB) particles as a porogen, chitosan (CS)-based hemostatic porous sponges were prepared in supercritical carbon dioxide due to its low viscosity, small surface tension, and good compatibility with organic solvent. Fourier transform infrared spectroscopy (FTIR) spectra demonstrated that the chemical compositions of CS and poly-(methyl vinyl ether-co-maleic anhydride) (PVM/MA) were not altered during the phase inversion process. The morphology and structure of the sponge after the supercritical fluid (SCF) process were observed by scanning electron microscopy (SEM). The resulting hemostatic sponges showed a relatively high porosity (about 80%) with a controllable pore size ranging from 0.1 to 200 μm. The concentration of PVM/MA had no significant influence on the porosity of the sponges. Comparative experiments on biological assessment and hemostatic effect between the resulting sponges and Avitene® were also carried out. With the incorporation of PVM/MA into the CS-based sponges, the water absorption rate of the sponges increased significantly, and the CS-PVM/MA sponges showed a similar water absorption rate (about 90%) to that of Avitene®. The results of the whole blood clotting experiment and animal experiment also demonstrated that the clotting ability of the CS-PVM/MA sponges was similar to that of Avitene®. All these results elementarily verified that the sponges prepared in this study were suitable for hemostasis and demonstrated the feasibility of using SCF-assisted phase inversion technology to produce hemostatic porous sponges. PMID:28788577

Animal model of respiratory syncytial virus: CD8+ T cells cause a cytokine storm that is chemically tractable by sphingosine-1-phosphate 1 receptor agonist therapy.

PubMed

Walsh, Kevin B; Teijaro, John R; Brock, Linda G; Fremgen, Daniel M; Collins, Peter L; Rosen, Hugh; Oldstone, Michael B A

2014-06-01

The cytokine storm is an intensified, dysregulated, tissue-injurious inflammatory response driven by cytokine and immune cell components. The cytokine storm during influenza virus infection, whereby the amplified innate immune response is primarily responsible for pulmonary damage, has been well characterized. Now we describe a novel event where virus-specific T cells induce a cytokine storm. The paramyxovirus pneumonia virus of mice (PVM) is a model of human respiratory syncytial virus (hRSV). Unexpectedly, when C57BL/6 mice were infected with PVM, the innate inflammatory response was undetectable until day 5 postinfection, at which time CD8(+) T cells infiltrated into the lung, initiating a cytokine storm by their production of gamma interferon (IFN-γ) and tumor necrosis factor alpha (TNF-α). Administration of an immunomodulatory sphingosine-1-phosphate (S1P) receptor 1 (S1P1R) agonist significantly inhibited PVM-elicited cytokine storm by blunting the PVM-specific CD8(+) T cell response, resulting in diminished pulmonary disease and enhanced survival. A dysregulated overly exuberant immune response, termed a "cytokine storm," accompanies virus-induced acute respiratory diseases (VARV), is primarily responsible for the accompanying high morbidity and mortality, and can be controlled therapeutically in influenza virus infection of mice and ferrets by administration of sphingosine-1-phosphate 1 receptor (S1P1R) agonists. Here, two novel findings are recorded. First, in contrast to influenza infection, where the cytokine storm is initiated early by the innate immune system, for pneumonia virus of mice (PVM), a model of RSV, the cytokine storm is initiated late in infection by the adaptive immune response: specifically, by virus-specific CD8 T cells via their release of IFN-γ and TNF-α. Blockading these cytokines with neutralizing antibodies blunts the cytokine storm and protects the host. Second, PVM infection is controlled by administration of an S1P1R agonist.

A Systems Engineering Framework for Implementing a Security and Critical Patch Management Process in Diverse Environments (Academic Departments' Workstations)

NASA Astrophysics Data System (ADS)

Mohammadi, Hadi

Use of the Patch Vulnerability Management (PVM) process should be seriously considered for any networked computing system. The PVM process prevents the operating system (OS) and software applications from being attacked due to security vulnerabilities, which lead to system failures and critical data leakage. The purpose of this research is to create and design a Security and Critical Patch Management Process (SCPMP) framework based on Systems Engineering (SE) principles. This framework will assist Information Technology Department Staff (ITDS) to reduce IT operating time and costs and mitigate the risk of security and vulnerability attacks. Further, this study evaluates implementation of the SCPMP in the networked computing systems of an academic environment in order to: 1. Meet patch management requirements by applying SE principles. 2. Reduce the cost of IT operations and PVM cycles. 3. Improve the current PVM methodologies to prevent networked computing systems from becoming the targets of security vulnerability attacks. 4. Embed a Maintenance Optimization Tool (MOT) in the proposed framework. The MOT allows IT managers to make the most practicable choice of methods for deploying and installing released patches and vulnerability remediation. In recent years, there has been a variety of frameworks for security practices in every networked computing system to protect computer workstations from becoming compromised or vulnerable to security attacks, which can expose important information and critical data. I have developed a new mechanism for implementing PVM for maximizing security-vulnerability maintenance, protecting OS and software packages, and minimizing SCPMP cost. To increase computing system security in any diverse environment, particularly in academia, one must apply SCPMP. I propose an optimal maintenance policy that will allow ITDS to measure and estimate the variation of PVM cycles based on their department's requirements. My results demonstrate that MOT optimizes the process of implementing SCPMP in academic workstations.

Dots and dashes: art, virtual reality, and the telegraph

NASA Astrophysics Data System (ADS)

Ruzanka, Silvia; Chang, Ben

2009-02-01

Dots and Dashes is a virtual reality artwork that explores online romance over the telegraph, based on Ella Cheever Thayer's novel Wired Love - a Romance in Dots and Dashes (an Old Story Told in a New Way)1. The uncanny similarities between this story and the world of today's virtual environments provides the springboard for an exploration of a wealth of anxieties and dreams, including the construction of identities in an electronically mediated environment, the shifting boundaries between the natural and machine worlds, and the spiritual dimensions of science and technology. In this paper we examine the parallels between the telegraph networks and our current conceptions of cyberspace, as well as unique social and cultural impacts specific to the telegraph. These include the new opportunities and roles available to women in the telegraph industry and the connection between the telegraph and the Spiritualist movement. We discuss the development of the artwork, its structure and aesthetics, and the technical development of the work.

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.

A parallel adaptive mesh refinement algorithm

NASA Technical Reports Server (NTRS)

Quirk, James J.; Hanebutte, Ulf R.

1993-01-01

Over recent years, Adaptive Mesh Refinement (AMR) algorithms which dynamically match the local resolution of the computational grid to the numerical solution being sought have emerged as powerful tools for solving problems that contain disparate length and time scales. In particular, several workers have demonstrated the effectiveness of employing an adaptive, block-structured hierarchical grid system for simulations of complex shock wave phenomena. Unfortunately, from the parallel algorithm developer's viewpoint, this class of scheme is quite involved; these schemes cannot be distilled down to a small kernel upon which various parallelizing strategies may be tested. However, because of their block-structured nature such schemes are inherently parallel, so all is not lost. In this paper we describe the method by which Quirk's AMR algorithm has been parallelized. This method is built upon just a few simple message passing routines and so it may be implemented across a broad class of MIMD machines. Moreover, the method of parallelization is such that the original serial code is left virtually intact, and so we are left with just a single product to support. The importance of this fact should not be underestimated given the size and complexity of the original algorithm.

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

Debugging Fortran on a shared memory machine

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

Allen, T.R.; Padua, D.A.

1987-01-01

Debugging on a parallel processor is more difficult than debugging on a serial machine because errors in a parallel program may introduce nondeterminism. The approach to parallel debugging presented here attempts to reduce the problem of debugging on a parallel machine to that of debugging on a serial machine by automatically detecting nondeterminism. 20 refs., 6 figs.

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.

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.

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

Generalization of soft phonon modes

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

Rudin, Sven P.

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. In this paper, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system withmore » $N$ atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, $${\\mathrm{PVM}}_{0}$$, represents the $3N$-dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, $${\\mathrm{PVM}}_{0}$$ serves as a generalization of soft phonon modes. At low temperatures, $${\\mathrm{PVM}}_{0}$$ reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case $${\\mathrm{PVM}}_{0}$$ culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, $${\\mathrm{PVM}}_{0}$$ can be equally well calculated on either side of the structural phase transition. Finally, two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the $${\\beta}$$ phase of uranium, the higher-symmetry structure of which stabilizes with temperature.« less

Generalization of soft phonon modes

DOE PAGES

Rudin, Sven P.

2018-04-27

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. In this paper, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system withmore » $N$ atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, $${\\mathrm{PVM}}_{0}$$, represents the $3N$-dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, $${\\mathrm{PVM}}_{0}$$ serves as a generalization of soft phonon modes. At low temperatures, $${\\mathrm{PVM}}_{0}$$ reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case $${\\mathrm{PVM}}_{0}$$ culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, $${\\mathrm{PVM}}_{0}$$ can be equally well calculated on either side of the structural phase transition. Finally, two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the $${\\beta}$$ phase of uranium, the higher-symmetry structure of which stabilizes with temperature.« less

CloudMC: a cloud computing application for Monte Carlo simulation.

PubMed

Miras, H; Jiménez, R; Miras, C; Gomà, C

2013-04-21

This work presents CloudMC, a cloud computing application-developed in Windows Azure®, the platform of the Microsoft® cloud-for the parallelization of Monte Carlo simulations in a dynamic virtual cluster. CloudMC is a web application designed to be independent of the Monte Carlo code in which the simulations are based-the simulations just need to be of the form: input files → executable → output files. To study the performance of CloudMC in Windows Azure®, Monte Carlo simulations with penelope were performed on different instance (virtual machine) sizes, and for different number of instances. The instance size was found to have no effect on the simulation runtime. It was also found that the decrease in time with the number of instances followed Amdahl's law, with a slight deviation due to the increase in the fraction of non-parallelizable time with increasing number of instances. A simulation that would have required 30 h of CPU on a single instance was completed in 48.6 min when executed on 64 instances in parallel (speedup of 37 ×). Furthermore, the use of cloud computing for parallel computing offers some advantages over conventional clusters: high accessibility, scalability and pay per usage. Therefore, it is strongly believed that cloud computing will play an important role in making Monte Carlo dose calculation a reality in future clinical practice.

A Systems Engineering Framework for Implementing a Security and Critical Patch Management Process in Diverse Environments (Academic Departments' Workstations)

ERIC Educational Resources Information Center

Mohammadi, Hadi

2014-01-01

Use of the Patch Vulnerability Management (PVM) process should be seriously considered for any networked computing system. The PVM process prevents the operating system (OS) and software applications from being attacked due to security vulnerabilities, which lead to system failures and critical data leakage. The purpose of this research is to…

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.

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

PubMed

Hess, Berk; Kutzner, Carsten; van der Spoel, David; Lindahl, Erik

2008-03-01

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.

Modeling and analysis of solar distributed generation

NASA Astrophysics Data System (ADS)

Ortiz Rivera, Eduardo Ivan

Recent changes in the global economy are creating a big impact in our daily life. The price of oil is increasing and the number of reserves are less every day. Also, dramatic demographic changes are impacting the viability of the electric infrastructure and ultimately the economic future of the industry. These are some of the reasons that many countries are looking for alternative energy to produce electric energy. The most common form of green energy in our daily life is solar energy. To convert solar energy into electrical energy is required solar panels, dc-dc converters, power control, sensors, and inverters. In this work, a photovoltaic module, PVM, model using the electrical characteristics provided by the manufacturer data sheet is presented for power system applications. Experimental results from testing are showed, verifying the proposed PVM model. Also in this work, three maximum power point tracker, MPPT, algorithms would be presented to obtain the maximum power from a PVM. The first MPPT algorithm is a method based on the Rolle's and Lagrange's Theorems and can provide at least an approximate answer to a family of transcendental functions that cannot be solved using differential calculus. The second MPPT algorithm is based on the approximation of the proposed PVM model using fractional polynomials where the shape, boundary conditions and performance of the proposed PVM model are satisfied. The third MPPT algorithm is based in the determination of the optimal duty cycle for a dc-dc converter and the previous knowledge of the load or load matching conditions. Also, four algorithms to calculate the effective irradiance level and temperature over a photovoltaic module are presented in this work. The main reasons to develop these algorithms are for monitoring climate conditions, the elimination of temperature and solar irradiance sensors, reductions in cost for a photovoltaic inverter system, and development of new algorithms to be integrated with maximum power point tracking algorithms. Finally, several PV power applications will be presented like circuit analysis for a load connected to two different PV arrays, speed control for a do motor connected to a PVM, and a novel single phase photovoltaic inverter system using the Z-source converter.

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

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.

Kinetic and kinematic evaluation of compensatory movements of the head, pelvis and thoracolumbar spine associated with asymmetric weight bearing of the pelvic limbs in trotting dogs.

PubMed

Hicks, D A; Millis, D L

2014-01-01

To determine ground reaction forces, head and pelvis vertical motion (HVM and PVM, respectively), and thoraco-lumbar lateral angular motion (LAM) of the spine using kinematic gait analysis in dogs with mild asymmetric weight-bearing of the pelvic limbs while trotting. Twenty-seven hound-type dogs were fitted with reflective markers placed on the sagittal crest of the skull, the ischiatic tuberosity, and thoracolumbar spine of dogs to track motion while trotting. Kinetic and kinematic data were used to characterize asymmetry between the left and right pelvic limbs, and to describe HVM, PVM and thoraco-lumbar LAM. Maximum and minimum position and total motion values were determined for each measured variable. Dogs with asymmetric weight bearing of the pelvic limbs had greater PVM on the side with a greater peak vertical force (PVF), and greater thoraco-lumbar LAM toward the side with a lower PVF while trotting. No differences in mean HVM were detected, and there were no significant correlations between the magnitude of HVM, PVM and thoraco-lumbar LAM and the degree of asymmetric weight bearing. Dogs with subtle asymmetric weight bearing of a pelvic limb had patterns of body motion that may be useful in identifying subtle lameness in dogs; greater PVM on the side with greater weight bearing and greater thoraco-lumbar LAM toward the side with less weight bearing while trotting. Description of these compensatory movements is valuable when evaluating dogs with subtle weight bearing asymmetry in the pelvic limbs and may improve the sensitivity of lameness detection during subjective clinical lameness examination.

Higher operation temperature quadrant photon detectors of 2-11 μm wavelength radiation with large photosensitive areas

NASA Astrophysics Data System (ADS)

Pawluczyk, J.; Sosna, A.; Wojnowski, D.; Koźniewski, A.; Romanis, M.; Gawron, W.; Piotrowski, J.

2017-10-01

We report on the quadrant photon HgCdTe detectors optimized for 2-11 μm wavelength spectral range and Peltier or no cooling, and photosensitive area of a quad-cell of 1×1 to 4×4 mm. The devices are fabricated as photoconductors or multiple photovoltaic cells connected in series (PVM). The former are characterized by a relatively uniform photosensitive area. The PVM photovoltaic cells are distributed along the wafer surface, comprising a periodical stripe structure with a period of 20 μm. Within each period, there is an insensitive gap/trench < 9 μm wide between stripe mesas. The resulting spatial quantization error prevents positioning of the beam spot of size close to the period, but becomes negligible for the optimal spot size comparable to a quadrant-cell area. The photoconductors produce 1/f noise with about 10 kHz knee frequency, due to bias necessary for their operation. The PVM photodiodes are typically operated at 0 V bias, so they generate no 1/f noise and operation from DC is enabled. At 230 K, upper corner frequency of 16 to 100 MHz is obtained for photoconductor and 60 to 80 MHz for PVM, normalized detectivity D* 6×107 cm×Hz1/2/W to >1.4×108 cm×Hz1/2/W for photoconductor and >1.7×108 cm·Hz1/2/W for PVM, allowing for position control of the radiation beam with submicron accuracy at 16 MHz, 10.6 μm wavelength of pulsed radiation spot of 0.8 mm dia at the close-to-maximal input radiation power density in a range of detector linear operation.

Characterization of the passive and active material parameters of the pubovisceralis muscle using an inverse numerical method.

PubMed

Silva, M E T; Parente, M P L; Brandão, S; Mascarenhas, T; Natal Jorge, R M

2018-04-11

The mechanical characteristics of the female pelvic floor are relevant to understand pelvic floor dysfunctions (PFD), and how they are related with changes in their biomechanical behavior. Urinary incontinence (UI) and pelvic organ prolapse (POP) are the most common pathologies, which can be associated with changes in the mechanical properties of the supportive structures in the female pelvic cavity. PFD have been studied through different methods, from experimental tensile tests using tissues from fresh female cadavers or tissues collected at the time of a transvaginal hysterectomy procedure, or by applying imaging techniques. In this work, an inverse finite element analysis (FEA) was applied to understand the passive and active behavior of the pubovisceralis muscle (PVM) during Valsalva maneuver and muscle active contraction, respectively. Individual numerical models of women without pathology, with stress UI (SUI) and POP were built based on magnetic resonance images, including the PVM and surrounding structures. The passive and active material parameters obtained for a transversely isotropic hyperelastic constitutive model were estimated for the three groups. The values for the material constants were significantly higher for the women with POP when compared with the other two groups. The PVM of women with POP showed the highest stiffness. Additionally, the influence of these parameters was analyzed by evaluating their stress-strain, and force-displacements responses. The force produced by the PVM in women with POP was 47% and 82% higher when compared to women without pathology and with SUI, respectively. The inverse FEA allowed estimating the material parameters of the PVM using input information acquired non-invasively. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Implementation and performance of parallel Prolog interpreter

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

Wei, S.; Kale, L.V.; Balkrishna, R.

1988-01-01

In this paper, the authors discuss the implementation of a parallel Prolog interpreter on different parallel machines. The implementation is based on the REDUCE--OR process model which exploits both AND and OR parallelism in logic programs. It is machine independent as it runs on top of the chare-kernel--a machine-independent parallel programming system. The authors also give the performance of the interpreter running a diverse set of benchmark pargrams on parallel machines including shared memory systems: an Alliant FX/8, Sequent and a MultiMax, and a non-shared memory systems: Intel iPSC/32 hypercube, in addition to its performance on a multiprocessor simulation system.

A high performance scientific cloud computing environment for materials simulations

NASA Astrophysics Data System (ADS)

Jorissen, K.; Vila, F. D.; Rehr, J. J.

2012-09-01

We describe the development of a scientific cloud computing (SCC) platform that offers high performance computation capability. The platform consists of a scientific virtual machine prototype containing a UNIX operating system and several materials science codes, together with essential interface tools (an SCC toolset) that offers functionality comparable to local compute clusters. In particular, our SCC toolset provides automatic creation of virtual clusters for parallel computing, including tools for execution and monitoring performance, as well as efficient I/O utilities that enable seamless connections to and from the cloud. Our SCC platform is optimized for the Amazon Elastic Compute Cloud (EC2). We present benchmarks for prototypical scientific applications and demonstrate performance comparable to local compute clusters. To facilitate code execution and provide user-friendly access, we have also integrated cloud computing capability in a JAVA-based GUI. Our SCC platform may be an alternative to traditional HPC resources for materials science or quantum chemistry applications.

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…

Heterogeneous Distributed Computing for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Sunderam, Vaidy S.

1998-01-01

The research supported under this award focuses on heterogeneous distributed computing for high-performance applications, with particular emphasis on computational aerosciences. The overall goal of this project was to and investigate issues in, and develop solutions to, efficient execution of computational aeroscience codes in heterogeneous concurrent computing environments. In particular, we worked in the context of the PVM[1] system and, subsequent to detailed conversion efforts and performance benchmarking, devising novel techniques to increase the efficacy of heterogeneous networked environments for computational aerosciences. Our work has been based upon the NAS Parallel Benchmark suite, but has also recently expanded in scope to include the NAS I/O benchmarks as specified in the NHT-1 document. In this report we summarize our research accomplishments under the auspices of the grant.

A general purpose subroutine for fast fourier transform on a distributed memory parallel machine

NASA Technical Reports Server (NTRS)

Dubey, A.; Zubair, M.; Grosch, C. E.

1992-01-01

One issue which is central in developing a general purpose Fast Fourier Transform (FFT) subroutine on a distributed memory parallel machine is the data distribution. It is possible that different users would like to use the FFT routine with different data distributions. Thus, there is a need to design FFT schemes on distributed memory parallel machines which can support a variety of data distributions. An FFT implementation on a distributed memory parallel machine which works for a number of data distributions commonly encountered in scientific applications is presented. The problem of rearranging the data after computing the FFT is also addressed. The performance of the implementation on a distributed memory parallel machine Intel iPSC/860 is evaluated.

Simplified Virtualization in a HEP/NP Environment with Condor

NASA Astrophysics Data System (ADS)

Strecker-Kellogg, W.; Caramarcu, C.; Hollowell, C.; Wong, T.

2012-12-01

In this work we will address the development of a simple prototype virtualized worker node cluster, using Scientific Linux 6.x as a base OS, KVM and the libvirt API for virtualization, and the Condor batch software to manage virtual machines. The discussion in this paper provides details on our experience with building, configuring, and deploying the various components from bare metal, including the base OS, creation and distribution of the virtualized OS images and the integration of batch services with the virtual machines. Our focus was on simplicity and interoperability with our existing architecture.

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

Supersonic civil airplane study and design: Performance and sonic boom

NASA Technical Reports Server (NTRS)

Cheung, Samson

1995-01-01

Since aircraft configuration plays an important role in aerodynamic performance and sonic boom shape, the configuration of the next generation supersonic civil transport has to be tailored to meet high aerodynamic performance and low sonic boom requirements. Computational fluid dynamics (CFD) can be used to design airplanes to meet these dual objectives. The work and results in this report are used to support NASA's High Speed Research Program (HSRP). CFD tools and techniques have been developed for general usages of sonic boom propagation study and aerodynamic design. Parallel to the research effort on sonic boom extrapolation, CFD flow solvers have been coupled with a numeric optimization tool to form a design package for aircraft configuration. This CFD optimization package has been applied to configuration design on a low-boom concept and an oblique all-wing concept. A nonlinear unconstrained optimizer for Parallel Virtual Machine has been developed for aerodynamic design and study.

Gilgamesh: A Multithreaded Processor-In-Memory Architecture for Petaflops Computing

NASA Technical Reports Server (NTRS)

Sterling, T. L.; Zima, H. P.

2002-01-01

Processor-in-Memory (PIM) architectures avoid the von Neumann bottleneck in conventional machines by integrating high-density DRAM and CMOS logic on the same chip. Parallel systems based on this new technology are expected to provide higher scalability, adaptability, robustness, fault tolerance and lower power consumption than current MPPs or commodity clusters. In this paper we describe the design of Gilgamesh, a PIM-based massively parallel architecture, and elements of its execution model. Gilgamesh extends existing PIM capabilities by incorporating advanced mechanisms for virtualizing tasks and data and providing adaptive resource management for load balancing and latency tolerance. The Gilgamesh execution model is based on macroservers, a middleware layer which supports object-based runtime management of data and threads allowing explicit and dynamic control of locality and load balancing. The paper concludes with a discussion of related research activities and an outlook to future work.

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.

Memory access in shared virtual memory

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

Berrendorf, R.

1992-01-01

Shared virtual memory (SVM) is a virtual memory layer with a single address space on top of a distributed real memory on parallel computers. We examine the behavior and performance of SVM running a parallel program with medium-grained, loop-level parallelism on top of it. A simulator for the underlying parallel architecture can be used to examine the behavior of SVM more deeply. The influence of several parameters, such as the number of processors, page size, cold or warm start, and restricted page replication, is studied.

Memory access in shared virtual memory

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

Berrendorf, R.

1992-09-01

Shared virtual memory (SVM) is a virtual memory layer with a single address space on top of a distributed real memory on parallel computers. We examine the behavior and performance of SVM running a parallel program with medium-grained, loop-level parallelism on top of it. A simulator for the underlying parallel architecture can be used to examine the behavior of SVM more deeply. The influence of several parameters, such as the number of processors, page size, cold or warm start, and restricted page replication, is studied.

Feasibility of Virtual Machine and Cloud Computing Technologies for High Performance Computing

DTIC Science & Technology

2014-05-01

Hat Enterprise Linux SaaS software as a service VM virtual machine vNUMA virtual non-uniform memory access WRF weather research and forecasting...previously mentioned in Chapter I Section B1 of this paper, which is used to run the weather research and forecasting ( WRF ) model in their experiments...against a VMware virtualization solution of WRF . The experiment consisted of running WRF in a standard configuration between the D-VTM and VMware while

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.

Status and Roadmap of CernVM

NASA Astrophysics Data System (ADS)

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

2015-12-01

Cloud resources nowadays contribute an essential share of resources for computing in high-energy physics. Such resources can be either provided by private or public IaaS clouds (e.g. OpenStack, Amazon EC2, Google Compute Engine) or by volunteers computers (e.g. LHC@Home 2.0). In any case, experiments need to prepare a virtual machine image that provides the execution environment for the physics application at hand. The CernVM virtual machine since version 3 is a minimal and versatile virtual machine image capable of booting different operating systems. The virtual machine image is less than 20 megabyte in size. The actual operating system is delivered on demand by the CernVM File System. CernVM 3 has matured from a prototype to a production environment. It is used, for instance, to run LHC applications in the cloud, to tune event generators using a network of volunteer computers, and as a container for the historic Scientific Linux 5 and Scientific Linux 4 based software environments in the course of long-term data preservation efforts of the ALICE, CMS, and ALEPH experiments. We present experience and lessons learned from the use of CernVM at scale. We also provide an outlook on the upcoming developments. These developments include adding support for Scientific Linux 7, the use of container virtualization, such as provided by Docker, and the streamlining of virtual machine contextualization towards the cloud-init industry standard.

Parallel machine architecture and compiler design facilities

NASA Technical Reports Server (NTRS)

Kuck, David J.; Yew, Pen-Chung; Padua, David; Sameh, Ahmed; Veidenbaum, Alex

1990-01-01

The objective is to provide an integrated simulation environment for studying and evaluating various issues in designing parallel systems, including machine architectures, parallelizing compiler techniques, and parallel algorithms. The status of Delta project (which objective is to provide a facility to allow rapid prototyping of parallelized compilers that can target toward different machine architectures) is summarized. Included are the surveys of the program manipulation tools developed, the environmental software supporting Delta, and the compiler research projects in which Delta has played a role.

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.

Improved approach to quantitative cardiac volumetrics using automatic thresholding and manual trimming: a cardiovascular MRI study.

PubMed

Rayarao, Geetha; Biederman, Robert W W; Williams, Ronald B; Yamrozik, June A; Lombardi, Richard; Doyle, Mark

2018-01-01

To establish the clinical validity and accuracy of automatic thresholding and manual trimming (ATMT) by comparing the method with the conventional contouring method for in vivo cardiac volume measurements. CMR was performed on 40 subjects (30 patients and 10 controls) using steady-state free precession cine sequences with slices oriented in the short-axis and acquired contiguously from base to apex. Left ventricular (LV) volumes, end-diastolic volume, end-systolic volume, and stroke volume (SV) were obtained with ATMT and with the conventional contouring method. Additionally, SV was measured independently using CMR phase velocity mapping (PVM) of the aorta for validation. Three methods of calculating SV were compared by applying Bland-Altman analysis. The Bland-Altman standard deviation of variation (SD) and offset bias for LV SV for the three sets of data were: ATMT-PVM (7.65, [Formula: see text]), ATMT-contours (7.85, [Formula: see text]), and contour-PVM (11.01, 4.97), respectively. Equating the observed range to the error contribution of each approach, the error magnitude of ATMT:PVM:contours was in the ratio 1:2.4:2.5. Use of ATMT for measuring ventricular volumes accommodates trabeculae and papillary structures more intuitively than contemporary contouring methods. This results in lower variation when analyzing cardiac structure and function and consequently improved accuracy in assessing chamber volumes.

Finding Tropical Cyclones on a Cloud Computing Cluster: Using Parallel Virtualization for Large-Scale Climate Simulation Analysis

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

Hasenkamp, Daren; Sim, Alexander; Wehner, Michael

Extensive computing power has been used to tackle issues such as climate changes, fusion energy, and other pressing scientific challenges. These computations produce a tremendous amount of data; however, many of the data analysis programs currently only run a single processor. In this work, we explore the possibility of using the emerging cloud computing platform to parallelize such sequential data analysis tasks. As a proof of concept, we wrap a program for analyzing trends of tropical cyclones in a set of virtual machines (VMs). This approach allows the user to keep their familiar data analysis environment in the VMs, whilemore » we provide the coordination and data transfer services to ensure the necessary input and output are directed to the desired locations. This work extensively exercises the networking capability of the cloud computing systems and has revealed a number of weaknesses in the current cloud system software. In our tests, we are able to scale the parallel data analysis job to a modest number of VMs and achieve a speedup that is comparable to running the same analysis task using MPI. However, compared to MPI based parallelization, the cloud-based approach has a number of advantages. The cloud-based approach is more flexible because the VMs can capture arbitrary software dependencies without requiring the user to rewrite their programs. The cloud-based approach is also more resilient to failure; as long as a single VM is running, it can make progress while as soon as one MPI node fails the whole analysis job fails. In short, this initial work demonstrates that a cloud computing system is a viable platform for distributed scientific data analyses traditionally conducted on dedicated supercomputing systems.« less

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

Taming Wild Horses: The Need for Virtual Time-based Scheduling of VMs in Network Simulations

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

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

2012-01-01

The next generation of scalable network simulators employ virtual machines (VMs) to act as high-fidelity models of traffic producer/consumer nodes in simulated networks. However, network simulations could be inaccurate if VMs are not scheduled according to virtual time, especially when many VMs are hosted per simulator core in a multi-core simulator environment. Since VMs are by default free-running, on the outset, it is not clear if, and to what extent, their untamed execution affects the results in simulated scenarios. Here, we provide the first quantitative basis for establishing the need for generalized virtual time scheduling of VMs in network simulators,more » based on an actual prototyped implementations. To exercise breadth, our system is tested with multiple disparate applications: (a) a set of message passing parallel programs, (b) a computer worm propagation phenomenon, and (c) a mobile ad-hoc wireless network simulation. We define and use error metrics and benchmarks in scaled tests to empirically report the poor match of traditional, fairness-based VM scheduling to VM-based network simulation, and also clearly show the better performance of our simulation-specific scheduler, with up to 64 VMs hosted on a 12-core simulator node.« less

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.

Start-up capabilities of photovoltaic module for the International Space Station

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

Hajela, G.; Hague, L.

1997-12-31

The International Space Station (ISS) uses four photovoltaic modules (PVMs) to supply electric power for the US On-Orbit Segment (USOS). The ISS is assembled on orbit over a period of about 5 years and over 40 stages. PVMs are launched and integrated with the ISS at different times during the ISS assembly. During early stages, the electric power is provided by the integrated truss segment (ITS) P6; subsequently, ITS P4, S4, and S6 are launched. PVMs are launched into space in the National Space Transportation System (NSTS) cargo bay. Each PVM consists of two independent power channels. The NSTS docksmore » with the ISS, the PVM is removed from the cargo bay and installed on the ISS. At this stage the PVM is in stowed configuration and its batteries are in fully discharged state. The start-up consists of initialization and checkout of all hardware, deployment of SAW and photovoltaic radiator (PVR), thermal conditioning batteries, and charging batteries; not necessarily in the same order for all PVMs. PVMs are designed to be capable of on-orbit start-up, within a specified time period, when external power is applied to a specified electrical interface. This paper describes the essential steps required for PVM start-up and how these operations are performed for various PVMs. The integrated operations scenarios (IOS) prepared by the NASA, Johnson Space Center, details specific procedures and timelines for start-up of each PVM. The paper describes how dormant batteries are brought to their normal operating temperature range and then charged to 100% state of charge (SOC). Total time required to complete start-up is computed and compared to the IOS timelines. External power required during start-up is computed and compared to the requirements and/or available power on ISS. Also described is how these start-up procedures can be adopted for restart of PVMs when required.« less

Performance Analysis of Ivshmem for High-Performance Computing in Virtual Machines

NASA Astrophysics Data System (ADS)

Ivanovic, Pavle; Richter, Harald

2018-01-01

High-Performance computing (HPC) is rarely accomplished via virtual machines (VMs). In this paper, we present a remake of ivshmem which can change this. Ivshmem was a shared memory (SHM) between virtual machines on the same server, with SHM-access synchronization included, until about 5 years ago when newer versions of Linux and its virtualization library libvirt evolved. We restored that SHM-access synchronization feature because it is indispensable for HPC and made ivshmem runnable with contemporary versions of Linux, libvirt, KVM, QEMU and especially MPICH, which is an implementation of MPI - the standard HPC communication library. Additionally, MPICH was transparently modified by us to get ivshmem included, resulting in a three to ten times performance improvement compared to TCP/IP. Furthermore, we have transparently replaced MPI_PUT, a single-side MPICH communication mechanism, by an own MPI_PUT wrapper. As a result, our ivshmem even surpasses non-virtualized SHM data transfers for block lengths greater than 512 KBytes, showing the benefits of virtualization. All improvements were possible without using SR-IOV.

Preconditioned implicit solvers for the Navier-Stokes equations on distributed-memory machines

NASA Technical Reports Server (NTRS)

Ajmani, Kumud; Liou, Meng-Sing; Dyson, Rodger W.

1994-01-01

The GMRES method is parallelized, and combined with local preconditioning to construct an implicit parallel solver to obtain steady-state solutions for the Navier-Stokes equations of fluid flow on distributed-memory machines. The new implicit parallel solver is designed to preserve the convergence rate of the equivalent 'serial' solver. A static domain-decomposition is used to partition the computational domain amongst the available processing nodes of the parallel machine. The SPMD (Single-Program Multiple-Data) programming model is combined with message-passing tools to develop the parallel code on a 32-node Intel Hypercube and a 512-node Intel Delta machine. The implicit parallel solver is validated for internal and external flow problems, and is found to compare identically with flow solutions obtained on a Cray Y-MP/8. A peak computational speed of 2300 MFlops/sec has been achieved on 512 nodes of the Intel Delta machine,k for a problem size of 1024 K equations (256 K grid points).

THE MODIFYING EFFECTS OF CERTAIN SUBSTANCES OF BACTERIAL ORIGIN ON THE COURSE OF INFECTION WITH PNEUMONIA VIRUS OF MICE (PVM)

PubMed Central

Horsfall, Frank L.; McCarty, Maclyn

1947-01-01

Evidence is presented which indicates that certain polysaccharide preparations derived from various bacterial species, as well as similar materials not of bacterial origin, are capable of lessening the severity of infection with pneumonia virus of mice (PVM) and inhibiting multiplication of the virus in mouse lungs infected with this agent. It seems probable that modification with respect to the virus is mediated by a substance which may be polysaccharide in nature. PMID:19871640

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.

Data communications in a parallel active messaging interface of a parallel computer

DOEpatents

Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

2014-09-02

Eager send data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints that specify a client, a context, and a task, including receiving an eager send data communications instruction with transfer data disposed in a send buffer characterized by a read/write send buffer memory address in a read/write virtual address space of the origin endpoint; determining for the send buffer a read-only send buffer memory address in a read-only virtual address space, the read-only virtual address space shared by both the origin endpoint and the target endpoint, with all frames of physical memory mapped to pages of virtual memory in the read-only virtual address space; and communicating by the origin endpoint to the target endpoint an eager send message header that includes the read-only send buffer memory address.

Data communications in a parallel active messaging interface of a parallel computer

DOEpatents

Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

2014-09-16

Eager send data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints that specify a client, a context, and a task, including receiving an eager send data communications instruction with transfer data disposed in a send buffer characterized by a read/write send buffer memory address in a read/write virtual address space of the origin endpoint; determining for the send buffer a read-only send buffer memory address in a read-only virtual address space, the read-only virtual address space shared by both the origin endpoint and the target endpoint, with all frames of physical memory mapped to pages of virtual memory in the read-only virtual address space; and communicating by the origin endpoint to the target endpoint an eager send message header that includes the read-only send buffer memory address.

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

Reflections on the ethics of participatory visual methods to engage communities in global health research

PubMed Central

Black, Gillian F.; Davies, Alun; Iskander, Dalia; Chambers, Mary

2018-01-01

ABSTRACT There is a growing body of literature describing conceptual frameworks for working with participatory visual methods (PVM). Through a global health lens, this paper examines some key themes within these frameworks. We reflect on our experiences of working with with an array of PVM to engage community members in Vietnam, Kenya, the Philippines and South Africa in biomedical research and public health. The participants that we have engaged in these processes live in under-resourced areas with high prevalence of communicable and non-communicable diseases. Our paper describes some of the challenges that we have encountered while using PVM to foster knowledge exchange, build relationships and facilitate change among individuals and families, community members, health workers, biomedical scientists and researchers. We consider multiple ethical situations that have arisen through our work and discuss the ways in which we have navigated and negotiated them. We offer our reflections and learning from facilitating these processes and in doing so we add novel contributions to ethical framework concepts. PMID:29434532

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.

Running accuracy analysis of a 3-RRR parallel kinematic machine considering the deformations of the links

NASA Astrophysics Data System (ADS)

Wang, Liping; Jiang, Yao; Li, Tiemin

2014-09-01

Parallel kinematic machines have drawn considerable attention and have been widely used in some special fields. However, high precision is still one of the challenges when they are used for advanced machine tools. One of the main reasons is that the kinematic chains of parallel kinematic machines are composed of elongated links that can easily suffer deformations, especially at high speeds and under heavy loads. A 3-RRR parallel kinematic machine is taken as a study object for investigating its accuracy with the consideration of the deformations of its links during the motion process. Based on the dynamic model constructed by the Newton-Euler method, all the inertia loads and constraint forces of the links are computed and their deformations are derived. Then the kinematic errors of the machine are derived with the consideration of the deformations of the links. Through further derivation, the accuracy of the machine is given in a simple explicit expression, which will be helpful to increase the calculating speed. The accuracy of this machine when following a selected circle path is simulated. The influences of magnitude of the maximum acceleration and external loads on the running accuracy of the machine are investigated. The results show that the external loads will deteriorate the accuracy of the machine tremendously when their direction coincides with the direction of the worst stiffness of the machine. The proposed method provides a solution for predicting the running accuracy of the parallel kinematic machines and can also be used in their design optimization as well as selection of suitable running parameters.

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.

A distributed monitoring system for photovoltaic arrays based on a two-level wireless sensor network

NASA Astrophysics Data System (ADS)

Su, F. P.; Chen, Z. C.; Zhou, H. F.; Wu, L. J.; Lin, P. J.; Cheng, S. Y.; Li, Y. F.

2017-11-01

In this paper, a distributed on-line monitoring system based on a two-level wireless sensor network (WSN) is proposed for real time status monitoring of photovoltaic (PV) arrays to support the fine management and maintenance of PV power plants. The system includes the sensing nodes installed on PV modules (PVM), sensing and routing nodes installed on combiner boxes of PV sub-arrays (PVA), a sink node and a data management centre (DMC) running on a host computer. The first level WSN is implemented by the low-cost wireless transceiver nRF24L01, and it is used to achieve single hop communication between the PVM nodes and their corresponding PVA nodes. The second level WSN is realized by the CC2530 based ZigBee network for multi-hop communication among PVA nodes and the sink node. The PVM nodes are used to monitor the PVM working voltage and backplane temperature, and they send the acquired data to their PVA node via the nRF24L01 based first level WSN. The PVA nodes are used to monitor the array voltage, PV string current and environment irradiance, and they send the acquired and received data to the DMC via the ZigBee based second level WSN. The DMC is designed using the MATLAB GUIDE and MySQL database. Laboratory experiment results show that the system can effectively acquire, display, store and manage the operating and environment parameters of PVA in real time.

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

The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.

PubMed

Schulte, Kathrin; Pawlowski, Nikolaus; Faelber, Katja; Fröhlich, Chris; Howard, Jonathan; Daumke, Oliver

2016-03-02

The immunity-related GTPases (IRGs) constitute a powerful cell-autonomous resistance system against several intracellular pathogens. Irga6 is a dynamin-like protein that oligomerizes at the parasitophorous vacuolar membrane (PVM) of Toxoplasma gondii leading to its vesiculation. Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. Contrary to the previous model, the structure shows that the GTPase domains dimerize in a parallel fashion. The nucleotides in the center of the interface participate in dimerization by forming symmetric contacts with each other and with the switch I region of the opposing Irga6 molecule. The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. Further dimerization contacts involve switch II, the G4 helix and the trans stabilizing loop. The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. This study contributes important insights into the assembly and catalytic mechanisms of IRG proteins as prerequisite to understand their anti-microbial action.

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…

The Tera Multithreaded Architecture and Unstructured Meshes

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.; Mavriplis, Dimitri J.

1998-01-01

The Tera Multithreaded Architecture (MTA) is a new parallel supercomputer currently being installed at San Diego Supercomputing Center (SDSC). This machine has an architecture quite different from contemporary parallel machines. The computational processor is a custom design and the machine uses hardware to support very fine grained multithreading. The main memory is shared, hardware randomized and flat. These features make the machine highly suited to the execution of unstructured mesh problems, which are difficult to parallelize on other architectures. We report the results of a study carried out during July-August 1998 to evaluate the execution of EUL3D, a code that solves the Euler equations on an unstructured mesh, on the 2 processor Tera MTA at SDSC. Our investigation shows that parallelization of an unstructured code is extremely easy on the Tera. We were able to get an existing parallel code (designed for a shared memory machine), running on the Tera by changing only the compiler directives. Furthermore, a serial version of this code was compiled to run in parallel on the Tera by judicious use of directives to invoke the "full/empty" tag bits of the machine to obtain synchronization. This version achieves 212 and 406 Mflop/s on one and two processors respectively, and requires no attention to partitioning or placement of data issues that would be of paramount importance in other parallel architectures.

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.

Empirical Analysis and Refinement of Expert System Knowledge Bases

DTIC Science & Technology

1990-03-31

the number of hidden units and the error rates is listed in Figure 6. 3.3. Cancer Data A data qet for eva!ukting th.- Frognosis of breast cancer ...Alternative Rule Induction Methods A data set for evaluating the prognosis of breast cancer recurrence was analyzed by Michalski’s AQI5 rule induction program...AQ15 7 2 32% PVM 2 1 23% Figure 6-3: Comparative Summa-y for AQI5 and PVM on Breast Cancer Data 6.2.2. Alternative Decision Tree Induction Methods

Development and Application of ANN Model for Worker Assignment into Virtual Cells of Large Sized Configurations

NASA Astrophysics Data System (ADS)

Murali, R. V.; Puri, A. B.; Fathi, Khalid

2010-10-01

This paper presents an extended version of study already undertaken on development of an artificial neural networks (ANNs) model for assigning workforce into virtual cells under virtual cellular manufacturing systems (VCMS) environments. Previously, the same authors have introduced this concept and applied it to virtual cells of two-cell configuration and the results demonstrated that ANNs could be a worth applying tool for carrying out workforce assignments. In this attempt, three-cell configurations problems are considered for worker assignment task. Virtual cells are formed under dual resource constraint (DRC) context in which the number of available workers is less than the total number of machines available. Since worker assignment tasks are quite non-linear and highly dynamic in nature under varying inputs & conditions and, in parallel, ANNs have the ability to model complex relationships between inputs and outputs and find similar patterns effectively, an attempt was earlier made to employ ANNs into the above task. In this paper, the multilayered perceptron with feed forward (MLP-FF) neural network model has been reused for worker assignment tasks of three-cell configurations under DRC context and its performance at different time periods has been analyzed. The previously proposed worker assignment model has been reconfigured and cell formation solutions available for three-cell configuration in the literature are used in combination to generate datasets for training ANNs framework. Finally, results of the study have been presented and discussed.

Reverse time migration: A seismic processing application on the connection machine

NASA Technical Reports Server (NTRS)

Fiebrich, Rolf-Dieter

1987-01-01

The implementation of a reverse time migration algorithm on the Connection Machine, a massively parallel computer is described. Essential architectural features of this machine as well as programming concepts are presented. The data structures and parallel operations for the implementation of the reverse time migration algorithm are described. The algorithm matches the Connection Machine architecture closely and executes almost at the peak performance of this machine.

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.

Can Multiple "Spatial" Virtual Timelines Convey the Relatedness of Chronological Knowledge across Parallel Domains?

ERIC Educational Resources Information Center

Korallo, Liliya; Foreman, Nigel; Boyd-Davis, Stephen; Moar, Magnus; Coulson, Mark

2012-01-01

Single linear virtual timelines have been used effectively with undergraduates and primary school children to convey the chronological ordering of historical items, improving on PowerPoint and paper/textual displays. In the present study, a virtual environment (VE) consisting of three parallel related timelines (world history and the histories of…

ATLAS TDAQ System Administration: evolution and re-design

NASA Astrophysics Data System (ADS)

Ballestrero, S.; Bogdanchikov, A.; Brasolin, F.; Contescu, C.; Dubrov, S.; Fazio, D.; Korol, A.; Lee, C. J.; Scannicchio, D. A.; Twomey, M. S.

2015-12-01

The ATLAS Trigger and Data Acquisition system is responsible for the online processing of live data, streaming from the ATLAS experiment at the Large Hadron Collider at CERN. The online farm is composed of ∼3000 servers, processing the data read out from ∼100 million detector channels through multiple trigger levels. During the two years of the first Long Shutdown there has been a tremendous amount of work done by the ATLAS Trigger and Data Acquisition System Administrators, implementing numerous new software applications, upgrading the OS and the hardware, changing some design philosophies and exploiting the High- Level Trigger farm with different purposes. The OS version has been upgraded to SLC6; for the largest part of the farm, which is composed of net booted nodes, this required a completely new design of the net booting system. In parallel, the migration to Puppet of the Configuration Management systems has been completed for both net booted and local booted hosts; the Post-Boot Scripts system and Quattor have been consequently dismissed. Virtual Machine usage has been investigated and tested and many of the core servers are now running on Virtual Machines. Virtualisation has also been used to adapt the High-Level Trigger farm as a batch system, which has been used for running Monte Carlo production jobs that are mostly CPU and not I/O bound. Finally, monitoring the health and the status of ∼3000 machines in the experimental area is obviously of the utmost importance, so the obsolete Nagios v2 has been replaced with Icinga, complemented by Ganglia as a performance data provider. This paper serves for reporting of the actions taken by the Systems Administrators in order to improve and produce a system capable of performing for the next three years of ATLAS data taking.

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

Volunteered Cloud Computing for Disaster Management

NASA Astrophysics Data System (ADS)

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

2014-12-01

Disaster management relies increasingly on interpreting earth observations and running numerical models; which require significant computing capacity - usually on short notice and at irregular intervals. Peak computing demand during event detection, hazard assessment, or incident response may exceed agency budgets; however some of it can be met through volunteered computing, which distributes subtasks to participating computers via the Internet. This approach has enabled large projects in mathematics, basic science, and climate research to harness the slack computing capacity of thousands of desktop computers. This capacity is likely to diminish as desktops give way to battery-powered mobile devices (laptops, smartphones, tablets) in the consumer market; but as cloud computing becomes commonplace, it may offer significant slack capacity -- if its users are given an easy, trustworthy mechanism for participating. Such a "volunteered cloud computing" mechanism would also offer several advantages over traditional volunteered computing: tasks distributed within a cloud have fewer bandwidth limitations; granular billing mechanisms allow small slices of "interstitial" computing at no marginal cost; and virtual storage volumes allow in-depth, reversible machine reconfiguration. Volunteered cloud computing is especially suitable for "embarrassingly parallel" tasks, including ones requiring large data volumes: examples in disaster management include near-real-time image interpretation, pattern / trend detection, or large model ensembles. In the context of a major disaster, we estimate that cloud users (if suitably informed) might volunteer hundreds to thousands of CPU cores across a large provider such as Amazon Web Services. To explore this potential, we are building a volunteered cloud computing platform and targeting it to a disaster management context. Using a lightweight, fault-tolerant network protocol, this platform helps cloud users join parallel computing projects; automates reconfiguration of their virtual machines; ensures accountability for donated computing; and optimizes the use of "interstitial" computing. Initial applications include fire detection from multispectral satellite imagery and flood risk mapping through hydrological simulations.

Line-drawing algorithms for parallel machines

NASA Technical Reports Server (NTRS)

Pang, Alex T.

1990-01-01

The fact that conventional line-drawing algorithms, when applied directly on parallel machines, can lead to very inefficient codes is addressed. It is suggested that instead of modifying an existing algorithm for a parallel machine, a more efficient implementation can be produced by going back to the invariants in the definition. Popular line-drawing algorithms are compared with two alternatives; distance to a line (a point is on the line if sufficiently close to it) and intersection with a line (a point on the line if an intersection point). For massively parallel single-instruction-multiple-data (SIMD) machines (with thousands of processors and up), the alternatives provide viable line-drawing algorithms. Because of the pixel-per-processor mapping, their performance is independent of the line length and orientation.

Immunobiotic Lactobacillus administered post-exposure averts the lethal sequelae of respiratory virus infection.

PubMed

Percopo, Caroline M; Rice, Tyler A; Brenner, Todd A; Dyer, Kimberly D; Luo, Janice L; Kanakabandi, Kishore; Sturdevant, Daniel E; Porcella, Stephen F; Domachowske, Joseph B; Keicher, Jesse D; Rosenberg, Helene F

2015-09-01

We reported previously that priming of the respiratory tract with immunobiotic Lactobacillus prior to virus challenge protects mice against subsequent lethal infection with pneumonia virus of mice (PVM). We present here the results of gene microarray which document differential expression of proinflammatory mediators in response to PVM infection alone and those suppressed in response to Lactobacillus plantarum. We also demonstrate for the first time that intranasal inoculation with live or heat-inactivated L. plantarum or Lactobacillus reuteri promotes full survival from PVM infection when administered within 24h after virus challenge. Survival in response to L. plantarum administered after virus challenge is associated with suppression of proinflammatory cytokines, limited virus recovery, and diminished neutrophil recruitment to lung tissue and airways. Utilizing this post-virus challenge protocol, we found that protective responses elicited by L. plantarum at the respiratory tract were distinct from those at the gastrointestinal mucosa, as mice devoid of the anti-inflammatory cytokine, interleukin (IL)-10, exhibit survival and inflammatory responses that are indistinguishable from those of their wild-type counterparts. Finally, although L. plantarum interacts specifically with pattern recognition receptors TLR2 and NOD2, the respective gene-deleted mice were fully protected against lethal PVM infection by L. plantarum, as are mice devoid of type I interferon receptors. Taken together, L. plantarum is a versatile and flexible agent that is capable of averting the lethal sequelae of severe respiratory infection both prior to and post-virus challenge via complex and potentially redundant mechanisms. Published by Elsevier B.V.

Crocodilian perivitelline membrane-bound sperm detection.

PubMed

Augustine, Lauren

2017-05-01

Advanced reproductive technologies (ART's) are often employed with various taxa to enhance captive breeding programs and maintain genetic diversity. Perivitelline membrane-bound (PVM-bound) sperm detection has previously been demonstrated in avian and chelonian species as a useful technique for breeding management. In the absence of embryotic development within an egg, this technique can detect the presence of sperm trapped on the oocyte membrane confirming breeding, male reproductive status, and pair compatibility. PVM-bound sperm were successfully detected in three clutches of Cuban crocodile (Crocodylus rhombifer) eggs at the Smithsonian's National Zoological Park (NZP) for the first time in any crocodilian species. PVM-bound sperm were detected in fresh and incubated C. rhombifer eggs, as well as eggs that were developing (banded) and those that were not (not banded). The results of this study showed significant differences in average sperm densities per egg between clutches (p = 0.001). Additionally, there was not a significant difference within clutches between eggs that banded and those that did not band (Clutch A, p = 0.505; Clutch B, p = 0.665; Clutch C, p = 0.266). The results of this study demonstrate the necessity to microscopically examine eggs that do not develop (do not band), to determine if sperm is present, which can help animal managers problem solve reproductive shortcomings. PVM-bound sperm detection could be a useful technique in assessing crocodilian breeding programs, as well as have potential uses in studies assessing sperm storage, artificial insemination, and artificial incubation. This article is a U.S. Government work and is in the public domain in the USA.

Torins are potent antimalarials that block replenishment of Plasmodium liver stage parasitophorous vacuole membrane proteins

PubMed Central

Hanson, Kirsten K.; Ressurreição, Ana S.; Buchholz, Kathrin; Prudêncio, Miguel; Herman-Ornelas, Jonathan D.; Rebelo, Maria; Beatty, Wandy L.; Wirth, Dyann F.; Hänscheid, Thomas; Moreira, Rui; Marti, Matthias; Mota, Maria M.

2013-01-01

Residence within a customized vacuole is a highly successful strategy used by diverse intracellular microorganisms. The parasitophorous vacuole membrane (PVM) is the critical interface between Plasmodium parasites and their possibly hostile, yet ultimately sustaining, host cell environment. We show that torins, developed as ATP-competitive mammalian target of rapamycin (mTOR) kinase inhibitors, are fast-acting antiplasmodial compounds that unexpectedly target the parasite directly, blocking the dynamic trafficking of the Plasmodium proteins exported protein 1 (EXP1) and upregulated in sporozoites 4 (UIS4) to the liver stage PVM and leading to efficient parasite elimination by the hepatocyte. Torin2 has single-digit, or lower, nanomolar potency in both liver and blood stages of infection in vitro and is likewise effective against both stages in vivo, with a single oral dose sufficient to clear liver stage infection. Parasite elimination and perturbed trafficking of liver stage PVM-resident proteins are both specific aspects of torin-mediated Plasmodium liver stage inhibition, indicating that torins have a distinct mode of action compared with currently used antimalarials. PMID:23836641

The Automated Instrumentation and Monitoring System (AIMS) reference manual

NASA Technical Reports Server (NTRS)

Yan, Jerry; Hontalas, Philip; Listgarten, Sherry

1993-01-01

Whether a researcher is designing the 'next parallel programming paradigm,' another 'scalable multiprocessor' or investigating resource allocation algorithms for multiprocessors, a facility that enables parallel program execution to be captured and displayed is invaluable. Careful analysis of execution traces can help computer designers and software architects to uncover system behavior and to take advantage of specific application characteristics and hardware features. A software tool kit that facilitates performance evaluation of parallel applications on multiprocessors is described. The Automated Instrumentation and Monitoring System (AIMS) has four major software components: a source code instrumentor which automatically inserts active event recorders into the program's source code before compilation; a run time performance-monitoring library, which collects performance data; a trace file animation and analysis tool kit which reconstructs program execution from the trace file; and a trace post-processor which compensate for data collection overhead. Besides being used as prototype for developing new techniques for instrumenting, monitoring, and visualizing parallel program execution, AIMS is also being incorporated into the run-time environments of various hardware test beds to evaluate their impact on user productivity. Currently, AIMS instrumentors accept FORTRAN and C parallel programs written for Intel's NX operating system on the iPSC family of multi computers. A run-time performance-monitoring library for the iPSC/860 is included in this release. We plan to release monitors for other platforms (such as PVM and TMC's CM-5) in the near future. Performance data collected can be graphically displayed on workstations (e.g. Sun Sparc and SGI) supporting X-Windows (in particular, Xl IR5, Motif 1.1.3).

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

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.

Proceedings: Sisal `93

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

Feo, J.T.

1993-10-01

This report contain papers on: Programmability and performance issues; The case of an iterative partial differential equation solver; Implementing the kernal of the Australian Region Weather Prediction Model in Sisal; Even and quarter-even prime length symmetric FFTs and their Sisal Implementations; Top-down thread generation for Sisal; Overlapping communications and computations on NUMA architechtures; Compiling technique based on dataflow analysis for funtional programming language Valid; Copy elimination for true multidimensional arrays in Sisal 2.0; Increasing parallelism for an optimization that reduces copying in IF2 graphs; Caching in on Sisal; Cache performance of Sisal Vs. FORTRAN; FFT algorithms on a shared-memory multiprocessor;more » A parallel implementation of nonnumeric search problems in Sisal; Computer vision algorithms in Sisal; Compilation of Sisal for a high-performance data driven vector processor; Sisal on distributed memory machines; A virtual shared addressing system for distributed memory Sisal; Developing a high-performance FFT algorithm in Sisal for a vector supercomputer; Implementation issues for IF2 on a static data-flow architechture; and Systematic control of parallelism in array-based data-flow computation. Selected papers have been indexed separately for inclusion in the Energy Science and Technology Database.« less

minimega

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

David Fritz, John Floren

2013-08-27

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

Parallel Computational Fluid Dynamics: Current Status and Future Requirements

NASA Technical Reports Server (NTRS)

Simon, Horst D.; VanDalsem, William R.; Dagum, Leonardo; Kutler, Paul (Technical Monitor)

1994-01-01

One or the key objectives of the Applied Research Branch in the Numerical Aerodynamic Simulation (NAS) Systems Division at NASA Allies Research Center is the accelerated introduction of highly parallel machines into a full operational environment. In this report we discuss the performance results obtained from the implementation of some computational fluid dynamics (CFD) applications on the Connection Machine CM-2 and the Intel iPSC/860. We summarize some of the experiences made so far with the parallel testbed machines at the NAS Applied Research Branch. Then we discuss the long term computational requirements for accomplishing some of the grand challenge problems in computational aerosciences. We argue that only massively parallel machines will be able to meet these grand challenge requirements, and we outline the computer science and algorithm research challenges ahead.

The " Swarm of Ants vs. Herd of Elephants" Debated Revisited: Performance Measurements of PVM-Overflow Across a Wide Spectrum of Architectures

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Jespersen, Dennis; Buning, Peter; Bailey, David (Technical Monitor)

1996-01-01

The Gorden Bell Prizes given out at Supercomputing every year includes at least two catergories: performance (highest GFLOP count) and price-performance (GFLOP/million $$) for real applications. In the past five years, the winners of the price-performance categories all came from networks of work-stations. This reflects three important facts: 1. supercomputers are still too expensive for the masses; 2. achieving high performance for real applications takes real work; and, most importantly; 3. it is possible to obtain acceptable performance for certain real applications on network of work stations. With the continued advance of network technology as well as increased performance of "desktop" workstation, the "Swarm of Ants vs. Herd of Elephants" debate, which began with vector multiprocessors (VPPs) against SIMD type multiprocessors (e.g. CM2), is now recast as VPPs against Symetric Multiprocessors (SMPs, e.g. SGI PowerChallenge). This paper reports on performance studies we performed solving a large scale (2-million grid pt.s) CFD problem involving a Boeing 747 based on a parallel version of OVERFLOW that utilizes message passing on PVM. A performance monitoring tool developed under NASA HPCC, called AIMS, was used to instrument and analyze the the performance data thus obtained. We plan to compare its performance data obtained across a wide spectrum of architectures including: the Cray C90, IBM/SP2, SGI/Power Challenge Cluster, to a group of workstations connected over a simple network. The metrics of comparison includes speed-up, price-performance, throughput, and turn-around time. We also plan to present a plan of attack for various issues that will make the execution of Grand Challenge Applications across the Global Information Infrastructure a reality.

[Parallel virtual reality visualization of extreme large medical datasets].

PubMed

Tang, Min

2010-04-01

On the basis of a brief description of grid computing, the essence and critical techniques of parallel visualization of extreme large medical datasets are discussed in connection with Intranet and common-configuration computers of hospitals. In this paper are introduced several kernel techniques, including the hardware structure, software framework, load balance and virtual reality visualization. The Maximum Intensity Projection algorithm is realized in parallel using common PC cluster. In virtual reality world, three-dimensional models can be rotated, zoomed, translated and cut interactively and conveniently through the control panel built on virtual reality modeling language (VRML). Experimental results demonstrate that this method provides promising and real-time results for playing the role in of a good assistant in making clinical diagnosis.

Quantum information, cognition, and music.

PubMed

Dalla Chiara, Maria L; Giuntini, Roberto; Leporini, Roberto; Negri, Eleonora; Sergioli, Giuseppe

2015-01-01

Parallelism represents an essential aspect of human mind/brain activities. One can recognize some common features between psychological parallelism and the characteristic parallel structures that arise in quantum theory and in quantum computation. The article is devoted to a discussion of the following questions: a comparison between classical probabilistic Turing machines and quantum Turing machines.possible applications of the quantum computational semantics to cognitive problems.parallelism in music.

Quantum information, cognition, and music

PubMed Central

Dalla Chiara, Maria L.; Giuntini, Roberto; Leporini, Roberto; Negri, Eleonora; Sergioli, Giuseppe

2015-01-01

Parallelism represents an essential aspect of human mind/brain activities. One can recognize some common features between psychological parallelism and the characteristic parallel structures that arise in quantum theory and in quantum computation. The article is devoted to a discussion of the following questions: a comparison between classical probabilistic Turing machines and quantum Turing machines.possible applications of the quantum computational semantics to cognitive problems.parallelism in music. PMID:26539139

The Language Grid: supporting intercultural collaboration

NASA Astrophysics Data System (ADS)

Ishida, T.

2018-03-01

A variety of language resources already exist online. Unfortunately, since many language resources have usage restrictions, it is virtually impossible for each user to negotiate with every language resource provider when combining several resources to achieve the intended purpose. To increase the accessibility and usability of language resources (dictionaries, parallel texts, part-of-speech taggers, machine translators, etc.), we proposed the Language Grid [1]; it wraps existing language resources as atomic services and enables users to create new services by combining the atomic services, and reduces the negotiation costs related to intellectual property rights [4]. Our slogan is “language services from language resources.” We believe that modularization with recombination is the key to creating a full range of customized language environments for various user communities.

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.

Reconditioning of Batteries on the International Space Station

NASA Technical Reports Server (NTRS)

Hajela, Gyan; Cohen, Fred; Dalton, Penni

2004-01-01

Primary source of electric power for the International Space Station (ISS) is the photovoltaic module (PVM). At assembly complete stage, the ISS will be served by 4 PVMs. Each PVM contains two independent power channels such that one failure will result in loss of only one power channel. During early stages of assembly, the ISS is served by only one PVM designated as P6. Solar arrays are used to convert solar flux into electrical power. Nickel hydrogen batteries are used to store electrical power for use during periods when the solar input is not adequate to support channel loads. Batteries are operated per established procedures that ensure that they are maintained within specified temperature limits, charge current is controlled to conform to a specified charge profile, and battery voltages are maintained within specified limits. Both power channels on the PVM P6 have been operating flawlessly since December 2000 with 100 percent power availability. All components, including batteries, are monitored regularly to ensure that they are operating within specified limits and to trend their wear out and age effects. The paper briefly describes the battery trend data. Batteries have started to show some effects of aging and a battery reconditioning procedure is being evaluated at this time. Reconditioning is expected to reduce cell voltage divergence and provide data that can be used to update the state of charge (SOC) computation in the software to account for battery age. During reconditioning, each battery, one at a time, will be discharged per a specified procedure and then returned to a full state of charge. The paper describes the reconditioning procedure and the expected benefits. The reconditioning procedures have been thoroughly coordinated by all affected technical teams and approved by all required boards. The reconditioning is tentatively scheduled for September 2004.

Lactobacillus priming of the respiratory tract: Heterologous immunity and protection against lethal pneumovirus infection.

PubMed

Garcia-Crespo, Katia E; Chan, Calvin C; Gabryszewski, Stanislaw J; Percopo, Caroline M; Rigaux, Peter; Dyer, Kimberly D; Domachowske, Joseph B; Rosenberg, Helene F

2013-03-01

We showed previously that wild-type mice primed via intranasal inoculation with live or heat-inactivated Lactobacillus species were fully (100%) protected against the lethal sequelae of infection with the virulent pathogen, pneumonia virus of mice (PVM), a response that is associated with diminished expression of proinflammatory cytokines and diminished virus recovery. We show here that 40% of the mice primed with live Lactobacillus survived when PVM challenge was delayed for 5months. This robust and sustained resistance to PVM infection resulting from prior interaction with an otherwise unrelated microbe is a profound example of heterologous immunity. We undertook the present study in order to understand the nature and unique features of this response. We found that intranasal inoculation with L. reuteri elicited rapid, transient neutrophil recruitment in association with proinflammatory mediators (CXCL1, CCL3, CCL2, CXCL10, TNF-alpha and IL-17A) but not Th1 cytokines. IFNγ does not contribute to survival promoted by Lactobacillus-priming. Live L. reuteri detected in lung tissue underwent rapid clearance, and was undetectable at 24h after inoculation. In contrast, L. reuteri peptidoglycan (PGN) and L. reuteri genomic DNA (gDNA) were detected at 24 and 48h after inoculation, respectively. In contrast to live bacteria, intranasal inoculation with isolated L. reuteri gDNA elicited no neutrophil recruitment, had minimal impact on virus recovery and virus-associated production of CCL3, and provided no protection against the negative sequelae of virus infection. Isolated PGN elicited neutrophil recruitment and proinflammatory cytokines but did not promote sustained survival in response to subsequent PVM infection. Overall, further evaluation of the responses leading to Lactobacillus-mediated heterologous immunity may provide insight into novel antiviral preventive modalities. Published by Elsevier B.V.

Lactobacillus priming of the respiratory tract: heterologous immunity and protection against lethal pneumovirus infection

PubMed Central

Garcia-Crespo, Katia E.; Chan, Calvin C.; Gabryszewski, Stanislaw J.; Percopo, Caroline M.; Rigaux, Peter; Dyer, Kimberly D.; Domachowske, Joseph B.; Rosenberg, Helene F.

2013-01-01

We showed previously that wild-type mice primed via intranasal inoculation with live or heat-inactivated Lactobacillus species were fully (100%) protected against the lethal sequelae of infection with the virulent pathogen, pneumonia virus of mice (PVM), a response that is associated with diminished expression of proinflammatory cytokines and diminished virus recovery. We show here that 40% of the mice primed with live Lactobacillus survived when PVM challenge was delayed for 5 months. This robust and sustained resistance to PVM infection resulting from prior interaction with an otherwise unrelated microbe is a profound example of heterologous immunity. We undertook the present study in order to understand the nature and unique features of this response. We found that intranasal inoculation with L. reuteri elicited rapid, transient neutrophil recruitment in association with proinflammatory mediators (CXCL1, CCL3, CCL2, CXCL10, TNF-alpha and IL-17A) but not Th1 cytokines. IFNγ does not contribute to survival promoted by Lactobacillus-priming. Live L. reuteri detected in lung tissue underwent rapid clearance, and was undetectable at 24 hrs after inoculation. In contrast, L. reuteri peptidoglycan (PGN) and L. reuteri genomic DNA (gDNA) were detected at 24 and 48 hours after inoculation, respectively. In contrast to live bacteria, intranasal inoculation with isolated L. reuteri gDNA elicited no neutrophil recruitment, had minimal impact on virus recovery and virus-associated production of CCL3, and provided no protection against the negative sequelae of virus infection. Isolated PGN elicited neutrophil recruitment and proinflammatory cytokines but did not promote sustained survival in response to subsequent PVM infection. Overall, further evaluation of the responses leading to Lactobacillus-mediated heterologous immunity may provide insight into novel antiviral preventive modalities. PMID:23274789

Effect of a triclosan/PVM/MA copolymer/fluoride dentifrice on volatile sulfur compounds in vitro.

PubMed

Pilch, S; Williams, M I; Cummins, D

2005-01-01

The objective of the investigation was to document the in vitro efficacy of a triclosan/PVM/MA copolymer/fluoride (TCF) dentifrice against the formation of volatile sulfur compounds (VSC) as well as the growth of H2S-producing bacteria. Clinical studies using organoleptic judges, gas chromatography, or a portable sulfide monitor have generally been employed in the assessment of treatments for the control of oral malodor. However, these studies are not appropriate for screening purposes because of the expense and time required. An in vitro method was developed for the purpose of screening new compounds, agents or formulations for their ability to control VSC formation and for determining bio-equivalence of efficacy when implementing changes in existing formulations. The method combines basic microbiological methods, dynamic flow cell techniques and head space analysis. The in vitro VSC method was validated by comparing the efficacy of two dentifrices containing TCF with a control fluoride dentifrice as the TCF products have been clinically proven to control oral malodor. In the validation studies, the TCF-containing dentifrices were significantly better (P < 0.05) than the control dentifrice in inhibiting VSC formation and reducing H(2)S-producing bacteria. For example, when compared with baseline, the TCF dentifrices reduced VSC formation between 42 and 49% compared with the control dentifrice which reduced VSC formation 3%. There was no significant difference (P > 0.05) between the two TCF dentifrice formulations. Using an in vitro breath VSC model, it has been demonstrated that two variants of a dentifrice containing triclosan, PVM/MA copolymer and fluoride have efficacy that is significantly better than a control fluoridated dentifrice and that there is no significant difference between the triclosan/PVM/MA copolymer/fluoride dentifrice variants.

A Virtual Astronomical Research Machine in No Time (VARMiNT)

NASA Astrophysics Data System (ADS)

Beaver, John

2012-05-01

We present early results of using virtual machine software to help make astronomical research computing accessible to a wider range of individuals. Our Virtual Astronomical Research Machine in No Time (VARMiNT) is an Ubuntu Linux virtual machine with free, open-source software already installed and configured (and in many cases documented). The purpose of VARMiNT is to provide a ready-to-go astronomical research computing environment that can be freely shared between researchers, or between amateur and professional, teacher and student, etc., and to circumvent the often-difficult task of configuring a suitable computing environment from scratch. Thus we hope that VARMiNT will make it easier for individuals to engage in research computing even if they have no ready access to the facilities of a research institution. We describe our current version of VARMiNT and some of the ways it is being used at the University of Wisconsin - Fox Valley, a two-year teaching campus of the University of Wisconsin System, as a means to enhance student independent study research projects and to facilitate collaborations with researchers at other locations. We also outline some future plans and prospects.

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.

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

The paradigm compiler: Mapping a functional language for the connection machine

NASA Technical Reports Server (NTRS)

Dennis, Jack B.

1989-01-01

The Paradigm Compiler implements a new approach to compiling programs written in high level languages for execution on highly parallel computers. The general approach is to identify the principal data structures constructed by the program and to map these structures onto the processing elements of the target machine. The mapping is chosen to maximize performance as determined through compile time global analysis of the source program. The source language is Sisal, a functional language designed for scientific computations, and the target language is Paris, the published low level interface to the Connection Machine. The data structures considered are multidimensional arrays whose dimensions are known at compile time. Computations that build such arrays usually offer opportunities for highly parallel execution; they are data parallel. The Connection Machine is an attractive target for these computations, and the parallel for construct of the Sisal language is a convenient high level notation for data parallel algorithms. The principles and organization of the Paradigm Compiler are discussed.

An M-step preconditioned conjugate gradient method for parallel computation

NASA Technical Reports Server (NTRS)

Adams, L.

1983-01-01

This paper describes a preconditioned conjugate gradient method that can be effectively implemented on both vector machines and parallel arrays to solve sparse symmetric and positive definite systems of linear equations. The implementation on the CYBER 203/205 and on the Finite Element Machine is discussed and results obtained using the method on these machines are given.

Virtual Oscillator Controls | Grid Modernization | NREL

Science.gov Websites

Virtual Oscillator Controls Virtual Oscillator Controls NREL is developing virtual oscillator Santa-Barbara, and SunPower. Publications Synthesizing Virtual Oscillators To Control Islanded Inverters Synchronization of Parallel Single-Phase Inverters Using Virtual Oscillator Control, IEEE Transactions on Power

Approximation algorithms for scheduling unrelated parallel machines with release dates

NASA Astrophysics Data System (ADS)

Avdeenko, T. V.; Mesentsev, Y. A.; Estraykh, I. V.

2017-01-01

In this paper we propose approaches to optimal scheduling of unrelated parallel machines with release dates. One approach is based on the scheme of dynamic programming modified with adaptive narrowing of search domain ensuring its computational effectiveness. We discussed complexity of the exact schedules synthesis and compared it with approximate, close to optimal, solutions. Also we explain how the algorithm works for the example of two unrelated parallel machines and five jobs with release dates. Performance results that show the efficiency of the proposed approach have been given.

Heterogeneous voter models

NASA Astrophysics Data System (ADS)

Masuda, Naoki; Gibert, N.; Redner, S.

2010-07-01

We introduce the heterogeneous voter model (HVM), in which each agent has its own intrinsic rate to change state, reflective of the heterogeneity of real people, and the partisan voter model (PVM), in which each agent has an innate and fixed preference for one of two possible opinion states. For the HVM, the time until consensus is reached is much longer than in the classic voter model. For the PVM in the mean-field limit, a population evolves to a preference-based state, where each agent tends to be aligned with its internal preference. For finite populations, discrete fluctuations ultimately lead to consensus being reached in a time that scales exponentially with population size.

Monitoring of antisolvent crystallization of sodium scutellarein by combined FBRM-PVM-NIR.

PubMed

Liu, Xuesong; Sun, Di; Wang, Feng; Wu, Yongjiang; Chen, Yong; Wang, Longhu

2011-06-01

Antisolvent crystallization can be used as an alternative to cooling or evaporation for the separation and purification of solid product in the pharmaceutical industry. To improve the process understanding of antisolvent crystallization, the use of in-line tools is vital. In this study, the process analytical technology (PAT) tools including focused beam reflectance measurement (FBRM), particle video microscope (PVM), and near-infrared spectroscopy (NIRS) were utilized to monitor antisolvent crystallization of sodium scutellarein. FBRM was used to monitor chord count and chord length distribution of sodium scutellarein particles in the crystallizer, and PVM, as an in-line video camera, provided pictures imaging particle shape and dimension. In addition, a quantitative model of PLS was established by in-line NIRS to detect the concentration of sodium scutellarein in the solvent and good calibration statistics were obtained (r(2) = 0.976) with the residual predictive deviation value of 11.3. The discussion over sensitivities, strengths, and weaknesses of the PAT tools may be helpful in selection of suitable PAT techniques. These in-line techniques eliminate the need for sample preparation and offer a time-saving approach to understand and monitor antisolvent crystallization process. Copyright © 2011 Wiley-Liss, Inc.

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

Impact of equalizing currents on losses and torque ripples in electrical machines with fractional slot concentrated windings

NASA Astrophysics Data System (ADS)

Toporkov, D. M.; Vialcev, G. B.

2017-10-01

The implementation of parallel branches is a commonly used manufacturing method of the realizing of fractional slot concentrated windings in electrical machines. If the rotor eccentricity is enabled in a machine with parallel branches, the equalizing currents can arise. The simulation approach of the equalizing currents in parallel branches of an electrical machine winding based on magnetic field calculation by using Finite Elements Method is discussed in the paper. The high accuracy of the model is provided by the dynamic improvement of the inductances in the differential equation system describing a machine. The pre-computed table flux linkage functions are used for that. The functions are the dependences of the flux linkage of parallel branches on the branches currents and rotor position angle. The functions permit to calculate self-inductances and mutual inductances by partial derivative. The calculated results obtained for the electric machine specimen are presented. The results received show that the adverse combination of design solutions and the rotor eccentricity leads to a high value of the equalizing currents and windings heating. Additional torque ripples also arise. The additional ripples harmonic content is not similar to the cogging torque or ripples caused by the rotor eccentricity.

GPURFSCREEN: a GPU based virtual screening tool using random forest classifier.

PubMed

Jayaraj, P B; Ajay, Mathias K; Nufail, M; Gopakumar, G; Jaleel, U C A

2016-01-01

In-silico methods are an integral part of modern drug discovery paradigm. Virtual screening, an in-silico method, is used to refine data models and reduce the chemical space on which wet lab experiments need to be performed. Virtual screening of a ligand data model requires large scale computations, making it a highly time consuming task. This process can be speeded up by implementing parallelized algorithms on a Graphical Processing Unit (GPU). Random Forest is a robust classification algorithm that can be employed in the virtual screening. A ligand based virtual screening tool (GPURFSCREEN) that uses random forests on GPU systems has been proposed and evaluated in this paper. This tool produces optimized results at a lower execution time for large bioassay data sets. The quality of results produced by our tool on GPU is same as that on a regular serial environment. Considering the magnitude of data to be screened, the parallelized virtual screening has a significantly lower running time at high throughput. The proposed parallel tool outperforms its serial counterpart by successfully screening billions of molecules in training and prediction phases.

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.

RTNN: The New Parallel Machine in Zaragoza

NASA Astrophysics Data System (ADS)

Sijs, A. J. V. D.

I report on the development of RTNN, a parallel computer designed as a 4^4 hypercube of 256 T9000 transputer nodes, each with 8 MB memory. The peak performance of the machine is expected to be 2.5 Gflops.

Six Years of Parallel Computing at NAS (1987 - 1993): What Have we Learned?

NASA Technical Reports Server (NTRS)

Simon, Horst D.; Cooper, D. M. (Technical Monitor)

1994-01-01

In the fall of 1987 the age of parallelism at NAS began with the installation of a 32K processor CM-2 from Thinking Machines. In 1987 this was described as an "experiment" in parallel processing. In the six years since, NAS acquired a series of parallel machines, and conducted an active research and development effort focused on the use of highly parallel machines for applications in the computational aerosciences. In this time period parallel processing for scientific applications evolved from a fringe research topic into the one of main activities at NAS. In this presentation I will review the history of parallel computing at NAS in the context of the major progress, which has been made in the field in general. I will attempt to summarize the lessons we have learned so far, and the contributions NAS has made to the state of the art. Based on these insights I will comment on the current state of parallel computing (including the HPCC effort) and try to predict some trends for the next six years.

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.

NGScloud: RNA-seq analysis of non-model species using cloud computing.

PubMed

Mora-Márquez, Fernando; Vázquez-Poletti, José Luis; López de Heredia, Unai

2018-05-03

RNA-seq analysis usually requires large computing infrastructures. NGScloud is a bioinformatic system developed to analyze RNA-seq data using the cloud computing services of Amazon that permit the access to ad hoc computing infrastructure scaled according to the complexity of the experiment, so its costs and times can be optimized. The application provides a user-friendly front-end to operate Amazon's hardware resources, and to control a workflow of RNA-seq analysis oriented to non-model species, incorporating the cluster concept, which allows parallel runs of common RNA-seq analysis programs in several virtual machines for faster analysis. NGScloud is freely available at https://github.com/GGFHF/NGScloud/. A manual detailing installation and how-to-use instructions is available with the distribution. unai.lopezdeheredia@upm.es.

The performance of low-cost commercial cloud computing as an alternative in computational chemistry.

PubMed

Thackston, Russell; Fortenberry, Ryan C

2015-05-05

The growth of commercial cloud computing (CCC) as a viable means of computational infrastructure is largely unexplored for the purposes of quantum chemistry. In this work, the PSI4 suite of computational chemistry programs is installed on five different types of Amazon World Services CCC platforms. The performance for a set of electronically excited state single-point energies is compared between these CCC platforms and typical, "in-house" physical machines. Further considerations are made for the number of cores or virtual CPUs (vCPUs, for the CCC platforms), but no considerations are made for full parallelization of the program (even though parallelization of the BLAS library is implemented), complete high-performance computing cluster utilization, or steal time. Even with this most pessimistic view of the computations, CCC resources are shown to be more cost effective for significant numbers of typical quantum chemistry computations. Large numbers of large computations are still best utilized by more traditional means, but smaller-scale research may be more effectively undertaken through CCC services. © 2015 Wiley Periodicals, Inc.

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.

Portable programming on parallel/networked computers using the Application Portable Parallel Library (APPL)

NASA Technical Reports Server (NTRS)

Quealy, Angela; Cole, Gary L.; Blech, Richard A.

1993-01-01

The Application Portable Parallel Library (APPL) is a subroutine-based library of communication primitives that is callable from applications written in FORTRAN or C. APPL provides a consistent programmer interface to a variety of distributed and shared-memory multiprocessor MIMD machines. The objective of APPL is to minimize the effort required to move parallel applications from one machine to another, or to a network of homogeneous machines. APPL encompasses many of the message-passing primitives that are currently available on commercial multiprocessor systems. This paper describes APPL (version 2.3.1) and its usage, reports the status of the APPL project, and indicates possible directions for the future. Several applications using APPL are discussed, as well as performance and overhead results.

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 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.

Robust Airborne Networking Extensions (RANGE)

DTIC Science & Technology

2008-02-01

IMUNES [13] project, which provides an entire network stack virtualization and topology control inside a single FreeBSD machine . The emulated topology...Multicast versus broadcast in a manet.” in ADHOC-NOW, 2004, pp. 14–27. [9] J. Mukherjee, R. Atwood , “ Rendezvous point relocation in protocol independent...computer with an Ethernet connection, or a Linux virtual machine on some other (e.g., Windows) operating system, should work. 2.1 Patching the source code

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.

Concurrent computation of attribute filters on shared memory parallel machines.

PubMed

Wilkinson, Michael H F; Gao, Hui; Hesselink, Wim H; Jonker, Jan-Eppo; Meijster, Arnold

2008-10-01

Morphological attribute filters have not previously been parallelized, mainly because they are both global and non-separable. We propose a parallel algorithm that achieves efficient parallelism for a large class of attribute filters, including attribute openings, closings, thinnings and thickenings, based on Salembier's Max-Trees and Min-trees. The image or volume is first partitioned in multiple slices. We then compute the Max-trees of each slice using any sequential Max-Tree algorithm. Subsequently, the Max-trees of the slices can be merged to obtain the Max-tree of the image. A C-implementation yielded good speed-ups on both a 16-processor MIPS 14000 parallel machine, and a dual-core Opteron-based machine. It is shown that the speed-up of the parallel algorithm is a direct measure of the gain with respect to the sequential algorithm used. Furthermore, the concurrent algorithm shows a speed gain of up to 72 percent on a single-core processor, due to reduced cache thrashing.

A real-time MPEG software decoder using a portable message-passing library

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

Kwong, Man Kam; Tang, P.T. Peter; Lin, Biquan

1995-12-31

We present a real-time MPEG software decoder that uses message-passing libraries such as MPL, p4 and MPI. The parallel MPEG decoder currently runs on the IBM SP system but can be easil ported to other parallel machines. This paper discusses our parallel MPEG decoding algorithm as well as the parallel programming environment under which it uses. Several technical issues are discussed, including balancing of decoding speed, memory limitation, 1/0 capacities, and optimization of MPEG decoding components. This project shows that a real-time portable software MPEG decoder is feasible in a general-purpose parallel machine.

Solution of a tridiagonal system of equations on the finite element machine

NASA Technical Reports Server (NTRS)

Bostic, S. W.

1984-01-01

Two parallel algorithms for the solution of tridiagonal systems of equations were implemented on the Finite Element Machine. The Accelerated Parallel Gauss method, an iterative method, and the Buneman algorithm, a direct method, are discussed and execution statistics are presented.

Scheduling Jobs with Variable Job Processing Times on Unrelated Parallel Machines

PubMed Central

Zhang, Guang-Qian; Wang, Jian-Jun; Liu, Ya-Jing

2014-01-01

m unrelated parallel machines scheduling problems with variable job processing times are considered, where the processing time of a job is a function of its position in a sequence, its starting time, and its resource allocation. The objective is to determine the optimal resource allocation and the optimal schedule to minimize a total cost function that dependents on the total completion (waiting) time, the total machine load, the total absolute differences in completion (waiting) times on all machines, and total resource cost. If the number of machines is a given constant number, we propose a polynomial time algorithm to solve the problem. PMID:24982933

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.

Implementation of a parallel unstructured Euler solver on the CM-5

NASA Technical Reports Server (NTRS)

Morano, Eric; Mavriplis, D. J.

1995-01-01

An efficient unstructured 3D Euler solver is parallelized on a Thinking Machine Corporation Connection Machine 5, distributed memory computer with vectoring capability. In this paper, the single instruction multiple data (SIMD) strategy is employed through the use of the CM Fortran language and the CMSSL scientific library. The performance of the CMSSL mesh partitioner is evaluated and the overall efficiency of the parallel flow solver is discussed.

Performance of a plasma fluid code on the Intel parallel computers

NASA Technical Reports Server (NTRS)

Lynch, V. E.; Carreras, B. A.; Drake, J. B.; Leboeuf, J. N.; Liewer, P.

1992-01-01

One approach to improving the real-time efficiency of plasma turbulence calculations is to use a parallel algorithm. A parallel algorithm for plasma turbulence calculations was tested on the Intel iPSC/860 hypercube and the Touchtone Delta machine. Using the 128 processors of the Intel iPSC/860 hypercube, a factor of 5 improvement over a single-processor CRAY-2 is obtained. For the Touchtone Delta machine, the corresponding improvement factor is 16. For plasma edge turbulence calculations, an extrapolation of the present results to the Intel (sigma) machine gives an improvement factor close to 64 over the single-processor CRAY-2.

On the suitability of the connection machine for direct particle simulation

NASA Technical Reports Server (NTRS)

Dagum, Leonard

1990-01-01

The algorithmic structure was examined of the vectorizable Stanford particle simulation (SPS) method and the structure is reformulated in data parallel form. Some of the SPS algorithms can be directly translated to data parallel, but several of the vectorizable algorithms have no direct data parallel equivalent. This requires the development of new, strictly data parallel algorithms. In particular, a new sorting algorithm is developed to identify collision candidates in the simulation and a master/slave algorithm is developed to minimize communication cost in large table look up. Validation of the method is undertaken through test calculations for thermal relaxation of a gas, shock wave profiles, and shock reflection from a stationary wall. A qualitative measure is provided of the performance of the Connection Machine for direct particle simulation. The massively parallel architecture of the Connection Machine is found quite suitable for this type of calculation. However, there are difficulties in taking full advantage of this architecture because of lack of a broad based tradition of data parallel programming. An important outcome of this work has been new data parallel algorithms specifically of use for direct particle simulation but which also expand the data parallel diction.

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…

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.

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

Characterization of robotics parallel algorithms and mapping onto a reconfigurable SIMD machine

NASA Technical Reports Server (NTRS)

Lee, C. S. G.; Lin, C. T.

1989-01-01

The kinematics, dynamics, Jacobian, and their corresponding inverse computations are six essential problems in the control of robot manipulators. Efficient parallel algorithms for these computations are discussed and analyzed. Their characteristics are identified and a scheme on the mapping of these algorithms to a reconfigurable parallel architecture is presented. Based on the characteristics including type of parallelism, degree of parallelism, uniformity of the operations, fundamental operations, data dependencies, and communication requirement, it is shown that most of the algorithms for robotic computations possess highly regular properties and some common structures, especially the linear recursive structure. Moreover, they are well-suited to be implemented on a single-instruction-stream multiple-data-stream (SIMD) computer with reconfigurable interconnection network. The model of a reconfigurable dual network SIMD machine with internal direct feedback is introduced. A systematic procedure internal direct feedback is introduced. A systematic procedure to map these computations to the proposed machine is presented. A new scheduling problem for SIMD machines is investigated and a heuristic algorithm, called neighborhood scheduling, that reorders the processing sequence of subtasks to reduce the communication time is described. Mapping results of a benchmark algorithm are illustrated and discussed.

NAS Parallel Benchmark. Results 11-96: Performance Comparison of HPF and MPI Based NAS Parallel Benchmarks. 1.0

NASA Technical Reports Server (NTRS)

Saini, Subash; Bailey, David; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

High Performance Fortran (HPF), the high-level language for parallel Fortran programming, is based on Fortran 90. HALF was defined by an informal standards committee known as the High Performance Fortran Forum (HPFF) in 1993, and modeled on TMC's CM Fortran language. Several HPF features have since been incorporated into the draft ANSI/ISO Fortran 95, the next formal revision of the Fortran standard. HPF allows users to write a single parallel program that can execute on a serial machine, a shared-memory parallel machine, or a distributed-memory parallel machine. HPF eliminates the complex, error-prone task of explicitly specifying how, where, and when to pass messages between processors on distributed-memory machines, or when to synchronize processors on shared-memory machines. HPF is designed in a way that allows the programmer to code an application at a high level, and then selectively optimize portions of the code by dropping into message-passing or calling tuned library routines as 'extrinsics'. Compilers supporting High Performance Fortran features first appeared in late 1994 and early 1995 from Applied Parallel Research (APR) Digital Equipment Corporation, and The Portland Group (PGI). IBM introduced an HPF compiler for the IBM RS/6000 SP/2 in April of 1996. Over the past two years, these implementations have shown steady improvement in terms of both features and performance. The performance of various hardware/ programming model (HPF and MPI (message passing interface)) combinations will be compared, based on latest NAS (NASA Advanced Supercomputing) Parallel Benchmark (NPB) results, thus providing a cross-machine and cross-model comparison. Specifically, HPF based NPB results will be compared with MPI based NPB results to provide perspective on performance currently obtainable using HPF versus MPI or versus hand-tuned implementations such as those supplied by the hardware vendors. In addition we would also present NPB (Version 1.0) performance results for the following systems: DEC Alpha Server 8400 5/440, Fujitsu VPP Series (VX, VPP300, and VPP700), HP/Convex Exemplar SPP2000, IBM RS/6000 SP P2SC node (120 MHz) NEC SX-4/32, SGI/CRAY T3E, SGI Origin2000.

The FORCE - A highly portable parallel programming language

NASA Technical Reports Server (NTRS)

Jordan, Harry F.; Benten, Muhammad S.; Alaghband, Gita; Jakob, Ruediger

1989-01-01

This paper explains why the FORCE parallel programming language is easily portable among six different shared-memory multiprocessors, and how a two-level macro preprocessor makes it possible to hide low-level machine dependencies and to build machine-independent high-level constructs on top of them. These FORCE constructs make it possible to write portable parallel programs largely independent of the number of processes and the specific shared-memory multiprocessor executing them.

The FORCE: A highly portable parallel programming language

NASA Technical Reports Server (NTRS)

Jordan, Harry F.; Benten, Muhammad S.; Alaghband, Gita; Jakob, Ruediger

1989-01-01

Here, it is explained why the FORCE parallel programming language is easily portable among six different shared-memory microprocessors, and how a two-level macro preprocessor makes it possible to hide low level machine dependencies and to build machine-independent high level constructs on top of them. These FORCE constructs make it possible to write portable parallel programs largely independent of the number of processes and the specific shared memory multiprocessor executing them.

Identification of Interesting Objects in Large Spectral Surveys Using Highly Parallelized Machine Learning

NASA Astrophysics Data System (ADS)

Škoda, Petr; Palička, Andrej; Koza, Jakub; Shakurova, Ksenia

2017-06-01

The current archives of LAMOST multi-object spectrograph contain millions of fully reduced spectra, from which the automatic pipelines have produced catalogues of many parameters of individual objects, including their approximate spectral classification. This is, however, mostly based on the global shape of the whole spectrum and on integral properties of spectra in given bandpasses, namely presence and equivalent width of prominent spectral lines, while for identification of some interesting object types (e.g. Be stars or quasars) the detailed shape of only a few lines is crucial. Here the machine learning is bringing a new methodology capable of improving the reliability of classification of such objects even in boundary cases. We present results of Spark-based semi-supervised machine learning of LAMOST spectra attempting to automatically identify the single and double-peak emission of Hα line typical for Be and B[e] stars. The labelled sample was obtained from archive of 2m Perek telescope at Ondřejov observatory. A simple physical model of spectrograph resolution was used in domain adaptation to LAMOST training domain. The resulting list of candidates contains dozens of Be stars (some are likely yet unknown), but also a bunch of interesting objects resembling spectra of quasars and even blazars, as well as many instrumental artefacts. The verification of a nature of interesting candidates benefited considerably from cross-matching and visualisation in the Virtual Observatory environment.

Dockres: a computer program that analyzes the output of virtual screening of small molecules

PubMed Central

2010-01-01

Background This paper describes a computer program named Dockres that is designed to analyze and summarize results of virtual screening of small molecules. The program is supplemented with utilities that support the screening process. Foremost among these utilities are scripts that run the virtual screening of a chemical library on a large number of processors in parallel. Methods Dockres and some of its supporting utilities are written Fortran-77; other utilities are written as C-shell scripts. They support the parallel execution of the screening. The current implementation of the program handles virtual screening with Autodock-3 and Autodock-4, but can be extended to work with the output of other programs. Results Analysis of virtual screening by Dockres led to both active and selective lead compounds. Conclusions Analysis of virtual screening was facilitated and enhanced by Dockres in both the authors' laboratories as well as laboratories elsewhere. PMID:20205801

Study on Parallel 2-DOF Rotation Machanism in Radar

NASA Astrophysics Data System (ADS)

Jiang, Ming; Hu, Xuelong; Liu, Lei; Yu, Yunfei

The spherical parallel machine has become the world's academic and industrial focus of the field in recent years due to its simple and economical manufacture as well as its structural compactness especially suitable for areas where space gesture changes. This paper dwells upon its present research and development home and abroad. The newer machine (RGRR-II) can rotate around the axis z within 360° and the axis y1 from -90° to +90°. It has the advantages such as less moving parts (only 3 parts), larger ratio of work space to machine size, zero mechanic coupling, no singularity. Constructing rotation machine with spherical parallel 2-DOF rotation join (RGRR-II) may realize semispherical movement with zero dead point and extent the range. Control card (PA8000NT Series CNC) is installed in the computer. The card can run the corresponding software which realizes radar movement control. The machine meets the need of radars in plane and satellite which require larger detection range, lighter weight and compacter structure.

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

Li, Ang; Song, Shuaiwen; Brugel, Eric

To continuously comply with Moore’s Law, modern parallel machines become increasingly complex. Effectively tuning application performance for these machines therefore becomes a daunting task. Moreover, identifying performance bottlenecks at application and architecture level, as well as evaluating various optimization strategies, are becoming extremely difficult when the entanglement of numerous correlated factors is being presented. To tackle these challenges, we present a visual analytical model named “X”. It is intuitive and sufficiently flexible to track all the typical features of a parallel 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

GATECloud.net: a platform for large-scale, open-source text processing on the cloud.

PubMed

Tablan, Valentin; Roberts, Ian; Cunningham, Hamish; Bontcheva, Kalina

2013-01-28

Cloud computing is increasingly being regarded as a key enabler of the 'democratization of science', because on-demand, highly scalable cloud computing facilities enable researchers anywhere to carry out data-intensive experiments. In the context of natural language processing (NLP), algorithms tend to be complex, which makes their parallelization and deployment on cloud platforms a non-trivial task. This study presents a new, unique, cloud-based platform for large-scale NLP research--GATECloud. net. It enables researchers to carry out data-intensive NLP experiments by harnessing the vast, on-demand compute power of the Amazon cloud. Important infrastructural issues are dealt with by the platform, completely transparently for the researcher: load balancing, efficient data upload and storage, deployment on the virtual machines, security and fault tolerance. We also include a cost-benefit analysis and usage evaluation.

minimega v. 3.0

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

Crussell, Jonathan; Erickson, Jeremy; Fritz, David

minimega is an emulytics platform for creating testbeds of networked devices. The platoform consists of easily deployable tools to facilitate bringing up large networks of virtual machines including Windows, Linux, and Android. minimega allows experiments to be brought up quickly with almost no configuration. minimega also includes tools for simple cluster, management, as well as tools for creating Linux-based virtual machines. This release of minimega includes new emulated sensors for Android devices to improve the fidelity of testbeds that include mobile devices. Emulated sensors include GPS and

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.

An integrated runtime and compile-time approach for parallelizing structured and block structured applications

NASA Technical Reports Server (NTRS)

Agrawal, Gagan; Sussman, Alan; Saltz, Joel

1993-01-01

Scientific and engineering applications often involve structured meshes. These meshes may be nested (for multigrid codes) and/or irregularly coupled (called multiblock or irregularly coupled regular mesh problems). A combined runtime and compile-time approach for parallelizing these applications on distributed memory parallel machines in an efficient and machine-independent fashion was described. A runtime library which can be used to port these applications on distributed memory machines was designed and implemented. The library is currently implemented on several different systems. To further ease the task of application programmers, methods were developed for integrating this runtime library with compilers for HPK-like parallel programming languages. How this runtime library was integrated with the Fortran 90D compiler being developed at Syracuse University is discussed. Experimental results to demonstrate the efficacy of our approach are presented. A multiblock Navier-Stokes solver template and a multigrid code were experimented with. Our experimental results show that our primitives have low runtime communication overheads. Further, the compiler parallelized codes perform within 20 percent of the code parallelized by manually inserting calls to the runtime library.

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.

Establishing a group of endpoints in a parallel computer

DOEpatents

Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.; Xue, Hanhong

2016-02-02

A parallel computer executes a number of tasks, each task includes a number of endpoints and the endpoints are configured to support collective operations. In such a parallel computer, establishing a group of endpoints receiving a user specification of a set of endpoints included in a global collection of endpoints, where the user specification defines the set in accordance with a predefined virtual representation of the endpoints, the predefined virtual representation is a data structure setting forth an organization of tasks and endpoints included in the global collection of endpoints and the user specification defines the set of endpoints without a user specification of a particular endpoint; and defining a group of endpoints in dependence upon the predefined virtual representation of the endpoints and the user specification.

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.

Automated Solar Module Assembly Line

NASA Technical Reports Server (NTRS)

Bycer, M.

1979-01-01

The gathering of information that led to the design approach of the machine, and a summary of the findings in the areas of study along with a description of each station of the machine are discussed. The machine is a cell stringing and string applique machine which is flexible in design, capable of handling a variety of cells and assembling strings of cells which can then be placed in a matrix up to 4 ft x 2 ft. in series or parallel arrangement. The target machine cycle is to be 5 seconds per cell. This machine is primarily adapted to 100 MM round cells with one or two tabs between cells. It places finished strings of up to twelve cells in a matrix of up to six such strings arranged in series or in parallel.

Simulation Exploration through Immersive Parallel Planes

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

Brunhart-Lupo, Nicholas J; Bush, Brian W; Gruchalla, Kenny M

We present a visualization-driven simulation system that tightly couples systems dynamics simulations with an immersive virtual environment to allow analysts to rapidly develop and test hypotheses in a high-dimensional parameter space. To accomplish this, we generalize the two-dimensional parallel-coordinates statistical graphic as an immersive 'parallel-planes' visualization for multivariate time series emitted by simulations running in parallel with the visualization. In contrast to traditional parallel coordinate's mapping the multivariate dimensions onto coordinate axes represented by a series of parallel lines, we map pairs of the multivariate dimensions onto a series of parallel rectangles. As in the case of parallel coordinates, eachmore » individual observation in the dataset is mapped to a polyline whose vertices coincide with its coordinate values. Regions of the rectangles can be 'brushed' to highlight and select observations of interest: a 'slider' control allows the user to filter the observations by their time coordinate. In an immersive virtual environment, users interact with the parallel planes using a joystick that can select regions on the planes, manipulate selection, and filter time. The brushing and selection actions are used to both explore existing data as well as to launch additional simulations corresponding to the visually selected portions of the input parameter space. As soon as the new simulations complete, their resulting observations are displayed in the virtual environment. This tight feedback loop between simulation and immersive analytics accelerates users' realization of insights about the simulation and its output.« less

Simulation Exploration through Immersive Parallel Planes: Preprint

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

Brunhart-Lupo, Nicholas; Bush, Brian W.; Gruchalla, Kenny

We present a visualization-driven simulation system that tightly couples systems dynamics simulations with an immersive virtual environment to allow analysts to rapidly develop and test hypotheses in a high-dimensional parameter space. To accomplish this, we generalize the two-dimensional parallel-coordinates statistical graphic as an immersive 'parallel-planes' visualization for multivariate time series emitted by simulations running in parallel with the visualization. In contrast to traditional parallel coordinate's mapping the multivariate dimensions onto coordinate axes represented by a series of parallel lines, we map pairs of the multivariate dimensions onto a series of parallel rectangles. As in the case of parallel coordinates, eachmore » individual observation in the dataset is mapped to a polyline whose vertices coincide with its coordinate values. Regions of the rectangles can be 'brushed' to highlight and select observations of interest: a 'slider' control allows the user to filter the observations by their time coordinate. In an immersive virtual environment, users interact with the parallel planes using a joystick that can select regions on the planes, manipulate selection, and filter time. The brushing and selection actions are used to both explore existing data as well as to launch additional simulations corresponding to the visually selected portions of the input parameter space. As soon as the new simulations complete, their resulting observations are displayed in the virtual environment. This tight feedback loop between simulation and immersive analytics accelerates users' realization of insights about the simulation and its output.« less

Contention Modeling for Multithreaded Distributed Shared Memory Machines: The Cray XMT

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

Secchi, Simone; Tumeo, Antonino; Villa, Oreste

Distributed Shared Memory (DSM) machines are a wide class of multi-processor computing systems where a large virtually-shared address space is mapped on a network of physically distributed memories. High memory latency and network contention are two of the main factors that limit performance scaling of such architectures. Modern high-performance computing DSM systems have evolved toward exploitation of massive hardware multi-threading and fine-grained memory hashing to tolerate irregular latencies, avoid network hot-spots and enable high scaling. In order to model the performance of such large-scale machines, parallel simulation has been proved to be a promising approach to achieve good accuracy inmore » reasonable times. One of the most critical factors in solving the simulation speed-accuracy trade-off is network modeling. The Cray XMT is a massively multi-threaded supercomputing architecture that belongs to the DSM class, since it implements a globally-shared address space abstraction on top of a physically distributed memory substrate. In this paper, we discuss the development of a contention-aware network model intended to be integrated in a full-system XMT simulator. We start by measuring the effects of network contention in a 128-processor XMT machine and then investigate the trade-off that exists between simulation accuracy and speed, by comparing three network models which operate at different levels of accuracy. The comparison and model validation is performed by executing a string-matching algorithm on the full-system simulator and on the XMT, using three datasets that generate noticeably different contention patterns.« less

Randomized clinical trial of two oral care regimens in reducing and controlling established dental plaque and gingivitis.

PubMed

Ayad, Farid; Mateo, Luis R; Dillon, Rensi; Miller, Jeffrey M; Pilch, Shira; Stewart, Bernal

2015-09-01

To evaluate the efficacy of a test regimen (TR) integrating the use of a commercially available triclosan, PVM/MA copolymer, and sodium fluoride containing toothpaste, an alcohol-free, fluoride-free cetylpyridinium chloride (CPC) mouthwash, and a manual toothbrush with cheek and tongue cleaner compared to a negative control regimen (NCR) integrating a commercially available 0.76% sodium monofluorophosphate toothpaste, a manual toothbrush and a fluoride-free and alcohol-free non-antibacterial mouthwash in the reduction and control of established plaque and gingivitis after 4 weeks of product use. A 4-week, two-cell, double-blind, parallel-group, randomized clinical study was conducted in Cedar Knolls, New Jersey, USA. Recruited subjects were randomly assigned to two regimens: (1) a commercially available toothpaste containing triclosan, PVM/MA copolymer, and 0.243% sodium fluoride, a manual toothbrush with cheek and tongue cleaner, and commercially available mouthwash containing 0.075% CPC in a fluoride-free and alcohol-free base (TR), or (2) a commercially available 0.76% sodium monofluorophosphate toothpaste, a manual toothbrush with rounded/polished bristles, and a fluoride-free and alcohol-free non-antibacterial mouthwash (NCR). Subjects were examined for dental plaque and gingivitis. Gingival, Gingival Severity, Gingival Interproximal, Plaque, Plaque Severity and Plaque Interproximal Index scores were calculated. For regimen comparison, independent t-test and ANCOVA analyses were performed. 130 subjects were screened; 120 enrolled; and 115 subjects completed the randomized clinical trial (RCT). After 4 weeks of product use, subjects using TR exhibited statistically significant (P < 0.001) reductions of 22.3%, 27.8% and 20.4% in mean Gingival, Gingival Severity and Gingival Interproximal Index scores, respectively, as compared to subjects using NCR. After 4 weeks of product use, subjects using TR exhibited statistically significant (P < 0.001) reductions of 28.2%, 60.7% and 27.6% in mean Plaque, Plaque Severity and Plaque Interproximal Index scores, respectively, as compared to subjects using NCR.

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.

Efficient Parallel Kernel Solvers for Computational Fluid Dynamics Applications

NASA Technical Reports Server (NTRS)

Sun, Xian-He

1997-01-01

Distributed-memory parallel computers dominate today's parallel computing arena. These machines, such as Intel Paragon, IBM SP2, and Cray Origin2OO, have successfully delivered high performance computing power for solving some of the so-called "grand-challenge" problems. Despite initial success, parallel machines have not been widely accepted in production engineering environments due to the complexity of parallel programming. On a parallel computing system, a task has to be partitioned and distributed appropriately among processors to reduce communication cost and to attain load balance. More importantly, even with careful partitioning and mapping, the performance of an algorithm may still be unsatisfactory, since conventional sequential algorithms may be serial in nature and may not be implemented efficiently on parallel machines. In many cases, new algorithms have to be introduced to increase parallel performance. In order to achieve optimal performance, in addition to partitioning and mapping, a careful performance study should be conducted for a given application to find a good algorithm-machine combination. This process, however, is usually painful and elusive. The goal of this project is to design and develop efficient parallel algorithms for highly accurate Computational Fluid Dynamics (CFD) simulations and other engineering applications. The work plan is 1) developing highly accurate parallel numerical algorithms, 2) conduct preliminary testing to verify the effectiveness and potential of these algorithms, 3) incorporate newly developed algorithms into actual simulation packages. The work plan has well achieved. Two highly accurate, efficient Poisson solvers have been developed and tested based on two different approaches: (1) Adopting a mathematical geometry which has a better capacity to describe the fluid, (2) Using compact scheme to gain high order accuracy in numerical discretization. The previously developed Parallel Diagonal Dominant (PDD) algorithm and Reduced Parallel Diagonal Dominant (RPDD) algorithm have been carefully studied on different parallel platforms for different applications, and a NASA simulation code developed by Man M. Rai and his colleagues has been parallelized and implemented based on data dependency analysis. These achievements are addressed in detail in the paper.

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.

Fundamental Roles of the Golgi-Associated Toxoplasma Aspartyl Protease, ASP5, at the Host-Parasite Interface

PubMed Central

Hammoudi, Pierre-Mehdi; Jacot, Damien; Mueller, Christina; Di Cristina, Manlio; Dogga, Sunil Kumar; Marq, Jean-Baptiste; Romano, Julia; Tosetti, Nicolò; Dubrot, Juan; Emre, Yalin; Lunghi, Matteo; Coppens, Isabelle; Yamamoto, Masahiro; Sojka, Daniel; Pino, Paco; Soldati-Favre, Dominique

2015-01-01

Toxoplasma gondii possesses sets of dense granule proteins (GRAs) that either assemble at, or cross the parasitophorous vacuole membrane (PVM) and exhibit motifs resembling the HT/PEXEL previously identified in a repertoire of exported Plasmodium proteins. Within Plasmodium spp., cleavage of the HT/PEXEL motif by the endoplasmic reticulum-resident protease Plasmepsin V precedes trafficking to and export across the PVM of proteins involved in pathogenicity and host cell remodelling. Here, we have functionally characterized the T. gondii aspartyl protease 5 (ASP5), a Golgi-resident protease that is phylogenetically related to Plasmepsin V. We show that deletion of ASP5 causes a significant loss in parasite fitness in vitro and an altered virulence in vivo. Furthermore, we reveal that ASP5 is necessary for the cleavage of GRA16, GRA19 and GRA20 at the PEXEL-like motif. In the absence of ASP5, the intravacuolar nanotubular network disappears and several GRAs fail to localize to the PVM, while GRA16 and GRA24, both known to be targeted to the host cell nucleus, are retained within the vacuolar space. Additionally, hypermigration of dendritic cells and bradyzoite cyst wall formation are impaired, critically impacting on parasite dissemination and persistence. Overall, the absence of ASP5 dramatically compromises the parasite’s ability to modulate host signalling pathways and immune responses. PMID:26473595

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.

Three-Dimensional High-Lift Analysis Using a Parallel Unstructured Multigrid Solver

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.

1998-01-01

A directional implicit unstructured agglomeration multigrid solver is ported to shared and distributed memory massively parallel machines using the explicit domain-decomposition and message-passing approach. Because the algorithm operates on local implicit lines in the unstructured mesh, special care is required in partitioning the problem for parallel computing. A weighted partitioning strategy is described which avoids breaking the implicit lines across processor boundaries, while incurring minimal additional communication overhead. Good scalability is demonstrated on a 128 processor SGI Origin 2000 machine and on a 512 processor CRAY T3E machine for reasonably fine grids. The feasibility of performing large-scale unstructured grid calculations with the parallel multigrid algorithm is demonstrated by computing the flow over a partial-span flap wing high-lift geometry on a highly resolved grid of 13.5 million points in approximately 4 hours of wall clock time on the CRAY T3E.

Clock Agreement Among Parallel Supercomputer Nodes

DOE Data Explorer

Jones, Terry R.; Koenig, Gregory A.

2014-04-30

This dataset presents measurements that quantify the clock synchronization time-agreement characteristics among several high performance computers including the current world's most powerful machine for open science, the U.S. Department of Energy's Titan machine sited at Oak Ridge National Laboratory. These ultra-fast machines derive much of their computational capability from extreme node counts (over 18000 nodes in the case of the Titan machine). Time-agreement is commonly utilized by parallel programming applications and tools, distributed programming application and tools, and system software. Our time-agreement measurements detail the degree of time variance between nodes and how that variance changes over time. The dataset includes empirical measurements and the accompanying spreadsheets.

Assessment of OLED displays for vision research.

PubMed

Cooper, Emily A; Jiang, Haomiao; Vildavski, Vladimir; Farrell, Joyce E; Norcia, Anthony M

2013-10-23

Vision researchers rely on visual display technology for the presentation of stimuli to human and nonhuman observers. Verifying that the desired and displayed visual patterns match along dimensions such as luminance, spectrum, and spatial and temporal frequency is an essential part of developing controlled experiments. With cathode-ray tubes (CRTs) becoming virtually unavailable on the commercial market, it is useful to determine the characteristics of newly available displays based on organic light emitting diode (OLED) panels to determine how well they may serve to produce visual stimuli. This report describes a series of measurements summarizing the properties of images displayed on two commercially available OLED displays: the Sony Trimaster EL BVM-F250 and PVM-2541. The results show that the OLED displays have large contrast ratios, wide color gamuts, and precise, well-behaved temporal responses. Correct adjustment of the settings on both models produced luminance nonlinearities that were well predicted by a power function ("gamma correction"). Both displays have adjustable pixel independence and can be set to have little to no spatial pixel interactions. OLED displays appear to be a suitable, or even preferable, option for many vision research applications.

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

Characterizing parallel file-access patterns on a large-scale multiprocessor

NASA Technical Reports Server (NTRS)

Purakayastha, A.; Ellis, Carla; Kotz, David; Nieuwejaar, Nils; Best, Michael L.

1995-01-01

High-performance parallel file systems are needed to satisfy tremendous I/O requirements of parallel scientific applications. The design of such high-performance parallel file systems depends on a comprehensive understanding of the expected workload, but so far there have been very few usage studies of multiprocessor file systems. This paper is part of the CHARISMA project, which intends to fill this void by measuring real file-system workloads on various production parallel machines. In particular, we present results from the CM-5 at the National Center for Supercomputing Applications. Our results are unique because we collect information about nearly every individual I/O request from the mix of jobs running on the machine. Analysis of the traces leads to various recommendations for parallel file-system design.

Parallel Computing Using Web Servers and "Servlets".

ERIC Educational Resources Information Center

Lo, Alfred; Bloor, Chris; Choi, Y. K.

2000-01-01

Describes parallel computing and presents inexpensive ways to implement a virtual parallel computer with multiple Web servers. Highlights include performance measurement of parallel systems; models for using Java and intranet technology including single server, multiple clients and multiple servers, single client; and a comparison of CGI (common…

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;

Application of high-performance computing to numerical simulation of human movement

NASA Technical Reports Server (NTRS)

Anderson, F. C.; Ziegler, J. M.; Pandy, M. G.; Whalen, R. T.

1995-01-01

We have examined the feasibility of using massively-parallel and vector-processing supercomputers to solve large-scale optimization problems for human movement. Specifically, we compared the computational expense of determining the optimal controls for the single support phase of gait using a conventional serial machine (SGI Iris 4D25), a MIMD parallel machine (Intel iPSC/860), and a parallel-vector-processing machine (Cray Y-MP 8/864). With the human body modeled as a 14 degree-of-freedom linkage actuated by 46 musculotendinous units, computation of the optimal controls for gait could take up to 3 months of CPU time on the Iris. Both the Cray and the Intel are able to reduce this time to practical levels. The optimal solution for gait can be found with about 77 hours of CPU on the Cray and with about 88 hours of CPU on the Intel. Although the overall speeds of the Cray and the Intel were found to be similar, the unique capabilities of each machine are better suited to different portions of the computational algorithm used. The Intel was best suited to computing the derivatives of the performance criterion and the constraints whereas the Cray was best suited to parameter optimization of the controls. These results suggest that the ideal computer architecture for solving very large-scale optimal control problems is a hybrid system in which a vector-processing machine is integrated into the communication network of a MIMD parallel machine.

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

Barrett, Brian; Brightwell, Ronald B.; Grant, Ryan

This report presents a specification for the Portals 4 networ k programming interface. Portals 4 is intended to allow scalable, high-performance network communication betwee n nodes of a parallel computing system. Portals 4 is well suited to massively parallel processing and embedded syste ms. Portals 4 represents an adaption of the data movement layer developed for massively parallel processing platfor ms, such as the 4500-node Intel TeraFLOPS machine. Sandia's Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4 is tarmore » geted to the next generation of machines employing advanced network interface architectures that support enh anced offload capabilities.« less

The Portals 4.0 network programming interface.

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

Barrett, Brian W.; Brightwell, Ronald Brian; Pedretti, Kevin

2012-11-01

This report presents a specification for the Portals 4.0 network programming interface. Portals 4.0 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4.0 is well suited to massively parallel processing and embedded systems. Portals 4.0 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandias Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4.0 is targeted to the next generationmore » of machines employing advanced network interface architectures that support enhanced offload capabilities.« less

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.

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.

Applications of Parallel Computation in Micro-Mechanics and Finite Element Method

NASA Technical Reports Server (NTRS)

Tan, Hui-Qian

1996-01-01

This project discusses the application of parallel computations related with respect to material analyses. Briefly speaking, we analyze some kind of material by elements computations. We call an element a cell here. A cell is divided into a number of subelements called subcells and all subcells in a cell have the identical structure. The detailed structure will be given later in this paper. It is obvious that the problem is "well-structured". SIMD machine would be a better choice. In this paper we try to look into the potentials of SIMD machine in dealing with finite element computation by developing appropriate algorithms on MasPar, a SIMD parallel machine. In section 2, the architecture of MasPar will be discussed. A brief review of the parallel programming language MPL also is given in that section. In section 3, some general parallel algorithms which might be useful to the project will be proposed. And, combining with the algorithms, some features of MPL will be discussed in more detail. In section 4, the computational structure of cell/subcell model will be given. The idea of designing the parallel algorithm for the model will be demonstrated. Finally in section 5, a summary will be given.

The R package "sperrorest" : Parallelized spatial error estimation and variable importance assessment for geospatial machine learning

NASA Astrophysics Data System (ADS)

Schratz, Patrick; Herrmann, Tobias; Brenning, Alexander

2017-04-01

Computational and statistical prediction methods such as the support vector machine have gained popularity in remote-sensing applications in recent years and are often compared to more traditional approaches like maximum-likelihood classification. However, the accuracy assessment of such predictive models in a spatial context needs to account for the presence of spatial autocorrelation in geospatial data by using spatial cross-validation and bootstrap strategies instead of their now more widely used non-spatial equivalent. The R package sperrorest by A. Brenning [IEEE International Geoscience and Remote Sensing Symposium, 1, 374 (2012)] provides a generic interface for performing (spatial) cross-validation of any statistical or machine-learning technique available in R. Since spatial statistical models as well as flexible machine-learning algorithms can be computationally expensive, parallel computing strategies are required to perform cross-validation efficiently. The most recent major release of sperrorest therefore comes with two new features (aside from improved documentation): The first one is the parallelized version of sperrorest(), parsperrorest(). This function features two parallel modes to greatly speed up cross-validation runs. Both parallel modes are platform independent and provide progress information. par.mode = 1 relies on the pbapply package and calls interactively (depending on the platform) parallel::mclapply() or parallel::parApply() in the background. While forking is used on Unix-Systems, Windows systems use a cluster approach for parallel execution. par.mode = 2 uses the foreach package to perform parallelization. This method uses a different way of cluster parallelization than the parallel package does. In summary, the robustness of parsperrorest() is increased with the implementation of two independent parallel modes. A new way of partitioning the data in sperrorest is provided by partition.factor.cv(). This function gives the user the possibility to perform cross-validation at the level of some grouping structure. As an example, in remote sensing of agricultural land uses, pixels from the same field contain nearly identical information and will thus be jointly placed in either the test set or the training set. Other spatial sampling resampling strategies are already available and can be extended by the user.

System software for the finite element machine

NASA Technical Reports Server (NTRS)

Crockett, T. W.; Knott, J. D.

1985-01-01

The Finite Element Machine is an experimental parallel computer developed at Langley Research Center to investigate the application of concurrent processing to structural engineering analysis. This report describes system-level software which has been developed to facilitate use of the machine by applications researchers. The overall software design is outlined, and several important parallel processing issues are discussed in detail, including processor management, communication, synchronization, and input/output. Based on experience using the system, the hardware architecture and software design are critiqued, and areas for further work are suggested.

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…

A clinical investigation of the efficacy of three commercially available dentifrices for controlling established gingivitis and supragingival plaque.

PubMed

Singh, Surrendra; Chaknis, Patricia; DeVizio, William; Petrone, Margaret; Panagakos, Fotinos S; Proskin, Howard M

2010-01-01

To assess the efficacy ofa dentifrice containing 0.3% triclosan/2.0% PVM/MA copolymer/0.243% sodium fluoride for controlling established gingivitis and supragingival plaque relative to that of a dentifrice containing 0.454% stannous fluoride, sodium hexametaphosphate, and zinc lactate, and a dentifrice containing 0.243% sodium fluoride as a negative control. Following a baseline examination for gingivitis and supragingival plaque, qualifying adult male and female subjects from the Piscataway, NJ, USA area were randomized into three dentifrice groups. Subjects were instructed to brush their teeth twice daily (morning and evening) for one minute with their assigned dentifrice and a soft-bristled toothbrush. Examinations for gingivitis and supragingival plaque were repeated after six weeks of product use. One-hundred and seventy-one (171) subjects complied with the protocol and completed the study. Relative to the group using the dentifrice with 0.243% sodium fluoride alone, the 0.3% triclosan/2.0% PVM/MA copolymer/0.243% sodium fluoride group exhibited statistically significant reductions in gingival index and supragingival plaque index scores of 25.3% and 33.0%, respectively, after six weeks of product use. Similarly, relative to the group using the 0.243% sodium fluoride dentifrice, the 0.454% stannous fluoride, sodium hexametaphosphate, and zinc lactate dentifrice group exhibited statistically significant reductions in gingival index and plaque index scores of 8.1% and 14.1% after six weeks of product use. Further, relative to the 0.454% stannous fluoride, sodium hexametaphosphate, and zinc lactate dentifrice group, the 0.3% triclosan/2.0% PVM/MA copolymer/0.243% sodium fluoride dentifrice group exhibited statistically significant reductions in gingival index and plaque index scores of 18.7% and 22%, respectively. The overall results of this double-blind clinical study support the conclusion that a dentifrice containing 0.3% triclosan/2.0% PVM/MA copolymer/0.243% sodium fluoride is efficacious for the control of established gingivitis and supragingival plaque as compared to a regular fluoride dentifrice, and that it provides a greater level of efficacy for the control of gingivitis and supragingival plaque than does a dentifrice containing 0.454% stannous fluoride, sodium hexametaphosphate, and zinc lactate.

Muscarinic excitation of parvalbumin-positive interneurons contributes to the severity of pilocarpine-induced seizures

PubMed Central

Yi, Feng; DeCan, Evan; Stoll, Kurt; Marceau, Eric; Deisseroth, Karl; Lawrence, J. Josh

2014-01-01

SUMMARY Objective A common rodent model in epilepsy research employs the muscarinic acetylcholine receptor (mAChR) agonist pilocarpine, yet the mechanisms underlying the induction of pilocarpine-induced seizures (PISs) remain unclear. Global M1 mAChR (M1R) knockout mice are resistant to PISs, implying that M1R activation disrupts excitation/inhibition balance. Parvalbumin-positive (PV) inhibitory neurons express M1 mAChRs, participate in cholinergically-induced oscillations, and can enter a state of depolarization block (DB) during epileptiform activity. Here, we test the hypothesis that pilocarpine activation of M1Rs expressed on PV cells contributes to PISs. Methods CA1 PV cells in PV-CRE mice were visualized with a floxed YFP or hM3Dq-mCherry adeno-associated virus, or by crossing PV-CRE mice with the RosaYFP reporter line. To eliminate M1Rs from PV cells, we generated PV-M1KO mice by crossing PV-CRE and floxed M1 mice. Action potential (AP) frequency was monitored during application of pilocarpine (200 µM). In behavioral experiments, locomotion and seizure symptoms were recorded in WT or PV-M1KO mice during PISs. Results Pilocarpine significantly increased AP frequency in CA1 PV cells into the gamma range. In the continued presence of pilocarpine, a subset (5/7) of PV cells progressed to DB, which was mimicked by hM3Dq activation of Gq-receptor signaling. Pilocarpine-induced depolarization, AP firing at gamma frequency, and progression to DB were prevented in CA1 PV cells of PV-M1KO mice. Finally, compared to WT mice, PV-M1KO mice were associated with reduced severity of PISs. Significance Pilocarpine can directly depolarize PV+ cells via M1R activation but a subset of these cells progress to DB. Our electrophysiological and behavioral results suggest that this mechanism is active during PISs, contributing to a collapse of PV-mediated GABAergic inhibition, dysregulation of excitation/inhibition balance, and increased susceptibility to PISs. PMID:25495999

Solving the Cauchy-Riemann equations on parallel computers

NASA Technical Reports Server (NTRS)

Fatoohi, Raad A.; Grosch, Chester E.

1987-01-01

Discussed is the implementation of a single algorithm on three parallel-vector computers. The algorithm is a relaxation scheme for the solution of the Cauchy-Riemann equations; a set of coupled first order partial differential equations. The computers were chosen so as to encompass a variety of architectures. They are: the MPP, and SIMD machine with 16K bit serial processors; FLEX/32, an MIMD machine with 20 processors; and CRAY/2, an MIMD machine with four vector processors. The machine architectures are briefly described. The implementation of the algorithm is discussed in relation to these architectures and measures of the performance on each machine are given. Simple performance models are used to describe the performance. These models highlight the bottlenecks and limiting factors for this algorithm on these architectures. Conclusions are presented.

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

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.

Solution of task related to control of swiss-type automatic lathe to get planes parallel to part axis

NASA Astrophysics Data System (ADS)

Tabekina, N. A.; Chepchurov, M. S.; Evtushenko, E. I.; Dmitrievsky, B. S.

2018-05-01

The work solves the problem of automation of machining process namely turning to produce parts having the planes parallel to an axis of rotation of part without using special tools. According to the results, the availability of the equipment of a high speed electromechanical drive to control the operative movements of lathe machine will enable one to get the planes parallel to the part axis. The method of getting planes parallel to the part axis is based on the mathematical model, which is presented as functional dependency between the conveying velocity of the driven element and the time. It describes the operative movements of lathe machine all over the tool path. Using the model of movement of the tool, it has been found that the conveying velocity varies from the maximum to zero value. It will allow one to carry out the reverse of the drive. The scheme of tool placement regarding the workpiece has been proposed for unidirectional movement of the driven element at high conveying velocity. The control method of CNC machines can be used for getting geometrically complex parts on the lathe without using special milling tools.

Wave scheduling - Decentralized scheduling of task forces in multicomputers

NASA Technical Reports Server (NTRS)

Van Tilborg, A. M.; Wittie, L. D.

1984-01-01

Decentralized operating systems that control large multicomputers need techniques to schedule competing parallel programs called task forces. Wave scheduling is a probabilistic technique that uses a hierarchical distributed virtual machine to schedule task forces by recursively subdividing and issuing wavefront-like commands to processing elements capable of executing individual tasks. Wave scheduling is highly resistant to processing element failures because it uses many distributed schedulers that dynamically assign scheduling responsibilities among themselves. The scheduling technique is trivially extensible as more processing elements join the host multicomputer. A simple model of scheduling cost is used by every scheduler node to distribute scheduling activity and minimize wasted processing capacity by using perceived workload to vary decentralized scheduling rules. At low to moderate levels of network activity, wave scheduling is only slightly less efficient than a central scheduler in its ability to direct processing elements to accomplish useful work.

A Latency-Tolerant Partitioner for Distributed Computing on the Information Power Grid

NASA Technical Reports Server (NTRS)

Das, Sajal K.; Harvey, Daniel J.; Biwas, Rupak; Kwak, Dochan (Technical Monitor)

2001-01-01

NASA's Information Power Grid (IPG) is an infrastructure designed to harness the power of graphically distributed computers, databases, and human expertise, in order to solve large-scale realistic computational problems. This type of a meta-computing environment is necessary to present a unified virtual machine to application developers that hides the intricacies of a highly heterogeneous environment and yet maintains adequate security. In this paper, we present a novel partitioning scheme. called MinEX, that dynamically balances processor workloads while minimizing data movement and runtime communication, for applications that are executed in a parallel distributed fashion on the IPG. We also analyze the conditions that are required for the IPG to be an effective tool for such distributed computations. Our results show that MinEX is a viable load balancer provided the nodes of the IPG are connected by a high-speed asynchronous interconnection network.

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

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

The portals 4.0.1 network programming interface.

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

Barrett, Brian W.; Brightwell, Ronald Brian; Pedretti, Kevin

2013-04-01

This report presents a specification for the Portals 4.0 network programming interface. Portals 4.0 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4.0 is well suited to massively parallel processing and embedded systems. Portals 4.0 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandias Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4.0 is targeted to the next generationmore » of machines employing advanced network interface architectures that support enhanced offload capabilities. 3« less

Execution models for mapping programs onto distributed memory parallel computers

NASA Technical Reports Server (NTRS)

Sussman, Alan

1992-01-01

The problem of exploiting the parallelism available in a program to efficiently employ the resources of the target machine is addressed. The problem is discussed in the context of building a mapping compiler for a distributed memory parallel machine. The paper describes using execution models to drive the process of mapping a program in the most efficient way onto a particular machine. Through analysis of the execution models for several mapping techniques for one class of programs, we show that the selection of the best technique for a particular program instance can make a significant difference in performance. On the other hand, the results of benchmarks from an implementation of a mapping compiler show that our execution models are accurate enough to select the best mapping technique for a given program.

Conception et mise au point d'un emulateur de machine Synchrone trapezoidale a aimants permanents

NASA Astrophysics Data System (ADS)

Lessard, Francois

The development of technology leads inevitably to higher systems' complexity faced by engineers. Over time, tools are often developed in parallel with the main systems to ensure their sustainability. The work presented in this document provides a new tool for testing motor drives. In general, this project refers to active loads, which are complex dynamic loads emulated electronically with a static converter. Specifically, this document proposes and implements a system whose purpose is to recreate the behaviour of a trapezoidal permanent magnets synchronous machine. The ultimate goal is to connect a motor drive to the three terminal of the motor emulator, as it would with a real motor. The emulator's response then obtained, when subjected to disturbances of the motor drive, is ideally identical to the one of a real motor. The motor emulator led to a significant versatility of a test bench because the electrical and mechanical parameters of the application can be easily modified. The work is divided into two main parts: the static converter and real-rime. Overall, these two entities form a PHIL (Power Hardware-in-the-loop) real-time simulation. The static converter enables the exchange of real power between the drive motor and the real-time simulation. The latter gives the application the intelligence needed to interact with the motor drive in a way which the desired behaviour is recreated. The main partner of this project, Opal-RT, ensures this development. Keywords: virtual machine, PHIL, real-time simulation, electronic load

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.

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.

Heterogeneous concurrent computing with exportable services

NASA Technical Reports Server (NTRS)

Sunderam, Vaidy

1995-01-01

Heterogeneous concurrent computing, based on the traditional process-oriented model, is approaching its functionality and performance limits. An alternative paradigm, based on the concept of services, supporting data driven computation, and built on a lightweight process infrastructure, is proposed to enhance the functional capabilities and the operational efficiency of heterogeneous network-based concurrent computing. TPVM is an experimental prototype system supporting exportable services, thread-based computation, and remote memory operations that is built as an extension of and an enhancement to the PVM concurrent computing system. TPVM offers a significantly different computing paradigm for network-based computing, while maintaining a close resemblance to the conventional PVM model in the interest of compatibility and ease of transition Preliminary experiences have demonstrated that the TPVM framework presents a natural yet powerful concurrent programming interface, while being capable of delivering performance improvements of upto thirty percent.

Preparation and characterization of mucoadhesive nanoparticles of poly (methyl vinyl ether-co-maleic anhydride) containing glycyrrhizic acid intended for vaginal administration.

PubMed

Aguilar-Rosas, Irene; Alcalá-Alcalá, Sergio; Llera-Rojas, Viridiana; Ganem-Rondero, Adriana

2015-01-01

Traditional vaginal preparations reside in the vaginal cavity for relatively a short period of time, requiring multiple doses in order to attain the desired therapeutic effect. Therefore, mucoadhesive systems appear to be appropriate to prolong the residence time in the vaginal cavity. In the current study, mucoadhesive nanoparticles based on poly(methyl vinyl ether-co-maleic anhydride) (PVM/MA) intended for vaginal delivery of glycyrrhizic acid (GA) (a drug with well-known antiviral properties) were prepared and characterized. Nanoparticles were generated by a solvent displacement method. Incorporation of GA was performed during nanoprecipitation, followed by adsorption of drug once nanoparticles were formed. The prepared nanoparticles were characterized in terms of size, Z-potential, morphology, drug loading, interaction of GA with PVM/MA (by differential scanning calorimetry) and the in vitro interaction of nanoparticles with pig mucin (at two pH values, 3.6 and 5; with and without GA adsorbed). The preparation method led to nanoparticles of a mean diameter of 198.5 ± 24.3 nm, zeta potential of -44.8 ± 2.8 mV and drug loading of 15.07 ± 0.86 µg/mg polymer. The highest mucin interaction resulted at pH 3.6 for nanoparticles without GA adsorbed. The data obtained suggest the promise of using mucoadhesive nanoparticles of PVM/MA for intravaginal delivery of GA.

Non-equilibrium plasma kinetics of reacting CO: an improved state to state approach

NASA Astrophysics Data System (ADS)

Pietanza, L. D.; Colonna, G.; Capitelli, M.

2017-12-01

Non-equilibrium plasma kinetics of reacting CO for conditions typically met in microwave discharges have been developed based on the coupling of excited state kinetics and the Boltzmann equation for the electron energy distribution function (EEDF). Particular attention is given to the insertion in the vibrational kinetics of a complete set of electron molecule resonant processes linking the whole vibrational ladder of the CO molecule, as well as to the role of Boudouard reaction, i.e. the process of forming CO2 by two vibrationally excited CO molecules, in shaping the vibrational distribution of CO and promoting reaction channels assisted by vibrational excitation (pure vibrational mechanisms, PVM). PVM mechanisms can become competitive with electron impact dissociation processes (DEM) in the activation of CO. A case study reproducing the conditions of a microwave discharge has been considered following the coupled kinetics also in the post discharge conditions. Results include the evolution of EEDF in discharge and post discharge conditions highlighting the role of superelastic vibrational and electronic collisions in shaping the EEDF. Moreover, PVM rate coefficients and DEM ones are studied as a function of gas temperature, showing a non-Arrhenius behavior, i.e. the rate coefficients increase with decreasing gas temperature as a result of a vibrational-vibrational (V-V) pumping up mechanism able to form plateaux in the vibrational distribution function. The accuracy of the results is discussed in particular in connection to the present knowledge of the activation energy of the Boudouard process.

Effects of Ramadan Gasting on Postural Balance and Attentional Capacities in Elderly People.

PubMed

Laatar, R; Borji, R; Baccouch, R; Zahaf, F; Rebai, H; Sahli, S

2016-01-01

To evaluate the effects of Ramadan fasting on postural balance and attentional capacities in older adults. the Neurophysiology department of a University Hospital. Fifteen males aged between 65 and 80 years were asked to perform a postural balance protocol and a simple reaction time (SRT) test in four testing phases: one week before Ramadan (BR), during the second (SWR) and the fourth week of Ramadan (FWR) and 3 weeks after Ramadan (AR). Postural balance measurements were recorded in the bipedal stance in four different conditions: firm surface/eyes open (EO), firm surface/eyes closed (EC), foam surface/EO and foam surface/EC using a force platform. Results of the present study demonstrated that center of pressure (CoP) mean velocity (CoPVm), medio-lateral length (CoPLX) and antero-posterior length (CoPLY) were significantly higher during the SWR than BR. Likewise, values of CoPVm and CoPLX increased significantly during the FWR compared to BR. The CoPLX decreased significantly in the FWR compared to the SWR. Values of CoPVm and CoPLX were significantly higher AR in comparison with BR. In addition, SRT values increased significantly during the SWR and the FWR than BR. Ramadan fasting affects postural balance and attentional capacities in the elderly mainly in the SWR and it may, therefore, increase the risk of fall and fall-related injuries. More than three weeks are needed for older adults to recover postural balance impairment due to Ramadan fasting.

Scheduling for Parallel Supercomputing: A Historical Perspective of Achievable Utilization

NASA Technical Reports Server (NTRS)

Jones, James Patton; Nitzberg, Bill

1999-01-01

The NAS facility has operated parallel supercomputers for the past 11 years, including the Intel iPSC/860, Intel Paragon, Thinking Machines CM-5, IBM SP-2, and Cray Origin 2000. Across this wide variety of machine architectures, across a span of 10 years, across a large number of different users, and through thousands of minor configuration and policy changes, the utilization of these machines shows three general trends: (1) scheduling using a naive FIFO first-fit policy results in 40-60% utilization, (2) switching to the more sophisticated dynamic backfilling scheduling algorithm improves utilization by about 15 percentage points (yielding about 70% utilization), and (3) reducing the maximum allowable job size further increases utilization. Most surprising is the consistency of these trends. Over the lifetime of the NAS parallel systems, we made hundreds, perhaps thousands, of small changes to hardware, software, and policy, yet, utilization was affected little. In particular these results show that the goal of achieving near 100% utilization while supporting a real parallel supercomputing workload is unrealistic.

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.

Specification and Analysis of Parallel Machine Architecture

DTIC Science & Technology

1990-03-17

Parallel Machine Architeture C.V. Ramamoorthy Computer Science Division Dept. of Electrical Engineering and Computer Science University of California...capacity. (4) Adaptive: The overhead in resolution of deadlocks, etc. should be in proportion to their frequency. (5) Avoid rollbacks: Rollbacks can be...snapshots of system state graphically at a rate proportional to simulation time. Some of the examples are as follow: (1) When the simulation clock of

Scaling Support Vector Machines On Modern HPC Platforms

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

You, Yang; Fu, Haohuan; Song, Shuaiwen

2015-02-01

We designed and implemented MIC-SVM, a highly efficient parallel SVM for x86 based multicore and many-core architectures, such as the Intel Ivy Bridge CPUs and Intel Xeon Phi co-processor (MIC). We propose various novel analysis methods and optimization techniques to fully utilize the multilevel parallelism provided by these architectures and serve as general optimization methods for other machine learning tools.

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.

Architectures for reasoning in parallel

NASA Technical Reports Server (NTRS)

Hall, Lawrence O.

1989-01-01

The research conducted has dealt with rule-based expert systems. The algorithms that may lead to effective parallelization of them were investigated. Both the forward and backward chained control paradigms were investigated in the course of this work. The best computer architecture for the developed and investigated algorithms has been researched. Two experimental vehicles were developed to facilitate this research. They are Backpac, a parallel backward chained rule-based reasoning system and Datapac, a parallel forward chained rule-based reasoning system. Both systems have been written in Multilisp, a version of Lisp which contains the parallel construct, future. Applying the future function to a function causes the function to become a task parallel to the spawning task. Additionally, Backpac and Datapac have been run on several disparate parallel processors. The machines are an Encore Multimax with 10 processors, the Concert Multiprocessor with 64 processors, and a 32 processor BBN GP1000. Both the Concert and the GP1000 are switch-based machines. The Multimax has all its processors hung off a common bus. All are shared memory machines, but have different schemes for sharing the memory and different locales for the shared memory. The main results of the investigations come from experiments on the 10 processor Encore and the Concert with partitions of 32 or less processors. Additionally, experiments have been run with a stripped down version of EMYCIN.

A parallel-machine scheduling problem with two competing agents

NASA Astrophysics Data System (ADS)

Lee, Wen-Chiung; Chung, Yu-Hsiang; Wang, Jen-Ya

2017-06-01

Scheduling with two competing agents has become popular in recent years. Most of the research has focused on single-machine problems. This article considers a parallel-machine problem, the objective of which is to minimize the total completion time of jobs from the first agent given that the maximum tardiness of jobs from the second agent cannot exceed an upper bound. The NP-hardness of this problem is also examined. A genetic algorithm equipped with local search is proposed to search for the near-optimal solution. Computational experiments are conducted to evaluate the proposed genetic algorithm.

On the relationship between parallel computation and graph embedding

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

Gupta, A.K.

1989-01-01

The problem of efficiently simulating an algorithm designed for an n-processor parallel machine G on an m-processor parallel machine H with n > m arises when parallel algorithms designed for an ideal size machine are simulated on existing machines which are of a fixed size. The author studies this problem when every processor of H takes over the function of a number of processors in G, and he phrases the simulation problem as a graph embedding problem. New embeddings presented address relevant issues arising from the parallel computation environment. The main focus centers around embedding complete binary trees into smaller-sizedmore » binary trees, butterflies, and hypercubes. He also considers simultaneous embeddings of r source machines into a single hypercube. Constant factors play a crucial role in his embeddings since they are not only important in practice but also lead to interesting theoretical problems. All of his embeddings minimize dilation and load, which are the conventional cost measures in graph embeddings and determine the maximum amount of time required to simulate one step of G on H. His embeddings also optimize a new cost measure called ({alpha},{beta})-utilization which characterizes how evenly the processors of H are used by the processors of G. Ideally, the utilization should be balanced (i.e., every processor of H simulates at most (n/m) processors of G) and the ({alpha},{beta})-utilization measures how far off from a balanced utilization the embedding is. He presents embeddings for the situation when some processors of G have different capabilities (e.g. memory or I/O) than others and the processors with different capabilities are to be distributed uniformly among the processors of H. Placing such conditions on an embedding results in an increase in some of the cost measures.« less

Parallel Preconditioning for CFD Problems on the CM-5

NASA Technical Reports Server (NTRS)

Simon, Horst D.; Kremenetsky, Mark D.; Richardson, John; Lasinski, T. A. (Technical Monitor)

1994-01-01

Up to today, preconditioning methods on massively parallel systems have faced a major difficulty. The most successful preconditioning methods in terms of accelerating the convergence of the iterative solver such as incomplete LU factorizations are notoriously difficult to implement on parallel machines for two reasons: (1) the actual computation of the preconditioner is not very floating-point intensive, but requires a large amount of unstructured communication, and (2) the application of the preconditioning matrix in the iteration phase (i.e. triangular solves) are difficult to parallelize because of the recursive nature of the computation. Here we present a new approach to preconditioning for very large, sparse, unsymmetric, linear systems, which avoids both difficulties. We explicitly compute an approximate inverse to our original matrix. This new preconditioning matrix can be applied most efficiently for iterative methods on massively parallel machines, since the preconditioning phase involves only a matrix-vector multiplication, with possibly a dense matrix. Furthermore the actual computation of the preconditioning matrix has natural parallelism. For a problem of size n, the preconditioning matrix can be computed by solving n independent small least squares problems. The algorithm and its implementation on the Connection Machine CM-5 are discussed in detail and supported by extensive timings obtained from real problem data.

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.

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...

Multi-objective problem of the modified distributed parallel machine and assembly scheduling problem (MDPMASP) with eligibility constraints

NASA Astrophysics Data System (ADS)

Amallynda, I.; Santosa, B.

2017-11-01

This paper proposes a new generalization of the distributed parallel machine and assembly scheduling problem (DPMASP) with eligibility constraints referred to as the modified distributed parallel machine and assembly scheduling problem (MDPMASP) with eligibility constraints. Within this generalization, we assume that there are a set non-identical factories or production lines, each one with a set unrelated parallel machine with different speeds in processing them disposed to a single assembly machine in series. A set of different products that are manufactured through an assembly program of a set of components (jobs) according to the requested demand. Each product requires several kinds of jobs with different sizes. Beside that we also consider to the multi-objective problem (MOP) of minimizing mean flow time and the number of tardy products simultaneously. This is known to be NP-Hard problem, is important to practice, as the former criterions to reflect the customer's demand and manufacturer's perspective. This is a realistic and complex problem with wide range of possible solutions, we propose four simple heuristics and two metaheuristics to solve it. Various parameters of the proposed metaheuristic algorithms are discussed and calibrated by means of Taguchi technique. All proposed algorithms are tested by Matlab software. Our computational experiments indicate that the proposed problem and fourth proposed algorithms are able to be implemented and can be used to solve moderately-sized instances, and giving efficient solutions, which are close to optimum in most cases.

From planes to brains: parallels between military development of virtual reality environments and virtual neurological surgery.

PubMed

Schmitt, Paul J; Agarwal, Nitin; Prestigiacomo, Charles J

2012-01-01

Military explorations of the practical role of simulators have served as a driving force for much of the virtual reality technology that we have today. The evolution of 3-dimensional and virtual environments from the early flight simulators used during World War II to the sophisticated training simulators in the modern military followed a path that virtual surgical and neurosurgical devices have already begun to parallel. By understanding the evolution of military simulators as well as comparing and contrasting that evolution with current and future surgical simulators, it may be possible to expedite the development of appropriate devices and establish their validity as effective training tools. As such, this article presents a historical perspective examining the progression of neurosurgical simulators, the establishment of effective and appropriate curricula for using them, and the contributions that the military has made during the ongoing maturation of this exciting treatment and training modality. Copyright © 2012. Published by Elsevier Inc.

Computer-Aided Parallelizer and Optimizer

NASA Technical Reports Server (NTRS)

Jin, Haoqiang

2011-01-01

The Computer-Aided Parallelizer and Optimizer (CAPO) automates the insertion of compiler directives (see figure) to facilitate parallel processing on Shared Memory Parallel (SMP) machines. While CAPO currently is integrated seamlessly into CAPTools (developed at the University of Greenwich, now marketed as ParaWise), CAPO was independently developed at Ames Research Center as one of the components for the Legacy Code Modernization (LCM) project. The current version takes serial FORTRAN programs, performs interprocedural data dependence analysis, and generates OpenMP directives. Due to the widely supported OpenMP standard, the generated OpenMP codes have the potential to run on a wide range of SMP machines. CAPO relies on accurate interprocedural data dependence information currently provided by CAPTools. Compiler directives are generated through identification of parallel loops in the outermost level, construction of parallel regions around parallel loops and optimization of parallel regions, and insertion of directives with automatic identification of private, reduction, induction, and shared variables. Attempts also have been made to identify potential pipeline parallelism (implemented with point-to-point synchronization). Although directives are generated automatically, user interaction with the tool is still important for producing good parallel codes. A comprehensive graphical user interface is included for users to interact with the parallelization process.

Long-Term Training with a Brain-Machine Interface-Based Gait Protocol Induces Partial Neurological Recovery in Paraplegic Patients.

PubMed

Donati, Ana R C; Shokur, Solaiman; Morya, Edgard; Campos, Debora S F; Moioli, Renan C; Gitti, Claudia M; Augusto, Patricia B; Tripodi, Sandra; Pires, Cristhiane G; Pereira, Gislaine A; Brasil, Fabricio L; Gallo, Simone; Lin, Anthony A; Takigami, Angelo K; Aratanha, Maria A; Joshi, Sanjay; Bleuler, Hannes; Cheng, Gordon; Rudolph, Alan; Nicolelis, Miguel A L

2016-08-11

Brain-machine interfaces (BMIs) provide a new assistive strategy aimed at restoring mobility in severely paralyzed patients. Yet, no study in animals or in human subjects has indicated that long-term BMI training could induce any type of clinical recovery. Eight chronic (3-13 years) spinal cord injury (SCI) paraplegics were subjected to long-term training (12 months) with a multi-stage BMI-based gait neurorehabilitation paradigm aimed at restoring locomotion. This paradigm combined intense immersive virtual reality training, enriched visual-tactile feedback, and walking with two EEG-controlled robotic actuators, including a custom-designed lower limb exoskeleton capable of delivering tactile feedback to subjects. Following 12 months of training with this paradigm, all eight patients experienced neurological improvements in somatic sensation (pain localization, fine/crude touch, and proprioceptive sensing) in multiple dermatomes. Patients also regained voluntary motor control in key muscles below the SCI level, as measured by EMGs, resulting in marked improvement in their walking index. As a result, 50% of these patients were upgraded to an incomplete paraplegia classification. Neurological recovery was paralleled by the reemergence of lower limb motor imagery at cortical level. We hypothesize that this unprecedented neurological recovery results from both cortical and spinal cord plasticity triggered by long-term BMI usage.

Long-Term Training with a Brain-Machine Interface-Based Gait Protocol Induces Partial Neurological Recovery in Paraplegic Patients

PubMed Central

Donati, Ana R. C.; Shokur, Solaiman; Morya, Edgard; Campos, Debora S. F.; Moioli, Renan C.; Gitti, Claudia M.; Augusto, Patricia B.; Tripodi, Sandra; Pires, Cristhiane G.; Pereira, Gislaine A.; Brasil, Fabricio L.; Gallo, Simone; Lin, Anthony A.; Takigami, Angelo K.; Aratanha, Maria A.; Joshi, Sanjay; Bleuler, Hannes; Cheng, Gordon; Rudolph, Alan; Nicolelis, Miguel A. L.

2016-01-01

Brain-machine interfaces (BMIs) provide a new assistive strategy aimed at restoring mobility in severely paralyzed patients. Yet, no study in animals or in human subjects has indicated that long-term BMI training could induce any type of clinical recovery. Eight chronic (3–13 years) spinal cord injury (SCI) paraplegics were subjected to long-term training (12 months) with a multi-stage BMI-based gait neurorehabilitation paradigm aimed at restoring locomotion. This paradigm combined intense immersive virtual reality training, enriched visual-tactile feedback, and walking with two EEG-controlled robotic actuators, including a custom-designed lower limb exoskeleton capable of delivering tactile feedback to subjects. Following 12 months of training with this paradigm, all eight patients experienced neurological improvements in somatic sensation (pain localization, fine/crude touch, and proprioceptive sensing) in multiple dermatomes. Patients also regained voluntary motor control in key muscles below the SCI level, as measured by EMGs, resulting in marked improvement in their walking index. As a result, 50% of these patients were upgraded to an incomplete paraplegia classification. Neurological recovery was paralleled by the reemergence of lower limb motor imagery at cortical level. We hypothesize that this unprecedented neurological recovery results from both cortical and spinal cord plasticity triggered by long-term BMI usage. PMID:27513629

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

Interactive Parallel Data Analysis within Data-Centric Cluster Facilities using the IPython Notebook

NASA Astrophysics Data System (ADS)

Pascoe, S.; Lansdowne, J.; Iwi, A.; Stephens, A.; Kershaw, P.

2012-12-01

The data deluge is making traditional analysis workflows for many researchers obsolete. Support for parallelism within popular tools such as matlab, IDL and NCO is not well developed and rarely used. However parallelism is necessary for processing modern data volumes on a timescale conducive to curiosity-driven analysis. Furthermore, for peta-scale datasets such as the CMIP5 archive, it is no longer practical to bring an entire dataset to a researcher's workstation for analysis, or even to their institutional cluster. Therefore, there is an increasing need to develop new analysis platforms which both enable processing at the point of data storage and which provides parallelism. Such an environment should, where possible, maintain the convenience and familiarity of our current analysis environments to encourage curiosity-driven research. We describe how we are combining the interactive python shell (IPython) with our JASMIN data-cluster infrastructure. IPython has been specifically designed to bridge the gap between the HPC-style parallel workflows and the opportunistic curiosity-driven analysis usually carried out using domain specific languages and scriptable tools. IPython offers a web-based interactive environment, the IPython notebook, and a cluster engine for parallelism all underpinned by the well-respected Python/Scipy scientific programming stack. JASMIN is designed to support the data analysis requirements of the UK and European climate and earth system modeling community. JASMIN, with its sister facility CEMS focusing the earth observation community, has 4.5 PB of fast parallel disk storage alongside over 370 computing cores provide local computation. Through the IPython interface to JASMIN, users can make efficient use of JASMIN's multi-core virtual machines to perform interactive analysis on all cores simultaneously or can configure IPython clusters across multiple VMs. Larger-scale clusters can be provisioned through JASMIN's batch scheduling system. Outputs can be summarised and visualised using the full power of Python's many scientific tools, including Scipy, Matplotlib, Pandas and CDAT. This rich user experience is delivered through the user's web browser; maintaining the interactive feel of a workstation-based environment with the parallel power of a remote data-centric processing facility.

A fast sorting algorithm for a hypersonic rarefied flow particle simulation on the connection machine

NASA Technical Reports Server (NTRS)

Dagum, Leonardo

1989-01-01

The data parallel implementation of a particle simulation for hypersonic rarefied flow described by Dagum associates a single parallel data element with each particle in the simulation. The simulated space is divided into discrete regions called cells containing a variable and constantly changing number of particles. The implementation requires a global sort of the parallel data elements so as to arrange them in an order that allows immediate access to the information associated with cells in the simulation. Described here is a very fast algorithm for performing the necessary ranking of the parallel data elements. The performance of the new algorithm is compared with that of the microcoded instruction for ranking on the Connection Machine.

Performance Comparison of a Set of Periodic and Non-Periodic Tridiagonal Solvers on SP2 and Paragon Parallel Computers

NASA Technical Reports Server (NTRS)

Sun, Xian-He; Moitra, Stuti

1996-01-01

Various tridiagonal solvers have been proposed in recent years for different parallel platforms. In this paper, the performance of three tridiagonal solvers, namely, the parallel partition LU algorithm, the parallel diagonal dominant algorithm, and the reduced diagonal dominant algorithm, is studied. These algorithms are designed for distributed-memory machines and are tested on an Intel Paragon and an IBM SP2 machines. Measured results are reported in terms of execution time and speedup. Analytical study are conducted for different communication topologies and for different tridiagonal systems. The measured results match the analytical results closely. In addition to address implementation issues, performance considerations such as problem sizes and models of speedup are also discussed.

Single product lot-sizing on unrelated parallel machines with non-decreasing processing times

NASA Astrophysics Data System (ADS)

Eremeev, A.; Kovalyov, M.; Kuznetsov, P.

2018-01-01

We consider a problem in which at least a given quantity of a single product has to be partitioned into lots, and lots have to be assigned to unrelated parallel machines for processing. In one version of the problem, the maximum machine completion time should be minimized, in another version of the problem, the sum of machine completion times is to be minimized. Machine-dependent lower and upper bounds on the lot size are given. The product is either assumed to be continuously divisible or discrete. The processing time of each machine is defined by an increasing function of the lot volume, given as an oracle. Setup times and costs are assumed to be negligibly small, and therefore, they are not considered. We derive optimal polynomial time algorithms for several special cases of the problem. An NP-hard case is shown to admit a fully polynomial time approximation scheme. An application of the problem in energy efficient processors scheduling is considered.

Early experiences in developing and managing the neuroscience gateway.

PubMed

Sivagnanam, Subhashini; Majumdar, Amit; Yoshimoto, Kenneth; Astakhov, Vadim; Bandrowski, Anita; Martone, MaryAnn; Carnevale, Nicholas T

2015-02-01

The last few decades have seen the emergence of computational neuroscience as a mature field where researchers are interested in modeling complex and large neuronal systems and require access to high performance computing machines and associated cyber infrastructure to manage computational workflow and data. The neuronal simulation tools, used in this research field, are also implemented for parallel computers and suitable for high performance computing machines. But using these tools on complex high performance computing machines remains a challenge because of issues with acquiring computer time on these machines located at national supercomputer centers, dealing with complex user interface of these machines, dealing with data management and retrieval. The Neuroscience Gateway is being developed to alleviate and/or hide these barriers to entry for computational neuroscientists. It hides or eliminates, from the point of view of the users, all the administrative and technical barriers and makes parallel neuronal simulation tools easily available and accessible on complex high performance computing machines. It handles the running of jobs and data management and retrieval. This paper shares the early experiences in bringing up this gateway and describes the software architecture it is based on, how it is implemented, and how users can use this for computational neuroscience research using high performance computing at the back end. We also look at parallel scaling of some publicly available neuronal models and analyze the recent usage data of the neuroscience gateway.

Early experiences in developing and managing the neuroscience gateway

PubMed Central

Sivagnanam, Subhashini; Majumdar, Amit; Yoshimoto, Kenneth; Astakhov, Vadim; Bandrowski, Anita; Martone, MaryAnn; Carnevale, Nicholas. T.

2015-01-01

SUMMARY The last few decades have seen the emergence of computational neuroscience as a mature field where researchers are interested in modeling complex and large neuronal systems and require access to high performance computing machines and associated cyber infrastructure to manage computational workflow and data. The neuronal simulation tools, used in this research field, are also implemented for parallel computers and suitable for high performance computing machines. But using these tools on complex high performance computing machines remains a challenge because of issues with acquiring computer time on these machines located at national supercomputer centers, dealing with complex user interface of these machines, dealing with data management and retrieval. The Neuroscience Gateway is being developed to alleviate and/or hide these barriers to entry for computational neuroscientists. It hides or eliminates, from the point of view of the users, all the administrative and technical barriers and makes parallel neuronal simulation tools easily available and accessible on complex high performance computing machines. It handles the running of jobs and data management and retrieval. This paper shares the early experiences in bringing up this gateway and describes the software architecture it is based on, how it is implemented, and how users can use this for computational neuroscience research using high performance computing at the back end. We also look at parallel scaling of some publicly available neuronal models and analyze the recent usage data of the neuroscience gateway. PMID:26523124

Modeling of spectral signatures of littoral waters

NASA Astrophysics Data System (ADS)

Haltrin, Vladimir I.

1997-12-01

The spectral values of remotely obtained radiance reflectance coefficient (RRC) are compared with the values of RRC computed from inherent optical properties measured during the shipborne experiment near the West Florida coast. The model calculations are based on the algorithm developed at the Naval Research Laboratory at Stennis Space Center and presented here. The algorithm is based on the radiation transfer theory and uses regression relationships derived from experimental data. Overall comparison of derived and measured RRCs shows that this algorithm is suitable for processing ground truth data for the purposes of remote data calibration. The second part of this work consists of the evaluation of the predictive visibility model (PVM). The simulated three-dimensional values of optical properties are compared with the measured ones. Preliminary results of comparison are encouraging and show that the PVM can qualitatively predict the evolution of inherent optical properties in littoral waters.

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.

Implementation and Assessment of a Virtual Laboratory of Parallel Robots Developed for Engineering Students

ERIC Educational Resources Information Center

Gil, Arturo; Peidró, Adrián; Reinoso, Óscar; Marín, José María

2017-01-01

This paper presents a tool, LABEL, oriented to the teaching of parallel robotics. The application, organized as a set of tools developed using Easy Java Simulations, enables the study of the kinematics of parallel robotics. A set of classical parallel structures was implemented such that LABEL can solve the inverse and direct kinematic problem of…

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.

Implementation and Characterization of Three-Dimensional Particle-in-Cell Codes on Multiple-Instruction-Multiple-Data Massively Parallel Supercomputers

NASA Technical Reports Server (NTRS)

Lyster, P. M.; Liewer, P. C.; Decyk, V. K.; Ferraro, R. D.

1995-01-01

A three-dimensional electrostatic particle-in-cell (PIC) plasma simulation code has been developed on coarse-grain distributed-memory massively parallel computers with message passing communications. Our implementation is the generalization to three-dimensions of the general concurrent particle-in-cell (GCPIC) algorithm. In the GCPIC algorithm, the particle computation is divided among the processors using a domain decomposition of the simulation domain. In a three-dimensional simulation, the domain can be partitioned into one-, two-, or three-dimensional subdomains ("slabs," "rods," or "cubes") and we investigate the efficiency of the parallel implementation of the push for all three choices. The present implementation runs on the Intel Touchstone Delta machine at Caltech; a multiple-instruction-multiple-data (MIMD) parallel computer with 512 nodes. We find that the parallel efficiency of the push is very high, with the ratio of communication to computation time in the range 0.3%-10.0%. The highest efficiency (> 99%) occurs for a large, scaled problem with 64(sup 3) particles per processing node (approximately 134 million particles of 512 nodes) which has a push time of about 250 ns per particle per time step. We have also developed expressions for the timing of the code which are a function of both code parameters (number of grid points, particles, etc.) and machine-dependent parameters (effective FLOP rate, and the effective interprocessor bandwidths for the communication of particles and grid points). These expressions can be used to estimate the performance of scaled problems--including those with inhomogeneous plasmas--to other parallel machines once the machine-dependent parameters are known.

Optimizing the way kinematical feed chains with great distance between slides are chosen for CNC machine tools

NASA Astrophysics Data System (ADS)

Lucian, P.; Gheorghe, S.

2017-08-01

This paper presents a new method, based on FRISCO formula, for optimizing the choice of the best control system for kinematical feed chains with great distance between slides used in computer numerical controlled machine tools. Such machines are usually, but not limited to, used for machining large and complex parts (mostly in the aviation industry) or complex casting molds. For such machine tools the kinematic feed chains are arranged in a dual-parallel drive structure that allows the mobile element to be moved by the two kinematical branches and their related control systems. Such an arrangement allows for high speed and high rigidity (a critical requirement for precision machining) during the machining process. A significant issue for such an arrangement it’s the ability of the two parallel control systems to follow the same trajectory accurately in order to address this issue it is necessary to achieve synchronous motion control for the two kinematical branches ensuring that the correct perpendicular position it’s kept by the mobile element during its motion on the two slides.

Communication Studies of DMP and SMP Machines

NASA Technical Reports Server (NTRS)

Sohn, Andrew; Biswas, Rupak; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

Understanding the interplay between machines and problems is key to obtaining high performance on parallel machines. This paper investigates the interplay between programming paradigms and communication capabilities of parallel machines. In particular, we explicate the communication capabilities of the IBM SP-2 distributed-memory multiprocessor and the SGI PowerCHALLENGEarray symmetric multiprocessor. Two benchmark problems of bitonic sorting and Fast Fourier Transform are selected for experiments. Communication-efficient algorithms are developed to exploit the overlapping capabilities of the machines. Programs are written in Message-Passing Interface for portability and identical codes are used for both machines. Various data sizes and message sizes are used to test the machines' communication capabilities. Experimental results indicate that the communication performance of the multiprocessors are consistent with the size of messages. The SP-2 is sensitive to message size but yields a much higher communication overlapping because of the communication co-processor. The PowerCHALLENGEarray is not highly sensitive to message size and yields a low communication overlapping. Bitonic sorting yields lower performance compared to FFT due to a smaller computation-to-communication ratio.

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.

A performance study of sparse Cholesky factorization on INTEL iPSC/860

NASA Technical Reports Server (NTRS)

Zubair, M.; Ghose, M.

1992-01-01

The problem of Cholesky factorization of a sparse matrix has been very well investigated on sequential machines. A number of efficient codes exist for factorizing large unstructured sparse matrices. However, there is a lack of such efficient codes on parallel machines in general, and distributed machines in particular. Some of the issues that are critical to the implementation of sparse Cholesky factorization on a distributed memory parallel machine are ordering, partitioning and mapping, load balancing, and ordering of various tasks within a processor. Here, we focus on the effect of various partitioning schemes on the performance of sparse Cholesky factorization on the Intel iPSC/860. Also, a new partitioning heuristic for structured as well as unstructured sparse matrices is proposed, and its performance is compared with other schemes.

FEM analysis of an single stator dual PM rotors axial synchronous machine

NASA Astrophysics Data System (ADS)

Tutelea, L. N.; Deaconu, S. I.; Popa, G. N.

2017-01-01

The actual e - continuously variable transmission (e-CVT) solution for the parallel Hybrid Electric Vehicle (HEV) requires two electric machines, two inverters, and a planetary gear. A distinct electric generator and a propulsion electric motor, both with full power converters, are typical for a series HEV. In an effort to simplify the planetary-geared e-CVT for the parallel HEV or the series HEV we hereby propose to replace the basically two electric machines and their two power converters by a single, axial-air-gap, electric machine central stator, fed from a single PWM converter with dual frequency voltage output and two independent PM rotors. The proposed topologies, the magneto-motive force analysis and quasi 3D-FEM analysis are the core of the paper.

Machining heavy plastic sections

NASA Technical Reports Server (NTRS)

Stalkup, O. M.

1967-01-01

Machining technique produces consistently satisfactory plane-parallel optical surfaces for pressure windows, made of plexiglass, required to support a photographic study of liquid rocket combustion processes. The surfaces are machined and polished to the required tolerances and show no degradation from stress relaxation over periods as long as 6 months.

Parallel processors and nonlinear structural dynamics algorithms and software

NASA Technical Reports Server (NTRS)

Belytschko, Ted; Gilbertsen, Noreen D.; Neal, Mark O.; Plaskacz, Edward J.

1989-01-01

The adaptation of a finite element program with explicit time integration to a massively parallel SIMD (single instruction multiple data) computer, the CONNECTION Machine is described. The adaptation required the development of a new algorithm, called the exchange algorithm, in which all nodal variables are allocated to the element with an exchange of nodal forces at each time step. The architectural and C* programming language features of the CONNECTION Machine are also summarized. Various alternate data structures and associated algorithms for nonlinear finite element analysis are discussed and compared. Results are presented which demonstrate that the CONNECTION Machine is capable of outperforming the CRAY XMP/14.

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.

Modeling the 1958 Lituya Bay mega-tsunami with a PVM-IFCP GPU-based model

NASA Astrophysics Data System (ADS)

González-Vida, José M.; Arcas, Diego; de la Asunción, Marc; Castro, Manuel J.; Macías, Jorge; Ortega, Sergio; Sánchez-Linares, Carlos; Titov, Vasily

2013-04-01

In this work we present a numerical study, performed in collaboration with the NOAA Center for Tsunami Research (USA), that uses a GPU version of the PVM-IFCP landslide model for the simulation of the 1958 landslide generated tsunami of Lituya Bay. In this model, a layer composed of fluidized granular material is assumed to flow within an upper layer of an inviscid fluid (e. g. water). The model is discretized using a two dimensional PVM-IFCP [Fernández - Castro - Parés. On an Intermediate Field Capturing Riemann Solver Based on a Parabolic Viscosity Matrix for the Two-Layer Shallow Water System, J. Sci. Comput., 48 (2011):117-140] finite volume scheme implemented on GPU cards for increasing the speed-up. This model has been previously validated by using the two-dimensional physical laboratory experiments data from H. Fritz [Lituya Bay Landslide Impact Generated Mega-Tsunami 50th Anniversary. Pure Appl. Geophys., 166 (2009) pp. 153-175]. In the present work, the first step was to reconstruct the topobathymetry of the Lituya Bay before this event ocurred, this is based on USGS geological surveys data. Then, a sensitivity analysis of some model parameters has been performed in order to determine the parameters that better fit to reality, when model results are compared against available event data, as run-up areas. In this presentation, the reconstruction of the pre-tsunami scenario will be shown, a detailed simulation of the tsunami presented and several comparisons with real data (runup, wave height, etc.) shown.

Long-term live imaging reveals cytosolic immune responses of host hepatocytes against Plasmodium infection and parasite escape mechanisms

PubMed Central

Prado, Monica; Eickel, Nina; De Niz, Mariana; Heitmann, Anna; Agop-Nersesian, Carolina; Wacker, Rahel; Schmuckli-Maurer, Jacqueline; Caldelari, Reto; Janse, Chris J; Khan, Shahid M; May, Jürgen; Meyer, Christian G; Heussler, Volker T

2015-01-01

Plasmodium parasites are transmitted by Anopheles mosquitoes to the mammalian host and actively infect hepatocytes after passive transport in the bloodstream to the liver. In their target host hepatocyte, parasites reside within a parasitophorous vacuole (PV). In the present study it was shown that the parasitophorous vacuole membrane (PVM) can be targeted by autophagy marker proteins LC3, ubiquitin, and SQSTM1/p62 as well as by lysosomes in a process resembling selective autophagy. The dynamics of autophagy marker proteins in individual Plasmodium berghei-infected hepatocytes were followed by live imaging throughout the entire development of the parasite in the liver. Although the host cell very efficiently recognized the invading parasite in its vacuole, the majority of parasites survived this initial attack. Successful parasite development correlated with the gradual loss of all analyzed autophagy marker proteins and associated lysosomes from the PVM. However, other autophagic events like nonselective canonical autophagy in the host cell continued. This was indicated as LC3, although not labeling the PVM anymore, still localized to autophagosomes in the infected host cell. It appears that growing parasites even benefit from this form of nonselective host cell autophagy as an additional source of nutrients, as in host cells deficient for autophagy, parasite growth was retarded and could partly be rescued by the supply of additional amino acid in the medium. Importantly, mouse infections with P. berghei sporozoites confirmed LC3 dynamics, the positive effect of autophagy activation on parasite growth, and negative effects upon autophagy inhibition. PMID:26208778

Social energy: mining energy from the society

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

Zhang, Jun Jason; Gao, David Wenzhong; Zhang, Yingchen

The inherent nature of energy, i.e., physicality, sociality and informatization, implies the inevitable and intensive interaction between energy systems and social systems. From this perspective, we define 'social energy' as a complex sociotechnical system of energy systems, social systems and the derived artificial virtual systems which characterize the intense intersystem and intra-system interactions. The recent advancement in intelligent technology, including artificial intelligence and machine learning technologies, sensing and communication in Internet of Things technologies, and massive high performance computing and extreme-scale data analytics technologies, enables the possibility of substantial advancement in socio-technical system optimization, scheduling, control and management. In thismore » paper, we provide a discussion on the nature of energy, and then propose the concept and intention of social energy systems for electrical power. A general methodology of establishing and investigating social energy is proposed, which is based on the ACP approach, i.e., 'artificial systems' (A), 'computational experiments' (C) and 'parallel execution' (P), and parallel system methodology. A case study on the University of Denver (DU) campus grid is provided and studied to demonstrate the social energy concept. In the concluding remarks, we discuss the technical pathway, in both social and nature sciences, to social energy, and our vision on its future.« less

Implementation and analysis of a Navier-Stokes algorithm on parallel computers

NASA Technical Reports Server (NTRS)

Fatoohi, Raad A.; Grosch, Chester E.

1988-01-01

The results of the implementation of a Navier-Stokes algorithm on three parallel/vector computers are presented. The object of this research is to determine how well, or poorly, a single numerical algorithm would map onto three different architectures. The algorithm is a compact difference scheme for the solution of the incompressible, two-dimensional, time-dependent Navier-Stokes equations. The computers were chosen so as to encompass a variety of architectures. They are the following: the MPP, an SIMD machine with 16K bit serial processors; Flex/32, an MIMD machine with 20 processors; and Cray/2. The implementation of the algorithm is discussed in relation to these architectures and measures of the performance on each machine are given. The basic comparison is among SIMD instruction parallelism on the MPP, MIMD process parallelism on the Flex/32, and vectorization of a serial code on the Cray/2. Simple performance models are used to describe the performance. These models highlight the bottlenecks and limiting factors for this algorithm on these architectures. Finally, conclusions are presented.

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.

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.

Distribution Locational Real-Time Pricing Based Smart Building Control and Management

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

Hao, Jun; Dai, Xiaoxiao; Zhang, Yingchen

This paper proposes an real-virtual parallel computing scheme for smart building operations aiming at augmenting overall social welfare. The University of Denver's campus power grid and Ritchie fitness center is used for demonstrating the proposed approach. An artificial virtual system is built in parallel to the real physical system to evaluate the overall social cost of the building operation based on the social science based working productivity model, numerical experiment based building energy consumption model and the power system based real-time pricing mechanism. Through interactive feedback exchanged between the real and virtual system, enlarged social welfare, including monetary cost reductionmore » and energy saving, as well as working productivity improvements, can be achieved.« less

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.

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.

Data parallel sorting for particle simulation

NASA Technical Reports Server (NTRS)

Dagum, Leonardo

1992-01-01

Sorting on a parallel architecture is a communications intensive event which can incur a high penalty in applications where it is required. In the case of particle simulation, only integer sorting is necessary, and sequential implementations easily attain the minimum performance bound of O (N) for N particles. Parallel implementations, however, have to cope with the parallel sorting problem which, in addition to incurring a heavy communications cost, can make the minimun performance bound difficult to attain. This paper demonstrates how the sorting problem in a particle simulation can be reduced to a merging problem, and describes an efficient data parallel algorithm to solve this merging problem in a particle simulation. The new algorithm is shown to be optimal under conditions usual for particle simulation, and its fieldwise implementation on the Connection Machine is analyzed in detail. The new algorithm is about four times faster than a fieldwise implementation of radix sort on the Connection Machine.

Assessment of OLED displays for vision research

PubMed Central

Cooper, Emily A.; Jiang, Haomiao; Vildavski, Vladimir; Farrell, Joyce E.; Norcia, Anthony M.

2013-01-01

Vision researchers rely on visual display technology for the presentation of stimuli to human and nonhuman observers. Verifying that the desired and displayed visual patterns match along dimensions such as luminance, spectrum, and spatial and temporal frequency is an essential part of developing controlled experiments. With cathode-ray tubes (CRTs) becoming virtually unavailable on the commercial market, it is useful to determine the characteristics of newly available displays based on organic light emitting diode (OLED) panels to determine how well they may serve to produce visual stimuli. This report describes a series of measurements summarizing the properties of images displayed on two commercially available OLED displays: the Sony Trimaster EL BVM-F250 and PVM-2541. The results show that the OLED displays have large contrast ratios, wide color gamuts, and precise, well-behaved temporal responses. Correct adjustment of the settings on both models produced luminance nonlinearities that were well predicted by a power function (“gamma correction”). Both displays have adjustable pixel independence and can be set to have little to no spatial pixel interactions. OLED displays appear to be a suitable, or even preferable, option for many vision research applications. PMID:24155345

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

A high performance parallel algorithm for 1-D FFT

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

Agarwal, R.C.; Gustavson, F.G.; Zubair, M.

1994-12-31

In this paper the authors propose a parallel high performance FFT algorithm based on a multi-dimensional formulation. They use this to solve a commonly encountered FFT based kernel on a distributed memory parallel machine, the IBM scalable parallel system, SP1. The kernel requires a forward FFT computation of an input sequence, multiplication of the transformed data by a coefficient array, and finally an inverse FFT computation of the resultant data. They show that the multi-dimensional formulation helps in reducing the communication costs and also improves the single node performance by effectively utilizing the memory system of the node. They implementedmore » this kernel on the IBM SP1 and observed a performance of 1.25 GFLOPS on a 64-node machine.« less

A Pervasive Parallel Processing Framework for Data Visualization and Analysis at Extreme Scale

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

Moreland, Kenneth; Geveci, Berk

2014-11-01

The evolution of the computing world from teraflop to petaflop has been relatively effortless, with several of the existing programming models scaling effectively to the petascale. The migration to exascale, however, poses considerable challenges. All industry trends infer that the exascale machine will be built using processors containing hundreds to thousands of cores per chip. It can be inferred that efficient concurrency on exascale machines requires a massive amount of concurrent threads, each performing many operations on a localized piece of data. Currently, visualization libraries and applications are based off what is known as the visualization pipeline. In the pipelinemore » model, algorithms are encapsulated as filters with inputs and outputs. These filters are connected by setting the output of one component to the input of another. Parallelism in the visualization pipeline is achieved by replicating the pipeline for each processing thread. This works well for today’s distributed memory parallel computers but cannot be sustained when operating on processors with thousands of cores. Our project investigates a new visualization framework designed to exhibit the pervasive parallelism necessary for extreme scale machines. Our framework achieves this by defining algorithms in terms of worklets, which are localized stateless operations. Worklets are atomic operations that execute when invoked unlike filters, which execute when a pipeline request occurs. The worklet design allows execution on a massive amount of lightweight threads with minimal overhead. Only with such fine-grained parallelism can we hope to fill the billions of threads we expect will be necessary for efficient computation on an exascale machine.« less

A Data Parallel Multizone Navier-Stokes Code

NASA Technical Reports Server (NTRS)

Jespersen, Dennis C.; Levit, Creon; Kwak, Dochan (Technical Monitor)

1995-01-01

We have developed a data parallel multizone compressible Navier-Stokes code on the Connection Machine CM-5. The code is set up for implicit time-stepping on single or multiple structured grids. For multiple grids and geometrically complex problems, we follow the "chimera" approach, where flow data on one zone is interpolated onto another in the region of overlap. We will describe our design philosophy and give some timing results for the current code. The design choices can be summarized as: 1. finite differences on structured grids; 2. implicit time-stepping with either distributed solves or data motion and local solves; 3. sequential stepping through multiple zones with interzone data transfer via a distributed data structure. We have implemented these ideas on the CM-5 using CMF (Connection Machine Fortran), a data parallel language which combines elements of Fortran 90 and certain extensions, and which bears a strong similarity to High Performance Fortran (HPF). One interesting feature is the issue of turbulence modeling, where the architecture of a parallel machine makes the use of an algebraic turbulence model awkward, whereas models based on transport equations are more natural. We will present some performance figures for the code on the CM-5, and consider the issues involved in transitioning the code to HPF for portability to other parallel platforms.

Ordered fast fourier transforms on a massively parallel hypercube multiprocessor

NASA Technical Reports Server (NTRS)

Tong, Charles; Swarztrauber, Paul N.

1989-01-01

Design alternatives for ordered Fast Fourier Transformation (FFT) algorithms were examined on massively parallel hypercube multiprocessors such as the Connection Machine. Particular emphasis is placed on reducing communication which is known to dominate the overall computing time. To this end, the order and computational phases of the FFT were combined, and the sequence to processor maps that reduce communication were used. The class of ordered transforms is expanded to include any FFT in which the order of the transform is the same as that of the input sequence. Two such orderings are examined, namely, standard-order and A-order which can be implemented with equal ease on the Connection Machine where orderings are determined by geometries and priorities. If the sequence has N = 2 exp r elements and the hypercube has P = 2 exp d processors, then a standard-order FFT can be implemented with d + r/2 + 1 parallel transmissions. An A-order sequence can be transformed with 2d - r/2 parallel transmissions which is r - d + 1 fewer than the standard order. A parallel method for computing the trigonometric coefficients is presented that does not use trigonometric functions or interprocessor communication. A performance of 0.9 GFLOPS was obtained for an A-order transform on the Connection Machine.

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.

Fast parallel 3D profilometer with DMD technology

NASA Astrophysics Data System (ADS)

Hou, Wenmei; Zhang, Yunbo

2011-12-01

Confocal microscope has been a powerful tool for three-dimensional profile analysis. Single mode confocal microscope is limited by scanning speed. This paper presents a 3D profilometer prototype of parallel confocal microscope based on DMD (Digital Micromirror Device). In this system the DMD takes the place of Nipkow Disk which is a classical parallel scanning scheme to realize parallel lateral scanning technique. Operated with certain pattern, the DMD generates a virtual pinholes array which separates the light into multi-beams. The key parameters that affect the measurement (pinhole size and the lateral scanning distance) can be configured conveniently by different patterns sent to DMD chip. To avoid disturbance between two virtual pinholes working at the same time, a scanning strategy is adopted. Depth response curve both axial and abaxial were extract. Measurement experiments have been carried out on silicon structured sample, and axial resolution of 55nm is achieved.

Conceptual Study of Permanent Magnet Machine Ship Propulsion Systems

DTIC Science & Technology

1977-12-01

cycloconverter subsystem is designed using advanced thyristors and can be either water or air cooled. The machine-cycloconverter, many-phase or parallel...Turnb, Phase, Poles, Air Gap ................................. 3-9 3-5 Machine Characteristics Versus Number of Poles (large machine, 40 000 hp). Poles...cylindrical permanent magnet generator forces the power conditioner to provide for both frequency change and voltage control. The complexity of this dual

Pre-resistance-welding resistance check

DOEpatents

Destefan, Dennis E.; Stompro, David A.

1991-01-01

A preweld resistance check for resistance welding machines uses an open circuited measurement to determine the welding machine resistance, a closed circuit measurement to determine the parallel resistance of a workpiece set and the machine, and a calculation to determine the resistance of the workpiece set. Any variation in workpiece set or machine resistance is an indication that the weld may be different from a control weld.

Advances in Parallelization for Large Scale Oct-Tree Mesh Generation

NASA Technical Reports Server (NTRS)

O'Connell, Matthew; Karman, Steve L.

2015-01-01

Despite great advancements in the parallelization of numerical simulation codes over the last 20 years, it is still common to perform grid generation in serial. Generating large scale grids in serial often requires using special "grid generation" compute machines that can have more than ten times the memory of average machines. While some parallel mesh generation techniques have been proposed, generating very large meshes for LES or aeroacoustic simulations is still a challenging problem. An automated method for the parallel generation of very large scale off-body hierarchical meshes is presented here. This work enables large scale parallel generation of off-body meshes by using a novel combination of parallel grid generation techniques and a hybrid "top down" and "bottom up" oct-tree method. Meshes are generated using hardware commonly found in parallel compute clusters. The capability to generate very large meshes is demonstrated by the generation of off-body meshes surrounding complex aerospace geometries. Results are shown including a one billion cell mesh generated around a Predator Unmanned Aerial Vehicle geometry, which was generated on 64 processors in under 45 minutes.

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.

Towards a Better Distributed Framework for Learning Big Data

DTIC Science & Technology

2017-06-14

UNLIMITED: PB Public Release 13. SUPPLEMENTARY NOTES 14. ABSTRACT This work aimed at solving issues in distributed machine learning. The PI’s team proposed...communication load. Finally, the team proposed the parallel least-squares policy iteration (parallel LSPI) to parallelize a reinforcement policy learning. 15

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

Parallelization of Rocket Engine Simulator Software (PRESS)

NASA Technical Reports Server (NTRS)

Cezzar, Ruknet

1998-01-01

We have outlined our work in the last half of the funding period. We have shown how a demo package for RESSAP using MPI can be done. However, we also mentioned the difficulties with the UNIX platform. We have reiterated some of the suggestions made during the presentation of the progress of the at Fourth Annual HBCU Conference. Although we have discussed, in some detail, how TURBDES/PUMPDES software can be run in parallel using MPI, at present, we are unable to experiment any further with either MPI or PVM. Due to X windows not being implemented, we are also not able to experiment further with XPVM, which it will be recalled, has a nice GUI interface. There are also some concerns, on our part, about MPI being an appropriate tool. The best thing about MPr is that it is public domain. Although and plenty of documentation exists for the intricacies of using MPI, little information is available on its actual implementations. Other than very typical, somewhat contrived examples, such as Jacobi algorithm for solving Laplace's equation, there are few examples which can readily be applied to real situations, such as in our case. In effect, the review of literature on both MPI and PVM, and there is a lot, indicate something similar to the enormous effort which was spent on LISP and LISP-like languages as tools for artificial intelligence research. During the development of a book on programming languages [12], when we searched the literature for very simple examples like taking averages, reading and writing records, multiplying matrices, etc., we could hardly find a any! Yet, so much was said and done on that topic in academic circles. It appears that we faced the same problem with MPI, where despite significant documentation, we could not find even a simple example which supports course-grain parallelism involving only a few processes. From the foregoing, it appears that a new direction may be required for more productive research during the extension period (10/19/98 - 10/18/99). At the least, the research would need to be done on Windows 95/Windows NT based platforms. Moreover, with the acquisition of Lahey Fortran package for PC platform, and the existing Borland C + + 5. 0, we can do work on C + + wrapper issues. We have carefully studied the blueprint for Space Transportation Propulsion Integrated Design Environment for the next 25 years [13] and found the inclusion of HBCUs in that effort encouraging. Especially in the long period for which a map is provided, there is no doubt that HBCUs will grow and become better equipped to do meaningful research. In the shorter period, as was suggested in our presentation at the HBCU conference, some key decisions regarding the aging Fortran based software for rocket propellants will need to be made. One important issue is whether or not object oriented languages such as C + + or Java should be used for distributed computing. Whether or not "distributed computing" is necessary for the existing software is yet another, larger, question to be tackled with.

Parallel-distributed mobile robot simulator

NASA Astrophysics Data System (ADS)

Okada, Hiroyuki; Sekiguchi, Minoru; Watanabe, Nobuo

1996-06-01

The aim of this project is to achieve an autonomous learning and growth function based on active interaction with the real world. It should also be able to autonomically acquire knowledge about the context in which jobs take place, and how the jobs are executed. This article describes a parallel distributed movable robot system simulator with an autonomous learning and growth function. The autonomous learning and growth function which we are proposing is characterized by its ability to learn and grow through interaction with the real world. When the movable robot interacts with the real world, the system compares the virtual environment simulation with the interaction result in the real world. The system then improves the virtual environment to match the real-world result more closely. This the system learns and grows. It is very important that such a simulation is time- realistic. The parallel distributed movable robot simulator was developed to simulate the space of a movable robot system with an autonomous learning and growth function. The simulator constructs a virtual space faithful to the real world and also integrates the interfaces between the user, the actual movable robot and the virtual movable robot. Using an ultrafast CG (computer graphics) system (FUJITSU AG series), time-realistic 3D CG is displayed.

Parallelizing serial code for a distributed processing environment with an application to high frequency electromagnetic scattering

NASA Astrophysics Data System (ADS)

Work, Paul R.

1991-12-01

This thesis investigates the parallelization of existing serial programs in computational electromagnetics for use in a parallel environment. Existing algorithms for calculating the radar cross section of an object are covered, and a ray-tracing code is chosen for implementation on a parallel machine. Current parallel architectures are introduced and a suitable parallel machine is selected for the implementation of the chosen ray-tracing algorithm. The standard techniques for the parallelization of serial codes are discussed, including load balancing and decomposition considerations, and appropriate methods for the parallelization effort are selected. A load balancing algorithm is modified to increase the efficiency of the application, and a high level design of the structure of the serial program is presented. A detailed design of the modifications for the parallel implementation is also included, with both the high level and the detailed design specified in a high level design language called UNITY. The correctness of the design is proven using UNITY and standard logic operations. The theoretical and empirical results show that it is possible to achieve an efficient parallel application for a serial computational electromagnetic program where the characteristics of the algorithm and the target architecture critically influence the development of such an implementation.

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

Establishing a group of endpoints to support collective operations without specifying unique identifiers for any endpoints

DOEpatents

Archer, Charles J.; Blocksom, Michael A.; Ratterman, Joseph D.; Smith, Brian E.; Xue, Hanghon

2016-02-02

A parallel computer executes a number of tasks, each task includes a number of endpoints and the endpoints are configured to support collective operations. In such a parallel computer, establishing a group of endpoints receiving a user specification of a set of endpoints included in a global collection of endpoints, where the user specification defines the set in accordance with a predefined virtual representation of the endpoints, the predefined virtual representation is a data structure setting forth an organization of tasks and endpoints included in the global collection of endpoints and the user specification defines the set of endpoints without a user specification of a particular endpoint; and defining a group of endpoints in dependence upon the predefined virtual representation of the endpoints and the user specification.

Towards the Teraflop CFD

NASA Technical Reports Server (NTRS)

Schreiber, Robert; Simon, Horst D.

1992-01-01

We are surveying current projects in the area of parallel supercomputers. The machines considered here will become commercially available in the 1990 - 1992 time frame. All are suitable for exploring the critical issues in applying parallel processors to large scale scientific computations, in particular CFD calculations. This chapter presents an overview of the surveyed machines, and a detailed analysis of the various architectural and technology approaches taken. Particular emphasis is placed on the feasibility of a Teraflops capability following the paths proposed by various developers.

Research on precision grinding technology of large scale and ultra thin optics

NASA Astrophysics Data System (ADS)

Zhou, Lian; Wei, Qiancai; Li, Jie; Chen, Xianhua; Zhang, Qinghua

2018-03-01

The flatness and parallelism error of large scale and ultra thin optics have an important influence on the subsequent polishing efficiency and accuracy. In order to realize the high precision grinding of those ductile elements, the low deformation vacuum chuck was designed first, which was used for clamping the optics with high supporting rigidity in the full aperture. Then the optics was planar grinded under vacuum adsorption. After machining, the vacuum system was turned off. The form error of optics was on-machine measured using displacement sensor after elastic restitution. The flatness would be convergenced with high accuracy by compensation machining, whose trajectories were integrated with the measurement result. For purpose of getting high parallelism, the optics was turned over and compensation grinded using the form error of vacuum chuck. Finally, the grinding experiment of large scale and ultra thin fused silica optics with aperture of 430mm×430mm×10mm was performed. The best P-V flatness of optics was below 3 μm, and parallelism was below 3 ″. This machining technique has applied in batch grinding of large scale and ultra thin optics.

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

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…

Parallel algorithms for boundary value problems

NASA Technical Reports Server (NTRS)

Lin, Avi

1990-01-01

A general approach to solve boundary value problems numerically in a parallel environment is discussed. The basic algorithm consists of two steps: the local step where all the P available processors work in parallel, and the global step where one processor solves a tridiagonal linear system of the order P. The main advantages of this approach are two fold. First, this suggested approach is very flexible, especially in the local step and thus the algorithm can be used with any number of processors and with any of the SIMD or MIMD machines. Secondly, the communication complexity is very small and thus can be used as easily with shared memory machines. Several examples for using this strategy are discussed.

Vascular system modeling in parallel environment - distributed and shared memory approaches

PubMed Central

Jurczuk, Krzysztof; Kretowski, Marek; Bezy-Wendling, Johanne

2011-01-01

The paper presents two approaches in parallel modeling of vascular system development in internal organs. In the first approach, new parts of tissue are distributed among processors and each processor is responsible for perfusing its assigned parts of tissue to all vascular trees. Communication between processors is accomplished by passing messages and therefore this algorithm is perfectly suited for distributed memory architectures. The second approach is designed for shared memory machines. It parallelizes the perfusion process during which individual processing units perform calculations concerning different vascular trees. The experimental results, performed on a computing cluster and multi-core machines, show that both algorithms provide a significant speedup. PMID:21550891

Parallel matrix multiplication on the Connection Machine

NASA Technical Reports Server (NTRS)

Tichy, Walter F.

1988-01-01

Matrix multiplication is a computation and communication intensive problem. Six parallel algorithms for matrix multiplication on the Connection Machine are presented and compared with respect to their performance and processor usage. For n by n matrices, the algorithms have theoretical running times of O(n to the 2nd power log n), O(n log n), O(n), and O(log n), and require n, n to the 2nd power, n to the 2nd power, and n to the 3rd power processors, respectively. With careful attention to communication patterns, the theoretically predicted runtimes can indeed be achieved in practice. The parallel algorithms illustrate the tradeoffs between performance, communication cost, and processor usage.

PCLIPS: Parallel CLIPS

NASA Technical Reports Server (NTRS)

Gryphon, Coranth D.; Miller, Mark D.

1991-01-01

PCLIPS (Parallel CLIPS) is a set of extensions to the C Language Integrated Production System (CLIPS) expert system language. PCLIPS is intended to provide an environment for the development of more complex, extensive expert systems. Multiple CLIPS expert systems are now capable of running simultaneously on separate processors, or separate machines, thus dramatically increasing the scope of solvable tasks within the expert systems. As a tool for parallel processing, PCLIPS allows for an expert system to add to its fact-base information generated by other expert systems, thus allowing systems to assist each other in solving a complex problem. This allows individual expert systems to be more compact and efficient, and thus run faster or on smaller machines.

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

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.

Parallel Algorithms for Computer Vision

DTIC Science & Technology

1990-04-01

NA86-1, Thinking Machines Corporation, Cambridge, MA, December 1986. [43] J. Little, G. Blelloch, and T. Cass. How to program the connection machine for... to program the connection machine for computer vision. In Proc. Workshop on Comp. Architecture for Pattern Analysis and Machine Intell., 1987. [92] J...In Proceedings of SPIE Conf. on Advances in Intelligent Robotics Systems, Bellingham, VA, 1987. SPIE. [91] J. Little, G. Blelloch, and T. Cass. How

Sputnik: ad hoc distributed computation.

PubMed

Völkel, Gunnar; Lausser, Ludwig; Schmid, Florian; Kraus, Johann M; Kestler, Hans A

2015-04-15

In bioinformatic applications, computationally demanding algorithms are often parallelized to speed up computation. Nevertheless, setting up computational environments for distributed computation is often tedious. Aim of this project were the lightweight ad hoc set up and fault-tolerant computation requiring only a Java runtime, no administrator rights, while utilizing all CPU cores most effectively. The Sputnik framework provides ad hoc distributed computation on the Java Virtual Machine which uses all supplied CPU cores fully. It provides a graphical user interface for deployment setup and a web user interface displaying the current status of current computation jobs. Neither a permanent setup nor administrator privileges are required. We demonstrate the utility of our approach on feature selection of microarray data. The Sputnik framework is available on Github http://github.com/sysbio-bioinf/sputnik under the Eclipse Public License. hkestler@fli-leibniz.de or hans.kestler@uni-ulm.de Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Design and manufacture of the integrated field unit for the NIRSpec spectrometer on JWST

NASA Astrophysics Data System (ADS)

Lobb, Daniel; Robertson, David; Closs, Martin; Barnes, Andy

2008-09-01

The NIRSpec imaging spectrometer, which forms part of the James Webb Space Telescope instrumentation, will include an integrated field unit (IFU). The IFU will be tasked specifically with efficient analysis of extended objects, including galaxies; it will accept a square image area at the spectrometer entrance field, dissect this area into 30 parallel sub-slits, and image the sub-slits end-to-end, forming a single virtual entrance slit. The IFU, uses all-mirror optics to operate over the spectral range 700nm to 5000nm. 95 mirrors and the main support structure are made in a common aluminium alloy, to achieve athermal performance down to an operating temperature of around 30K. Relatively complex mirror surface shapes are produced by diamond machining. The IFU has been designed and constructed by SSTL, with optics produced by CfAI; the unit is currently undergoing performance tests. This paper describes the IFU optical design and performance, and outlines the mirror manufacturing methods and alignment procedures.

Analysis of multigrid methods on massively parallel computers: Architectural implications

NASA Technical Reports Server (NTRS)

Matheson, Lesley R.; Tarjan, Robert E.

1993-01-01

We study the potential performance of multigrid algorithms running on massively parallel computers with the intent of discovering whether presently envisioned machines will provide an efficient platform for such algorithms. We consider the domain parallel version of the standard V cycle algorithm on model problems, discretized using finite difference techniques in two and three dimensions on block structured grids of size 10(exp 6) and 10(exp 9), respectively. Our models of parallel computation were developed to reflect the computing characteristics of the current generation of massively parallel multicomputers. These models are based on an interconnection network of 256 to 16,384 message passing, 'workstation size' processors executing in an SPMD mode. The first model accomplishes interprocessor communications through a multistage permutation network. The communication cost is a logarithmic function which is similar to the costs in a variety of different topologies. The second model allows single stage communication costs only. Both models were designed with information provided by machine developers and utilize implementation derived parameters. With the medium grain parallelism of the current generation and the high fixed cost of an interprocessor communication, our analysis suggests an efficient implementation requires the machine to support the efficient transmission of long messages, (up to 1000 words) or the high initiation cost of a communication must be significantly reduced through an alternative optimization technique. Furthermore, with variable length message capability, our analysis suggests the low diameter multistage networks provide little or no advantage over a simple single stage communications network.

Plasmacytoid Dendritic Cells Promote Host Defense Against Acute Pneumovirus Infection via the TLR7-MyD88-Dependent Signaling Pathway

PubMed Central

Davidson, Sophia; Kaiko, Gerard; Loh, Zhixuan; Lalwani, Amit; Zhang, Vivian; Spann, Kirsten; Foo, Shen Yun; Hansbro, Nicole; Uematsu, Satoshi; Akira, Shizuo; Matthaei, Klaus I.; Rosenberg, Helene F.; Foster, Paul S.; Phipps, Simon

2012-01-01

Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection in infants. In human infants, plasmacytoid dendritic cells (pDC) are recruited to the nasal compartment during infection and initiate host defense through the secretion of type I IFN, IL-12 and IL-6. However, RSV-infected pDCs are refractory to TLR7-mediated activation. Here, we used the rodent-specific pathogen, pneumonia virus of mice (PVM), to determine the contribution of pDC and TLR7-signaling to the development of the innate inflammatory and early adaptive immune response. In wild-type (WT) but not TLR7- or myeloid differentiation protein 88 (MyD88)-deficient mice, PVM inoculation led to a marked infiltration of pDCs and increased expression of type I, II and III IFNs. The delayed induction of IFNs in the absence of TLR7 or MyD88 was associated with a diminished innate inflammatory response and augmented virus recovery from lung tissue. In the absence of TLR7, PVM-specific CD8+ T cell cytokine production was abrogated. The adoptive transfer of TLR7-sufficient but not TLR7-deficient pDC to TLR7-gene-deleted mice recapitulated the antiviral responses observed in WT mice and promoted virus clearance. In summary, TLR7-mediated signaling by pDC is required for appropriate innate responses to acute pneumovirus infection. It is conceivable that as-yet-unidentified defects in the TLR7 signaling pathway may be associated with elevated levels of RSV-associated morbidity and mortality among otherwise healthy human infants. PMID:21482736

Culture media-based selection of endothelial cells, pericytes, and perivascular-resident macrophage-like melanocytes from the young mouse vestibular system.

PubMed

Zhang, Jinhui; Chen, Songlin; Cai, Jing; Hou, Zhiqiang; Wang, Xiaohan; Kachelmeier, Allan; Shi, Xiaorui

2017-03-01

The vestibular blood-labyrinth barrier (BLB) is comprised of perivascular-resident macrophage-like melanocytes (PVM/Ms) and pericytes (PCs), in addition to endothelial cells (ECs) and basement membrane (BM), and bears strong resemblance to the cochlear BLB in the stria vascularis. Over the past few decades, in vitro cell-based models have been widely used in blood-brain barrier (BBB) and blood-retina barrier (BRB) research, and have proved to be powerful tools for studying cell-cell interactions in their respective organs. Study of both the vestibular and strial BLB has been limited by the unavailability of primary culture cells from these barriers. To better understand how barrier component cells interact in the vestibular system to control BLB function, we developed a novel culture medium-based method for obtaining EC, PC, and PVM/M primary cells from tiny explants of the semicircular canal, sacculus, utriculus, and ampullae tissue of young mouse ears at post-natal age 8-12 d. Each phenotype is grown in a specific culture medium which selectively supports the phenotype in a mixed population of vestibular cell types. The unwanted phenotypes do not survive passaging. The protocol does not require additional equipment or special enzyme treatment. The harvesting process takes less than 2 h. Primary cell types are generated within 7-10 d. The primary culture ECs, PCs, and PVM/M shave consistent phenotypes more than 90% pure after two passages (∼ 3 weeks). The highly purified primary cell lines can be used for studying cell-cell interactions, barrier permeability, and angiogenesis. Copyright © 2017 Elsevier B.V. All rights reserved.

Dynamic Load Balancing for Grid Partitioning on a SP-2 Multiprocessor: A Framework

NASA Technical Reports Server (NTRS)

Sohn, Andrew; Simon, Horst; Lasinski, T. A. (Technical Monitor)

1994-01-01

Computational requirements of full scale computational fluid dynamics change as computation progresses on a parallel machine. The change in computational intensity causes workload imbalance of processors, which in turn requires a large amount of data movement at runtime. If parallel CFD is to be successful on a parallel or massively parallel machine, balancing of the runtime load is indispensable. Here a framework is presented for dynamic load balancing for CFD applications, called Jove. One processor is designated as a decision maker Jove while others are assigned to computational fluid dynamics. Processors running CFD send flags to Jove in a predetermined number of iterations to initiate load balancing. Jove starts working on load balancing while other processors continue working with the current data and load distribution. Jove goes through several steps to decide if the new data should be taken, including preliminary evaluate, partition, processor reassignment, cost evaluation, and decision. Jove running on a single EBM SP2 node has been completely implemented. Preliminary experimental results show that the Jove approach to dynamic load balancing can be effective for full scale grid partitioning on the target machine IBM SP2.

Dynamic Load Balancing For Grid Partitioning on a SP-2 Multiprocessor: A Framework

NASA Technical Reports Server (NTRS)

Sohn, Andrew; Simon, Horst; Lasinski, T. A. (Technical Monitor)

1994-01-01

Computational requirements of full scale computational fluid dynamics change as computation progresses on a parallel machine. The change in computational intensity causes workload imbalance of processors, which in turn requires a large amount of data movement at runtime. If parallel CFD is to be successful on a parallel or massively parallel machine, balancing of the runtime load is indispensable. Here a framework is presented for dynamic load balancing for CFD applications, called Jove. One processor is designated as a decision maker Jove while others are assigned to computational fluid dynamics. Processors running CFD send flags to Jove in a predetermined number of iterations to initiate load balancing. Jove starts working on load balancing while other processors continue working with the current data and load distribution. Jove goes through several steps to decide if the new data should be taken, including preliminary evaluate, partition, processor reassignment, cost evaluation, and decision. Jove running on a single IBM SP2 node has been completely implemented. Preliminary experimental results show that the Jove approach to dynamic load balancing can be effective for full scale grid partitioning on the target machine IBM SP2.

The influence of foot position on scrum kinetics during machine scrummaging.

PubMed

Bayne, Helen; Kat, Cor-Jacques

2018-05-23

The purpose of this study was to investigate the effect of variations in the alignment of the feet on scrum kinetics during machine scrummaging. Twenty nine rugby forwards from amateur-level teams completed maximal scrum efforts against an instrumented scrum machine, with the feet in parallel and non-parallel positions. Three-dimensional forces, the moment about the vertical axis and sagittal plane joint angles were measured during the sustained pushing phase. There was a decrease in the magnitude of the resultant force and compression force in both of the non-parallel conditions compared to parallel and larger compression forces were associated with more extended hip and knee angles. Scrummaging with the left foot forward resulted in the lateral force being directed more towards the left and the turning moment becoming more clockwise. These directional changes were reversed when scrummaging with the right foot forward. Scrummaging with the right foot positioned ahead of the left may serve to counteract the natural clockwise wheel of the live scrum and could be used to achieve an anti-clockwise rotation of the scrum for tactical reasons. However, this would be associated with lower resultant forces and a greater lateral shear force component directed towards the right.

On-Line Scheduling of Parallel Machines

DTIC Science & Technology

1990-11-01

machine without losing any work; this is referred to as the preemptive model. In contrast to the nonpreemptive model which we have considered in this paper...that there exists no schedule of length d. The 2-relaxed decision procedure is as follows. Put each job into the queue of the slowest machine Mk such...in their queues . If a machine’s queue is empty it takes jobs to process from the queue of the first machine that is slower than it and that has a

Design, Results, Evolution and Status of the ATLAS Simulation at Point1 Project

NASA Astrophysics Data System (ADS)

Ballestrero, S.; Batraneanu, S. M.; Brasolin, F.; Contescu, C.; Fazio, D.; Di Girolamo, A.; Lee, C. J.; Pozo Astigarraga, M. E.; Scannicchio, D. A.; Sedov, A.; Twomey, M. S.; Wang, F.; Zaytsev, A.

2015-12-01

During the LHC Long Shutdown 1 (LSI) period, that started in 2013, the Simulation at Point1 (Sim@P1) project takes advantage, in an opportunistic way, of the TDAQ (Trigger and Data Acquisition) HLT (High-Level Trigger) farm of the ATLAS experiment. This farm provides more than 1300 compute nodes, which are particularly suited for running event generation and Monte Carlo production jobs that are mostly CPU and not I/O bound. It is capable of running up to 2700 Virtual Machines (VMs) each with 8 CPU cores, for a total of up to 22000 parallel jobs. This contribution gives a review of the design, the results, and the evolution of the Sim@P1 project, operating a large scale OpenStack based virtualized platform deployed on top of the ATLAS TDAQ HLT farm computing resources. During LS1, Sim@P1 was one of the most productive ATLAS sites: it delivered more than 33 million CPU-hours and it generated more than 1.1 billion Monte Carlo events. The design aspects are presented: the virtualization platform exploited by Sim@P1 avoids interferences with TDAQ operations and it guarantees the security and the usability of the ATLAS private network. The cloud mechanism allows the separation of the needed support on both infrastructural (hardware, virtualization layer) and logical (Grid site support) levels. This paper focuses on the operational aspects of such a large system during the upcoming LHC Run 2 period: simple, reliable, and efficient tools are needed to quickly switch from Sim@P1 to TDAQ mode and back, to exploit the resources when they are not used for the data acquisition, even for short periods. The evolution of the central OpenStack infrastructure is described, as it was upgraded from Folsom to the Icehouse release, including the scalability issues addressed.

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

Implementation of an ADI method on parallel computers

NASA Technical Reports Server (NTRS)

Fatoohi, Raad A.; Grosch, Chester E.

1987-01-01

The implementation of an ADI method for solving the diffusion equation on three parallel/vector computers is discussed. The computers were chosen so as to encompass a variety of architectures. They are: the MPP, an SIMD machine with 16K bit serial processors; FLEX/32, an MIMD machine with 20 processors; and CRAY/2, an MIMD machine with four vector processors. The Gaussian elimination algorithm is used to solve a set of tridiagonal systems on the FLEX/32 and CRAY/2 while the cyclic elimination algorithm is used to solve these systems on the MPP. The implementation of the method is discussed in relation to these architectures and measures of the performance on each machine are given. Simple performance models are used to describe the performance. These models highlight the bottlenecks and limiting factors for this algorithm on these architectures. Finally, conclusions are presented.

Implementation of an ADI method on parallel computers

NASA Technical Reports Server (NTRS)

Fatoohi, Raad A.; Grosch, Chester E.

1987-01-01

In this paper the implementation of an ADI method for solving the diffusion equation on three parallel/vector computers is discussed. The computers were chosen so as to encompass a variety of architectures. They are the MPP, an SIMD machine with 16-Kbit serial processors; Flex/32, an MIMD machine with 20 processors; and Cray/2, an MIMD machine with four vector processors. The Gaussian elimination algorithm is used to solve a set of tridiagonal systems on the Flex/32 and Cray/2 while the cyclic elimination algorithm is used to solve these systems on the MPP. The implementation of the method is discussed in relation to these architectures and measures of the performance on each machine are given. Simple performance models are used to describe the performance. These models highlight the bottlenecks and limiting factors for this algorithm on these architectures. Finally conclusions are presented.

Empirical Evaluation of Conservative and Optimistic Discrete Event Execution on Cloud and VM Platforms

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

Yoginath, Srikanth B; Perumalla, Kalyan S

2013-01-01

Virtual machine (VM) technologies, especially those offered via Cloud platforms, present new dimensions with respect to performance and cost in executing parallel discrete event simulation (PDES) applications. Due to the introduction of overall cost as a metric, the choice of the highest-end computing configuration is no longer the most economical one. Moreover, runtime dynamics unique to VM platforms introduce new performance characteristics, and the variety of possible VM configurations give rise to a range of choices for hosting a PDES run. Here, an empirical study of these issues is undertaken to guide an understanding of the dynamics, trends and trade-offsmore » in executing PDES on VM/Cloud platforms. Performance results and cost measures are obtained from actual execution of a range of scenarios in two PDES benchmark applications on the Amazon Cloud offerings and on a high-end VM host machine. The data reveals interesting insights into the new VM-PDES dynamics that come into play and also leads to counter-intuitive guidelines with respect to choosing the best and second-best configurations when overall cost of execution is considered. In particular, it is found that choosing the highest-end VM configuration guarantees neither the best runtime nor the least cost. Interestingly, choosing a (suitably scaled) low-end VM configuration provides the least overall cost without adversely affecting the total runtime.« less

Testing an Open Source installation and server provisioning tool for the INFN CNAF Tierl Storage system

NASA Astrophysics Data System (ADS)

Pezzi, M.; Favaro, M.; Gregori, D.; Ricci, P. P.; Sapunenko, V.

2014-06-01

In large computing centers, such as the INFN CNAF Tier1 [1], is essential to be able to configure all the machines, depending on use, in an automated way. For several years at the Tier1 has been used Quattor[2], a server provisioning tool, which is currently used in production. Nevertheless we have recently started a comparison study involving other tools able to provide specific server installation and configuration features and also offer a proper full customizable solution as an alternative to Quattor. Our choice at the moment fell on integration between two tools: Cobbler [3] for the installation phase and Puppet [4] for the server provisioning and management operation. The tool should provide the following properties in order to replicate and gradually improve the current system features: implement a system check for storage specific constraints such as kernel modules black list at boot time to avoid undesired SAN (Storage Area Network) access during disk partitioning; a simple and effective mechanism for kernel upgrade and downgrade; the ability of setting package provider using yum, rpm or apt; easy to use Virtual Machine installation support including bonding and specific Ethernet configuration; scalability for managing thousands of nodes and parallel installations. This paper describes the results of the comparison and the tests carried out to verify the requirements and the new system suitability in the INFN-T1 environment.

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.

Performance Evaluation of Communication Software Systems for Distributed Computing

NASA Technical Reports Server (NTRS)

Fatoohi, Rod

1996-01-01

In recent years there has been an increasing interest in object-oriented distributed computing since it is better quipped to deal with complex systems while providing extensibility, maintainability, and reusability. At the same time, several new high-speed network technologies have emerged for local and wide area networks. However, the performance of networking software is not improving as fast as the networking hardware and the workstation microprocessors. This paper gives an overview and evaluates the performance of the Common Object Request Broker Architecture (CORBA) standard in a distributed computing environment at NASA Ames Research Center. The environment consists of two testbeds of SGI workstations connected by four networks: Ethernet, FDDI, HiPPI, and ATM. The performance results for three communication software systems are presented, analyzed and compared. These systems are: BSD socket programming interface, IONA's Orbix, an implementation of the CORBA specification, and the PVM message passing library. The results show that high-level communication interfaces, such as CORBA and PVM, can achieve reasonable performance under certain conditions.

RAGE deficiency predisposes mice to virus-induced paucigranulocytic asthma

PubMed Central

Arikkatt, Jaisy; Ullah, Md Ashik; Short, Kirsty Renfree; Zhang, Vivan; Gan, Wan Jun; Loh, Zhixuan; Werder, Rhiannon B; Simpson, Jennifer; Sly, Peter D; Mazzone, Stuart B; Spann, Kirsten M; Ferreira, Manuel AR; Upham, John W; Sukkar, Maria B; Phipps, Simon

2017-01-01

Asthma is a chronic inflammatory disease. Although many patients with asthma develop type-2 dominated eosinophilic inflammation, a number of individuals develop paucigranulocytic asthma, which occurs in the absence of eosinophilia or neutrophilia. The aetiology of paucigranulocytic asthma is unknown. However, both respiratory syncytial virus (RSV) infection and mutations in the receptor for advanced glycation endproducts (RAGE) are risk factors for asthma development. Here, we show that RAGE deficiency impairs anti-viral immunity during an early-life infection with pneumonia virus of mice (PVM; a murine analogue of RSV). The elevated viral load was associated with the release of high mobility group box-1 (HMGB1) which triggered airway smooth muscle remodelling in early-life. Re-infection with PVM in later-life induced many of the cardinal features of asthma in the absence of eosinophilic or neutrophilic inflammation. Anti-HMGB1 mitigated both early-life viral disease and asthma-like features, highlighting HMGB1 as a possible novel therapeutic target. DOI: http://dx.doi.org/10.7554/eLife.21199.001 PMID:28099113

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

Performance verification of network function virtualization in software defined optical transport networks

NASA Astrophysics Data System (ADS)

Zhao, Yongli; Hu, Liyazhou; Wang, Wei; Li, Yajie; Zhang, Jie

2017-01-01

With the continuous opening of resource acquisition and application, there are a large variety of network hardware appliances deployed as the communication infrastructure. To lunch a new network application always implies to replace the obsolete devices and needs the related space and power to accommodate it, which will increase the energy and capital investment. Network function virtualization1 (NFV) aims to address these problems by consolidating many network equipment onto industry standard elements such as servers, switches and storage. Many types of IT resources have been deployed to run Virtual Network Functions (vNFs), such as virtual switches and routers. Then how to deploy NFV in optical transport networks is a of great importance problem. This paper focuses on this problem, and gives an implementation architecture of NFV-enabled optical transport networks based on Software Defined Optical Networking (SDON) with the procedure of vNFs call and return. Especially, an implementation solution of NFV-enabled optical transport node is designed, and a parallel processing method for NFV-enabled OTN nodes is proposed. To verify the performance of NFV-enabled SDON, the protocol interaction procedures of control function virtualization and node function virtualization are demonstrated on SDON testbed. Finally, the benefits and challenges of the parallel processing method for NFV-enabled OTN nodes are simulated and analyzed.

Heavy Analysis and Light Virtualization of Water Use Data with Python

NASA Astrophysics Data System (ADS)

Kim, H.; Bijoor, N.; Famiglietti, J. S.

2014-12-01

Water utilities possess a large amount of water data that could be used to inform urban ecohydrology, management decisions, and conservation policies, but such data are rarely analyzed owing to difficulty in analyzation, visualization, and interpretion. We have developed a high performance computing resource for this purpose. We partnered with 6 water agencies in Orange County who provided 10 years of parcel-level monthly water use billing data for a pilot study. The first challenge that we overcame was to refine all human errors and unify the many different formats of data over all agencies. Second, we tested and applied experimental approaches to the data, including complex calculations, with high efficiency. Third, we developed a method to refine the data so it can be browsed along a time series index and/or geo-spatial queries with high efficiency, no matter how large the data. Python scientific libraries were the best match to handle arbitrary data sets in our environment. Further milestones include agency entry, sets of formulae, and maintaining 15M rows X 70 columns of data with high performance of cpu-bound processes. To deal with billions of rows, we performed an analysis virtualization stack by leveraging iPython parallel computing. With this architecture, one agency could be considered one computing node or virtual machine that maintains its own data sets respectively. For example, a big agency could use a large node, and a small agency could use a micro node. Under the minimum required raw data specs, more agencies could be analyzed. The program developed in this study simplifies data analysis, visualization, and interpretation of large water datasets, and can be used to analyze large data volumes from water agencies nationally or worldwide.

Interfacing HTCondor-CE with OpenStack

NASA Astrophysics Data System (ADS)

Bockelman, B.; Caballero Bejar, J.; Hover, J.

2017-10-01

Over the past few years, Grid Computing technologies have reached a high level of maturity. One key aspect of this success has been the development and adoption of newer Compute Elements to interface the external Grid users with local batch systems. These new Compute Elements allow for better handling of jobs requirements and a more precise management of diverse local resources. However, despite this level of maturity, the Grid Computing world is lacking diversity in local execution platforms. As Grid Computing technologies have historically been driven by the needs of the High Energy Physics community, most resource providers run the platform (operating system version and architecture) that best suits the needs of their particular users. In parallel, the development of virtualization and cloud technologies has accelerated recently, making available a variety of solutions, both commercial and academic, proprietary and open source. Virtualization facilitates performing computational tasks on platforms not available at most computing sites. This work attempts to join the technologies, allowing users to interact with computing sites through one of the standard Computing Elements, HTCondor-CE, but running their jobs within VMs on a local cloud platform, OpenStack, when needed. The system will re-route, in a transparent way, end user jobs into dynamically-launched VM worker nodes when they have requirements that cannot be satisfied by the static local batch system nodes. Also, once the automated mechanisms are in place, it becomes straightforward to allow an end user to invoke a custom Virtual Machine at the site. This will allow cloud resources to be used without requiring the user to establish a separate account. Both scenarios are described in this work.

Software architecture and design of the web services facilitating climate model diagnostic analysis

NASA Astrophysics Data System (ADS)

Pan, L.; Lee, S.; Zhang, J.; Tang, B.; Zhai, C.; Jiang, J. H.; Wang, W.; Bao, Q.; Qi, M.; Kubar, T. L.; Teixeira, J.

2015-12-01

Climate model diagnostic analysis is a computationally- and data-intensive task because it involves multiple numerical model outputs and satellite observation data that can both be high resolution. We have built an online tool that facilitates this process. The tool is called Climate Model Diagnostic Analyzer (CMDA). It employs the web service technology and provides a web-based user interface. The benefits of these choices include: (1) No installation of any software other than a browser, hence it is platform compatable; (2) Co-location of computation and big data on the server side, and small results and plots to be downloaded on the client side, hence high data efficiency; (3) multi-threaded implementation to achieve parallel performance on multi-core servers; and (4) cloud deployment so each user has a dedicated virtual machine. In this presentation, we will focus on the computer science aspects of this tool, namely the architectural design, the infrastructure of the web services, the implementation of the web-based user interface, the mechanism of provenance collection, the approach to virtualization, and the Amazon Cloud deployment. As an example, We will describe our methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks (i.e., Flask, Gunicorn, and Tornado). Another example is the use of Docker, a light-weight virtualization container, to distribute and deploy CMDA onto an Amazon EC2 instance. Our tool of CMDA has been successfully used in the 2014 Summer School hosted by the JPL Center for Climate Science. Students had positive feedbacks in general and we will report their comments. An enhanced version of CMDA with several new features, some requested by the 2014 students, will be used in the 2015 Summer School soon.

Concurrent extensions to the FORTRAN language for parallel programming of computational fluid dynamics algorithms

NASA Technical Reports Server (NTRS)

Weeks, Cindy Lou

1986-01-01

Experiments were conducted at NASA Ames Research Center to define multi-tasking software requirements for multiple-instruction, multiple-data stream (MIMD) computer architectures. The focus was on specifying solutions for algorithms in the field of computational fluid dynamics (CFD). The program objectives were to allow researchers to produce usable parallel application software as soon as possible after acquiring MIMD computer equipment, to provide researchers with an easy-to-learn and easy-to-use parallel software language which could be implemented on several different MIMD machines, and to enable researchers to list preferred design specifications for future MIMD computer architectures. Analysis of CFD algorithms indicated that extensions of an existing programming language, adaptable to new computer architectures, provided the best solution to meeting program objectives. The CoFORTRAN Language was written in response to these objectives and to provide researchers a means to experiment with parallel software solutions to CFD algorithms on machines with parallel architectures.

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.

Large-Scale Linear Optimization through Machine Learning: From Theory to Practical System Design and Implementation

DTIC Science & Technology

2016-08-10

AFRL-AFOSR-JP-TR-2016-0073 Large-scale Linear Optimization through Machine Learning: From Theory to Practical System Design and Implementation ...2016 4.  TITLE AND SUBTITLE Large-scale Linear Optimization through Machine Learning: From Theory to Practical System Design and Implementation 5a...performances on various machine learning tasks and it naturally lends itself to fast parallel implementations . Despite this, very little work has been

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

Decomposition method for fast computation of gigapixel-sized Fresnel holograms on a graphics processing unit cluster.

PubMed

Jackin, Boaz Jessie; Watanabe, Shinpei; Ootsu, Kanemitsu; Ohkawa, Takeshi; Yokota, Takashi; Hayasaki, Yoshio; Yatagai, Toyohiko; Baba, Takanobu

2018-04-20

A parallel computation method for large-size Fresnel computer-generated hologram (CGH) is reported. The method was introduced by us in an earlier report as a technique for calculating Fourier CGH from 2D object data. In this paper we extend the method to compute Fresnel CGH from 3D object data. The scale of the computation problem is also expanded to 2 gigapixels, making it closer to real application requirements. The significant feature of the reported method is its ability to avoid communication overhead and thereby fully utilize the computing power of parallel devices. The method exhibits three layers of parallelism that favor small to large scale parallel computing machines. Simulation and optical experiments were conducted to demonstrate the workability and to evaluate the efficiency of the proposed technique. A two-times improvement in computation speed has been achieved compared to the conventional method, on a 16-node cluster (one GPU per node) utilizing only one layer of parallelism. A 20-times improvement in computation speed has been estimated utilizing two layers of parallelism on a very large-scale parallel machine with 16 nodes, where each node has 16 GPUs.

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.

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.

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

Reed, D.A.; Grunwald, D.C.

The spectrum of parallel processor designs can be divided into three sections according to the number and complexity of the processors. At one end there are simple, bit-serial processors. Any one of thee processors is of little value, but when it is coupled with many others, the aggregate computing power can be large. This approach to parallel processing can be likened to a colony of termites devouring a log. The most notable examples of this approach are the NASA/Goodyear Massively Parallel Processor, which has 16K one-bit processors, and the Thinking Machines Connection Machine, which has 64K one-bit processors. At themore » other end of the spectrum, a small number of processors, each built using the fastest available technology and the most sophisticated architecture, are combined. An example of this approach is the Cray X-MP. This type of parallel processing is akin to four woodmen attacking the log with chainsaws.« less

Large-scale virtual screening on public cloud resources with Apache Spark.

PubMed

Capuccini, Marco; Ahmed, Laeeq; Schaal, Wesley; Laure, Erwin; Spjuth, Ola

2017-01-01

Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, however it constitutes a trivially parallelizable task. Most of the available parallel implementations are based on message passing interface, relying on low failure rate hardware and fast network connection. Google's MapReduce revolutionized large-scale analysis, enabling the processing of massive datasets on commodity hardware and cloud resources, providing transparent scalability and fault tolerance at the software level. Open source implementations of MapReduce include Apache Hadoop and the more recent Apache Spark. We developed a method to run existing docking-based screening software on distributed cloud resources, utilizing the MapReduce approach. We benchmarked our method, which is implemented in Apache Spark, docking a publicly available target receptor against [Formula: see text]2.2 M compounds. The performance experiments show a good parallel efficiency (87%) when running in a public cloud environment. Our method enables parallel Structure-based virtual screening on public cloud resources or commodity computer clusters. The degree of scalability that we achieve allows for trying out our method on relatively small libraries first and then to scale to larger libraries. Our implementation is named Spark-VS and it is freely available as open source from GitHub (https://github.com/mcapuccini/spark-vs).Graphical abstract.

Scan line graphics generation on the massively parallel processor

NASA Technical Reports Server (NTRS)

Dorband, John E.

1988-01-01

Described here is how researchers implemented a scan line graphics generation algorithm on the Massively Parallel Processor (MPP). Pixels are computed in parallel and their results are applied to the Z buffer in large groups. To perform pixel value calculations, facilitate load balancing across the processors and apply the results to the Z buffer efficiently in parallel requires special virtual routing (sort computation) techniques developed by the author especially for use on single-instruction multiple-data (SIMD) architectures.

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.

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

Yang, C.

Almost every computer architect dreams of achieving high system performance with low implementation costs. A multigauge machine can reconfigure its data-path width, provide parallelism, achieve better resource utilization, and sometimes can trade computational precision for increased speed. A simple experimental method is used here to capture the main characteristics of multigauging. The measurements indicate evidence of near-optimal speedups. Adapting these ideas in designing parallel processors incurs low costs and provides flexibility. Several operational aspects of designing a multigauge machine are discussed as well. Thus, this research reports the technical, economical, and operational feasibility studies of multigauging.

Progressive Vector Quantization on a massively parallel SIMD machine with application to multispectral image data

NASA Technical Reports Server (NTRS)

Manohar, Mareboyana; Tilton, James C.

1994-01-01

A progressive vector quantization (VQ) compression approach is discussed which decomposes image data into a number of levels using full search VQ. The final level is losslessly compressed, enabling lossless reconstruction. The computational difficulties are addressed by implementation on a massively parallel SIMD machine. We demonstrate progressive VQ on multispectral imagery obtained from the Advanced Very High Resolution Radiometer instrument and other Earth observation image data, and investigate the trade-offs in selecting the number of decomposition levels and codebook training method.

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.

Telescoping magnetic ball bar test gage

DOEpatents

Bryan, J.B.

1982-03-15

A telescoping magnetic ball bar test gage for determining the accuracy of machine tools, including robots, and those measuring machines having non-disengagable servo drives which cannot be clutched out. Two gage balls are held and separated from one another by a telescoping fixture which allows them relative radial motional freedom but not relative lateral motional freedom. The telescoping fixture comprises a parallel reed flexure unit and a rigid member. One gage ball is secured by a magnetic socket knuckle assembly which fixes its center with respect to the machine being tested. The other gage ball is secured by another magnetic socket knuckle assembly which is engaged or held by the machine in such manner that the center of that ball is directed to execute a prescribed trajectory, all points of which are equidistant from the center of the fixed gage ball. As the moving ball executes its trajectory, changes in the radial distance between the centers of the two balls caused by inaccuracies in the machine are determined or measured by a linear variable differential transformer (LVDT) assembly actuated by the parallel reed flexure unit. Measurements can be quickly and easily taken for multiple trajectories about several different fixed ball locations, thereby determining the accuracy of the machine.

A compositional reservoir simulator on distributed memory parallel computers

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

Rame, M.; Delshad, M.

1995-12-31

This paper presents the application of distributed memory parallel computes to field scale reservoir simulations using a parallel version of UTCHEM, The University of Texas Chemical Flooding Simulator. The model is a general purpose highly vectorized chemical compositional simulator that can simulate a wide range of displacement processes at both field and laboratory scales. The original simulator was modified to run on both distributed memory parallel machines (Intel iPSC/960 and Delta, Connection Machine 5, Kendall Square 1 and 2, and CRAY T3D) and a cluster of workstations. A domain decomposition approach has been taken towards parallelization of the code. Amore » portion of the discrete reservoir model is assigned to each processor by a set-up routine that attempts a data layout as even as possible from the load-balance standpoint. Each of these subdomains is extended so that data can be shared between adjacent processors for stencil computation. The added routines that make parallel execution possible are written in a modular fashion that makes the porting to new parallel platforms straight forward. Results of the distributed memory computing performance of Parallel simulator are presented for field scale applications such as tracer flood and polymer flood. A comparison of the wall-clock times for same problems on a vector supercomputer is also presented.« less

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.

High Performance Distributed Computing in a Supercomputer Environment: Computational Services and Applications Issues

NASA Technical Reports Server (NTRS)

Kramer, Williams T. C.; Simon, Horst D.

1994-01-01

This tutorial proposes to be a practical guide for the uninitiated to the main topics and themes of high-performance computing (HPC), with particular emphasis to distributed computing. The intent is first to provide some guidance and directions in the rapidly increasing field of scientific computing using both massively parallel and traditional supercomputers. Because of their considerable potential computational power, loosely or tightly coupled clusters of workstations are increasingly considered as a third alternative to both the more conventional supercomputers based on a small number of powerful vector processors, as well as high massively parallel processors. Even though many research issues concerning the effective use of workstation clusters and their integration into a large scale production facility are still unresolved, such clusters are already used for production computing. In this tutorial we will utilize the unique experience made at the NAS facility at NASA Ames Research Center. Over the last five years at NAS massively parallel supercomputers such as the Connection Machines CM-2 and CM-5 from Thinking Machines Corporation and the iPSC/860 (Touchstone Gamma Machine) and Paragon Machines from Intel were used in a production supercomputer center alongside with traditional vector supercomputers such as the Cray Y-MP and C90.

ProperCAD: A portable object-oriented parallel environment for VLSI CAD

NASA Technical Reports Server (NTRS)

Ramkumar, Balkrishna; Banerjee, Prithviraj

1993-01-01

Most parallel algorithms for VLSI CAD proposed to date have one important drawback: they work efficiently only on machines that they were designed for. As a result, algorithms designed to date are dependent on the architecture for which they are developed and do not port easily to other parallel architectures. A new project under way to address this problem is described. A Portable object-oriented parallel environment for CAD algorithms (ProperCAD) is being developed. The objectives of this research are (1) to develop new parallel algorithms that run in a portable object-oriented environment (CAD algorithms using a general purpose platform for portable parallel programming called CARM is being developed and a C++ environment that is truly object-oriented and specialized for CAD applications is also being developed); and (2) to design the parallel algorithms around a good sequential algorithm with a well-defined parallel-sequential interface (permitting the parallel algorithm to benefit from future developments in sequential algorithms). One CAD application that has been implemented as part of the ProperCAD project, flat VLSI circuit extraction, is described. The algorithm, its implementation, and its performance on a range of parallel machines are discussed in detail. It currently runs on an Encore Multimax, a Sequent Symmetry, Intel iPSC/2 and i860 hypercubes, a NCUBE 2 hypercube, and a network of Sun Sparc workstations. Performance data for other applications that were developed are provided: namely test pattern generation for sequential circuits, parallel logic synthesis, and standard cell placement.

The development of a scalable parallel 3-D CFD algorithm for turbomachinery. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Luke, Edward Allen

1993-01-01

Two algorithms capable of computing a transonic 3-D inviscid flow field about rotating machines are considered for parallel implementation. During the study of these algorithms, a significant new method of measuring the performance of parallel algorithms is developed. The theory that supports this new method creates an empirical definition of scalable parallel algorithms that is used to produce quantifiable evidence that a scalable parallel application was developed. The implementation of the parallel application and an automated domain decomposition tool are also discussed.

The OpenMP Implementation of NAS Parallel Benchmarks and its Performance

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Yan, Jerry

1999-01-01

As the new ccNUMA architecture became popular in recent years, parallel programming with compiler directives on these machines has evolved to accommodate new needs. In this study, we examine the effectiveness of OpenMP directives for parallelizing the NAS Parallel Benchmarks. Implementation details will be discussed and performance will be compared with the MPI implementation. We have demonstrated that OpenMP can achieve very good results for parallelization on a shared memory system, but effective use of memory and cache is very important.

Parallelization and automatic data distribution for nuclear reactor simulations

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

Liebrock, L.M.

1997-07-01

Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directlymore » affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed.« less