Sample records for multiprocessing

  1. Improvement of multiprocessing performance by using optical centralized shared bus

    NASA Astrophysics Data System (ADS)

    Han, Xuliang; Chen, Ray T.

    2004-06-01

    With the ever-increasing need to solve larger and more complex problems, multiprocessing is attracting more and more research efforts. One of the challenges facing the multiprocessor designers is to fulfill in an effective manner the communications among the processes running in parallel on multiple multiprocessors. The conventional electrical backplane bus provides narrow bandwidth as restricted by the physical limitations of electrical interconnects. In the electrical domain, in order to operate at high frequency, the backplane topology has been changed from the simple shared bus to the complicated switched medium. However, the switched medium is an indirect network. It cannot support multicast/broadcast as effectively as the shared bus. Besides the additional latency of going through the intermediate switching nodes, signal routing introduces substantial delay and considerable system complexity. Alternatively, optics has been well known for its interconnect capability. Therefore, it has become imperative to investigate how to improve multiprocessing performance by utilizing optical interconnects. From the implementation standpoint, the existing optical technologies still cannot fulfill the intelligent functions that a switch fabric should provide as effectively as their electronic counterparts. Thus, an innovative optical technology that can provide sufficient bandwidth capacity, while at the same time, retaining the essential merits of the shared bus topology, is highly desirable for the multiprocessing performance improvement. In this paper, the optical centralized shared bus is proposed for use in the multiprocessing systems. This novel optical interconnect architecture not only utilizes the beneficial characteristics of optics, but also retains the desirable properties of the shared bus topology. Meanwhile, from the architecture standpoint, it fits well in the centralized shared-memory multiprocessing scheme. Therefore, a smooth migration with substantial multiprocessing performance improvement is expected. To prove the technical feasibility from the architecture standpoint, a conceptual emulation of the centralized shared-memory multiprocessing scheme is demonstrated on a generic PCI subsystem with an optical centralized shared bus.

  2. Comparing host and target environments for distributed Ada programs

    NASA Technical Reports Server (NTRS)

    Paulk, Mark C.

    1986-01-01

    The Ada programming language provides a means of specifying logical concurrency by using multitasking. Extending the Ada multitasking concurrency mechanism into a physically concurrent distributed environment which imposes its own requirements can lead to incompatibilities. These problems are discussed. Using distributed Ada for a target system may be appropriate, but when using the Ada language in a host environment, a multiprocessing model may be more suitable than retargeting an Ada compiler for the distributed environment. The tradeoffs between multitasking on distributed targets and multiprocessing on distributed hosts are discussed. Comparisons of the multitasking and multiprocessing models indicate different areas of application.

  3. Multiprocessing MCNP on an IBM RS/6000 cluster

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

    McKinney, G.W.; West, J.T.

    1993-01-01

    The advent of high-performance computer systems has brought to maturity programming concepts like vectorization, multiprocessing, and multitasking. While there are many schools of thought as to the most significant factor in obtaining order-of-magnitude increases in performance, such speedup can only be achieved by integrating the computer system and application code. Vectorization leads to faster manipulation of arrays by overlapping instruction CPU cycles. Discrete ordinates codes, which require the solving of large matrices, have proved to be major benefactors of vectorization. Monte Carlo transport, on the other hand, typically contains numerous logic statements and requires extensive redevelopment to benefit from vectorization.more » Multiprocessing and multitasking provide additional CPU cycles via multiple processors. Such systems are generally designed with either common memory access (multitasking) or distributed memory access. In both cases, theoretical speedup, as a function of the number of processors (P) and the fraction of task time that multiprocesses (f), can be formulated using Amdahl's Law S ((f,P) = 1 f + f/P). However, for most applications this theoretical limit cannot be achieved, due to additional terms not included in Amdahl's Law. Monte Carlo transport is a natural candidate for multiprocessing, since the particle tracks are generally independent and the precision of the result increases as the square root of the number of particles tracked.« less

  4. Multi-processing control system for the SEL 840MP (MPCS/1) users guide. Volume 2: Operations guide

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The generation and operational use of the SEL 840MP multiprocessing control system (MPCS) are considered. System initialization, job task table generation, the MPCS command language, display library generation, and system error summary are reviewed.

  5. Distributed Network and Multiprocessing Minicomputer State-of-the-Art Capabilities.

    ERIC Educational Resources Information Center

    Theis, Douglas J.

    An examination of the capabilities of minicomputers and midicomputers now on the market reveals two basic items which users should evaluate when selecting computers for their own applications: distributed networking systems and multiprocessing architectures. Variables which should be considered in evaluating a distributed networking system…

  6. Multiprocessing MCNP on an IBN RS/6000 cluster

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

    McKinney, G.W.; West, J.T.

    1993-01-01

    The advent of high-performance computer systems has brought to maturity programming concepts like vectorization, multiprocessing, and multitasking. While there are many schools of thought as to the most significant factor in obtaining order-of-magnitude increases in performance, such speedup can only be achieved by integrating the computer system and application code. Vectorization leads to faster manipulation of arrays by overlapping instruction CPU cycles. Discrete ordinates codes, which require the solving of large matrices, have proved to be major benefactors of vectorization. Monte Carlo transport, on the other hand, typically contains numerous logic statements and requires extensive redevelopment to benefit from vectorization.more » Multiprocessing and multitasking provide additional CPU cycles via multiple processors. Such systems are generally designed with either common memory access (multitasking) or distributed memory access. In both cases, theoretical speedup, as a function of the number of processors P and the fraction f of task time that multiprocesses, can be formulated using Amdahl's law: S(f, P) =1/(1-f+f/P). However, for most applications, this theoretical limit cannot be achieved because of additional terms (e.g., multitasking overhead, memory overlap, etc.) that are not included in Amdahl's law. Monte Carlo transport is a natural candidate for multiprocessing because the particle tracks are generally independent, and the precision of the result increases as the square Foot of the number of particles tracked.« less

  7. Multiprocessing MCNP on an IBM RS/6000 cluster

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

    McKinney, G.W.; West, J.T.

    1993-03-01

    The advent of high-performance computer systems has brought to maturity programming concepts like vectorization, multiprocessing, and multitasking. While there are many schools of thought as to the most significant factor in obtaining order-of-magnitude increases in performance, such speedup can only be achieved by integrating the computer system and application code. Vectorization leads to faster manipulation of arrays by overlapping instruction CPU cycles. Discrete ordinates codes, which require the solving of large matrices, have proved to be major benefactors of vectorization. Monte Carlo transport, on the other hand, typically contains numerous logic statements and requires extensive redevelopment to benefit from vectorization.more » Multiprocessing and multitasking provide additional CPU cycles via multiple processors. Such systems are generally designed with either common memory access (multitasking) or distributed memory access. In both cases, theoretical speedup, as a function of the number of processors (P) and the fraction of task time that multiprocesses (f), can be formulated using Amdahl`s Law S ((f,P) = 1 f + f/P). However, for most applications this theoretical limit cannot be achieved, due to additional terms not included in Amdahl`s Law. Monte Carlo transport is a natural candidate for multiprocessing, since the particle tracks are generally independent and the precision of the result increases as the square root of the number of particles tracked.« less

  8. Concept of a programmable maintenance processor applicable to multiprocessing systems

    NASA Technical Reports Server (NTRS)

    Glover, Richard D.

    1988-01-01

    A programmable maintenance processor concept applicable to multiprocessing systems has been developed at the NASA Ames Research Center's Dryden Flight Research Facility. This stand-alone-processor is intended to provide support for system and application software testing as well as hardware diagnostics. An initial machanization has been incorporated into the extended aircraft interrogation and display system (XAIDS) which is multiprocessing general-purpose ground support equipment. The XAIDS maintenance processor has independent terminal and printer interfaces and a dedicated magnetic bubble memory that stores system test sequences entered from the terminal. This report describes the hardware and software embodied in this processor and shows a typical application in the check-out of a new XAIDS.

  9. C-MOS array design techniques: SUMC multiprocessor system study

    NASA Technical Reports Server (NTRS)

    Clapp, W. A.; Helbig, W. A.; Merriam, A. S.

    1972-01-01

    The current capabilities of LSI techniques for speed and reliability, plus the possibilities of assembling large configurations of LSI logic and storage elements, have demanded the study of multiprocessors and multiprocessing techniques, problems, and potentialities. Evaluated are three previous systems studies for a space ultrareliable modular computer multiprocessing system, and a new multiprocessing system is proposed that is flexibly configured with up to four central processors, four 1/0 processors, and 16 main memory units, plus auxiliary memory and peripheral devices. This multiprocessor system features a multilevel interrupt, qualified S/360 compatibility for ground-based generation of programs, virtual memory management of a storage hierarchy through 1/0 processors, and multiport access to multiple and shared memory units.

  10. When Do Words Hurt? A Multiprocess View of the Effects of Verbalization on Visual Memory

    ERIC Educational Resources Information Center

    Brown, Charity; Brandimonte, Maria A.; Wickham, Lee H. V.; Bosco, Andrea; Schooler, Jonathan W.

    2014-01-01

    Verbal overshadowing reflects the impairment in memory performance following verbalization of nonverbal stimuli. However, it is not clear whether the same mechanisms are responsible for verbal overshadowing effects observed with different stimuli and task demands. In the present article, we propose a multiprocess view that reconciles the main…

  11. Validity of Multiprocess IRT Models for Separating Content and Response Styles

    ERIC Educational Resources Information Center

    Plieninger, Hansjörg; Meiser, Thorsten

    2014-01-01

    Response styles, the tendency to respond to Likert-type items irrespective of content, are a widely known threat to the reliability and validity of self-report measures. However, it is still debated how to measure and control for response styles such as extreme responding. Recently, multiprocess item response theory models have been proposed that…

  12. Increasing component functionality via multi-process additive manufacturing

    NASA Astrophysics Data System (ADS)

    Coronel, Jose L.; Fehr, Katherine H.; Kelly, Dominic D.; Espalin, David; Wicker, Ryan B.

    2017-05-01

    Additively manufactured components, although extensively customizable, are often limited in functionality. Multi-process additive manufacturing (AM) grants the ability to increase the functionality of components via subtractive manufacturing, wire embedding, foil embedding and pick and place. These processes are scalable to include several platforms ranging from desktop to large area printers. The Multi3D System is highlighted, possessing the capability to perform the above mentioned processes, all while transferring a fabricated component with a robotic arm. Work was conducted to fabricate a patent inspired, printed missile seeker. The seeker demonstrated the advantage of multi-process AM via introduction of the pick and place process. Wire embedding was also explored, with the successful interconnect of two layers of embedded wires in different planes. A final demonstration of a printed contour bracket, served to show the reduction of surface roughness on a printed part is 87.5% when subtractive manufacturing is implemented in tandem with AM. Functionality of the components on all the cases was improved. Results included optical components embedded within the printed housing, wires embedded with interconnection, and reduced surface roughness. These results highlight the improved functionality of components through multi-process AM, specifically through work conducted with the Multi3D System.

  13. Checkout/demonstration application program for the SEL 840MP Multi-Processing Control System: Version 1 (MPCS/1)

    NASA Technical Reports Server (NTRS)

    Anderson, W. F.; Conway, J. R.; Keller, L. C.

    1972-01-01

    The characteristics of the application program were developed to verify and demonstrate the SEL 840MP Multi-Processing Control System - Version I (MPCS/1). The application program emphasizes the display support and task control capabilities. The application program is further intended to be used as an aid to familization with MPCS/1. It complements the information provided in the MPCS/1 Users Guide, Volume I and II.

  14. Expressing Parallelism with ROOT

    NASA Astrophysics Data System (ADS)

    Piparo, D.; Tejedor, E.; Guiraud, E.; Ganis, G.; Mato, P.; Moneta, L.; Valls Pla, X.; Canal, P.

    2017-10-01

    The need for processing the ever-increasing amount of data generated by the LHC experiments in a more efficient way has motivated ROOT to further develop its support for parallelism. Such support is being tackled both for shared-memory and distributed-memory environments. The incarnations of the aforementioned parallelism are multi-threading, multi-processing and cluster-wide executions. In the area of multi-threading, we discuss the new implicit parallelism and related interfaces, as well as the new building blocks to safely operate with ROOT objects in a multi-threaded environment. Regarding multi-processing, we review the new MultiProc framework, comparing it with similar tools (e.g. multiprocessing module in Python). Finally, as an alternative to PROOF for cluster-wide executions, we introduce the efforts on integrating ROOT with state-of-the-art distributed data processing technologies like Spark, both in terms of programming model and runtime design (with EOS as one of the main components). For all the levels of parallelism, we discuss, based on real-life examples and measurements, how our proposals can increase the productivity of scientists.

  15. Performance Modeling and Measurement of Parallelized Code for Distributed Shared Memory Multiprocessors

    NASA Technical Reports Server (NTRS)

    Waheed, Abdul; Yan, Jerry

    1998-01-01

    This paper presents a model to evaluate the performance and overhead of parallelizing sequential code using compiler directives for multiprocessing on distributed shared memory (DSM) systems. With increasing popularity of shared address space architectures, it is essential to understand their performance impact on programs that benefit from shared memory multiprocessing. We present a simple model to characterize the performance of programs that are parallelized using compiler directives for shared memory multiprocessing. We parallelized the sequential implementation of NAS benchmarks using native Fortran77 compiler directives for an Origin2000, which is a DSM system based on a cache-coherent Non Uniform Memory Access (ccNUMA) architecture. We report measurement based performance of these parallelized benchmarks from four perspectives: efficacy of parallelization process; scalability; parallelization overhead; and comparison with hand-parallelized and -optimized version of the same benchmarks. Our results indicate that sequential programs can conveniently be parallelized for DSM systems using compiler directives but realizing performance gains as predicted by the performance model depends primarily on minimizing architecture-specific data locality overhead.

  16. Expressing Parallelism with ROOT

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

    Piparo, D.; Tejedor, E.; Guiraud, E.

    The need for processing the ever-increasing amount of data generated by the LHC experiments in a more efficient way has motivated ROOT to further develop its support for parallelism. Such support is being tackled both for shared-memory and distributed-memory environments. The incarnations of the aforementioned parallelism are multi-threading, multi-processing and cluster-wide executions. In the area of multi-threading, we discuss the new implicit parallelism and related interfaces, as well as the new building blocks to safely operate with ROOT objects in a multi-threaded environment. Regarding multi-processing, we review the new MultiProc framework, comparing it with similar tools (e.g. multiprocessing module inmore » Python). Finally, as an alternative to PROOF for cluster-wide executions, we introduce the efforts on integrating ROOT with state-of-the-art distributed data processing technologies like Spark, both in terms of programming model and runtime design (with EOS as one of the main components). For all the levels of parallelism, we discuss, based on real-life examples and measurements, how our proposals can increase the productivity of scientists.« less

  17. A multi-process model of self-regulation: influences of mindfulness, integrative self-knowledge and self-control in Iran.

    PubMed

    Ghorbani, Nima; Watson, P J; Farhadi, Mehran; Chen, Zhuo

    2014-04-01

    Self-regulation presumably rests upon multiple processes that include an awareness of ongoing self-experience, enduring self-knowledge and self-control. The present investigation tested this multi-process model using the Five-Facet Mindfulness Questionnaire (FFMQ) and the Integrative Self-Knowledge and Brief Self-Control Scales. Using a sample of 1162 Iranian university students, we confirmed the five-factor structure of the FFMQ in Iran and documented its factorial invariance across males and females. Self-regulatory variables correlated negatively with Perceived Stress, Depression, and Anxiety and positively with Self-Esteem and Satisfaction with Life. Partial mediation effects confirmed that self-regulatory measures ameliorated the disturbing effects of Perceived Stress. Integrative Self-Knowledge and Self-Control interacted to partially mediate the association of Perceived Stress with lower levels of Satisfaction with Life. Integrative Self-Knowledge, alone or in interaction with Self-Control, was the only self-regulation variable to display the expected mediation of Perceived Stress associations with all other measures. Self-Control failed to be implicated in self-regulation only in the mediation of Anxiety. These data confirmed the need to further examine this multi-process model of self-regulation. © 2014 International Union of Psychological Science.

  18. CHIMERA II - A real-time multiprocessing environment for sensor-based robot control

    NASA Technical Reports Server (NTRS)

    Stewart, David B.; Schmitz, Donald E.; Khosla, Pradeep K.

    1989-01-01

    A multiprocessing environment for a wide variety of sensor-based robot system, providing the flexibility, performance, and UNIX-compatible interface needed for fast development of real-time code is addressed. The requirements imposed on the design of a programming environment for sensor-based robotic control is outlined. The details of the current hardware configuration are presented, along with the details of the CHIMERA II software. Emphasis is placed on the kernel, low-level interboard communication, user interface, extended file system, user-definable and dynamically selectable real-time schedulers, remote process synchronization, and generalized interprocess communication. A possible implementation of a hierarchical control model, the NASA/NBS standard reference model for telerobot control system is demonstrated.

  19. Integrated Multi-process Microfluidic Systems for Automating Analysis

    PubMed Central

    Yang, Weichun; Woolley, Adam T.

    2010-01-01

    Microfluidic technologies have been applied extensively in rapid sample analysis. Some current challenges for standard microfluidic systems are relatively high detection limits, and reduced resolving power and peak capacity compared to conventional approaches. The integration of multiple functions and components onto a single platform can overcome these separation and detection limitations of microfluidics. Multiplexed systems can greatly increase peak capacity in multidimensional separations and can increase sample throughput by analyzing many samples simultaneously. On-chip sample preparation, including labeling, preconcentration, cleanup and amplification, can all serve to speed up and automate processes in integrated microfluidic systems. This paper summarizes advances in integrated multi-process microfluidic systems for automated analysis, their benefits and areas for needed improvement. PMID:20514343

  20. The Dynamic Multiprocess Framework: Evidence from Prospective Memory with Contextual Variability

    PubMed Central

    Scullin, Michael K.; McDaniel, Mark A.; Shelton, Jill Talley

    2013-01-01

    The ability to remember to execute delayed intentions is referred to as prospective memory. Previous theoretical and empirical work has focused on isolating whether a particular prospective memory task is supported either by effortful monitoring processes or by cue-driven spontaneous processes. In the present work, we advance the Dynamic Multiprocess Framework, which contends that both monitoring and spontaneous retrieval may be utilized dynamically to support prospective remembering. To capture the dynamic interplay between monitoring and spontaneous retrieval we had participants perform many ongoing tasks and told them that their prospective memory cue may occur in any context. Following either a 20-min or a 12-hr retention interval, the prospective memory cues were presented infrequently across three separate ongoing tasks. The monitoring patterns (measured as ongoing task cost relative to a between-subjects control condition) were consistent and robust across the three contexts. There was no evidence for monitoring prior to the initial prospective memory cue; however, individuals who successfully spontaneously retrieved the prospective memory intention, thereby realizing that prospective memory cues could be expected within that context, subsequently monitored. These data support the Dynamic Multiprocess Framework, which contends that individuals will engage monitoring when prospective memory cues are expected, disengage monitoring when cues are not expected, and that when monitoring is disengaged, a probabilistic spontaneous retrieval mechanism can support prospective remembering. PMID:23916951

  1. LibIsopach

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

    Brunhart-Lupo, Nicholas

    2016-12-06

    LibIsopach is a toolkit for high performance distributed immersive visualization, leveraging modern OpenGL. It features a multi-process scenegraph, explicit instance rendering, mesh generation, and three-dimensional user interaction event processing.

  2. Mars Science Laboratory CHIMRA/IC/DRT Flight Software for Sample Acquisition and Processing

    NASA Technical Reports Server (NTRS)

    Kim, Won S.; Leger, Chris; Carsten, Joseph; Helmick, Daniel; Kuhn, Stephen; Redick, Richard; Trujillo, Diana

    2013-01-01

    The design methodologies of using sequence diagrams, multi-process functional flow diagrams, and hierarchical state machines were successfully applied in designing three MSL (Mars Science Laboratory) flight software modules responsible for handling actuator motions of the CHIMRA (Collection and Handling for In Situ Martian Rock Analysis), IC (Inlet Covers), and DRT (Dust Removal Tool) mechanisms. The methodologies were essential to specify complex interactions with other modules, support concurrent foreground and background motions, and handle various fault protections. Studying task scenarios with multi-process functional flow diagrams yielded great insight to overall design perspectives. Since the three modules require three different levels of background motion support, the methodologies presented in this paper provide an excellent comparison. All three modules are fully operational in flight.

  3. Design of a modular digital computer system

    NASA Technical Reports Server (NTRS)

    1973-01-01

    A design tradeoff study is reported for a modular spaceborne computer system that is responsive to many mission types and phases. The computer uses redundancy to maximize reliability, and multiprocessing to maximize processing capacity. Fault detection and recovery features provide optimal reliability.

  4. Automatic Management of Parallel and Distributed System Resources

    NASA Technical Reports Server (NTRS)

    Yan, Jerry; Ngai, Tin Fook; Lundstrom, Stephen F.

    1990-01-01

    Viewgraphs on automatic management of parallel and distributed system resources are presented. Topics covered include: parallel applications; intelligent management of multiprocessing systems; performance evaluation of parallel architecture; dynamic concurrent programs; compiler-directed system approach; lattice gaseous cellular automata; and sparse matrix Cholesky factorization.

  5. Real-time synchronized multiple-sensor IR/EO scene generation utilizing the SGI Onyx2

    NASA Astrophysics Data System (ADS)

    Makar, Robert J.; O'Toole, Brian E.

    1998-07-01

    An approach to utilize the symmetric multiprocessing environment of the Silicon Graphics Inc.R (SGI) Onyx2TM has been developed to support the generation of IR/EO scenes in real-time. This development, supported by the Naval Air Warfare Center Aircraft Division (NAWC/AD), focuses on high frame rate hardware-in-the-loop testing of multiple sensor avionics systems. In the past, real-time IR/EO scene generators have been developed as custom architectures that were often expensive and difficult to maintain. Previous COTS scene generation systems, designed and optimized for visual simulation, could not be adapted for accurate IR/EO sensor stimulation. The new Onyx2 connection mesh architecture made it possible to develop a more economical system while maintaining the fidelity needed to stimulate actual sensors. An SGI based Real-time IR/EO Scene Simulator (RISS) system was developed to utilize the Onyx2's fast multiprocessing hardware to perform real-time IR/EO scene radiance calculations. During real-time scene simulation, the multiprocessors are used to update polygon vertex locations and compute radiometrically accurate floating point radiance values. The output of this process can be utilized to drive a variety of scene rendering engines. Recent advancements in COTS graphics systems, such as the Silicon Graphics InfiniteRealityR make a total COTS solution possible for some classes of sensors. This paper will discuss the critical technologies that apply to infrared scene generation and hardware-in-the-loop testing using SGI compatible hardware. Specifically, the application of RISS high-fidelity real-time radiance algorithms on the SGI Onyx2's multiprocessing hardware will be discussed. Also, issues relating to external real-time control of multiple synchronized scene generation channels will be addressed.

  6. Development of Targeting UAVs Using Electric Helicopters and Yamaha RMAX

    DTIC Science & Technology

    2007-05-17

    including the QNX real - time operating system . The video overlay board is useful to display the onboard camera’s image with important information such as... real - time operating system . Fully utilizing the built-in multi-processing architecture with inter-process synchronization and communication

  7. CubiCal: Suite for fast radio interferometric calibration

    NASA Astrophysics Data System (ADS)

    Kenyon, J. S.; Smirnov, O. M.; Grobler, T. L.; Perkins, S. J.

    2018-05-01

    CubiCal implements several accelerated gain solvers which exploit complex optimization for fast radio interferometric gain calibration. The code can be used for both direction-independent and direction-dependent self-calibration. CubiCal is implemented in Python and Cython, and multiprocessing is fully supported.

  8. Veridical and False Memory for Text: A Multiprocess Analysis

    ERIC Educational Resources Information Center

    Singer, Murray; Remillard, Gilbert

    2008-01-01

    People report recognizing discourse inferences at rates that approach target acceptance. Brainerd et al. [Brainerd, C. J., Wright, R., Reyna, V. F., & Mojardin, A. H. (2001). "Conjoint recognition and phantom recollection." "Journal of Experimental Psychology: Learning, Memory, and Cognition, 27", 307-329] proposed that…

  9. An integrated dexterous robotic testbed for space applications

    NASA Technical Reports Server (NTRS)

    Li, Larry C.; Nguyen, Hai; Sauer, Edward

    1992-01-01

    An integrated dexterous robotic system was developed as a testbed to evaluate various robotics technologies for advanced space applications. The system configuration consisted of a Utah/MIT Dexterous Hand, a PUMA 562 arm, a stereo vision system, and a multiprocessing computer control system. In addition to these major subsystems, a proximity sensing system was integrated with the Utah/MIT Hand to provide capability for non-contact sensing of a nearby object. A high-speed fiber-optic link was used to transmit digitized proximity sensor signals back to the multiprocessing control system. The hardware system was designed to satisfy the requirements for both teleoperated and autonomous operations. The software system was designed to exploit parallel processing capability, pursue functional modularity, incorporate artificial intelligence for robot control, allow high-level symbolic robot commands, maximize reusable code, minimize compilation requirements, and provide an interactive application development and debugging environment for the end users. An overview is presented of the system hardware and software configurations, and implementation is discussed of subsystem functions.

  10. Towards Formalizing the Java Security Architecture of JDK 1.2

    DTIC Science & Technology

    1998-01-01

    and Richard E. Newman for their contributions to this paper. References 1. Balfanz , D. and Gong, L.: Experience with Secure Multi-Processing in Java...Privacy, IEEE Computer Society, Oakland, California, Pages 122-136, 1992. 18. Wallach, D. S., Balfanz , D., Dean, D., and Felton, E. W.: Extensible

  11. Microfabrication Technology for Photonics

    DTIC Science & Technology

    1990-06-01

    specifically addressed by a "folded," parallel architecture currently being proposed by A. Huang(35) who calls it "Computational Origami ." 25 IV...34Computational Origami " U.S. Patent Pending; H.M. Lu, "computatiortal Origami : A Geometric Approach to Regular Multiprocessing," MIT Master’s Thesis in

  12. Phantom Recollection of Bridging and Elaborative Inferences

    ERIC Educational Resources Information Center

    Singer, Murray; Spear, Jackie

    2015-01-01

    The phantom recollection model is a multiprocess analysis according to which memory judgments are collaboratively supported by one's recollection of an item in its context, a vaguer sense of stimulus familiarity, and the phantom recollection of the substance and even perceptual details of unstudied but related lures. Phantom recollection has…

  13. Post-processing, energy production use of sugarcane bagasse ash

    USDA-ARS?s Scientific Manuscript database

    Sugarcane bagasse ash (SBA) is a multi-process by-product produced from the milling of sugarcane. Bagasse is the fibrous material remaining after removing the sugar, water, and other impurities from the sugarcane delivered to the mill. Louisiana produces an estimated 2.7 mt of bagasse each year. In ...

  14. Post-processing, energy production use of sugarcane bagasse ash

    USDA-ARS?s Scientific Manuscript database

    Sugarcane bagasse ash (SBA) is a multi-processed by-product produced from the milling of sugarcane. Bagasse is the fibrous material remaining after removing the sugar, water, and other impurities from the sugarcane delivered to the mill. Louisiana produces an estimated 3 million tons of bagasse each...

  15. Two Fundamental Issues in Multiprocessing.

    DTIC Science & Technology

    1987-10-01

    Structural Model of a Multiprocessor 6 Figure 5: Operational Model of a Multiprocessor 7 Figure 6: The von Neumann Processor (from Gajski and Peir [201) 10...Computer Society, June, 1983. 20. Gajski , D. D. & J-K. Peir. "Essential Issues in Multiprocessor Systems". Computer 18, 6 (June 1985), 9-27. 21. Gurd

  16. Robust, High-Speed Network Design for Large-Scale Multiprocessing

    DTIC Science & Technology

    1993-09-01

    3.17 Left: Non-expansive Wiring of Processors to First Stage Routing Elements . ... 38 3.18 Right: Expansive Wiring of Processors to First Stage...162 8.2 RNI Micro -architecture ........ .............................. 163 8.3 Packaged RN I IC...169 11.1 MLUNK Message Formats ........ .............................. 173 12.1 Routing Board Arrangement for 64- processor Machine

  17. Running ATLAS workloads within massively parallel distributed applications using Athena Multi-Process framework (AthenaMP)

    NASA Astrophysics Data System (ADS)

    Calafiura, Paolo; Leggett, Charles; Seuster, Rolf; Tsulaia, Vakhtang; Van Gemmeren, Peter

    2015-12-01

    AthenaMP is a multi-process version of the ATLAS reconstruction, simulation and data analysis framework Athena. By leveraging Linux fork and copy-on-write mechanisms, it allows for sharing of memory pages between event processors running on the same compute node with little to no change in the application code. Originally targeted to optimize the memory footprint of reconstruction jobs, AthenaMP has demonstrated that it can reduce the memory usage of certain configurations of ATLAS production jobs by a factor of 2. AthenaMP has also evolved to become the parallel event-processing core of the recently developed ATLAS infrastructure for fine-grained event processing (Event Service) which allows the running of AthenaMP inside massively parallel distributed applications on hundreds of compute nodes simultaneously. We present the architecture of AthenaMP, various strategies implemented by AthenaMP for scheduling workload to worker processes (for example: Shared Event Queue and Shared Distributor of Event Tokens) and the usage of AthenaMP in the diversity of ATLAS event processing workloads on various computing resources: Grid, opportunistic resources and HPC.

  18. Dual pathways to prospective remembering

    PubMed Central

    McDaniel, Mark A.; Umanath, Sharda; Einstein, Gilles O.; Waldum, Emily R.

    2015-01-01

    According to the multiprocess framework (McDaniel and Einstein, 2000), the cognitive system can support prospective memory (PM) retrieval through two general pathways. One pathway depends on top–down attentional control processes that maintain activation of the intention and/or monitor the environment for the triggering or target cues that indicate that the intention should be executed. A second pathway depends on (bottom–up) spontaneous retrieval processes, processes that are often triggered by a PM target cue; critically, spontaneous retrieval is assumed not to require monitoring or active maintenance of the intention. Given demand characteristics associated with experimental settings, however, participants are often inclined to monitor, thereby potentially masking discovery of bottom–up spontaneous retrieval processes. In this article, we discuss parameters of laboratory PM paradigms to discourage monitoring and review recent behavioral evidence from such paradigms that implicate spontaneous retrieval in PM. We then re-examine the neuro-imaging evidence from the lens of the multiprocess framework and suggest some critical modifications to existing neuro-cognitive interpretations of the neuro-imaging results. These modifications illuminate possible directions and refinements for further neuro-imaging investigations of PM. PMID:26236213

  19. A comparison of transfer-appropriate processing and multi-process frameworks for prospective memory performance.

    PubMed

    McBride, Dawn M; Abney, Drew H

    2012-01-01

    We examined multi-process (MP) and transfer-appropriate processing descriptions of prospective memory (PM). Three conditions were compared that varied the overlap in processing type (perceptual/conceptual) between the ongoing and PM tasks such that two conditions involved a match of perceptual processing and one condition involved a mismatch in processing (conceptual ongoing task/perceptual PM task). One of the matched processing conditions also created a focal PM task, whereas the other two conditions were considered non-focal (Einstein & McDaniel, 2005). PM task accuracy and ongoing task completion speed in baseline and PM task conditions were measured. Accuracy results indicated a higher PM task completion rate for the focal condition than the non-focal conditions, a finding that is consistent with predictions made by the MP view. However, reaction time (RT) analyses indicated that PM task cost did not differ across conditions when practice effects are considered. Thus, the PM accuracy results are consistent with a MP description of PM, but RT results did not support the MP view predictions regarding PM cost.

  20. Engineering study for the functional design of a multiprocessor system

    NASA Technical Reports Server (NTRS)

    Miller, J. S.; Vandever, W. H.; Stanten, S. F.; Avakian, A. E.; Kosmala, A. L.

    1972-01-01

    The results are presented of a study to generate a functional system design of a multiprocessing computer system capable of satisfying the computational requirements of a space station. These data management system requirements were specified to include: (1) real time control, (2) data processing and storage, (3) data retrieval, and (4) remote terminal servicing.

  1. Measuring Moral Thinking from a Neo-Kohlbergian Perspective

    ERIC Educational Resources Information Center

    Thoma, Stephen J.

    2014-01-01

    The neo-Kohlbergian model revises and extends Lawrence Kohlberg's model of moral reasoning development to better reflect advances in research and theory. In moving from Kohlberg's global stage model to a multi-process description of moral functioning, these modifications are most evident in the ways in which moral thinking is described,…

  2. The Development of Design Guides for the Implementation of Multiprocessing Element Systems.

    DTIC Science & Technology

    1985-09-01

    Conclusions............................ 30 -~-.4 IMPLEMENTATION OF CHILL SIGNALS . COMMUNICATION PRIMITIVES ON A DISTRIBUTED SYSTEM ........................ 31...Architecture of a Distributed System .......... ........................... 32 4.2 Algorithm for the SEND Signal Operation ...... 35 4.3 Algorithm for the...elements operating concurrently. Such Multi Processing-element Systems are clearly going to be complex and it is important that the designers of such

  3. Role of Thermochemical Decomposition in Energetic Material Initiation Sensitivity and Explosive Performance

    DTIC Science & Technology

    2007-02-05

    Electronic excitation has been suggested as one contributing mechanistic step in a multiprocess detonation model [18], and such electronic...and, (b) Dick, J. J., Orientation Dependence of the Shock Initiation Sensitivity of PETN: A Steric Hindrance Model , Workshop on Desensitization of...Explosives and Propellants, Rijswijk, The Netherlands, 11-13 Nov 1991. [15] Piermarini, G. J., Block, S., Miller , P. J., Effects of Pressure on

  4. Acoustic simulation in architecture with parallel algorithm

    NASA Astrophysics Data System (ADS)

    Li, Xiaohong; Zhang, Xinrong; Li, Dan

    2004-03-01

    In allusion to complexity of architecture environment and Real-time simulation of architecture acoustics, a parallel radiosity algorithm was developed. The distribution of sound energy in scene is solved with this method. And then the impulse response between sources and receivers at frequency segment, which are calculated with multi-process, are combined into whole frequency response. The numerical experiment shows that parallel arithmetic can improve the acoustic simulating efficiency of complex scene.

  5. ACCESS: A Communicating and Cooperating Expert Systems System.

    DTIC Science & Technology

    1988-01-31

    therefore more quickly accepted by programmers. This is in part due to the already familiar concepts of multi-processing environments (e.g. semaphores ...Di68] and monitors [Br75]) which can be viewed as a special case of synchronized shared memory models [Di6S]. Heterogeneous systems however, are by...locality of nodes is not possible and frequent access of memory is required. Synchronization of processes also suffers from a loss of efficiency in

  6. Integrated testing and verification system for research flight software

    NASA Technical Reports Server (NTRS)

    Taylor, R. N.

    1979-01-01

    The MUST (Multipurpose User-oriented Software Technology) program is being developed to cut the cost of producing research flight software through a system of software support tools. An integrated verification and testing capability was designed as part of MUST. Documentation, verification and test options are provided with special attention on real-time, multiprocessing issues. The needs of the entire software production cycle were considered, with effective management and reduced lifecycle costs as foremost goals.

  7. On Performance of Linear Multiuser Detectors for Wireless Multimedia Applications

    NASA Astrophysics Data System (ADS)

    Agarwal, Rekha; Reddy, B. V. R.; Bindu, E.; Nayak, Pinki

    In this paper, performance of different multi-rate schemes in DS-CDMA system is evaluated. The analysis of multirate linear multiuser detectors with multiprocessing gain is analyzed for synchronous Code Division Multiple Access (CDMA) systems. Variable data rate is achieved by varying the processing gain. Our conclusion is that bit error rate for multirate and single rate systems can be made same with a tradeoff with number of users in linear multiuser detectors.

  8. C-130 Automated Digital Data System (CADDS)

    NASA Technical Reports Server (NTRS)

    Scofield, C. P.; Nguyen, Chien

    1991-01-01

    Real time airborne data acquisition, archiving and distribution on the NASA/Ames Research Center (ARC) C-130 has been improved over the past three years due to the implementation of the C-130 Automated Digital Data System (CADDS). CADDS is a real time, multitasking, multiprocessing ROM-based system. CADDS acquires data from both avionics and environmental sensors inflight for all C-130 data lines. The system also displays the data on video monitors throughout the aircraft.

  9. ARTS BETA testing report

    NASA Technical Reports Server (NTRS)

    Mccune, M. C.

    1981-01-01

    The advanced real time system (ARTS) was tested utilizing existing commercial system hardware and software which has been operating under advanced operating system (AOS) for several years in a multitasking, multiprocessing, and multiple computer environment. Experiences with ARTS in terms of compatibility with AOS, ease of transmission between AOS and ARTS, and functional areas of ARTS which were tested are discussed. Relative and absolute performance of ARTS versus AOS as measured in the system environment are also presented.

  10. Submesoscale Flows and Mixing in the Oceanic Surface Layer Using the Regional Oceanic Modeling System (ROMS)

    DTIC Science & Technology

    2014-09-30

    continuation of the evolution of the Regional Oceanic Modeling System (ROMS) as a multi-scale, multi-process model and its utilization for...hydrostatic component of ROMS (Kanarska et al., 2007) is required to increase its efficiency and generality. The non-hydrostatic ROMS involves the solution...instability and wind-driven mixing. For the computational regime where those processes can be partially, but not yet fully resolved, it will

  11. Development and Flight Results of a PC104/QNX-Based On-Board Computer and Software for the YES2 Tether Experiment

    NASA Astrophysics Data System (ADS)

    Spiliotopoulos, I.; Mirmont, M.; Kruijff, M.

    2008-08-01

    This paper highlights the flight preparation and mission performance of a PC104-based On-Board Computer for ESA's second Young Engineer's Satellite (YES2), with additional attention to the flight software design and experience of QNX as multi-process real-time operating system. This combination of Commercial-Of-The-Shelf (COTS) technologies is an accessible option for small satellites with high computational demands.

  12. The Design, Development and Testing of a Multi-process Real-time Software System

    DTIC Science & Technology

    2007-03-01

    programming large systems stems from the complexity of dealing with many different details at one time. A sound engineering approach is to break...controls and 3) is portable to other OS platforms such as Microsoft Windows. Next, to reduce the complexity of the programming tasks, the system...processes depending on how often the process has to check to see if common data was modified. A good method for one process to quickly notify another

  13. UFMulti: A new parallel processing software system for HEP

    NASA Astrophysics Data System (ADS)

    Avery, Paul; White, Andrew

    1989-12-01

    UFMulti is a multiprocessing software package designed for general purpose high energy physics applications, including physics and detector simulation, data reduction and DST physics analysis. The system is particularly well suited for installations where several workstation or computers are connected through a local area network (LAN). The initial configuration of the software is currently running on VAX/VMS machines with a planned extension to ULTRIX, using the new RISC CPUs from Digital, in the near future.

  14. A software tool for dataflow graph scheduling

    NASA Technical Reports Server (NTRS)

    Jones, Robert L., III

    1994-01-01

    A graph-theoretic design process and software tool is presented for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described using a dataflow graph and are intended to be executed repetitively on multiple processors. The dataflow paradigm is very useful in exposing the parallelism inherent in algorithms. It provides a graphical and mathematical model which describes a partial ordering of algorithm tasks based on data precedence.

  15. Master/Programmable-Slave Computer

    NASA Technical Reports Server (NTRS)

    Smaistrla, David; Hall, William A.

    1990-01-01

    Unique modular computer features compactness, low power, mass storage of data, multiprocessing, and choice of various input/output modes. Master processor communicates with user via usual keyboard and video display terminal. Coordinates operations of as many as 24 slave processors, each dedicated to different experiment. Each slave circuit card includes slave microprocessor and assortment of input/output circuits for communication with external equipment, with master processor, and with other slave processors. Adaptable to industrial process control with selectable degrees of automatic control, automatic and/or manual monitoring, and manual intervention.

  16. User's manual for the two-dimensional transputer graphics toolkit

    NASA Technical Reports Server (NTRS)

    Ellis, Graham K.

    1988-01-01

    The user manual for the 2-D graphics toolkit for a transputer based parallel processor is presented. The toolkit consists of a package of 2-D display routines that can be used for the simulation visualizations. It supports multiple windows, double buffered screens for animations, and simple graphics transformations such as translation, rotation, and scaling. The display routines are written in occam to take advantage of the multiprocessing features available on transputers. The package is designed to run on a transputer separate from the graphics board.

  17. Event Oriented Design and Adaptive Multiprocessing

    DTIC Science & Technology

    1991-08-31

    System 5 2.3 The Classification 5 2.4 Real-Time Systems 7 2.5 Non Real-Time Systems 10 2.6 Common Characterizations of all Software Systems 10 2.7... Non -Optimal Guarantee Test Theorem 37 6.3.2 Chetto’s Optimal Guarantee Test Theorem 37 6.3.3 Multistate Case: An Extended Guarantee 39 Test Theorem...which subdivides all software systems according to the way in which they operate, such as interactive, non interactive, real-time, etc. Having defined

  18. The Use of Shrinkage Techniques in the Estimation of Attrition Rates for Large Scale Manpower Models

    DTIC Science & Technology

    1988-07-27

    auto regressive model combined with a linear program that solves for the coefficients using MAD. But this success has diminished with time (Rowe...8217Harrison-Stevens Forcasting and the Multiprocess Dy- namic Linear Model ", The American Statistician, v.40, pp. 12 9 - 1 3 5 . 1986. 8. Box, G. E. P. and...1950. 40. McCullagh, P. and Nelder, J., Generalized Linear Models , Chapman and Hall. 1983. 41. McKenzie, E. General Exponential Smoothing and the

  19. Computational structural mechanics for engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.

    1988-01-01

    The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.

  20. Computational structural mechanics for engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.

    1989-01-01

    The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.

  1. Modeling heterogeneous processor scheduling for real time systems

    NASA Technical Reports Server (NTRS)

    Leathrum, J. F.; Mielke, R. R.; Stoughton, J. W.

    1994-01-01

    A new model is presented to describe dataflow algorithms implemented in a multiprocessing system. Called the resource/data flow graph (RDFG), the model explicitly represents cyclo-static processor schedules as circuits of processor arcs which reflect the order that processors execute graph nodes. The model also allows the guarantee of meeting hard real-time deadlines. When unfolded, the model identifies statically the processor schedule. The model therefore is useful for determining the throughput and latency of systems with heterogeneous processors. The applicability of the model is demonstrated using a space surveillance algorithm.

  2. Computer-aided programming for message-passing system; Problems and a solution

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

    Wu, M.Y.; Gajski, D.D.

    1989-12-01

    As the number of processors and the complexity of problems to be solved increase, programming multiprocessing systems becomes more difficult and error-prone. Program development tools are necessary since programmers are not able to develop complex parallel programs efficiently. Parallel models of computation, parallelization problems, and tools for computer-aided programming (CAP) are discussed. As an example, a CAP tool that performs scheduling and inserts communication primitives automatically is described. It also generates the performance estimates and other program quality measures to help programmers in improving their algorithms and programs.

  3. Multiphase modeling of geologic carbon sequestration in saline aquifers.

    PubMed

    Bandilla, Karl W; Celia, Michael A; Birkholzer, Jens T; Cihan, Abdullah; Leister, Evan C

    2015-01-01

    Geologic carbon sequestration (GCS) is being considered as a climate change mitigation option in many future energy scenarios. Mathematical modeling is routinely used to predict subsurface CO2 and resident brine migration for the design of injection operations, to demonstrate the permanence of CO2 storage, and to show that other subsurface resources will not be degraded. Many processes impact the migration of CO2 and brine, including multiphase flow dynamics, geochemistry, and geomechanics, along with the spatial distribution of parameters such as porosity and permeability. In this article, we review a set of multiphase modeling approaches with different levels of conceptual complexity that have been used to model GCS. Model complexity ranges from coupled multiprocess models to simplified vertical equilibrium (VE) models and macroscopic invasion percolation models. The goal of this article is to give a framework of conceptual model complexity, and to show the types of modeling approaches that have been used to address specific GCS questions. Application of the modeling approaches is shown using five ongoing or proposed CO2 injection sites. For the selected sites, the majority of GCS models follow a simplified multiphase approach, especially for questions related to injection and local-scale heterogeneity. Coupled multiprocess models are only applied in one case where geomechanics have a strong impact on the flow. Owing to their computational efficiency, VE models tend to be applied at large scales. A macroscopic invasion percolation approach was used to predict the CO2 migration at one site to examine details of CO2 migration under the caprock. © 2015, National Ground Water Association.

  4. A distributed infrastructure for publishing VO services: an implementation

    NASA Astrophysics Data System (ADS)

    Cepparo, Francesco; Scagnetto, Ivan; Molinaro, Marco; Smareglia, Riccardo

    2016-07-01

    This contribution describes both the design and the implementation details of a new solution for publishing VO services, enlightening its maintainable, distributed, modular and scalable architecture. Indeed, the new publisher is multithreaded and multiprocess. Multiple instances of the modules can run on different machines to ensure high performance and high availability, and this will be true both for the interface modules of the services and the back end data access ones. The system uses message passing to let its components communicate through an AMQP message broker that can itself be distributed to provide better scalability and availability.

  5. Multiprocessor switch with selective pairing

    DOEpatents

    Gara, Alan; Gschwind, Michael K; Salapura, Valentina

    2014-03-11

    System, method and computer program product for a multiprocessing system to offer selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). Each paired microprocessor or processor cores that provide one highly reliable thread for high-reliability connect with a system components such as a memory "nest" (or memory hierarchy), an optional system controller, and optional interrupt controller, optional I/O or peripheral devices, etc. The memory nest is attached to a selective pairing facility via a switch or a bus

  6. Scheduler for multiprocessor system switch with selective pairing

    DOEpatents

    Gara, Alan; Gschwind, Michael Karl; Salapura, Valentina

    2015-01-06

    System, method and computer program product for scheduling threads in a multiprocessing system with selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). The method configures the selective pairing facility to use checking provide one highly reliable thread for high-reliability and allocate threads to corresponding processor cores indicating need for hardware checking. The method configures the selective pairing facility to provide multiple independent cores and allocate threads to corresponding processor cores indicating inherent resilience.

  7. Adaptive runtime for a multiprocessing API

    DOEpatents

    Antao, Samuel F.; Bertolli, Carlo; Eichenberger, Alexandre E.; O'Brien, John K.

    2016-11-15

    A computer-implemented method includes selecting a runtime for executing a program. The runtime includes a first combination of feature implementations, where each feature implementation implements a feature of an application programming interface (API). Execution of the program is monitored, and the execution uses the runtime. Monitor data is generated based on the monitoring. A second combination of feature implementations are selected, by a computer processor, where the selection is based at least in part on the monitor data. The runtime is modified by activating the second combination of feature implementations to replace the first combination of feature implementations.

  8. Adaptive runtime for a multiprocessing API

    DOEpatents

    Antao, Samuel F.; Bertolli, Carlo; Eichenberger, Alexandre E.; O'Brien, John K.

    2016-10-11

    A computer-implemented method includes selecting a runtime for executing a program. The runtime includes a first combination of feature implementations, where each feature implementation implements a feature of an application programming interface (API). Execution of the program is monitored, and the execution uses the runtime. Monitor data is generated based on the monitoring. A second combination of feature implementations are selected, by a computer processor, where the selection is based at least in part on the monitor data. The runtime is modified by activating the second combination of feature implementations to replace the first combination of feature implementations.

  9. Controlling multiple security robots in a warehouse environment

    NASA Technical Reports Server (NTRS)

    Everett, H. R.; Gilbreath, G. A.; Heath-Pastore, T. A.; Laird, R. T.

    1994-01-01

    The Naval Command Control and Ocean Surveillance Center (NCCOSC) has developed an architecture to provide coordinated control of multiple autonomous vehicles from a single host console. The multiple robot host architecture (MRHA) is a distributed multiprocessing system that can be expanded to accommodate as many as 32 robots. The initial application will employ eight Cybermotion K2A Navmaster robots configured as remote security platforms in support of the Mobile Detection Assessment and Response System (MDARS) Program. This paper discusses developmental testing of the MRHA in an operational warehouse environment, with two actual and four simulated robotic platforms.

  10. ATAMM enhancement and multiprocessing performance evaluation

    NASA Technical Reports Server (NTRS)

    Stoughton, John W.

    1994-01-01

    The algorithm to architecture mapping model (ATAAM) is a Petri net based model which provides a strategy for periodic execution of a class of real-time algorithms on multicomputer dataflow architecture. The execution of large-grained, decision-free algorithms on homogeneous processing elements is studied. The ATAAM provides an analytical basis for calculating performance bounds on throughput characteristics. Extension of the ATAMM as a strategy for cyclo-static scheduling provides for a truly distributed ATAMM multicomputer operating system. An ATAAM testbed consisting of a centralized graph manager and three processors is described using embedded firmware on 68HC11 microcontrollers.

  11. Research of improved banker algorithm

    NASA Astrophysics Data System (ADS)

    Yuan, Xingde; Xu, Hong; Qiao, Shijiao

    2013-03-01

    In the multi-process operating system, resource management strategy of system is a critical global issue, especially when many processes implicating for the limited resources, since unreasonable scheduling will cause dead lock. The most classical solution for dead lock question is the banker algorithm; however, it has its own deficiency and only can avoid dead lock occurring in a certain extent. This article aims at reducing unnecessary safety checking, and then uses the new allocation strategy to improve the banker algorithm. Through full analysis and example verification of the new allocation strategy, the results show the improved banker algorithm obtains substantial increase in performance.

  12. The impact of age, ongoing task difficulty, and cue salience on preschoolers' prospective memory performance: the role of executive function.

    PubMed

    Mahy, Caitlin E V; Moses, Louis J; Kliegel, Matthias

    2014-11-01

    The current study examined the impact of age, ongoing task (OT) difficulty, and cue salience on 4- and 5-year-old children's prospective memory (PM) and also explored the relation between individual differences in executive function (working memory, inhibition, and shifting) and PM. OT difficulty and cue salience are predicted to affect the detection of PM cues based on the multiprocess framework, yet neither has been thoroughly investigated in young children. OT difficulty was manipulated by requiring children to sort cards according to the size of pictured items (easy) or by opposite size (difficult), and cue salience was manipulated by placing a red border around half of the target cues (salient) and no border around the other cues (non-salient). The 5-year-olds outperformed the 4-year-olds on the PM task, and salient PM cues resulted in better PM cues compared with non-salient cues. There was no main effect of OT difficulty, and the interaction between cue salience and OT difficulty was not significant. However, a planned comparison revealed that the combination of non-salient cues and a difficult OT resulted in significantly worse PM performance than that in all of the other conditions. Inhibition accounted for significant variance in PM performance for non-salient cues and for marginally significant variance for salient cues. Furthermore, individual differences in inhibition fully mediated the effect of age on PM performance. Results are discussed in the context of the multiprocess framework and with reference to preschoolers' difficulty with the executive demands of dividing attention between the OT and PM task. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations.

    PubMed

    Ojeda-May, Pedro; Nam, Kwangho

    2017-08-08

    The strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in CHARMM are described. The serial version of the code was first profiled to identify routines that required parallelization. Afterward, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM message passage interface (MPI) machinery. In the second approach, two different self-consistent field (SCF) energy convergence accelerators were implemented using density and Fock matrices as targets for their extrapolations in the SCF procedure. In the third approach, the entire QM/MM and MM energy routines were accelerated by implementing the hybrid MPI/open multiprocessing (OpenMP) model in which both the task- and loop-level parallelization strategies were adopted to balance loads between different OpenMP threads. The present implementation was tested on two solvated enzyme systems (including <100 QM atoms) and an S N 2 symmetric reaction in water. The MPI version exceeded existing SE QM methods in CHARMM, which include the SCC-DFTB and SQUANTUM methods, by at least 4-fold. The use of SCF convergence accelerators further accelerated the code by ∼12-35% depending on the size of the QM region and the number of CPU cores used. Although the MPI version displayed good scalability, the performance was diminished for large numbers of MPI processes due to the overhead associated with MPI communications between nodes. This issue was partially overcome by the hybrid MPI/OpenMP approach which displayed a better scalability for a larger number of CPU cores (up to 64 CPUs in the tested systems).

  14. Improvement and speed optimization of numerical tsunami modelling program using OpenMP technology

    NASA Astrophysics Data System (ADS)

    Chernov, A.; Zaytsev, A.; Yalciner, A.; Kurkin, A.

    2009-04-01

    Currently, the basic problem of tsunami modeling is low speed of calculations which is unacceptable for services of the operative notification. Existing algorithms of numerical modeling of hydrodynamic processes of tsunami waves are developed without taking the opportunities of modern computer facilities. There is an opportunity to have considerable acceleration of process of calculations by using parallel algorithms. We discuss here new approach to parallelization tsunami modeling code using OpenMP Technology (for multiprocessing systems with the general memory). Nowadays, multiprocessing systems are easily accessible for everyone. The cost of the use of such systems becomes much lower comparing to the costs of clusters. This opportunity also benefits all programmers to apply multithreading algorithms on desktop computers of researchers. Other important advantage of the given approach is the mechanism of the general memory - there is no necessity to send data on slow networks (for example Ethernet). All memory is the common for all computing processes; it causes almost linear scalability of the program and processes. In the new version of NAMI DANCE using OpenMP technology and multi-threading algorithm provide 80% gain in speed in comparison with the one-thread version for dual-processor unit. The speed increased and 320% gain was attained for four core processor unit of PCs. Thus, it was possible to reduce considerably time of performance of calculations on the scientific workstations (desktops) without complete change of the program and user interfaces. The further modernization of algorithms of preparation of initial data and processing of results using OpenMP looks reasonable. The final version of NAMI DANCE with the increased computational speed can be used not only for research purposes but also in real time Tsunami Warning Systems.

  15. Visualization of Octree Adaptive Mesh Refinement (AMR) in Astrophysical Simulations

    NASA Astrophysics Data System (ADS)

    Labadens, M.; Chapon, D.; Pomaréde, D.; Teyssier, R.

    2012-09-01

    Computer simulations are important in current cosmological research. Those simulations run in parallel on thousands of processors, and produce huge amount of data. Adaptive mesh refinement is used to reduce the computing cost while keeping good numerical accuracy in regions of interest. RAMSES is a cosmological code developed by the Commissariat à l'énergie atomique et aux énergies alternatives (English: Atomic Energy and Alternative Energies Commission) which uses Octree adaptive mesh refinement. Compared to grid based AMR, the Octree AMR has the advantage to fit very precisely the adaptive resolution of the grid to the local problem complexity. However, this specific octree data type need some specific software to be visualized, as generic visualization tools works on Cartesian grid data type. This is why the PYMSES software has been also developed by our team. It relies on the python scripting language to ensure a modular and easy access to explore those specific data. In order to take advantage of the High Performance Computer which runs the RAMSES simulation, it also uses MPI and multiprocessing to run some parallel code. We would like to present with more details our PYMSES software with some performance benchmarks. PYMSES has currently two visualization techniques which work directly on the AMR. The first one is a splatting technique, and the second one is a custom ray tracing technique. Both have their own advantages and drawbacks. We have also compared two parallel programming techniques with the python multiprocessing library versus the use of MPI run. The load balancing strategy has to be smartly defined in order to achieve a good speed up in our computation. Results obtained with this software are illustrated in the context of a massive, 9000-processor parallel simulation of a Milky Way-like galaxy.

  16. 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.

  17. Spacelab Life Sciences-1 electrical diagnostic expert system

    NASA Technical Reports Server (NTRS)

    Kao, C. Y.; Morris, W. S.

    1989-01-01

    The Spacelab Life Sciences-1 (SLS-1) Electrical Diagnostic (SLED) expert system is a continuous, real time knowledge-based system to monitor and diagnose electrical system problems in the Spacelab. After fault isolation, the SLED system provides corrective procedures and advice to the ground-based console operator. The SLED system updates its knowledge about the status of Spacelab every 3 seconds. The system supports multiprocessing of malfunctions and allows multiple failures to be handled simultaneously. Information which is readily available via a mouse click includes: general information about the system and each component, the electrical schematics, the recovery procedures of each malfunction, and an explanation of the diagnosis.

  18. Design tool for multiprocessor scheduling and evaluation of iterative dataflow algorithms

    NASA Technical Reports Server (NTRS)

    Jones, Robert L., III

    1995-01-01

    A graph-theoretic design process and software tool is defined for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described with a dataflow graph and are intended to be executed repetitively on a set of identical processors. Typical applications include signal processing and control law problems. Graph-search algorithms and analysis techniques are introduced and shown to effectively determine performance bounds, scheduling constraints, and resource requirements. The software tool applies the design process to a given problem and includes performance optimization through the inclusion of additional precedence constraints among the schedulable tasks.

  19. Quantum Clock Synchronization with a Single Qudit

    NASA Astrophysics Data System (ADS)

    Tavakoli, Armin; Cabello, Adán; Żukowski, Marek; Bourennane, Mohamed

    2015-01-01

    Clock synchronization for nonfaulty processes in multiprocess networks is indispensable for a variety of technologies. A reliable system must be able to resynchronize the nonfaulty processes upon some components failing causing the distribution of incorrect or conflicting information in the network. The task of synchronizing such networks is related to Byzantine agreement (BA), which can classically be solved using recursive algorithms if and only if less than one-third of the processes are faulty. Here we introduce a nonrecursive quantum algorithm, based on a quantum solution of the detectable BA, which achieves clock synchronization in the presence of arbitrary many faulty processes by using only a single quantum system.

  20. A comparison of multiprocessor scheduling methods for iterative data flow architectures

    NASA Technical Reports Server (NTRS)

    Storch, Matthew

    1993-01-01

    A comparative study is made between the Algorithm to Architecture Mapping Model (ATAMM) and three other related multiprocessing models from the published literature. The primary focus of all four models is the non-preemptive scheduling of large-grain iterative data flow graphs as required in real-time systems, control applications, signal processing, and pipelined computations. Important characteristics of the models such as injection control, dynamic assignment, multiple node instantiations, static optimum unfolding, range-chart guided scheduling, and mathematical optimization are identified. The models from the literature are compared with the ATAMM for performance, scheduling methods, memory requirements, and complexity of scheduling and design procedures.

  1. Protection against hostile algorithms in UNIX software

    NASA Astrophysics Data System (ADS)

    Radatti, Peter V.

    1996-03-01

    Protection against hostile algorithms contained in Unix software is a growing concern without easy answers. Traditional methods used against similar attacks in other operating system environments such as MS-DOS or Macintosh are insufficient in the more complex environment provided by Unix. Additionally, Unix provides a special and significant problem in this regard due to its open and heterogeneous nature. These problems are expected to become both more common and pronounced as 32 bit multiprocess network operating systems become popular. Therefore, the problems experienced today are a good indicator of the problems and the solutions that will be experienced in the future, no matter which operating system becomes predominate.

  2. Model-based vision for space applications

    NASA Technical Reports Server (NTRS)

    Chaconas, Karen; Nashman, Marilyn; Lumia, Ronald

    1992-01-01

    This paper describes a method for tracking moving image features by combining spatial and temporal edge information with model based feature information. The algorithm updates the two-dimensional position of object features by correlating predicted model features with current image data. The results of the correlation process are used to compute an updated model. The algorithm makes use of a high temporal sampling rate with respect to spatial changes of the image features and operates in a real-time multiprocessing environment. Preliminary results demonstrate successful tracking for image feature velocities between 1.1 and 4.5 pixels every image frame. This work has applications for docking, assembly, retrieval of floating objects and a host of other space-related tasks.

  3. Improving the reliability of inverter-based welding machines

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

    Schiedermayer, M.

    1997-02-01

    Although inverter-based welding power sources have been available since the late 1980s, many people hesitated to purchase them because of reliability issues. Unfortunately, their hesitancy had a basis, until now. Recent improvements give some inverters a reliability level that approaches that of traditional, transformer-based industrial welding machines, which have a failure rate of about 1%. Acceptance of inverter-based welding machines is important because, for many welding applications, they provide capabilities that solid-state, transformer-based machines cannot deliver. These advantages include enhanced pulsed gas metal arc welding (GMAW-P), lightweight portability, an ultrastable arc, and energy efficiency--all while producing highly aesthetic weld beadsmore » and delivering multiprocess capabilities.« less

  4. A parallel finite-difference method for computational aerodynamics

    NASA Technical Reports Server (NTRS)

    Swisshelm, Julie M.

    1989-01-01

    A finite-difference scheme for solving complex three-dimensional aerodynamic flow on parallel-processing supercomputers is presented. The method consists of a basic flow solver with multigrid convergence acceleration, embedded grid refinements, and a zonal equation scheme. Multitasking and vectorization have been incorporated into the algorithm. Results obtained include multiprocessed flow simulations from the Cray X-MP and Cray-2. Speedups as high as 3.3 for the two-dimensional case and 3.5 for segments of the three-dimensional case have been achieved on the Cray-2. The entire solver attained a factor of 2.7 improvement over its unitasked version on the Cray-2. The performance of the parallel algorithm on each machine is analyzed.

  5. Environments for online maritime simulators with cloud computing capabilities

    NASA Astrophysics Data System (ADS)

    Raicu, Gabriel; Raicu, Alexandra

    2016-12-01

    This paper presents the cloud computing environments, network principles and methods for graphical development in realistic naval simulation, naval robotics and virtual interactions. The aim of this approach is to achieve a good simulation quality in large networked environments using open source solutions designed for educational purposes. Realistic rendering of maritime environments requires near real-time frameworks with enhanced computing capabilities during distance interactions. E-Navigation concepts coupled with the last achievements in virtual and augmented reality will enhance the overall experience leading to new developments and innovations. We have to deal with a multiprocessing situation using advanced technologies and distributed applications using remote ship scenario and automation of ship operations.

  6. Error recovery in shared memory multiprocessors using private caches

    NASA Technical Reports Server (NTRS)

    Wu, Kun-Lung; Fuchs, W. Kent; Patel, Janak H.

    1990-01-01

    The problem of recovering from processor transient faults in shared memory multiprocesses systems is examined. A user-transparent checkpointing and recovery scheme using private caches is presented. Processes can recover from errors due to faulty processors by restarting from the checkpointed computation state. Implementation techniques using checkpoint identifiers and recovery stacks are examined as a means of reducing performance degradation in processor utilization during normal execution. This cache-based checkpointing technique prevents rollback propagation, provides rapid recovery, and can be integrated into standard cache coherence protocols. An analytical model is used to estimate the relative performance of the scheme during normal execution. Extensions to take error latency into account are presented.

  7. A VLSI VAX chip set

    NASA Astrophysics Data System (ADS)

    Johnson, W. N.; Herrick, W. V.; Grundmann, W. J.

    1984-10-01

    For the first time, VLSI technology is used to compress the full functinality and comparable performance of the VAX 11/780 super-minicomputer into a 1.2 M transistor microprocessor chip set. There was no subsetting of the 304 instruction set and the 17 data types, nor reduction in hardware support for the 4 Gbyte virtual memory management architecture. The chipset supports an integral 8 kbyte memory cache, a 13.3 Mbyte/s system bus, and sophisticated multiprocessing. High performance is achieved through microcode optimizations afforded by the large control store, tightly coupled address and data caches, the use of internal and external 32 bit datapaths, the extensive aplication of both microlevel and macrolevel pipelining, and the use of specialized hardware assists.

  8. Development of capability for microtopography-resolving simulations of hydrologic processes in permafrost affected regions

    NASA Astrophysics Data System (ADS)

    Painter, S.; Moulton, J. D.; Berndt, M.; Coon, E.; Garimella, R.; Lewis, K. C.; Manzini, G.; Mishra, P.; Travis, B. J.; Wilson, C. J.

    2012-12-01

    The frozen soils of the Arctic and subarctic regions contain vast amounts of stored organic carbon. This carbon is vulnerable to release to the atmosphere as temperatures warm and permafrost degrades. Understanding the response of the subsurface and surface hydrologic system to degrading permafrost is key to understanding the rate, timing, and chemical form of potential carbon releases to the atmosphere. Simulating the hydrologic system in degrading permafrost regions is challenging because of the potential for topographic evolution and associated drainage network reorganization as permafrost thaws and massive ground ice melts. The critical process models required for simulating hydrology include subsurface thermal hydrology of freezing/thawing soils, thermal processes within ice wedges, mechanical deformation processes, overland flow, and surface energy balances including snow dynamics. A new simulation tool, the Arctic Terrestrial Simulator (ATS), is being developed to simulate these coupled processes. The computational infrastructure must accommodate fully unstructured grids that track evolving topography, allow accurate solutions on distorted grids, provide robust and efficient solutions on highly parallel computer architectures, and enable flexibility in the strategies for coupling among the various processes. The ATS is based on Amanzi (Moulton et al. 2012), an object-oriented multi-process simulator written in C++ that provides much of the necessary computational infrastructure. Status and plans for the ATS including major hydrologic process models and validation strategies will be presented. Highly parallel simulations of overland flow using high-resolution digital elevation maps of polygonal patterned ground landscapes demonstrate the feasibility of the approach. Simulations coupling three-phase subsurface thermal hydrology with a simple thaw-induced subsidence model illustrate the strong feedbacks among the processes. D. Moulton, M. Berndt, M. Day, J. Meza, et al., High-Level Design of Amanzi, the Multi-Process High Performance Computing Simulator, Technical Report ASCEM-HPC-2011-03-1, DOE Environmental Management, 2012.

  9. NASA's In-Space Manufacturing Project: Development of a Multimaterial, Multiprocess Fabrication Laboratory for the International Space Station

    NASA Technical Reports Server (NTRS)

    Prater, T.; Werkheiser, N.; Bean, Q.; Ledbetter, F.; Soohoo, H.; Wilkerson, M.; Hipp, B.

    2017-01-01

    NASA's long term goal is to send humans to Mars. Over the next two decades, NASA will work with private industry to develop and demonstrate the technologies and capabilities needed to support exploration of the red planet by humans and ensure their safe return to earth. To accomplish this goal, NASA is employing a capability driven approach to its human spaceflight strategy. This approach will develop a suite of evolving capabilities which provide specific functions to solve exploration challenges. One challenge that is critical to sustainable and safer exploration is the ability to manufacture and recycle materials in space. This paper provides an overview of NASA's in-space manufacturing project, its past and current activities, and how technologies under development will ultimately culminate in a multimaterial, multiprocess fabrication laboratory ('FabLab') to be deployed on the International Space Station in the early 2020s. ISM is a critical capability for the long endurance missions NASA seeks to undertake in the coming decades. An unanticipated failure that can be adapted for in low earth orbit may result in a loss of mission in transit to Mars. In order to have a suite of functional ISM capabilities that are compatible with NASA's exploration timeline, ISM must be equipped with the resources necessary to develop these technologies and deploy them for testing prior to the scheduled de-orbit of ISS in 2024. The paper will discuss the phased approach to FabLab development, desired capabilities, and requirements for the hardware. The FabLab will move NASA and private industry significantly closer to changing historical paradigms for human spaceflight where all materials used in space are launched from earth. While the FabLab will be tested on ISS, the system is ultimately intended for use in a deep space habitat or transit vehicle.

  10. A Cross-Platform Infrastructure for Scalable Runtime Application Performance Analysis

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

    Jack Dongarra; Shirley Moore; Bart Miller, Jeffrey Hollingsworth

    2005-03-15

    The purpose of this project was to build an extensible cross-platform infrastructure to facilitate the development of accurate and portable performance analysis tools for current and future high performance computing (HPC) architectures. Major accomplishments include tools and techniques for multidimensional performance analysis, as well as improved support for dynamic performance monitoring of multithreaded and multiprocess applications. Previous performance tool development has been limited by the burden of having to re-write a platform-dependent low-level substrate for each architecture/operating system pair in order to obtain the necessary performance data from the system. Manual interpretation of performance data is not scalable for large-scalemore » long-running applications. The infrastructure developed by this project provides a foundation for building portable and scalable performance analysis tools, with the end goal being to provide application developers with the information they need to analyze, understand, and tune the performance of terascale applications on HPC architectures. The backend portion of the infrastructure provides runtime instrumentation capability and access to hardware performance counters, with thread-safety for shared memory environments and a communication substrate to support instrumentation of multiprocess and distributed programs. Front end interfaces provides tool developers with a well-defined, platform-independent set of calls for requesting performance data. End-user tools have been developed that demonstrate runtime data collection, on-line and off-line analysis of performance data, and multidimensional performance analysis. The infrastructure is based on two underlying performance instrumentation technologies. These technologies are the PAPI cross-platform library interface to hardware performance counters and the cross-platform Dyninst library interface for runtime modification of executable images. The Paradyn and KOJAK projects have made use of this infrastructure to build performance measurement and analysis tools that scale to long-running programs on large parallel and distributed systems and that automate much of the search for performance bottlenecks.« less

  11. Multi-process herbicide transport in structured soil columns: Experiments and model analysis

    NASA Astrophysics Data System (ADS)

    Köhne, J. Maximilian; Köhne, Sigrid; Šimůnek, Jirka

    2006-05-01

    Model predictions of pesticide transport in structured soils are complicated by multiple processes acting concurrently. In this study, the hydraulic, physical, and chemical nonequilibrium (HNE, PNE, and CNE, respectively) processes governing herbicide transport under variably saturated flow conditions were studied. Bromide (Br -), isoproturon (IPU, 3-(4-isoprpylphenyl)-1,1-dimethylurea) and terbuthylazine (TER, N2-tert-butyl-6-chloro- N4-ethyl-1,3,5-triazine-2,4-diamine) were applied to two soil columns. An aggregated Ap soil column and a macroporous, aggregated Ah soil column were irrigated at a rate of 1 cm h - 1 for 3 h. Two more irrigations at the same rate and duration followed in weekly intervals. Nonlinear (Freundlich) equilibrium and two-site kinetic sorption parameters were determined for IPU and TER using batch experiments. The observed water flow and Br - transport were inversely simulated using mobile-immobile (MIM), dual-permeability (DPM), and combined triple-porosity (DP-MIM) numerical models implemented in HYDRUS-1D, with improving correspondence between empirical data and model results. Using the estimated HNE and PNE parameters together with batch-test derived equilibrium sorption parameters, the preferential breakthrough of the weakly adsorbed IPU in the Ah soil could be reasonably well predicted with the DPM approach, whereas leaching of the strongly adsorbed TER was predicted less well. The transport of IPU and TER through the aggregated Ap soil could be described consistently only when HNE, PNE, and CNE were simultaneously accounted for using the DPM. Inverse parameter estimation suggested that two-site kinetic sorption in inter-aggregate flow paths was reduced as compared to within aggregates, and that large values for the first-order degradation rate were an artifact caused by irreversible sorption. Overall, our results should be helpful to enhance the understanding and modeling of multi-process pesticide transport through structured soils during variably saturated water flow.

  12. [Series: Medical Applications of the PHITS Code (2): Acceleration by Parallel Computing].

    PubMed

    Furuta, Takuya; Sato, Tatsuhiko

    2015-01-01

    Time-consuming Monte Carlo dose calculation becomes feasible owing to the development of computer technology. However, the recent development is due to emergence of the multi-core high performance computers. Therefore, parallel computing becomes a key to achieve good performance of software programs. A Monte Carlo simulation code PHITS contains two parallel computing functions, the distributed-memory parallelization using protocols of message passing interface (MPI) and the shared-memory parallelization using open multi-processing (OpenMP) directives. Users can choose the two functions according to their needs. This paper gives the explanation of the two functions with their advantages and disadvantages. Some test applications are also provided to show their performance using a typical multi-core high performance workstation.

  13. Information technologies for astrophysics circa 2001

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1990-01-01

    It is easy to extrapolate current trends to see where technologies relating to information systems in astrophysics and other disciplines will be by the end of the decade. These technologies include mineaturization, multiprocessing, software technology, networking, databases, graphics, pattern computation, and interdisciplinary studies. It is easy to see what limits our current paradigms place on our thinking about technologies that will allow us to understand the laws governing very large systems about which we have large datasets. Three limiting paradigms are saving all the bits collected by instruments or generated by supercomputers; obtaining technology for information compression, storage and retrieval off the shelf; and the linear mode of innovation. We must extend these paradigms to meet our goals for information technology at the end of the decade.

  14. FAST - A multiprocessed environment for visualization of computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

    1991-01-01

    The paper presents the Flow Analysis Software Toolset (FAST) to be used for fluid-mechanics analysis. The design criteria for FAST including the minimization of the data path in the computational fluid-dynamics (CFD) process, consistent user interface, extensible software architecture, modularization, and the isolation of three-dimensional tasks from the application programmer are outlined. Each separate process communicates through the FAST Hub, while other modules such as FAST Central, NAS file input, CFD calculator, surface extractor and renderer, titler, tracer, and isolev might work together to generate the scene. An interprocess communication package making it possible for FAST to operate as a modular environment where resources could be shared among different machines as well as a single host is discussed.

  15. Art and brain: insights from neuropsychology, biology and evolution.

    PubMed

    Zaidel, Dahlia W

    2010-02-01

    Art is a uniquely human activity associated fundamentally with symbolic and abstract cognition. Its practice in human societies throughout the world, coupled with seeming non-functionality, has led to three major brain theories of art. (1) The localized brain regions and pathways theory links art to multiple neural regions. (2) The display of art and its aesthetics theory is tied to the biological motivation of courtship signals and mate selection strategies in animals. (3) The evolutionary theory links the symbolic nature of art to critical pivotal brain changes in Homo sapiens supporting increased development of language and hierarchical social grouping. Collectively, these theories point to art as a multi-process cognition dependent on diverse brain regions and on redundancy in art-related functional representation.

  16. Effects on Vibration and Surface Roughness in High Speed Micro End-Milling of Inconel 718 with Minimum Quantity Lubrication

    NASA Astrophysics Data System (ADS)

    Rahman, Mohamed Abd; Yeakub Ali, Mohammad; Saddam Khairuddin, Amir

    2017-03-01

    This paper presents the study on vibration and surface roughness of Inconel 718 workpiece produced by micro end-milling using Mikrotools Integrated Multi-Process machine tool DT-110 with control parameters; spindle speed (15000 rpm and 30000 rpm), feed rate (2 mm/min and 4 mm/min) and depth of cut (0.10 mm and 0.15mm). The vibration was measured using DYTRAN accelerometer instrument and the average surface roughness Ra was measured using Wyko NT1100. The analysis of variance (ANOVA) by using Design Expert software revealed that feed rate and depth of cut are the most significant factors on vibration meanwhile for average surface roughness, Ra, spindle speed is the most significant factor.

  17. Art and brain: insights from neuropsychology, biology and evolution

    PubMed Central

    Zaidel, Dahlia W

    2010-01-01

    Art is a uniquely human activity associated fundamentally with symbolic and abstract cognition. Its practice in human societies throughout the world, coupled with seeming non-functionality, has led to three major brain theories of art. (1) The localized brain regions and pathways theory links art to multiple neural regions. (2) The display of art and its aesthetics theory is tied to the biological motivation of courtship signals and mate selection strategies in animals. (3) The evolutionary theory links the symbolic nature of art to critical pivotal brain changes in Homo sapiens supporting increased development of language and hierarchical social grouping. Collectively, these theories point to art as a multi-process cognition dependent on diverse brain regions and on redundancy in art-related functional representation. PMID:19490399

  18. Computational structural mechanics for engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1989-01-01

    The computational structural mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures. It is structured to mainly supplement, complement, and whenever possible replace, costly experimental efforts which are unavoidable during engineering research and development programs. Specific objectives include: investigate unique advantages of parallel and multiprocesses for: reformulating/solving structural mechanics and formulating/solving multidisciplinary mechanics and develop integrated structural system computational simulators for: predicting structural performances, evaluating newly developed methods, and for identifying and prioritizing improved/missing methods needed. Herein the CSM program is summarized with emphasis on the Engine Structures Computational Simulator (ESCS). Typical results obtained using ESCS are described to illustrate its versatility.

  19. Spaceborne computer executive routine functional design specification. Volume 2: Computer executive design for space station/base

    NASA Technical Reports Server (NTRS)

    Kennedy, J. R.; Fitzpatrick, W. S.

    1971-01-01

    The computer executive functional system design concepts derived from study of the Space Station/Base are presented. Information Management System hardware configuration as directly influencing the executive design is reviewed. The hardware configuration and generic executive design requirements are considered in detail in a previous report (System Configuration and Executive Requirements Specifications for Reusable Shuttle and Space Station/Base, 9/25/70). This report defines basic system primitives and delineates processes and process control. Supervisor states are considered for describing basic multiprogramming and multiprocessing systems. A high-level computer executive including control of scheduling, allocation of resources, system interactions, and real-time supervisory functions is defined. The description is oriented to provide a baseline for a functional simulation of the computer executive system.

  20. Integrated testing and verification system for research flight software design document

    NASA Technical Reports Server (NTRS)

    Taylor, R. N.; Merilatt, R. L.; Osterweil, L. J.

    1979-01-01

    The NASA Langley Research Center is developing the MUST (Multipurpose User-oriented Software Technology) program to cut the cost of producing research flight software through a system of software support tools. The HAL/S language is the primary subject of the design. Boeing Computer Services Company (BCS) has designed an integrated verification and testing capability as part of MUST. Documentation, verification and test options are provided with special attention on real time, multiprocessing issues. The needs of the entire software production cycle have been considered, with effective management and reduced lifecycle costs as foremost goals. Capabilities have been included in the design for static detection of data flow anomalies involving communicating concurrent processes. Some types of ill formed process synchronization and deadlock also are detected statically.

  1. A survey on the design of multiprocessing systems for artificial intelligence applications

    NASA Technical Reports Server (NTRS)

    Wah, Benjamin W.; Li, Guo Jie

    1989-01-01

    Some issues in designing computers for artificial intelligence (AI) processing are discussed. These issues are divided into three levels: the representation level, the control level, and the processor level. The representation level deals with the knowledge and methods used to solve the problem and the means to represent it. The control level is concerned with the detection of dependencies and parallelism in the algorithmic and program representations of the problem, and with the synchronization and sheduling of concurrent tasks. The processor level addresses the hardware and architectural components needed to evaluate the algorithmic and program representations. Solutions for the problems of each level are illustrated by a number of representative systems. Design decisions in existing projects on AI computers are classed into top-down, bottom-up, and middle-out approaches.

  2. Design and initial application of the extended aircraft interrogation and display system: Multiprocessing ground support equipment for digital flight systems

    NASA Technical Reports Server (NTRS)

    Glover, Richard D.

    1987-01-01

    A pipelined, multiprocessor, general-purpose ground support equipment for digital flight systems has been developed and placed in service at the NASA Ames Research Center's Dryden Flight Research Facility. The design is an outgrowth of the earlier aircraft interrogation and display system (AIDS) used in support of several research projects to provide engineering-units display of internal control system parameters during development and qualification testing activities. The new system, incorporating multiple 16-bit processors, is called extended AIDS (XAIDS) and is now supporting the X-29A forward-swept-wing aircraft project. This report describes the design and mechanization of XAIDS and shows the steps whereby a typical user may take advantage of its high throughput and flexible features.

  3. A high-order language for a system of closely coupled processing elements

    NASA Technical Reports Server (NTRS)

    Feyock, S.; Collins, W. R.

    1986-01-01

    The research reported in this paper was occasioned by the requirements on part of the Real-Time Digital Simulator (RTDS) project under way at NASA Lewis Research Center. The RTDS simulation scheme employs a network of CPUs running lock-step cycles in the parallel computations of jet airplane simulations. Their need for a high order language (HOL) that would allow non-experts to write simulation applications and that could be implemented on a possibly varying network can best be fulfilled by using the programming language Ada. We describe how the simulation problems can be modeled in Ada, how to map a single, multi-processing Ada program into code for individual processors, regardless of network reconfiguration, and why some Ada language features are particulary well-suited to network simulations.

  4. Information technologies for astrophysics circa 2001

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1991-01-01

    It is easy to extrapolate current trends to see where technologies relating to information systems in astrophysics and other disciplines will be by the end of the decade. These technologies include miniaturization, multiprocessing, software technology, networking, databases, graphics, pattern computation, and interdisciplinary studies. It is less easy to see what limits our current paradigms place on our thinking about technologies that will allow us to understand the laws governing very large systems about which we have large data sets. Three limiting paradigms are as follows: saving all the bits collected by instruments or generated by supercomputers; obtaining technology for information compression, storage, and retrieval off the shelf; and the linear model of innovation. We must extend these paradigms to meet our goals for information technology at the end of the decade.

  5. A strategy for the observation of volcanism on Earth from space.

    PubMed

    Wadge, G

    2003-01-15

    Heat, strain, topography and atmospheric emissions associated with volcanism are well observed by satellites orbiting the Earth. Gravity and electromagnetic transients from volcanoes may also prove to be measurable from space. The nature of eruptions means that the best strategy for measuring their dynamic properties remotely from space is to employ two modes with different spatial and temporal samplings: eruption mode and background mode. Such observational programmes are best carried out at local or regional volcano observatories by coupling them with numerical models of volcanic processes. Eventually, such models could become multi-process, operational forecast models that assimilate the remote and other observables to constrain their uncertainties. The threat posed by very large magnitude explosive eruptions is global and best addressed by a spaceborne observational programme with a global remit.

  6. The Palomar Testbed Interferometer

    NASA Technical Reports Server (NTRS)

    Colavita, M. M.; Wallace, J. K.; Hines, B. E.; Gursel, Y.; Malbet, F.; Palmer, D. L.; Pan, X. P.; Shao, M.; Yu, J. W.; Boden, A. F.

    1999-01-01

    The Palomar Testbed Interferometer (PTI) is a long-baseline infrared interferometer located at Palomar Observatory, California. It was built as a testbed for interferometric techniques applicable to the Keck Interferometer. First fringes were obtained in 1995 July. PTI implements a dual-star architecture, tracking two stars simultaneously for phase referencing and narrow-angle astrometry. The three fixed 40 cm apertures can be combined pairwise to provide baselines to 110 m. The interferometer actively tracks the white-light fringe using an array detector at 2.2 microns and active delay lines with a range of +/-38 m. Laser metrology of the delay lines allows for servo control, and laser metrology of the complete optical path enables narrow-angle astrometric measurements. The instrument is highly automated, using a multiprocessing computer system for instrument control and sequencing.

  7. Extension of On-Surface Radiation Condition (OSRC) theory to full-vector electromagnetic wave scattering by three-dimensional conducting, dielectric, and coated targets

    NASA Astrophysics Data System (ADS)

    Taflove, Allen; Umashankar, Korada R.

    1993-08-01

    This project introduced radiation boundary condition (RBC) and absorbing boundary condition (ABC) theory to the engineering electromagnetics community. An approximate method for obtaining the scattering of 2-D and 3-D bodies, the on-surface radiation condition (OSRC) method, was formulated and validated. RBC's and ABC's were shown to work well at points closer to scatterers than anyone had expected. Finite-difference time domain (FD-TD) methods exploiting these ABC's were pursued for applications in scattering, radiation, penetration, biomedical studies, and nonlinear optics. Multiprocessing supercomputer software was developed for FD-TD, leading to the largest scale detailed electromagnetic wave interaction models ever conducted, including entire jet fighter aircraft modeled for radar cross section (RCS) at UHF frequencies up to 500 MHz.

  8. FAST: A multi-processed environment for visualization of computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

    1991-01-01

    Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

  9. Development of a prototype multi-processing interactive software invocation system

    NASA Technical Reports Server (NTRS)

    Berman, W. J.

    1983-01-01

    The Interactive Software Invocation System (NASA-ISIS) was first transported to the M68000 microcomputer, and then rewritten in the programming language Path Pascal. Path Pascal is a significantly enhanced derivative of Pascal, allowing concurrent algorithms to be expressed using the simple and elegant concept of Path Expressions. The primary results of this contract was to verify the viability of Path Pascal as a system's development language. The NASA-ISIS implementation using Path Pascal is a prototype of a large, interactive system in Path Pascal. As such, it is an excellent demonstration of the feasibility of using Path Pascal to write even more extensive systems. It is hoped that future efforts will build upon this research and, ultimately, that a full Path Pascal/ISIS Operating System (PPIOS) might be developed.

  10. MPI_XSTAR: MPI-based Parallelization of the XSTAR Photoionization Program

    NASA Astrophysics Data System (ADS)

    Danehkar, Ashkbiz; Nowak, Michael A.; Lee, Julia C.; Smith, Randall K.

    2018-02-01

    We describe a program for the parallel implementation of multiple runs of XSTAR, a photoionization code that is used to predict the physical properties of an ionized gas from its emission and/or absorption lines. The parallelization program, called MPI_XSTAR, has been developed and implemented in the C++ language by using the Message Passing Interface (MPI) protocol, a conventional standard of parallel computing. We have benchmarked parallel multiprocessing executions of XSTAR, using MPI_XSTAR, against a serial execution of XSTAR, in terms of the parallelization speedup and the computing resource efficiency. Our experience indicates that the parallel execution runs significantly faster than the serial execution, however, the efficiency in terms of the computing resource usage decreases with increasing the number of processors used in the parallel computing.

  11. Parallel-aware, dedicated job co-scheduling within/across symmetric multiprocessing nodes

    DOEpatents

    Jones, Terry R.; Watson, Pythagoras C.; Tuel, William; Brenner, Larry; ,Caffrey, Patrick; Fier, Jeffrey

    2010-10-05

    In a parallel computing environment comprising a network of SMP nodes each having at least one processor, a parallel-aware co-scheduling method and system for improving the performance and scalability of a dedicated parallel job having synchronizing collective operations. The method and system uses a global co-scheduler and an operating system kernel dispatcher adapted to coordinate interfering system and daemon activities on a node and across nodes to promote intra-node and inter-node overlap of said interfering system and daemon activities as well as intra-node and inter-node overlap of said synchronizing collective operations. In this manner, the impact of random short-lived interruptions, such as timer-decrement processing and periodic daemon activity, on synchronizing collective operations is minimized on large processor-count SPMD bulk-synchronous programming styles.

  12. Implications of recent new concepts on the future of mainstream laser processing

    NASA Astrophysics Data System (ADS)

    La Rocca, Aldo V.

    2000-07-01

    According to one of today's most accepted visualizations of the first viable realizations of The Computer Integrated Manufacturing Plant, C.I.M.P., the manufacturing systems herein discussed tend to be multiprocessing, and tend to incorporate the lasers to take advantage of the unique capacities of the laser as a processing tool. Finally also the present laser sources, while having been for a long time more than sufficient, inevitably tend also to new generations. Said visualizations stand in the belief that the first realizations of the C I M P most likely will use flexible multiprocessing machines, which, for flexibility requirements, grow in multi-station cells, in their aggregation in isles and finally in complete manufacturing centers. To constitute the CIMP all partaking elements must be the most easily amenable to Computer Aided Design, CAD, and Computer Aided Manufacturing, CAM. Another basic requirement is that all elements constituting the CIMP must possess the highest System Efficiency and Energy Efficiency at the level of the single element and of its aggregations throughout the various combinations at each and every operating level of said aggregations, up to that of the CIMP. The mastering of the CIMP design constitute a New Discipline that presents very formidable but necessary tasks. Of these the first examples were those related to the early flexible manufacturing system Design Programs. For what concerns the laser processing machines and their integration in manufacturing systems, attention must be given to not repeat the events that hindered their diffusion in the production field keeping it at a level much lower than the expectations and their true potential. Said events stemmed from the confusion between System Efficiency and Energy Efficiency, which persisted for too long and is still common. This has taken place at the levels of introduction of a single element into the combination of the several elements constituting a linear arrangement such as a Transfer Production Line. It because greater and with graver consequences in the case of arrangements possessing more than one degree of product routings, arrangements, as previously mentioned, which evolved in the Flexible Manufacturing Centers.

  13. Comparative Implementation of High Performance Computing for Power System Dynamic Simulations

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

    Jin, Shuangshuang; Huang, Zhenyu; Diao, Ruisheng

    Dynamic simulation for transient stability assessment is one of the most important, but intensive, computations for power system planning and operation. Present commercial software is mainly designed for sequential computation to run a single simulation, which is very time consuming with a single processer. The application of High Performance Computing (HPC) to dynamic simulations is very promising in accelerating the computing process by parallelizing its kernel algorithms while maintaining the same level of computation accuracy. This paper describes the comparative implementation of four parallel dynamic simulation schemes in two state-of-the-art HPC environments: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP).more » These implementations serve to match the application with dedicated multi-processor computing hardware and maximize the utilization and benefits of HPC during the development process.« less

  14. The Boom in 3D-Printed Sensor Technology

    PubMed Central

    Xu, Yuanyuan; Wu, Xiaoyue; Guo, Xiao; Kong, Bin; Zhang, Min; Qian, Xiang; Mi, Shengli; Sun, Wei

    2017-01-01

    Future sensing applications will include high-performance features, such as toxin detection, real-time monitoring of physiological events, advanced diagnostics, and connected feedback. However, such multi-functional sensors require advancements in sensitivity, specificity, and throughput with the simultaneous delivery of multiple detection in a short time. Recent advances in 3D printing and electronics have brought us closer to sensors with multiplex advantages, and additive manufacturing approaches offer a new scope for sensor fabrication. To this end, we review the recent advances in 3D-printed cutting-edge sensors. These achievements demonstrate the successful application of 3D-printing technology in sensor fabrication, and the selected studies deeply explore the potential for creating sensors with higher performance. Further development of multi-process 3D printing is expected to expand future sensor utility and availability. PMID:28534832

  15. schwimmbad: A uniform interface to parallel processing pools in Python

    NASA Astrophysics Data System (ADS)

    Price-Whelan, Adrian M.; Foreman-Mackey, Daniel

    2017-09-01

    Many scientific and computing problems require doing some calculation on all elements of some data set. If the calculations can be executed in parallel (i.e. without any communication between calculations), these problems are said to be perfectly parallel. On computers with multiple processing cores, these tasks can be distributed and executed in parallel to greatly improve performance. A common paradigm for handling these distributed computing problems is to use a processing "pool": the "tasks" (the data) are passed in bulk to the pool, and the pool handles distributing the tasks to a number of worker processes when available. schwimmbad provides a uniform interface to parallel processing pools and enables switching easily between local development (e.g., serial processing or with multiprocessing) and deployment on a cluster or supercomputer (via, e.g., MPI or JobLib).

  16. Multi-processing on supercomputers for computational aerodynamics

    NASA Technical Reports Server (NTRS)

    Yarrow, Maurice; Mehta, Unmeel B.

    1990-01-01

    The MIMD concept is applied, through multitasking, with relatively minor modifications to an existing code for a single processor. This approach maps the available memory to multiple processors, exploiting the C-FORTRAN-Unix interface. An existing single processor algorithm is mapped without the need for developing a new algorithm. The procedure of designing a code utilizing this approach is automated with the Unix stream editor. A Multiple Processor Multiple Grid (MPMG) code is developed as a demonstration of this approach. This code solves the three-dimensional, Reynolds-averaged, thin-layer and slender-layer Navier-Stokes equations with an implicit, approximately factored and diagonalized method. This solver is applied to a generic, oblique-wing aircraft problem on a four-processor computer using one process for data management and nonparallel computations and three processes for pseudotime advance on three different grid systems.

  17. Multiprocessing on supercomputers for computational aerodynamics

    NASA Technical Reports Server (NTRS)

    Yarrow, Maurice; Mehta, Unmeel B.

    1991-01-01

    Little use is made of multiple processors available on current supercomputers (computers with a theoretical peak performance capability equal to 100 MFLOPS or more) to improve turnaround time in computational aerodynamics. The productivity of a computer user is directly related to this turnaround time. In a time-sharing environment, such improvement in this speed is achieved when multiple processors are used efficiently to execute an algorithm. The concept of multiple instructions and multiple data (MIMD) is applied through multitasking via a strategy that requires relatively minor modifications to an existing code for a single processor. This approach maps the available memory to multiple processors, exploiting the C-Fortran-Unix interface. The existing code is mapped without the need for developing a new algorithm. The procedure for building a code utilizing this approach is automated with the Unix stream editor.

  18. Synergistic effect of manganese dioxide and diatomite for fast decolorization and high removal capacity of methyl orange.

    PubMed

    Peng, Hui Hua; Chen, Jie; Jiang, De Yi; Li, Min; Feng, Li; Losic, Dusan; Dong, Fan; Zhang, Yu Xin

    2016-12-15

    MnO 2 nanostructures with two different morphologies (nanowires and nanosheets) were uniformly deposited on diatomite via a one-pot hydrothermal method. The fast decolorization and high removal capacity for anionic dye-MO over synthesized composites had been clarified. The results revealed that the equilibrium time was shortened to as low as 10-30min, and the maximum adsorption capacities were 325mgg -1 and 420mgg -1 for nanowires and nanosheets composites, respectively, under the condition of initial pH 3 and ambient temperature. Indeed, the proposed decolorization mechanism was considered to be simultaneous multi-processes during the dye removal, including physical, physicochemical and chemical process. In principle, well-controlled cost-effective composites have promising ability to remove anionic dye pollutants for environmental remediation. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Efficient parallel architecture for highly coupled real-time linear system applications

    NASA Technical Reports Server (NTRS)

    Carroll, Chester C.; Homaifar, Abdollah; Barua, Soumavo

    1988-01-01

    A systematic procedure is developed for exploiting the parallel constructs of computation in a highly coupled, linear system application. An overall top-down design approach is adopted. Differential equations governing the application under consideration are partitioned into subtasks on the basis of a data flow analysis. The interconnected task units constitute a task graph which has to be computed in every update interval. Multiprocessing concepts utilizing parallel integration algorithms are then applied for efficient task graph execution. A simple scheduling routine is developed to handle task allocation while in the multiprocessor mode. Results of simulation and scheduling are compared on the basis of standard performance indices. Processor timing diagrams are developed on the basis of program output accruing to an optimal set of processors. Basic architectural attributes for implementing the system are discussed together with suggestions for processing element design. Emphasis is placed on flexible architectures capable of accommodating widely varying application specifics.

  20. CICADA -- Configurable Instrument Control and Data Acquisition

    NASA Astrophysics Data System (ADS)

    Young, Peter J.; Roberts, William H.; Sebo, Kim M.

    CICADA (Young et al. 1997) is a multi-process, distributed application for the control of astronomical data acquisition systems. It comprises elements that control the operation of, and data flow from CCD camera systems; and the operation of telescope instrument control systems. CICADA can be used to dynamically configure support for astronomical instruments that can be made up of multiple cameras and multiple instrument controllers. Each camera is described by a hierarchy of parts that are each individually configured and linked together. Most of CICADA is written in C++ and much of the configurability of CICADA comes from the use of inheritance and polymorphism. An example of a multiple part instrument configuration -- a wide field imager (WFI) -- is described here. WFI, presently under construction, is made up of eight 2k x 4k CCDs with dual SDSU II controllers and will be used at Siding Spring's ANU 40in and AAO 3.9m telescopes.

  1. Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods.

    PubMed

    Liu, Bin; Wu, Hao; Zhang, Deyuan; Wang, Xiaolong; Chou, Kuo-Chen

    2017-02-21

    To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful package can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All the work a user needs to do is to input a benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset, Pse-Analysis will automatically construct an ideal predictor, followed by yielding the predicted results for the submitted query samples. All the aforementioned tedious jobs can be automatically done by the computer. Moreover, the multiprocessing technique was adopted to enhance computational speed by about 6 folds. The Pse-Analysis Python package is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/Pse-Analysis/, and can be directly run on Windows, Linux, and Unix.

  2. Multiprocess evolution of landforms in the Kharga Region, Egypt: Applications to Mars

    NASA Technical Reports Server (NTRS)

    Breed, C. S.; Mccauley, J. F.; Grolier, M. J.

    1984-01-01

    In order to understand better the polygenetic evolution of landforms on the martian surface, field studies were conducted in and around the Kharga Depression, Egypt. The Kharga region, on the eastern edge of Egypt's Western Desert, was subject to erosion under mostly hyperarid climatic conditions, punctuated by brief pluvial episodes of lesser aridity, since early Pleistocene time. The region contains numerous landforms analogous to features on the martian surface: yardangs carved in layered surficial deposits and in bedrock, invasive dune trains, wind-modified channels and interfluves, and depressions bounded by steep scarps. Like many of the topographic depresions on Mars, the Kharga Depression was invaded by crescentic dunes. In Egypt, stratigraphic relations between dunes, yardangs, mass-wasting debris, and wind-eroded flash-flood deposits record shifts in the relative effectiveness of wind, water, and mass-wasting processes as a function of climate change.

  3. Architectural development of an advanced EVA Electronic System

    NASA Technical Reports Server (NTRS)

    Lavelle, Joseph

    1992-01-01

    An advanced electronic system for future EVA missions (including zero gravity, the lunar surface, and the surface of Mars) is under research and development within the Advanced Life Support Division at NASA Ames Research Center. As a first step in the development, an optimum system architecture has been derived from an analysis of the projected requirements for these missions. The open, modular architecture centers around a distributed multiprocessing concept where the major subsystems independently process their own I/O functions and communicate over a common bus. Supervision and coordination of the subsystems is handled by an embedded real-time operating system kernel employing multitasking software techniques. A discussion of how the architecture most efficiently meets the electronic system functional requirements, maximizes flexibility for future development and mission applications, and enhances the reliability and serviceability of the system in these remote, hostile environments is included.

  4. Education and the Transition to Fatherhood: The Role of Selection Into Union.

    PubMed

    Trimarchi, Alessandra; Van Bavel, Jan

    2017-02-01

    Although advanced education has been found to be consistently associated with a later transition to parenthood for women, findings about education and the transition to parenthood have been much less consistent for men, and no stylized fact has emerged from the literature. We argue that the inconsistency of findings for men is due to the fact that the selection process involved in union formation has been disregarded in earlier studies. We hypothesize that men's educational attainment consistently and positively affects the transition to fatherhood via higher rates of union formation. We apply multiprocess event-history analysis to data from the Generations and Gender Surveys for 10 European countries. Our results show indeed a consistent positive effect of education on the transition to fatherhood, but it operates chiefly through selection into union. Failing to account for this selection process leads to a major underestimation of the salience of education for the transition to fatherhood.

  5. System Architecture For High Speed Sorting Of Potatoes

    NASA Astrophysics Data System (ADS)

    Marchant, J. A.; Onyango, C. M.; Street, M. J.

    1989-03-01

    This paper illustrates an industrial application of vision processing in which potatoes are sorted according to their size and shape at speeds of up to 40 objects per second. The result is a multi-processing approach built around the VME bus. A hardware unit has been designed and constructed to encode the boundary of the potatoes, to reducing the amount of data to be processed. A master 68000 processor is used to control this unit and to handle data transfers along the bus. Boundary data is passed to one of three 68010 slave processors each responsible for a line of potatoes across a conveyor belt. The slave processors calculate attributes such as shape, size and estimated weight of each potato and the master processor uses this data to operate the sorting mechanism. The system has been interfaced with a commercial grading machine and performance trials are now in progress.

  6. EOS: A project to investigate the design and construction of real-time distributed embedded operating systems

    NASA Technical Reports Server (NTRS)

    Campbell, R. H.; Essick, R. B.; Grass, J.; Johnston, G.; Kenny, K.; Russo, V.

    1986-01-01

    The EOS project is investigating the design and construction of a family of real-time distributed embedded operating systems for reliable, distributed aerospace applications. Using the real-time programming techniques developed in co-operation with NASA in earlier research, the project staff is building a kernel for a multiple processor networked system. The first six months of the grant included a study of scheduling in an object-oriented system, the design philosophy of the kernel, and the architectural overview of the operating system. In this report, the operating system and kernel concepts are described. An environment for the experiments has been built and several of the key concepts of the system have been prototyped. The kernel and operating system is intended to support future experimental studies in multiprocessing, load-balancing, routing, software fault-tolerance, distributed data base design, and real-time processing.

  7. Neural priming in human frontal cortex: multiple forms of learning reduce demands on the prefrontal executive system.

    PubMed

    Race, Elizabeth A; Shanker, Shanti; Wagner, Anthony D

    2009-09-01

    Past experience is hypothesized to reduce computational demands in PFC by providing bottom-up predictive information that informs subsequent stimulus-action mapping. The present fMRI study measured cortical activity reductions ("neural priming"/"repetition suppression") during repeated stimulus classification to investigate the mechanisms through which learning from the past decreases demands on the prefrontal executive system. Manipulation of learning at three levels of representation-stimulus, decision, and response-revealed dissociable neural priming effects in distinct frontotemporal regions, supporting a multiprocess model of neural priming. Critically, three distinct patterns of neural priming were identified in lateral frontal cortex, indicating that frontal computational demands are reduced by three forms of learning: (a) cortical tuning of stimulus-specific representations, (b) retrieval of learned stimulus-decision mappings, and (c) retrieval of learned stimulus-response mappings. The topographic distribution of these neural priming effects suggests a rostrocaudal organization of executive function in lateral frontal cortex.

  8. Method for routing events from key strokes in a multi-processing computer systems

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

    Rhodes, D.A.; Rustici, E.; Carter, K.H.

    1990-01-23

    The patent describes a method of routing user input in a computer system which concurrently runs a plurality of processes. It comprises: generating keycodes representative of keys typed by a user; distinguishing generated keycodes by looking up each keycode in a routing table which assigns each possible keycode to an individual assigned process of the plurality of processes, one of which processes being a supervisory process; then, sending each keycode to its assigned process until a keycode assigned to the supervisory process is received; sending keycodes received subsequent to the keycode assigned to the supervisory process to a buffer; next,more » providing additional keycodes to the supervisory process from the buffer until the supervisory process has completed operation; and sending keycodes stored in the buffer to processes assigned therewith after the supervisory process has completedoperation.« less

  9. Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

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

    Jin, Shuangshuang; Chen, Yousu; Wu, Di

    2015-12-09

    Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Messagemore » Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.« less

  10. Immunomodulation of multiple myeloma.

    PubMed

    Tohnya, Tanyifor M; Figg, William D

    2004-11-01

    Multiple myeloma is a multi-process disease, and these different processes are responsible for the reduced sensitivity to chemotherapy and radiotherapy, hence the relapse and refractory nature of multiple myeloma. Emphasis is now placed on the hypothesis that myeloma cell growth, inhibition of apoptosis and drug resistance are dependent on immunomodulatory cytokines such as IL-6 and pro-angiogenic factors such as VEGF. In addition to its anti-angiogenic effects, the immunomodulatory properties of thalidomide make it a possible therapy for patients with advanced multiple myeloma. This has lead to the clinical development of a number of immunomodulatory thalidomide analogues (IMiDs) which are more potent and have less side effects than the parent drug, thalidomide. In the August 15(th) issue of Journal of Clinical Oncology, Schey SA et al. suggested that an IMiD (CC-4047) maybe efficacious due to T-cell co-stimulation, and safe in patients with relapsed or refractory multiple myeloma. This article demonstrates a supporting role for IMiDs as immunomodulatory adjuvant therapy.

  11. Control of cost in prospective memory: evidence for spontaneous retrieval processes.

    PubMed

    Scullin, Michael K; McDaniel, Mark A; Einstein, Gilles O

    2010-01-01

    To examine the processes that support prospective remembering, previous research has often examined whether the presence of a prospective memory task slows overall responding on an ongoing task. Although slowed task performance suggests that monitoring is present, this method does not clearly establish whether monitoring is functionally related to prospective memory performance. According to the multiprocess theory (McDaniel & Einstein, 2000), monitoring should be necessary to prospective memory performance with nonfocal cues but not with focal cues. To test this hypothesis, we varied monitoring by presenting items that were related (or unrelated) to the prospective memory task proximal to target events. Notably, whereas monitoring proximal to target events led to a large increase in nonfocal prospective memory performance, focal prospective remembering was high in the absence of monitoring, and monitoring in this condition provided no additional benefits. These results suggest that when monitoring is absent, spontaneous retrieval processes can support focal prospective remembering. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

  12. New Python-based methods for data processing

    PubMed Central

    Sauter, Nicholas K.; Hattne, Johan; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel

    2013-01-01

    Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2 TB h−1) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in real time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femto­second crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units. PMID:23793153

  13. What Costs Do Reveal and Moving Beyond the Cost Debate: Reply to Einstein and McDaniel (in press)

    PubMed Central

    Smith, Rebekah E.

    2010-01-01

    Einstein et al., (2005) predicted no cost to an ongoing task when a prospective memory task meet certain criteria. Smith et al. (2007) used prospective memory tasks that met these criteria and found a cost to the ongoing task, contrary to Einstein et al.'s prediction. Einstein and McDaniel (in press) correctly note that there are limitations to using ongoing task performance as a measure of the processes that contribute to prospective memory performance, however, the alternatives suggested by Einstein and McDaniel all focus on ongoing task performance and therefore do not move beyond the cost debate. This article describes why the Smith et al. findings are important, provides recommendations for issues to consider when investigating cost, and discusses individual cost measures. Finally, noting the blurry distinction between Einstein and McDaniel's description of the reflexive associative processes and preparatory attentional processes and difficulties in extending the multiprocess view to nonlaboratory tasks, suggestions are made for moving beyond the cost debate. PMID:20852726

  14. Array processor architecture

    NASA Technical Reports Server (NTRS)

    Barnes, George H. (Inventor); Lundstrom, Stephen F. (Inventor); Shafer, Philip E. (Inventor)

    1983-01-01

    A high speed parallel array data processing architecture fashioned under a computational envelope approach includes a data base memory for secondary storage of programs and data, and a plurality of memory modules interconnected to a plurality of processing modules by a connection network of the Omega gender. Programs and data are fed from the data base memory to the plurality of memory modules and from hence the programs are fed through the connection network to the array of processors (one copy of each program for each processor). Execution of the programs occur with the processors operating normally quite independently of each other in a multiprocessing fashion. For data dependent operations and other suitable operations, all processors are instructed to finish one given task or program branch before all are instructed to proceed in parallel processing fashion on the next instruction. Even when functioning in the parallel processing mode however, the processors are not locked-step but execute their own copy of the program individually unless or until another overall processor array synchronization instruction is issued.

  15. Parallelization of NAS Benchmarks for Shared Memory Multiprocessors

    NASA Technical Reports Server (NTRS)

    Waheed, Abdul; Yan, Jerry C.; Saini, Subhash (Technical Monitor)

    1998-01-01

    This paper presents our experiences of parallelizing the sequential implementation of NAS benchmarks using compiler directives on SGI Origin2000 distributed shared memory (DSM) system. Porting existing applications to new high performance parallel and distributed computing platforms is a challenging task. Ideally, a user develops a sequential version of the application, leaving the task of porting to new generations of high performance computing systems to parallelization tools and compilers. Due to the simplicity of programming shared-memory multiprocessors, compiler developers have provided various facilities to allow the users to exploit parallelism. Native compilers on SGI Origin2000 support multiprocessing directives to allow users to exploit loop-level parallelism in their programs. Additionally, supporting tools can accomplish this process automatically and present the results of parallelization to the users. We experimented with these compiler directives and supporting tools by parallelizing sequential implementation of NAS benchmarks. Results reported in this paper indicate that with minimal effort, the performance gain is comparable with the hand-parallelized, carefully optimized, message-passing implementations of the same benchmarks.

  16. Latent error detection: A golden two hours for detection.

    PubMed

    Saward, Justin R E; Stanton, Neville A

    2017-03-01

    Undetected error in safety critical contexts generates a latent condition that can contribute to a future safety failure. The detection of latent errors post-task completion is observed in naval air engineers using a diary to record work-related latent error detection (LED) events. A systems view is combined with multi-process theories to explore sociotechnical factors associated with LED. Perception of cues in different environments facilitates successful LED, for which the deliberate review of past tasks within two hours of the error occurring and whilst remaining in the same or similar sociotechnical environment to that which the error occurred appears most effective. Identified ergonomic interventions offer potential mitigation for latent errors; particularly in simple everyday habitual tasks. It is thought safety critical organisations should look to engineer further resilience through the application of LED techniques that engage with system cues across the entire sociotechnical environment, rather than relying on consistent human performance. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

  17. Shared performance monitor in a multiprocessor system

    DOEpatents

    Chiu, George; Gara, Alan G.; Salapura, Valentina

    2012-07-24

    A performance monitoring unit (PMU) and method for monitoring performance of events occurring in a multiprocessor system. The multiprocessor system comprises a plurality of processor devices units, each processor device for generating signals representing occurrences of events in the processor device, and, a single shared counter resource for performance monitoring. The performance monitor unit is shared by all processor cores in the multiprocessor system. The PMU comprises: a plurality of performance counters each for counting signals representing occurrences of events from one or more the plurality of processor units in the multiprocessor system; and, a plurality of input devices for receiving the event signals from one or more processor devices of the plurality of processor units, the plurality of input devices programmable to select event signals for receipt by one or more of the plurality of performance counters for counting, wherein the PMU is shared between multiple processing units, or within a group of processors in the multiprocessing system. The PMU is further programmed to monitor event signals issued from non-processor devices.

  18. Multitasking a three-dimensional Navier-Stokes algorithm on the Cray-2

    NASA Technical Reports Server (NTRS)

    Swisshelm, Julie M.

    1989-01-01

    A three-dimensional computational aerodynamics algorithm has been multitasked for efficient parallel execution on the Cray-2. It provides a means for examining the multitasking performance of a complete CFD application code. An embedded zonal multigrid scheme is used to solve the Reynolds-averaged Navier-Stokes equations for an internal flow model problem. The explicit nature of each component of the method allows a spatial partitioning of the computational domain to achieve a well-balanced task load for MIMD computers with vector-processing capability. Experiments have been conducted with both two- and three-dimensional multitasked cases. The best speedup attained by an individual task group was 3.54 on four processors of the Cray-2, while the entire solver yielded a speedup of 2.67 on four processors for the three-dimensional case. The multiprocessing efficiency of various types of computational tasks is examined, performance on two Cray-2s with different memory access speeds is compared, and extrapolation to larger problems is discussed.

  19. State recovery and lockstep execution restart in a system with multiprocessor pairing

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

    Gara, Alan; Gschwind, Michael K; Salapura, Valentina

    System, method and computer program product for a multiprocessing system to offer selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). Each paired microprocessor or processor cores that provide one highly reliable thread for high-reliability connect with a system components such as a memory "nest" (or memory hierarchy), an optional system controller, and optional interrupt controller, optional I/O or peripheral devices, etc. The memory nest is attached to a selective pairing facility via a switchmore » or a bus. Each selectively paired processor core is includes a transactional execution facility, whereing the system is configured to enable processor rollback to a previous state and reinitialize lockstep execution in order to recover from an incorrect execution when an incorrect execution has been detected by the selective pairing facility.« less

  20. An Ada inference engine for expert systems

    NASA Technical Reports Server (NTRS)

    Lavallee, David B.

    1986-01-01

    The purpose is to investigate the feasibility of using Ada for rule-based expert systems with real-time performance requirements. This includes exploring the Ada features which give improved performance to expert systems as well as optimizing the tradeoffs or workarounds that the use of Ada may require. A prototype inference engine was built using Ada, and rule firing rates in excess of 500 per second were demonstrated on a single MC68000 processor. The knowledge base uses a directed acyclic graph to represent production lines. The graph allows the use of AND, OR, and NOT logical operators. The inference engine uses a combination of both forward and backward chaining in order to reach goals as quickly as possible. Future efforts will include additional investigation of multiprocessing to improve performance and creating a user interface allowing rule input in an Ada-like syntax. Investigation of multitasking and alternate knowledge base representations will help to analyze some of the performance issues as they relate to larger problems.

  1. Individual differences in event-based prospective memory: Evidence for multiple processes supporting cue detection.

    PubMed

    Brewer, Gene A; Knight, Justin B; Marsh, Richard L; Unsworth, Nash

    2010-04-01

    The multiprocess view proposes that different processes can be used to detect event-based prospective memory cues, depending in part on the specificity of the cue. According to this theory, attentional processes are not necessary to detect focal cues, whereas detection of nonfocal cues requires some form of controlled attention. This notion was tested using a design in which we compared performance on a focal and on a nonfocal prospective memory task by participants with high or low working memory capacity. An interaction was found, such that participants with high and low working memory performed equally well on the focal task, whereas the participants with high working memory performed significantly better on the nonfocal task than did their counterparts with low working memory. Thus, controlled attention was only necessary for detecting event-based prospective memory cues in the nonfocal task. These results have implications for theories of prospective memory, the processes necessary for cue detection, and the successful fulfillment of intentions.

  2. Open system magnetic evolution of the taos plateau volcanic field, Northern New Mexico. I - The petrology and geochemistry of the servilleta basalt

    NASA Technical Reports Server (NTRS)

    Dungan, M. A.; Lindstrom, M. M.; Mcmillan, N. J.; Moorbath, S.; Hoefs, J.

    1986-01-01

    MULTIFIT, an embodiment of the conceptual structure needed in modeling multisource and multiprocess magmatic systems, is described. This program, which uses familiar materials balance methodology and the equilibrium form of the Rayleigh equations, links evolutionary arrays, which is turn collectively relate the starting and final compositions of a given magmatic system. Moreover, MULTIFIT incorporates variations within major element data arrays; the linkage between them can be tested using an extension of the least squares algorithm, which selects the best branch point according to the minimum-sum-of-squared-residuals criterion. Advantages and disadvantages of the materials balance approach used in this program are discussed, an example is provided, and equations utilized by MULTIFIT are summarized. While MULTIFIT may not be the best approach for poorly constrained models involving partial melting for complex mixing, it may ultimately prove useful for ascertaining trace element partition coefficients in magnetic systems.

  3. Automatic Generation of Cycle-Approximate TLMs with Timed RTOS Model Support

    NASA Astrophysics Data System (ADS)

    Hwang, Yonghyun; Schirner, Gunar; Abdi, Samar

    This paper presents a technique for automatically generating cycle-approximate transaction level models (TLMs) for multi-process applications mapped to embedded platforms. It incorporates three key features: (a) basic block level timing annotation, (b) RTOS model integration, and (c) RTOS overhead delay modeling. The inputs to TLM generation are application C processes and their mapping to processors in the platform. A processor data model, including pipelined datapath, memory hierarchy and branch delay model is used to estimate basic block execution delays. The delays are annotated to the C code, which is then integrated with a generated SystemC RTOS model. Our abstract RTOS provides dynamic scheduling and inter-process communication (IPC) with processor- and RTOS-specific pre-characterized timing. Our experiments using a MP3 decoder and a JPEG encoder show that timed TLMs, with integrated RTOS models, can be automatically generated in less than a minute. Our generated TLMs simulated three times faster than real-time and showed less than 10% timing error compared to board measurements.

  4. Automating the parallel processing of fluid and structural dynamics calculations

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.; Cole, Gary L.

    1987-01-01

    The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilities to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.

  5. Performance analysis of the GR712RC dual-core LEON3FT SPARC V8 processor in an asymmetric multi-processing environment

    NASA Astrophysics Data System (ADS)

    Giusi, Giovanni; Liu, Scige J.; Galli, Emanuele; Di Giorgio, Anna M.; Farina, Maria; Vertolli, Nello; Di Lellis, Andrea M.

    2016-07-01

    In this paper we present the results of a series of performance tests carried out on a prototype board mounting the Cobham Gaisler GR712RC Dual Core LEON3FT processor. The aim was the characterization of the performances of the dual core processor when used for executing a highly demanding lossless compression task, acting on data segments continuously copied from the static memory to the processor RAM. The selection of the compression activity to evaluate the performances was driven by the possibility of a comparison with previously executed tests on the Cobham/Aeroflex Gaisler UT699 LEON3FT SPARC™ V8. The results of the test activity have shown a factor 1.6 of improvement with respect to the previous tests, which can easily be improved by adopting a faster onboard board clock, and provided indications on the best size of the data chunks to be used in the compression activity.

  6. Global computing for bioinformatics.

    PubMed

    Loewe, Laurence

    2002-12-01

    Global computing, the collaboration of idle PCs via the Internet in a SETI@home style, emerges as a new way of massive parallel multiprocessing with potentially enormous CPU power. Its relations to the broader, fast-moving field of Grid computing are discussed without attempting a review of the latter. This review (i) includes a short table of milestones in global computing history, (ii) lists opportunities global computing offers for bioinformatics, (iii) describes the structure of problems well suited for such an approach, (iv) analyses the anatomy of successful projects and (v) points to existing software frameworks. Finally, an evaluation of the various costs shows that global computing indeed has merit, if the problem to be solved is already coded appropriately and a suitable global computing framework can be found. Then, either significant amounts of computing power can be recruited from the general public, or--if employed in an enterprise-wide Intranet for security reasons--idle desktop PCs can substitute for an expensive dedicated cluster.

  7. Corral framework: Trustworthy and fully functional data intensive parallel astronomical pipelines

    NASA Astrophysics Data System (ADS)

    Cabral, J. B.; Sánchez, B.; Beroiz, M.; Domínguez, M.; Lares, M.; Gurovich, S.; Granitto, P.

    2017-07-01

    Data processing pipelines represent an important slice of the astronomical software library that include chains of processes that transform raw data into valuable information via data reduction and analysis. In this work we present Corral, a Python framework for astronomical pipeline generation. Corral features a Model-View-Controller design pattern on top of an SQL Relational Database capable of handling: custom data models; processing stages; and communication alerts, and also provides automatic quality and structural metrics based on unit testing. The Model-View-Controller provides concept separation between the user logic and the data models, delivering at the same time multi-processing and distributed computing capabilities. Corral represents an improvement over commonly found data processing pipelines in astronomysince the design pattern eases the programmer from dealing with processing flow and parallelization issues, allowing them to focus on the specific algorithms needed for the successive data transformations and at the same time provides a broad measure of quality over the created pipeline. Corral and working examples of pipelines that use it are available to the community at https://github.com/toros-astro.

  8. Mechanical Properties and Microstructure of High-Strength Steel Controlled by Hot Stamping Process

    NASA Astrophysics Data System (ADS)

    Ou, Hang; Zhang, Xu; Xu, Junrui; Li, Guangyao; Cui, Junjia

    2018-03-01

    A novel design and manufacturing method, dubbed "precast," of the cooling system and tools for a hot forming process was proposed in this paper. The integrated structures of the punch and blank holder were determined by analyzing the bending and reverse-bending deformation of the forming parts. The desired crashworthiness performance of an automotive front bumper constructed with this process was obtained by a tailored phase transformation, which generated martensite-bainite in the middle and full martensite transformation in the corner areas. Varying cooling effects in the formed parts caused the highest temperature to be located in the bottom and the lowest on the end of the formed parts. Moreover, the microstructural distributions demonstrated that the bottom possessed a relatively lower content of martensite, while, conversely, the end possessed a higher content. This was precisely the most desired phase distributions for the hot formed parts. For the six-process cycle stamping, the temperatures reached a stable status after an initial rapid increase in the first three process cycles. The microstructural results verified the feasibility of the hot forming tools under multiprocess cycles.

  9. PARALLELISATION OF THE MODEL-BASED ITERATIVE RECONSTRUCTION ALGORITHM DIRA.

    PubMed

    Örtenberg, A; Magnusson, M; Sandborg, M; Alm Carlsson, G; Malusek, A

    2016-06-01

    New paradigms for parallel programming have been devised to simplify software development on multi-core processors and many-core graphical processing units (GPU). Despite their obvious benefits, the parallelisation of existing computer programs is not an easy task. In this work, the use of the Open Multiprocessing (OpenMP) and Open Computing Language (OpenCL) frameworks is considered for the parallelisation of the model-based iterative reconstruction algorithm DIRA with the aim to significantly shorten the code's execution time. Selected routines were parallelised using OpenMP and OpenCL libraries; some routines were converted from MATLAB to C and optimised. Parallelisation of the code with the OpenMP was easy and resulted in an overall speedup of 15 on a 16-core computer. Parallelisation with OpenCL was more difficult owing to differences between the central processing unit and GPU architectures. The resulting speedup was substantially lower than the theoretical peak performance of the GPU; the cause was explained. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. Neural evidence of the strategic choice between working memory and episodic memory in prospective remembering.

    PubMed

    Lewis-Peacock, Jarrod A; Cohen, Jonathan D; Norman, Kenneth A

    2016-12-01

    Theories of prospective memory (PM) posit that it can be subserved either by working memory (WM) or episodic memory (EM). Testing and refining these multiprocess theories of PM requires a way of tracking participants' reliance on WM versus EM. Here we use multi-voxel pattern analysis (MVPA) to derive a trial-by-trial measure of WM use in prospective memory. We manipulated strategy demands by varying the degree of proactive interference (which impairs EM) and the memory load required to perform the secondary task (which impairs WM). For the condition in which participants were pushed to rely more on WM, our MVPA measures showed 1) greater WM use and 2) a trial-by-trial correlation between WM use and PM behavior. Finally, we also showed that MVPA measures of WM use are not redundant with other behavioral measures: in the condition in which participants were pushed more to rely on WM, using neural and behavioral measures together led to better prediction of PM accuracy than either measure on its own. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. pypet: A Python Toolkit for Data Management of Parameter Explorations

    PubMed Central

    Meyer, Robert; Obermayer, Klaus

    2016-01-01

    pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines. PMID:27610080

  12. MULTIPROCESSOR AND DISTRIBUTED PROCESSING BIBLIOGRAPHIC DATA BASE SOFTWARE SYSTEM

    NASA Technical Reports Server (NTRS)

    Miya, E. N.

    1994-01-01

    Multiprocessors and distributed processing are undergoing increased scientific scrutiny for many reasons. It is more and more difficult to keep track of the existing research in these fields. This package consists of a large machine-readable bibliographic data base which, in addition to the usual keyword searches, can be used for producing citations, indexes, and cross-references. The data base is compiled from smaller existing multiprocessing bibliographies, and tables of contents from journals and significant conferences. There are approximately 4,000 entries covering topics such as parallel and vector processing, networks, supercomputers, fault-tolerant computers, and cellular automata. Each entry is represented by 21 fields including keywords, author, referencing book or journal title, volume and page number, and date and city of publication. The data base contains UNIX 'refer' formatted ASCII data and can be implemented on any computer running under the UNIX operating system. The data base requires approximately one megabyte of secondary storage. The documentation for this program is included with the distribution tape, although it can be purchased for the price below. This bibliography was compiled in 1985 and updated in 1988.

  13. Parallelization strategies for continuum-generalized method of moments on the multi-thread systems

    NASA Astrophysics Data System (ADS)

    Bustamam, A.; Handhika, T.; Ernastuti, Kerami, D.

    2017-07-01

    Continuum-Generalized Method of Moments (C-GMM) covers the Generalized Method of Moments (GMM) shortfall which is not as efficient as Maximum Likelihood estimator by using the continuum set of moment conditions in a GMM framework. However, this computation would take a very long time since optimizing regularization parameter. Unfortunately, these calculations are processed sequentially whereas in fact all modern computers are now supported by hierarchical memory systems and hyperthreading technology, which allowing for parallel computing. This paper aims to speed up the calculation process of C-GMM by designing a parallel algorithm for C-GMM on the multi-thread systems. First, parallel regions are detected for the original C-GMM algorithm. There are two parallel regions in the original C-GMM algorithm, that are contributed significantly to the reduction of computational time: the outer-loop and the inner-loop. Furthermore, this parallel algorithm will be implemented with standard shared-memory application programming interface, i.e. Open Multi-Processing (OpenMP). The experiment shows that the outer-loop parallelization is the best strategy for any number of observations.

  14. pypet: A Python Toolkit for Data Management of Parameter Explorations.

    PubMed

    Meyer, Robert; Obermayer, Klaus

    2016-01-01

    pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.

  15. The effect of modifying response and performance feedback parameters on the CNV in humans

    NASA Technical Reports Server (NTRS)

    Otto, D. A.; Leifer, L. J.

    1972-01-01

    The effect on the CNV of sustained and delayed motor response with the dominant and nondominant hand in the presence and absence of visual performance feedback, was studied in 15 male adults. Monopolar scalp recordings were obtained at Fz, Cz, Pz, and bilaterally over the motor hand area. Results indicated that the magnitude of the CNV was greater in the delayed than sustained response task, greater in the presence than absence of feedback, and greater over the motor hand area contralateral to movement. Frontal CNV habituated in the sustained, but not the delayed response task, suggested that frontal negative variations in the former case signify an orienting response to novelty or uncertainty. The absence of habituation in the delay condition was interpreted in terms of the motor inhibitory function of frontal association cortex. Performance feedback appeared to enhance CNV indirectly by increasing the motivation of subjects. A multiprocess conception of CNV was proposed in which vortex-negative slow potentials reflect a multiplicity of psychophysiological processes occurring at a variety of cortical and subcortical locations in the brain preparatory to a motor or mental action.

  16. MLP: A Parallel Programming Alternative to MPI for New Shared Memory Parallel Systems

    NASA Technical Reports Server (NTRS)

    Taft, James R.

    1999-01-01

    Recent developments at the NASA AMES Research Center's NAS Division have demonstrated that the new generation of NUMA based Symmetric Multi-Processing systems (SMPs), such as the Silicon Graphics Origin 2000, can successfully execute legacy vector oriented CFD production codes at sustained rates far exceeding processing rates possible on dedicated 16 CPU Cray C90 systems. This high level of performance is achieved via shared memory based Multi-Level Parallelism (MLP). This programming approach, developed at NAS and outlined below, is distinct from the message passing paradigm of MPI. It offers parallelism at both the fine and coarse grained level, with communication latencies that are approximately 50-100 times lower than typical MPI implementations on the same platform. Such latency reductions offer the promise of performance scaling to very large CPU counts. The method draws on, but is also distinct from, the newly defined OpenMP specification, which uses compiler directives to support a limited subset of multi-level parallel operations. The NAS MLP method is general, and applicable to a large class of NASA CFD codes.

  17. Passive serialization in a multitasking environment

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

    Hennessey, J.P.; Osisek, D.L.; Seigh, J.W. II

    1989-02-28

    In a multiprocessing system having a control program in which data objects are shared among processes, this patent describes a method for serializing references to a data object by the processes so as to prevent invalid references to the data object by any process when an operation requiring exclusive access is performed by another process, comprising the steps of: permitting the processes to reference data objects on a shared access basis without obtaining a shared lock; monitoring a point of execution of the control program which is common to all processes in the system, which occurs regularly in the process'more » execution and across which no references to any data object can be maintained by any process, except references using locks; establishing a system reference point which occurs after each process in the system has passed the point of execution at least once since the last such system reference point; requesting an operation requiring exclusive access on a selected data object; preventing subsequent references by other processes to the selected data object; waiting until two of the system references points have occurred; and then performing the requested operation.« less

  18. Active weld control

    NASA Technical Reports Server (NTRS)

    Powell, Bradley W.; Burroughs, Ivan A.

    1994-01-01

    Through the two phases of this contract, sensors for welding applications and parameter extraction algorithms have been developed. These sensors form the foundation of a weld control system which can provide action weld control through the monitoring of the weld pool and keyhole in a VPPA welding process. Systems of this type offer the potential of quality enhancement and cost reduction (minimization of rework on faulty welds) for high-integrity welding applications. Sensors for preweld and postweld inspection, weld pool monitoring, keyhole/weld wire entry monitoring, and seam tracking were developed. Algorithms for signal extraction were also developed and analyzed to determine their application to an adaptive weld control system. The following sections discuss findings for each of the three sensors developed under this contract: (1) weld profiling sensor; (2) weld pool sensor; and (3) stereo seam tracker/keyhole imaging sensor. Hardened versions of these sensors were designed and built under this contract. A control system, described later, was developed on a multiprocessing/multitasking operating system for maximum power and flexibility. Documentation for sensor mechanical and electrical design is also included as appendices in this report.

  19. A Robust Concurrent Approach for Road Extraction and Urbanization Monitoring Based on Superpixels Acquired from Spectral Remote Sensing Images

    NASA Astrophysics Data System (ADS)

    Seppke, Benjamin; Dreschler-Fischer, Leonie; Wilms, Christian

    2016-08-01

    The extraction of road signatures from remote sensing images as a promising indicator for urbanization is a classical segmentation problem. However, some segmentation algorithms often lead to non-sufficient results. One way to overcome this problem is the usage of superpixels, that represent a locally coherent cluster of connected pixels. Superpixels allow flexible, highly adaptive segmentation approaches due to the possibility of merging as well as splitting and form new basic image entities. On the other hand, superpixels require an appropriate representation containing all relevant information about topology and geometry to maximize their advantages.In this work, we present a combined geometric and topological representation based on a special graph representation, the so-called RS-graph. Moreover, we present the use of the RS-graph by means of a case study: the extraction of partially occluded road networks in rural areas from open source (spectral) remote sensing images by tracking. In addition, multiprocessing and GPU-based parallelization is used to speed up the construction of the representation and the application.

  20. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    PubMed Central

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques-Philippe

    2015-01-01

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering. PMID:25945583

  1. Multi-GPU parallel algorithm design and analysis for improved inversion of probability tomography with gravity gradiometry data

    NASA Astrophysics Data System (ADS)

    Hou, Zhenlong; Huang, Danian

    2017-09-01

    In this paper, we make a study on the inversion of probability tomography (IPT) with gravity gradiometry data at first. The space resolution of the results is improved by multi-tensor joint inversion, depth weighting matrix and the other methods. Aiming at solving the problems brought by the big data in the exploration, we present the parallel algorithm and the performance analysis combining Compute Unified Device Architecture (CUDA) with Open Multi-Processing (OpenMP) based on Graphics Processing Unit (GPU) accelerating. In the test of the synthetic model and real data from Vinton Dome, we get the improved results. It is also proved that the improved inversion algorithm is effective and feasible. The performance of parallel algorithm we designed is better than the other ones with CUDA. The maximum speedup could be more than 200. In the performance analysis, multi-GPU speedup and multi-GPU efficiency are applied to analyze the scalability of the multi-GPU programs. The designed parallel algorithm is demonstrated to be able to process larger scale of data and the new analysis method is practical.

  2. A General Approach to Access Morphologies of Polyoxometalates in Solution by Using SAXS: An Ab Initio Modeling Protocol.

    PubMed

    Li, Mu; Wang, Weiyu; Yin, Panchao

    2018-05-02

    Herein, we reported a general protocol for an ab initio modeling approach to deduce structure information of polyoxometalates (POMs) in solutions from scattering data collected by the small-angle X-ray scattering (SAXS) technique. To validate the protocol, the morphologies of a serious of known POMs in either aqueous or organic solvents were analyzed. The obtained particle morphologies were compared and confirmed with previous reported crystal structures. To extend the feasibility of the protocol to an unknown system of aqueous solutions of Na 2 MoO 4 with the pH ranging from -1 to 8.35, the formation of {Mo 36 } clusters was probed, identified, and confirmed by SAXS. The approach was further optimized with a multi-processing capability to achieve fast analysis of experimental data, thereby, facilitating in situ studies of formations of POMs in solutions. The advantage of this approach is to generate intuitive 3D models of POMs in solutions without confining information such as symmetries and possible sizes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. ALFA: The new ALICE-FAIR software framework

    NASA Astrophysics Data System (ADS)

    Al-Turany, M.; Buncic, P.; Hristov, P.; Kollegger, T.; Kouzinopoulos, C.; Lebedev, A.; Lindenstruth, V.; Manafov, A.; Richter, M.; Rybalchenko, A.; Vande Vyvre, P.; Winckler, N.

    2015-12-01

    The commonalities between the ALICE and FAIR experiments and their computing requirements led to the development of large parts of a common software framework in an experiment independent way. The FairRoot project has already shown the feasibility of such an approach for the FAIR experiments and extending it beyond FAIR to experiments at other facilities[1, 2]. The ALFA framework is a joint development between ALICE Online- Offline (O2) and FairRoot teams. ALFA is designed as a flexible, elastic system, which balances reliability and ease of development with performance using multi-processing and multithreading. A message- based approach has been adopted; such an approach will support the use of the software on different hardware platforms, including heterogeneous systems. Each process in ALFA assumes limited communication and reliance on other processes. Such a design will add horizontal scaling (multiple processes) to vertical scaling provided by multiple threads to meet computing and throughput demands. ALFA does not dictate any application protocols. Potentially, any content-based processor or any source can change the application protocol. The framework supports different serialization standards for data exchange between different hardware and software languages.

  4. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

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

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore » resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

  5. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams.

    PubMed

    Coquelle, Nicolas; Brewster, Aaron S; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques Philippe

    2015-05-01

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

  6. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    DOE PAGES

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; ...

    2015-04-25

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore » resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

  7. CubiCal - Fast radio interferometric calibration suite exploiting complex optimisation

    NASA Astrophysics Data System (ADS)

    Kenyon, J. S.; Smirnov, O. M.; Grobler, T. L.; Perkins, S. J.

    2018-05-01

    It has recently been shown that radio interferometric gain calibration can be expressed succinctly in the language of complex optimisation. In addition to providing an elegant framework for further development, it exposes properties of the calibration problem which can be exploited to accelerate traditional non-linear least squares solvers such as Gauss-Newton and Levenberg-Marquardt. We extend existing derivations to chains of Jones terms: products of several gains which model different aberrant effects. In doing so, we find that the useful properties found in the single term case still hold. We also develop several specialised solvers which deal with complex gains parameterised by real values. The newly developed solvers have been implemented in a Python package called CubiCal, which uses a combination of Cython, multiprocessing and shared memory to leverage the power of modern hardware. We apply CubiCal to both simulated and real data, and perform both direction-independent and direction-dependent self-calibration. Finally, we present the results of some rudimentary profiling to show that CubiCal is competitive with respect to existing calibration tools such as MeqTrees.

  8. Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations.

    PubMed

    Procacci, Piero

    2016-06-27

    We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .

  9. GEANT4 distributed computing for compact clusters

    NASA Astrophysics Data System (ADS)

    Harrawood, Brian P.; Agasthya, Greeshma A.; Lakshmanan, Manu N.; Raterman, Gretchen; Kapadia, Anuj J.

    2014-11-01

    A new technique for distribution of GEANT4 processes is introduced to simplify running a simulation in a parallel environment such as a tightly coupled computer cluster. Using a new C++ class derived from the GEANT4 toolkit, multiple runs forming a single simulation are managed across a local network of computers with a simple inter-node communication protocol. The class is integrated with the GEANT4 toolkit and is designed to scale from a single symmetric multiprocessing (SMP) machine to compact clusters ranging in size from tens to thousands of nodes. User designed 'work tickets' are distributed to clients using a client-server work flow model to specify the parameters for each individual run of the simulation. The new g4DistributedRunManager class was developed and well tested in the course of our Neutron Stimulated Emission Computed Tomography (NSECT) experiments. It will be useful for anyone running GEANT4 for large discrete data sets such as covering a range of angles in computed tomography, calculating dose delivery with multiple fractions or simply speeding the through-put of a single model.

  10. A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding.

    PubMed

    Scemama, Anthony; Renon, Nicolas; Rapacioli, Mathias

    2014-06-10

    We present an algorithm and its parallel implementation for solving a self-consistent problem as encountered in Hartree-Fock or density functional theory. The algorithm takes advantage of the sparsity of matrices through the use of local molecular orbitals. The implementation allows one to exploit efficiently modern symmetric multiprocessing (SMP) computer architectures. As a first application, the algorithm is used within the density-functional-based tight binding method, for which most of the computational time is spent in the linear algebra routines (diagonalization of the Fock/Kohn-Sham matrix). We show that with this algorithm (i) single point calculations on very large systems (millions of atoms) can be performed on large SMP machines, (ii) calculations involving intermediate size systems (1000-100 000 atoms) are also strongly accelerated and can run efficiently on standard servers, and (iii) the error on the total energy due to the use of a cutoff in the molecular orbital coefficients can be controlled such that it remains smaller than the SCF convergence criterion.

  11. Divorce, Separation, and Housing Changes: A Multiprocess Analysis of Longitudinal Data from England and Wales.

    PubMed

    Mikolai, Júlia; Kulu, Hill

    2018-02-01

    This study investigates the effect of marital and nonmarital separation on individuals' residential and housing trajectories. Using rich data from the British Household Panel Survey (BHPS) and applying multilevel competing-risks event history models, we analyze the risk of a move of single, married, cohabiting, and separated men and women to different housing types. We distinguish moves due to separation from moves of separated people and account for unobserved codeterminants of moving and separation risks. Our analysis shows that many individuals move due to separation, as expected, but that the likelihood of moving is also relatively high among separated individuals. We find that separation has a long-term effect on individuals' residential careers. Separated women exhibit high moving risks regardless of whether they moved out of the joint home upon separation, whereas separated men who did not move out upon separation are less likely to move. Interestingly, separated women are most likely to move to terraced houses, whereas separated men are equally likely to move to flats (apartments) and terraced (row) houses, suggesting that family structure shapes moving patterns of separated individuals.

  12. Purple L1 Milestone Review Panel TotalView Debugger Functionality and Performance for ASC Purple

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

    Wolfe, M

    2006-12-12

    ASC code teams require a robust software debugging tool to help developers quickly find bugs in their codes and get their codes running. Development debugging commonly runs up to 512 processes. Production jobs run up to full ASC Purple scale, and at times require introspection while running. Developers want a debugger that runs on all their development and production platforms and that works with all compilers and runtimes used with ASC codes. The TotalView Multiprocess Debugger made by Etnus was specified for ASC Purple to address this needed capability. The ASC Purple environment builds on the environment seen by TotalViewmore » on ASCI White. The debugger must now operate with the Power5 CPU, Federation switch, AIX 5.3 operating system including large pages, IBM compilers 7 and 9, POE 4.2 parallel environment, and rs6000 SLURM resource manager. Users require robust, basic debugger functionality with acceptable performance at development debugging scale. A TotalView installation must be provided at the beginning of the early user access period that meets these requirements. A functional enhancement, fast conditional data watchpoints, and a scalability enhancement, capability up to 8192 processes, are to be demonstrated.« less

  13. Parallel Execution of Functional Mock-up Units in Buildings Modeling

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

    Ozmen, Ozgur; Nutaro, James J.; New, Joshua Ryan

    2016-06-30

    A Functional Mock-up Interface (FMI) defines a standardized interface to be used in computer simulations to develop complex cyber-physical systems. FMI implementation by a software modeling tool enables the creation of a simulation model that can be interconnected, or the creation of a software library called a Functional Mock-up Unit (FMU). This report describes an FMU wrapper implementation that imports FMUs into a C++ environment and uses an Euler solver that executes FMUs in parallel using Open Multi-Processing (OpenMP). The purpose of this report is to elucidate the runtime performance of the solver when a multi-component system is imported asmore » a single FMU (for the whole system) or as multiple FMUs (for different groups of components as sub-systems). This performance comparison is conducted using two test cases: (1) a simple, multi-tank problem; and (2) a more realistic use case based on the Modelica Buildings Library. In both test cases, the performance gains are promising when each FMU consists of a large number of states and state events that are wrapped in a single FMU. Load balancing is demonstrated to be a critical factor in speeding up parallel execution of multiple FMUs.« less

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

    PubMed

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

    2016-01-01

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

  15. Modeling and Simulating Multiple Failure Masking enabled by Local Recovery for Stencil-based Applications at Extreme Scales

    DOE PAGES

    Gamell, Marc; Teranishi, Keita; Mayo, Jackson; ...

    2017-04-24

    By obtaining multi-process hard failure resilience at the application level is a key challenge that must be overcome before the promise of exascale can be fully realized. Some previous work has shown that online global recovery can dramatically reduce the overhead of failures when compared to the more traditional approach of terminating the job and restarting it from the last stored checkpoint. If online recovery is performed in a local manner further scalability is enabled, not only due to the intrinsic lower costs of recovering locally, but also due to derived effects when using some application types. In this papermore » we model one such effect, namely multiple failure masking, that manifests when running Stencil parallel computations on an environment when failures are recovered locally. First, the delay propagation shape of one or multiple failures recovered locally is modeled to enable several analyses of the probability of different levels of failure masking under certain Stencil application behaviors. These results indicate that failure masking is an extremely desirable effect at scale which manifestation is more evident and beneficial as the machine size or the failure rate increase.« less

  16. Hybrid multicore/vectorisation technique applied to the elastic wave equation on a staggered grid

    NASA Astrophysics Data System (ADS)

    Titarenko, Sofya; Hildyard, Mark

    2017-07-01

    In modern physics it has become common to find the solution of a problem by solving numerically a set of PDEs. Whether solving them on a finite difference grid or by a finite element approach, the main calculations are often applied to a stencil structure. In the last decade it has become usual to work with so called big data problems where calculations are very heavy and accelerators and modern architectures are widely used. Although CPU and GPU clusters are often used to solve such problems, parallelisation of any calculation ideally starts from a single processor optimisation. Unfortunately, it is impossible to vectorise a stencil structured loop with high level instructions. In this paper we suggest a new approach to rearranging the data structure which makes it possible to apply high level vectorisation instructions to a stencil loop and which results in significant acceleration. The suggested method allows further acceleration if shared memory APIs are used. We show the effectiveness of the method by applying it to an elastic wave propagation problem on a finite difference grid. We have chosen Intel architecture for the test problem and OpenMP (Open Multi-Processing) since they are extensively used in many applications.

  17. Optics Program Modified for Multithreaded Parallel Computing

    NASA Technical Reports Server (NTRS)

    Lou, John; Bedding, Dave; Basinger, Scott

    2006-01-01

    A powerful high-performance computer program for simulating and analyzing adaptive and controlled optical systems has been developed by modifying the serial version of the Modeling and Analysis for Controlled Optical Systems (MACOS) program to impart capabilities for multithreaded parallel processing on computing systems ranging from supercomputers down to Symmetric Multiprocessing (SMP) personal computers. The modifications included the incorporation of OpenMP, a portable and widely supported application interface software, that can be used to explicitly add multithreaded parallelism to an application program under a shared-memory programming model. OpenMP was applied to parallelize ray-tracing calculations, one of the major computing components in MACOS. Multithreading is also used in the diffraction propagation of light in MACOS based on pthreads [POSIX Thread, (where "POSIX" signifies a portable operating system for UNIX)]. In tests of the parallelized version of MACOS, the speedup in ray-tracing calculations was found to be linear, or proportional to the number of processors, while the speedup in diffraction calculations ranged from 50 to 60 percent, depending on the type and number of processors. The parallelized version of MACOS is portable, and, to the user, its interface is basically the same as that of the original serial version of MACOS.

  18. Mesh infrastructure for coupled multiprocess geophysical simulations

    DOE PAGES

    Garimella, Rao V.; Perkins, William A.; Buksas, Mike W.; ...

    2014-01-01

    We have developed a sophisticated mesh infrastructure capability to support large scale multiphysics simulations such as subsurface flow and reactive contaminant transport at storage sites as well as the analysis of the effects of a warming climate on the terrestrial arctic. These simulations involve a wide range of coupled processes including overland flow, subsurface flow, freezing and thawing of ice rich soil, accumulation, redistribution and melting of snow, biogeochemical processes involving plant matter and finally, microtopography evolution due to melting and degradation of ice wedges below the surface. In addition to supporting the usual topological and geometric queries about themore » mesh, the mesh infrastructure adds capabilities such as identifying columnar structures in the mesh, enabling deforming of the mesh subject to constraints and enabling the simultaneous use of meshes of different dimensionality for subsurface and surface processes. The generic mesh interface is capable of using three different open source mesh frameworks (MSTK, MOAB and STKmesh) under the hood allowing the developers to directly compare them and choose one that is best suited for the application's needs. We demonstrate the results of some simulations using these capabilities as well as present a comparison of the performance of the different mesh frameworks.« less

  19. Modeling and Simulating Multiple Failure Masking enabled by Local Recovery for Stencil-based Applications at Extreme Scales

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

    Gamell, Marc; Teranishi, Keita; Mayo, Jackson

    By obtaining multi-process hard failure resilience at the application level is a key challenge that must be overcome before the promise of exascale can be fully realized. Some previous work has shown that online global recovery can dramatically reduce the overhead of failures when compared to the more traditional approach of terminating the job and restarting it from the last stored checkpoint. If online recovery is performed in a local manner further scalability is enabled, not only due to the intrinsic lower costs of recovering locally, but also due to derived effects when using some application types. In this papermore » we model one such effect, namely multiple failure masking, that manifests when running Stencil parallel computations on an environment when failures are recovered locally. First, the delay propagation shape of one or multiple failures recovered locally is modeled to enable several analyses of the probability of different levels of failure masking under certain Stencil application behaviors. These results indicate that failure masking is an extremely desirable effect at scale which manifestation is more evident and beneficial as the machine size or the failure rate increase.« less

  20. Prospective memory across adolescence: the effects of age and cue focality.

    PubMed

    Wang, Lijuan; Altgassen, Mareike; Liu, Wei; Xiong, Weirui; Akgün, Canan; Kliegel, Matthias

    2011-01-01

    The present study examined the role of controlled attention in age differences in event-based prospective memory performance across adolescence. The researchers tested whether presenting the prospective memory cue in or out of focal awareness of the ongoing task (resulting in low versus high demands for controlled attention, respectively) might affect age-related prospective memory performance. In total, 119 Chinese participants ages 13 to 20 took part in this study (60 adolescents: age M = 13.26 years, SD = 0.50; 23 boys; 59 young adults: age M = 19.70 years, SD = 0.87; 19 men). Findings demonstrated a significant interaction, F(1, 114) = 6.41, p < .05. No effect of age on prospective memory performance was revealed when a focal cue was used (F < 1), whereas there was a reliable age effect between adolescents and young adults when nonfocal prospective memory cues were presented, F(1, 59) = 16.13, p < .01. This pattern of results suggests that the interplay of both available resources of controlled attention and working memory, along with specific task demands, may contribute to possible age differences in prospective memory performance across adolescence. Results are discussed in the context of the multiprocess theory of prospective memory.

  1. Laser direct-write and crystallization of FeSi II micro-dot array for NIR light-emitting device application

    NASA Astrophysics Data System (ADS)

    Narazaki, Aiko; Kurosaki, Ryozo; Sato, Tadatake; Kawaguchi, Yoshizo; Niino, Hiroyuki

    2007-02-01

    We printed FeSi II micro-dot array on various kinds of substrates utilizing laser-induced forward transfer (LIFT). An amorphous FeSi II was deposited by sputtering on a transparent plate as a source film. A single KrF excimer laser pulse through a mask-projection system was imaged with a small micrometer-sized grid pattern onto a film/plate interface, resulting in the deposition of FeSi II micro-dot array on a facing substrate with a high number density of 10 4 mm -2. FeSi II in the β crystalline phase is a promising eco-friendly semiconductor because of NIR electroluminescence used for optical networking as well as abundant components reserve on the earth and non-toxicity. However, the β-FeSi II film fabrication generally required high-temperature multi-processes which hamper its integration and performance reproducibility. Using the LIFT of micro-dot array, we succeeded in room-temperature preparation of β-FeSi II. Micro-Raman spectroscopy confirmed the β crystalline phase in the micro-dots deposited on an unheated silica glass substrate. Thus, the LIFT is useful for integrating functional micro-dot array accompanied by the crystallization at lower temperatures.

  2. Understanding the dark and bright sides of anxiety: A theory of workplace anxiety.

    PubMed

    Cheng, Bonnie Hayden; McCarthy, Julie M

    2018-05-01

    Researchers have uncovered inconsistent relations between anxiety and performance. Although the prominent view is a "dark side," where anxiety has a negative relation with performance, a "bright side" of anxiety has also been suggested. We reconcile past findings by presenting a comprehensive multilevel, multiprocess model of workplace anxiety called the theory of workplace anxiety (TWA). This model highlights the processes and conditions through which workplace anxiety may lead to debilitative and facilitative job performance and includes 19 theoretical propositions. Drawing on past theories of anxiety, resource depletion, cognitive-motivational processing, and performance, we uncover the debilitative and facilitative nature of dispositional and situational workplace anxiety by positioning emotional exhaustion, self-regulatory processing, and cognitive interference as distinct contrasting processes underlying the relationship between workplace anxiety and job performance. Extending our theoretical model, we pinpoint motivation, ability, and emotional intelligence as critical conditions that shape when workplace anxiety will debilitate and facilitate job performance. We also identify the unique employee, job, and situational characteristics that serve as antecedents of dispositional and situational workplace anxiety. The TWA offers a nuanced perspective on workplace anxiety and serves as a foundation for future work. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  3. A low-cost transportable ground station for capture and processing of direct broadcast EOS satellite data

    NASA Technical Reports Server (NTRS)

    Davis, Don; Bennett, Toby; Short, Nicholas M., Jr.

    1994-01-01

    The Earth Observing System (EOS), part of a cohesive national effort to study global change, will deploy a constellation of remote sensing spacecraft over a 15 year period. Science data from the EOS spacecraft will be processed and made available to a large community of earth scientists via NASA institutional facilities. A number of these spacecraft are also providing an additional interface to broadcast data directly to users. Direct broadcast of real-time science data from overhead spacecraft has valuable applications including validation of field measurements, planning science campaigns, and science and engineering education. The success and usefulness of EOS direct broadcast depends largely on the end-user cost of receiving the data. To extend this capability to the largest possible user base, the cost of receiving ground stations must be as low as possible. To achieve this goal, NASA Goddard Space Flight Center is developing a prototype low-cost transportable ground station for EOS direct broadcast data based on Very Large Scale Integration (VLSI) components and pipelined, multiprocessing architectures. The targeted reproduction cost of this system is less than $200K. This paper describes a prototype ground station and its constituent components.

  4. Flexible Biomanufacturing Processes that Address the Needs of the Future.

    PubMed

    Diel, Bernhard; Manzke, Christian; Peuker, Thorsten

    2014-01-01

    : As the age of the blockbuster drug recedes, the business model for the biopharmaceutical industry is evolving at an ever-increasing pace. The personalization of medicine, the emergence of biosimilars and biobetters, and the need to provide vaccines globally are just some of the factors forcing biomanufacturers to rethink how future manufacturing capability is implemented. One thing is clear: the traditional manufacturing strategy of constructing large-scale, purpose-built, capital-intensive facilities will no longer meet the industry's emerging production and economic requirements. Therefore, the authors of this chapter describe the new approach for designing and implementing flexible production processes for monoclonal antibodies and focus on the points to consider as well as the lessons learned from past experience in engineering such systems. A conceptual integrated design is presented that can be used as a blueprint for next-generation biomanufacturing facilities. In addition, this chapter discusses the benefits of the new approach with respect to flexibility, cost, and schedule. The concept presented here can be applied to other biopharmaceutical manufacturing processes and facilities, including-but not limited to-vaccine manufacturing, multiproduct and/or multiprocess capability, clinical manufacturing, and so on.

  5. Numerical simualtions and implications of air inclusions on the microdynamics of ice and firn

    NASA Astrophysics Data System (ADS)

    Steinbach, Florian; Weikusat, Ilka; Bons, Paul; Griera, Albert; Kerch, Johanna; Kuiper, Ernst-Jan; Llorens-Verde, Maria-Gema

    2016-04-01

    Although ice sheets are valuable paleo-climate archives, they can loose their integrity by ice flow (Faria et al. 2010). Consequently, understanding the dynamic processes that control the flow of ice is essential when investigating the past and future climate. While recent research successfully modelled the microdynamics of pure ice (e.g. Montagnat et al., 2014; Llorens et al., 2015), work taking into account second phases is scarce. Only a few studies also show the microstructural influence of air inclusions (Azuma et al., 2012, Roessiger et al., 2014). Therefore, modelling was performed focussing on the implications of the presence of bubbles on the microdynamical mechanisms and microstructure evolution. The full-field theory crystal plasticity code (FFT) of Lebensohn (2001), was coupled to the 2D multi-process modelling platform Elle (Bons et al., 2008), following the approach by Griera et al. (2013). FFT calculates the viscoplastic response of polycrystalline materials deforming by dislocation glide, taking into account mechanical anisotropy. The models further incorporate surface- and stored strain energy driven grain boundary migration (GBM) and intracrystalline recovery simulating annihilation and rearrangement of dislocations by reduction of internal misorientations. GBM was refined for polyphase materials following Becker et al. (2008) and Roessiger et al. (2014). Additionally, the formation of new high angle grain boundaries by nucleation and polygonisation based on critical internal misorientations has been implemented. Successively running the codes for different processes in very short numerical timesteps effectively enables multi-process modelling of deformation and concurrent recrystallisation. Results show how air inclusions control and increase strain localisation, leading to locally enhanced dynamic recrystallisation. This is in compliance with Faria et al. (2014), who theoretically predicted these localizations based on firn data from EPICA Dronning Maud Land (EDML) ice core. We propose that strain localisation has a strong control on the dominating recrystallisation mechanisms and can account for microstructural observations from alpine and polar ice cores. Our results confirm dynamic recrystallisation occurring in the uppermost levels of ice sheets as observed by Kipfstuhl et al. (2009) and Weikusat et al. (2009) in EDML core. References Azuma, N., et al. (2012) Journal of Structural Geology, 42, 184-193 Becker, J.K., et al. (2008) Computers & Geosciences, 34, 201-212 Bons, P.D., et al. (2008) Lecture Notes in Earth Sciences, 106 Faria, S.H., et al. (2010) Quaternary Science Reviews, 29, 338-351 Faria, S.H., et al. (2014) Journal of Structural Geology, 61, 21-49 Griera, A., et al. (2013) Tectonophysics, 587, 4-29 Kipfstuhl, S., et al. (2009) Journal of Geophysical Research, 114, B05204 Lebensohn, R.A. (2001) Acta Materialia, 49, 2723-2737 Llorens, M.G., et al. (2015) Journal of Glaciology, in press, doi:10.1017/jog.2016.28 Montagnat, M., et al. (2014) Journal of Structural Geology, 61, 78-108 Roessiger, J., et al. (2014) Journal of Structural Geology, 61, 123-132 Weikusat, I., et al. (2009) Journal of Glaciology, 55, 461-472

  6. Precise positioning method for multi-process connecting based on binocular vision

    NASA Astrophysics Data System (ADS)

    Liu, Wei; Ding, Lichao; Zhao, Kai; Li, Xiao; Wang, Ling; Jia, Zhenyuan

    2016-01-01

    With the rapid development of aviation and aerospace, the demand for metal coating parts such as antenna reflector, eddy-current sensor and signal transmitter, etc. is more and more urgent. Such parts with varied feature dimensions, complex three-dimensional structures, and high geometric accuracy are generally fabricated by the combination of different manufacturing technology. However, it is difficult to ensure the machining precision because of the connection error between different processing methods. Therefore, a precise positioning method is proposed based on binocular micro stereo vision in this paper. Firstly, a novel and efficient camera calibration method for stereoscopic microscope is presented to solve the problems of narrow view field, small depth of focus and too many nonlinear distortions. Secondly, the extraction algorithms for law curve and free curve are given, and the spatial position relationship between the micro vision system and the machining system is determined accurately. Thirdly, a precise positioning system based on micro stereovision is set up and then embedded in a CNC machining experiment platform. Finally, the verification experiment of the positioning accuracy is conducted and the experimental results indicated that the average errors of the proposed method in the X and Y directions are 2.250 μm and 1.777 μm, respectively.

  7. Akuna: An Open Source User Environment for Managing Subsurface Simulation Workflows

    NASA Astrophysics Data System (ADS)

    Freedman, V. L.; Agarwal, D.; Bensema, K.; Finsterle, S.; Gable, C. W.; Keating, E. H.; Krishnan, H.; Lansing, C.; Moeglein, W.; Pau, G. S. H.; Porter, E.; Scheibe, T. D.

    2014-12-01

    The U.S. Department of Energy (DOE) is investing in development of a numerical modeling toolset called ASCEM (Advanced Simulation Capability for Environmental Management) to support modeling analyses at legacy waste sites. ASCEM is an open source and modular computing framework that incorporates new advances and tools for predicting contaminant fate and transport in natural and engineered systems. The ASCEM toolset includes both a Platform with Integrated Toolsets (called Akuna) and a High-Performance Computing multi-process simulator (called Amanzi). The focus of this presentation is on Akuna, an open-source user environment that manages subsurface simulation workflows and associated data and metadata. In this presentation, key elements of Akuna are demonstrated, which includes toolsets for model setup, database management, sensitivity analysis, parameter estimation, uncertainty quantification, and visualization of both model setup and simulation results. A key component of the workflow is in the automated job launching and monitoring capabilities, which allow a user to submit and monitor simulation runs on high-performance, parallel computers. Visualization of large outputs can also be performed without moving data back to local resources. These capabilities make high-performance computing accessible to the users who might not be familiar with batch queue systems and usage protocols on different supercomputers and clusters.

  8. A high-rate PCI-based telemetry processor system

    NASA Astrophysics Data System (ADS)

    Turri, R.

    2002-07-01

    The high performances reached by the Satellite on-board telemetry generation and transmission, as consequently, will impose the design of ground facilities with higher processing capabilities at low cost to allow a good diffusion of these ground station. The equipment normally used are based on complex, proprietary bus and computing architectures that prevent the systems from exploiting the continuous and rapid increasing in computing power available on market. The PCI bus systems now allow processing of high-rate data streams in a standard PC-system. At the same time the Windows NT operating system supports multitasking and symmetric multiprocessing, giving the capability to process high data rate signals. In addition, high-speed networking, 64 bit PCI-bus technologies and the increase in processor power and software, allow creating a system based on COTS products (which in future may be easily and inexpensively upgraded). In the frame of EUCLID RTP 9.8 project, a specific work element was dedicated to develop the architecture of a system able to acquire telemetry data of up to 600 Mbps. Laben S.p.A - a Finmeccanica Company -, entrusted of this work, has designed a PCI-based telemetry system making possible the communication between a satellite down-link and a wide area network at the required rate.

  9. Multiprocessing the Sieve of Eratosthenes

    NASA Technical Reports Server (NTRS)

    Bokhari, S.

    1986-01-01

    The Sieve of Eratosthenes for finding prime numbers in recent years has seen much use as a benchmark algorithm for serial computers while its intrinsically parallel nature has gone largely unnoticed. The implementation of a parallel version of this algorithm for a real parallel computer, the Flex/32, is described and its performance discussed. It is shown that the algorithm is sensitive to several fundamental performance parameters of parallel machines, such as spawning time, signaling time, memory access, and overhead of process switching. Because of the nature of the algorithm, it is impossible to get any speedup beyond 4 or 5 processors unless some form of dynamic load balancing is employed. We describe the performance of our algorithm with and without load balancing and compare it with theoretical lower bounds and simulated results. It is straightforward to understand this algorithm and to check the final results. However, its efficient implementation on a real parallel machine requires thoughtful design, especially if dynamic load balancing is desired. The fundamental operations required by the algorithm are very simple: this means that the slightest overhead appears prominently in performance data. The Sieve thus serves not only as a very severe test of the capabilities of a parallel processor but is also an interesting challenge for the programmer.

  10. Prospective Memory Deficits in Ecstasy Users: Effects of Longer Ongoing Task Delay Interval

    PubMed Central

    WEINBORN, MICHAEL; WOODS, STEVEN PAUL; NULSEN, CLAIRE; PARK, KATHERINE

    2011-01-01

    Ecstasy use has been associated with neurotoxicity and neurocognitive impairment in a variety of domains, including prospective memory (ProM), which involves the delayed execution of a previously encoded intention in response to a specific cue. The present study adopted the multiprocess theory of ProM to evaluate the hypothesis that ecstasy users would evidence differentially impaired ProM on longer versus shorter ongoing task delays. Ecstasy (n = 31) users, high-risk alcohol users (n = 21) and healthy nonusers (n = 31) completed the short (2-min) and long (15-min) delay ProM scales of the Memory for Intentions Screening Test. Results showed a significant group by ProM delay interaction, such that ecstasy users performed comparably to the comparison groups on short-delay trials, but were impaired on long-delay ProM, particularly for time-based cues. Among the ecstasy users, long-delay ProM was positively associated with risky decision-making, but not with retrospective memory or other aspects of executive functions. These findings suggest that ecstasy users may be particularly susceptible to deficits in strategic target monitoring and maintenance of cue-intention pairings over longer ProM delays. Findings are discussed in the context of their potential everyday functioning (e.g., academic, vocational) and treatment implications for ecstasy users. PMID:22047194

  11. OpenMP parallelization of a gridded SWAT (SWATG)

    NASA Astrophysics Data System (ADS)

    Zhang, Ying; Hou, Jinliang; Cao, Yongpan; Gu, Juan; Huang, Chunlin

    2017-12-01

    Large-scale, long-term and high spatial resolution simulation is a common issue in environmental modeling. A Gridded Hydrologic Response Unit (HRU)-based Soil and Water Assessment Tool (SWATG) that integrates grid modeling scheme with different spatial representations also presents such problems. The time-consuming problem affects applications of very high resolution large-scale watershed modeling. The OpenMP (Open Multi-Processing) parallel application interface is integrated with SWATG (called SWATGP) to accelerate grid modeling based on the HRU level. Such parallel implementation takes better advantage of the computational power of a shared memory computer system. We conducted two experiments at multiple temporal and spatial scales of hydrological modeling using SWATG and SWATGP on a high-end server. At 500-m resolution, SWATGP was found to be up to nine times faster than SWATG in modeling over a roughly 2000 km2 watershed with 1 CPU and a 15 thread configuration. The study results demonstrate that parallel models save considerable time relative to traditional sequential simulation runs. Parallel computations of environmental models are beneficial for model applications, especially at large spatial and temporal scales and at high resolutions. The proposed SWATGP model is thus a promising tool for large-scale and high-resolution water resources research and management in addition to offering data fusion and model coupling ability.

  12. AthenaMT: upgrading the ATLAS software framework for the many-core world with multi-threading

    NASA Astrophysics Data System (ADS)

    Leggett, Charles; Baines, John; Bold, Tomasz; Calafiura, Paolo; Farrell, Steven; van Gemmeren, Peter; Malon, David; Ritsch, Elmar; Stewart, Graeme; Snyder, Scott; Tsulaia, Vakhtang; Wynne, Benjamin; ATLAS Collaboration

    2017-10-01

    ATLAS’s current software framework, Gaudi/Athena, has been very successful for the experiment in LHC Runs 1 and 2. However, its single threaded design has been recognized for some time to be increasingly problematic as CPUs have increased core counts and decreased available memory per core. Even the multi-process version of Athena, AthenaMP, will not scale to the range of architectures we expect to use beyond Run2. After concluding a rigorous requirements phase, where many design components were examined in detail, ATLAS has begun the migration to a new data-flow driven, multi-threaded framework, which enables the simultaneous processing of singleton, thread unsafe legacy Algorithms, cloned Algorithms that execute concurrently in their own threads with different Event contexts, and fully re-entrant, thread safe Algorithms. In this paper we report on the process of modifying the framework to safely process multiple concurrent events in different threads, which entails significant changes in the underlying handling of features such as event and time dependent data, asynchronous callbacks, metadata, integration with the online High Level Trigger for partial processing in certain regions of interest, concurrent I/O, as well as ensuring thread safety of core services. We also report on upgrading the framework to handle Algorithms that are fully re-entrant.

  13. Process Capability of High Speed Micro End-Milling of Inconel 718 with Minimum Quantity Lubrication

    NASA Astrophysics Data System (ADS)

    Rahman, Mohamed Abd; Yeakub Ali, Mohammad; Rahman Shah Rosli, Abdul; Banu, Asfana

    2017-03-01

    The demand for micro-parts is expected to grow and micro-machining has been shown to be a viable manufacturing process to produce these products. These micro-products may be produced from hard-to-machine materials such as superalloys under little or no metal cutting fluids to reduce machining cost or drawbacks associated with health and environment. This project aims to investigate the capability of micro end-milling process of Inconel 718 with minimum quantity lubrication (MQL). Microtools DT-110 multi-process micro machine was used to machine 10 micro-channels with MQL and 10 more under dry condition while maintaining the same machining parameters. The width of the micro-channels was measured using digital microscope and used to determine the process capability indices, Cp and Cpk. QI Macros SPC for Excel was used to analyze the resultant machining data. The results indicated that micro end-milling process of Inconel 718 was not capable under both MQL and dry cutting conditions as indicated by the Cp values of less than 1.0. However, the use of MQL helped the process to be more stable and capable. Results obtained showed that the process variation was greatly reduced by using MQL in micro end-milling of Inconel 718.

  14. The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication.

    NASA Astrophysics Data System (ADS)

    Ragan-Kelley, M.; Perez, F.; Granger, B.; Kluyver, T.; Ivanov, P.; Frederic, J.; Bussonnier, M.

    2014-12-01

    IPython has provided terminal-based tools for interactive computing in Python since 2001. The notebook document format and multi-process architecture introduced in 2011 have expanded the applicable scope of IPython into teaching, presenting, and sharing computational work, in addition to interactive exploration. The new architecture also allows users to work in any language, with implementations in Python, R, Julia, Haskell, and several other languages. The language agnostic parts of IPython have been renamed to Jupyter, to better capture the notion that a cross-language design can encapsulate commonalities present in computational research regardless of the programming language being used. This architecture offers components like the web-based Notebook interface, that supports rich documents that combine code and computational results with text narratives, mathematics, images, video and any media that a modern browser can display. This interface can be used not only in research, but also for publication and education, as notebooks can be converted to a variety of output formats, including HTML and PDF. Recent developments in the Jupyter project include a multi-user environment for hosting notebooks for a class or research group, a live collaboration notebook via Google Docs, and better support for languages other than Python.

  15. Feedback control impedance matching system using liquid stub tuner for ion cyclotron heating

    NASA Astrophysics Data System (ADS)

    Nomura, G.; Yokota, M.; Kumazawa, R.; Takahashi, C.; Torii, Y.; Saito, K.; Yamamoto, T.; Takeuchi, N.; Shimpo, F.; Kato, A.; Seki, T.; Mutoh, T.; Watari, T.; Zhao, Y.

    2001-10-01

    A long pulse discharge more than 2 minutes was achieved using Ion Cyclotron Range of Frequency (ICRF) heating only on the Large Helical Device (LHD). The final goal is a steady state operation (30 minutes) at MW level. A liquid stub tuner was newly invented to cope with the long pulse discharge. The liquid surface level was shifted under a high RF voltage operation without breakdown. In the long pulse discharge the reflected power was observed to gradually increase. The shift of the liquid surface was thought to be inevitably required at the further longer discharge. An ICRF heating system consisting of a liquid stub tuner was fabricated to demonstrate a feedback control impedance matching. The required shift of the liquid surface was predicted using a forward and a reflected RF powers as well as the phase difference between them. A liquid stub tuner was controlled by the multiprocessing computer system with CINOS (CHS Integration No Operating System) methods. The prime objective was to improve the performance of data processing and controlling a signal response. By employing this method a number of the program steps was remarkably reduced. A real time feedback control was demonstrated in the system using a temporally changed electric resistance.

  16. Electron Microscopic Observations of the Carotid Body of the Cat

    PubMed Central

    Ross, Leonard L.

    1959-01-01

    Carotid bodies were removed from cats, fixed in buffered 1 per cent osmic acid, embedded in deaerated, nitrogenated methacrylate, and cut into thin sections for electron microscopic study. The carotid body is seen to be composed of islands of chemoreceptor and sustentacular cells surrounded by wide irregular sinusoids. These cells are separated from the sinusoids by relatively broad interstitial spaces which are filled with collagen, fibroblasts, and many unmyelinated nerve fibers with their Schwann cell sheaths. The chemoreceptor cells are surrounded by the flattened, multiprocessed sustentacular cells which serve to convey the axons from an interstitial to a pericellular location. These sustentacular cells are assumed to be lemmoblastic in origin. Relatively few axons are seen to abut on the chemoreceptor cells. The cytoplasm of the chemoreceptor cell is characterized by numerous small mitochondria, units of granular endoplasmic reticulum, a small Golgi complex, and a variety of vesicles. There are many small vesicles diffusely scattered throughout the cytoplasm. In addition, there is a small number of dark-cored vesicles of the type which has been previously described in the adrenal medulla. These are usually associated with the Golgi complex. These findings are discussed in relation to the concepts of the origin of the chemoreceptor cell and the nature of the synapse. PMID:14439171

  17. Incentive Compatible Online Scheduling of Malleable Parallel Jobs with Individual Deadlines

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

    Carroll, Thomas E.; Grosu, Daniel

    2010-09-13

    We consider the online scheduling of malleable jobs on parallel systems, such as clusters, symmetric multiprocessing computers, and multi-core processor computers. Malleable jobs is a model of parallel processing in which jobs adapt to the number of processors assigned to them. This model permits the scheduler and resource manager to make more efficient use of the available resources. Each malleable job is characterized by arrival time, deadline, and value. If the job completes by its deadline, the user earns the payoff indicated by the value; otherwise, she earns a payoff of zero. The scheduling objective is to maximize the summore » of the values of the jobs that complete by their associated deadlines. Complicating the matter is that users in the real world are rational and they will attempt to manipulate the scheduler by misreporting their jobs’ parameters if it benefits them to do so. To mitigate this behavior, we design an incentive compatible online scheduling mechanism. Incentive compatibility assures us that the users will obtain the maximum payoff only if they truthfully report their jobs’ parameters to the scheduler. Finally, we simulate and study the mechanism to show the effects of misreports on the cheaters and on the system.« less

  18. Evaluative Conditioning: The “How” Question

    PubMed Central

    Jones, Christopher R.; Olson, Michael A.; Fazio, Russell H.

    2011-01-01

    Evaluative conditioning (EC) refers to attitude formation or change toward an object due to that object's mere co-occurrence with another valenced object or objects. This chapter focuses on the “how” question, that is, the question of what cognitive processes intervene between mere co-occurrence and attitude formation or change. Though EC has typically been thought of as occurring through a single, albeit contentious, mechanism, we begin by pointing out that both the heterogeneity of EC methodologies and the abundance of inconsistent results suggest that multiple processes with different characteristics can produce EC. We describe how the earliest posited process of EC, Pavlovian conditioning or signal learning, is a valid mechanism of EC that appears to have operated in some experiments but is unlikely to have operated in others and also cannot account for various EC findings. We describe other mechanisms of EC, when they can be expected to occur, and what characteristics they have. We particularly focus our attention on a process model of EC we have recently introduced, the implicit misattribution model. Finally, we describe the implications of a multi-process view of EC, which we argue can help resolve theoretical controversies and further the application of EC as a practical intervention for influencing attitudes in various domains. PMID:22241936

  19. A multiprocessing architecture for real-time monitoring

    NASA Technical Reports Server (NTRS)

    Schmidt, James L.; Kao, Simon M.; Read, Jackson Y.; Weitzenkamp, Scott M.; Laffey, Thomas J.

    1988-01-01

    A multitasking architecture for performing real-time monitoring and analysis using knowledge-based problem solving techniques is described. To handle asynchronous inputs and perform in real time, the system consists of three or more distributed processes which run concurrently and communicate via a message passing scheme. The Data Management Process acquires, compresses, and routes the incoming sensor data to other processes. The Inference Process consists of a high performance inference engine that performs a real-time analysis on the state and health of the physical system. The I/O Process receives sensor data from the Data Management Process and status messages and recommendations from the Inference Process, updates its graphical displays in real time, and acts as the interface to the console operator. The distributed architecture has been interfaced to an actual spacecraft (NASA's Hubble Space Telescope) and is able to process the incoming telemetry in real-time (i.e., several hundred data changes per second). The system is being used in two locations for different purposes: (1) in Sunnyville, California at the Space Telescope Test Control Center it is used in the preflight testing of the vehicle; and (2) in Greenbelt, Maryland at NASA/Goddard it is being used on an experimental basis in flight operations for health and safety monitoring.

  20. Pattern differences in experimental fevers induced by endotoxin, endogenous pyrogen, and prostaglandins.

    PubMed

    Morimoto, A; Nakamori, T; Watanabe, T; Ono, T; Murakami, N

    1988-04-01

    To distinguish pattern differences in experimentally induced fevers, we investigated febrile responses induced by intravenous (IV), intracerebroventricular (ICV), and intra-preoptic/anterior hypothalamic (POA) administration of bacterial endotoxin (lipopolysaccharide, LPS), endogenous pyrogen (EP), human recombinant interleukin-1 alpha (IL-1), and prostaglandins E2 and F2 alpha (PGE2 and PGF2 alpha). Intravenous LPS, EP, or IL-1 in high concentrations caused biphasic fever. In low concentrations, they induced only the first phase of fever. Latency to onset and time to first peak of fever induced by IV injection of LPS or EP were almost the same as those after ICV or POA injection of PGE2. Fever induced by ICV or POA administration of LPS, EP, IL-1, or PGF2 alpha had a long latency to onset and a prolonged time course. There were significant differences among the latencies to fever onset exhibited by groups that received ICV or POA injections of LPS, EP, or PGF2 alpha and by groups given IV injections of LPS or EP and ICV or POA injections of PGE2. Present observations indicate different patterns of fever produced by several kinds of pyrogens when given by various routes. These results permit us to consider the possibility that there are several mediators or multiprocesses underlying the pathogenesis of fever.

  1. Seizure Prediction and its Applications

    PubMed Central

    Iasemidis, Leon D.

    2011-01-01

    Epilepsy is characterized by intermittent, paroxysmal, hypersynchronous electrical activity, that may remain localized and/or spread and severely disrupt the brain’s normal multi-task and multi-processing function. Epileptic seizures are the hallmarks of such activity and had been considered unpredictable. It is only recently that research on the dynamics of seizure generation by analysis of the brain’s electrographic activity (EEG) has shed ample light on the predictability of seizures, and illuminated the way to automatic, prospective, long-term prediction of seizures. The ability to issue warnings in real time of impending seizures (e.g., tens of minutes prior to seizure occurrence in the case of focal epilepsy), may lead to novel diagnostic tools and treatments for epilepsy. Applications may range from a simple warning to the patient, in order to avert seizure-associated injuries, to intervention by automatic timely administration of an appropriate stimulus, for example of a chemical nature like an anti-epileptic drug (AED), electromagnetic nature like vagus nerve stimulation (VNS), deep brain stimulation (DBS), transcranial direct current (TDC) or transcranial magnetic stimulation (TMS), and/or of another nature (e.g., ultrasonic, cryogenic, biofeedback operant conditioning). It is thus expected that seizure prediction could readily become an integral part of the treatment of epilepsy through neuromodulation, especially in the new generation of closed-loop seizure control systems. PMID:21939848

  2. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

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

    Coquelle, Nicolas; CNRS, IBS, 38044 Grenoble; CEA, IBS, 38044 Grenoble

    A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced. High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able tomore » read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

  3. ATLAS Metadata Infrastructure Evolution for Run 2 and Beyond

    NASA Astrophysics Data System (ADS)

    van Gemmeren, P.; Cranshaw, J.; Malon, D.; Vaniachine, A.

    2015-12-01

    ATLAS developed and employed for Run 1 of the Large Hadron Collider a sophisticated infrastructure for metadata handling in event processing jobs. This infrastructure profits from a rich feature set provided by the ATLAS execution control framework, including standardized interfaces and invocation mechanisms for tools and services, segregation of transient data stores with concomitant object lifetime management, and mechanisms for handling occurrences asynchronous to the control framework's state machine transitions. This metadata infrastructure is evolving and being extended for Run 2 to allow its use and reuse in downstream physics analyses, analyses that may or may not utilize the ATLAS control framework. At the same time, multiprocessing versions of the control framework and the requirements of future multithreaded frameworks are leading to redesign of components that use an incident-handling approach to asynchrony. The increased use of scatter-gather architectures, both local and distributed, requires further enhancement of metadata infrastructure in order to ensure semantic coherence and robust bookkeeping. This paper describes the evolution of ATLAS metadata infrastructure for Run 2 and beyond, including the transition to dual-use tools—tools that can operate inside or outside the ATLAS control framework—and the implications thereof. It further examines how the design of this infrastructure is changing to accommodate the requirements of future frameworks and emerging event processing architectures.

  4. Group implicit concurrent algorithms in nonlinear structural dynamics

    NASA Technical Reports Server (NTRS)

    Ortiz, M.; Sotelino, E. D.

    1989-01-01

    During the 70's and 80's, considerable effort was devoted to developing efficient and reliable time stepping procedures for transient structural analysis. Mathematically, the equations governing this type of problems are generally stiff, i.e., they exhibit a wide spectrum in the linear range. The algorithms best suited to this type of applications are those which accurately integrate the low frequency content of the response without necessitating the resolution of the high frequency modes. This means that the algorithms must be unconditionally stable, which in turn rules out explicit integration. The most exciting possibility in the algorithms development area in recent years has been the advent of parallel computers with multiprocessing capabilities. So, this work is mainly concerned with the development of parallel algorithms in the area of structural dynamics. A primary objective is to devise unconditionally stable and accurate time stepping procedures which lend themselves to an efficient implementation in concurrent machines. Some features of the new computer architecture are summarized. A brief survey of current efforts in the area is presented. A new class of concurrent procedures, or Group Implicit algorithms is introduced and analyzed. The numerical simulation shows that GI algorithms hold considerable promise for application in coarse grain as well as medium grain parallel computers.

  5. Comparisons of Particle Tracking Techniques and Galerkin Finite Element Methods in Flow Simulations on Watershed Scales

    NASA Astrophysics Data System (ADS)

    Shih, D.; Yeh, G.

    2009-12-01

    This paper applies two numerical approximations, the particle tracking technique and Galerkin finite element method, to solve the diffusive wave equation in both one-dimensional and two-dimensional flow simulations. The finite element method is one of most commonly approaches in numerical problems. It can obtain accurate solutions, but calculation times may be rather extensive. The particle tracking technique, using either single-velocity or average-velocity tracks to efficiently perform advective transport, could use larger time-step sizes than the finite element method to significantly save computational time. Comparisons of the alternative approximations are examined in this poster. We adapt the model WASH123D to examine the work. WASH123D is an integrated multimedia, multi-processes, physics-based computational model suitable for various spatial-temporal scales, was first developed by Yeh et al., at 1998. The model has evolved in design capability and flexibility, and has been used for model calibrations and validations over the course of many years. In order to deliver a locally hydrological model in Taiwan, the Taiwan Typhoon and Flood Research Institute (TTFRI) is working with Prof. Yeh to develop next version of WASH123D. So, the work of our preliminary cooperationx is also sketched in this poster.

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

    Sauter, Nicholas K., E-mail: nksauter@lbl.gov; Hattne, Johan; Grosse-Kunstleve, Ralf W.

    The Computational Crystallography Toolbox (cctbx) is a flexible software platform that has been used to develop high-throughput crystal-screening tools for both synchrotron sources and X-ray free-electron lasers. Plans for data-processing and visualization applications are discussed, and the benefits and limitations of using graphics-processing units are evaluated. Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2 TB h{sup −1}) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in realmore » time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units.« less

  7. Solutions and debugging for data consistency in multiprocessors with noncoherent caches

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

    Bernstein, D.; Mendelson, B.; Breternitz, M. Jr.

    1995-02-01

    We analyze two important problems that arise in shared-memory multiprocessor systems. The stale data problem involves ensuring that data items in local memory of individual processors are current, independent of writes done by other processors. False sharing occurs when two processors have copies of the same shared data block but update different portions of the block. The false sharing problem involves guaranteeing that subsequent writes are properly combined. In modern architectures these problems are usually solved in hardware, by exploiting mechanisms for hardware controlled cache consistency. This leads to more expensive and nonscalable designs. Therefore, we are concentrating on softwaremore » methods for ensuring cache consistency that would allow for affordable and scalable multiprocessing systems. Unfortunately, providing software control is nontrivial, both for the compiler writer and for the application programmer. For this reason we are developing a debugging environment that will facilitate the development of compiler-based techniques and will help the programmer to tune his or her application using explicit cache management mechanisms. We extend the notion of a race condition for IBM Shared Memory System POWER/4, taking into consideration its noncoherent caches, and propose techniques for detection of false sharing problems. Identification of the stale data problem is discussed as well, and solutions are suggested.« less

  8. Cold Test and Performance Evaluation of Prototype Cryoline-X

    NASA Astrophysics Data System (ADS)

    Shah, N.; Choukekar, K.; Kapoor, H.; Muralidhara, S.; Garg, A.; Kumar, U.; Jadon, M.; Dash, B.; Bhattachrya, R.; Badgujar, S.; Billot, V.; Bravais, P.; Cadeau, P.

    2017-12-01

    The multi-process pipe vacuum jacketed cryolines for the ITER project are probably world’s most complex cryolines in terms of layout, load cases, quality, safety and regulatory requirements. As a risk mitigation plan, design, manufacturing and testing of prototype cryoline (PTCL) was planned before the approval of final design of ITER cryolines. The 29 meter long PTCL consist of 6 process pipes encased by thermal shield inside Outer Vacuum Jacket of DN 600 size and carries cold helium at 4.5 K and 80 K. The global heat load limit was defined as 1.2 W/m at 4.5 K and 4.5 W/m at 80 K. The PTCL-X (PTCL for Group-X cryolines) was specified in detail by ITER-India and designed as well as manufactured by Air Liquide. PTCL-X was installed and tested at cryogenic temperature at ITER-India Cryogenic Laboratory in 2016. The heat load at 4.5 K and 80 K, estimated using enthalpy difference method, was found to be approximately 0.8 W/m at 4.5 K, 4.2 W/m at 80 K, which is well within the defined limits. Thermal shield temperature profile was also found to be satisfactory. Paper summarizes the cold test results of PTCL-X

  9. Executive Functions Predict the Success of Top-Soccer Players

    PubMed Central

    Vestberg, Torbjörn; Gustafson, Roland; Maurex, Liselotte; Ingvar, Martin; Petrovic, Predrag

    2012-01-01

    While the importance of physical abilities and motor coordination is non-contested in sport, more focus has recently been turned toward cognitive processes important for different sports. However, this line of studies has often investigated sport-specific cognitive traits, while few studies have focused on general cognitive traits. We explored if measures of general executive functions can predict the success of a soccer player. The present study used standardized neuropsychological assessment tools assessing players' general executive functions including on-line multi-processing such as creativity, response inhibition, and cognitive flexibility. In a first cross-sectional part of the study we compared the results between High Division players (HD), Lower Division players (LD) and a standardized norm group. The result shows that both HD and LD players had significantly better measures of executive functions in comparison to the norm group for both men and women. Moreover, the HD players outperformed the LD players in these tests. In the second prospective part of the study, a partial correlation test showed a significant correlation between the result from the executive test and the numbers of goals and assists the players had scored two seasons later. The results from this study strongly suggest that results in cognitive function tests predict the success of ball sport players. PMID:22496850

  10. Proceedings of the First NASA Formal Methods Symposium

    NASA Technical Reports Server (NTRS)

    Denney, Ewen (Editor); Giannakopoulou, Dimitra (Editor); Pasareanu, Corina S. (Editor)

    2009-01-01

    Topics covered include: Model Checking - My 27-Year Quest to Overcome the State Explosion Problem; Applying Formal Methods to NASA Projects: Transition from Research to Practice; TLA+: Whence, Wherefore, and Whither; Formal Methods Applications in Air Transportation; Theorem Proving in Intel Hardware Design; Building a Formal Model of a Human-Interactive System: Insights into the Integration of Formal Methods and Human Factors Engineering; Model Checking for Autonomic Systems Specified with ASSL; A Game-Theoretic Approach to Branching Time Abstract-Check-Refine Process; Software Model Checking Without Source Code; Generalized Abstract Symbolic Summaries; A Comparative Study of Randomized Constraint Solvers for Random-Symbolic Testing; Component-Oriented Behavior Extraction for Autonomic System Design; Automated Verification of Design Patterns with LePUS3; A Module Language for Typing by Contracts; From Goal-Oriented Requirements to Event-B Specifications; Introduction of Virtualization Technology to Multi-Process Model Checking; Comparing Techniques for Certified Static Analysis; Towards a Framework for Generating Tests to Satisfy Complex Code Coverage in Java Pathfinder; jFuzz: A Concolic Whitebox Fuzzer for Java; Machine-Checkable Timed CSP; Stochastic Formal Correctness of Numerical Algorithms; Deductive Verification of Cryptographic Software; Coloured Petri Net Refinement Specification and Correctness Proof with Coq; Modeling Guidelines for Code Generation in the Railway Signaling Context; Tactical Synthesis Of Efficient Global Search Algorithms; Towards Co-Engineering Communicating Autonomous Cyber-Physical Systems; and Formal Methods for Automated Diagnosis of Autosub 6000.

  11. The Effect of NUMA Tunings on CPU Performance

    NASA Astrophysics Data System (ADS)

    Hollowell, Christopher; Caramarcu, Costin; Strecker-Kellogg, William; Wong, Antonio; Zaytsev, Alexandr

    2015-12-01

    Non-Uniform Memory Access (NUMA) is a memory architecture for symmetric multiprocessing (SMP) systems where each processor is directly connected to separate memory. Indirect access to other CPU's (remote) RAM is still possible, but such requests are slower as they must also pass through that memory's controlling CPU. In concert with a NUMA-aware operating system, the NUMA hardware architecture can help eliminate the memory performance reductions generally seen in SMP systems when multiple processors simultaneously attempt to access memory. The x86 CPU architecture has supported NUMA for a number of years. Modern operating systems such as Linux support NUMA-aware scheduling, where the OS attempts to schedule a process to the CPU directly attached to the majority of its RAM. In Linux, it is possible to further manually tune the NUMA subsystem using the numactl utility. With the release of Red Hat Enterprise Linux (RHEL) 6.3, the numad daemon became available in this distribution. This daemon monitors a system's NUMA topology and utilization, and automatically makes adjustments to optimize locality. As the number of cores in x86 servers continues to grow, efficient NUMA mappings of processes to CPUs/memory will become increasingly important. This paper gives a brief overview of NUMA, and discusses the effects of manual tunings and numad on the performance of the HEPSPEC06 benchmark, and ATLAS software.

  12. Real-time implementations of image segmentation algorithms on shared memory multicore architecture: a survey (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Akil, Mohamed

    2017-05-01

    The real-time processing is getting more and more important in many image processing applications. Image segmentation is one of the most fundamental tasks image analysis. As a consequence, many different approaches for image segmentation have been proposed. The watershed transform is a well-known image segmentation tool. The watershed transform is a very data intensive task. To achieve acceleration and obtain real-time processing of watershed algorithms, parallel architectures and programming models for multicore computing have been developed. This paper focuses on the survey of the approaches for parallel implementation of sequential watershed algorithms on multicore general purpose CPUs: homogeneous multicore processor with shared memory. To achieve an efficient parallel implementation, it's necessary to explore different strategies (parallelization/distribution/distributed scheduling) combined with different acceleration and optimization techniques to enhance parallelism. In this paper, we give a comparison of various parallelization of sequential watershed algorithms on shared memory multicore architecture. We analyze the performance measurements of each parallel implementation and the impact of the different sources of overhead on the performance of the parallel implementations. In this comparison study, we also discuss the advantages and disadvantages of the parallel programming models. Thus, we compare the OpenMP (an application programming interface for multi-Processing) with Ptheads (POSIX Threads) to illustrate the impact of each parallel programming model on the performance of the parallel implementations.

  13. Continued Development of Python-Based Thomson Data Analysis and Associated Visualization Tool for NSTX-U

    NASA Astrophysics Data System (ADS)

    Wallace, William; Miller, Jared; Diallo, Ahmed

    2015-11-01

    MultiPoint Thomson Scattering (MPTS) is an established, accurate method of finding the temperature, density, and pressure of a magnetically confined plasma. Two Nd:YAG (1064 nm) lasers are fired into the plasma with a effective frequency of 60 Hz, and the light is Doppler shifted by Thomson scattering. Polychromators on the NSTX-U midplane collect the scattered photons at various radii/scattering angles, and the avalanche photodiode voltages are saved to an MDSplus tree for later analysis. IDL code is then used to determine plasma temperature, pressure, and density from the captured polychromator measurements via Selden formulas. [1] Previous work [2] converted the single-processor IDL code into Python code, and prepared a new architecture for multiprocessing MPTS in parallel. However, that work was not completed to the generation of output data and curve fits that match with the previous IDL. This project refactored the Python code into a object-oriented architecture, and created a software test suite for the new architecture which allowed identification of the code which generated the difference in output. Another effort currently underway is to display the Thomson data in an intuitive, interactive format. This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Community College Internship (CCI) program.

  14. Performance analysis of distributed symmetric sparse matrix vector multiplication algorithm for multi-core architectures

    DOE PAGES

    Oryspayev, Dossay; Aktulga, Hasan Metin; Sosonkina, Masha; ...

    2015-07-14

    In this article, sparse matrix vector multiply (SpMVM) is an important kernel that frequently arises in high performance computing applications. Due to its low arithmetic intensity, several approaches have been proposed in literature to improve its scalability and efficiency in large scale computations. In this paper, our target systems are high end multi-core architectures and we use messaging passing interface + open multiprocessing hybrid programming model for parallelism. We analyze the performance of recently proposed implementation of the distributed symmetric SpMVM, originally developed for large sparse symmetric matrices arising in ab initio nuclear structure calculations. We also study important featuresmore » of this implementation and compare with previously reported implementations that do not exploit underlying symmetry. Our SpMVM implementations leverage the hybrid paradigm to efficiently overlap expensive communications with computations. Our main comparison criterion is the "CPU core hours" metric, which is the main measure of resource usage on supercomputers. We analyze the effects of topology-aware mapping heuristic using simplified network load model. Furthermore, we have tested the different SpMVM implementations on two large clusters with 3D Torus and Dragonfly topology. Our results show that the distributed SpMVM implementation that exploits matrix symmetry and hides communication yields the best value for the "CPU core hours" metric and significantly reduces data movement overheads.« less

  15. Hot melt extrusion of ion-exchange resin for taste masking.

    PubMed

    Tan, David Cheng Thiam; Ong, Jeremy Jianming; Gokhale, Rajeev; Heng, Paul Wan Sia

    2018-05-30

    Taste masking is important for some unpleasant tasting bioactives in oral dosage forms. Among many methods available for taste-masking, use of ion-exchange resin (IER) holds promise. IER combined with hot melt extrusion (HME) may offer additional advantages over solvent methods. IER provides taste masking by complexing with the drug ions and preventing drug dissolution in the mouth. Drug-IER complexation approaches described in literatures are mainly based either on batch processing or column eluting. These methods of drug-IER complexation have obvious limitations such as high solvent volume requirements, multiprocessing steps and extended processing time. Thus, the objective of this study was to develop a single-step, solvent-free, continuous HME process for complexation of drug-IER. The screening study evaluated drug to IER ratio, types of IER and drug complexation methods. In the screening study, a potassium salt of a weakly acidic carboxylate-based cationic IER was found suitable for the HME method. Thereafter, optimization study was conducted by varying HME process parameters such as screw speed, extrusion temperature and drug to IER ratio. It was observed that extrusion temperature and drug to IER ratio are imperative in drug-IER complexation through HME. In summary, this study has established the feasibility of a continuous complexation method for drug to IER using HME for taste masking. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. New generation of content addressable memories for associative processing

    NASA Astrophysics Data System (ADS)

    Lewis, H. G., Jr.; Giambalov, Paul

    2000-05-01

    Content addressable memories (CAMS) store both key and association data. A key is presented to the CAN when it is searched and all of the addresses are scanned in parallel to find the address referenced by the key. When a match occurs, the corresponding association is returned. With the explosion of telecommunications packet switching protocols, large data base servers, routers and search engines a new generation of dense sub-micron high throughput CAMS has been developed. The introduction of this paper presents a brief history and tutorial on CAMS, their many uses and advantages, and describes the architecture and functionality of several of MUSIC Semiconductors CAM devices. In subsequent sections of the paper we address using Associative Processing to accommodate the continued increase in sensor resolution, number of spectral bands, required coverage, the desire to implement real-time target cueing, and the data flow and image processing required for optimum performance of reconnaissance and surveillance Unmanned Aerial Vehicles (UAVs). To be competitive the system designer must provide the most computational power, per watt, per dollar, per cubic inch, within the boundaries of cost effective UAV environmental control systems. To address these problems we demonstrate leveraging DARPA and DoD funded Commercial Off-the-Shelf technology to integrate CAM based Associative Processing into a real-time heterogenous multiprocessing system for UAVs and other platforms with limited weight, volume and power budgets.

  17. HiCAT Software Infrastructure: Safe hardware control with object oriented Python

    NASA Astrophysics Data System (ADS)

    Moriarty, Christopher; Brooks, Keira; Soummer, Remi

    2018-01-01

    High contrast imaging for Complex Aperture Telescopes (HiCAT) is a testbed designed to demonstrate coronagraphy and wavefront control for segmented on-axis space telescopes such as envisioned for LUVOIR. To limit the air movements in the testbed room, software interfaces for several different hardware components were developed to completely automate operations. When developing software interfaces for many different pieces of hardware, unhandled errors are commonplace and can prevent the software from properly closing a hardware resource. Some fragile components (e.g. deformable mirrors) can be permanently damaged because of this. We present an object oriented Python-based infrastructure to safely automate hardware control and optical experiments. Specifically, conducting high-contrast imaging experiments while monitoring humidity and power status along with graceful shutdown processes even for unexpected errors. Python contains a construct called a “context manager” that allows you define code to run when a resource is opened or closed. Context managers ensure that a resource is properly closed, even when unhandled errors occur. Harnessing the context manager design, we also use Python’s multiprocessing library to monitor humidity and power status without interrupting the experiment. Upon detecting a safety problem, the master process sends an event to the child process that triggers the context managers to gracefully close any open resources. This infrastructure allows us to queue up several experiments and safely operate the testbed without a human in the loop.

  18. Does predictability matter? Effects of cue predictability on neurocognitive mechanisms underlying prospective memory.

    PubMed

    Cona, Giorgia; Arcara, Giorgio; Tarantino, Vincenza; Bisiacchi, Patrizia S

    2015-01-01

    Prospective memory (PM) represents the ability to successfully realize intentions when the appropriate moment or cue occurs. In this study, we used event-related potentials (ERPs) to explore the impact of cue predictability on the cognitive and neural mechanisms supporting PM. Participants performed an ongoing task and, simultaneously, had to remember to execute a pre-specified action when they encountered the PM cues. The occurrence of the PM cues was predictable (being signaled by a warning cue) for some participants and was completely unpredictable for others. In the predictable cue condition, the behavioral and ERP correlates of strategic monitoring were observed mainly in the ongoing trials wherein the PM cue was expected. In the unpredictable cue condition they were instead shown throughout the whole PM block. This pattern of results suggests that, in the predictable cue condition, participants engaged monitoring only when subjected to a context wherein the PM cue was expected, and disengaged monitoring when the PM cue was not expected. Conversely, participants in the unpredictable cue condition distributed their resources for strategic monitoring in more continuous manner. The findings of this study support the most recent views-the "Dynamic Multiprocess Framework" and the "Attention to Delayed Intention" (AtoDI) model-confirming that strategic monitoring is a flexible mechanism that is recruited mainly when a PM cue is expected and that may interact with bottom-up spontaneous processes.

  19. The effects of HIV disease and older age on laboratory-based, naturalistic, and self-perceived symptoms of prospective memory: does retrieval cue type and delay interval matter?

    PubMed

    Avci, G; Loft, S; Sheppard, D P; Woods, S P

    2016-11-01

    There is a rising prevalence of older HIV+ adults who are at risk of deficits in higher order neurocognitive functions and associated problems in everyday functioning. The current study applied multiprocess theory to examine the effects of HIV and aging on measures of laboratory-based, naturalistic, and self-perceived symptoms of prospective memory (PM). Participants included 125 Younger (48 with HIV, age = 32 ± 4.6 years) and 189 Older (112 with HIV, age = 56 ± 4.9 years) adults. Controlling for global neurocognitive functioning, mood, and other demographics, older age and HIV had independent effects on long-delay time-based PM in the laboratory, whereas on a naturalistic PM task older HIV- adults performed better than older HIV+ adults and younger persons. In line with the naturalistic findings, older age, but not HIV, was associated with a relative sparing of self-perceived PM failures in daily life across longer delay self-cued intervals. Findings suggest that, even in relatively younger aging cohorts, the effects of HIV and older age on PM can vary across PM delay intervals by the strategic demands of the retrieval cue type, are expressed differently in the laboratory and in daily life, and are independent of other higher order neurocognitive functions (e.g., retrospective memory).

  20. The Effects of HIV Disease and Older Age on Laboratory-based, Naturalistic, and Self-Perceived Symptoms of Prospective Memory: Does Retrieval Cue Type and Delay Interval Matter?

    PubMed Central

    Avci, G.; Loft, S.; Sheppard, D.P.; Woods, S.P.

    2016-01-01

    There is a rising prevalence of older HIV+ adults who are at risk of deficits in higher-order neurocognitive functions and associated problems in everyday functioning. The current study applied Multiprocess Theory to examine the effects of HIV and aging on measures of laboratory-based, naturalistic, and self-perceived symptoms of prospective memory (PM). Participants included 125 Younger (48 with HIV, age = 32±4.6 years) and 189 Older (112 with HIV, age = 56±4.9 years) adults. Controlling for global neurocognitive functioning, mood, and other demographics, older age and HIV had independent effects on long-delay time-based PM in the laboratory, whereas on a naturalistic PM task older HIV− adults performed better than older HIV+ adults and younger persons. In line with the naturalistic findings, older age, but not HIV, was associated with a relative sparing of self-perceived PM failures in daily life across longer delay self-cued intervals. Findings suggest that, even in relatively younger aging cohorts, the effects of HIV and older age on PM can vary across PM delay intervals by the strategic demands of the retrieval cue type, are expressed differently in the laboratory and in daily life, and are independent of other higher-order neurocognitive functions (e.g., retrospective memory). PMID:27002287

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

    Morishita, Sadaharu; Goto, Tetsuya; Nagase, Masaaki

    Multiprocesses in a single plasma process chamber with high throughput require precise, sequential, high-speed alteration of partial pressures of multiple gas species. A conventional gas-distribution system cannot realize this because the system seriously overshoots gas pressure immediately following valve operation. Furthermore, chamber volume and conductance of gas piping between the system and chamber should both be considered because they delay the stabilizing time of gas pressure. Therefore, the authors proposed a new gas-distribution system without overshoot by controlling gas flow rate based on pressure measurement, as well as a method of pulse-controlled gas injection immediately following valve operation. Time variationmore » of measured partial pressure agrees well with a calculation based on an equivalent-circuit model that represents the chamber and gas piping between the system and chamber. Using pulse-controlled gas injection, the stabilizing time can be reduced drastically to 0.6 s for HBr added to pure Ar plasma, and 0.7 s for O{sub 2} added to Ar/HBr plasma; without the pulse control, the stabilizing times are 3 and 7 s, respectively. In the O{sub 2} addition case, rapid stabilization can be achieved during the period of line/space pattern etching of poly-Si on a thin SiO{sub 2} film. This occurs without anomalous etching of the underlying SiO{sub 2} film or the Si substrate near the sidewall, thus obtaining a wide process margin with high throughput.« less

  2. Prospective memory and aging: evidence for preserved spontaneous retrieval with exact but not related cues.

    PubMed

    Mullet, Hillary G; Scullin, Michael K; Hess, Theodore J; Scullin, Rachel B; Arnold, Kathleen M; Einstein, Gilles O

    2013-12-01

    We examined whether normal aging spares or compromises cue-driven spontaneous retrieval processes that support prospective remembering. In Experiment 1, young and older adults performed prospective-memory tasks that required either strategic monitoring processes for retrieval (nonfocal) or for which participants relied on spontaneous retrieval processes (focal). We found age differences for nonfocal, but not focal, prospective-memory performance. Experiments 2 and 3 used an intention-interference paradigm in which participants were asked to perform a prospective-memory task (e.g., press "Q" when the word money appears) in the context of an image-rating task and were then told to suspend their prospective-memory intention until after completing an intervening lexical-decision task. During the lexical-decision task, we presented the exact prospective-memory cue (e.g., money; Experiments 2 and 3) or a semantically related lure (e.g., wallet; Experiment 3), and we inferred spontaneous retrieval from slowed lexical-decision responses to these items relative to matched control items. Young and older adults showed significant slowing when the exact prospective-memory cue was presented. Only young adults, however, showed significant slowing to the semantically related lure items. Collectively, these results partially support the multiprocess theory prediction that aging spares spontaneous retrieval processes. Spontaneous retrieval processes may become less sensitive with aging, such that older adults are less likely to respond to cues that do not exactly match their encoded targets. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  3. Multi-processor including data flow accelerator module

    DOEpatents

    Davidson, George S.; Pierce, Paul E.

    1990-01-01

    An accelerator module for a data flow computer includes an intelligent memory. The module is added to a multiprocessor arrangement and uses a shared tagged memory architecture in the data flow computer. The intelligent memory module assigns locations for holding data values in correspondence with arcs leading to a node in a data dependency graph. Each primitive computation is associated with a corresponding memory cell, including a number of slots for operands needed to execute a primitive computation, a primitive identifying pointer, and linking slots for distributing the result of the cell computation to other cells requiring that result as an operand. Circuitry is provided for utilizing tag bits to determine automatically when all operands required by a processor are available and for scheduling the primitive for execution in a queue. Each memory cell of the module may be associated with any of the primitives, and the particular primitive to be executed by the processor associated with the cell is identified by providing an index, such as the cell number for the primitive, to the primitive lookup table of starting addresses. The module thus serves to perform functions previously performed by a number of sections of data flow architectures and coexists with conventional shared memory therein. A multiprocessing system including the module operates in a hybrid mode, wherein the same processing modules are used to perform some processing in a sequential mode, under immediate control of an operating system, while performing other processing in a data flow mode.

  4. A scalable multi-process model of root nitrogen uptake

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

    Walker, Anthony P.

    This article is a Commentary on McMurtrie & Näsholm et al., 218: 119–130. Roots are represented in Terrestrial Ecosystem Models (TEMs) in much less detail than their equivalent above-ground resource acquisition organs – leaves. Often roots in TEMs are simply resource sinks, and below-ground resource acquisition is commonly simulated without any relationship to root dynamics at all, though there are exceptions (e.g. Zaehle & Friend, 2010). The representation of roots as carbon (C) and nitrogen (N) sinks without complementary source functions can lead to strange sensitivities in a model. For example, reducing root lifespans in the Community Land Model (versionmore » 4.5) increases plant production as N cycles more rapidly through the ecosystem without loss of plant function (D. M. Ricciuto, unpublished). The primary reasons for the poorer representation of roots compared with leaves in TEMs are three-fold: (1) data are much harder won, especially in the field; (2) no simple mechanistic models of root function are available; and (3) scaling root function from an individual root to a root system lags behind methods of scaling leaf function to a canopy. Here in this issue of New Phytologist, McMurtrie & Näsholm (pp. 119–130) develop a relatively simple model for root N uptake that mechanistically accounts for processes of N supply (mineralization and transport by diffusion and mass flow) and N demand (root uptake and microbial immobilization).« less

  5. A scalable multi-process model of root nitrogen uptake

    DOE PAGES

    Walker, Anthony P.

    2018-02-28

    This article is a Commentary on McMurtrie & Näsholm et al., 218: 119–130. Roots are represented in Terrestrial Ecosystem Models (TEMs) in much less detail than their equivalent above-ground resource acquisition organs – leaves. Often roots in TEMs are simply resource sinks, and below-ground resource acquisition is commonly simulated without any relationship to root dynamics at all, though there are exceptions (e.g. Zaehle & Friend, 2010). The representation of roots as carbon (C) and nitrogen (N) sinks without complementary source functions can lead to strange sensitivities in a model. For example, reducing root lifespans in the Community Land Model (versionmore » 4.5) increases plant production as N cycles more rapidly through the ecosystem without loss of plant function (D. M. Ricciuto, unpublished). The primary reasons for the poorer representation of roots compared with leaves in TEMs are three-fold: (1) data are much harder won, especially in the field; (2) no simple mechanistic models of root function are available; and (3) scaling root function from an individual root to a root system lags behind methods of scaling leaf function to a canopy. Here in this issue of New Phytologist, McMurtrie & Näsholm (pp. 119–130) develop a relatively simple model for root N uptake that mechanistically accounts for processes of N supply (mineralization and transport by diffusion and mass flow) and N demand (root uptake and microbial immobilization).« less

  6. Multiprocessor smalltalk: Implementation, performance, and analysis

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

    Pallas, J.I.

    1990-01-01

    Multiprocessor Smalltalk demonstrates the value of object-oriented programming on a multiprocessor. Its implementation and analysis shed light on three areas: concurrent programming in an object oriented language without special extensions, implementation techniques for adapting to multiprocessors, and performance factors in the resulting system. Adding parallelism to Smalltalk code is easy, because programs already use control abstractions like iterators. Smalltalk's basic control and concurrency primitives (lambda expressions, processes and semaphores) can be used to build parallel control abstractions, including parallel iterators, parallel objects, atomic objects, and futures. Language extensions for concurrency are not required. This implementation demonstrates that it is possiblemore » to build an efficient parallel object-oriented programming system and illustrates techniques for doing so. Three modification tools-serialization, replication, and reorganization-adapted the Berkeley Smalltalk interpreter to the Firefly multiprocessor. Multiprocessor Smalltalk's performance shows that the combination of multiprocessing and object-oriented programming can be effective: speedups (relative to the original serial version) exceed 2.0 for five processors on all the benchmarks; the median efficiency is 48%. Analysis shows both where performance is lost and how to improve and generalize the experimental results. Changes in the interpreter to support concurrency add at most 12% overhead; better access to per-process variables could eliminate much of that. Changes in the user code to express concurrency add as much as 70% overhead; this overhead could be reduced to 54% if blocks (lambda expressions) were reentrant. Performance is also lost when the program cannot keep all five processors busy.« less

  7. Multiprocessing on supercomputers for computational aerodynamics

    NASA Technical Reports Server (NTRS)

    Yarrow, Maurice; Mehta, Unmeel B.

    1990-01-01

    Very little use is made of multiple processors available on current supercomputers (computers with a theoretical peak performance capability equal to 100 MFLOPs or more) in computational aerodynamics to significantly improve turnaround time. The productivity of a computer user is directly related to this turnaround time. In a time-sharing environment, the improvement in this speed is achieved when multiple processors are used efficiently to execute an algorithm. The concept of multiple instructions and multiple data (MIMD) through multi-tasking is applied via a strategy which requires relatively minor modifications to an existing code for a single processor. Essentially, this approach maps the available memory to multiple processors, exploiting the C-FORTRAN-Unix interface. The existing single processor code is mapped without the need for developing a new algorithm. The procedure for building a code utilizing this approach is automated with the Unix stream editor. As a demonstration of this approach, a Multiple Processor Multiple Grid (MPMG) code is developed. It is capable of using nine processors, and can be easily extended to a larger number of processors. This code solves the three-dimensional, Reynolds averaged, thin-layer and slender-layer Navier-Stokes equations with an implicit, approximately factored and diagonalized method. The solver is applied to generic oblique-wing aircraft problem on a four processor Cray-2 computer. A tricubic interpolation scheme is developed to increase the accuracy of coupling of overlapped grids. For the oblique-wing aircraft problem, a speedup of two in elapsed (turnaround) time is observed in a saturated time-sharing environment.

  8. myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.

    PubMed

    Kasahara, Kota; Ma, Benson; Goto, Kota; Dasgupta, Bhaskar; Higo, Junichi; Fukuda, Ikuo; Mashimo, Tadaaki; Akiyama, Yutaka; Nakamura, Haruki

    2016-01-01

    Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named "myPresto/omegagene" that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods, e.g. , the virtual-system-coupled multi-canonical MD (V-McMD) method, replace a multi-process parallelized run with multiple independent runs to avoid inter-node communication overhead. In addition, adopting the non-Ewald-based zero-multipole summation method (ZMM) makes it possible to eliminate the Fourier space calculations altogether. The combination of these state-of-the-art techniques realizes efficient and accurate calculations of the conformational ensemble at an equilibrium state. By taking these advantages, myPresto/omegagene is specialized for the single process execution with Graphics Processing Unit (GPU). We performed benchmark simulations for the 20-mer peptide, Trp-cage, with explicit solvent. One of the most thermodynamically stable conformations generated by the V-McMD simulation is very similar to an experimentally solved native conformation. Furthermore, the computation speed is four-times faster than that of our previous simulation engine, myPresto/psygene-G. The new simulator, myPresto/omegagene, is freely available at the following URLs: http://www.protein.osaka-u.ac.jp/rcsfp/pi/omegagene/ and http://presto.protein.osaka-u.ac.jp/myPresto4/.

  9. Parallel fuzzy connected image segmentation on GPU

    PubMed Central

    Zhuge, Ying; Cao, Yong; Udupa, Jayaram K.; Miller, Robert W.

    2011-01-01

    Purpose: Image segmentation techniques using fuzzy connectedness (FC) principles have shown their effectiveness in segmenting a variety of objects in several large applications. However, one challenge in these algorithms has been their excessive computational requirements when processing large image datasets. Nowadays, commodity graphics hardware provides a highly parallel computing environment. In this paper, the authors present a parallel fuzzy connected image segmentation algorithm implementation on NVIDIA’s compute unified device Architecture (cuda) platform for segmenting medical image data sets. Methods: In the FC algorithm, there are two major computational tasks: (i) computing the fuzzy affinity relations and (ii) computing the fuzzy connectedness relations. These two tasks are implemented as cuda kernels and executed on GPU. A dramatic improvement in speed for both tasks is achieved as a result. Results: Our experiments based on three data sets of small, medium, and large data size demonstrate the efficiency of the parallel algorithm, which achieves a speed-up factor of 24.4x, 18.1x, and 10.3x, correspondingly, for the three data sets on the NVIDIA Tesla C1060 over the implementation of the algorithm on CPU, and takes 0.25, 0.72, and 15.04 s, correspondingly, for the three data sets. Conclusions: The authors developed a parallel algorithm of the widely used fuzzy connected image segmentation method on the NVIDIA GPUs, which are far more cost- and speed-effective than both cluster of workstations and multiprocessing systems. A near-interactive speed of segmentation has been achieved, even for the large data set. PMID:21859037

  10. Parallel fuzzy connected image segmentation on GPU.

    PubMed

    Zhuge, Ying; Cao, Yong; Udupa, Jayaram K; Miller, Robert W

    2011-07-01

    Image segmentation techniques using fuzzy connectedness (FC) principles have shown their effectiveness in segmenting a variety of objects in several large applications. However, one challenge in these algorithms has been their excessive computational requirements when processing large image datasets. Nowadays, commodity graphics hardware provides a highly parallel computing environment. In this paper, the authors present a parallel fuzzy connected image segmentation algorithm implementation on NVIDIA's compute unified device Architecture (CUDA) platform for segmenting medical image data sets. In the FC algorithm, there are two major computational tasks: (i) computing the fuzzy affinity relations and (ii) computing the fuzzy connectedness relations. These two tasks are implemented as CUDA kernels and executed on GPU. A dramatic improvement in speed for both tasks is achieved as a result. Our experiments based on three data sets of small, medium, and large data size demonstrate the efficiency of the parallel algorithm, which achieves a speed-up factor of 24.4x, 18.1x, and 10.3x, correspondingly, for the three data sets on the NVIDIA Tesla C1060 over the implementation of the algorithm on CPU, and takes 0.25, 0.72, and 15.04 s, correspondingly, for the three data sets. The authors developed a parallel algorithm of the widely used fuzzy connected image segmentation method on the NVIDIA GPUs, which are far more cost- and speed-effective than both cluster of workstations and multiprocessing systems. A near-interactive speed of segmentation has been achieved, even for the large data set.

  11. Enhancement of Local Climate Analysis Tool

    NASA Astrophysics Data System (ADS)

    Horsfall, F. M.; Timofeyeva, M. M.; Dutton, J.

    2012-12-01

    The National Oceanographic and Atmospheric Administration (NOAA) National Weather Service (NWS) will enhance its Local Climate Analysis Tool (LCAT) to incorporate specific capabilities to meet the needs of various users including energy, health, and other communities. LCAT is an online interactive tool that provides quick and easy access to climate data and allows users to conduct analyses at the local level such as time series analysis, trend analysis, compositing, correlation and regression techniques, with others to be incorporated as needed. LCAT uses principles of Artificial Intelligence in connecting human and computer perceptions on application of data and scientific techniques in multiprocessing simultaneous users' tasks. Future development includes expanding the type of data currently imported by LCAT (historical data at stations and climate divisions) to gridded reanalysis and General Circulation Model (GCM) data, which are available on global grids and thus will allow for climate studies to be conducted at international locations. We will describe ongoing activities to incorporate NOAA Climate Forecast System (CFS) reanalysis data (CFSR), NOAA model output data, including output from the National Multi Model Ensemble Prediction System (NMME) and longer term projection models, and plans to integrate LCAT into the Earth System Grid Federation (ESGF) and its protocols for accessing model output and observational data to ensure there is no redundancy in development of tools that facilitate scientific advancements and use of climate model information in applications. Validation and inter-comparison of forecast models will be included as part of the enhancement to LCAT. To ensure sustained development, we will investigate options for open sourcing LCAT development, in particular, through the University Corporation for Atmospheric Research (UCAR).

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

    Jennings, E.; Madigan, M.

    Given the complexity of modern cosmological parameter inference where we arefaced with non-Gaussian data and noise, correlated systematics and multi-probecorrelated data sets, the Approximate Bayesian Computation (ABC) method is apromising alternative to traditional Markov Chain Monte Carlo approaches in thecase where the Likelihood is intractable or unknown. The ABC method is called"Likelihood free" as it avoids explicit evaluation of the Likelihood by using aforward model simulation of the data which can include systematics. Weintroduce astroABC, an open source ABC Sequential Monte Carlo (SMC) sampler forparameter estimation. A key challenge in astrophysics is the efficient use oflarge multi-probe datasets to constrainmore » high dimensional, possibly correlatedparameter spaces. With this in mind astroABC allows for massive parallelizationusing MPI, a framework that handles spawning of jobs across multiple nodes. Akey new feature of astroABC is the ability to create MPI groups with differentcommunicators, one for the sampler and several others for the forward modelsimulation, which speeds up sampling time considerably. For smaller jobs thePython multiprocessing option is also available. Other key features include: aSequential Monte Carlo sampler, a method for iteratively adapting tolerancelevels, local covariance estimate using scikit-learn's KDTree, modules forspecifying optimal covariance matrix for a component-wise or multivariatenormal perturbation kernel, output and restart files are backed up everyiteration, user defined metric and simulation methods, a module for specifyingheterogeneous parameter priors including non-standard prior PDFs, a module forspecifying a constant, linear, log or exponential tolerance level,well-documented examples and sample scripts. This code is hosted online athttps://github.com/EliseJ/astroABC« less

  13. Atlas-guided cluster analysis of large tractography datasets.

    PubMed

    Ros, Christian; Güllmar, Daniel; Stenzel, Martin; Mentzel, Hans-Joachim; Reichenbach, Jürgen Rainer

    2013-01-01

    Diffusion Tensor Imaging (DTI) and fiber tractography are important tools to map the cerebral white matter microstructure in vivo and to model the underlying axonal pathways in the brain with three-dimensional fiber tracts. As the fast and consistent extraction of anatomically correct fiber bundles for multiple datasets is still challenging, we present a novel atlas-guided clustering framework for exploratory data analysis of large tractography datasets. The framework uses an hierarchical cluster analysis approach that exploits the inherent redundancy in large datasets to time-efficiently group fiber tracts. Structural information of a white matter atlas can be incorporated into the clustering to achieve an anatomically correct and reproducible grouping of fiber tracts. This approach facilitates not only the identification of the bundles corresponding to the classes of the atlas; it also enables the extraction of bundles that are not present in the atlas. The new technique was applied to cluster datasets of 46 healthy subjects. Prospects of automatic and anatomically correct as well as reproducible clustering are explored. Reconstructed clusters were well separated and showed good correspondence to anatomical bundles. Using the atlas-guided cluster approach, we observed consistent results across subjects with high reproducibility. In order to investigate the outlier elimination performance of the clustering algorithm, scenarios with varying amounts of noise were simulated and clustered with three different outlier elimination strategies. By exploiting the multithreading capabilities of modern multiprocessor systems in combination with novel algorithms, our toolkit clusters large datasets in a couple of minutes. Experiments were conducted to investigate the achievable speedup and to demonstrate the high performance of the clustering framework in a multiprocessing environment.

  14. A Differential Deficit in Time- versus Event-based Prospective Memory in Parkinson's Disease

    PubMed Central

    Raskin, Sarah A.; Woods, Steven Paul; Poquette, Amelia J.; McTaggart, April B.; Sethna, Jim; Williams, Rebecca C.; Tröster, Alexander I.

    2010-01-01

    Objective The aim of the current study was to clarify the nature and extent of impairment in time- versus event-based prospective memory in Parkinson's disease (PD). Prospective memory is thought to involve cognitive processes that are mediated by prefrontal systems and are executive in nature. Given that individuals with PD frequently show executive dysfunction, it is important to determine whether these individuals may have deficits in prospective memory that could impact daily functions, such as taking medications. Although it has been reported that individuals with PD evidence impairment in prospective memory, it is still unclear whether they show a greater deficit for time- versus event-based cues. Method Fifty-four individuals with PD and 34 demographically similar healthy adults were administered a standardized measure of prospective memory that allows for a direct comparison of time-based and event-based cues. In addition, participants were administered a series of standardized measures of retrospective memory and executive functions. Results Individuals with PD demonstrated impaired prospective memory performance compared to the healthy adults, with a greater impairment demonstrated for the time-based tasks. Time-based prospective memory performance was moderately correlated with measures of executive functioning, but only the Stroop Neuropsychological Screening Test emerged as a unique predictor in a linear regression. Conclusions Findings are interpreted within the context of McDaniel and Einstein's (2000) multi-process theory to suggest that individuals with PD experience particular difficulty executing a future intention when the cue to execute the prescribed intention requires higher levels of executive control. PMID:21090895

  15. FairMQ for Online Reconstruction - An example on \\overline{{\\rm{P}}}ANDA test beam data

    NASA Astrophysics Data System (ADS)

    Stockmanns, Tobias; PANDA Collaboration

    2017-10-01

    One of the large challenges of future particle physics experiments is the trend to run without a first level hardware trigger. The typical data rates exceed easily hundreds of GBytes/s, which is way too much to be stored permanently for an offline analysis. Therefore a strong data reduction has to be done by selection of only those data, which are physically interesting. This implies that all detector data are read out and have to be processed with the same rate as it is produced. Several different hardware approaches from FPGAs, GPUs to multicore CPUs and mixtures of these systems are under study. Common to all of them is the need to process the data in massive parallel systems. One very convenient way to realize parallel systems on heterogeneous systems is the usage of message queue based multiprocessing. One package that allow development of such application is the FairMQ module in the FairRoot simulation framework developed at GSI. FairRoot is used by several different experiments at and outside the GSI including the \\overline{{{P}}}ANDA experiment. FairMQ is an abstract layer for message queue base application, it has up to now two implementations: ZeroMQ and nanomsg. For the \\overline{{{P}}}ANDA experiment, FairMQ is under test in two different ways. On the one hand side for online processing test beam data of prototypes of sub-detectors of \\overline{{{P}}}ANDA and, in a more generalized way, on time-based simulated data of the complete detector system. The first test on test beam data is presented in this paper.

  16. `Dhara': An Open Framework for Critical Zone Modeling

    NASA Astrophysics Data System (ADS)

    Le, P. V.; Kumar, P.

    2016-12-01

    Processes in the Critical Zone, which sustain terrestrial life, are tightly coupled across hydrological, physical, biological, chemical, pedological, geomorphological and ecological domains over both short and long timescales. Observations and quantification of the Earth's surface across these domains using emerging high resolution measurement technologies such as light detection and ranging (lidar) and hyperspectral remote sensing are enabling us to characterize fine scale landscape attributes over large spatial areas. This presents a unique opportunity to develop novel approaches to model the Critical Zone that can capture fine scale intricate dependencies across the different processes in 3D. The development of interdisciplinary tools that transcend individual disciplines and capture new levels of complexity and emergent properties is at the core of Critical Zone science. Here we introduce an open framework for high-performance computing model (`Dhara') for modeling complex processes in the Critical Zone. The framework is designed to be modular in structure with the aim to create uniform and efficient tools to facilitate and leverage process modeling. It also provides flexibility to maintain, collaborate, and co-develop additional components by the scientific community. We show the essential framework that simulates ecohydrologic dynamics, and surface - sub-surface coupling in 3D using hybrid parallel CPU-GPU. We demonstrate that the open framework in Dhara is feasible for detailed, multi-processes, and large-scale modeling of the Critical Zone, which opens up exciting possibilities. We will also present outcomes from a Modeling Summer Institute led by Intensively Managed Critical Zone Observatory (IMLCZO) with representation from several CZOs and international representatives.

  17. Developing Daily Quantitative Damage Estimates From Geospatial Layers To Support Post Event Recovery

    NASA Astrophysics Data System (ADS)

    Woods, B. K.; Wei, L. H.; Connor, T. C.

    2014-12-01

    With the growth of natural hazard data available in near real-time it is increasingly feasible to deliver damage estimates caused by natural disasters. These estimates can be used in disaster management setting or by commercial entities to optimize the deployment of resources and/or routing of goods and materials. This work outlines an end-to-end, modular process to generate estimates of damage caused by severe weather. The processing stream consists of five generic components: 1) Hazard modules that provide quantitate data layers for each peril. 2) Standardized methods to map the hazard data to an exposure layer based on atomic geospatial blocks. 3) Peril-specific damage functions that compute damage metrics at the atomic geospatial block level. 4) Standardized data aggregators, which map damage to user-specific geometries. 5) Data dissemination modules, which provide resulting damage estimates in a variety of output forms. This presentation provides a description of this generic tool set, and an illustrated example using HWRF-based hazard data for Hurricane Arthur (2014). In this example, the Python-based real-time processing ingests GRIB2 output from the HWRF numerical model, dynamically downscales it in conjunctions with a land cover database using a multiprocessing pool, and a just-in-time compiler (JIT). The resulting wind fields are contoured, and ingested into a PostGIS database using OGR. Finally, the damage estimates are calculated at the atomic block level and aggregated to user-defined regions using PostgreSQL queries to construct application specific tabular and graphics output.

  18. An efficient approach for treating composition-dependent diffusion within organic particles

    DOE PAGES

    O'Meara, Simon; Topping, David O.; Zaveri, Rahul A.; ...

    2017-09-07

    Mounting evidence demonstrates that under certain conditions the rate of component partitioning between the gas and particle phase in atmospheric organic aerosol is limited by particle-phase diffusion. To date, however, particle-phase diffusion has not been incorporated into regional atmospheric models. An analytical rather than numerical solution to diffusion through organic particulate matter is desirable because of its comparatively small computational expense in regional models. Current analytical models assume diffusion to be independent of composition and therefore use a constant diffusion coefficient. To realistically model diffusion, however, it should be composition-dependent (e.g. due to the partitioning of components that plasticise, vitrifymore » or solidify). This study assesses the modelling capability of an analytical solution to diffusion corrected to account for composition dependence against a numerical solution. Results show reasonable agreement when the gas-phase saturation ratio of a partitioning component is constant and particle-phase diffusion limits partitioning rate (<10% discrepancy in estimated radius change). However, when the saturation ratio of the partitioning component varies, a generally applicable correction cannot be found, indicating that existing methodologies are incapable of deriving a general solution. Until such time as a general solution is found, caution should be given to sensitivity studies that assume constant diffusivity. Furthermore, the correction was implemented in the polydisperse, multi-process Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) and is used to illustrate how the evolution of number size distribution may be accelerated by condensation of a plasticising component onto viscous organic particles.« less

  19. Performance Study of Monte Carlo Codes on Xeon Phi Coprocessors — Testing MCNP 6.1 and Profiling ARCHER Geometry Module on the FS7ONNi Problem

    NASA Astrophysics Data System (ADS)

    Liu, Tianyu; Wolfe, Noah; Lin, Hui; Zieb, Kris; Ji, Wei; Caracappa, Peter; Carothers, Christopher; Xu, X. George

    2017-09-01

    This paper contains two parts revolving around Monte Carlo transport simulation on Intel Many Integrated Core coprocessors (MIC, also known as Xeon Phi). (1) MCNP 6.1 was recompiled into multithreading (OpenMP) and multiprocessing (MPI) forms respectively without modification to the source code. The new codes were tested on a 60-core 5110P MIC. The test case was FS7ONNi, a radiation shielding problem used in MCNP's verification and validation suite. It was observed that both codes became slower on the MIC than on a 6-core X5650 CPU, by a factor of 4 for the MPI code and, abnormally, 20 for the OpenMP code, and both exhibited limited capability of strong scaling. (2) We have recently added a Constructive Solid Geometry (CSG) module to our ARCHER code to provide better support for geometry modelling in radiation shielding simulation. The functions of this module are frequently called in the particle random walk process. To identify the performance bottleneck we developed a CSG proxy application and profiled the code using the geometry data from FS7ONNi. The profiling data showed that the code was primarily memory latency bound on the MIC. This study suggests that despite low initial porting e_ort, Monte Carlo codes do not naturally lend themselves to the MIC platform — just like to the GPUs, and that the memory latency problem needs to be addressed in order to achieve decent performance gain.

  20. An efficient approach for treating composition-dependent diffusion within organic particles

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

    O'Meara, Simon; Topping, David O.; Zaveri, Rahul A.

    Mounting evidence demonstrates that under certain conditions the rate of component partitioning between the gas and particle phase in atmospheric organic aerosol is limited by particle-phase diffusion. To date, however, particle-phase diffusion has not been incorporated into regional atmospheric models. An analytical rather than numerical solution to diffusion through organic particulate matter is desirable because of its comparatively small computational expense in regional models. Current analytical models assume diffusion to be independent of composition and therefore use a constant diffusion coefficient. To realistically model diffusion, however, it should be composition-dependent (e.g. due to the partitioning of components that plasticise, vitrifymore » or solidify). This study assesses the modelling capability of an analytical solution to diffusion corrected to account for composition dependence against a numerical solution. Results show reasonable agreement when the gas-phase saturation ratio of a partitioning component is constant and particle-phase diffusion limits partitioning rate (<10% discrepancy in estimated radius change). However, when the saturation ratio of the partitioning component varies, a generally applicable correction cannot be found, indicating that existing methodologies are incapable of deriving a general solution. Until such time as a general solution is found, caution should be given to sensitivity studies that assume constant diffusivity. Furthermore, the correction was implemented in the polydisperse, multi-process Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) and is used to illustrate how the evolution of number size distribution may be accelerated by condensation of a plasticising component onto viscous organic particles.« less

  1. The Development of High-speed Full-function Storm Surge Model and the Case Study of 2013 Typhoon Haiyan

    NASA Astrophysics Data System (ADS)

    Tsai, Y. L.; Wu, T. R.; Lin, C. Y.; Chuang, M. H.; Lin, C. W.

    2016-02-01

    An ideal storm surge operational model should feature as: 1. Large computational domain which covers the complete typhoon life cycle. 2. Supporting both parametric and atmospheric models. 3. Capable of calculating inundation area for risk assessment. 4. Tides are included for accurate inundation simulation. Literature review shows that not many operational models reach the goals for the fast calculation, and most of the models have limited functions. In this paper, a well-developed COMCOT (COrnell Multi-grid Coupled of Tsunami Model) tsunami model is chosen as the kernel to establish a storm surge model which solves the nonlinear shallow water equations on both spherical and Cartesian coordinates directly. The complete evolution of storm surge including large-scale propagation and small-scale offshore run-up can be simulated by nested-grid scheme. The global tide model TPXO 7.2 established by Oregon State University is coupled to provide astronomical boundary conditions. The atmospheric model named WRF (Weather Research and Forecasting Model) is also coupled to provide metrological fields. The high-efficiency thin-film method is adopted to evaluate the storm surge inundation. Our in-house model has been optimized by OpenMp (Open Multi-Processing) with the performance which is 10 times faster than the original version and makes it an early-warning storm surge model. In this study, the thorough simulation of 2013 Typhoon Haiyan is performed. The detailed results will be presented in Oceanic Science Meeting of 2016 in terms of surge propagation and high-resolution inundation areas.

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

    Dritz, K.W.; Boyle, J.M.

    This paper addresses the problem of measuring and analyzing the performance of fine-grained parallel programs running on shared-memory multiprocessors. Such processors use locking (either directly in the application program, or indirectly in a subroutine library or the operating system) to serialize accesses to global variables. Given sufficiently high rates of locking, the chief factor preventing linear speedup (besides lack of adequate inherent parallelism in the application) is lock contention - the blocking of processes that are trying to acquire a lock currently held by another process. We show how a high-resolution, low-overhead clock may be used to measure both lockmore » contention and lack of parallel work. Several ways of presenting the results are covered, culminating in a method for calculating, in a single multiprocessing run, both the speedup actually achieved and the speedup lost to contention for each lock and to lack of parallel work. The speedup losses are reported in the same units, ''processor-equivalents,'' as the speedup achieved. Both are obtained without having to perform the usual one-process comparison run. We chronicle also a variety of experiments motivated by actual results obtained with our measurement method. The insights into program performance that we gained from these experiments helped us to refine the parts of our programs concerned with communication and synchronization. Ultimately these improvements reduced lock contention to a negligible amount and yielded nearly linear speedup in applications not limited by lack of parallel work. We describe two generally applicable strategies (''code motion out of critical regions'' and ''critical-region fissioning'') for reducing lock contention and one (''lock/variable fusion'') applicable only on certain architectures.« less

  3. Dispel4py: An Open-Source Python library for Data-Intensive Seismology

    NASA Astrophysics Data System (ADS)

    Filgueira, Rosa; Krause, Amrey; Spinuso, Alessandro; Klampanos, Iraklis; Danecek, Peter; Atkinson, Malcolm

    2015-04-01

    Scientific workflows are a necessary tool for many scientific communities as they enable easy composition and execution of applications on computing resources while scientists can focus on their research without being distracted by the computation management. Nowadays, scientific communities (e.g. Seismology) have access to a large variety of computing resources and their computational problems are best addressed using parallel computing technology. However, successful use of these technologies requires a lot of additional machinery whose use is not straightforward for non-experts: different parallel frameworks (MPI, Storm, multiprocessing, etc.) must be used depending on the computing resources (local machines, grids, clouds, clusters) where applications are run. This implies that for achieving the best applications' performance, users usually have to change their codes depending on the features of the platform selected for running them. This work presents dispel4py, a new open-source Python library for describing abstract stream-based workflows for distributed data-intensive applications. Special care has been taken to provide dispel4py with the ability to map abstract workflows to different platforms dynamically at run-time. Currently dispel4py has four mappings: Apache Storm, MPI, multi-threading and sequential. The main goal of dispel4py is to provide an easy-to-use tool to develop and test workflows in local resources by using the sequential mode with a small dataset. Later, once a workflow is ready for long runs, it can be automatically executed on different parallel resources. dispel4py takes care of the underlying mappings by performing an efficient parallelisation. Processing Elements (PE) represent the basic computational activities of any dispel4Py workflow, which can be a seismologic algorithm, or a data transformation process. For creating a dispel4py workflow, users only have to write very few lines of code to describe their PEs and how they are connected by using Python, which is widely supported on many platforms and is popular in many scientific domains, such as in geosciences. Once, a dispel4py workflow is written, a user only has to select which mapping they would like to use, and everything else (parallelisation, distribution of data) is carried on by dispel4py without any cost to the user. Among all dispel4py features we would like to highlight the following: * The PEs are connected by streams and not by writing to and reading from intermediate files, avoiding many IO operations. * The PEs can be stored into a registry. Therefore, different users can recombine PEs in many different workflows. * dispel4py has been enriched with a provenance mechanism to support runtime provenance analysis. We have adopted the W3C-PROV data model, which is accessible via a prototypal browser-based user interface and a web API. It supports the users with the visualisation of graphical products and offers combined operations to access and download the data, which may be selectively stored at runtime, into dedicated data archives. dispel4py has been already used by seismologists in the VERCE project to develop different seismic workflows. One of them is the Seismic Ambient Noise Cross-Correlation workflow, which preprocesses and cross-correlates traces from several stations. First, this workflow was tested on a local machine by using a small number of stations as input data. Later, it was executed on different parallel platforms (SuperMUC cluster, and Terracorrelator machine), automatically scaling up by using MPI and multiprocessing mappings and up to 1000 stations as input data. The results show that the dispel4py achieves scalable performance in both mappings tested on different parallel platforms.

  4. GPU accelerated dynamic functional connectivity analysis for functional MRI data.

    PubMed

    Akgün, Devrim; Sakoğlu, Ünal; Esquivel, Johnny; Adinoff, Bryon; Mete, Mutlu

    2015-07-01

    Recent advances in multi-core processors and graphics card based computational technologies have paved the way for an improved and dynamic utilization of parallel computing techniques. Numerous applications have been implemented for the acceleration of computationally-intensive problems in various computational science fields including bioinformatics, in which big data problems are prevalent. In neuroimaging, dynamic functional connectivity (DFC) analysis is a computationally demanding method used to investigate dynamic functional interactions among different brain regions or networks identified with functional magnetic resonance imaging (fMRI) data. In this study, we implemented and analyzed a parallel DFC algorithm based on thread-based and block-based approaches. The thread-based approach was designed to parallelize DFC computations and was implemented in both Open Multi-Processing (OpenMP) and Compute Unified Device Architecture (CUDA) programming platforms. Another approach developed in this study to better utilize CUDA architecture is the block-based approach, where parallelization involves smaller parts of fMRI time-courses obtained by sliding-windows. Experimental results showed that the proposed parallel design solutions enabled by the GPUs significantly reduce the computation time for DFC analysis. Multicore implementation using OpenMP on 8-core processor provides up to 7.7× speed-up. GPU implementation using CUDA yielded substantial accelerations ranging from 18.5× to 157× speed-up once thread-based and block-based approaches were combined in the analysis. Proposed parallel programming solutions showed that multi-core processor and CUDA-supported GPU implementations accelerated the DFC analyses significantly. Developed algorithms make the DFC analyses more practical for multi-subject studies with more dynamic analyses. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Dynamics and mixing mechanism of transverse jet injection into a supersonic combustor with cavity flameholder

    NASA Astrophysics Data System (ADS)

    Liu, Chaoyang; Zhao, Yanhui; Wang, Zhenguo; Wang, Hongbo; Sun, Mingbo

    2017-07-01

    The interaction between sonic transverse jet and supersonic crossflow coupled with a cavity flameholder is investigated using large eddy simulation (LES), where the compressible flow dynamics and fuel mixing mechanism are analyzed emphatically. An adaptive central-upwind 6th-order weighted essentially non-oscillatory (WENO-CU6) scheme along with multi-threaded and multi-process MPI/OpenMP parallel is adopted to improve the accuracy and parallel efficiency of the solver. This simulation aims to reproduce the flow conditions in the experiment, and the results show fairly good agreement with the experimental data for distributions of streamwise and normal velocity components. Instantaneous structures such as the shock, large scale vortices and recirculation zone are identified, and their spatial deformation and temporal evolution are presented to reveal the effect on the subsequent mixing. Then some time-averaged and statistical results are obtained to explain the interesting phenomenon observed in the experiment, that there are two pairs of counter-rotating streamwise vortices existing in and above the cavity with the same rotation direction. The above pair is induced by the transverse momentum of jet in supersonic crossflow, which is so-called counter-rotating vortices (CRVs) in the flat-plate injection. On account of the entrainment, the reflux in the cavity transports to the core of jet wakes, and then another pair of counter-rotating streamwise vortices is formed below with the effect of cavity. A pair of trailing CRVs is generated at the trailing edge of cavity, and the turbulent kinetic energy (TKE) here is obviously higher than that in other regions. To some extent, the cavity can enhance the mixing, but will not bring excess total pressure loss.

  6. [Influence of elevated atmospheric CO2 concentration on photosynthesis and leaf nitrogen partition in process of photosynthetic carbon cycle in Musa paradisiaca].

    PubMed

    Sun, G; Zhao, P; Zeng, X; Peng, S

    2001-06-01

    The photosynthetic rate (Pn) in leaves of Musa paradisiaca grown under elevated CO2 concentration (700 +/- 56 microliters.L-1) for one week was 5.14 +/- 0.32 mumol.m-2.s-1, 22.1% higher than that under ambient CO2 concentration, while under elevated CO2 concentration for 8 week, the Pn decreased by 18.1%. It can be inferred that the photosynthetic acclimation to elevated CO2 concentration and the Pn inhibition occurred in leaves of M. paradisiaca. The respiration rate in light (Rd) was lower in leaves under higher CO2 concentration, compared with that under ambient CO2 concentration. If the respiration in light was not included, the difference in CO2 compensation point for the leaves of both plants was not significant. Under higher CO2 concentration for 8 weeks, the maximum carboxylation rate(Vcmax) and electron transportation rate (J) in leaves decreased respectively by 30.5% and 14.8%, compared with that under ambient CO2 concentration. The calculated apparent quantum yield (alpha) in leaves under elevated CO2 concentration according to the initial slope of Pn/PAR was reduced to 0.014 +/- 0.010 molCO2.mol-1 quanta, compared with the value of 0.025 +/- 0.005 molCO2.mol-1 quanta in the control. The efficiency of light energy conversion also decreased from 0.203 to 0.136 electrons.quanta-1 in plants under elevated CO2 concentration. A lower partitioning coefficient for leaf nitrogen in Rubisco, bioenergetics and thylakoid light-harvesting components was observed in plants under higher CO2 concentration. The results indicated that the multi-process of photosynthesis was suppressed significantly by a long-term (8 weeks) higher CO2 concentration incubation.

  7. Amanzi: An Open-Source Multi-process Simulator for Environmental Applications

    NASA Astrophysics Data System (ADS)

    Moulton, J. D.; Molins, S.; Johnson, J. N.; Coon, E.; Lipnikov, K.; Day, M.; Barker, E.

    2014-12-01

    The Advanced Simulation Capabililty for Environmental Management (ASCEM) program is developing an approach and open-source tool suite for standardized risk and performance assessments at legacy nuclear waste sites. These assessments begin with simplified models, and add geometric and geologic complexity as understanding is gained. The Platform toolsets (Akuna) generates these conceptual models and Amanzi provides the computational engine to perform the simulations, returning the results for analysis and visualization. In this presentation we highlight key elements of the design, algorithms and implementations used in Amanzi. In particular, the hierarchical and modular design is aligned with the coupled processes being sumulated, and naturally supports a wide range of model complexity. This design leverages a dynamic data manager and the synergy of two graphs (one from the high-level perspective of the models the other from the dependencies of the variables in the model) to enable this flexible model configuration at run time. Moreover, to model sites with complex hydrostratigraphy, as well as engineered systems, we are developing a dual unstructured/structured capability. Recently, these capabilities have been collected in a framework named Arcos, and efforts have begun to improve interoperability between the unstructured and structured AMR approaches in Amanzi. To leverage a range of biogeochemistry capability from the community (e.g., CrunchFlow, PFLOTRAN, etc.), a biogeochemistry interface library was developed called Alquimia. To ensure that Amanzi is truly an open-source community code we require a completely open-source tool chain for our development. We will comment on elements of this tool chain, including the testing and documentation development tools such as docutils, and Sphinx. Finally, we will show simulation results from our phased demonstrations, including the geochemically complex Savannah River F-Area seepage basins.

  8. Atlas-Guided Cluster Analysis of Large Tractography Datasets

    PubMed Central

    Ros, Christian; Güllmar, Daniel; Stenzel, Martin; Mentzel, Hans-Joachim; Reichenbach, Jürgen Rainer

    2013-01-01

    Diffusion Tensor Imaging (DTI) and fiber tractography are important tools to map the cerebral white matter microstructure in vivo and to model the underlying axonal pathways in the brain with three-dimensional fiber tracts. As the fast and consistent extraction of anatomically correct fiber bundles for multiple datasets is still challenging, we present a novel atlas-guided clustering framework for exploratory data analysis of large tractography datasets. The framework uses an hierarchical cluster analysis approach that exploits the inherent redundancy in large datasets to time-efficiently group fiber tracts. Structural information of a white matter atlas can be incorporated into the clustering to achieve an anatomically correct and reproducible grouping of fiber tracts. This approach facilitates not only the identification of the bundles corresponding to the classes of the atlas; it also enables the extraction of bundles that are not present in the atlas. The new technique was applied to cluster datasets of 46 healthy subjects. Prospects of automatic and anatomically correct as well as reproducible clustering are explored. Reconstructed clusters were well separated and showed good correspondence to anatomical bundles. Using the atlas-guided cluster approach, we observed consistent results across subjects with high reproducibility. In order to investigate the outlier elimination performance of the clustering algorithm, scenarios with varying amounts of noise were simulated and clustered with three different outlier elimination strategies. By exploiting the multithreading capabilities of modern multiprocessor systems in combination with novel algorithms, our toolkit clusters large datasets in a couple of minutes. Experiments were conducted to investigate the achievable speedup and to demonstrate the high performance of the clustering framework in a multiprocessing environment. PMID:24386292

  9. First Applications of the New Parallel Krylov Solver for MODFLOW on a National and Global Scale

    NASA Astrophysics Data System (ADS)

    Verkaik, J.; Hughes, J. D.; Sutanudjaja, E.; van Walsum, P.

    2016-12-01

    Integrated high-resolution hydrologic models are increasingly being used for evaluating water management measures at field scale. Their drawbacks are large memory requirements and long run times. Examples of such models are The Netherlands Hydrological Instrument (NHI) model and the PCRaster Global Water Balance (PCR-GLOBWB) model. Typical simulation periods are 30-100 years with daily timesteps. The NHI model predicts water demands in periods of drought, supporting operational and long-term water-supply decisions. The NHI is a state-of-the-art coupling of several models: a 7-layer MODFLOW groundwater model ( 6.5M 250m cells), a MetaSWAP model for the unsaturated zone (Richards emulator of 0.5M cells), and a surface water model (MOZART-DM). The PCR-GLOBWB model provides a grid-based representation of global terrestrial hydrology and this work uses the version that includes a 2-layer MODFLOW groundwater model ( 4.5M 10km cells). The Parallel Krylov Solver (PKS) speeds up computation by both distributed memory parallelization (Message Passing Interface) and shared memory parallelization (Open Multi-Processing). PKS includes conjugate gradient, bi-conjugate gradient stabilized, and generalized minimal residual linear accelerators that use an overlapping additive Schwarz domain decomposition preconditioner. PKS can be used for both structured and unstructured grids and has been fully integrated in MODFLOW-USG using METIS partitioning and in iMODFLOW using RCB partitioning. iMODFLOW is an accelerated version of MODFLOW-2005 that is implicitly and online coupled to MetaSWAP. Results for benchmarks carried out on the Cartesius Dutch supercomputer (https://userinfo.surfsara.nl/systems/cartesius) for the PCRGLOB-WB model and on a 2x16 core Windows machine for the NHI model show speedups up to 10-20 and 5-10, respectively.

  10. TOMO3D: 3-D joint refraction and reflection traveltime tomography parallel code for active-source seismic data—synthetic test

    NASA Astrophysics Data System (ADS)

    Meléndez, A.; Korenaga, J.; Sallarès, V.; Miniussi, A.; Ranero, C. R.

    2015-10-01

    We present a new 3-D traveltime tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the velocity distribution and the geometry of reflecting boundaries in the subsurface. This code is based on its popular 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The traveltime calculations are done using a hybrid ray-tracing technique combining the graph and bending methods. The LSQR algorithm is used to perform the iterative regularized inversion to improve the initial velocity and depth models. In order to cope with an increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes most of the run time (˜90 per cent in the test presented here), has been parallelized with a combination of multi-processing and message passing interface standards. This parallelization distributes the ray-tracing and traveltime calculations among available computational resources. The code's performance is illustrated with a realistic synthetic example, including a checkerboard anomaly and two reflectors, which simulates the geometry of a subduction zone. The code is designed to invert for a single reflector at a time. A data-driven layer-stripping strategy is proposed for cases involving multiple reflectors, and it is tested for the successive inversion of the two reflectors. Layers are bound by consecutive reflectors, and an initial velocity model for each inversion step incorporates the results from previous steps. This strategy poses simpler inversion problems at each step, allowing the recovery of strong velocity discontinuities that would otherwise be smoothened.

  11. A nonrecursive order N preconditioned conjugate gradient: Range space formulation of MDOF dynamics

    NASA Technical Reports Server (NTRS)

    Kurdila, Andrew J.

    1990-01-01

    While excellent progress has been made in deriving algorithms that are efficient for certain combinations of system topologies and concurrent multiprocessing hardware, several issues must be resolved to incorporate transient simulation in the control design process for large space structures. Specifically, strategies must be developed that are applicable to systems with numerous degrees of freedom. In addition, the algorithms must have a growth potential in that they must also be amenable to implementation on forthcoming parallel system architectures. For mechanical system simulation, this fact implies that algorithms are required that induce parallelism on a fine scale, suitable for the emerging class of highly parallel processors; and transient simulation methods must be automatically load balancing for a wider collection of system topologies and hardware configurations. These problems are addressed by employing a combination range space/preconditioned conjugate gradient formulation of multi-degree-of-freedom dynamics. The method described has several advantages. In a sequential computing environment, the method has the features that: by employing regular ordering of the system connectivity graph, an extremely efficient preconditioner can be derived from the 'range space metric', as opposed to the system coefficient matrix; because of the effectiveness of the preconditioner, preliminary studies indicate that the method can achieve performance rates that depend linearly upon the number of substructures, hence the title 'Order N'; and the method is non-assembling. Furthermore, the approach is promising as a potential parallel processing algorithm in that the method exhibits a fine parallel granularity suitable for a wide collection of combinations of physical system topologies/computer architectures; and the method is easily load balanced among processors, and does not rely upon system topology to induce parallelism.

  12. Development of a Next Generation Concurrent Framework for the ATLAS Experiment

    NASA Astrophysics Data System (ADS)

    Calafiura, P.; Lampl, W.; Leggett, C.; Malon, D.; Stewart, G.; Wynne, B.

    2015-12-01

    The ATLAS experiment has successfully used its Gaudi/Athena software framework for data taking and analysis during the first LHC run, with billions of events successfully processed. However, the design of Gaudi/Athena dates from early 2000 and the software and the physics code has been written using a single threaded, serial design. This programming model has increasing difficulty in exploiting the potential of current CPUs, which offer their best performance only through taking full advantage of multiple cores and wide vector registers. Future CPU evolution will intensify this trend, with core counts increasing and memory per core falling. With current memory consumption for 64 bit ATLAS reconstruction in a high luminosity environment approaching 4GB, it will become impossible to fully occupy all cores in a machine without exhausting available memory. However, since maximizing performance per watt will be a key metric, a mechanism must be found to use all cores as efficiently as possible. In this paper we report on our progress with a practical demonstration of the use of multithreading in the ATLAS reconstruction software, using the GaudiHive framework. We have expanded support to Calorimeter, Inner Detector, and Tracking code, discussing what changes were necessary in order to allow the serially designed ATLAS code to run, both to the framework and to the tools and algorithms used. We report on both the performance gains, and what general lessons were learned about the code patterns that had been employed in the software and which patterns were identified as particularly problematic for multi-threading. We also present our findings on implementing a hybrid multi-threaded / multi-process framework, to take advantage of the strengths of each type of concurrency, while avoiding some of their corresponding limitations.

  13. Mitochondrial-targeted DNA delivery using a DF-MITO-Porter, an innovative nano carrier with cytoplasmic and mitochondrial fusogenic envelopes

    NASA Astrophysics Data System (ADS)

    Yamada, Yuma; Kawamura, Eriko; Harashima, Hideyoshi

    2012-08-01

    Mitochondrial gene therapy has the potential for curing a variety of diseases that are associated with mitochondrial DNA mutations and/or defects. To achieve this, it will be necessary to deliver therapeutic agents into the mitochondria in diseased cells. A number of mitochondrial drug delivery systems have been reported to date. However, reports of mitochondrial-targeted DNA delivery are limited. To achieve this, the therapeutic agent must be taken up by the cell (1), after which, the multi-processes associated with intracellular trafficking must be sophisticatedly regulated so as to release the agent from the endosome and deliver it to the cytosol (2) and to pass through the mitochondrial membrane (3). We report herein on the mitochondrial delivery of oligo DNA as a model therapeutic using a Dual Function (DF)-MITO-Porter, an innovative nano carrier designed for mitochondrial delivery. The critical structural elements of the DF-MITO-Porter include mitochondria-fusogenic inner envelopes and endosome-fusogenic outer envelopes, modified with octaarginine which greatly assists in cellular uptake. Inside the cell, the carrier passes through the endosomal and mitochondrial membranes via step-wise membrane fusion. When the oligo DNA was packaged in the DF-MITO-Porter, cellular uptake efficiency was strongly enhanced. Intracellular observation using confocal laser scanning microscopy showed that the DF-MITO-Porter was effectively released from endosomes. Moreover, the findings confirmed that the mitochondrial targeting activity of the DF-MITO-Porter was significantly higher than that of a carrier without outer endosome-fusogenic envelopes. These results support the conclusion that mitochondrial-targeted DNA delivery using a DF-MITO-Porter can be achieved when intracellular trafficking is optimally regulated.

  14. Retrieval cue and delay interval influence the relationship between prospective memory and activities of daily living in older adults.

    PubMed

    Tierney, Savanna M; Bucks, Romola S; Weinborn, Michael; Hodgson, Erica; Woods, Steven Paul

    2016-01-01

    Older adults commonly experience mild declines in everyday functioning and the strategic aspects of prospective memory (PM). This study used multiprocess theory to examine whether the strategic demands of retrieval cue type (event vs. time based) and delay interval length (2 vs. 15 min) influence the relationship between PM and activities of daily living (ADLs) in older adults. Participants included 97 community-dwelling older adults recruited from the Western Australia Participant Pool. Participants were administered the Memory for Intentions Screening Test (MIST) and Prospective and Retrospective Memory Questionnaire (PRMQ) as part of a larger neurocognitive assessment. A knowledgeable informant completed the Activities of Daily Living Questionnaire (ADLQ), from which a cutpoint of ≥ 1 was used to classify participants into "ADL normal" (n = 37) or "mild ADL problems" (n = 60) groups. Repeated measures multivariate analysis of variance (MANOVA) controlling for age was conducted with ADL group as the between-subjects factor and either MIST or PRMQ cue and delay scores as the within-subjects factors. We observed a significant ADL group by PM interaction on the MIST, with pair-wise analyses showing that the mild ADL problems group performed worse than ADL normal participants on the 15-min time-based scale (p < .001, Cohen's d = 0.71). No other MIST or PRMQ cue-delay variable differed between the two ADL groups (ps > .10). Findings indicate that decrements in strategically demanding cue monitoring and detection over longer PM delays may partly explain older adults' mild problems in everyday functioning. Findings may inform neuropsychological interventions aimed at maintaining ADL independence and enhancing quality of life in older adults.

  15. Technologies for network-centric C4ISR

    NASA Astrophysics Data System (ADS)

    Dunkelberger, Kirk A.

    2003-07-01

    Three technologies form the heart of any network-centric command, control, communication, intelligence, surveillance, and reconnaissance (C4ISR) system: distributed processing, reconfigurable networking, and distributed resource management. Distributed processing, enabled by automated federation, mobile code, intelligent process allocation, dynamic multiprocessing groups, check pointing, and other capabilities creates a virtual peer-to-peer computing network across the force. Reconfigurable networking, consisting of content-based information exchange, dynamic ad-hoc routing, information operations (perception management) and other component technologies forms the interconnect fabric for fault tolerant inter processor and node communication. Distributed resource management, which provides the means for distributed cooperative sensor management, foe sensor utilization, opportunistic collection, symbiotic inductive/deductive reasoning and other applications provides the canonical algorithms for network-centric enterprises and warfare. This paper introduces these three core technologies and briefly discusses a sampling of their component technologies and their individual contributions to network-centric enterprises and warfare. Based on the implied requirements, two new algorithms are defined and characterized which provide critical building blocks for network centricity: distributed asynchronous auctioning and predictive dynamic source routing. The first provides a reliable, efficient, effective approach for near-optimal assignment problems; the algorithm has been demonstrated to be a viable implementation for ad-hoc command and control, object/sensor pairing, and weapon/target assignment. The second is founded on traditional dynamic source routing (from mobile ad-hoc networking), but leverages the results of ad-hoc command and control (from the contributed auctioning algorithm) into significant increases in connection reliability through forward prediction. Emphasis is placed on the advantages gained from the closed-loop interaction of the multiple technologies in the network-centric application environment.

  16. CIRF.B Reaction-Transport-Mechanical Simulator: Applications to CO2 Injection and Reservoir Integrity Prediction

    NASA Astrophysics Data System (ADS)

    Park, A. J.; Tuncay, K.; Ortoleva, P. J.

    2003-12-01

    An important component of CO2 sequestration in geologic formations is the reactions between the injected fluid and the resident geologic material. In particular, carbonate mineral reaction rates are several orders of magnitude faster than those of siliciclastic minerals. The reactions between resident and injected components can create complex flow regime modifications, and potentially undermine the reservoir integrity by changing their mineralogic and textural compositions on engineering time scale. This process can be further enhanced due to differences in pH and temperature of the injectant from the resident sediments and fluids. CIRF.B is a multi-process simulator originally developed for basin simulations. Implemented processes include kinetic and thermodynamic reactions between minerals and fluid, fluid flow, mass-transfer, composite-media approach to sediment textural description and dynamics, elasto-visco-plastic rheology, and fracturing dynamics. To test the feasibility of applying CIRF.B to CO2 sequestration, a number of engineering scale simulations are carried out to delineate the effects of changing injectant chemistry and injection rates on both carbonate and siliciclastic sediments. Initial findings indicate that even moderate amounts of CO2 introduced into sediments can create low pH environments, which affects feldspar-clay interactions. While the amount of feldspars reacting in engineering time scale may be small, its consequence to clay alteration and permeability modfication can be significant. Results also demonstrate that diffusion-imported H+ can affect sealing properties of both siliciclastic and carbonate formations. In carbonate systems significant mass transfer can occur due to dissolution and reprecipitation. The resulting shifts in in-situ stresses can be sufficient to initiate fracturing. These simulations allow characterization of injectant fluids, thus assisting in the implementation of effective sequestration procedures.

  17. Elaboration d'une structure de collecte des matieres residuelles selon la Theorie Constructale

    NASA Astrophysics Data System (ADS)

    Al-Maalouf, George

    Currently, more than 80% of the waste management costs are attributed to the waste collection phase. In order to reduce these costs, one current solution resides in the implementation of waste transfer stations. In these stations, at least 3 collection vehicles transfer their load into a larger hauling truck. This cost reduction is based on the principle of economy of scale applied to the transportation sector. This solution improves the efficiency of the system; nevertheless, it does not optimize it. Recent studies show that the compactor trucks used in the collection phase generate significant economic losses mainly due to the frequent stops and the transportation to transfer stations often far from the collection area. This study suggests the restructuring of the waste collection process by dividing it into two phases: the collection phase, and the transportation to the transfer station phase. To achieve this, a deterministic theory called: "the Constructal Theory" (CT) is used. The results show that starting a certain density threshold, the application of the CT minimizes energy losses in the system. In fact, the collection is optimal if it is done using a combination of low capacity vehicle to collect door to door and transfer their charge into high-capacity trucks. These trucks will then transport their load to the transfer station. To minimize the costs of labor, this study proposes the use of Cybernetic Transport System (CTS) as an automated collection vehicle to collect small amounts of waste. Finally, the optimization method proposed is part of a decentralized approach to the collection and treatment of waste. This allows the implementation of multi-process waste treatment facilities on a territory scale. Keywords: Waste collection, Constructal Theory, Cybernetic Transportation Systems.

  18. The Rational Patient and Beyond: Implications for Treatment Adherence in People with Psychiatric Disabilities

    PubMed Central

    Corrigan, Patrick W.; Rüsch, Nicolas; Ben-Zeev, Dror; Sher, Tamara

    2014-01-01

    Purpose/Objective Many people with psychiatric disabilities do not benefit from evidence-based practices because they often do not seek out or fully adhere to them. One way psychologists have made sense of this rehabilitation and health decision process and subsequent behaviors (of which adherence might be viewed as one) is by proposing a “rational patient;” namely, that decisions are made deliberatively by weighing perceived costs and benefits of intervention options. Social psychological research, however, suggests limitations to a rational patient theory that impact models of health decision making. Design The research literature was reviewed for studies of rational patient models and alternative theories with empirical support. Special focus was on models specifically related to decisions about rehabilitation strategies for psychiatric disability. Results Notions of the rational patient evolved out of several psychological models including the health belief model, protection motivation theory, and theory of planned behavior. A variety of practice strategies evolved to promote rational decision making. However, research also suggests limitations to rational deliberations of health. (1) Rather than carefully and consciously considered, many health decisions are implicit, potentially occurring outside awareness. (2) Decisions are not always planful; often it is the immediate exigencies of a context rather than an earlier balance of costs and benefits that has the greatest effects. (3) Cool cognitions often do not dictate the process; emotional factors have an important role in health decisions. Each of these limitations suggests additional practice strategies that facilitate a person’s health decisions. Conclusions/Implications Old models of rational decision making need to be supplanted by multi-process models that explain supra-deliberative factors in health decisions and behaviors. PMID:24446671

  19. Three-dimensional electrical resistivity model of a nuclear waste disposal site

    NASA Astrophysics Data System (ADS)

    Rucker, Dale F.; Levitt, Marc T.; Greenwood, William J.

    2009-12-01

    A three-dimensional (3D) modeling study was completed on a very large electrical resistivity survey conducted at a nuclear waste site in eastern Washington. The acquisition included 47 pole-pole two-dimensional (2D) resistivity profiles collected along parallel and orthogonal lines over an area of 850 m × 570 m. The data were geo-referenced and inverted using EarthImager3D (EI3D). EI3D runs on a Microsoft 32-bit operating system (e.g. WIN-2K, XP) with a maximum usable memory of 2 GB. The memory limits the size of the domain for the inversion model to 200 m × 200 m, based on the survey electrode density. Therefore, a series of increasing overlapping models were run to evaluate the effectiveness of dividing the survey area into smaller subdomains. The results of the smaller subdomains were compared to the inversion results of a single domain over a larger area using an upgraded form of EI3D that incorporates multi-processing capabilities and 32 GB of RAM memory. The contours from the smaller subdomains showed discontinuity at the boundaries between the adjacent models, which do not match the hydrogeologic expectations given the nature of disposal at the site. At several boundaries, the contours of the low resistivity areas close, leaving the appearance of disconnected plumes or open contours at boundaries are not met with a continuance of the low resistivity plume into the adjacent subdomain. The model results of the single large domain show a continuous monolithic plume within the central and western portion of the site, directly beneath the elongated trenches. It is recommended that where possible, the domain not be subdivided, but instead include as much of the domain as possible given the memory of available computing resources.

  20. PhreeqcRM: A reaction module for transport simulators based on the geochemical model PHREEQC

    USGS Publications Warehouse

    Parkhurst, David L.; Wissmeier, Laurin

    2015-01-01

    PhreeqcRM is a geochemical reaction module designed specifically to perform equilibrium and kinetic reaction calculations for reactive transport simulators that use an operator-splitting approach. The basic function of the reaction module is to take component concentrations from the model cells of the transport simulator, run geochemical reactions, and return updated component concentrations to the transport simulator. If multicomponent diffusion is modeled (e.g., Nernst–Planck equation), then aqueous species concentrations can be used instead of component concentrations. The reaction capabilities are a complete implementation of the reaction capabilities of PHREEQC. In each cell, the reaction module maintains the composition of all of the reactants, which may include minerals, exchangers, surface complexers, gas phases, solid solutions, and user-defined kinetic reactants.PhreeqcRM assigns initial and boundary conditions for model cells based on standard PHREEQC input definitions (files or strings) of chemical compositions of solutions and reactants. Additional PhreeqcRM capabilities include methods to eliminate reaction calculations for inactive parts of a model domain, transfer concentrations and other model properties, and retrieve selected results. The module demonstrates good scalability for parallel processing by using multiprocessing with MPI (message passing interface) on distributed memory systems, and limited scalability using multithreading with OpenMP on shared memory systems. PhreeqcRM is written in C++, but interfaces allow methods to be called from C or Fortran. By using the PhreeqcRM reaction module, an existing multicomponent transport simulator can be extended to simulate a wide range of geochemical reactions. Results of the implementation of PhreeqcRM as the reaction engine for transport simulators PHAST and FEFLOW are shown by using an analytical solution and the reactive transport benchmark of MoMaS.

  1. Impact of Scale-Dependent Coupled Processes on Solute Fate and Transport in the Critical Zone: Case Studies Involving Inorganic and Radioactive Contaminants

    NASA Astrophysics Data System (ADS)

    Jardine, P. M.; Gentry, R. W.

    2011-12-01

    Soil, the thin veneer of matter covering the Earths surface that supports a web of living diversity, is often abused through anthropogenic inputs of toxic waste. This subsurface regime, coupled with life sustaining surface water and groundwater is known as the "Critical Zone". The disposal of radioactive and toxic organic and inorganic waste generated by industry and various government agencies has historically involved shallow land burial or the use of surface impoundments in unsaturated soils and sediments. Presently, contaminated sites have been closing rapidly and many remediation strategies have chosen to leave contaminants in-place. As such, contaminants will continue to interact with the geosphere and investigations on long term changes and interactive processes is imperative to verify risks. In this presentation we provide a snap-shot of subsurface science research from the past 25 y that seeks to provide an improved understanding and predictive capability of multi-scale contaminant fate and transport processes in heterogeneous unsaturated and saturated environments. Investigations focus on coupled hydrological, geochemical, and microbial processes that control reactive contaminant transport and that involve multi-scale fundamental research ranging from the molecular scale (e.g. synchrotrons, electron sources, arrays) to in situ plume interrogation strategies at the macroscopic scale (e.g. geophysics, field biostimulation, coupled processes monitoring). We show how this fundamental research is used to provide multi-process, multi-scale predictive monitoring and modeling tools that can be used at contaminated sites to (1) inform and improve the technical basis for decision making, and (2) assess which sites are amenable to natural attenuation and which would benefit from source zone remedial intervention.

  2. Real-time classification of signals from three-component seismic sensors using neural nets

    NASA Astrophysics Data System (ADS)

    Bowman, B. C.; Dowla, F.

    1992-05-01

    Adaptive seismic data acquisition systems with capabilities of signal discrimination and event classification are important in treaty monitoring, proliferation, and earthquake early detection systems. Potential applications include monitoring underground chemical explosions, as well as other military, cultural, and natural activities where characteristics of signals change rapidly and without warning. In these applications, the ability to detect and interpret events rapidly without falling behind the influx of the data is critical. We developed a system for real-time data acquisition, analysis, learning, and classification of recorded events employing some of the latest technology in computer hardware, software, and artificial neural networks methods. The system is able to train dynamically, and updates its knowledge based on new data. The software is modular and hardware-independent; i.e., the front-end instrumentation is transparent to the analysis system. The software is designed to take advantage of the multiprocessing environment of the Unix operating system. The Unix System V shared memory and static RAM protocols for data access and the semaphore mechanism for interprocess communications were used. As the three-component sensor detects a seismic signal, it is displayed graphically on a color monitor using X11/Xlib graphics with interactive screening capabilities. For interesting events, the triaxial signal polarization is computed, a fast Fourier Transform (FFT) algorithm is applied, and the normalized power spectrum is transmitted to a backpropagation neural network for event classification. The system is currently capable of handling three data channels with a sampling rate of 500 Hz, which covers the bandwidth of most seismic events. The system has been tested in laboratory setting with artificial events generated in the vicinity of a three-component sensor.

  3. Modeling multi-process connectivity in river deltas: extending the single layer network analysis to a coupled multilayer network framework

    NASA Astrophysics Data System (ADS)

    Tejedor, A.; Longjas, A.; Foufoula-Georgiou, E.

    2017-12-01

    Previous work [e.g. Tejedor et al., 2016 - GRL] has demonstrated the potential of using graph theory to study key properties of the structure and dynamics of river delta channel networks. Although the distribution of fluxes in river deltas is mostly driven by the connectivity of its channel network a significant part of the fluxes might also arise from connectivity between the channels and islands due to overland flow and seepage. This channel-island-subsurface interaction creates connectivity pathways which facilitate or inhibit transport depending on their degree of coupling. The question we pose here is how to collectively study system connectivity that emerges from the aggregated action of different processes (different in nature, intensity and time scales). Single-layer graphs as those introduced for delta channel networks are inadequate as they lack the ability to represent coupled processes, and neglecting across-process interactions can lead to mis-representation of the overall system dynamics. We present here a framework that generalizes the traditional representation of networks (single-layer graphs) to the so-called multi-layer networks or multiplex. A multi-layer network conceptualizes the overall connectivity arising from different processes as distinct graphs (layers), while allowing at the same time to represent interactions between layers by introducing interlayer links (across process interactions). We illustrate this framework using a study of the joint connectivity that arises from the coupling of the confined flow on the channel network and the overland flow on islands, on a prototype delta. We show the potential of the multi-layer framework to answer quantitatively questions related to the characteristic time scales to steady-state transport in the system as a whole when different levels of channel-island coupling are modulated by different magnitudes of discharge rates.

  4. The rational patient and beyond: implications for treatment adherence in people with psychiatric disabilities.

    PubMed

    Corrigan, Patrick W; Rüsch, Nicolas; Ben-Zeev, Dror; Sher, Tamara

    2014-02-01

    Many people with psychiatric disabilities do not benefit from evidence-based practices because they often do not seek out or fully adhere to them. One way psychologists have made sense of this rehabilitation and health decision process and subsequent behaviors (of which adherence might be viewed as one) is by proposing a "rational patient"; namely, that decisions are made deliberatively by weighing perceived costs and benefits of intervention options. Social psychological research, however, suggests limitations to a rational patient theory that impact models of health decision making. The research literature was reviewed for studies of rational patient models and alternative theories with empirical support. Special focus was on models specifically related to decisions about rehabilitation strategies for psychiatric disability. Notions of the rational patient evolved out of several psychological models including the health belief model, protection motivation theory, and theory of planned behavior. A variety of practice strategies evolved to promote rational decision making. However, research also suggests limitations to rational deliberations of health. (1) Rather than carefully and consciously considered, many health decisions are implicit, potentially occurring outside awareness. (2) Decisions are not always planful; often it is the immediate exigencies of a context rather than an earlier balance of costs and benefits that has the greatest effects. (3) Cool cognitions often do not dictate the process; emotional factors have an important role in health decisions. Each of these limitations suggests additional practice strategies that facilitate a person's health decisions. Old models of rational decision making need to be supplanted by multiprocess models that explain supradeliberative factors in health decisions and behaviors. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  5. Understanding action control of daily walking behavior among dog owners: a community survey.

    PubMed

    Rhodes, Ryan E; Lim, Clarise

    2016-11-16

    Walking among dog owners may be a means to achieve health benefits, yet almost half of owners (approximately 30% of households) are not regularly walking their dogs. Current research on the correlates of dog walking has generally considered intention as the primary determinant of behavior, yet the intention-behavior relationship is modest. The purpose of this paper was to apply a framework designed to evaluate the intention-behavior gap, known as multi-process action control (M-PAC), to understand daily walking among dog owners. A community sample of adult dog owners (N = 227) in Victoria, Canada completed M-PAC measures of motivational (dog and human outcome expectations, affective judgments, perceived capability and opportunity), regulatory (planning), and reflexive (automaticity, identity) processes as well as intention to walk and behavior. Three intention-behavior profiles emerged: a) non-intenders who were not active (26%; n = 59), b) unsuccessful intenders who failed to enact their positive intentions (33%; n = 75), and c) successful intenders who were active (40%; n = 91). Congruent with M-PAC, a discriminant function analysis showed that affective judgements (r = 0.33), automaticity (r = 0.38), and planning (r = 0.33) distinguished between all three intention-behavior profiles, while identity (r = 0.22) and dog breed size (r = 0.28) differentiated between successful and unsuccessful intenders. The majority of dog owners have positive intentions to walk, yet almost half fail to meet these intentions. Interventions focused on affective judgments (e.g., more enjoyable places to walk), behavioral regulation (e.g., setting a concrete plan), habit (e.g., making routines and cues) and identity formation (e.g., affirmations of commitment) may help overcome difficulties with translating these intentions into action, thus increasing overall levels of walking.

  6. Neutron Capture Experiments on Unstable Nuclei

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

    Schwantes, Jon M.; Sudowe, Ralf; Folden, Charles M., III

    2005-01-15

    The overall objective of this project is the measurement of neutron capture cross sections of importance to stewardship science and astrophysical modeling of nucleosynthesis, while at the same time helping to train the next generation of scientists with expertise relevant to U.S. national nuclear security missions and to stewardship science. A primary objective of this project is to study neutron capture cross sections for various stable and unstable isotopes that will contribute to the Science Based Stockpile Stewardship (SBSS) program by providing improved data for modeling and interpretation of nuclear device performance. Much of the information obtained will also bemore » important in astrophysical modeling of nucleosynthesis. Measurements of these neutron capture cross sections are being conducted in collaboration with researchers at the Los Alamos Neutron Science Center (LANSCE) facility using the unique Detector for Advanced Neutron Capture Experiments (DANCE). In our early discussions with the DANCE group, decisions were made on the first cross sections to be measured and how our expertise in target preparation, radiochemical separations chemistry, and data analysis could best be applied. The initial emphasis of the project was on preparing suitable targets of both natural and separated stable europium isotopes in preparation for the ultimate goal of preparing a sufficiently large target of radioactive 155Eu (t1/2 = 4.7 years) and other radioactive and stable species for neutron cross-section measurements at DANCE. Our Annual Report, ''Neutron Capture Experiments on Unstable Nuclei'' by J. M. Schwantes, R. Sudowe, C. M. Folden III, H. Nitsche, and D. C. Hoffman, submitted to NNSA in December 2003, gives details about the initial considerations and scope of the project. During the current reporting period, electroplated targets of natural Eu together with valuable, stable, and isotopically pure 151Eu and 153Eu, and isotopically separated 154Sm were measured for the first time at the DANCE facility in early 2004. The Eu targets, suitable blanks, Be backing foils, and standards had been sent to the DANCE group in early fall 2003. Some preliminary data analysis was performed and more sophisticated analysis has begun. We developed plans for a suitable computer system for data analysis within our group at Berkeley and had meetings with counterparts at Lawrence Livermore National Laboratory (LLNL) and LANL concerning analysis of these data. Our major emphasis in 2004 has been to develop the separations and processes ultimately required to prepare radioactive targets of 4.7-year 155Eu. Efforts continued to devise an optimum multiprocess procedure suitable for use in separating radioactive 155Eu already produced by irradiation of stable 154Sm in a high neutron flux reactor at the Institut Laue-Langevin in France and shipped to LANL (the 22-min 155Sm neutron-capture product decays to 155Eu). This separation is extremely demanding because the highly radioactive 155Eu must be isolated from about 20 times as much mass of samarium before a target can be prepared for DANCE measurements. After all the procedures have been fully tested the radioactive 155Eu will be separated. The same electroplating methods already used successfully to prepare stable Eu isotope targets will be used to prepare the 155Eu target for DANCE. Discussions were held with LANL radiochemists in the Chemistry (C) Division about appropriate facilities at LANL for conducting the full-scale separation and purification of the radioactive targets. Three more multiprocess separations were developed that generated less chemical and radioactive waste, but they must still be adapted for processing hundred-milligram quantities. Until these separations can be successfully implemented at this scale, standard HPLC procedures will be used for separating and preparing radioactive 155Eu, 2.6-year 147Pm, and 1.9-year 171Tm target materials. Future directions beyond the preparation of radioactive lanthanide targets include closer collaboration with both LLNL and LANL to prepare actinide targets such as plutonium, americium, and curium. Also, the applicability of established and novel techniques will be evaluated for rapid separations of Am and Cm required in the irradiation of 241Am. Lastly, we will conduct a series of experiments aimed at enhancing current methods used to electrodeposit lanthanide and actinide targets on thin Ti and Be backings.« less

  7. Measurement of the electroweak top quark production cross section and the CKM matrix element Vtb with the D0 experiment

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

    Kirsch, Matthias

    2009-06-29

    At particle accelerators the Standard Model has been tested and will be tested further to a great precision. The data analyzed in this thesis have been collected at the world's highest energetic-collider, the Tevatron, located at the Fermi National Accelerator Laboratory (FNAL) in the vicinity of Chicago, IL, USA. There, protons and antiprotons are collided at a center-of-mass energy of {radical}s = 1.96 TeV. The discovery of the top quark was one of the remarkable results not only for the CDF and D0 experiments at the Tevatron collider, but also for the Standard Model, which had predicted the existence ofmore » the top quark because of symmetry arguments long before already. Still, the Tevatron is the only facility able to produce top quarks. The predominant production mechanism of top quarks is the production of a top-antitop quark pair via the strong force. However, the Standard Model also allows the production of single top quarks via the electroweak interaction. This process features the unique opportunity to measure the |V tb| matrix element of the Cabbibo-Kobayashi-Maskawa (CKM) matrix directly, without assuming unitarity of the matrix or assuming that the number of quark generations is three. Hence, the measurement of the cross section of electroweak top quark production is more than the technical challenge to extract a physics process that only occurs one out of ten billion collisions. It is also an important test of the V-A structure of the electroweak interaction and a potential window to physics beyond the Standard Model in the case where the measurement of |V{sub tb}| would result in a value significantly different from 1, the value predicted by the Standard Model. At the Tevatron two production processes contribute significantly to the production of single top quarks: the production via the t-channel, also called W-gluon fusion, and the production via the s-channel, known as well as W* process. This analysis searches for the combined s+t channel production cross section, assuming the ratio of s-channel production over t-channel production is realized in nature as predicted by the Standard Model. A data set of approximately 1 fb -1 is analyzed, the data set used by the D0 collaboration to claim evidence for single top quark production. Events with two, three, and four jets are used in the analysis if they contain one or two jets that were tagged as originating from the decay of a b hadron, an isolated muon or electron, and a significant amount of missing transverse energy. This selection of events follows the signature that the single top quark events are expected to show in the detector. In the meantime, both collaborations D0 and CDF have analyzed a larger data set and have celebrated the joint observation of single top quark production. The novelty of the analysis presented here is the way discriminating observables are determined. A so-called Multi-Process Factory evaluates each event under several hypotheses. A common analysis technique for example in top quark properties studies is to reconstruct the intermediate particles in the decay chain of the signal process from the final state objects measured in the various subdetectors. An essential part of such a method is to resolve the ambiguities that arise in the assignment of the final state objects to the partons of the decay chain. In a Multi-Process Factory this approach is extended and not only the decay chain of the signal process is reconstructed, but also the decay chains of the most important background processes. From the numerous possible event configurations for each of the signal and background decay chains the most probable configuration is selected based on a likelihood measure. Properties of this configuration, such as mass of the reconstructed top quark, are then used in a multivariate analysis technique to separate the expected signal contribution from the background processes. The technique which is used is called Boosted Decision Trees and has only recently been introduced in high energy physics analyses. A Bayesian approach is used to finally extract the cross section from the discriminant output of Boosted Decision Trees.« less

  8. The EOSDIS software challenge

    NASA Astrophysics Data System (ADS)

    Jaworski, Allan

    1993-08-01

    The Earth Observing System (EOS) Data and Information System (EOSDIS) will serve as a major resource for the earth science community, supporting both command and control of complex instruments onboard the EOS spacecraft and the archiving, distribution, and analysis of data. The scale of EOSDIS and the volume of multidisciplinary research to be conducted using EOSDIS resources will produce unparalleled needs for technology transparency, data integration, and system interoperability. The scale of this effort far outscopes any previous scientific data system in its breadth or operational and performance needs. Modern hardware technology can meet the EOSDIS technical challenge. Multiprocessing speeds of many giga-flops are being realized by modern computers. Online storage disk, optical disk, and videocassette libraries with storage capacities of many terabytes are now commercially available. Radio frequency and fiber optics communications networks with gigabit rates are demonstrable today. It remains, of course, to perform the system engineering to establish the requirements, architectures, and designs that will implement the EOSDIS systems. Software technology, however, has not enjoyed the price/performance advances of hardware. Although we have learned to engineer hardware systems which have several orders of magnitude greater complexity and performance than those built in the 1960's, we have not made comparable progress in dramatically reducing the cost of software development. This lack of progress may significantly reduce our capabilities to achieve economically the types of highly interoperable, responsive, integraded, and productive environments which are needed by the earth science community. This paper describes some of the EOSDIS software requirements and current activities in the software community which are applicable to meeting the EOSDIS challenge. Some of these areas include intelligent user interfaces, software reuse libraries, and domain engineering. Also included are discussions of applicable standards in the areas of operating systems interfaces, user interfaces, communications interfaces, data transport, and science algorithm support, and their role in supporting the software development process.

  9. A DNA-based semantic fusion model for remote sensing data.

    PubMed

    Sun, Heng; Weng, Jian; Yu, Guangchuang; Massawe, Richard H

    2013-01-01

    Semantic technology plays a key role in various domains, from conversation understanding to algorithm analysis. As the most efficient semantic tool, ontology can represent, process and manage the widespread knowledge. Nowadays, many researchers use ontology to collect and organize data's semantic information in order to maximize research productivity. In this paper, we firstly describe our work on the development of a remote sensing data ontology, with a primary focus on semantic fusion-driven research for big data. Our ontology is made up of 1,264 concepts and 2,030 semantic relationships. However, the growth of big data is straining the capacities of current semantic fusion and reasoning practices. Considering the massive parallelism of DNA strands, we propose a novel DNA-based semantic fusion model. In this model, a parallel strategy is developed to encode the semantic information in DNA for a large volume of remote sensing data. The semantic information is read in a parallel and bit-wise manner and an individual bit is converted to a base. By doing so, a considerable amount of conversion time can be saved, i.e., the cluster-based multi-processes program can reduce the conversion time from 81,536 seconds to 4,937 seconds for 4.34 GB source data files. Moreover, the size of result file recording DNA sequences is 54.51 GB for parallel C program compared with 57.89 GB for sequential Perl. This shows that our parallel method can also reduce the DNA synthesis cost. In addition, data types are encoded in our model, which is a basis for building type system in our future DNA computer. Finally, we describe theoretically an algorithm for DNA-based semantic fusion. This algorithm enables the process of integration of the knowledge from disparate remote sensing data sources into a consistent, accurate, and complete representation. This process depends solely on ligation reaction and screening operations instead of the ontology.

  10. Assessing Potential Additional PFAS Retention Processes in the Subsurface

    NASA Astrophysics Data System (ADS)

    Brusseau, M. L.

    2017-12-01

    Understanding the transport and fate of per- and poly-fluorinated alkyl substances (PFASs) in the subsurface is critical for accurate risk assessments and design of effective remedial actions. Current conceptual and mathematical models are based on an assumption that solid-phase adsorption is the sole source of retention for PFASs. However, additional retention processes may be relevant for PFAS compounds in vadose-zone systems and in source zones that contain trapped immiscible organic liquids. These include adsorption at the air-water interface, partitioning to the soil atmosphere, adsorption at the NAPL-water interface, and absorption by NAPL. A multi-process retention model is proposed to account for these potential additional sources of PFAS retardation. An initial assessment of the relative magnitudes and significance of these retention processes was conducted for three representative PFASs, perfluorooctanoic acid (PFOA), perfluorooctane sulfonate (PFOS), and 8:2 fluorotelomer alcohol (FTOH). Data collected from the literature were used to determine measured or estimated values for the relevant distribution coefficients, which were in turn used to calculate retardation factors for a representative porous medium. Adsorption at the air-water interface was shown to be a primary source of retention for PFOA and PFOS, contributing approximately 80% of total retardation. Adsorption to NAPL-water interfaces and absorption by bulk NAPL were also shown to be significant sources of retention for PFOS and PFOA. The latter process was the predominant source of retention for 8:2 FTOH, contributing 98% of total retardation. These results indicate that we may anticipate significant retention of PFASs by these additional processes. In such cases, retardation of PFASs in source areas may be significantly greater than what is typically estimated based on the standard assumption of solid-phase adsorption as the sole retention mechanism. This has significant ramifications for accurate determination of the migration potential and magnitude of mass flux to groundwater, as well as for calculations of contaminant mass residing in source zones.

  11. astroABC : An Approximate Bayesian Computation Sequential Monte Carlo sampler for cosmological parameter estimation

    NASA Astrophysics Data System (ADS)

    Jennings, E.; Madigan, M.

    2017-04-01

    Given the complexity of modern cosmological parameter inference where we are faced with non-Gaussian data and noise, correlated systematics and multi-probe correlated datasets,the Approximate Bayesian Computation (ABC) method is a promising alternative to traditional Markov Chain Monte Carlo approaches in the case where the Likelihood is intractable or unknown. The ABC method is called "Likelihood free" as it avoids explicit evaluation of the Likelihood by using a forward model simulation of the data which can include systematics. We introduce astroABC, an open source ABC Sequential Monte Carlo (SMC) sampler for parameter estimation. A key challenge in astrophysics is the efficient use of large multi-probe datasets to constrain high dimensional, possibly correlated parameter spaces. With this in mind astroABC allows for massive parallelization using MPI, a framework that handles spawning of processes across multiple nodes. A key new feature of astroABC is the ability to create MPI groups with different communicators, one for the sampler and several others for the forward model simulation, which speeds up sampling time considerably. For smaller jobs the Python multiprocessing option is also available. Other key features of this new sampler include: a Sequential Monte Carlo sampler; a method for iteratively adapting tolerance levels; local covariance estimate using scikit-learn's KDTree; modules for specifying optimal covariance matrix for a component-wise or multivariate normal perturbation kernel and a weighted covariance metric; restart files output frequently so an interrupted sampling run can be resumed at any iteration; output and restart files are backed up at every iteration; user defined distance metric and simulation methods; a module for specifying heterogeneous parameter priors including non-standard prior PDFs; a module for specifying a constant, linear, log or exponential tolerance level; well-documented examples and sample scripts. This code is hosted online at https://github.com/EliseJ/astroABC.

  12. A DNA-Based Semantic Fusion Model for Remote Sensing Data

    PubMed Central

    Sun, Heng; Weng, Jian; Yu, Guangchuang; Massawe, Richard H.

    2013-01-01

    Semantic technology plays a key role in various domains, from conversation understanding to algorithm analysis. As the most efficient semantic tool, ontology can represent, process and manage the widespread knowledge. Nowadays, many researchers use ontology to collect and organize data's semantic information in order to maximize research productivity. In this paper, we firstly describe our work on the development of a remote sensing data ontology, with a primary focus on semantic fusion-driven research for big data. Our ontology is made up of 1,264 concepts and 2,030 semantic relationships. However, the growth of big data is straining the capacities of current semantic fusion and reasoning practices. Considering the massive parallelism of DNA strands, we propose a novel DNA-based semantic fusion model. In this model, a parallel strategy is developed to encode the semantic information in DNA for a large volume of remote sensing data. The semantic information is read in a parallel and bit-wise manner and an individual bit is converted to a base. By doing so, a considerable amount of conversion time can be saved, i.e., the cluster-based multi-processes program can reduce the conversion time from 81,536 seconds to 4,937 seconds for 4.34 GB source data files. Moreover, the size of result file recording DNA sequences is 54.51 GB for parallel C program compared with 57.89 GB for sequential Perl. This shows that our parallel method can also reduce the DNA synthesis cost. In addition, data types are encoded in our model, which is a basis for building type system in our future DNA computer. Finally, we describe theoretically an algorithm for DNA-based semantic fusion. This algorithm enables the process of integration of the knowledge from disparate remote sensing data sources into a consistent, accurate, and complete representation. This process depends solely on ligation reaction and screening operations instead of the ontology. PMID:24116207

  13. Projected impacts of urbanisation on hydrological resource flows: A case study within the uMngeni Catchment, South Africa.

    PubMed

    Schütte, S; Schulze, R E

    2017-07-01

    Significant land use changes from natural/agricultural to urban land uses have been proposed within the Mpushini/Mkhondeni sub-catchments of the uMngeni Catchment in South Africa. A better understanding of the influences which such land use changes are likely to have on hydrological flows, is required, in order to make informed land use decisions for a sustainable future. As a point of departure, an overview of linkages between urbanisation and hydrological flow responses within this sub-humid study area is given. The urban characteristics of increased impervious areas and the potential return flows from transfers of potable water from outside the catchment were identified as being important in regard to hydrological flow responses. A methodology was developed to model urban response scenarios with urban characteristics as variables, using the daily time-step process based ACRU model. This is a hydrological multi-process model and not an urban hydraulic model and it addresses the landscape as well as the channel components of a catchment, and in addition to runoff components includes evaporation and transpiration losses as outputs. For the study area strong links between proposed urbanisation and hydrological resource flow responses were found, with increases in stormflows, together with increased and more regulated baseflows, and with impacts varying markedly between dry or wet years and by season. The impacts will depend on the fractions of impervious areas, whether or not these are connected to permeable areas, the amount of imported water and water system leaks. Furthermore, the urban hydrological impacts were found to be relatively greater in more arid than humid areas because of changes in the rainfall to runoff conversion. Flow changes due to urbanisation are considered to have important environmental impacts, requiring mitigation. The methodology used in this paper could be used for other urbanising areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Fast Gas Replacement in Plasma Process Chamber by Improving Gas Flow Pattern

    NASA Astrophysics Data System (ADS)

    Morishita, Sadaharu; Goto, Tetsuya; Akutsu, Isao; Ohyama, Kenji; Ito, Takashi; Ohmi, Tadahiro

    2009-01-01

    The precise and high-speed alteration of various gas species is important for realizing precise and well-controlled multiprocesses in a single plasma process chamber with high throughput. The gas replacement times in the replacement of N2 by Ar and that of H2 by Ar are measured in a microwave excited high-density and low electron-temperature plasma process chamber at various working pressures and gas flow rates, incorporating a new gas flow control system, which can avoid overshoot of the gas pressure in the chamber immediately after the valve operation, and a gradational lead screw booster pump, which can maintain excellent pumping capability for various gas species including lightweight gases such as H2 in a wide pressure region from 10-1 to 104 Pa. Furthermore, to control the gas flow pattern in the chamber, upper ceramic shower plates, which have thousands of very fine gas injection holes (numbers of 1200 and 2400) formed with optimized allocation on the plates, are adopted, while the conventional gas supply method in the microwave-excited plasma chamber uses many holes only opened at the sidewall of the chamber (gas ring). It has been confirmed that, in the replacement of N2 by Ar, a short replacement time of approximately 1 s in the cases of 133 and 13.3 Pa and approximately 3 s in the case of 4 Pa can be achieved when the upper shower plate has 2400 holes, while a replacement time longer than approximately 10 s is required for all pressure cases where the gas ring is used. In addition, thanks to the excellent pumping capability of the gradational lead screw booster pump for lightweight gases, it has also been confirmed that the replacement time of H2 by Ar is almost the same as that of N2 by Ar.

  15. DasPy – Open Source Multivariate Land Data Assimilation Framework with High Performance Computing

    NASA Astrophysics Data System (ADS)

    Han, Xujun; Li, Xin; Montzka, Carsten; Kollet, Stefan; Vereecken, Harry; Hendricks Franssen, Harrie-Jan

    2015-04-01

    Data assimilation has become a popular method to integrate observations from multiple sources with land surface models to improve predictions of the water and energy cycles of the soil-vegetation-atmosphere continuum. In recent years, several land data assimilation systems have been developed in different research agencies. Because of the software availability or adaptability, these systems are not easy to apply for the purpose of multivariate land data assimilation research. Multivariate data assimilation refers to the simultaneous assimilation of observation data for multiple model state variables into a simulation model. Our main motivation was to develop an open source multivariate land data assimilation framework (DasPy) which is implemented using the Python script language mixed with C++ and Fortran language. This system has been evaluated in several soil moisture, L-band brightness temperature and land surface temperature assimilation studies. The implementation allows also parameter estimation (soil properties and/or leaf area index) on the basis of the joint state and parameter estimation approach. LETKF (Local Ensemble Transform Kalman Filter) is implemented as the main data assimilation algorithm, and uncertainties in the data assimilation can be represented by perturbed atmospheric forcings, perturbed soil and vegetation properties and model initial conditions. The CLM4.5 (Community Land Model) was integrated as the model operator. The CMEM (Community Microwave Emission Modelling Platform), COSMIC (COsmic-ray Soil Moisture Interaction Code) and the two source formulation were integrated as observation operators for assimilation of L-band passive microwave, cosmic-ray soil moisture probe and land surface temperature measurements, respectively. DasPy is parallelized using the hybrid MPI (Message Passing Interface) and OpenMP (Open Multi-Processing) techniques. All the input and output data flow is organized efficiently using the commonly used NetCDF file format. Online 1D and 2D visualization of data assimilation results is also implemented to facilitate the post simulation analysis. In summary, DasPy is a ready to use open source parallel multivariate land data assimilation framework.

  16. Compositional diversity in peridotites as result of a multi-process history: The Pacific-derived Santa Elena ophiolite, northwest Costa Rica

    NASA Astrophysics Data System (ADS)

    Escuder-Viruete, Javier; Baumgartner, Peter O.; Castillo-Carrión, Mercedes

    2015-08-01

    The Santa Elena ophiolite (SEO) is an ultramafic nappe of more than 270 km2 overlying a tectonic serpentinite-matrix mélange in northwest Costa Rica. It is mainly composed of Cpx-rich and Cpx-poor harzburgites (~ 2.5 km-thick), with minor lherzolite, dunite and chromitite, as well as intrusive mafic sills and subvertical dikes, which coalesce into an upper Isla Negritos gabbroic sill complex. Minerals and whole-rock features of the Cpx-rich and Cpx-poor harzburgites share features of the abyssal and supra-subduction zone (SSZ) peridotites, respectively. To explain these characteristics two-stages of melting and refertilization processes are required. By means of trace element modeling, the composition of Cpx-rich harzburgites may be reproduced by up to ~ 5-10% melting of a primitive mantle source, and the composition of Cpx-poor harzburgites and dunites by ~ 15-18% melting of an already depleted mantle. Therefore, the Cpx-rich harzburgites can be interpreted as product of first-stage melting and low-degrees of melt-rock interaction in a mid-ocean ridge environment, and the Cpx-poor harzburgites and dunites as the product of second-stage melting and refertilization in a SSZ setting. The mafic sills and the Isla Negrito gabbros are genetically related and can be explained as crystallization from the liquids that were extracted from the lower SSZ mantle levels and emplaced at shallow conditions. The Murciélagos Island basalts are not directly related to the ultramafic and mafic rocks of the SEO. Their E-MORB-like composition is similar to most of the CLIP mafic lavas and suggests a common Caribbean plume-related source. The SEO represents a fragment of Pacific-derived, SSZ oceanic lithosphere emplaced onto the southern North America margin during the late Cretaceous. Because of the predominance of rollback-induced extension during its history, only a limited amount of crustal rocks were formed and preserved in the SEO.

  17. Nonrecursive formulations of multibody dynamics and concurrent multiprocessing

    NASA Technical Reports Server (NTRS)

    Kurdila, Andrew J.; Menon, Ramesh

    1993-01-01

    Since the late 1980's, research in recursive formulations of multibody dynamics has flourished. Historically, much of this research can be traced to applications of low dimensionality in mechanism and vehicle dynamics. Indeed, there is little doubt that recursive order N methods are the method of choice for this class of systems. This approach has the advantage that a minimal number of coordinates are utilized, parallelism can be induced for certain system topologies, and the method is of order N computational cost for systems of N rigid bodies. Despite the fact that many authors have dismissed redundant coordinate formulations as being of order N(exp 3), and hence less attractive than recursive formulations, we present recent research that demonstrates that at least three distinct classes of redundant, nonrecursive multibody formulations consistently achieve order N computational cost for systems of rigid and/or flexible bodies. These formulations are as follows: (1) the preconditioned range space formulation; (2) penalty methods; and (3) augmented Lagrangian methods for nonlinear multibody dynamics. The first method can be traced to its foundation in equality constrained quadratic optimization, while the last two methods have been studied extensively in the context of coercive variational boundary value problems in computational mechanics. Until recently, however, they have not been investigated in the context of multibody simulation, and present theoretical questions unique to nonlinear dynamics. All of these nonrecursive methods have additional advantages with respect to recursive order N methods: (1) the formalisms retain the highly desirable order N computational cost; (2) the techniques are amenable to concurrent simulation strategies; (3) the approaches do not depend upon system topology to induce concurrency; and (4) the methods can be derived to balance the computational load automatically on concurrent multiprocessors. In addition to the presentation of the fundamental formulations, this paper presents new theoretical results regarding the rate of convergence of order N constraint stabilization schemes associated with the newly introduced class of methods.

  18. Benchmark tests on the digital equipment corporation Alpha AXP 21164-based AlphaServer 8400, including a comparison of optimized vector and superscalar processing

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

    Wasserman, H.J.

    1996-02-01

    The second generation of the Digital Equipment Corp. (DEC) DECchip Alpha AXP microprocessor is referred to as the 21164. From the viewpoint of numerically-intensive computing, the primary difference between it and its predecessor, the 21064, is that the 21164 has twice the multiply/add throughput per clock period (CP), a maximum of two floating point operations (FLOPS) per CP vs. one for 21064. The AlphaServer 8400 is a shared-memory multiprocessor server system that can accommodate up to 12 CPUs and up to 14 GB of memory. In this report we will compare single processor performance of the 8400 system with thatmore » of the International Business Machines Corp. (IBM) RISC System/6000 POWER-2 microprocessor running at 66 MHz, the Silicon Graphics, Inc. (SGI) MIPS R8000 microprocessor running at 75 MHz, and the Cray Research, Inc. CRAY J90. The performance comparison is based on a set of Fortran benchmark codes that represent a portion of the Los Alamos National Laboratory supercomputer workload. The advantage of using these codes, is that the codes also span a wide range of computational characteristics, such as vectorizability, problem size, and memory access pattern. The primary disadvantage of using them is that detailed, quantitative analysis of performance behavior of all codes on all machines is difficult. One important addition to the benchmark set appears for the first time in this report. Whereas the older version was written for a vector processor, the newer version is more optimized for microprocessor architectures. Therefore, we have for the first time, an opportunity to measure performance on a single application using implementations that expose the respective strengths of vector and superscalar architecture. All results in this report are from single processors. A subsequent article will explore shared-memory multiprocessing performance of the 8400 system.« less

  19. Understanding strength exercise intentions and behavior in hematologic cancer survivors: an analysis of the intention-behavior gap.

    PubMed

    Vallerand, James R; Rhodes, Ryan E; Walker, Gordon J; Courneya, Kerry S

    2016-12-01

    Strength exercise improves many health outcomes in cancer survivors but the prevalence and correlates of strength exercise have not been well-described. Moreover, no study has examined the critical intention-behavior gap for exercise in cancer survivors. The aims of this study are to quantify the intention-behavior gap for strength exercise in hematologic cancer survivors (HCS) and examine correlates of both intention formation and translation using the multi-process action control framework (M-PAC). A random sample of 2100 HCS in Alberta, Canada, were mailed a survey assessing strength exercise behavior, the M-PAC, and demographic/medical variables. Separate logistic regressions were used to analyze the relationships between the correlates and intention formation and translation. Surveys were completed by 606 HCS with 58 % (n = 353) intending to do strength exercise. HCS who were not retired (OR = 1.56, p = 0.001), were highly educated (OR = 1.32, p = 0.001), and had a favorable attitude (OR = 1.56, p < 0.001), descriptive norm (OR = 1.38, p = 0.006), injunctive norm (OR = 1.45, p = 0.004), and perceived control (OR = 1.38, p < 0.001), were more likely to form an exercise intention. Of those with an exercise intention, 51 % (n = 181) reported regular strength exercise. HCS with a detailed plan (OR = 1.86, p < 0.001), favorable attitude (OR = 1.68, p = 0.001), sense of obligation (OR = 1.38, p = 0.010), and self-regulated their affinity for competing activities (OR = 1.35, p = 0.012), were more likely to translate their intention into behavior. Just over half of HCS intended to do strength exercise and only half of intenders translated that intention into behavior. Interventions targeting both intention formation and translation may provide the best approach for increasing strength exercise in HCS.

  20. Large-scale 3D simulations of ICF and HEDP targets

    NASA Astrophysics Data System (ADS)

    Marinak, Michael M.

    2000-10-01

    The radiation hydrodynamics code HYDRA continues to be developed and applied to 3D simulations of a variety of targets for both inertial confinement fusion (ICF) and high energy density physics. Several packages have been added enabling this code to perform ICF target simulations with similar accuracy as two-dimensional codes of long-time historical use. These include a laser ray trace and deposition package, a heavy ion deposition package, implicit Monte Carlo photonics, and non-LTE opacities, derived from XSN or the linearized response matrix approach.(R. More, T. Kato, Phys. Rev. Lett. 81, 814 (1998), S. Libby, F. Graziani, R. More, T. Kato, Proceedings of the 13th International Conference on Laser Interactions and Related Plasma Phenomena, (AIP, New York, 1997).) LTE opacities can also be calculated for arbitrary mixtures online by combining tabular values generated by different opacity codes. Thermonuclear burn, charged particle transport, neutron energy deposition, electron-ion coupling and conduction, and multigroup radiation diffusion packages are also installed. HYDRA can employ ALE hydrodynamics; a number of grid motion algorithms are available. Multi-material flows are resolved using material interface reconstruction. Results from large-scale simulations run on up to 1680 processors, using a combination of massively parallel processing and symmetric multiprocessing, will be described. A large solid angle simulation of Rayleigh-Taylor instability growth in a NIF ignition capsule has resolved simultaneously the full spectrum of the most dangerous modes that grow from surface roughness. Simulations of a NIF hohlraum illuminated with the initial 96 beam configuration have also been performed. The effect of the hohlraum’s 3D intrinsic drive asymmetry on the capsule implosion will be considered. We will also discuss results from a Nova experiment in which a copper sphere is crushed by a planar shock. Several interacting hydrodynamic instabilities, including the Widnall instability, cause breakup of the resulting vortex ring.

  1. Correlates of meeting the combined and independent aerobic and strength exercise guidelines in hematologic cancer survivors.

    PubMed

    Vallerand, James R; Rhodes, Ryan E; Walker, Gordon J; Courneya, Kerry S

    2017-03-28

    Most previous research on the correlates of physical activity has examined the aerobic or strength exercise guidelines separately. Such an approach does not allow an examination of the correlates of meeting the combined guidelines versus a single guideline, or one guideline versus the other. Here, we report the prevalence and correlates of meeting the combined and independent exercise guidelines in hematologic cancer survivors (HCS). In a population-based, cross-sectional survey of 606 HCS from Alberta, Canada using a mailed questionnaire, we obtained separate assessments of aerobic and strength exercise behaviors, as well as separate assessments for motivations, regulations, and reflective processes using the multi-process action control framework (M-PAC). Overall, 22% of HCS met the combined exercise guideline, 22% met aerobic-only, 10% met strength-only, and 46% met neither exercise guideline. HCS were more likely to meet the combined guideline over the aerobic-only guideline if they had no children living at home, and over both the aerobic and strength-only guidelines if they had completed university. As hypothesized, those meeting the combined guideline also had a more favorable strength-specific M-PAC profile (i.e., motivations, regulations, and reflective processes) than those meeting the aerobic-only guideline, and a more favorable aerobic-specific M-PAC profile than those meeting the strength-only guideline. Interestingly and unexpectedly, HCS meeting the combined guidelines also reported significantly greater aerobic-specific perceived control, planning, and obligation/regret than those meeting the aerobic-only guideline, and greater strength-specific perceived control, planning, and obligation/regret than those meeting the strength-only guideline. Few HCS are meeting the combined exercise guidelines. M-PAC based variables are strong correlates of meeting the combined guidelines compared to aerobic or strength only guidelines. Strategies to help HCS meet the combined guidelines may need to promote more favorable behavioral regulations and reflective processes for both types of exercise rather than just the type of exercise in which HCS are deficient.

  2. The relevance of grain dissection for grain size reduction in polar ice: insights from numerical models and ice core microstructure analysis

    NASA Astrophysics Data System (ADS)

    Steinbach, Florian; Kuiper, Ernst-Jan N.; Eichler, Jan; Bons, Paul D.; Drury, Martyn R.; Griera, Albert; Pennock, Gill M.; Weikusat, Ilka

    2017-09-01

    The flow of ice depends on the properties of the aggregate of individual ice crystals, such as grain size or lattice orientation distributions. Therefore, an understanding of the processes controlling ice micro-dynamics is needed to ultimately develop a physically based macroscopic ice flow law. We investigated the relevance of the process of grain dissection as a grain-size-modifying process in natural ice. For that purpose, we performed numerical multi-process microstructure modelling and analysed microstructure and crystallographic orientation maps from natural deep ice-core samples from the North Greenland Eemian Ice Drilling (NEEM) project. Full crystallographic orientations measured by electron backscatter diffraction (EBSD) have been used together with c-axis orientations using an optical technique (Fabric Analyser). Grain dissection is a feature of strain-induced grain boundary migration. During grain dissection, grain boundaries bulge into a neighbouring grain in an area of high dislocation energy and merge with the opposite grain boundary. This splits the high dislocation-energy grain into two parts, effectively decreasing the local grain size. Currently, grain size reduction in ice is thought to be achieved by either the progressive transformation from dislocation walls into new high-angle grain boundaries, called subgrain rotation or polygonisation, or bulging nucleation that is assisted by subgrain rotation. Both our time-resolved numerical modelling and NEEM ice core samples show that grain dissection is a common mechanism during ice deformation and can provide an efficient process to reduce grain sizes and counter-act dynamic grain-growth in addition to polygonisation or bulging nucleation. Thus, our results show that solely strain-induced boundary migration, in absence of subgrain rotation, can reduce grain sizes in polar ice, in particular if strain energy gradients are high. We describe the microstructural characteristics that can be used to identify grain dissection in natural microstructures.

  3. List-mode PET image reconstruction for motion correction using the Intel XEON PHI co-processor

    NASA Astrophysics Data System (ADS)

    Ryder, W. J.; Angelis, G. I.; Bashar, R.; Gillam, J. E.; Fulton, R.; Meikle, S.

    2014-03-01

    List-mode image reconstruction with motion correction is computationally expensive, as it requires projection of hundreds of millions of rays through a 3D array. To decrease reconstruction time it is possible to use symmetric multiprocessing computers or graphics processing units. The former can have high financial costs, while the latter can require refactoring of algorithms. The Xeon Phi is a new co-processor card with a Many Integrated Core architecture that can run 4 multiple-instruction, multiple data threads per core with each thread having a 512-bit single instruction, multiple data vector register. Thus, it is possible to run in the region of 220 threads simultaneously. The aim of this study was to investigate whether the Xeon Phi co-processor card is a viable alternative to an x86 Linux server for accelerating List-mode PET image reconstruction for motion correction. An existing list-mode image reconstruction algorithm with motion correction was ported to run on the Xeon Phi coprocessor with the multi-threading implemented using pthreads. There were no differences between images reconstructed using the Phi co-processor card and images reconstructed using the same algorithm run on a Linux server. However, it was found that the reconstruction runtimes were 3 times greater for the Phi than the server. A new version of the image reconstruction algorithm was developed in C++ using OpenMP for mutli-threading and the Phi runtimes decreased to 1.67 times that of the host Linux server. Data transfer from the host to co-processor card was found to be a rate-limiting step; this needs to be carefully considered in order to maximize runtime speeds. When considering the purchase price of a Linux workstation with Xeon Phi co-processor card and top of the range Linux server, the former is a cost-effective computation resource for list-mode image reconstruction. A multi-Phi workstation could be a viable alternative to cluster computers at a lower cost for medical imaging applications.

  4. DasPy 1.0 - the Open Source Multivariate Land Data Assimilation Framework in combination with the Community Land Model 4.5

    NASA Astrophysics Data System (ADS)

    Han, X.; Li, X.; He, G.; Kumbhar, P.; Montzka, C.; Kollet, S.; Miyoshi, T.; Rosolem, R.; Zhang, Y.; Vereecken, H.; Franssen, H.-J. H.

    2015-08-01

    Data assimilation has become a popular method to integrate observations from multiple sources with land surface models to improve predictions of the water and energy cycles of the soil-vegetation-atmosphere continuum. Multivariate data assimilation refers to the simultaneous assimilation of observation data from multiple model state variables into a simulation model. In recent years, several land data assimilation systems have been developed in different research agencies. Because of the software availability or adaptability, these systems are not easy to apply for the purpose of multivariate land data assimilation research. We developed an open source multivariate land data assimilation framework (DasPy) which is implemented using the Python script language mixed with the C++ and Fortran programming languages. LETKF (Local Ensemble Transform Kalman Filter) is implemented as the main data assimilation algorithm, and uncertainties in the data assimilation can be introduced by perturbed atmospheric forcing data, and represented by perturbed soil and vegetation parameters and model initial conditions. The Community Land Model (CLM) was integrated as the model operator. The implementation allows also parameter estimation (soil properties and/or leaf area index) on the basis of the joint state and parameter estimation approach. The Community Microwave Emission Modelling platform (CMEM), COsmic-ray Soil Moisture Interaction Code (COSMIC) and the Two-Source Formulation (TSF) were integrated as observation operators for the assimilation of L-band passive microwave, cosmic-ray soil moisture probe and land surface temperature measurements, respectively. DasPy has been evaluated in several assimilation studies of neutron count intensity (soil moisture), L-band brightness temperature and land surface temperature. DasPy is parallelized using the hybrid Message Passing Interface and Open Multi-Processing techniques. All the input and output data flows are organized efficiently using the commonly used NetCDF file format. Online 1-D and 2-D visualization of data assimilation results is also implemented to facilitate the post simulation analysis. In summary, DasPy is a ready to use open source parallel multivariate land data assimilation framework.

  5. Modelling of runoff generation and soil moisture dynamics for hillslopes and micro-catchments

    NASA Astrophysics Data System (ADS)

    Bronstert, Axel; Plate, Erich J.

    1997-11-01

    The modelling of hillslope hydrology is of great importance not only for the reason that all non-plain, i.e. hilly or mountainous, landscapes can be considered as being composed of a mosaic of hillslopes. A hillslope model may also be used for both research purposes and for application-oriented, detailed, hillslope-scale hydrological studies in conjunction with related scientific disciplines such as geotechnics, geo-chemistry and environmental technology. Despite the current limited application of multi-process and multi-dimensional hydrological models (particularly at the hillslope scale), hardly any comprehensive model has been available for operational use. In this paper we introduce a model which considers most of the relevant hillslope hydrological processes. Some recent applications are described which demonstrate its ability to narrow the stated gap in hillslope hydrological modelling. The modelling system accounts for the hydrological processes of interception, evapotranspiration, infiltration, soil-moisture movement (where the flow processes can be modelled in three dimensions), surface runoff, subsurface stormflow and streamflow discharge. The relevant process interactions are also included. Special regard has been given to consideration of state-of-the-art knowledge concerning rapid soilwater flow processes during storm conditions (e.g. macropore infiltration, lateral subsurface stormflow, return flow) and to its transfer to and inclusion within an operational modelling scheme. The model is "physically based" in the sense that its parameters have a physical meaning and can be obtained or derived from field measurements. This somewhat weaker than usual definition of a physical basis implies that some of the sub-models (still) contain empirical components, that the effects of the high spatial and temporal variability found in nature cannot always be expressed within the various physical laws, i.e. that the laws are scale dependent, and that due to limitations of measurements and data processing, one can express only averaged and incomplete data conditions. Several applications demonstrate the reliable performance of the model for one-, two- and three-dimensional simulations. The described examples of application are part of a comprehensive erosion and agro-chemical transport study in a loessy agricultural catchment in southwestern Germany, and of a study on the sealing efficacy of capillary barriers in landfill covers.

  6. Utilizing High-Performance Computing to Investigate Parameter Sensitivity of an Inversion Model for Vadose Zone Flow and Transport

    NASA Astrophysics Data System (ADS)

    Fang, Z.; Ward, A. L.; Fang, Y.; Yabusaki, S.

    2011-12-01

    High-resolution geologic models have proven effective in improving the accuracy of subsurface flow and transport predictions. However, many of the parameters in subsurface flow and transport models cannot be determined directly at the scale of interest and must be estimated through inverse modeling. A major challenge, particularly in vadose zone flow and transport, is the inversion of the highly-nonlinear, high-dimensional problem as current methods are not readily scalable for large-scale, multi-process models. In this paper we describe the implementation of a fully automated approach for addressing complex parameter optimization and sensitivity issues on massively parallel multi- and many-core systems. The approach is based on the integration of PNNL's extreme scale Subsurface Transport Over Multiple Phases (eSTOMP) simulator, which uses the Global Array toolkit, with the Beowulf-Cluster inspired parallel nonlinear parameter estimation software, BeoPEST in the MPI mode. In the eSTOMP/BeoPEST implementation, a pre-processor generates all of the PEST input files based on the eSTOMP input file. Simulation results for comparison with observations are extracted automatically at each time step eliminating the need for post-process data extractions. The inversion framework was tested with three different experimental data sets: one-dimensional water flow at Hanford Grass Site; irrigation and infiltration experiment at the Andelfingen Site; and a three-dimensional injection experiment at Hanford's Sisson and Lu Site. Good agreements are achieved in all three applications between observations and simulations in both parameter estimates and water dynamics reproduction. Results show that eSTOMP/BeoPEST approach is highly scalable and can be run efficiently with hundreds or thousands of processors. BeoPEST is fault tolerant and new nodes can be dynamically added and removed. A major advantage of this approach is the ability to use high-resolution geologic models to preserve the spatial structure in the inverse model, which leads to better parameter estimates and improved predictions when using the inverse-conditioned realizations of parameter fields.

  7. TWOS - TIME WARP OPERATING SYSTEM, VERSION 2.5.1

    NASA Technical Reports Server (NTRS)

    Bellenot, S. F.

    1994-01-01

    The Time Warp Operating System (TWOS) is a special-purpose operating system designed to support parallel discrete-event simulation. TWOS is a complete implementation of the Time Warp mechanism, a distributed protocol for virtual time synchronization based on process rollback and message annihilation. Version 2.5.1 supports simulations and other computations using both virtual time and dynamic load balancing; it does not support general time-sharing or multi-process jobs using conventional message synchronization and communication. The program utilizes the underlying operating system's resources. TWOS runs a single simulation at a time, executing it concurrently on as many processors of a distributed system as are allocated. The simulation needs only to be decomposed into objects (logical processes) that interact through time-stamped messages. TWOS provides transparent synchronization. The user does not have to add any more special logic to aid in synchronization, nor give any synchronization advice, nor even understand much about how the Time Warp mechanism works. The Time Warp Simulator (TWSIM) subdirectory contains a sequential simulation engine that is interface compatible with TWOS. This means that an application designer and programmer who wish to use TWOS can prototype code on TWSIM on a single processor and/or workstation before having to deal with the complexity of working on a distributed system. TWSIM also provides statistics about the application which may be helpful for determining the correctness of an application and for achieving good performance on TWOS. Version 2.5.1 has an updated interface that is not compatible with 2.0. The program's user manual assists the simulation programmer in the design, coding, and implementation of discrete-event simulations running on TWOS. The manual also includes a practical user's guide to the TWOS application benchmark, Colliding Pucks. TWOS supports simulations written in the C programming language. It is designed to run on the Sun3/Sun4 series computers and the BBN "Butterfly" GP-1000 computer. The standard distribution medium for this package is a .25 inch tape cartridge in TAR format. TWOS was developed in 1989 and updated in 1991. This program is a copyrighted work with all copyright vested in NASA. Sun3 and Sun4 are trademarks of Sun Microsystems, Inc.

  8. Implementation of the ATLAS trigger within the multi-threaded software framework AthenaMT

    NASA Astrophysics Data System (ADS)

    Wynne, Ben; ATLAS Collaboration

    2017-10-01

    We present an implementation of the ATLAS High Level Trigger, HLT, that provides parallel execution of trigger algorithms within the ATLAS multithreaded software framework, AthenaMT. This development will enable the ATLAS HLT to meet future challenges due to the evolution of computing hardware and upgrades of the Large Hadron Collider, LHC, and ATLAS Detector. During the LHC data-taking period starting in 2021, luminosity will reach up to three times the original design value. Luminosity will increase further, to up to 7.5 times the design value, in 2026 following LHC and ATLAS upgrades. This includes an upgrade of the ATLAS trigger architecture that will result in an increase in the HLT input rate by a factor of 4 to 10 compared to the current maximum rate of 100 kHz. The current ATLAS multiprocess framework, AthenaMP, manages a number of processes that each execute algorithms sequentially for different events. AthenaMT will provide a fully multi-threaded environment that will additionally enable concurrent execution of algorithms within an event. This has the potential to significantly reduce the memory footprint on future manycore devices. An additional benefit of the HLT implementation within AthenaMT is that it facilitates the integration of offline code into the HLT. The trigger must retain high rejection in the face of increasing numbers of pileup collisions. This will be achieved by greater use of offline algorithms that are designed to maximize the discrimination of signal from background. Therefore a unification of the HLT and offline reconstruction software environment is required. This has been achieved while at the same time retaining important HLT-specific optimisations that minimize the computation performed to reach a trigger decision. Such optimizations include early event rejection and reconstruction within restricted geometrical regions. We report on an HLT prototype in which the need for HLT-specific components has been reduced to a minimum. Promising results have been obtained with a prototype that includes the key elements of trigger functionality including regional reconstruction and early event rejection. We report on the first experience of migrating trigger selections to this new framework and present the next steps towards a full implementation of the ATLAS trigger.

  9. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data.

    PubMed

    Chen, Shifu; Huang, Tanxiao; Zhou, Yanqing; Han, Yue; Xu, Mingyan; Gu, Jia

    2017-03-14

    Some applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed to profile the sequencing quality, but few of them can quantify or correct the sequencing errors. This unmet requirement motivated us to develop AfterQC, a tool with functions to profile sequencing errors and correct most of them, plus highly automated quality control and data filtering features. Different from most tools, AfterQC analyses the overlapping of paired sequences for pair-end sequencing data. Based on overlapping analysis, AfterQC can detect and cut adapters, and furthermore it gives a novel function to correct wrong bases in the overlapping regions. Another new feature is to detect and visualise sequencing bubbles, which can be commonly found on the flowcell lanes and may raise sequencing errors. Besides normal per cycle quality and base content plotting, AfterQC also provides features like polyX (a long sub-sequence of a same base X) filtering, automatic trimming and K-MER based strand bias profiling. For each single or pair of FastQ files, AfterQC filters out bad reads, detects and eliminates sequencer's bubble effects, trims reads at front and tail, detects the sequencing errors and corrects part of them, and finally outputs clean data and generates HTML reports with interactive figures. AfterQC can run in batch mode with multiprocess support, it can run with a single FastQ file, a single pair of FastQ files (for pair-end sequencing), or a folder for all included FastQ files to be processed automatically. Based on overlapping analysis, AfterQC can estimate the sequencing error rate and profile the error transform distribution. The results of our error profiling tests show that the error distribution is highly platform dependent. Much more than just another new quality control (QC) tool, AfterQC is able to perform quality control, data filtering, error profiling and base correction automatically. Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations. While providing rich configurable options, AfterQC can detect and set all the options automatically and require no argument in most cases.

  10. Assessing the potential contributions of additional retention processes to PFAS retardation in the subsurface.

    PubMed

    Brusseau, Mark L

    2018-02-01

    A comprehensive understanding of the transport and fate of per- and poly-fluoroalkyl substances (PFAS) in the subsurface is critical for accurate risk assessments and design of effective remedial actions. A multi-process retention model is proposed to account for potential additional sources of retardation for PFAS transport in source zones. These include partitioning to the soil atmosphere, adsorption at air-water interfaces, partitioning to trapped organic liquids (NAPL), and adsorption at NAPL-water interfaces. An initial assessment of the relative magnitudes and significance of these retention processes was conducted for two PFAS of primary concern, perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), and an example precursor (fluorotelomer alcohol, FTOH). The illustrative evaluation was conducted using measured porous-medium properties representative of a sandy vadose-zone soil. Data collected from the literature were used to determine measured or estimated values for the relevant distribution coefficients, which were in turn used to calculate retardation factors for the model system. The results showed that adsorption at the air-water interface was a primary source of retention for both PFOA and PFOS, contributing approximately 50% of total retention for the conditions employed. Adsorption to NAPL-water interfaces and partitioning to bulk NAPL were also shown to be significant sources of retention. NAPL partitioning was the predominant source of retention for FTOH, contributing ~98% of total retention. These results indicate that these additional processes may be, in some cases, significant sources of retention for subsurface transport of PFAS. The specific magnitudes and significance of the individual retention processes will depend upon the properties and conditions of the specific system of interest (e.g., PFAS constituent and concentration, porous medium, aqueous chemistry, fluid saturations, co-contaminants). In cases wherein these additional retention processes are significant, retardation of PFAS in source areas would likely be greater than what is typically estimated based on the standard assumption of solid-phase adsorption as the sole retention mechanism. This has significant ramifications for accurate determination of the migration potential and magnitude of mass flux to groundwater, as well as for calculations of contaminant mass residing in source zones. Both of which have critical implications for human-health risk assessments. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. A generalized reconstruction framework for unconventional PET systems

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

    Mathews, Aswin John, E-mail: amathews@wustl.edu; Li, Ke; O’Sullivan, Joseph A.

    2015-08-15

    Purpose: Quantitative estimation of the radionuclide activity concentration in positron emission tomography (PET) requires precise modeling of PET physics. The authors are focused on designing unconventional PET geometries for specific applications. This work reports the creation of a generalized reconstruction framework, capable of reconstructing tomographic PET data for systems that use right cuboidal detector elements positioned at arbitrary geometry using a regular Cartesian grid of image voxels. Methods: The authors report on a variety of design choices and optimization for the creation of the generalized framework. The image reconstruction algorithm is maximum likelihood-expectation–maximization. System geometry can be specified using amore » simple script. Given the geometry, a symmetry seeking algorithm finds existing symmetry in the geometry with respect to the image grid to improve the memory usage/speed. Normalization is approached from a geometry independent perspective. The system matrix is computed using the Siddon’s algorithm and subcrystal approach. The program is parallelized through open multiprocessing and message passing interface libraries. A wide variety of systems can be modeled using the framework. This is made possible by modeling the underlying physics and data correction, while generalizing the geometry dependent features. Results: Application of the framework for three novel PET systems, each designed for a specific application, is presented to demonstrate the robustness of the framework in modeling PET systems of unconventional geometry. Three PET systems of unconventional geometry are studied. (1) Virtual-pinhole half-ring insert integrated into Biograph-40: although the insert device improves image quality over conventional whole-body scanner, the image quality varies depending on the position of the insert and the object. (2) Virtual-pinhole flat-panel insert integrated into Biograph-40: preliminary results from an investigation into a modular flat-panel insert are presented. (3) Plant PET system: a reconfigurable PET system for imaging plants, with resolution of greater than 3.3 mm, is shown. Using the automated symmetry seeking algorithm, the authors achieved a compression ratio of the storage and memory requirement by a factor of approximately 50 for the half-ring and flat-panel systems. For plant PET system, the compression ratio is approximately five. The ratio depends on the level of symmetry that exists in different geometries. Conclusions: This work brings the field closer to arbitrary geometry reconstruction. A generalized reconstruction framework can be used to validate multiple hypotheses and the effort required to investigate each system is reduced. Memory usage/speed can be improved with certain optimizations.« less

  12. A generalized reconstruction framework for unconventional PET systems.

    PubMed

    Mathews, Aswin John; Li, Ke; Komarov, Sergey; Wang, Qiang; Ravindranath, Bosky; O'Sullivan, Joseph A; Tai, Yuan-Chuan

    2015-08-01

    Quantitative estimation of the radionuclide activity concentration in positron emission tomography (PET) requires precise modeling of PET physics. The authors are focused on designing unconventional PET geometries for specific applications. This work reports the creation of a generalized reconstruction framework, capable of reconstructing tomographic PET data for systems that use right cuboidal detector elements positioned at arbitrary geometry using a regular Cartesian grid of image voxels. The authors report on a variety of design choices and optimization for the creation of the generalized framework. The image reconstruction algorithm is maximum likelihood-expectation-maximization. System geometry can be specified using a simple script. Given the geometry, a symmetry seeking algorithm finds existing symmetry in the geometry with respect to the image grid to improve the memory usage/speed. Normalization is approached from a geometry independent perspective. The system matrix is computed using the Siddon's algorithm and subcrystal approach. The program is parallelized through open multiprocessing and message passing interface libraries. A wide variety of systems can be modeled using the framework. This is made possible by modeling the underlying physics and data correction, while generalizing the geometry dependent features. Application of the framework for three novel PET systems, each designed for a specific application, is presented to demonstrate the robustness of the framework in modeling PET systems of unconventional geometry. Three PET systems of unconventional geometry are studied. (1) Virtual-pinhole half-ring insert integrated into Biograph-40: although the insert device improves image quality over conventional whole-body scanner, the image quality varies depending on the position of the insert and the object. (2) Virtual-pinhole flat-panel insert integrated into Biograph-40: preliminary results from an investigation into a modular flat-panel insert are presented. (3) Plant PET system: a reconfigurable PET system for imaging plants, with resolution of greater than 3.3 mm, is shown. Using the automated symmetry seeking algorithm, the authors achieved a compression ratio of the storage and memory requirement by a factor of approximately 50 for the half-ring and flat-panel systems. For plant PET system, the compression ratio is approximately five. The ratio depends on the level of symmetry that exists in different geometries. This work brings the field closer to arbitrary geometry reconstruction. A generalized reconstruction framework can be used to validate multiple hypotheses and the effort required to investigate each system is reduced. Memory usage/speed can be improved with certain optimizations.

  13. A generalized reconstruction framework for unconventional PET systems

    PubMed Central

    Mathews, Aswin John; Li, Ke; Komarov, Sergey; Wang, Qiang; Ravindranath, Bosky; O’Sullivan, Joseph A.; Tai, Yuan-Chuan

    2015-01-01

    Purpose: Quantitative estimation of the radionuclide activity concentration in positron emission tomography (PET) requires precise modeling of PET physics. The authors are focused on designing unconventional PET geometries for specific applications. This work reports the creation of a generalized reconstruction framework, capable of reconstructing tomographic PET data for systems that use right cuboidal detector elements positioned at arbitrary geometry using a regular Cartesian grid of image voxels. Methods: The authors report on a variety of design choices and optimization for the creation of the generalized framework. The image reconstruction algorithm is maximum likelihood-expectation–maximization. System geometry can be specified using a simple script. Given the geometry, a symmetry seeking algorithm finds existing symmetry in the geometry with respect to the image grid to improve the memory usage/speed. Normalization is approached from a geometry independent perspective. The system matrix is computed using the Siddon’s algorithm and subcrystal approach. The program is parallelized through open multiprocessing and message passing interface libraries. A wide variety of systems can be modeled using the framework. This is made possible by modeling the underlying physics and data correction, while generalizing the geometry dependent features. Results: Application of the framework for three novel PET systems, each designed for a specific application, is presented to demonstrate the robustness of the framework in modeling PET systems of unconventional geometry. Three PET systems of unconventional geometry are studied. (1) Virtual-pinhole half-ring insert integrated into Biograph-40: although the insert device improves image quality over conventional whole-body scanner, the image quality varies depending on the position of the insert and the object. (2) Virtual-pinhole flat-panel insert integrated into Biograph-40: preliminary results from an investigation into a modular flat-panel insert are presented. (3) Plant PET system: a reconfigurable PET system for imaging plants, with resolution of greater than 3.3 mm, is shown. Using the automated symmetry seeking algorithm, the authors achieved a compression ratio of the storage and memory requirement by a factor of approximately 50 for the half-ring and flat-panel systems. For plant PET system, the compression ratio is approximately five. The ratio depends on the level of symmetry that exists in different geometries. Conclusions: This work brings the field closer to arbitrary geometry reconstruction. A generalized reconstruction framework can be used to validate multiple hypotheses and the effort required to investigate each system is reduced. Memory usage/speed can be improved with certain optimizations. PMID:26233187

  14. OFF, Open source Finite volume Fluid dynamics code: A free, high-order solver based on parallel, modular, object-oriented Fortran API

    NASA Astrophysics Data System (ADS)

    Zaghi, S.

    2014-07-01

    OFF, an open source (free software) code for performing fluid dynamics simulations, is presented. The aim of OFF is to solve, numerically, the unsteady (and steady) compressible Navier-Stokes equations of fluid dynamics by means of finite volume techniques: the research background is mainly focused on high-order (WENO) schemes for multi-fluids, multi-phase flows over complex geometries. To this purpose a highly modular, object-oriented application program interface (API) has been developed. In particular, the concepts of data encapsulation and inheritance available within Fortran language (from standard 2003) have been stressed in order to represent each fluid dynamics "entity" (e.g. the conservative variables of a finite volume, its geometry, etc…) by a single object so that a large variety of computational libraries can be easily (and efficiently) developed upon these objects. The main features of OFF can be summarized as follows: Programming LanguageOFF is written in standard (compliant) Fortran 2003; its design is highly modular in order to enhance simplicity of use and maintenance without compromising the efficiency; Parallel Frameworks Supported the development of OFF has been also targeted to maximize the computational efficiency: the code is designed to run on shared-memory multi-cores workstations and distributed-memory clusters of shared-memory nodes (supercomputers); the code's parallelization is based on Open Multiprocessing (OpenMP) and Message Passing Interface (MPI) paradigms; Usability, Maintenance and Enhancement in order to improve the usability, maintenance and enhancement of the code also the documentation has been carefully taken into account; the documentation is built upon comprehensive comments placed directly into the source files (no external documentation files needed): these comments are parsed by means of doxygen free software producing high quality html and latex documentation pages; the distributed versioning system referred as git has been adopted in order to facilitate the collaborative maintenance and improvement of the code; CopyrightsOFF is a free software that anyone can use, copy, distribute, study, change and improve under the GNU Public License version 3. The present paper is a manifesto of OFF code and presents the currently implemented features and ongoing developments. This work is focused on the computational techniques adopted and a detailed description of the main API characteristics is reported. OFF capabilities are demonstrated by means of one and two dimensional examples and a three dimensional real application.

  15. Advances in understanding, models and parameterisations of biosphere-atmosphere ammonia exchange

    NASA Astrophysics Data System (ADS)

    Flechard, C. R.; Massad, R.-S.; Loubet, B.; Personne, E.; Simpson, D.; Bash, J. O.; Cooter, E. J.; Nemitz, E.; Sutton, M. A.

    2013-03-01

    Atmospheric ammonia (NH3) dominates global emissions of total reactive nitrogen (Nr), while emissions from agricultural production systems contribute about two thirds of global NH3 emissions; the remaining third emanates from oceans, natural vegetation, humans, wild animals and biomass burning. On land, NH3 emitted from the various sources eventually returns to the biosphere by dry deposition to sink areas, predominantly semi-natural vegetation, and by wet and dry deposition as ammonium (NH4+) to all surfaces. However, the land/atmosphere exchange of gaseous NH3 is in fact bi-directional over unfertilized as well as fertilized ecosystems, with periods and areas of emission and deposition alternating in time (diurnal, seasonal) and space (patchwork landscapes). The exchange is controlled by a range of environmental factors, including meteorology, surface layer turbulence, thermodynamics, air and surface heterogeneous-phase chemistry, canopy geometry, plant development stage, leaf age, organic matter decomposition, soil microbial turnover, and, in agricultural systems, by fertilizer application rate, fertilizer type, soil type, crop type, and agricultural management practices. We review the range of processes controlling NH3 emission and uptake in the different parts of the soil-canopy-atmosphere continuum, with NH3 emission potentials defined at the substrate and leaf levels by different [NH4+] / [H+] ratios (Γ). Surface/atmosphere exchange models for NH3 are necessary to compute the temporal and spatial patterns of emissions and deposition at the soil, plant, field, landscape, regional and global scales, in order to assess the multiple environmental impacts of air-borne and deposited NH3 and NH4+. Models of soil/vegetation/atmosphereem NH3 exchange are reviewed from the substrate and leaf scales to the global scale. They range from simple steady-state, "big leaf" canopy resistance models, to dynamic, multi-layer, multi-process, multi-chemical species schemes. Their level of complexity depends on their purpose, the spatial scale at which they are applied, the current level of parameterisation, and the availability of the input data they require. State-of-the-art solutions for determining the emission/sink Γ potentials through the soil/canopy system include coupled, interactive chemical transport models (CTM) and soil/ecosystem modelling at the regional scale. However, it remains a matter for debate to what extent realistic options for future regional and global models should be based on process-based mechanistic versus empirical and regression-type models. Further discussion is needed on the extent and timescale by which new approaches can be used, such as integration with ecosystem models and satellite observations.

  16. Advances in understanding, models and parameterizations of biosphere-atmosphere ammonia exchange

    NASA Astrophysics Data System (ADS)

    Flechard, C. R.; Massad, R.-S.; Loubet, B.; Personne, E.; Simpson, D.; Bash, J. O.; Cooter, E. J.; Nemitz, E.; Sutton, M. A.

    2013-07-01

    Atmospheric ammonia (NH3) dominates global emissions of total reactive nitrogen (Nr), while emissions from agricultural production systems contribute about two-thirds of global NH3 emissions; the remaining third emanates from oceans, natural vegetation, humans, wild animals and biomass burning. On land, NH3 emitted from the various sources eventually returns to the biosphere by dry deposition to sink areas, predominantly semi-natural vegetation, and by wet and dry deposition as ammonium (NH4+) to all surfaces. However, the land/atmosphere exchange of gaseous NH3 is in fact bi-directional over unfertilized as well as fertilized ecosystems, with periods and areas of emission and deposition alternating in time (diurnal, seasonal) and space (patchwork landscapes). The exchange is controlled by a range of environmental factors, including meteorology, surface layer turbulence, thermodynamics, air and surface heterogeneous-phase chemistry, canopy geometry, plant development stage, leaf age, organic matter decomposition, soil microbial turnover, and, in agricultural systems, by fertilizer application rate, fertilizer type, soil type, crop type, and agricultural management practices. We review the range of processes controlling NH3 emission and uptake in the different parts of the soil-canopy-atmosphere continuum, with NH3 emission potentials defined at the substrate and leaf levels by different [NH4+] / [H+] ratios (Γ). Surface/atmosphere exchange models for NH3 are necessary to compute the temporal and spatial patterns of emissions and deposition at the soil, plant, field, landscape, regional and global scales, in order to assess the multiple environmental impacts of airborne and deposited NH3 and NH4+. Models of soil/vegetation/atmosphere NH3 exchange are reviewed from the substrate and leaf scales to the global scale. They range from simple steady-state, "big leaf" canopy resistance models, to dynamic, multi-layer, multi-process, multi-chemical species schemes. Their level of complexity depends on their purpose, the spatial scale at which they are applied, the current level of parameterization, and the availability of the input data they require. State-of-the-art solutions for determining the emission/sink Γ potentials through the soil/canopy system include coupled, interactive chemical transport models (CTM) and soil/ecosystem modelling at the regional scale. However, it remains a matter for debate to what extent realistic options for future regional and global models should be based on process-based mechanistic versus empirical and regression-type models. Further discussion is needed on the extent and timescale by which new approaches can be used, such as integration with ecosystem models and satellite observations.

  17. Investigating the Influence of Remedial Capping on the Hydrological, Geochemical, and Microbial Processes that Control Subsurface Contaminant Migration at WAG 5 on the Oak Ridge Reservation: Implications toward Long-Term Stewardship

    NASA Astrophysics Data System (ADS)

    Jardine, P. M.; Mehlhorn, T. L.

    2006-05-01

    The following research investigated the effectiveness of an aggressive, large scale remedial action that is occurring to subsurface waste trenches containing radioactive and organic waste at the Oak Ridge National Laboratory. The site is being remediated as one of the top cleanup prioritization for the Oak Ridge Accelerated Remediation endeavor. Site landlords, Bechtel Jacobs Co., LLC (BJC) are installing a minimal RCRA cap with the primary objective of controlling the infiltration of storm water into the hundreds of unconfined waste trenches containing radioactive and organic waste. The site now offers a unique scientific opportunity to track the kinetic evolution of post-cap processes influencing contaminant migration and immobilization, because we have many years of pre-cap coupled processes information and knowledge. Since the cap is certain to disrupt the near steady-state contaminant discharge profiles that have existed for many years from the site, we have been quantifying the influence of post-cap hydrological, geochemical, and microbial processes on contaminant discharge as a function of scale and time in an effort to assess local-scale cap influences versus regional scale groundwater flow influences on contaminant discharge. We have been allowed to maintain numerous groundwater monitoring wells at a field site and these have a rich historical data set with regard to hydrology, geochemistry, microbiology, and contaminant flux. Our objectives are to investigate cap induced changes in (1) groundwater and surface hydrology and contaminant flux, (2) geochemistry and contaminant speciation, and (3) microbial community structure and organic contaminant degradation and inorganic contaminant immobilization. Our approach monitors coupled processes during base-flow and during storm events in both the groundwater and surface water discharge from the site and the surrounding watershed. Pre- and post-cap data will than be modeled with a multiprocess, multicomponent, transport model which is linked to pre- and post-cap surface water hydrograph analysis from the site and the surrounding watershed. Our goal is to provide an improved fundamental understanding of the long-term fate and transport of contaminants and an improved ability to predict system response to remedial actions. The experimental and numerical results from this investigation will provide knowledge and information in previously unexplored areas of cap performance with regard to coupled hydrology, geochemistry, microbiology, and contaminant flux in humid regimes. The products will support DOE's mission of long-term stewardship of contaminated environments and be transferable to other site where similar remediation exists or is planned.

  18. Grain dissection as a grain size reducing mechanism during ice microdynamics

    NASA Astrophysics Data System (ADS)

    Steinbach, Florian; Kuiper, Ernst N.; Eichler, Jan; Bons, Paul D.; Drury, Martin R.; Griera, Albert; Pennock, Gill M.; Weikusat, Ilka

    2017-04-01

    Ice sheets are valuable paleo-climate archives, but can lose their integrity by ice flow. An understanding of the microdynamic mechanisms controlling the flow of ice is essential when assessing climatic and environmental developments related to ice sheets and glaciers. For instance, the development of a consistent mechanistic grain size law would support larger scale ice flow models. Recent research made significant progress in numerically modelling deformation and recrystallisation mechanisms in the polycrystalline ice and ice-air aggregate (Llorens et al., 2016a,b; Steinbach et al., 2016). The numerical setup assumed grain size reduction is achieved by the progressive transformation of subgrain boundaries into new high angle grain boundaries splitting an existing grain. This mechanism is usually termed polygonisation. Analogue experiments suggested, that strain induced grain boundary migration can cause bulges to migrate through the whole of a grain separating one region of the grain from another (Jessell, 1986; Urai, 1987). This mechanism of grain dissection could provide an alternative grain size reducing mechanism, but has not yet been observed during ice microdynamics. In this contribution, we present results using an updated numerical approach allowing for grain dissection. The approach is based on coupling the full field theory crystal visco-plasticity code (VPFFT) of Lebensohn (2001) to the multi-process modelling platform Elle (Bons et al., 2008). VPFFT predicts the mechanical fields resulting from short strain increments, dynamic recrystallisation process are implemented in Elle. The novel approach includes improvements to allow for grain dissection, which was topologically impossible during earlier simulations. The simulations are supported by microstructural observations from NEEM (North Greenland Eemian Ice Drilling) ice core. Mappings of c-axis orientations using the automatic fabric analyser and full crystallographic orientations using electron backscatter diffraction (EBSD) are presented. Numerical simulations predict and resolve the microstructural evolution over strain and time. The occurrence of processes such as grain dissection can only be proven using such time resolved movies of microstructure evolution. We will present movies that show grain dissection as a common process during the simulations. Microstructures obtained from NEEM ice core support the observations and we provide evidence for grain dissection in natural ice. Grain dissection is observed to be most efficient relative to polygonisation, when the microstructure approaches steady state grain sizes. This is consistent with analogue experiments observing grain dissection by Jessell (1986) and Urai (1987). Our research suggests a novel grain size reducing mechanisms in ice microdynamics that should be considered when developing a consistent grain size law.

  19. Fast 2D FWI on a multi and many-cores workstation.

    NASA Astrophysics Data System (ADS)

    Thierry, Philippe; Donno, Daniela; Noble, Mark

    2014-05-01

    Following the introduction of x86 co-processors (Xeon Phi) and the performance increase of standard 2-socket workstations using the latest 12 cores E5-v2 x86-64 CPU, we present here a MPI + OpenMP implementation of an acoustic 2D FWI (full waveform inversion) code which simultaneously runs on the CPUs and on the co-processors installed in a workstation. The main advantage of running a 2D FWI on a workstation is to be able to quickly evaluate new features such as more complicated wave equations, new cost functions, finite-difference stencils or boundary conditions. Since the co-processor is made of 61 in-order x86 cores, each of them having up to 4 threads, this many-core can be seen as a shared memory SMP (symmetric multiprocessing) machine with its own IP address. Depending on the vendor, a single workstation can handle several co-processors making the workstation as a personal cluster under the desk. The original Fortran 90 CPU version of the 2D FWI code is just recompiled to get a Xeon Phi x86 binary. This multi and many-core configuration uses standard compilers and associated MPI as well as math libraries under Linux; therefore, the cost of code development remains constant, while improving computation time. We choose to implement the code with the so-called symmetric mode to fully use the capacity of the workstation, but we also evaluate the scalability of the code in native mode (i.e running only on the co-processor) thanks to the Linux ssh and NFS capabilities. Usual care of optimization and SIMD vectorization is used to ensure optimal performances, and to analyze the application performances and bottlenecks on both platforms. The 2D FWI implementation uses finite-difference time-domain forward modeling and a quasi-Newton (with L-BFGS algorithm) optimization scheme for the model parameters update. Parallelization is achieved through standard MPI shot gathers distribution and OpenMP for domain decomposition within the co-processor. Taking advantage of the 16 GB of memory available on the co-processor we are able to keep wavefields in memory to achieve the gradient computation by cross-correlation of forward and back-propagated wavefields needed by our time-domain FWI scheme, without heavy traffic on the i/o subsystem and PCIe bus. In this presentation we will also review some simple methodologies to determine performance expectation compared to real performances in order to get optimization effort estimation before starting any huge modification or rewriting of research codes. The key message is the ease of use and development of this hybrid configuration to reach not the absolute peak performance value but the optimal one that ensures the best balance between geophysical and computer developments.

  20. Spatially-Distributed Stream Flow and Nutrient Dynamics Simulations Using the Component-Based AgroEcoSystem-Watershed (AgES-W) Model

    NASA Astrophysics Data System (ADS)

    Ascough, J. C.; David, O.; Heathman, G. C.; Smith, D. R.; Green, T. R.; Krause, P.; Kipka, H.; Fink, M.

    2010-12-01

    The Object Modeling System 3 (OMS3), currently being developed by the USDA-ARS Agricultural Systems Research Unit and Colorado State University (Fort Collins, CO), provides a component-based environmental modeling framework which allows the implementation of single- or multi-process modules that can be developed and applied as custom-tailored model configurations. OMS3 as a “lightweight” modeling framework contains four primary foundations: modeling resources (e.g., components) annotated with modeling metadata; domain specific knowledge bases and ontologies; tools for calibration, sensitivity analysis, and model optimization; and methods for model integration and performance scalability. The core is able to manage modeling resources and development tools for model and simulation creation, execution, evaluation, and documentation. OMS3 is based on the Java platform but is highly interoperable with C, C++, and FORTRAN on all major operating systems and architectures. The ARS Conservation Effects Assessment Project (CEAP) Watershed Assessment Study (WAS) Project Plan provides detailed descriptions of ongoing research studies at 14 benchmark watersheds in the United States. In order to satisfy the requirements of CEAP WAS Objective 5 (“develop and verify regional watershed models that quantify environmental outcomes of conservation practices in major agricultural regions”), a new watershed model development approach was initiated to take advantage of OMS3 modeling framework capabilities. Specific objectives of this study were to: 1) disaggregate and refactor various agroecosystem models (e.g., J2K-S, SWAT, WEPP) and implement hydrological, N dynamics, and crop growth science components under OMS3, 2) assemble a new modular watershed scale model for fully-distributed transfer of water and N loading between land units and stream channels, and 3) evaluate the accuracy and applicability of the modular watershed model for estimating stream flow and N dynamics. The Cedar Creek watershed (CCW) in northeastern Indiana, USA was selected for application of the OMS3-based AgroEcoSystem-Watershed (AgES-W) model. AgES-W performance for stream flow and N loading was assessed using Nash-Sutcliffe model efficiency (ENS) and percent bias (PBIAS) model evaluation statistics. Comparisons of daily and average monthly simulated and observed stream flow and N loads for the 1997-2005 simulation period resulted in PBIAS and ENS values that were similar or better than those reported in the literature for SWAT stream flow and N loading predictions at a similar scale. The results show that the AgES-W model was able to reproduce the hydrological and N dynamics of the CCW with sufficient quality, and should serve as a foundation upon which to better quantify additional water quality indicators (e.g., sediment transport and P dynamics) at the watershed scale.

  1. A numerical differentiation library exploiting parallel architectures

    NASA Astrophysics Data System (ADS)

    Voglis, C.; Hadjidoukas, P. E.; Lagaris, I. E.; Papageorgiou, D. G.

    2009-08-01

    We present a software library for numerically estimating first and second order partial derivatives of a function by finite differencing. Various truncation schemes are offered resulting in corresponding formulas that are accurate to order O(h), O(h), and O(h), h being the differencing step. The derivatives are calculated via forward, backward and central differences. Care has been taken that only feasible points are used in the case where bound constraints are imposed on the variables. The Hessian may be approximated either from function or from gradient values. There are three versions of the software: a sequential version, an OpenMP version for shared memory architectures and an MPI version for distributed systems (clusters). The parallel versions exploit the multiprocessing capability offered by computer clusters, as well as modern multi-core systems and due to the independent character of the derivative computation, the speedup scales almost linearly with the number of available processors/cores. Program summaryProgram title: NDL (Numerical Differentiation Library) Catalogue identifier: AEDG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 73 030 No. of bytes in distributed program, including test data, etc.: 630 876 Distribution format: tar.gz Programming language: ANSI FORTRAN-77, ANSI C, MPI, OPENMP Computer: Distributed systems (clusters), shared memory systems Operating system: Linux, Solaris Has the code been vectorised or parallelized?: Yes RAM: The library uses O(N) internal storage, N being the dimension of the problem Classification: 4.9, 4.14, 6.5 Nature of problem: The numerical estimation of derivatives at several accuracy levels is a common requirement in many computational tasks, such as optimization, solution of nonlinear systems, etc. The parallel implementation that exploits systems with multiple CPUs is very important for large scale and computationally expensive problems. Solution method: Finite differencing is used with carefully chosen step that minimizes the sum of the truncation and round-off errors. The parallel versions employ both OpenMP and MPI libraries. Restrictions: The library uses only double precision arithmetic. Unusual features: The software takes into account bound constraints, in the sense that only feasible points are used to evaluate the derivatives, and given the level of the desired accuracy, the proper formula is automatically employed. Running time: Running time depends on the function's complexity. The test run took 15 ms for the serial distribution, 0.6 s for the OpenMP and 4.2 s for the MPI parallel distribution on 2 processors.

  2. Strategies for Large Scale Implementation of a Multiscale, Multiprocess Integrated Hydrologic Model

    NASA Astrophysics Data System (ADS)

    Kumar, M.; Duffy, C.

    2006-05-01

    Distributed models simulate hydrologic state variables in space and time while taking into account the heterogeneities in terrain, surface, subsurface properties and meteorological forcings. Computational cost and complexity associated with these model increases with its tendency to accurately simulate the large number of interacting physical processes at fine spatio-temporal resolution in a large basin. A hydrologic model run on a coarse spatial discretization of the watershed with limited number of physical processes needs lesser computational load. But this negatively affects the accuracy of model results and restricts physical realization of the problem. So it is imperative to have an integrated modeling strategy (a) which can be universally applied at various scales in order to study the tradeoffs between computational complexity (determined by spatio- temporal resolution), accuracy and predictive uncertainty in relation to various approximations of physical processes (b) which can be applied at adaptively different spatial scales in the same domain by taking into account the local heterogeneity of topography and hydrogeologic variables c) which is flexible enough to incorporate different number and approximation of process equations depending on model purpose and computational constraint. An efficient implementation of this strategy becomes all the more important for Great Salt Lake river basin which is relatively large (~89000 sq. km) and complex in terms of hydrologic and geomorphic conditions. Also the types and the time scales of hydrologic processes which are dominant in different parts of basin are different. Part of snow melt runoff generated in the Uinta Mountains infiltrates and contributes as base flow to the Great Salt Lake over a time scale of decades to centuries. The adaptive strategy helps capture the steep topographic and climatic gradient along the Wasatch front. Here we present the aforesaid modeling strategy along with an associated hydrologic modeling framework which facilitates a seamless, computationally efficient and accurate integration of the process model with the data model. The flexibility of this framework leads to implementation of multiscale, multiresolution, adaptive refinement/de-refinement and nested modeling simulations with least computational burden. However, performing these simulations and related calibration of these models over a large basin at higher spatio- temporal resolutions is computationally intensive and requires use of increasing computing power. With the advent of parallel processing architectures, high computing performance can be achieved by parallelization of existing serial integrated-hydrologic-model code. This translates to running the same model simulation on a network of large number of processors thereby reducing the time needed to obtain solution. The paper also discusses the implementation of the integrated model on parallel processors. Also will be discussed the mapping of the problem on multi-processor environment, method to incorporate coupling between hydrologic processes using interprocessor communication models, model data structure and parallel numerical algorithms to obtain high performance.

  3. Review of unsaturated-zone transport and attenuation of volatile organic compound (VOC) plumes leached from shallow source zones

    NASA Astrophysics Data System (ADS)

    Rivett, Michael O.; Wealthall, Gary P.; Dearden, Rachel A.; McAlary, Todd A.

    2011-04-01

    Reliable prediction of the unsaturated zone transport and attenuation of dissolved-phase VOC (volatile organic compound) plumes leached from shallow source zones is a complex, multi-process, environmental problem. It is an important problem as sources, which include solid-waste landfills, aqueous-phase liquid discharge lagoons and NAPL releases partially penetrating the unsaturated zone, may persist for decades. Natural attenuation processes operating in the unsaturated zone that, uniquely for VOCs includes volatilisation, may, however, serve to protect underlying groundwater and potentially reduce the need for expensive remedial actions. Review of the literature indicates that only a few studies have focused upon the overall leached VOC source and plume scenario as a whole. These are mostly modelling studies that often involve high strength, non-aqueous phase liquid (NAPL) sources for which density-induced and diffusive vapour transport is significant. Occasional dissolved-phase aromatic hydrocarbon controlled infiltration field studies also exist. Despite this lack of focus on the overall problem, a wide range of process-based unsaturated zone — VOC research has been conducted that may be collated to build good conceptual model understanding of the scenario, particularly for the much studied aromatic hydrocarbons and chlorinated aliphatic hydrocarbons (CAHs). In general, the former group is likely to be attenuated in the unsaturated zone due to their ready aerobic biodegradation, albeit with rate variability across the literature, whereas the fate of the latter is far less likely to be dominated by a single mechanism and dependent upon the relative importance of the various attenuation processes within individual site — VOC scenarios. Analytical and numerical modelling tools permit effective process representation of the whole scenario, albeit with potential for inclusion of additional processes — e.g., multi-mechanistic sorption phase partitioning, and provide good opportunity for further sensitivity analysis and development to practitioner use. There remains a significant need to obtain intermediate laboratory-scale and particularly field-scale (actual site and controlled release) datasets that address the scenario as a whole and permit validation of the available models. Integrated assessment of the range of simultaneous processes that combine to influence leached plume generation, transport and attenuation in the unsaturated zone is required. Component process research needs are required across the problem scenario and include: the simultaneous volatilisation and dissolution of source zones; development of appropriate field-scale dispersion estimates for the unsaturated zone; assessment of transient VOC exchanges between aqueous, vapour and sorbed phases and their influence upon plume attenuation; development of improved field methods to recognise and quantify biodegradation of CAHs; establishment of the influence of co-contaminants; and, finally, translation of research findings into more robust practitioner practice.

  4. Geologic support for the putative Borealis basin (Mega-Impact) on Mars

    NASA Astrophysics Data System (ADS)

    Bleamaster, L. F.

    2008-12-01

    A series of recent papers (all in Nature v. 453) using Martian gravity and topography [Andrews-Hanna et al., 2008], 3-D hydrodynamic simulations [Marinova et al., 2008], and 2-D hydrocode models [Nimmo et al., 2008] have eloquently reintroduced the single mega-impact hypothesis for the formation of the Martian hemispheric dichotomy boundary. Although geophysical models often return non-unique solutions, the coalition front presented by these three independent methods to test such a hypothesis lends credibility and demands further evaluation. The central tenet of these works is the proposition that an elliptical basin (long axis 10,600km, ellipticity 1.25) centered at 67N, 208E marks the pre-Tharsis crustal thickness transition and thus the real dichotomy boundary. Evaluation of this new boundary with respect to the geologic record offers new avenues, especially since geologic tests of the mega-impact hypothesis have mostly proved inconclusive because of Mars' multi-stage and multi-process geologic history. Within this survey, a slightly larger ellipse with a long axis of 12,500 km, ellipticity of 1.48, and centered at 65.3N, 250E expands the putative Borealis impact basin (which does not necessarily represent the transient or final impact cavity dimensions, but defines a potential 'affected zone') while maintaining agreement with the original observations with respect to gravity and topography. The 'affected zone' can be defined by basement structure that may become susceptible to later deformation, or it may in fact have been the paleo- topographic expression of the basin. By expanding the overall area (nearly twice the area of the original mega-impact basin proposed by Wilhelms and Squyres in 1984) several geologic features become significant in evaluating the mega-impact story. 1) Valles Marineris is concentric to the putative basin interior and parallels the ellipse margin suggesting that it is the structural manifestation of localized crustal relaxation of the Tharsis volcanic pile over pre-existing basement structure related to Borealis basin subsidence. The present day Valles Marineris may actually represent the 'missing portion' of the original crustal dichotomy trace underneath Tharsis. 2) The 'great faults' (Connerney et al., 2005) that offset the magnetic field pattern radiate from near the center of the putative basin, again suggesting basement structural control related to basin formation. 3) The mysterious Medusa Fossae Formation is completely enclosed within the basin margin and the units' southern contacts fall within 5 km of the same elliptical trace that bisects central Valles Marineris. 4) Chaos regions at the eastern end of Valles Marineris are wholly contained within the basin margin and suggest some kind of marginal control on their locations. 5) Valley network (channel) densities sharply increase outside the basin and are truncated by the Borealis ellipse. Integrating these and other geologic observations (still ongoing) with the newly formulated geophysical methods suggests that a single mega-impact is reemerging as a viable and perhaps preferred mechanism for dichotomy formation.

  5. Implementing the PM Programming Language using MPI and OpenMP - a New Tool for Programming Geophysical Models on Parallel Systems

    NASA Astrophysics Data System (ADS)

    Bellerby, Tim

    2015-04-01

    PM (Parallel Models) is a new parallel programming language specifically designed for writing environmental and geophysical models. The language is intended to enable implementers to concentrate on the science behind the model rather than the details of running on parallel hardware. At the same time PM leaves the programmer in control - all parallelisation is explicit and the parallel structure of any given program may be deduced directly from the code. This paper describes a PM implementation based on the Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) standards, looking at issues involved with translating the PM parallelisation model to MPI/OpenMP protocols and considering performance in terms of the competing factors of finer-grained parallelisation and increased communication overhead. In order to maximise portability, the implementation stays within the MPI 1.3 standard as much as possible, with MPI-2 MPI-IO file handling the only significant exception. Moreover, it does not assume a thread-safe implementation of MPI. PM adopts a two-tier abstract representation of parallel hardware. A PM processor is a conceptual unit capable of efficiently executing a set of language tasks, with a complete parallel system consisting of an abstract N-dimensional array of such processors. PM processors may map to single cores executing tasks using cooperative multi-tasking, to multiple cores or even to separate processing nodes, efficiently sharing tasks using algorithms such as work stealing. While tasks may move between hardware elements within a PM processor, they may not move between processors without specific programmer intervention. Tasks are assigned to processors using a nested parallelism approach, building on ideas from Reyes et al. (2009). The main program owns all available processors. When the program enters a parallel statement then either processors are divided out among the newly generated tasks (number of new tasks < number of processors) or tasks are divided out among the available processors (number of tasks > number of processors). Nested parallel statements may further subdivide the processor set owned by a given task. Tasks or processors are distributed evenly by default, but uneven distributions are possible under programmer control. It is also possible to explicitly enable child tasks to migrate within the processor set owned by their parent task, reducing load unbalancing at the potential cost of increased inter-processor message traffic. PM incorporates some programming structures from the earlier MIST language presented at a previous EGU General Assembly, while adopting a significantly different underlying parallelisation model and type system. PM code is available at www.pm-lang.org under an unrestrictive MIT license. Reference Ruymán Reyes, Antonio J. Dorta, Francisco Almeida, Francisco de Sande, 2009. Automatic Hybrid MPI+OpenMP Code Generation with llc, Recent Advances in Parallel Virtual Machine and Message Passing Interface, Lecture Notes in Computer Science Volume 5759, 185-195

  6. Application of Geologic Mapping Techniques and Autonomous Feature Detection to Future Exploration of Europa

    NASA Astrophysics Data System (ADS)

    Bunte, M. K.; Tanaka, K. L.; Doggett, T.; Figueredo, P. H.; Lin, Y.; Greeley, R.; Saripalli, S.; Bell, J. F.

    2013-12-01

    Europa's extremely young surface age, evidence for extensive resurfacing, and indications of a sub-surface ocean elevate its astrobiological potential for habitable environments and make it a compelling focus for study. Knowledge of the global distribution and timing of Europan geologic units is a key step in understanding the history of the satellite and for identifying areas relevant for exploration. I have produced a 1:15M scale global geologic map of Europa which represents a proportionate distribution of four unit types and associated features: plains, linea, chaos, and crater materials. Mapping techniques differ somewhat from other planetary maps but do provide a method to establish stratigraphic markers and to illustrate the surface history through four periods of formation as a function of framework lineament cross-cutting relationships. Correlations of observed features on Europa with Earth analogs enforce a multi-process theory for formation rather than the typical reliance on the principle of parsimony. Lenticulae and microchaos are genetically similar and most likely form by diapirism. Platy and blocky chaos units, endmembers of archetypical chaos, are best explained by brine mobilization. Ridges account for the majority of lineaments and may form by a number of methods indicative of local conditions; most form by either tidal pumping or shear heating. The variety of morphologies exhibited by bands indicates that multiple formation mechanisms apply once fracturing of the brittle surface over a ductile subsurface is initiated. Mapping results support the interpretation that Europa's shell has thickened over time resulting in changes in the style and intensity of deformation. Mapping serves as an index for change detection and classification, aids in pre-encounter targeting, and supports the selection of potential landing sites. Highest priority target areas are those which indicate geophysical activity by the presence of volcanic plumes, outgassing, or disrupted surface morphologies. Areas of high interest include lineaments and chaos margins. The limitations on detecting activity at these locations are approximated by studying similar observed conditions on other bodies. By adapting machine learning and data mining techniques to signatures of plumes and morphology, I have demonstrated autonomous rule-based detection of known features using edge-detection and supervised classification methods. These methods successfully detect ≤94% of known volcanic plumes or jets at Io, Enceladus, and comets. They also allow recognition of multiple feature types. Applying these results to conditions expected for Europa enables a prediction of the potential for detection of similar features and enables recommendations for mission concepts to increase the science return and efficiency of future missions to observe Europa. This post-Galileo view of Europa provides a synthesis of the overall history of this unique icy satellite and will be a useful frame of reference for future exploration of the jovian system and other potentially active outer solar system bodies.

  7. GIAnT - Generic InSAR Analysis Toolbox

    NASA Astrophysics Data System (ADS)

    Agram, P.; Jolivet, R.; Riel, B. V.; Simons, M.; Doin, M.; Lasserre, C.; Hetland, E. A.

    2012-12-01

    We present a computing framework for studying the spatio-temporal evolution of ground deformation from interferometric synthetic aperture radar (InSAR) data. Several open-source tools including Repeat Orbit Interferometry PACkage (ROI-PAC) and InSAR Scientific Computing Environment (ISCE) from NASA-JPL, and Delft Object-oriented Repeat Interferometric Software (DORIS), have enabled scientists to generate individual interferograms from raw radar data with relative ease. Numerous computational techniques and algorithms that reduce phase information from multiple interferograms to a deformation time-series have been developed and verified over the past decade. However, the sharing and direct comparison of products from multiple processing approaches has been hindered by - 1) absence of simple standards for sharing of estimated time-series products, 2) use of proprietary software tools with license restrictions and 3) the closed source nature of the exact implementation of many of these algorithms. We have developed this computing framework to address all of the above issues. We attempt to take the first steps towards creating a community software repository for InSAR time-series analysis. To date, we have implemented the short baseline subset algorithm (SBAS), NSBAS and multi-scale interferometric time-series (MInTS) in this framework and the associated source code is included in the GIAnT distribution. A number of the associated routines have been optimized for performance and scalability with large data sets. Some of the new features in our processing framework are - 1) the use of daily solutions from continuous GPS stations to correct for orbit errors, 2) the use of meteorological data sets to estimate the tropospheric delay screen and 3) a data-driven bootstrapping approach to estimate the uncertainties associated with estimated time-series products. We are currently working on incorporating tidal load corrections for individual interferograms and propagation of noise covariance models through the processing chain for robust estimation of uncertainties in the deformation estimates. We will demonstrate the ease of use of our framework with results ranging from regional scale analysis around Long Valley, CA and Parkfield, CA to continental scale analysis in Western South America. We will also present preliminary results from a new time-series approach that simultaneously estimates deformation over the complete spatial domain at all time epochs on a distributed computing platform. GIAnT has been developed entirely using open source tools and uses Python as the underlying platform. We build on the extensive numerical (NumPy) and scientific (SciPy) computing Python libraries to develop an object-oriented, flexible and modular framework for time-series InSAR applications. The toolbox is currently configured to work with outputs from ROI-PAC, ISCE and DORIS, but can easily be extended to support products from other SAR/InSAR processors. The toolbox libraries include support for hierarchical data format (HDF5) memory mapped files, parallel processing with Python's multi-processing module and support for many convex optimization solvers like CSDP, CVXOPT etc. An extensive set of routines to deal with ASCII and XML files has also been included for controlling the processing parameters.

  8. Soil process modelling in CZO research: gains in data harmonisation and model validation

    NASA Astrophysics Data System (ADS)

    van Gaans, Pauline; Andrianaki, Maria; Kobierska, Florian; Kram, Pavel; Lamacova, Anna; Lair, Georg; Nikolaidis, Nikos; Duffy, Chris; Regelink, Inge; van Leeuwen, Jeroen P.; de Ruiter, Peter

    2014-05-01

    Various soil process models were applied to four European Critical Zone observatories (CZOs), the core research sites of the FP7 project SoilTrEC: the Damma glacier forefield (CH), a set of three forested catchments on geochemically contrasing bedrocks in the Slavkov Forest (CZ), a chronosequence of soils in the former floodplain of the Danube of Fuchsenbigl/Marchfeld (AT), and the Koiliaris catchments in the north-western part of Crete, (GR). The aim of the modelling exercises was to apply and test soil process models with data from the CZOs for calibration/validation, identify potential limits to the application scope of the models, interpret soil state and soil functions at key stages of the soil life cycle, represented by the four SoilTrEC CZOs, contribute towards harmonisation of data and data acquisition. The models identified as specifically relevant were: The Penn State Integrated Hydrologic Model (PIHM), a fully coupled, multiprocess, multi-scale hydrologic model, to get a better understanding of water flow and pathways, The Soil and Water Assessment Tool (SWAT), a deterministic, continuous time (daily time step) basin scale model, to evaluate the impact of soil management practices, The Rothamsted Carbon model (Roth-C) to simulate organic carbon turnover and the Carbon, Aggregation, and Structure Turnover (CAST) model to include the role of soil aggregates in carbon dynamics, The Ligand Charge Distribution (LCD) model, to understand the interaction between organic matter and oxide surfaces in soil aggregate formation, and The Terrestrial Ecology Model (TEM) to obtain insight into the link between foodweb structure and carbon and nutrient turnover. With some exceptions all models were applied to all four CZOs. The need for specific model input contributed largely to data harmonisation. The comparisons between the CZOs turned out to be of great value for understanding the strength and limitations of the models, as well as the differences in soil conditions between the CZOs. The CZO modelling led to further developments of the PIHM, with incorporation of functionality for karstic fracture flow (Koiliaris) and fracture flow anisotropy (Damma). The Damma case also provided experience on how to use results from geophysical investigations in model refinement. The SWAT modelling showed variability among the CZOs in hydraulic conductivity, the curve number that determines how fast rainfall results in runoff, and soil moisture capacity. Roth-C and CAST showed carbon sequestration fluxes to be low for old cultivated soils (Koiliaris) and high for new soils (Damma), where the latter site also had very high turnover rates. The LCD modelling, so far limited to the calcareous floodplain soils in Austria, explains differences in C-sequestration capacity between forest and agricultural soils from competition between phosphate and soil organic matter for adsorption sites on Fe-(hydr)oxides. The wide variety of soil (eco)system conditions challenged the TEM model and showed important directions for refinement: 1) differentiating between various fractions of organic matter and concomitant microbial decomposition pathways, and 2) the need to better define the physiological traits of the organisms in relation to local environmental conditions.

  9. Augmenting Parametric Optimal Ascent Trajectory Modeling with Graph Theory

    NASA Technical Reports Server (NTRS)

    Dees, Patrick D.; Zwack, Matthew R.; Edwards, Stephen; Steffens, Michael

    2016-01-01

    It has been well documented that decisions made in the early stages of Conceptual and Pre-Conceptual design commit up to 80% of total Life-Cycle Cost (LCC) while engineers know the least about the product they are designing [1]. Once within Preliminary and Detailed design however, making changes to the design becomes far more difficult to enact in both cost and schedule. Primarily this has been due to a lack of detailed data usually uncovered later during the Preliminary and Detailed design phases. In our current budget-constrained environment, making decisions within Conceptual and Pre-Conceptual design which minimize LCC while meeting requirements is paramount to a program's success. Within the arena of launch vehicle design, optimizing the ascent trajectory is critical for minimizing the costs present within such concerns as propellant, aerodynamic, aeroheating, and acceleration loads while meeting requirements such as payload delivered to a desired orbit. In order to optimize the vehicle design its constraints and requirements must be known, however as the design cycle proceeds it is all but inevitable that the conditions will change. Upon that change, the previously optimized trajectory may no longer be optimal, or meet design requirements. The current paradigm for adjusting to these updates is generating point solutions for every change in the design's requirements [2]. This can be a tedious, time-consuming task as changes in virtually any piece of a launch vehicle's design can have a disproportionately large effect on the ascent trajectory, as the solution space of the trajectory optimization problem is both non-linear and multimodal [3]. In addition, an industry standard tool, Program to Optimize Simulated Trajectories (POST), requires an expert analyst to produce simulated trajectories that are feasible and optimal [4]. In a previous publication the authors presented a method for combatting these challenges [5]. In order to bring more detailed information into Conceptual and Pre-Conceptual design, knowledge of the effects originating from changes to the vehicle must be calculated. In order to do this, a model capable of quantitatively describing any vehicle within the entire design space under consideration must be constructed. This model must be based upon analysis of acceptable fidelity, which in this work comes from POST. Design space interrogation can be achieved with surrogate modeling, a parametric, polynomial equation representing a tool. A surrogate model must be informed by data from the tool with enough points to represent the solution space for the chosen number of variables with an acceptable level of error. Therefore, Design Of Experiments (DOE) is used to select points within the design space to maximize information gained on the design space while minimizing number of data points required. To represent a design space with a non-trivial number of variable parameters the number of points required still represent an amount of work which would take an inordinate amount of time via the current paradigm of manual analysis, and so an automated method was developed. The best practices of expert trajectory analysts working within NASA Marshall's Advanced Concepts Office (ACO) were implemented within a tool called multiPOST. These practices include how to use the output data from a previous run of POST to inform the next, determining whether a trajectory solution is feasible from a real-world perspective, and how to handle program execution errors. The tool was then augmented with multiprocessing capability to enable analysis on multiple trajectories simultaneously, allowing throughput to scale with available computational resources. In this update to the previous work the authors discuss issues with the method and solutions.

  10. Assessment by regional modelling of the impact of monopile foundations on the hydrodynamics and sediment transport: case of Courseulles-sur-Mer (France) wind farm

    NASA Astrophysics Data System (ADS)

    Rivier, Aurélie; Bennis, Anne-Claire; Pinon, Grégory; Magar, Vanesa; Gross, Markus

    2015-04-01

    Offshore monopile foundations of wind turbines modify hydrodynamics and sediment transport at local scale and also at regional scale. The aim of this work is to assess these changes and to parametrize them in a regional model. These modifications were previously evaluated using the regional circulation model MARS3D (Lazure and Dumas, 2008) in tests-cases (Rivier et al., 2014) using two approaches: in the first approach, monopiles are explicitly modelled in the mesh as dry cells and in the second approach a sub-grid parametrization which considers the drag force exerted by a monopile on the flow is used. The sub-grid parametrization is improved close to the bed in this paper by adding a drag force term in the momentum equations, source terms in the turbulence model and by increasing the bed shear stress at monopile location. Changes in hydrodynamics regime, especially near-bed, affect sediment transport regime and modifications due to monopiles on sediment dynamics is also investigated using the MARS3D sediment transport module (Le Hir et al., 2011) which solves the advection-diffusion equations. Test-cases are run using hydrodynamical conditions and sediment grain sizes typical from the area located off Courseulles-sur-Mer (Normandy, France) where an offshore wind farm is planned to be built. Velocity, turbulent kinetic energy and bed thickness changes due to the monopile simulated by both approaches are compared to each other and to experimental measurements made in a flume at the University of Caen or to published data (e.g. Roulund et al., 2005; Dargahi,1989). Then the model is applied in a real configuration on an area including the future offshore wind farm of Courseulles-sur-Mer. Four monopiles are represented in the model using both approaches and modifications of the hydrodynamics and sediment transport are assessed along a tidal cycle. Currents increase at the side edge of the monopile and decrease in front of and downstream the monopile. Turbulent kinetic energy strongly increase as expected upstream the monopile. Resuspension and erosion occurs around the monopile in locations where current speeds increase due to the monopile presence and sediments deposit downstream where the bed shear stress is lower. The pattern of bed erosion is modified depending of current velocity. References Dargahi, B. 1989. The turbulent flow field around a circular cylinder. Experiments in Fluids, 8(1-2), 1-12. Lazure, P. and Dumas, F. (2008). external-internal mode coupling for a 3D hydrodynamical model for applications at regional scale (MARS). Advances in Water Resources 31(2), 233-250. Le Hir, P., Cayocca, F. and Waeles, B. (2011). Dynamics of sand and mud mixtures: a multiprocess-based modelling strategy. Continental Shelf Research 31(10), 135-149. Rivier, A., Bennis, A.-C., Pinon, G., Gross, M. and Magar, V. (2014). Regional numerical modelling of offshore monopile wind turbine impacts on hydrodynamics and sediment transport. Proceeding of the 1st International Conference on Renewable Energies Offshore, November 2014, Lisbonne, Portugal. Roulund, A., Sumer, B. M., Fredsøe, J., & Michelsen, J. 2005. Numerical and experimental investigation of flow and scour around a circular pile. Journal of Fluid Mechanics, 534, 351-401.

  11. Visualisation methods for large provenance collections in data-intensive collaborative platforms

    NASA Astrophysics Data System (ADS)

    Spinuso, Alessandro; Fligueira, Rosa; Atkinson, Malcolm; Gemuend, Andre

    2016-04-01

    This work investigates improving the methods of visually representing provenance information in the context of modern data-driven scientific research. It explores scenarios where data-intensive workflows systems are serving communities of researchers within collaborative environments, supporting the sharing of data and methods, and offering a variety of computation facilities, including HPC, HTC and Cloud. It focuses on the exploration of big-data visualization techniques aiming at producing comprehensive and interactive views on top of large and heterogeneous provenance data. The same approach is applicable to control-flow and data-flow workflows or to combinations of the two. This flexibility is achieved using the W3C-PROV recommendation as a reference model, especially its workflow oriented profiles such as D-PROV (Messier et al. 2013). Our implementation is based on the provenance records produced by the dispel4py data-intensive processing library (Filgueira et al. 2015). dispel4py is an open-source Python framework for describing abstract stream-based workflows for distributed data-intensive applications, developed during the VERCE project. dispel4py enables scientists to develop their scientific methods and applications on their laptop and then run them at scale on a wide range of e-Infrastructures (Cloud, Cluster, etc.) without making changes. Users can therefore focus on designing their workflows at an abstract level, describing actions, input and output streams, and how they are connected. The dispel4py system then maps these descriptions to the enactment platforms, such as MPI, Storm, multiprocessing. It provides a mechanism which allows users to determine the provenance information to be collected and to analyze it at runtime. For this work we consider alternative visualisation methods for provenance data, from infinite lists and localised interactive graphs, to radial-views. The latter technique has been positively explored in many fields, from text data visualisation to genomics and social networking analysis. Its adoption for provenance has been presented in literature (Borkin et al. 2013) in the context of parent-child relationships across processes, constructed from control-flow information. Computer graphics research has focused on the advantage of this radial distribution of interlinked information and on ways to improve the visual efficiency and tunability of such representations, like the Hierarchical Edge Bundles visualisation method, (Holten et al. 2006), which aims at reducing visual clutter of highly connected structures via the generation of bundles. Our approach explores the potential of the combination of these methods. It serves environments where the size of the provenance collection, coupled with the diversity of the infrastructures and the domain metadata, make the extrapolation of usage trends extremely challenging. Applications of such visualisation systems can engage groups of scientists, data providers and computational engineers, by serving visual snapshots that highlight relationships between an item and its connected processes. We will present examples of comprehensive views on the distribution of processing and data transfers during a workflow's execution in HPC, as well as cross workflows interactions and internal dynamics. The latter in the context of faceted searches on domain metadata values-range. These are obtained from the analysis of real provenance data generated by the processing of seismic traces performed through the VERCE platform.

  12. E2GPR - Edit your geometry, Execute GprMax2D and Plot the Results!

    NASA Astrophysics Data System (ADS)

    Pirrone, Daniele; Pajewski, Lara

    2015-04-01

    In order to predict correctly the Ground Penetrating Radar (GPR) response from a particular scenario, Maxwell's equations have to be solved, subject to the physical and geometrical properties of the considered problem and to its initial conditions. Several techniques have been developed in computational electromagnetics, for the solution of Maxwell's equations. These methods can be classified into two main categories: differential and integral equation solvers, which can be implemented in the time or spectral domain. All of the different methods present compromises between computational efficiency, stability, and the ability to model complex geometries. The Finite-Difference Time-Domain (FDTD) technique has several advantages over alternative approaches: it has inherent simplicity, efficiency and conditional stability; it is suitable to treat impulsive behavior of the electromagnetic field and can provide either ultra-wideband temporal waveforms or the sinusoidal steady-state response at any frequency within the excitation spectrum; it is accurate and highly versatile; and it has become a mature and well-researched technique. Moreover, the FDTD technique is suitable to be executed on parallel-processing CPU-based computers and to exploit the modern computer visualisation capabilities. GprMax [1] is a very well-known and largely validated FDTD software tool, implemented by A. Giannopoulos and available for free public download on www.gprmax.com, together with examples and a detailled user guide. The tool includes two electromagnetic wave simulators, GprMax2D and GprMax3D, for the full-wave simulation of two-dimensional and three-dimensional GPR models. In GprMax, everything can be done with the aid of simple commands that are used to define the model parameters and results to be calculated. These commands need to be entered in a simple ASCII text file. GprMax output files can be stored in ASCII or binary format. The software is provided with MATLAB functions, which can be employed to import synthetic data created by GprMax using the binary-format option into MATLAB, in order to be processed and/or visualized. Further MATLAB procedures for the visualization of GprMax synthetic data have been developed within the COST Action TU1208 [2] and are available for free public download on www.GPRadar.eu. The current version of GprMax3D is compiled with OpenMP, supporting multi-platform shared memory multiprocessing which allows GprMax3D to take advantage of multiple cores/CPUs. GprMax2D, instead, exploits a single core when executed. E2GPR is a new software tool, available free of charge for both academic and commercial use, conceived to: 1) assist in the creation, modification and analysis of GprMax2D models, through a Computer-Aided Design (CAD) system; 2) allow parallel and/or distributed computing with GprMax2D, on a network of computers; 3) automatically plot A-scans and B-scans generated by GprMax2D. The CAD and plotter parts of the tool are implemented in Java and can run on any Java Virtual Machine (JVM) regardless of computer architecture. The part of the tool devoted to supporting parallel and/or distributed computing, instead, requires the set up of a Web-Service (on a server emulator or server); in fact, it is currently configured only for Windows Server and Internet Information Services (IIS). In this work, E2GPR is presented and examples are provided which demonstrate its use. The tool can be currently obtained by contacting the authors. It will soon be possible to download it from www.GPRadar.eu. Acknowledgement This work is a contribution to the COST Action TU1208 'Civil Engineering Applications of Ground Penetrating Radar.' The authors thank COST for funding the Action TU1208. References [1] A. Giannopoulos, 'Modelling ground penetrating radar by GprMax,' Construction and Building Materials, vol. 19, pp. 755-762, 2005. [2] L. Pajewski, A. Benedetto, X. Dérobert, A. Giannopoulos, A. Loizos, G. Manacorda, M. Marciniak, C. Plati, G. Schettini, I. Trinks, "Applications of Ground Penetrating Radar in Civil Engineering - COST Action TU1208," Proc. 7th International Workshop on Advanced Ground Penetrating Radar (IWAGPR), 2-5 July 2013, Nantes, France, pp. 1-6.

  13. Resonant coherent excitation of hydrogen-like ions planar channeled in a crystal; Transition into the first excited state

    NASA Astrophysics Data System (ADS)

    Babaev, A.; Pivovarov, Yu. L.

    2012-03-01

    The presented program is designed to simulate the characteristics of resonant coherent excitation of hydrogen-like ions planar-channeled in a crystal. The program realizes the numerical algorithm to solve the Schrödinger equation for the ion-bound electron at a special resonance excitation condition. The calculated wave function of the bound electron defines probabilities for the ion to be in the either ground or first excited state, or to be ionized. Finally, in the outgoing beam the fractions of ions in the ground state, in the first excited state, and ionized by collisions with target electrons, are defined. The program code is written on C++ and is designed for multiprocessing systems (clusters). The output data are presented in the table. Program summaryProgram title: RCE_H-like_1 Catalogue identifier: AEKX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2813 No. of bytes in distributed program, including test data, etc.: 34 667 Distribution format: tar.gz Programming language: C++ (g++, icc compilers) Computer: Multiprocessor systems (clusters) Operating system: Any OS based on LINUX; program was tested under Novell SLES 10 Has the code been vectorized or parallelized?: Yes. Contains MPI directives RAM: <1 MB per processor Classification: 2.1, 2.6, 7.10 External routines: MPI library for GNU C++, Intel C++ compilers Nature of problem: When relativistic hydrogen-like ion moves in the crystal in the planar channeling regime, in the ion rest frame the time-periodic electric field acts on the bound electron. If the frequency of this field matches the transition frequency between electronic energy levels, the resonant coherent excitation can take place. Therefore, ions in the different states may be observed in the outgoing beam behind the crystal. To get the probabilities for the ion to be in the ground state or in the first excited state, or to be ionized, the Schrödinger equation is solved for the electron of ion. The numerical solving of the Schrödinger equation is carried out taking into account the fine structure of electronic energy levels, the Stark effect due to the influence of the crystal electric field on electronic energy levels and the ionization of ion due to the collisions with crystal electrons. Solution method: The wave function of the electron of ion is the superposition of the wave functions of stationary states with time-dependent coefficients. These stationary wave functions and corresponding energies are defined from the stationary Schrödinger equation. The equation is reduced to the problem of the eigen values and vectors of Hermitian matrix. The corresponding matrix equation is considered as the linear equation system. Then the time-dependent coefficients of the electron wave function are defined from the Schrödinger equation, with a time-periodic crystal field. The time-periodic field is responsible for the transitions between the stationary states. The final time-dependent Schrödinger equation represents the matrix equation which has been solved by means of the QR-algorithm. Restrictions: As expected the program gives the correct results for relativistic hydrogen-like ions with the kinetic energies up to 1 GeV/u and at the crystal thicknesses of 1-100 μm. The restrictions are: first, the program might give inadequate results, when the ion kinetic energy is too large (>10 GeV/u); second, the unaccounted physical factors may be significant at specific conditions. For example, the spontaneous emission by exited highly charged ions, as well as both energy and angular spread of the incident beam, could lead to additional broadening of the resonance. The medium polarization by the electric field of ion can influence the electronic energy levels of the ion in the non-relativistic case. The role of these factors was discussed in the references. Also, the large crystal thickness may require large computational time. Running time: In general, the running time depends on the number of processors. In our tests we used the crystal thickness up to 100 μm and the number of 2.66 GHz processors was up to 100. The running time was about 1 hour in these conditions.

  14. OpenMP GNU and Intel Fortran programs for solving the time-dependent Gross-Pitaevskii equation

    NASA Astrophysics Data System (ADS)

    Young-S., Luis E.; Muruganandam, Paulsamy; Adhikari, Sadhan K.; Lončar, Vladimir; Vudragović, Dušan; Balaž, Antun

    2017-11-01

    We present Open Multi-Processing (OpenMP) version of Fortran 90 programs for solving the Gross-Pitaevskii (GP) equation for a Bose-Einstein condensate in one, two, and three spatial dimensions, optimized for use with GNU and Intel compilers. We use the split-step Crank-Nicolson algorithm for imaginary- and real-time propagation, which enables efficient calculation of stationary and non-stationary solutions, respectively. The present OpenMP programs are designed for computers with multi-core processors and optimized for compiling with both commercially-licensed Intel Fortran and popular free open-source GNU Fortran compiler. The programs are easy to use and are elaborated with helpful comments for the users. All input parameters are listed at the beginning of each program. Different output files provide physical quantities such as energy, chemical potential, root-mean-square sizes, densities, etc. We also present speedup test results for new versions of the programs. Program files doi:http://dx.doi.org/10.17632/y8zk3jgn84.2 Licensing provisions: Apache License 2.0 Programming language: OpenMP GNU and Intel Fortran 90. Computer: Any multi-core personal computer or workstation with the appropriate OpenMP-capable Fortran compiler installed. Number of processors used: All available CPU cores on the executing computer. Journal reference of previous version: Comput. Phys. Commun. 180 (2009) 1888; ibid.204 (2016) 209. Does the new version supersede the previous version?: Not completely. It does supersede previous Fortran programs from both references above, but not OpenMP C programs from Comput. Phys. Commun. 204 (2016) 209. Nature of problem: The present Open Multi-Processing (OpenMP) Fortran programs, optimized for use with commercially-licensed Intel Fortran and free open-source GNU Fortran compilers, solve the time-dependent nonlinear partial differential (GP) equation for a trapped Bose-Einstein condensate in one (1d), two (2d), and three (3d) spatial dimensions for six different trap symmetries: axially and radially symmetric traps in 3d, circularly symmetric traps in 2d, fully isotropic (spherically symmetric) and fully anisotropic traps in 2d and 3d, as well as 1d traps, where no spatial symmetry is considered. Solution method: We employ the split-step Crank-Nicolson algorithm to discretize the time-dependent GP equation in space and time. The discretized equation is then solved by imaginary- or real-time propagation, employing adequately small space and time steps, to yield the solution of stationary and non-stationary problems, respectively. Reasons for the new version: Previously published Fortran programs [1,2] have now become popular tools [3] for solving the GP equation. These programs have been translated to the C programming language [4] and later extended to the more complex scenario of dipolar atoms [5]. Now virtually all computers have multi-core processors and some have motherboards with more than one physical computer processing unit (CPU), which may increase the number of available CPU cores on a single computer to several tens. The C programs have been adopted to be very fast on such multi-core modern computers using general-purpose graphic processing units (GPGPU) with Nvidia CUDA and computer clusters using Message Passing Interface (MPI) [6]. Nevertheless, previously developed Fortran programs are also commonly used for scientific computation and most of them use a single CPU core at a time in modern multi-core laptops, desktops, and workstations. Unless the Fortran programs are made aware and capable of making efficient use of the available CPU cores, the solution of even a realistic dynamical 1d problem, not to mention the more complicated 2d and 3d problems, could be time consuming using the Fortran programs. Previously, we published auto-parallel Fortran programs [2] suitable for Intel (but not GNU) compiler for solving the GP equation. Hence, a need for the full OpenMP version of the Fortran programs to reduce the execution time cannot be overemphasized. To address this issue, we provide here such OpenMP Fortran programs, optimized for both Intel and GNU Fortran compilers and capable of using all available CPU cores, which can significantly reduce the execution time. Summary of revisions: Previous Fortran programs [1] for solving the time-dependent GP equation in 1d, 2d, and 3d with different trap symmetries have been parallelized using the OpenMP interface to reduce the execution time on multi-core processors. There are six different trap symmetries considered, resulting in six programs for imaginary-time propagation and six for real-time propagation, totaling to 12 programs included in BEC-GP-OMP-FOR software package. All input data (number of atoms, scattering length, harmonic oscillator trap length, trap anisotropy, etc.) are conveniently placed at the beginning of each program, as before [2]. Present programs introduce a new input parameter, which is designated by Number_of_Threads and defines the number of CPU cores of the processor to be used in the calculation. If one sets the value 0 for this parameter, all available CPU cores will be used. For the most efficient calculation it is advisable to leave one CPU core unused for the background system's jobs. For example, on a machine with 20 CPU cores such that we used for testing, it is advisable to use up to 19 CPU cores. However, the total number of used CPU cores can be divided into more than one job. For instance, one can run three simulations simultaneously using 10, 4, and 5 CPU cores, respectively, thus totaling to 19 used CPU cores on a 20-core computer. The Fortran source programs are located in the directory src, and can be compiled by the make command using the makefile in the root directory BEC-GP-OMP-FOR of the software package. The examples of produced output files can be found in the directory output, although some large density files are omitted, to save space. The programs calculate the values of actually used dimensionless nonlinearities from the physical input parameters, where the input parameters correspond to the identical nonlinearity values as in the previously published programs [1], so that the output files of the old and new programs can be directly compared. The output files are conveniently named such that their contents can be easily identified, following the naming convention introduced in Ref. [2]. For example, a file named -out.txt, where is a name of the individual program, represents the general output file containing input data, time and space steps, nonlinearity, energy and chemical potential, and was named fort.7 in the old Fortran version of programs [1]. A file named -den.txt is the output file with the condensate density, which had the names fort.3 and fort.4 in the old Fortran version [1] for imaginary- and real-time propagation programs, respectively. Other possible density outputs, such as the initial density, are commented out in the programs to have a simpler set of output files, but users can uncomment and re-enable them, if needed. In addition, there are output files for reduced (integrated) 1d and 2d densities for different programs. In the real-time programs there is also an output file reporting the dynamics of evolution of root-mean-square sizes after a perturbation is introduced. The supplied real-time programs solve the stationary GP equation, and then calculate the dynamics. As the imaginary-time programs are more accurate than the real-time programs for the solution of a stationary problem, one can first solve the stationary problem using the imaginary-time programs, adapt the real-time programs to read the pre-calculated wave function and then study the dynamics. In that case the parameter NSTP in the real-time programs should be set to zero and the space mesh and nonlinearity parameters should be identical in both programs. The reader is advised to consult our previous publication where a complete description of the output files is given [2]. A readme.txt file, included in the root directory, explains the procedure to compile and run the programs. We tested our programs on a workstation with two 10-core Intel Xeon E5-2650 v3 CPUs. The parameters used for testing are given in sample input files, provided in the corresponding directory together with the programs. In Table 1 we present wall-clock execution times for runs on 1, 6, and 19 CPU cores for programs compiled using Intel and GNU Fortran compilers. The corresponding columns "Intel speedup" and "GNU speedup" give the ratio of wall-clock execution times of runs on 1 and 19 CPU cores, and denote the actual measured speedup for 19 CPU cores. In all cases and for all numbers of CPU cores, although the GNU Fortran compiler gives excellent results, the Intel Fortran compiler turns out to be slightly faster. Note that during these tests we always ran only a single simulation on a workstation at a time, to avoid any possible interference issues. Therefore, the obtained wall-clock times are more reliable than the ones that could be measured with two or more jobs running simultaneously. We also studied the speedup of the programs as a function of the number of CPU cores used. The performance of the Intel and GNU Fortran compilers is illustrated in Fig. 1, where we plot the speedup and actual wall-clock times as functions of the number of CPU cores for 2d and 3d programs. We see that the speedup increases monotonically with the number of CPU cores in all cases and has large values (between 10 and 14 for 3d programs) for the maximal number of cores. This fully justifies the development of OpenMP programs, which enable much faster and more efficient solving of the GP equation. However, a slow saturation in the speedup with the further increase in the number of CPU cores is observed in all cases, as expected. The speedup tends to increase for programs in higher dimensions, as they become more complex and have to process more data. This is why the speedups of the supplied 2d and 3d programs are larger than those of 1d programs. Also, for a single program the speedup increases with the size of the spatial grid, i.e., with the number of spatial discretization points, since this increases the amount of calculations performed by the program. To demonstrate this, we tested the supplied real2d-th program and varied the number of spatial discretization points NX=NY from 20 to 1000. The measured speedup obtained when running this program on 19 CPU cores as a function of the number of discretization points is shown in Fig. 2. The speedup first increases rapidly with the number of discretization points and eventually saturates. Additional comments: Example inputs provided with the programs take less than 30 minutes to run on a workstation with two Intel Xeon E5-2650 v3 processors (2 QPI links, 10 CPU cores, 25 MB cache, 2.3 GHz).

  15. INTRODUCTION Summary of Papers Summary of Papers

    NASA Astrophysics Data System (ADS)

    Gauthier, Serge; Abarzhi, Snezhana I.; Sreenivasan, Katepalli R.

    2010-12-01

    Turbulent mixing is the generic name for processes by which two initially distinct fluids tend towards a homogeneous substance under the action of a vigorous stirring agent. The fluids may be miscible or immiscible, their molecular diffusivities may be comparable or disparate, they may be in single phase or multiphase, and may be contained in simple or complex geometries. Moreover, the thermodynamic and fluid dynamic conditions may be different: incompressible or compressible, low or high speeds, with the dominant stirring mechanism arising from buoyancy, shear or inertial effects. Each of these circumstances has its physical characteristics and requires specific mathematical tools of investigation, but there are also some generic features. Turbulent mixing is an intellectually challenging problem in terms of the underlying physics as well as the tools needed to describe, simulate and predict it. The understanding of turbulent mixing is important since it occurs in numerous and diverse circumstances, involving elementary and idealized flows, on the one hand, and a variety of complex flows in technological applications, on the other. Mixing occurs in many contexts such as inertial confinement, magnetic fusion and non-equilibrium heat transport, material transformation under the action of high strain rates, strong shocks, explosions, blast waves, supernovae and accretion disks, stellar non-Boussinesq and magneto-convection, planetary interiors in astrophysics, mantle-lithosphere tectonics, volcanic eruptions, atmospheric and oceanographic flows in geophysics, premixed and non-premixed combustion, unsteady boundary layers, pollution transport in urban areas, as well as hypersonic and supersonic flows in aerodynamics. A deep understanding of turbulent mixing requires one to go above and beyond studies of canonical turbulence, and include walls, non-equilibrium situations, interfaces, strong and isolated vortices, combustion, and so forth. In this article we briefly review various aspects of Turbulent Mixing that were discussed at the Second International Conference and Advanced School 'Turbulent Mixing and Beyond', TMB-2009, held in summer 2009 at the Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy. The papers are arranged by TMB themes and within each theme they are ordered alphabetically by the last name of the first author, with tutorials following research contributions. Canonical turbulence and turbulent mixing. The theme of canonical turbulence and turbulent mixing is considered by several authors. Casciola et al investigate the dynamics of inertial particles dispersed in a turbulent jet and compare their numerical modeling results with the classical similarity theory of the jet far-field. Remarkable agreement is found between the theory and the direct numerical simulations (DNS), including decay of Stokes numbers with the distance from the origin, self-similarity of the mean axial particle velocity profile, etc. Nagata considers complex turbulent flows, which are known to exhibit no linear critical point for the laminar states, and which are linearly stable at finite Reynolds numbers. Square duct flow and sliding Couette flow in an annulus are considered and nonlinear traveling-wave states are found for the flows with the use of the homotopy approach developed by the author. These states may constitute a skeleton around which a time-dependent trajectory in the phase space is organized. Teitelbaum and Mininni study a decaying 3D incompressible turbulence, which mimicks turbulent mixing in geophysical flows, with rotation rendering the flow anisotropic at large scales. The authors analyze three DNS results (without and with rotation, and with helicity), observe a decoupling of the modes normal to the rotation axis, and show that the helicity decreases the decay rate of turbulence. Wang and Peters investigate the structure of turbulence by studying strain rates of various scalars, including a passive scalar, a velocity component, turbulent kinetic energy and dissipation rate. The analyses of the DNS data for homogeneous shear flows show that statistically the gradient vectors with large magnitudes align with each other, while gradients with small magnitudes tend to be randomly organized. Zybin et al study turbulence structure through a model of vortex filament. In this way, they show that contraction and stretching out of a filament provide an energy flux from larger to smaller scales. The authors obtain the scaling exponents for both Lagrangian and transverse Eulerian structure functions and report good agreement with the existing data. Wall-bounded flows. Six papers are focused on the theme of wall-bounded flows. Cassel and Obabko perform numerical simulations of the two-dimensional flow induced by a thick-core vortex. This problem is important for studies of unsteady separation in the vortex-induced flows. Their accurate investigations convicingly justify that the Rayleigh instability does exist at large Reynolds numbers. Cvitanović and Gibson study the effects of geometry on transitional turbulent flow and focus on wall-bounded shear flows at moderate Reynolds numbers. The authors determine a set of unstable periodic orbits from close recurrences of the turbulent flow, identify a few equilibria that resemble frequently observed but unstable coherent structures, and construct a low-dimensional state-space projection from the extremely high-dimensional data sets. The approach developed by the authors can be a useful tool for understanding massive data sets. Seidel et al focus on developing feedback flow control strategies, i.e., they attempt to achieve a desired flow state for the turbulent shear layer behind a backward facing step. The authors show that the Proper Orthogonal Decomposition (POD) of the density field is a better marker than that for the velocity field, as in the former case the contribution of small scale structures is effectively eliminated. Tuğluk and Tarman use solenoidal bases to numerically solve incompressible fluid flow problems. Within this approach the solution remains strictly solenoidal throughout the solution domain. The approach effectively eliminates possible errors which can be induced by the continuity equation. Voropayev and Zagumennyi investigate the receptivity of a laminar boundary layer over an actively deforming surface by means of the stability analysis and the DNS. The study is focused on tracking the energy transport between turbulent fluctuations of the velocity components as well as the energy transfer from the mean flow to fluctuations, and vice versa. Ziaei-Rad presents a parallel finite-volume/finite-element method for compressible turbulent flows with a modified k - epsilon turbulent model. Some test cases (open flow and a transient flow generated after an accidental rupture in a pipeline) show the efficiency of the method. Non-equilibrium processes. A number of papers considers non-equilibrium turbulent processes. Abarzhi and Rosner perform a comparative study of modeling approaches of Rayleigh-Taylor turbulent mixing. The authors consider similarities and differences in governing mechanisms and basic properties of turbulent mixing, as discussed in recent theoretical and heuristic modeling studies, and briefly outline how these mechanisms and properties may be explored in experiments and simulations. Grinstein presents numerical simulations of turbulent velocity fields based on subgrid modeling implicitly provided by a class of high-resolution finite-volume algorithms. The approach is successfully applied to the problem of turbulent mixing. Lim et al present a study of the verification and validation of front tracking numerical simulations on two experiments on turbulent mixing. The experiments include the quasi-immiscible case at a very large Schmidt number and the case of miscible fluids. The simulations successfully reproduce results of both experiments and find that the dominant short wavelength of the initial perturbations may significantly influence the mixing process. Livescu et al provide an overview of the variable density effects in buoyancy-driven turbulence at low to moderate Atwood numbers within a single-fluid approximation. The two cases considered are the classical Rayleigh-Taylor (RT) case and an idealized triply periodic RT-flow, between which several important differences are found. Among them, there is a mixing asymmetry in variable density flows and an anomalous small-scale anisotropy. Nevmerzhitsky et al report new experimental results obtained at the experimental facilities at the VNIIEF (Sarov, Russia). In particular, the authors investigate turbulent mixing induced by the Richtmyer-Meshkov (RM) instability in gases with weak and strong shock waves. They obtain accurate quantitative results which can be used as benchmarks for theoretical analysis and the validation of numerical codes. Scagliarini et al present results from numerical simulations of RT-type turbulence, performed with the use of the lattice Boltzmann method, which is able to describe consistently a thermal compressible flow subject to an external forcing. The authors show that the presence of the adiabatic gradient terminates the mixing process, in agreement with results of theoretical analysis and other computational approaches. Interfacial dynamics. Four papers are focused on the dynamics of interfaces and hydrodynamic instabilities. Bazarov et al report an experimental study of the dynamics of a gas bubble rising in a water channel. The experiments are designed to accurately analyze the effects induced by the joint action and development of gravitational and shear instability in a two-dimensional flow. It is shown that initial short-wavelength perturbations on the dome of a rising bubble quickly decay. This decay is not attributed to dissipative mechanisms, such as viscosity or surface tension, but is rather a manifestation of a hydrodynamic consequence of the so-called sub-harmonic instability. Igonin et al study the perturbation growth at a free surface of condensed matter with deterministic initial perturbations under the effect of a shock wave, which induces the RM instability. Two- and three-dimensional initial perturbations at the surface are imposed, and pulsed radiography and a two-piston shock tube technique are applied for experimental diagnostics. The authors quantify the dependency of the linear growth-rate on shock strength and geometry of the perturbation, show that the growth of the perturbations strongly depends on material compression in the shock tube, and find that 3D perturbations grow faster than 2D perturbations in the nonlinear regime of RMI. Matsuoka uses analytical and numerical methods to investigate the RT and RM instabilities in the incompressible limit. The author considers the interfacial dynamics in planar geometry and accounts for the effect of surface tension. Under certain conditions in the parameter regime, a mode-mode interaction leads to a 'resonance' type of behavior in the interfacial dynamics, and this resonant motion is studied in detail. Nevmerzhitsky et al report new experimental results on turbulent mixing induced by the RT instability at the gas-liquid interface. The width of the mixing zone spans a substantial dynamic range, thus allowing for accurate quantification of the mixing growth-rate. The authors find that the prefactor in the gt2 scaling law varies with time and depends on the Reynolds number in the range Re~104-106. Some interesting features of the front dynamics are observed, including front pulsation and formation of secondary structures. High energy density physics. The theme of high energy density physics is of special interest to the TMB community. Huete Ruiz de Lira investigates the classical problem of turbulence generation by a shock wave interacting with a random density inhomogeneity field, and proposes an exact small-amplitude linear theory to describe such interaction. The analysis is applied to study time-space evolution of the perturbed quantities behind a corrugated shock front, and yields the closed-form exact analytical expressions for the turbulent kinetic energy, degree of anisotropy of velocity and vorticity fields in the compressed fluid, shock amplification of the density non-uniformity, and the sonic energy flux radiated downstream. Ktitorov obtains self-similar solution of isentropic compression of a gas in convergent geometry. The stability of shell motion is considered by means of two-dimensional numerical simulations. The perturbation amplitude growth is given for both plane and cylindrical geometries. Lebo and Lebo apply a model of energy transport in turbulent sub-critical laser plasmas of porous targets. This model is proposed for studying powerful laser pulse interaction with a low-density porous target. The interaction is strongly inhomogeneous and turbulent. Material science. Three papers consider the materials aspect of turbulent mixing. Aprelkov et al investigate the RM instability development on the free surface of a metal (lead). The disturbances are regular grooves of a triangular cross-section and a pulsed radiography method is used to visualize the interface after the passage of a strong shock. Numerical computations are in good agreement with experiments. Demianov et al make an attempt to describe RT instability in solid state by the volume-of-fluid numerical method, and their hydrodynamic simulation are based on the Bingham rheological model to include plastic effects. Desai et al report the possibility of laser generated craters to investigate planetary events such as meteorite impact craters. Experiments are performed using a laser beam on aluminum foil targets and results are well explained by two-dimensional hydrodynamic numerical simulations including radiation. Astrophysics. Astrophysical problems are considered in the following papers. Brandenburg et al study the transport in hydromagnetic turbulence and dynamos and examine the predictive power of a mean-field theory by comparing its outcome with simulations under controlled conditions. A recently developed test-field method is used to extract turbulent transport coefficients in kinematic and quasi-kinematic cases. The latter is illustrated by magnetic buoyancy-driven flows. Chernyshov et al provide a survey of various subgrid models for strong compressible magneto-hydrodynamic (MHD) turbulence and perform the large eddy simulation (LES) of weakly compressible turbulence in a local interstellar medium. They observe that density fluctuations exhibit a Kolmogorov-like spectrum over a range of scales with a spectral index close to -5/3, presumably because the density fluctuations behave like a passive scalar. Gibson deals with turbulence and turbulent mixing in natural fluids, i.e., fluids in the Universe. He claims that many recent observations show that the standard cosmological model must be strongly modified to take basic fluid mechanics into account. Ustyugov carries out three-dimensional numerical simulations of solar magneto-convection using a realistic physical model (fully compressible radiation MHD equations, dynamical viscosity, equation of state and opacities of stellar matter) and provides a detailed discussion of the results. Magneto-hydrodynamics. The following four contributions consider the problems of magnetic field line reconnection and turbulence in magnetized plasmas. Gekelman et al study experimentally the reconnection of magnetic field lines in plasma current systems. The authors present experimental results on undriven reconnection, which occurs when two magnetic flux ropes are generated from initially adjacent pulsed current channels in a background magnetoplasma. They also present 3D magnetic fields and currents associated with the colliding laser produced plasmas. The reconnection regions (which are three-dimensional) are directly observed in the experiments. The authors argue that reconnection is not an independent topic but is part of a variety of phenomena associated with the much broader subject of 3D current systems in plasmas. Malyshkin presents a two-fluid magneto-hydrodynamic (MHD) model of quasi-stationary, two-dimensional, magnetic reconnection in an incompressible plasma composed of electrons and ions. The author finds two distinct regimes of slow and fast reconnection, which may serve to explain the initial slow build up and subsequent rapid release of magnetic energy frequently observed in cosmic and laboratory plasmas. Malyshkin and Kulsrud present two theoretical approaches for the calculation of the rate of quasi-stationary, two-dimensional magnetic reconnection with nonuniform anomalous resistivity within the framework of incompressible MHD. These MHD equations are solved for the entire reconnection layer and across the reconnection layer. The approaches give the same approximate answer for the reconnection rate and agree with some recent simulations. Krommes reviews the state-of-the-art in the field of nonlinear gyrokinetics, which is a description of low-frequency dynamics in magnetized plasmas, providing the fundamental basis for numerical simulations of micro-turbulence in magnetic-confinement fusion and astrophysical applications. The author sketches the derivation of the novel dynamical system comprising the nonlinear gyrokinetic equation and the coupled electrostatic gyrokinetic Poisson equation with the use of modern perturbative approaches. This tutorial is accessible to a broad audience and allows the reader to fully appreciate the gyro-kinetic equation as a powerful theoretical tool for studies of turbulence in magnetized plasmas. Canonical plasmas. Several contributions are devoted to experiments and observations on canonical plasmas, including hydrodynamics of discharges and ionosphere. Bagautdinova et al study the influence of the RT instability and turbulent plasma-electrolyte mixing on multichannel discharges in various experimental conditions of particular interest. Their experiments were carried out at atmospheric pressure. They conclude that the process of development of turbulent mixing instability is significantly influenced by discharge current value, the composition and concentration of the electrolyte, a well as the immersion depth of the electrode. Baryshnikov et al investigate the shock wave instabilities in glow discharge, which play an important role in applications as they may lead to a significant reduction of aerodynamic drag. The authors conduct experiments in which a shock wave enters the region of positive glow-discharge column with a lowered density of gas, and study the RM instability developing at the interface between the two media. The authors consider the effects of the shock strength, plasma decay, humidity and the dustiness of air, and show that humidity and small degree of the dustiness have little influence on the evolution of the instability. Kayumov et al have developed an experimental device to investigate the stability of the discharge plasma between a droplet cathode and electrolytes and the induced turbulent mixing of the electrolytes. Physical properties of the plasma discharges and their characterization in the atmospheric and lower pressure regimes is an "unexplored" research area. The authors perform a systematic experimental study spanning a broad parameter regime, of the influence of multi-channel discharge plasma on the creation of plasma swirls and on turbulent mixing, which develops on the boundary between the droplet cathode and electrolyte anode. Son and Tereshonok present a theoretical study of the thermal and plasma effect from discharge influence on air flow. The electron energy distribution function has been found numerically, using the parallel package Gas Dynamics Tool and solving the Boltzmann equation in the two-term approximation. These theoretical studies provide a better understanding of the experimental results described earlier. Cohen et al report an investigation of ionospheric ducts having the shape of large plasma sheets, generated by the vertically transmitted High Frequency Active Auroral Research Program (HFAARP) heater waves in several experiments conducted in Gakona (Alaska). Depending on the polarizations of the heater waves, these large-scale ionospheric plasma structures have different configurations. The authors study in detail the effect of the plasma sheets on the ionosonde signals in the presence of distant plasma blobs, and report good agreement between their theoretical studies and field experiments. Physics of atmosphere. Three manuscripts are devoted to turbulence and turbulent mixing in the atmosphere. Mukund et al deal with the interaction between turbulence and radiative processes within the nocturnal atmospheric boundary layer. They propose a flux-emissivity formulation that eliminates the near-ground anomalous cooling ('Ramdas paradox'). O'Kane and Frederiksen apply a statistical dynamical closure theory of turbulence to the problem of data assimilation in strongly nonlinear settings. Data assimilation aims to obtain a near-optimal estimate of the state of the atmosphere, based on observations and short term forecasts, and to provide the so-called background states with information in the data-void areas. Sofieva et al recall that the main source of turbulence in the stratosphere is the breaking of gravity waves which leads to effective turbulent mixing of the atmosphere. The authors propose the new methodology for reconstructing gravity waves and turbulence spectra parameters from scintillation satellite measurements, and discuss the results of their unique state-of-the-art observations. Geophysics and Earth science. One paper details geophysics and Earth science. To study geophysical phenomena in the laboratory, Cotel performs mixing experiments by impinging a turbulent jet across a stratified interface. The author distinguishes between entrainment and mixing, and suggests that entrainment can be characterized by a new parameter called 'persistence' to allow a proper interpretation of the experiments. Combustion. The following papers are devoted to combustion and mixing in the turbulent regime. Chorny et al verify the potentialities of the Reynolds averaged Navier-Stokes approach to model incompressible turbulent mixing at large Schmidt numbers in a co-axial mixer. Two different mixing regime modes can be observed, with and without a recirculation zone developing just behind the tube. Hicks and Rosner compare the evolution of a burning interface between denser fuel and less dense ashes to the evolution of a non-burning interface, in the presence of gravity. The developments of the subsequent 2D turbulent flows are compared. Meshram investigates the mixing of chemical elements of the type A + B → C by using the two-point closure method. The equations describing the turbulence under study are written in terms of two-point correlation functions and two-point triple correlation functions. Various length scales involved can be evaluated by integrating these equations. Zhang et al study the importance of scalar dissipation rate on the quenching of the steady laminar flamelet model at different stoichiometric ratios in a one-step reversible reaction with Arrhenius rate. The difference between the mixing and quenched states is investigated. Mathematical aspects of non-equilibrium flows. Dynamics of turbulent flows is an intellectually rich problem, and four contributions analyze the mathematical aspects. Fukumoto et al study the stability of a vortex tube embedded in a strain flow (the Moore-Saffman-Tsai-Widnall instability). The Lagrangian approach of the weakly nonlinear analysis is developed. It is shown that this approach facilitates the calculation of the wave-induced mean flow and allows one to study the evolution of three-dimensional disturbances. Goldobin studies the transport of a pollutant in a fluid layer by spatially localized two-dimensional thermo-convective currents appearing under frozen parametric disorder in the presence of an imposed longitudinal advection. The author employs the eddy diffusivity approach and shows that the effective diffusivity can be several orders of magnitude larger than that in the absence of advection. Troshkin exhibits a new exact solution of the Navier-Stokes equations for a rotating gas tube. This solution improves the well-known rigid-body rotation with a constant temperature, and applies to the centrifugation of a gas mixture. Zakharov presents theoretical results about the self-consistent analytical theory for wind-driven sea. He offers answers to some outstanding questions of great importance for the development of self-consistent analytical theory for wind-driven sea, without which experiments and theory cannot make useful contact. Stochastic processes and probabilistic description. The following papers are devoted to stochastic processes, probabilistic description and data analysis aspects of turbulent mixing and beyond. Kim et al present a statistical theory of self-organization of shear flows, modeled by a nonlinear diffusion equation with a stochastic forcing. A non-perturbative method based on a coherent structure is utilized for the prediction of the probability distribution functions. The results are confirmed by numerical simulations. Klimenko introduces non-conservative and competitive mixing within the framework of stochastic simulations where particles move with a fluid flow and are engaged in a random-walk. Traditional mixing is conservative (i.e., the total amount of scalar is preserved during mixing) while, in non-conservative mixing, the post-mixing average of the particles becomes biased towards those participating in mixing. Vesper and Khokhlov remark that many physical objects have a dynamical scale and cannot be numerically simulated with a fixed computational grid. They suggest the use of a proportional-integral-derivative to automatically control the expansion or contraction of the computational grid. The example of the rarefaction wave is discussed. Advanced numerical simulations. Several works are devoted to numerical methods and their applications in TMB-related problems. Belotserkovskaya and Konyukhov carry out three-dimensional numerical simulations of branching patterns that occur when a less viscous fluid filtrates through a porous medium saturated by a more viscous one. They use a finite-volume weighted essentially non-oscillatory scheme (WENO). Belotserkovskii presents a review of numerical modeling studies performed under his leadership at the Institute for Computer Aided Design of the Russian Academy of Sciences. This work describes effective parallel algorithms for the solution of complex problems governed by nonlinear partial differential equations. The algorithms allow a dramatic reduction of the computational time and effective use of the multiprocessing computing resources. Examples from fluid dynamics (RT, RM and Kelvin-Helmholtz instabilities, as well as transitional and turbulent flows) and from medicine (modeling of circulatory and respiratory systems of human organism, and of cranial trauma) are displayed. Fortova studies the initial stage of the onset of turbulence in three-dimensional free shear flows of an ideal compressible gas. It turns out that the birth of turbulence is connected with large vortex structures. Griffond et al build a statistical numerical model of fully developed turbulence in compressible flows. The authors develop a Reynolds stress model that matches shock-turbulence interactions to the predictions of the linear interaction analysis, which, 'à la Ribner', relies on Kovasznay's decomposition and allows for the computation of the waves transmitted or produced at the shock front. The authors demonstrate close agreement between the linear interaction analysis and the Reynolds stress model for any shock strength. Jayakumar et al developed a hybrid (structured/unstructured) finite-volume method capable of handling turbulent flows and conjugate heat transfer. A two-equation turbulence model is implemented and the backward-facing step flow is simulated and studied, since this configuration plays an important role in the design of heating or cooling equipment. Jin et al make an assessment of the LES capability in capturing preferential concentration of heavy particles in isotropic turbulent flows. In such flows, heavy particles tend to accumulate preferentially in regions of high strain rate and low vorticity due to the inertial bias. The authors call for new subgrid-scale models including particle-flow interactions. Lim et al combine a front tracking method with a dynamic subgrid-scale model to compensate the unresolved scales in LES methods. As a result, the authors observe a converging trend for the micro observables for the reshocked RM turbulent mixing flow. They compare their results to a simple model based on 1D diffusion that takes place in the geometry that is defined statistically by the interface between the two fluids. Liu carries out a numerical study of the turbulent mixing in a convergent shock tube, induced by the RM instability. The author characterizes the turbulent mixing flow by a number of quantities and mimics in the simulations the presence of macroscopic perturbations by imposing at the interface some artificial perturbations. He observes that these disturbances influence the mixing flow characteristics significantly. Reckinger et al present an extension of the adaptive wavelet collocation method to simulations of the RT instability. Such a method seems to be promising due to the localized nature of this instability. Numerical tests show that the method successfully captures the characteristics of a weakly compressible single-mode perturbation. Suzuki et al investigate turbulent mixing in regular as well as fractal grid turbulence by means of DNS, and relate to experiments performed in a water channel (see below). Turbulent mixing is enhanced in the fractal grid, especially at large times. They point out the usefulness of employing fractal grids in high-performance mixers. Grinstein et al present a tutorial on implicit large-eddy-simulations methods, i.e., numerical simulations of turbulent velocity fields based on subgrid modeling implicitly provided by a class of high-resolution, finite-volume algorithms. Experimental diagnostics. A substantial part of modern discoveries is provided by state-of-the-art experimental capabilities. The four contributions below are devoted to the methods of experimental design and diagnostics. Haehn et al present experiments performed at the Wisconsin Shock Tube Laboratory, which study the behavior of a twice-shocked spherical density inhomogeneity. High speed cameras are used to observe the development of the vortex ring after reshock. Nevmerzhitsky et al report experiments performed at the Federal Nuclear Center (VNIIEF) in Sarov, Russia, on a dispersion of liquid drop under the effect of an air shock wave. This shock wave is created through the explosion of C2H2+2.5O2 mixture in a shock tube. The drop liquid is tributyl phosphate, and the flow is recorded by high-speed filming. The experimental results have remarkable accuracy and precision, and their high quality allows for the direct comparison with the results of theoretical and numerical models. Suzuki et al perform experiments on high Schmidt number scalar transfer in regular and fractal grid turbulence. The time-series particle image velocimetry and the planar laser induced fluorescence technique are used to measure the velocity and concentration fields. The authors show that turbulent mixing for the fractal grid turbulence is strongly enhanced compared to that for a regular grid turbulence. Niemela considers turbulent flows produced with the use of gaseous 4He as a working fluid. His tutorial highlights some of the motivations, advantages and disadvantages of this experimental approach. It discusses how the use of cryogenic helium enables advances and explorations in classical (especially in high Rayleigh number convection) and quantum turbulence, and how it helps to gain a better understanding of the fundamental aspects of both. Some practical examples are also outlined. Conclusion. In conclusion, the authors of the introductory article hope that this Topical Issue will expose Turbulent Mixing and Beyond phenomena to a broad scientific community and will serve to integrate our knowledge of the field and further enrich its development.

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