Science.gov

Sample records for parallel discrete-event simulation

  1. Synchronization Of Parallel Discrete Event Simulations

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S.

    1992-01-01

    Adaptive, parallel, discrete-event-simulation-synchronization algorithm, Breathing Time Buckets, developed in Synchronous Parallel Environment for Emulation and Discrete Event Simulation (SPEEDES) operating system. Algorithm allows parallel simulations to process events optimistically in fluctuating time cycles that naturally adapt while simulation in progress. Combines best of optimistic and conservative synchronization strategies while avoiding major disadvantages. Algorithm processes events optimistically in time cycles adapting while simulation in progress. Well suited for modeling communication networks, for large-scale war games, for simulated flights of aircraft, for simulations of computer equipment, for mathematical modeling, for interactive engineering simulations, and for depictions of flows of information.

  2. Running Parallel Discrete Event Simulators on Sierra

    SciTech Connect

    Barnes, P. D.; Jefferson, D. R.

    2015-12-03

    In this proposal we consider porting the ROSS/Charm++ simulator and the discrete event models that run under its control so that they run on the Sierra architecture and make efficient use of the Volta GPUs.

  3. An adaptive synchronization protocol for parallel discrete event simulation

    SciTech Connect

    Bisset, K.R.

    1998-12-01

    Simulation, especially discrete event simulation (DES), is used in a variety of disciplines where numerical methods are difficult or impossible to apply. One problem with this method is that a sufficiently detailed simulation may take hours or days to execute, and multiple runs may be needed in order to generate the desired results. Parallel discrete event simulation (PDES) has been explored for many years as a method to decrease the time taken to execute a simulation. Many protocols have been developed which work well for particular types of simulations, but perform poorly when used for other types of simulations. Often it is difficult to know a priori whether a particular protocol is appropriate for a given problem. In this work, an adaptive synchronization method (ASM) is developed which works well on an entire spectrum of problems. The ASM determines, using an artificial neural network (ANN), the likelihood that a particular event is safe to process.

  4. The effects of parallel processing architectures on discrete event simulation

    NASA Astrophysics Data System (ADS)

    Cave, William; Slatt, Edward; Wassmer, Robert E.

    2005-05-01

    As systems become more complex, particularly those containing embedded decision algorithms, mathematical modeling presents a rigid framework that often impedes representation to a sufficient level of detail. Using discrete event simulation, one can build models that more closely represent physical reality, with actual algorithms incorporated in the simulations. Higher levels of detail increase simulation run time. Hardware designers have succeeded in producing parallel and distributed processor computers with theoretical speeds well into the teraflop range. However, the practical use of these machines on all but some very special problems is extremely limited. The inability to use this power is due to great difficulties encountered when trying to translate real world problems into software that makes effective use of highly parallel machines. This paper addresses the application of parallel processing to simulations of real world systems of varying inherent parallelism. It provides a brief background in modeling and simulation validity and describes a parameter that can be used in discrete event simulation to vary opportunities for parallel processing at the expense of absolute time synchronization and is constrained by validity. It focuses on the effects of model architecture, run-time software architecture, and parallel processor architecture on speed, while providing an environment where modelers can achieve sufficient model accuracy to produce valid simulation results. It describes an approach to simulation development that captures subject area expert knowledge to leverage inherent parallelism in systems in the following ways: * Data structures are separated from instructions to track which instruction sets share what data. This is used to determine independence and thus the potential for concurrent processing at run-time. * Model connectivity (independence) can be inspected visually to determine if the inherent parallelism of a physical system is properly represented. Models need not be changed to move from a single processor to parallel processor hardware architectures. * Knowledge of the architectural parallelism is stored within the system and used during run time to allocate processors to processes in a maximally efficient way.

  5. Parallel discrete-event simulation of FCFS stochastic queueing networks

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1988-01-01

    Physical systems are inherently parallel. Intuition suggests that simulations of these systems may be amenable to parallel execution. The parallel execution of a discrete-event simulation requires careful synchronization of processes in order to ensure the execution's correctness; this synchronization can degrade performance. Largely negative results were recently reported in a study which used a well-known synchronization method on queueing network simulations. Discussed here is a synchronization method (appointments), which has proven itself to be effective on simulations of FCFS queueing networks. The key concept behind appointments is the provision of lookahead. Lookahead is a prediction on a processor's future behavior, based on an analysis of the processor's simulation state. It is shown how lookahead can be computed for FCFS queueing network simulations, give performance data that demonstrates the method's effectiveness under moderate to heavy loads, and discuss performance tradeoffs between the quality of lookahead, and the cost of computing lookahead.

  6. Parallel discrete event simulation: A shared memory approach

    NASA Technical Reports Server (NTRS)

    Reed, Daniel A.; Malony, Allen D.; Mccredie, Bradley D.

    1987-01-01

    With traditional event list techniques, evaluating a detailed discrete event simulation model can often require hours or even days of computation time. Parallel simulation mimics the interacting servers and queues of a real system by assigning each simulated entity to a processor. By eliminating the event list and maintaining only sufficient synchronization to insure causality, parallel simulation can potentially provide speedups that are linear in the number of processors. A set of shared memory experiments is presented using the Chandy-Misra distributed simulation algorithm to simulate networks of queues. Parameters include queueing network topology and routing probabilities, number of processors, and assignment of network nodes to processors. These experiments show that Chandy-Misra distributed simulation is a questionable alternative to sequential simulation of most queueing network models.

  7. The cost of conservative synchronization in parallel discrete event simulations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1990-01-01

    The performance of a synchronous conservative parallel discrete-event simulation protocol is analyzed. The class of simulation models considered is oriented around a physical domain and possesses a limited ability to predict future behavior. A stochastic model is used to show that as the volume of simulation activity in the model increases relative to a fixed architecture, the complexity of the average per-event overhead due to synchronization, event list manipulation, lookahead calculations, and processor idle time approach the complexity of the average per-event overhead of a serial simulation. The method is therefore within a constant factor of optimal. The analysis demonstrates that on large problems--those for which parallel processing is ideally suited--there is often enough parallel workload so that processors are not usually idle. The viability of the method is also demonstrated empirically, showing how good performance is achieved on large problems using a thirty-two node Intel iPSC/2 distributed memory multiprocessor.

  8. Synchronous parallel system for emulation and discrete event simulation

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S. (Inventor)

    1992-01-01

    A synchronous parallel system for emulation and discrete event simulation having parallel nodes responds to received messages at each node by generating event objects having individual time stamps, stores only the changes to state variables of the simulation object attributable to the event object, and produces corresponding messages. The system refrains from transmitting the messages and changing the state variables while it determines whether the changes are superseded, and then stores the unchanged state variables in the event object for later restoral to the simulation object if called for. This determination preferably includes sensing the time stamp of each new event object and determining which new event object has the earliest time stamp as the local event horizon, determining the earliest local event horizon of the nodes as the global event horizon, and ignoring the events whose time stamps are less than the global event horizon. Host processing between the system and external terminals enables such a terminal to query, monitor, command or participate with a simulation object during the simulation process.

  9. Model for the evolution of the time profile in optimistic parallel discrete event simulations

    NASA Astrophysics Data System (ADS)

    Ziganurova, L.; Novotny, M. A.; Shchur, L. N.

    2016-02-01

    We investigate synchronisation aspects of an optimistic algorithm for parallel discrete event simulations (PDES). We present a model for the time evolution in optimistic PDES. This model evaluates the local virtual time profile of the processing elements. We argue that the evolution of the time profile is reminiscent of the surface profile in the directed percolation problem and in unrestricted surface growth. We present results of the simulation of the model and emphasise predictive features of our approach.

  10. SPEEDES - A multiple-synchronization environment for parallel discrete-event simulation

    NASA Technical Reports Server (NTRS)

    Steinman, Jeff S.

    1992-01-01

    Synchronous Parallel Environment for Emulation and Discrete-Event Simulation (SPEEDES) is a unified parallel simulation environment. It supports multiple-synchronization protocols without requiring users to recompile their code. When a SPEEDES simulation runs on one node, all the extra parallel overhead is removed automatically at run time. When the same executable runs in parallel, the user preselects the synchronization algorithm from a list of options. SPEEDES currently runs on UNIX networks and on the California Institute of Technology/Jet Propulsion Laboratory Mark III Hypercube. SPEEDES also supports interactive simulations. Featured in the SPEEDES environment is a new parallel synchronization approach called Breathing Time Buckets. This algorithm uses some of the conservative techniques found in Time Bucket synchronization, along with the optimism that characterizes the Time Warp approach. A mathematical model derived from first principles predicts the performance of Breathing Time Buckets. Along with the Breathing Time Buckets algorithm, this paper discusses the rules for processing events in SPEEDES, describes the implementation of various other synchronization protocols supported by SPEEDES, describes some new ones for the future, discusses interactive simulations, and then gives some performance results.

  11. Explicit spatial scattering for load balancing in conservatively synchronized parallel discrete-event simulations

    SciTech Connect

    Thulasidasan, Sunil; Kasiviswanathan, Shiva; Eidenbenz, Stephan; Romero, Philip

    2010-01-01

    We re-examine the problem of load balancing in conservatively synchronized parallel, discrete-event simulations executed on high-performance computing clusters, focusing on simulations where computational and messaging load tend to be spatially clustered. Such domains are frequently characterized by the presence of geographic 'hot-spots' - regions that generate significantly more simulation events than others. Examples of such domains include simulation of urban regions, transportation networks and networks where interaction between entities is often constrained by physical proximity. Noting that in conservatively synchronized parallel simulations, the speed of execution of the simulation is determined by the slowest (i.e most heavily loaded) simulation process, we study different partitioning strategies in achieving equitable processor-load distribution in domains with spatially clustered load. In particular, we study the effectiveness of partitioning via spatial scattering to achieve optimal load balance. In this partitioning technique, nearby entities are explicitly assigned to different processors, thereby scattering the load across the cluster. This is motivated by two observations, namely, (i) since load is spatially clustered, spatial scattering should, intuitively, spread the load across the compute cluster, and (ii) in parallel simulations, equitable distribution of CPU load is a greater determinant of execution speed than message passing overhead. Through large-scale simulation experiments - both of abstracted and real simulation models - we observe that scatter partitioning, even with its greatly increased messaging overhead, significantly outperforms more conventional spatial partitioning techniques that seek to reduce messaging overhead. Further, even if hot-spots change over the course of the simulation, if the underlying feature of spatial clustering is retained, load continues to be balanced with spatial scattering leading us to the observation that spatial scattering can often obviate the need for dynamic load balancing.

  12. Optimized Hypervisor Scheduler for Parallel Discrete Event Simulations on Virtual Machine Platforms

    SciTech Connect

    Yoginath, Srikanth B; Perumalla, Kalyan S

    2013-01-01

    With the advent of virtual machine (VM)-based platforms for parallel computing, it is now possible to execute parallel discrete event simulations (PDES) over multiple virtual machines, in contrast to executing in native mode directly over hardware as is traditionally done over the past decades. While mature VM-based parallel systems now offer new, compelling benefits such as serviceability, dynamic reconfigurability and overall cost effectiveness, the runtime performance of parallel applications can be significantly affected. In particular, most VM-based platforms are optimized for general workloads, but PDES execution exhibits unique dynamics significantly different from other workloads. Here we first present results from experiments that highlight the gross deterioration of the runtime performance of VM-based PDES simulations when executed using traditional VM schedulers, quantitatively showing the bad scaling properties of the scheduler as the number of VMs is increased. The mismatch is fundamental in nature in the sense that any fairness-based VM scheduler implementation would exhibit this mismatch with PDES runs. We also present a new scheduler optimized specifically for PDES applications, and describe its design and implementation. Experimental results obtained from running PDES benchmarks (PHOLD and vehicular traffic simulations) over VMs show over an order of magnitude improvement in the run time of the PDES-optimized scheduler relative to the regular VM scheduler, with over 20 reduction in run time of simulations using up to 64 VMs. The observations and results are timely in the context of emerging systems such as cloud platforms and VM-based high performance computing installations, highlighting to the community the need for PDES-specific support, and the feasibility of significantly reducing the runtime overhead for scalable PDES on VM platforms.

  13. Synchronous Parallel Emulation and Discrete Event Simulation System with Self-Contained Simulation Objects and Active Event Objects

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S. (Inventor)

    1998-01-01

    The present invention is embodied in a method of performing object-oriented simulation and a system having inter-connected processor nodes operating in parallel to simulate mutual interactions of a set of discrete simulation objects distributed among the nodes as a sequence of discrete events changing state variables of respective simulation objects so as to generate new event-defining messages addressed to respective ones of the nodes. The object-oriented simulation is performed at each one of the nodes by assigning passive self-contained simulation objects to each one of the nodes, responding to messages received at one node by generating corresponding active event objects having user-defined inherent capabilities and individual time stamps and corresponding to respective events affecting one of the passive self-contained simulation objects of the one node, restricting the respective passive self-contained simulation objects to only providing and receiving information from die respective active event objects, requesting information and changing variables within a passive self-contained simulation object by the active event object, and producing corresponding messages specifying events resulting therefrom by the active event objects.

  14. The IDES framework: A case study in development of a parallel discrete-event simulation system

    SciTech Connect

    Nicol, D.M.; Johnson, M.M.; Yoshimura, A.S.

    1997-12-31

    This tutorial describes considerations in the design and development of the IDES parallel simulation system. IDES is a Java-based parallel/distributed simulation system designed to support the study of complex large-scale enterprise systems. Using the IDES system as an example, the authors discuss how anticipated model and system constraints molded the design decisions with respect to modeling, synchronization, and communication strategies.

  15. Distributed discrete event simulation. Final report

    SciTech Connect

    De Vries, R.C.

    1988-02-01

    The presentation given here is restricted to discrete event simulation. The complexity of and time required for many present and potential discrete simulations exceeds the reasonable capacity of most present serial computers. The desire, then, is to implement the simulations on a parallel machine. However, certain problems arise in an effort to program the simulation on a parallel machine. In one category of methods deadlock care arise and some method is required to either detect deadlock and recover from it or to avoid deadlock through information passing. In the second category of methods, potentially incorrect simulations are allowed to proceed. If the situation is later determined to be incorrect, recovery from the error must be initiated. In either case, computation and information passing are required which would not be required in a serial implementation. The net effect is that the parallel simulation may not be much better than a serial simulation. In an effort to determine alternate approaches, important papers in the area were reviewed. As a part of that review process, each of the papers was summarized. The summary of each paper is presented in this report in the hopes that those doing future work in the area will be able to gain insight that might not otherwise be available, and to aid in deciding which papers would be most beneficial to pursue in more detail. The papers are broken down into categories and then by author. Conclusions reached after examining the papers and other material, such as direct talks with an author, are presented in the last section. Also presented there are some ideas that surfaced late in the research effort. These promise to be of some benefit in limiting information which must be passed between processes and in better understanding the structure of a distributed simulation. Pursuit of these ideas seems appropriate.

  16. Optimization of Operations Resources via Discrete Event Simulation Modeling

    NASA Technical Reports Server (NTRS)

    Joshi, B.; Morris, D.; White, N.; Unal, R.

    1996-01-01

    The resource levels required for operation and support of reusable launch vehicles are typically defined through discrete event simulation modeling. Minimizing these resources constitutes an optimization problem involving discrete variables and simulation. Conventional approaches to solve such optimization problems involving integer valued decision variables are the pattern search and statistical methods. However, in a simulation environment that is characterized by search spaces of unknown topology and stochastic measures, these optimization approaches often prove inadequate. In this paper, we have explored the applicability of genetic algorithms to the simulation domain. Genetic algorithms provide a robust search strategy that does not require continuity and differentiability of the problem domain. The genetic algorithm successfully minimized the operation and support activities for a space vehicle, through a discrete event simulation model. The practical issues associated with simulation optimization, such as stochastic variables and constraints, were also taken into consideration.

  17. On constructing optimistic simulation algorithms for the discrete event system specification

    SciTech Connect

    Nutaro, James J

    2008-01-01

    This article describes a Time Warp simulation algorithm for discrete event models that are described in terms of the Discrete Event System Specification (DEVS). The article shows how the total state transition and total output function of a DEVS atomic model can be transformed into an event processing procedure for a logical process. A specific Time Warp algorithm is constructed around this logical process, and it is shown that the algorithm correctly simulates a DEVS coupled model that consists entirely of interacting atomic models. The simulation algorithm is presented abstractly; it is intended to provide a basis for implementing efficient and scalable parallel algorithms that correctly simulate DEVS models.

  18. Synchronization of autonomous objects in discrete event simulation

    NASA Technical Reports Server (NTRS)

    Rogers, Ralph V.

    1990-01-01

    Autonomous objects in event-driven discrete event simulation offer the potential to combine the freedom of unrestricted movement and positional accuracy through Euclidean space of time-driven models with the computational efficiency of event-driven simulation. The principal challenge to autonomous object implementation is object synchronization. The concept of a spatial blackboard is offered as a potential methodology for synchronization. The issues facing implementation of a spatial blackboard are outlined and discussed.

  19. Reversible Discrete Event Formulation and Optimistic Parallel Execution of Vehicular Traffic Models

    SciTech Connect

    Yoginath, Srikanth B; Perumalla, Kalyan S

    2009-01-01

    Vehicular traffic simulations are useful in applications such as emergency planning and traffic management. High speed of traffic simulations translates to speed of response and level of resilience in those applications. Discrete event formulation of traffic flow at the level of individual vehicles affords both the flexibility of simulating complex scenarios of vehicular flow behavior as well as rapid simulation time advances. However, efficient parallel/distributed execution of the models becomes challenging due to synchronization overheads. Here, a parallel traffic simulation approach is presented that is aimed at reducing the time for simulating emergency vehicular traffic scenarios. Our approach resolves the challenges that arise in parallel execution of microscopic, vehicular-level models of traffic. We apply a reverse computation-based optimistic execution approach to address the parallel synchronization problem. This is achieved by formulating a reversible version of a discrete event model of vehicular traffic, and by utilizing this reversible model in an optimistic execution setting. Three unique aspects of this effort are: (1) exploration of optimistic simulation applied to vehicular traffic simulation (2) addressing reverse computation challenges specific to optimistic vehicular traffic simulation (3) achieving absolute (as opposed to self-relative) speedup with a sequential speed close to that of a fast, de facto standard sequential simulator for emergency traffic. The design and development of the parallel simulation system is presented, along with a performance study that demonstrates excellent sequential performance as well as parallel performance. The benefits of optimistic execution are demonstrated, including a speed up of nearly 20 on 32 processors observed on a vehicular network of over 65,000 intersections and over 13 million vehicles.

  20. Reversible Parallel Discrete-Event Execution of Large-scale Epidemic Outbreak Models

    SciTech Connect

    Perumalla, Kalyan S; Seal, Sudip K

    2010-01-01

    The spatial scale, runtime speed and behavioral detail of epidemic outbreak simulations together require the use of large-scale parallel processing. In this paper, an optimistic parallel discrete event execution of a reaction-diffusion simulation model of epidemic outbreaks is presented, with an implementation over the $\\mu$sik simulator. Rollback support is achieved with the development of a novel reversible model that combines reverse computation with a small amount of incremental state saving. Parallel speedup and other runtime performance metrics of the simulation are tested on a small (8,192-core) Blue Gene / P system, while scalability is demonstrated on 65,536 cores of a large Cray XT5 system. Scenarios representing large population sizes (up to several hundred million individuals in the largest case) are exercised.

  1. Quality Improvement With Discrete Event Simulation: A Primer for Radiologists.

    PubMed

    Booker, Michael T; O'Connell, Ryan J; Desai, Bhushan; Duddalwar, Vinay A

    2016-04-01

    The application of simulation software in health care has transformed quality and process improvement. Specifically, software based on discrete-event simulation (DES) has shown the ability to improve radiology workflows and systems. Nevertheless, despite the successful application of DES in the medical literature, the power and value of simulation remains underutilized. For this reason, the basics of DES modeling are introduced, with specific attention to medical imaging. In an effort to provide readers with the tools necessary to begin their own DES analyses, the practical steps of choosing a software package and building a basic radiology model are discussed. In addition, three radiology system examples are presented, with accompanying DES models that assist in analysis and decision making. Through these simulations, we provide readers with an understanding of the theory, requirements, and benefits of implementing DES in their own radiology practices. PMID:26922594

  2. Advances in Discrete-Event Simulation for MSL Command Validation

    NASA Technical Reports Server (NTRS)

    Patrikalakis, Alexander; O'Reilly, Taifun

    2013-01-01

    In the last five years, the discrete event simulator, SEQuence GENerator (SEQGEN), developed at the Jet Propulsion Laboratory to plan deep-space missions, has greatly increased uplink operations capacity to deal with increasingly complicated missions. In this paper, we describe how the Mars Science Laboratory (MSL) project makes full use of an interpreted environment to simulate change in more than fifty thousand flight software parameters and conditional command sequences to predict the result of executing a conditional branch in a command sequence, and enable the ability to warn users whenever one or more simulated spacecraft states change in an unexpected manner. Using these new SEQGEN features, operators plan more activities in one sol than ever before.

  3. Discrete Event Modeling and Massively Parallel Execution of Epidemic Outbreak Phenomena

    SciTech Connect

    Perumalla, Kalyan S; Seal, Sudip K

    2011-01-01

    In complex phenomena such as epidemiological outbreaks, the intensity of inherent feedback effects and the significant role of transients in the dynamics make simulation the only effective method for proactive, reactive or post-facto analysis. The spatial scale, runtime speed, and behavioral detail needed in detailed simulations of epidemic outbreaks make it necessary to use large-scale parallel processing. Here, an optimistic parallel execution of a new discrete event formulation of a reaction-diffusion simulation model of epidemic propagation is presented to facilitate in dramatically increasing the fidelity and speed by which epidemiological simulations can be performed. Rollback support needed during optimistic parallel execution is achieved by combining reverse computation with a small amount of incremental state saving. Parallel speedup of over 5,500 and other runtime performance metrics of the system are observed with weak-scaling execution on a small (8,192-core) Blue Gene / P system, while scalability with a weak-scaling speedup of over 10,000 is demonstrated on 65,536 cores of a large Cray XT5 system. Scenarios representing large population sizes exceeding several hundreds of millions of individuals in the largest cases are successfully exercised to verify model scalability.

  4. Metrics for Availability Analysis Using a Discrete Event Simulation Method

    SciTech Connect

    Schryver, Jack C; Nutaro, James J; Haire, Marvin Jonathan

    2012-01-01

    The system performance metric 'availability' is a central concept with respect to the concerns of a plant's operators and owners, yet it can be abstract enough to resist explanation at system levels. Hence, there is a need for a system-level metric more closely aligned with a plant's (or, more generally, a system's) raison d'etre. Historically, availability of repairable systems - intrinsic, operational, or otherwise - has been defined as a ratio of times. This paper introduces a new concept of availability, called endogenous availability, defined in terms of a ratio of quantities of product yield. Endogenous availability can be evaluated using a discrete event simulation analysis methodology. A simulation example shows that endogenous availability reduces to conventional availability in a simple series system with different processing rates and without intermediate storage capacity, but diverges from conventional availability when storage capacity is progressively increased. It is shown that conventional availability tends to be conservative when a design includes features, such as in - process storage, that partially decouple the components of a larger system.

  5. Enhancing Complex System Performance Using Discrete-Event Simulation

    SciTech Connect

    Allgood, Glenn O; Olama, Mohammed M; Lake, Joe E

    2010-01-01

    In this paper, we utilize discrete-event simulation (DES) merged with human factors analysis to provide the venue within which the separation and deconfliction of the system/human operating principles can occur. A concrete example is presented to illustrate the performance enhancement gains for an aviation cargo flow and security inspection system achieved through the development and use of a process DES. The overall performance of the system is computed, analyzed, and optimized for the different system dynamics. Various performance measures are considered such as system capacity, residual capacity, and total number of pallets waiting for inspection in the queue. These metrics are performance indicators of the system's ability to service current needs and respond to additional requests. We studied and analyzed different scenarios by changing various model parameters such as the number of pieces per pallet ratio, number of inspectors and cargo handling personnel, number of forklifts, number and types of detection systems, inspection modality distribution, alarm rate, and cargo closeout time. The increased physical understanding resulting from execution of the queuing model utilizing these vetted performance measures identified effective ways to meet inspection requirements while maintaining or reducing overall operational cost and eliminating any shipping delays associated with any proposed changes in inspection requirements. With this understanding effective operational strategies can be developed to optimally use personnel while still maintaining plant efficiency, reducing process interruptions, and holding or reducing costs.

  6. Discrete event simulation of fuel transfer strategies for defueling a nuclear reactor.

    SciTech Connect

    Garcia, H. E.; Houshyar, A.; Engineering Division; Western Michigan Univ.

    1998-02-01

    Fuel handling and conditioning activities for the decommissioning of the Experimental Breeder Reactor Il are being performed at Argonne National Laboratory. Discrete event simulation and optimization techniques are being investigated to plan, supervise and perform these activities in such a way that productivity can be improved. The idea is to characterize this operation as a collection of interconnected serving cells, and then apply operational research techniques to identify appropriate planning schedules for the given scenarios. This paper describes an application of discrete event simulation to evaluate fuel transfer strategies and identify optimal solutions among distributed resources.

  7. DISCRETE EVENT SIMULATION OF OPTICAL SWITCH MATRIX PERFORMANCE IN COMPUTER NETWORKS

    SciTech Connect

    Imam, Neena; Poole, Stephen W

    2013-01-01

    In this paper, we present application of a Discrete Event Simulator (DES) for performance modeling of optical switching devices in computer networks. Network simulators are valuable tools in situations where one cannot investigate the system directly. This situation may arise if the system under study does not exist yet or the cost of studying the system directly is prohibitive. Most available network simulators are based on the paradigm of discrete-event-based simulation. As computer networks become increasingly larger and more complex, sophisticated DES tool chains have become available for both commercial and academic research. Some well-known simulators are NS2, NS3, OPNET, and OMNEST. For this research, we have applied OMNEST for the purpose of simulating multi-wavelength performance of optical switch matrices in computer interconnection networks. Our results suggest that the application of DES to computer interconnection networks provides valuable insight in device performance and aids in topology and system optimization.

  8. The use of discrete-event simulation modeling to compare handwritten and electronic prescribing systems.

    PubMed

    Ghany, Ahmad; Vassanji, Karim; Kuziemsky, Craig; Keshavjee, Karim

    2013-01-01

    Electronic prescribing (e-prescribing) is expected to bring many benefits to Canadian healthcare, such as a reduction in errors and adverse drug reactions. As there currently is no functioning e-prescribing system in Canada that is completely electronic, we are unable to evaluate the performance of a live system. An alternative approach is to use simulation modeling for evaluation. We developed two discrete-event simulation models, one of the current handwritten prescribing system and one of a proposed e-prescribing system, to compare the performance of these two systems. We were able to compare the number of processes in each model, workflow efficiency, and the distribution of patients or prescriptions. Although we were able to compare these models to each other, using discrete-event simulation software was challenging. We were limited in the number of variables we could measure. We discovered non-linear processes and feedback loops in both models that could not be adequately represented using discrete-event simulation software. Finally, interactions between entities in both models could not be modeled using this type of software. We have come to the conclusion that a more appropriate approach to modeling both the handwritten and electronic prescribing systems would be to use a complex adaptive systems approach using agent-based modeling or systems-based modeling. PMID:23388319

  9. Discrete event simulation of the Defense Waste Processing Facility (DWPF) analytical laboratory

    SciTech Connect

    Shanahan, K.L.

    1992-02-01

    A discrete event simulation of the Savannah River Site (SRS) Defense Waste Processing Facility (DWPF) analytical laboratory has been constructed in the GPSS language. It was used to estimate laboratory analysis times at process analytical hold points and to study the effect of sample number on those times. Typical results are presented for three different simultaneous representing increasing levels of complexity, and for different sampling schemes. Example equipment utilization time plots are also included. SRS DWPF laboratory management and chemists found the simulations very useful for resource and schedule planning.

  10. Using Discrete Event Simulation to predict KPI's at a Projected Emergency Room.

    PubMed

    Concha, Pablo; Neriz, Liliana; Parada, Danilo; Ramis, Francisco

    2015-01-01

    Discrete Event Simulation (DES) is a powerful factor in the design of clinical facilities. DES enables facilities to be built or adapted to achieve the expected Key Performance Indicators (KPI's) such as average waiting times according to acuity, average stay times and others. Our computational model was built and validated using expert judgment and supporting statistical data. One scenario studied resulted in a 50% decrease in the average cycle time of patients compared to the original model, mainly by modifying the patient's attention model. PMID:26262262

  11. A Framework for the Optimization of Discrete-Event Simulation Models

    NASA Technical Reports Server (NTRS)

    Joshi, B. D.; Unal, R.; White, N. H.; Morris, W. D.

    1996-01-01

    With the growing use of computer modeling and simulation, in all aspects of engineering, the scope of traditional optimization has to be extended to include simulation models. Some unique aspects have to be addressed while optimizing via stochastic simulation models. The optimization procedure has to explicitly account for the randomness inherent in the stochastic measures predicted by the model. This paper outlines a general purpose framework for optimization of terminating discrete-event simulation models. The methodology combines a chance constraint approach for problem formulation, together with standard statistical estimation and analyses techniques. The applicability of the optimization framework is illustrated by minimizing the operation and support resources of a launch vehicle, through a simulation model.

  12. Discrete-event simulation for the design and evaluation of physical protection systems

    SciTech Connect

    Jordan, S.E.; Snell, M.K.; Madsen, M.M.; Smith, J.S.; Peters, B.A.

    1998-08-01

    This paper explores the use of discrete-event simulation for the design and control of physical protection systems for fixed-site facilities housing items of significant value. It begins by discussing several modeling and simulation activities currently performed in designing and analyzing these protection systems and then discusses capabilities that design/analysis tools should have. The remainder of the article then discusses in detail how some of these new capabilities have been implemented in software to achieve a prototype design and analysis tool. The simulation software technology provides a communications mechanism between a running simulation and one or more external programs. In the prototype security analysis tool, these capabilities are used to facilitate human-in-the-loop interaction and to support a real-time connection to a virtual reality (VR) model of the facility being analyzed. This simulation tool can be used for both training (in real-time mode) and facility analysis and design (in fast mode).

  13. DeMO: An Ontology for Discrete-event Modeling and Simulation

    PubMed Central

    Silver, Gregory A; Miller, John A; Hybinette, Maria; Baramidze, Gregory; York, William S

    2011-01-01

    Several fields have created ontologies for their subdomains. For example, the biological sciences have developed extensive ontologies such as the Gene Ontology, which is considered a great success. Ontologies could provide similar advantages to the Modeling and Simulation community. They provide a way to establish common vocabularies and capture knowledge about a particular domain with community-wide agreement. Ontologies can support significantly improved (semantic) search and browsing, integration of heterogeneous information sources, and improved knowledge discovery capabilities. This paper discusses the design and development of an ontology for Modeling and Simulation called the Discrete-event Modeling Ontology (DeMO), and it presents prototype applications that demonstrate various uses and benefits that such an ontology may provide to the Modeling and Simulation community. PMID:22919114

  14. CONFIG - Adapting qualitative modeling and discrete event simulation for design of fault management systems

    NASA Technical Reports Server (NTRS)

    Malin, Jane T.; Basham, Bryan D.

    1989-01-01

    CONFIG is a modeling and simulation tool prototype for analyzing the normal and faulty qualitative behaviors of engineered systems. Qualitative modeling and discrete-event simulation have been adapted and integrated, to support early development, during system design, of software and procedures for management of failures, especially in diagnostic expert systems. Qualitative component models are defined in terms of normal and faulty modes and processes, which are defined by invocation statements and effect statements with time delays. System models are constructed graphically by using instances of components and relations from object-oriented hierarchical model libraries. Extension and reuse of CONFIG models and analysis capabilities in hybrid rule- and model-based expert fault-management support systems are discussed.

  15. A conceptual modeling framework for discrete event simulation using hierarchical control structures

    PubMed Central

    Furian, N.; O’Sullivan, M.; Walker, C.; Vössner, S.; Neubacher, D.

    2015-01-01

    Conceptual Modeling (CM) is a fundamental step in a simulation project. Nevertheless, it is only recently that structured approaches towards the definition and formulation of conceptual models have gained importance in the Discrete Event Simulation (DES) community. As a consequence, frameworks and guidelines for applying CM to DES have emerged and discussion of CM for DES is increasing. However, both the organization of model-components and the identification of behavior and system control from standard CM approaches have shortcomings that limit CM’s applicability to DES. Therefore, we discuss the different aspects of previous CM frameworks and identify their limitations. Further, we present the Hierarchical Control Conceptual Modeling framework that pays more attention to the identification of a models’ system behavior, control policies and dispatching routines and their structured representation within a conceptual model. The framework guides the user step-by-step through the modeling process and is illustrated by a worked example. PMID:26778940

  16. A generic discrete-event simulation model for outpatient clinics in a large public hospital.

    PubMed

    Weerawat, Waressara; Pichitlamken, Juta; Subsombat, Peerapong

    2013-01-01

    The orthopedic outpatient department (OPD) ward in a large Thai public hospital is modeled using Discrete-Event Stochastic (DES) simulation. Key Performance Indicators (KPIs) are used to measure effects across various clinical operations during different shifts throughout the day. By considering various KPIs such as wait times to see doctors, percentage of patients who can see a doctor within a target time frame, and the time that the last patient completes their doctor consultation, bottlenecks are identified and resource-critical clinics can be prioritized. The simulation model quantifies the chronic, high patient congestion that is prevalent amongst Thai public hospitals with very high patient-to-doctor ratios. Our model can be applied across five different OPD wards by modifying the model parameters. Throughout this work, we show how DES models can be used as decision-support tools for hospital management. PMID:23778015

  17. Developing Flexible Discrete Event Simulation Models in an Uncertain Policy Environment

    NASA Technical Reports Server (NTRS)

    Miranda, David J.; Fayez, Sam; Steele, Martin J.

    2011-01-01

    On February 1st, 2010 U.S. President Barack Obama submitted to Congress his proposed budget request for Fiscal Year 2011. This budget included significant changes to the National Aeronautics and Space Administration (NASA), including the proposed cancellation of the Constellation Program. This change proved to be controversial and Congressional approval of the program's official cancellation would take many months to complete. During this same period an end-to-end discrete event simulation (DES) model of Constellation operations was being built through the joint efforts of Productivity Apex Inc. (PAl) and Science Applications International Corporation (SAIC) teams under the guidance of NASA. The uncertainty in regards to the Constellation program presented a major challenge to the DES team, as to: continue the development of this program-of-record simulation, while at the same time remain prepared for possible changes to the program. This required the team to rethink how it would develop it's model and make it flexible enough to support possible future vehicles while at the same time be specific enough to support the program-of-record. This challenge was compounded by the fact that this model was being developed through the traditional DES process-orientation which lacked the flexibility of object-oriented approaches. The team met this challenge through significant pre-planning that led to the "modularization" of the model's structure by identifying what was generic, finding natural logic break points, and the standardization of interlogic numbering system. The outcome of this work resulted in a model that not only was ready to be easily modified to support any future rocket programs, but also a model that was extremely structured and organized in a way that facilitated rapid verification. This paper discusses in detail the process the team followed to build this model and the many advantages this method provides builders of traditional process-oriented discrete event simulations.

  18. Statistical and Probabilistic Extensions to Ground Operations' Discrete Event Simulation Modeling

    NASA Technical Reports Server (NTRS)

    Trocine, Linda; Cummings, Nicholas H.; Bazzana, Ashley M.; Rychlik, Nathan; LeCroy, Kenneth L.; Cates, Grant R.

    2010-01-01

    NASA's human exploration initiatives will invest in technologies, public/private partnerships, and infrastructure, paving the way for the expansion of human civilization into the solar system and beyond. As it is has been for the past half century, the Kennedy Space Center will be the embarkation point for humankind's journey into the cosmos. Functioning as a next generation space launch complex, Kennedy's launch pads, integration facilities, processing areas, launch and recovery ranges will bustle with the activities of the world's space transportation providers. In developing this complex, KSC teams work through the potential operational scenarios: conducting trade studies, planning and budgeting for expensive and limited resources, and simulating alternative operational schemes. Numerous tools, among them discrete event simulation (DES), were matured during the Constellation Program to conduct such analyses with the purpose of optimizing the launch complex for maximum efficiency, safety, and flexibility while minimizing life cycle costs. Discrete event simulation is a computer-based modeling technique for complex and dynamic systems where the state of the system changes at discrete points in time and whose inputs may include random variables. DES is used to assess timelines and throughput, and to support operability studies and contingency analyses. It is applicable to any space launch campaign and informs decision-makers of the effects of varying numbers of expensive resources and the impact of off nominal scenarios on measures of performance. In order to develop representative DES models, methods were adopted, exploited, or created to extend traditional uses of DES. The Delphi method was adopted and utilized for task duration estimation. DES software was exploited for probabilistic event variation. A roll-up process was used, which was developed to reuse models and model elements in other less - detailed models. The DES team continues to innovate and expand DES capabilities to address KSC's planning needs.

  19. Discrete Event Simulation Model of Sudden Cardiac Death Predicts High Impact of Preventive Interventions

    NASA Astrophysics Data System (ADS)

    Andreev, Victor P.; Head, Trajen; Johnson, Neil; Deo, Sapna K.; Daunert, Sylvia; Goldschmidt-Clermont, Pascal J.

    2013-05-01

    Sudden Cardiac Death (SCD) is responsible for at least 180,000 deaths a year and incurs an average cost of $286 billion annually in the United States alone. Herein, we present a novel discrete event simulation model of SCD, which quantifies the chains of events associated with the formation, growth, and rupture of atheroma plaques, and the subsequent formation of clots, thrombosis and on-set of arrhythmias within a population. The predictions generated by the model are in good agreement both with results obtained from pathological examinations on the frequencies of three major types of atheroma, and with epidemiological data on the prevalence and risk of SCD. These model predictions allow for identification of interventions and importantly for the optimal time of intervention leading to high potential impact on SCD risk reduction (up to 8-fold reduction in the number of SCDs in the population) as well as the increase in life expectancy.

  20. The effects of indoor environmental exposures on pediatric asthma: a discrete event simulation model

    PubMed Central

    2012-01-01

    Background In the United States, asthma is the most common chronic disease of childhood across all socioeconomic classes and is the most frequent cause of hospitalization among children. Asthma exacerbations have been associated with exposure to residential indoor environmental stressors such as allergens and air pollutants as well as numerous additional factors. Simulation modeling is a valuable tool that can be used to evaluate interventions for complex multifactorial diseases such as asthma but in spite of its flexibility and applicability, modeling applications in either environmental exposures or asthma have been limited to date. Methods We designed a discrete event simulation model to study the effect of environmental factors on asthma exacerbations in school-age children living in low-income multi-family housing. Model outcomes include asthma symptoms, medication use, hospitalizations, and emergency room visits. Environmental factors were linked to percent predicted forced expiratory volume in 1 second (FEV1%), which in turn was linked to risk equations for each outcome. Exposures affecting FEV1% included indoor and outdoor sources of NO2 and PM2.5, cockroach allergen, and dampness as a proxy for mold. Results Model design parameters and equations are described in detail. We evaluated the model by simulating 50,000 children over 10 years and showed that pollutant concentrations and health outcome rates are comparable to values reported in the literature. In an application example, we simulated what would happen if the kitchen and bathroom exhaust fans were improved for the entire cohort, and showed reductions in pollutant concentrations and healthcare utilization rates. Conclusions We describe the design and evaluation of a discrete event simulation model of pediatric asthma for children living in low-income multi-family housing. Our model simulates the effect of environmental factors (combustion pollutants and allergens), medication compliance, seasonality, and medical history on asthma outcomes (symptom-days, medication use, hospitalizations, and emergency room visits). The model can be used to evaluate building interventions and green building construction practices on pollutant concentrations, energy savings, and asthma healthcare utilization costs, and demonstrates the value of a simulation approach for studying complex diseases such as asthma. PMID:22989068

  1. Discrete event simulation tool for analysis of qualitative models of continuous processing systems

    NASA Technical Reports Server (NTRS)

    Malin, Jane T. (Inventor); Basham, Bryan D. (Inventor); Harris, Richard A. (Inventor)

    1990-01-01

    An artificial intelligence design and qualitative modeling tool is disclosed for creating computer models and simulating continuous activities, functions, and/or behavior using developed discrete event techniques. Conveniently, the tool is organized in four modules: library design module, model construction module, simulation module, and experimentation and analysis. The library design module supports the building of library knowledge including component classes and elements pertinent to a particular domain of continuous activities, functions, and behavior being modeled. The continuous behavior is defined discretely with respect to invocation statements, effect statements, and time delays. The functionality of the components is defined in terms of variable cluster instances, independent processes, and modes, further defined in terms of mode transition processes and mode dependent processes. Model construction utilizes the hierarchy of libraries and connects them with appropriate relations. The simulation executes a specialized initialization routine and executes events in a manner that includes selective inherency of characteristics through a time and event schema until the event queue in the simulator is emptied. The experimentation and analysis module supports analysis through the generation of appropriate log files and graphics developments and includes the ability of log file comparisons.

  2. Towards High Performance Discrete-Event Simulations of Smart Electric Grids

    SciTech Connect

    Perumalla, Kalyan S; Nutaro, James J; Yoginath, Srikanth B

    2011-01-01

    Future electric grid technology is envisioned on the notion of a smart grid in which responsive end-user devices play an integral part of the transmission and distribution control systems. Detailed simulation is often the primary choice in analyzing small network designs, and the only choice in analyzing large-scale electric network designs. Here, we identify and articulate the high-performance computing needs underlying high-resolution discrete event simulation of smart electric grid operation large network scenarios such as the entire Eastern Interconnect. We focus on the simulator's most computationally intensive operation, namely, the dynamic numerical solution for the electric grid state, for both time-integration as well as event-detection. We explore solution approaches using general-purpose dense and sparse solvers, and propose a scalable solver specialized for the sparse structures of actual electric networks. Based on experiments with an implementation in the THYME simulator, we identify performance issues and possible solution approaches for smart grid experimentation in the large.

  3. Implementation of Tree and Butterfly Barriers with Optimistic Time Management Algorithms for Discrete Event Simulation

    NASA Astrophysics Data System (ADS)

    Rizvi, Syed S.; Shah, Dipali; Riasat, Aasia

    The Time Wrap algorithm [3] offers a run time recovery mechanism that deals with the causality errors. These run time recovery mechanisms consists of rollback, anti-message, and Global Virtual Time (GVT) techniques. For rollback, there is a need to compute GVT which is used in discrete-event simulation to reclaim the memory, commit the output, detect the termination, and handle the errors. However, the computation of GVT requires dealing with transient message problem and the simultaneous reporting problem. These problems can be dealt in an efficient manner by the Samadi's algorithm [8] which works fine in the presence of causality errors. However, the performance of both Time Wrap and Samadi's algorithms depends on the latency involve in GVT computation. Both algorithms give poor latency for large simulation systems especially in the presence of causality errors. To improve the latency and reduce the processor ideal time, we implement tree and butterflies barriers with the optimistic algorithm. Our analysis shows that the use of synchronous barriers such as tree and butterfly with the optimistic algorithm not only minimizes the GVT latency but also minimizes the processor idle time.

  4. StratBAM: A Discrete-Event Simulation Model to Support Strategic Hospital Bed Capacity Decisions.

    PubMed

    Devapriya, Priyantha; Strömblad, Christopher T B; Bailey, Matthew D; Frazier, Seth; Bulger, John; Kemberling, Sharon T; Wood, Kenneth E

    2015-10-01

    The ability to accurately measure and assess current and potential health care system capacities is an issue of local and national significance. Recent joint statements by the Institute of Medicine and the Agency for Healthcare Research and Quality have emphasized the need to apply industrial and systems engineering principles to improving health care quality and patient safety outcomes. To address this need, a decision support tool was developed for planning and budgeting of current and future bed capacity, and evaluating potential process improvement efforts. The Strategic Bed Analysis Model (StratBAM) is a discrete-event simulation model created after a thorough analysis of patient flow and data from Geisinger Health System's (GHS) electronic health records. Key inputs include: timing, quantity and category of patient arrivals and discharges; unit-level length of care; patient paths; and projected patient volume and length of stay. Key outputs include: admission wait time by arrival source and receiving unit, and occupancy rates. Electronic health records were used to estimate parameters for probability distributions and to build empirical distributions for unit-level length of care and for patient paths. Validation of the simulation model against GHS operational data confirmed its ability to model real-world data consistently and accurately. StratBAM was successfully used to evaluate the system impact of forecasted patient volumes and length of stay in terms of patient wait times, occupancy rates, and cost. The model is generalizable and can be appropriately scaled for larger and smaller health care settings. PMID:26310949

  5. Discrete event simulation for exploring strategies: an urban water management case.

    PubMed

    Huang, Dong-Bin; Scholz, Roland W; Gujer, Willi; Chitwood, Derek E; Loukopoulos, Peter; Schertenleib, Roland; Siegrist, Hansruedi

    2007-02-01

    This paper presents a model structure aimed at offering an overview of the various elements of a strategy and exploring their multidimensional effects through time in an efficient way. It treats a strategy as a set of discrete events planned to achieve a certain strategic goal and develops a new form of causal networks as an interfacing component between decision makers and environment models, e.g., life cycle inventory and material flow models. The causal network receives a strategic plan as input in a discrete manner and then outputs the updated parameter sets to the subsequent environmental models. Accordingly, the potential dynamic evolution of environmental systems caused by various strategies can be stepwise simulated. It enables a way to incorporate discontinuous change in models for environmental strategy analysis, and enhances the interpretability and extendibility of a complex model by its cellular constructs. It is exemplified using an urban water management case in Kunming, a major city in Southwest China. By utilizing the presented method, the case study modeled the cross-scale interdependencies of the urban drainage system and regional water balance systems, and evaluated the effectiveness of various strategies for improving the situation of Dianchi Lake. PMID:17328203

  6. Discrete event simulation for healthcare organizations: a tool for decision making.

    PubMed

    Hamrock, Eric; Paige, Kerrie; Parks, Jennifer; Scheulen, James; Levin, Scott

    2013-01-01

    Healthcare organizations face challenges in efficiently accommodating increased patient demand with limited resources and capacity. The modern reimbursement environment prioritizes the maximization of operational efficiency and the reduction of unnecessary costs (i.e., waste) while maintaining or improving quality. As healthcare organizations adapt, significant pressures are placed on leaders to make difficult operational and budgetary decisions. In lieu of hard data, decision makers often base these decisions on subjective information. Discrete event simulation (DES), a computerized method of imitating the operation of a real-world system (e.g., healthcare delivery facility) over time, can provide decision makers with an evidence-based tool to develop and objectively vet operational solutions prior to implementation. DES in healthcare commonly focuses on (1) improving patient flow, (2) managing bed capacity, (3) scheduling staff, (4) managing patient admission and scheduling procedures, and (5) using ancillary resources (e.g., labs, pharmacies). This article describes applicable scenarios, outlines DES concepts, and describes the steps required for development. An original DES model developed to examine crowding and patient flow for staffing decision making at an urban academic emergency department serves as a practical example. PMID:23650696

  7. Discrete-event simulation of a wide-area health care network.

    PubMed Central

    McDaniel, J G

    1995-01-01

    OBJECTIVE: Predict the behavior and estimate the telecommunication cost of a wide-area message store-and-forward network for health care providers that uses the telephone system. DESIGN: A tool with which to perform large-scale discrete-event simulations was developed. Network models for star and mesh topologies were constructed to analyze the differences in performances and telecommunication costs. The distribution of nodes in the network models approximates the distribution of physicians, hospitals, medical labs, and insurers in the Province of Saskatchewan, Canada. Modeling parameters were based on measurements taken from a prototype telephone network and a survey conducted at two medical clinics. Simulation studies were conducted for both topologies. RESULTS: For either topology, the telecommunication cost of a network in Saskatchewan is projected to be less than $100 (Canadian) per month per node. The estimated telecommunication cost of the star topology is approximately half that of the mesh. Simulations predict that a mean end-to-end message delivery time of two hours or less is achievable at this cost. A doubling of the data volume results in an increase of less than 50% in the mean end-to-end message transfer time. CONCLUSION: The simulation models provided an estimate of network performance and telecommunication cost in a specific Canadian province. At the expected operating point, network performance appeared to be relatively insensitive to increases in data volume. Similar results might be anticipated in other rural states and provinces in North America where a telephone-based network is desired. PMID:7583646

  8. Using Discrete Event Simulation for Programming Model Exploration at Extreme-Scale: Macroscale Components for the Structural Simulation Toolkit (SST).

    SciTech Connect

    Wilke, Jeremiah J; Kenny, Joseph P.

    2015-02-01

    Discrete event simulation provides a powerful mechanism for designing and testing new extreme- scale programming models for high-performance computing. Rather than debug, run, and wait for results on an actual system, design can first iterate through a simulator. This is particularly useful when test beds cannot be used, i.e. to explore hardware or scales that do not yet exist or are inaccessible. Here we detail the macroscale components of the structural simulation toolkit (SST). Instead of depending on trace replay or state machines, the simulator is architected to execute real code on real software stacks. Our particular user-space threading framework allows massive scales to be simulated even on small clusters. The link between the discrete event core and the threading framework allows interesting performance metrics like call graphs to be collected from a simulated run. Performance analysis via simulation can thus become an important phase in extreme-scale programming model and runtime system design via the SST macroscale components.

  9. Using Discrete Event Computer Simulation to Improve Patient Flow in a Ghanaian Acute Care Hospital

    PubMed Central

    Best, Allyson M.; Dixon, Cinnamon A.; Kelton, W. David; Lindsell, Christopher J.

    2014-01-01

    Objectives Crowding and limited resources have increased the strain on acute care facilities and emergency departments (EDs) worldwide. These problems are particularly prevalent in developing countries. Discrete event simulation (DES) is a computer-based tool that can be used to estimate how changes to complex healthcare delivery systems, such as EDs, will affect operational performance. Using this modality, our objective was to identify operational interventions that could potentially improve patient throughput of one acute care setting in a developing country. Methods We developed a simulation model of acute care at a district level hospital in Ghana to test the effects of resource-neutral (e.g. modified staff start times and roles) and resource-additional (e.g. increased staff) operational interventions on patient throughput. Previously captured, de-identified time-and-motion data from 487 acute care patients were used to develop and test the model. The primary outcome was the modeled effect of interventions on patient length of stay (LOS). Results The base-case (no change) scenario had a mean LOS of 292 minutes (95% CI 291, 293). In isolation, neither adding staffing, changing staff roles, nor varying shift times affected overall patient LOS. Specifically, adding two registration workers, history takers, and physicians resulted in a 23.8 (95% CI 22.3, 25.3) minute LOS decrease. However, when shift start-times were coordinated with patient arrival patterns, potential mean LOS was decreased by 96 minutes (95% CI 94, 98); and with the simultaneous combination of staff roles (Registration and History-taking) there was an overall mean LOS reduction of 152 minutes (95% CI 150, 154). Conclusions Resource-neutral interventions identified through DES modeling have the potential to improve acute care throughput in this Ghanaian municipal hospital. DES offers another approach to identifying potentially effective interventions to improve patient flow in emergency and acute care in resource-limited settings. PMID:24953788

  10. Modeling Temporal Processes in Early Spacecraft Design: Application of Discrete-Event Simulations for Darpa's F6 Program

    NASA Technical Reports Server (NTRS)

    Dubos, Gregory F.; Cornford, Steven

    2012-01-01

    While the ability to model the state of a space system over time is essential during spacecraft operations, the use of time-based simulations remains rare in preliminary design. The absence of the time dimension in most traditional early design tools can however become a hurdle when designing complex systems whose development and operations can be disrupted by various events, such as delays or failures. As the value delivered by a space system is highly affected by such events, exploring the trade space for designs that yield the maximum value calls for the explicit modeling of time.This paper discusses the use of discrete-event models to simulate spacecraft development schedule as well as operational scenarios and on-orbit resources in the presence of uncertainty. It illustrates how such simulations can be utilized to support trade studies, through the example of a tool developed for DARPA's F6 program to assist the design of "fractionated spacecraft".

  11. Discrete-event simulation of nuclear-waste transport in geologic sites subject to disruptive events. Final report

    SciTech Connect

    Aggarwal, S.; Ryland, S.; Peck, R.

    1980-06-19

    This report outlines a methodology to study the effects of disruptive events on nuclear waste material in stable geologic sites. The methodology is based upon developing a discrete events model that can be simulated on the computer. This methodology allows a natural development of simulation models that use computer resources in an efficient manner. Accurate modeling in this area depends in large part upon accurate modeling of ion transport behavior in the storage media. Unfortunately, developments in this area are not at a stage where there is any consensus on proper models for such transport. Consequently, our work is directed primarily towards showing how disruptive events can be properly incorporated in such a model, rather than as a predictive tool at this stage. When and if proper geologic parameters can be determined, then it would be possible to use this as a predictive model. Assumptions and their bases are discussed, and the mathematical and computer model are described.

  12. The Activity-tracking paradigm in discrete-event modeling and simulation: The case of spatially continuous distributed systems

    SciTech Connect

    Muzy,; Jammalamadaka, Rajanikanth; Zeigler, Bernard P; Nutaro, James J

    2011-01-01

    From a modeling and simulation perspective, studying dynamic systems consists of focusing on changes in states. According to the precision of state changes, generic algorithms can be developed to track the activity of sub-systems. This paper aims at describing and applying this more natural and intuitive way to describe and implement dynamic systems. Activity is defined mathematically. A generic application case of diffusion is experimented with to compare the efficiency of quantized state methods using this new approach with traditional methods which do not focus computations on active areas. Our goal is to demonstrate that the concept of activity can estimate the computational effort required by a quantized state method. Specifically, when properly designed, a discrete-event simulator for such a method achieves a reduction in the number of state transitions that more than compensates for the overhead it imposes.

  13. Using Discrete Event Simulation to Model Integrated Commodities Consumption for a Launch Campaign of the Space Launch System

    NASA Technical Reports Server (NTRS)

    Leonard, Daniel; Parsons, Jeremy W.; Cates, Grant

    2014-01-01

    In May 2013, NASA's GSDO Program requested a study to develop a discrete event simulation (DES) model that analyzes the launch campaign process of the Space Launch System (SLS) from an integrated commodities perspective. The scope of the study includes launch countdown and scrub turnaround and focuses on four core launch commodities: hydrogen, oxygen, nitrogen, and helium. Previously, the commodities were only analyzed individually and deterministically for their launch support capability, but this study was the first to integrate them to examine the impact of their interactions on a launch campaign as well as the effects of process variability on commodity availability. The study produced a validated DES model with Rockwell Arena that showed that Kennedy Space Center's ground systems were capable of supporting a 48-hour scrub turnaround for the SLS. The model will be maintained and updated to provide commodity consumption analysis of future ground system and SLS configurations.

  14. Simulating an emergency department: the importance of modeling the interactions between physicians and delegates in a discrete event simulation

    PubMed Central

    2013-01-01

    Background Computer simulation studies of the emergency department (ED) are often patient driven and consider the physician as a human resource whose primary activity is interacting directly with the patient. In many EDs, physicians supervise delegates such as residents, physician assistants and nurse practitioners each with different skill sets and levels of independence. The purpose of this study is to present an alternative approach where physicians and their delegates in the ED are modeled as interacting pseudo-agents in a discrete event simulation (DES) and to compare it with the traditional approach ignoring such interactions. Methods The new approach models a hierarchy of heterogeneous interacting pseudo-agents in a DES, where pseudo-agents are entities with embedded decision logic. The pseudo-agents represent a physician and delegate, where the physician plays a senior role to the delegate (i.e. treats high acuity patients and acts as a consult for the delegate). A simple model without the complexity of the ED is first created in order to validate the building blocks (programming) used to create the pseudo-agents and their interaction (i.e. consultation). Following validation, the new approach is implemented in an ED model using data from an Ontario hospital. Outputs from this model are compared with outputs from the ED model without the interacting pseudo-agents. They are compared based on physician and delegate utilization, patient waiting time for treatment, and average length of stay. Additionally, we conduct sensitivity analyses on key parameters in the model. Results In the hospital ED model, comparisons between the approach with interaction and without showed physician utilization increase from 23% to 41% and delegate utilization increase from 56% to 71%. Results show statistically significant mean time differences for low acuity patients between models. Interaction time between physician and delegate results in increased ED length of stay and longer waits for beds. Conclusion This example shows the importance of accurately modeling physician relationships and the roles in which they treat patients. Neglecting these relationships could lead to inefficient resource allocation due to inaccurate estimates of physician and delegate time spent on patient related activities and length of stay. PMID:23692710

  15. SimPackJ/S: a web-oriented toolkit for discrete event simulation

    NASA Astrophysics Data System (ADS)

    Park, Minho; Fishwick, Paul A.

    2002-07-01

    SimPackJ/S is the JavaScript and Java version of SimPack, which means SimPackJ/S is a collection of JavaScript and Java libraries and executable programs for computer simulations. The main purpose of creating SimPackJ/S is that we allow existing SimPack users to expand simulation areas and provide future users with a freeware simulation toolkit to simulate and model a system in web environments. One of the goals for this paper is to introduce SimPackJ/S. The other goal is to propose translation rules for converting C to JavaScript and Java. Most parts demonstrate the translation rules with examples. In addition, we discuss a 3D dynamic system model and overview an approach to 3D dynamic systems using SimPackJ/S. We explain an interface between SimPackJ/S and the 3D language--Virtual Reality Modeling Language (VRML). This paper documents how to translate C to JavaScript and Java and how to utilize SimPackJ/S within a 3D web environment.

  16. Discrete event simulation of a proton therapy facility: a case study.

    PubMed

    Corazza, Uliana; Filippini, Roberto; Setola, Roberto

    2011-06-01

    Proton therapy is a type of particle therapy which utilizes a beam of protons to irradiate diseased tissue. The main difference with respect to conventional radiotherapy (X-rays, γ-rays) is the capability to target tumors with extreme precision, which makes it possible to treat deep-seated tumors and tumors affecting noble tissues as brain, eyes, etc. However, proton therapy needs high-energy cyclotrons and this requires sophisticated control-supervision schema to guarantee, further than the prescribed performance, the safety of the patients and of the operators. In this paper we present the modeling and simulation of the irradiation process of the PROSCAN facility at the Paul Scherrer Institut. This is a challenging task because of the complexity of the operation scenario, which consists of deterministic and stochastic processes resulting from the coordination-interaction among diverse entities such as distributed automatic control systems, safety protection systems, and human operators. PMID:20675013

  17. Forest biomass supply logistics for a power plant using the discrete-event simulation approach

    SciTech Connect

    Mobini, Mahdi; Sowlati, T.; Sokhansanj, Shahabaddine

    2011-04-01

    This study investigates the logistics of supplying forest biomass to a potential power plant. Due to the complexities in such a supply logistics system, a simulation model based on the framework of Integrated Biomass Supply Analysis and Logistics (IBSAL) is developed in this study to evaluate the cost of delivered forest biomass, the equilibrium moisture content, and carbon emissions from the logistics operations. The model is applied to a proposed case of 300 MW power plant in Quesnel, BC, Canada. The results show that the biomass demand of the power plant would not be met every year. The weighted average cost of delivered biomass to the gate of the power plant is about C$ 90 per dry tonne. Estimates of equilibrium moisture content of delivered biomass and CO2 emissions resulted from the processes are also provided.

  18. Evaluating the cost effectiveness of donepezil in the treatment of Alzheimer's disease in Germany using discrete event simulation

    PubMed Central

    2012-01-01

    Background Previous cost-effectiveness studies of cholinesterase inhibitors have modeled Alzheimer's disease (AD) progression and treatment effects through single or global severity measures, or progression to "Full Time Care". This analysis evaluates the cost-effectiveness of donepezil versus memantine or no treatment in Germany by considering correlated changes in cognition, behavior and function. Methods Rates of change were modeled using trial and registry-based patient level data. A discrete event simulation projected outcomes for three identical patient groups: donepezil 10 mg, memantine 20 mg and no therapy. Patient mix, mortality and costs were developed using Germany-specific sources. Results Treatment of patients with mild to moderately severe AD with donepezil compared to no treatment was associated with 0.13 QALYs gained per patient, and 0.01 QALYs gained per caregiver and resulted in average savings of €7,007 and €9,893 per patient from the healthcare system and societal perspectives, respectively. In patients with moderate to moderately-severe AD, donepezil compared to memantine resulted in QALY gains averaging 0.01 per patient, and savings averaging €1,960 and €2,825 from the healthcare system and societal perspective, respectively. In probabilistic sensitivity analyses, donepezil dominated no treatment in most replications and memantine in over 70% of the replications. Donepezil leads to savings in 95% of replications versus memantine. Conclusions Donepezil is highly cost-effective in patients with AD in Germany, leading to improvements in health outcomes and substantial savings compared to no treatment. This holds across a variety of sensitivity analyses. PMID:22316501

  19. Parallelized direct execution simulation of message-passing parallel programs

    NASA Technical Reports Server (NTRS)

    Dickens, Phillip M.; Heidelberger, Philip; Nicol, David M.

    1994-01-01

    As massively parallel computers proliferate, there is growing interest in findings ways by which performance of massively parallel codes can be efficiently predicted. This problem arises in diverse contexts such as parallelizing computers, parallel performance monitoring, and parallel algorithm development. In this paper we describe one solution where one directly executes the application code, but uses a discrete-event simulator to model details of the presumed parallel machine such as operating system and communication network behavior. Because this approach is computationally expensive, we are interested in its own parallelization specifically the parallelization of the discrete-event simulator. We describe methods suitable for parallelized direct execution simulation of message-passing parallel programs, and report on the performance of such a system, Large Application Parallel Simulation Environment (LAPSE), we have built on the Intel Paragon. On all codes measured to date, LAPSE predicts performance well typically within 10 percent relative error. Depending on the nature of the application code, we have observed low slowdowns (relative to natively executing code) and high relative speedups using up to 64 processors.

  20. Simulating Billion-Task Parallel Programs

    SciTech Connect

    Perumalla, Kalyan S; Park, Alfred J

    2014-01-01

    In simulating large parallel systems, bottom-up approaches exercise detailed hardware models with effects from simplified software models or traces, whereas top-down approaches evaluate the timing and functionality of detailed software models over coarse hardware models. Here, we focus on the top-down approach and significantly advance the scale of the simulated parallel programs. Via the direct execution technique combined with parallel discrete event simulation, we stretch the limits of the top-down approach by simulating message passing interface (MPI) programs with millions of tasks. Using a timing-validated benchmark application, a proof-of-concept scaling level is achieved to over 0.22 billion virtual MPI processes on 216,000 cores of a Cray XT5 supercomputer, representing one of the largest direct execution simulations to date, combined with a multiplexing ratio of 1024 simulated tasks per real task.

  1. Analysis hierarchical model for discrete event systems

    NASA Astrophysics Data System (ADS)

    Ciortea, E. M.

    2015-11-01

    The This paper presents the hierarchical model based on discrete event network for robotic systems. Based on the hierarchical approach, Petri network is analysed as a network of the highest conceptual level and the lowest level of local control. For modelling and control of complex robotic systems using extended Petri nets. Such a system is structured, controlled and analysed in this paper by using Visual Object Net ++ package that is relatively simple and easy to use, and the results are shown as representations easy to interpret. The hierarchical structure of the robotic system is implemented on computers analysed using specialized programs. Implementation of hierarchical model discrete event systems, as a real-time operating system on a computer network connected via a serial bus is possible, where each computer is dedicated to local and Petri model of a subsystem global robotic system. Since Petri models are simplified to apply general computers, analysis, modelling, complex manufacturing systems control can be achieved using Petri nets. Discrete event systems is a pragmatic tool for modelling industrial systems. For system modelling using Petri nets because we have our system where discrete event. To highlight the auxiliary time Petri model using transport stream divided into hierarchical levels and sections are analysed successively. Proposed robotic system simulation using timed Petri, offers the opportunity to view the robotic time. Application of goods or robotic and transmission times obtained by measuring spot is obtained graphics showing the average time for transport activity, using the parameters sets of finished products. individually.

  2. The split system approach to managing time in simulations of hybrid systems having continuous and discrete event components

    SciTech Connect

    Nutaro, James J.; Kuruganti, Phani Teja; Protopopescu, Vladimir A.; Shankar, Mallikarjun

    2012-02-08

    The efficient and accurate management of time in simulations of hybrid models is an outstanding engineering problem. General a priori knowledge about the dynamic behavior of the hybrid system (i.e. essentially continuous, essentially discrete, or 'truly hybrid') facilitates this task. Indeed, for essentially discrete and essentially continuous systems, existing software packages can be conveniently used to perform quite sophisticated and satisfactory simulations. The situation is different for 'truly hybrid' systems, for which direct application of existing software packages results in a lengthy design process, cumbersome software assemblies, inaccurate results, or some combination of these independent of the designer's a priori knowledge about the system's structure and behavior. The main goal of this paper is to provide a methodology whereby simulation designers can use a priori knowledge about the hybrid model's structure to build a straightforward, efficient, and accurate simulator with existing software packages. The proposed methodology is based on a formal decomposition and re-articulation of the hybrid system; this is the main theoretical result of the paper. To set the result in the right perspective, we briefly review the essentially continuous and essentially discrete approaches, which are illustrated with typical examples. Then we present our new, split system approach, first in a general formal context, then in three more specific guises that reflect the viewpoints of three main communities of hybrid system researchers and practitioners. For each of these variants we indicate an implementation path. Our approach is illustrated with an archetypal problem of power grid control.

  3. Estimating the Unknown Parameters of the Natural History of Metachronous Colorectal Cancer Using Discrete-Event Simulation

    PubMed Central

    Erenay, Fatih Safa; Alagoz, Oguzhan; Banerjee, Ritesh; Cima, Robert R.

    2011-01-01

    Objectives Some aspects of the natural history of metachronous colorectal cancer (MCRC), such as the rate of progression from adenomatous polyp to MCRC, are unknown. The objective of this study is to estimate a set of parameters revealing some of these unknown characteristics of MCRC. Methods The authors developed a computer simulation model that mimics the progression of MCRC for a 5-year period following the treatment of primary colorectal cancer (CRC). They obtained the inputs of the simulation model using longitudinal data for 284 CRC patients from the Mayo Clinic, Rochester. Results Five-year MCRC incidence and all-cause mortality were 7.4% and 12.7% in the patient cohort, respectively. Statistical analysis showed that 5-year MCRC incidence was associated with gender (P = 0.05), whereas both all-cause and CRC-related mortalities were associated with age (P < 0.001 and P = 0.01). Estimated annual probabilities of progression from adenomatous polyp to MCRC and from MCRC to metastatic MCRC were 0.14 and 0.28, respectively. Annual probabilities of mortality after MCRC and metastatic MCRC treatments were estimated to be 0.06 and 0.26, respectively. The estimated annual probability of mortality due to undetected MCRC was 0.16. Conclusions The results imply that MCRC, especially in women, may be more common than suggested by previous studies. In addition, statistics derived from the clinical data and results of the simulation model indicate that gender and age affect the progression of MCRC. PMID:21212440

  4. Budget Impact Analysis of Switching to Digital Mammography in a Population-Based Breast Cancer Screening Program: A Discrete Event Simulation Model

    PubMed Central

    Comas, Mercè; Arrospide, Arantzazu; Mar, Javier; Sala, Maria; Vilaprinyó, Ester; Hernández, Cristina; Cots, Francesc; Martínez, Juan; Castells, Xavier

    2014-01-01

    Objective To assess the budgetary impact of switching from screen-film mammography to full-field digital mammography in a population-based breast cancer screening program. Methods A discrete-event simulation model was built to reproduce the breast cancer screening process (biennial mammographic screening of women aged 50 to 69 years) combined with the natural history of breast cancer. The simulation started with 100,000 women and, during a 20-year simulation horizon, new women were dynamically entered according to the aging of the Spanish population. Data on screening were obtained from Spanish breast cancer screening programs. Data on the natural history of breast cancer were based on US data adapted to our population. A budget impact analysis comparing digital with screen-film screening mammography was performed in a sample of 2,000 simulation runs. A sensitivity analysis was performed for crucial screening-related parameters. Distinct scenarios for recall and detection rates were compared. Results Statistically significant savings were found for overall costs, treatment costs and the costs of additional tests in the long term. The overall cost saving was 1,115,857€ (95%CI from 932,147 to 1,299,567) in the 10th year and 2,866,124€ (95%CI from 2,492,610 to 3,239,638) in the 20th year, representing 4.5% and 8.1% of the overall cost associated with screen-film mammography. The sensitivity analysis showed net savings in the long term. Conclusions Switching to digital mammography in a population-based breast cancer screening program saves long-term budget expense, in addition to providing technical advantages. Our results were consistent across distinct scenarios representing the different results obtained in European breast cancer screening programs. PMID:24832200

  5. On extending parallelism to serial simulators

    NASA Technical Reports Server (NTRS)

    Nicol, David; Heidelberger, Philip

    1994-01-01

    This paper describes an approach to discrete event simulation modeling that appears to be effective for developing portable and efficient parallel execution of models of large distributed systems and communication networks. In this approach, the modeler develops submodels using an existing sequential simulation modeling tool, using the full expressive power of the tool. A set of modeling language extensions permit automatically synchronized communication between submodels; however, the automation requires that any such communication must take a nonzero amount off simulation time. Within this modeling paradigm, a variety of conservative synchronization protocols can transparently support conservative execution of submodels on potentially different processors. A specific implementation of this approach, U.P.S. (Utilitarian Parallel Simulator), is described, along with performance results on the Intel Paragon.

  6. Inflated speedups in parallel simulations via malloc()

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1990-01-01

    Discrete-event simulation programs make heavy use of dynamic memory allocation in order to support simulation's very dynamic space requirements. When programming in C one is likely to use the malloc() routine. However, a parallel simulation which uses the standard Unix System V malloc() implementation may achieve an overly optimistic speedup, possibly superlinear. An alternate implementation provided on some (but not all systems) can avoid the speedup anomaly, but at the price of significantly reduced available free space. This is especially severe on most parallel architectures, which tend not to support virtual memory. It is shown how a simply implemented user-constructed interface to malloc() can both avoid artificially inflated speedups, and make efficient use of the dynamic memory space. The interface simply catches blocks on the basis of their size. The problem is demonstrated empirically, and the effectiveness of the solution is shown both empirically and analytically.

  7. Expected lifetime numbers and costs of fractures in postmenopausal women with and without osteoporosis in Germany: a discrete event simulation model

    PubMed Central

    2014-01-01

    Background Osteoporotic fractures cause a large health burden and substantial costs. This study estimated the expected fracture numbers and costs for the remaining lifetime of postmenopausal women in Germany. Methods A discrete event simulation (DES) model which tracks changes in fracture risk due to osteoporosis, a previous fracture or institutionalization in a nursing home was developed. Expected lifetime fracture numbers and costs per capita were estimated for postmenopausal women (aged 50 and older) at average osteoporosis risk (AOR) and for those never suffering from osteoporosis. Direct and indirect costs were modeled. Deterministic univariate and probabilistic sensitivity analyses were conducted. Results The expected fracture numbers over the remaining lifetime of a 50 year old woman with AOR for each fracture type (% attributable to osteoporosis) were: hip 0.282 (57.9%), wrist 0.229 (18.2%), clinical vertebral 0.206 (39.2%), humerus 0.147 (43.5%), pelvis 0.105 (47.5%), and other femur 0.033 (52.1%). Expected discounted fracture lifetime costs (excess cost attributable to osteoporosis) per 50 year old woman with AOR amounted to €4,479 (€1,995). Most costs were accrued in the hospital €1,743 (€751) and long-term care sectors €1,210 (€620). Univariate sensitivity analysis resulted in percentage changes between -48.4% (if fracture rates decreased by 2% per year) and +83.5% (if fracture rates increased by 2% per year) compared to base case excess costs. Costs for women with osteoporosis were about 3.3 times of those never getting osteoporosis (€7,463 vs. €2,247), and were markedly increased for women with a previous fracture. Conclusion The results of this study indicate that osteoporosis causes a substantial share of fracture costs in postmenopausal women, which strongly increase with age and previous fractures. PMID:24981316

  8. Parallel simulation today

    NASA Technical Reports Server (NTRS)

    Nicol, David; Fujimoto, Richard

    1992-01-01

    This paper surveys topics that presently define the state of the art in parallel simulation. Included in the tutorial are discussions on new protocols, mathematical performance analysis, time parallelism, hardware support for parallel simulation, load balancing algorithms, and dynamic memory management for optimistic synchronization.

  9. Parallel Atomistic Simulations

    SciTech Connect

    HEFFELFINGER,GRANT S.

    2000-01-18

    Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.

  10. Scaling Time Warp-based Discrete Event Execution to 104 Processors on Blue Gene Supercomputer

    SciTech Connect

    Perumalla, Kalyan S

    2007-01-01

    Lately, important large-scale simulation applications, such as emergency/event planning and response, are emerging that are based on discrete event models. The applications are characterized by their scale (several millions of simulated entities), their fine-grained nature of computation (microseconds per event), and their highly dynamic inter-entity event interactions. The desired scale and speed together call for highly scalable parallel discrete event simulation (PDES) engines. However, few such parallel engines have been designed or tested on platforms with thousands of processors. Here an overview is given of a unique PDES engine that has been designed to support Time Warp-style optimistic parallel execution as well as a more generalized mixed, optimistic-conservative synchronization. The engine is designed to run on massively parallel architectures with minimal overheads. A performance study of the engine is presented, including the first results to date of PDES benchmarks demonstrating scalability to as many as 16,384 processors, on an IBM Blue Gene supercomputer. The results show, for the first time, the promise of effectively sustaining very large scale discrete event execution on up to 104 processors.

  11. Xyce parallel electronic simulator.

    SciTech Connect

    Keiter, Eric Richard; Mei, Ting; Russo, Thomas V.; Rankin, Eric Lamont; Schiek, Richard Louis; Thornquist, Heidi K.; Fixel, Deborah A.; Coffey, Todd Stirling; Pawlowski, Roger Patrick; Santarelli, Keith R.

    2010-05-01

    This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide.

  12. Parallel Dislocation Simulator

    Energy Science and Technology Software Center (ESTSC)

    2006-10-30

    ParaDiS is software capable of simulating the motion, evolution, and interaction of dislocation networks in single crystals using massively parallel computer architectures. The software is capable of outputting the stress-strain response of a single crystal whose plastic deformation is controlled by the dislocation processes.

  13. An algebra of discrete event processes

    NASA Technical Reports Server (NTRS)

    Heymann, Michael; Meyer, George

    1991-01-01

    This report deals with an algebraic framework for modeling and control of discrete event processes. The report consists of two parts. The first part is introductory, and consists of a tutorial survey of the theory of concurrency in the spirit of Hoare's CSP, and an examination of the suitability of such an algebraic framework for dealing with various aspects of discrete event control. To this end a new concurrency operator is introduced and it is shown how the resulting framework can be applied. It is further shown that a suitable theory that deals with the new concurrency operator must be developed. In the second part of the report the formal algebra of discrete event control is developed. At the present time the second part of the report is still an incomplete and occasionally tentative working paper.

  14. Optimal Discrete Event Supervisory Control of Aircraft Gas Turbine Engines

    NASA Technical Reports Server (NTRS)

    Litt, Jonathan (Technical Monitor); Ray, Asok

    2004-01-01

    This report presents an application of the recently developed theory of optimal Discrete Event Supervisory (DES) control that is based on a signed real measure of regular languages. The DES control techniques are validated on an aircraft gas turbine engine simulation test bed. The test bed is implemented on a networked computer system in which two computers operate in the client-server mode. Several DES controllers have been tested for engine performance and reliability.

  15. Discrete Events as Units of Perceived Time

    ERIC Educational Resources Information Center

    Liverence, Brandon M.; Scholl, Brian J.

    2012-01-01

    In visual images, we perceive both space (as a continuous visual medium) and objects (that inhabit space). Similarly, in dynamic visual experience, we perceive both continuous time and discrete events. What is the relationship between these units of experience? The most intuitive answer may be similar to the spatial case: time is perceived as an…

  16. Discrete Events as Units of Perceived Time

    ERIC Educational Resources Information Center

    Liverence, Brandon M.; Scholl, Brian J.

    2012-01-01

    In visual images, we perceive both space (as a continuous visual medium) and objects (that inhabit space). Similarly, in dynamic visual experience, we perceive both continuous time and discrete events. What is the relationship between these units of experience? The most intuitive answer may be similar to the spatial case: time is perceived as an

  17. Nonlinear Control and Discrete Event Systems

    NASA Technical Reports Server (NTRS)

    Meyer, George; Null, Cynthia H. (Technical Monitor)

    1995-01-01

    As the operation of large systems becomes ever more dependent on extensive automation, the need for an effective solution to the problem of design and validation of the underlying software becomes more critical. Large systems possesses much detailed structure, typically hierarchical, and they are hybrid. Information processing at the top of the hierarchy is by means of formal logic and sentences; on the bottom it is by means of simple scalar differential equations and functions of time; and in the middle it is by an interacting mix of nonlinear multi-axis differential equations and automata, and functions of time and discrete events. The lecture will address the overall problem as it relates to flight vehicle management, describe the middle level, and offer a design approach that is based on Differential Geometry and Discrete Event Dynamic Systems Theory.

  18. Multiple Autonomous Discrete Event Controllers for Constellations

    NASA Technical Reports Server (NTRS)

    Esposito, Timothy C.

    2003-01-01

    The Multiple Autonomous Discrete Event Controllers for Constellations (MADECC) project is an effort within the National Aeronautics and Space Administration Goddard Space Flight Center's (NASA/GSFC) Information Systems Division to develop autonomous positioning and attitude control for constellation satellites. It will be accomplished using traditional control theory and advanced coordination algorithms developed by the Johns Hopkins University Applied Physics Laboratory (JHU/APL). This capability will be demonstrated in the discrete event control test-bed located at JHU/APL. This project will be modeled for the Leonardo constellation mission, but is intended to be adaptable to any constellation mission. To develop a common software architecture. the controllers will only model very high-level responses. For instance, after determining that a maneuver must be made. the MADECC system will output B (Delta)V (velocity change) value. Lower level systems must then decide which thrusters to fire and for how long to achieve that (Delta)V.

  19. Parallel implementation of VHDL simulations on the Intel iPSC/2 hypercube. Master's thesis

    SciTech Connect

    Comeau, R.C.

    1991-12-01

    VHDL models are executed sequentially in current commercial simulators. As chip designs grow larger and more complex, simulations must run faster. One approach to increasing simulation speed is through parallel processors. This research transforms the behavioral and structural models created by Intermetrics' sequential VHDL simulator into models for parallel execution. The models are simulated on an Intel iPSC/2 hypercube with synchronization of the nodes being achieved by utilizing the Chandy Misra paradigm for discrete-event simulations. Three eight-bit adders, the ripple carry, the carry save, and the carry-lookahead, are each run through the parallel simulator. Simulation time is cut in at least half for all three test cases over the sequential Intermetrics model. Results with regard to speedup are given to show effects of different mappings, varying workloads per node, and overhead due to output messages.

  20. Discrete Event Execution with One-Sided and Two-Sided GVT Algorithms on 216,000 Processor Cores

    SciTech Connect

    Perumalla, Kalyan S; Park, Alfred J; Tipparaju, Vinod

    2014-01-01

    Global virtual time (GVT) computation is a key determinant of the efficiency and runtime dynamics of parallel discrete event simulations (PDES), especially on large-scale parallel platforms. Here, three execution modes of a generalized GVT computation algorithm are studied on high-performance parallel computing systems: (1) a synchronous GVT algorithm that affords ease of implementation, (2) an asynchronous GVT algorithm that is more complex to implement but can relieve blocking latencies, and (3) a variant of the asynchronous GVT algorithm to exploit one-sided communication in extant supercomputing platforms. Performance results are presented of implementations of these algorithms on up to 216,000 cores of a Cray XT5 system, exercised on a range of parameters: optimistic and conservative synchronization, fine- to medium-grained event computation, synthetic and non-synthetic applications, and different lookahead values. Performance of up to 54 billion events executed per second is registered. Detailed PDES-specific runtime metrics are presented to further the understanding of tightly-coupled discrete event dynamics on massively parallel platforms.

  1. Planning and supervision of reactor defueling using discrete event techniques

    SciTech Connect

    Garcia, H.E.; Imel, G.R.; Houshyar, A.

    1995-12-31

    New fuel handling and conditioning activities for the defueling of the Experimental Breeder Reactor II are being performed at Argonne National Laboratory. Research is being conducted to investigate the use of discrete event simulation, analysis, and optimization techniques to plan, supervise, and perform these activities in such a way that productivity can be improved. The central idea is to characterize this defueling operation as a collection of interconnected serving cells, and then apply operational research techniques to identify appropriate planning schedules for given scenarios. In addition, a supervisory system is being developed to provide personnel with on-line information on the progress of fueling tasks and to suggest courses of action to accommodate changing operational conditions. This paper provides an introduction to the research in progress at ANL. In particular, it briefly describes the fuel handling configuration for reactor defueling at ANL, presenting the flow of material from the reactor grid to the interim storage location, and the expected contributions of this work. As an example of the studies being conducted for planning and supervision of fuel handling activities at ANL, an application of discrete event simulation techniques to evaluate different fuel cask transfer strategies is given at the end of the paper.

  2. Parallel Power Grid Simulation Toolkit

    Energy Science and Technology Software Center (ESTSC)

    2015-09-14

    ParGrid is a 'wrapper' that integrates a coupled Power Grid Simulation toolkit consisting of a library to manage the synchronization and communication of independent simulations. The included library code in ParGid, named FSKIT, is intended to support the coupling multiple continuous and discrete even parallel simulations. The code is designed using modern object oriented C++ methods utilizing C++11 and current Boost libraries to ensure compatibility with multiple operating systems and environments.

  3. Parallelizing Timed Petri Net simulations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1993-01-01

    The possibility of using parallel processing to accelerate the simulation of Timed Petri Nets (TPN's) was studied. It was recognized that complex system development tools often transform system descriptions into TPN's or TPN-like models, which are then simulated to obtain information about system behavior. Viewed this way, it was important that the parallelization of TPN's be as automatic as possible, to admit the possibility of the parallelization being embedded in the system design tool. Later years of the grant were devoted to examining the problem of joint performance and reliability analysis, to explore whether both types of analysis could be accomplished within a single framework. In this final report, the results of our studies are summarized. We believe that the problem of parallelizing TPN's automatically for MIMD architectures has been almost completely solved for a large and important class of problems. Our initial investigations into joint performance/reliability analysis are two-fold; it was shown that Monte Carlo simulation, with importance sampling, offers promise of joint analysis in the context of a single tool, and methods for the parallel simulation of general Continuous Time Markov Chains, a model framework within which joint performance/reliability models can be cast, were developed. However, very much more work is needed to determine the scope and generality of these approaches. The results obtained in our two studies, future directions for this type of work, and a list of publications are included.

  4. LAN attack detection using Discrete Event Systems.

    PubMed

    Hubballi, Neminath; Biswas, Santosh; Roopa, S; Ratti, Ritesh; Nandi, Sukumar

    2011-01-01

    Address Resolution Protocol (ARP) is used for determining the link layer or Medium Access Control (MAC) address of a network host, given its Internet Layer (IP) or Network Layer address. ARP is a stateless protocol and any IP-MAC pairing sent by a host is accepted without verification. This weakness in the ARP may be exploited by malicious hosts in a Local Area Network (LAN) by spoofing IP-MAC pairs. Several schemes have been proposed in the literature to circumvent these attacks; however, these techniques either make IP-MAC pairing static, modify the existing ARP, patch operating systems of all the hosts etc. In this paper we propose a Discrete Event System (DES) approach for Intrusion Detection System (IDS) for LAN specific attacks which do not require any extra constraint like static IP-MAC, changing the ARP etc. A DES model is built for the LAN under both a normal and compromised (i.e., spoofed request/response) situation based on the sequences of ARP related packets. Sequences of ARP events in normal and spoofed scenarios are similar thereby rendering the same DES models for both the cases. To create different ARP events under normal and spoofed conditions the proposed technique uses active ARP probing. However, this probing adds extra ARP traffic in the LAN. Following that a DES detector is built to determine from observed ARP related events, whether the LAN is operating under a normal or compromised situation. The scheme also minimizes extra ARP traffic by probing the source IP-MAC pair of only those ARP packets which are yet to be determined as genuine/spoofed by the detector. Also, spoofed IP-MAC pairs determined by the detector are stored in tables to detect other LAN attacks triggered by spoofing namely, man-in-the-middle (MiTM), denial of service etc. The scheme is successfully validated in a test bed. PMID:20804980

  5. Analytic Perturbation Analysis of Discrete Event Dynamic Systems

    SciTech Connect

    Uryasev, S.

    1994-09-01

    This paper considers a new Analytic Perturbation Analysis (APA) approach for Discrete Event Dynamic Systems (DEDS) with discontinuous sample-path functions with respect to control parameters. The performance functions for DEDS usually are formulated as mathematical expectations, which can be calculated only numerically. APA is based on new analytic formulas for the gradients of expectations of indicator functions; therefore, it is called an analytic perturbation analysis. The gradient of performance function may not coincide with the expectation of a gradient of sample-path function (i.e., the interchange formula for the gradient and expectation sign may not be valid). Estimates of gradients can be obtained with one simulation run of the models.

  6. Parallel Event-Driven Global Magnetospheric Hybrid Simulations

    NASA Astrophysics Data System (ADS)

    Omelchenko, Y. A.; Karimabadi, H.; Saule, E.; Catalyurek, U. V.

    2010-12-01

    Global MHD/Hall-MHD magnetospheric models are not able to capture the full diversity of scales and processes that control the Earth's magnetosphere. In order to significantly improve the predictive capabilities of global space weather models, new CPU-efficient algorithms are needed, which could properly account for ion kinetic effects in a large computational domain over long simulation times. To achieve this much expected breakthrough in hybrid (particle ions and fluid electrons) simulations we developed a novel asynchronous time integration technique known as Discrete-Event Simulation (DES). DES replaces conventional time stepping with event processing, which allows to update macro-particles and grid-based fields on their own timescales. This unique capability of DES removes the traditional CFL constraint on the global timestep and enables natural (event-driven) coupling of multi-physics components in a global application model. We report first-ever parallel 2D hybrid DES (HYPERS) runs and compare them with similar time-stepped simulations. We also discuss our undergoing efforts on developing efficient load-balancing strategies for future 3D HYPERS runs on petascale architectures.

  7. Xyce parallel electronic simulator design.

    SciTech Connect

    Thornquist, Heidi K.; Rankin, Eric Lamont; Mei, Ting; Schiek, Richard Louis; Keiter, Eric Richard; Russo, Thomas V.

    2010-09-01

    This document is the Xyce Circuit Simulator developer guide. Xyce has been designed from the 'ground up' to be a SPICE-compatible, distributed memory parallel circuit simulator. While it is in many respects a research code, Xyce is intended to be a production simulator. As such, having software quality engineering (SQE) procedures in place to insure a high level of code quality and robustness are essential. Version control, issue tracking customer support, C++ style guildlines and the Xyce release process are all described. The Xyce Parallel Electronic Simulator has been under development at Sandia since 1999. Historically, Xyce has mostly been funded by ASC, the original focus of Xyce development has primarily been related to circuits for nuclear weapons. However, this has not been the only focus and it is expected that the project will diversify. Like many ASC projects, Xyce is a group development effort, which involves a number of researchers, engineers, scientists, mathmaticians and computer scientists. In addition to diversity of background, it is to be expected on long term projects for there to be a certain amount of staff turnover, as people move on to different projects. As a result, it is very important that the project maintain high software quality standards. The point of this document is to formally document a number of the software quality practices followed by the Xyce team in one place. Also, it is hoped that this document will be a good source of information for new developers.

  8. Modelling machine ensembles with discrete event dynamical system theory

    NASA Technical Reports Server (NTRS)

    Hunter, Dan

    1990-01-01

    Discrete Event Dynamical System (DEDS) theory can be utilized as a control strategy for future complex machine ensembles that will be required for in-space construction. The control strategy involves orchestrating a set of interactive submachines to perform a set of tasks for a given set of constraints such as minimum time, minimum energy, or maximum machine utilization. Machine ensembles can be hierarchically modeled as a global model that combines the operations of the individual submachines. These submachines are represented in the global model as local models. Local models, from the perspective of DEDS theory , are described by the following: a set of system and transition states, an event alphabet that portrays actions that takes a submachine from one state to another, an initial system state, a partial function that maps the current state and event alphabet to the next state, and the time required for the event to occur. Each submachine in the machine ensemble is presented by a unique local model. The global model combines the local models such that the local models can operate in parallel under the additional logistic and physical constraints due to submachine interactions. The global model is constructed from the states, events, event functions, and timing requirements of the local models. Supervisory control can be implemented in the global model by various methods such as task scheduling (open-loop control) or implementing a feedback DEDS controller (closed-loop control).

  9. Discrete Event Supervisory Control Applied to Propulsion Systems

    NASA Technical Reports Server (NTRS)

    Litt, Jonathan S.; Shah, Neerav

    2005-01-01

    The theory of discrete event supervisory (DES) control was applied to the optimal control of a twin-engine aircraft propulsion system and demonstrated in a simulation. The supervisory control, which is implemented as a finite-state automaton, oversees the behavior of a system and manages it in such a way that it maximizes a performance criterion, similar to a traditional optimal control problem. DES controllers can be nested such that a high-level controller supervises multiple lower level controllers. This structure can be expanded to control huge, complex systems, providing optimal performance and increasing autonomy with each additional level. The DES control strategy for propulsion systems was validated using a distributed testbed consisting of multiple computers--each representing a module of the overall propulsion system--to simulate real-time hardware-in-the-loop testing. In the first experiment, DES control was applied to the operation of a nonlinear simulation of a turbofan engine (running in closed loop using its own feedback controller) to minimize engine structural damage caused by a combination of thermal and structural loads. This enables increased on-wing time for the engine through better management of the engine-component life usage. Thus, the engine-level DES acts as a life-extending controller through its interaction with and manipulation of the engine s operation.

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

    SciTech Connect

    Yoginath, Srikanth B; Perumalla, Kalyan S

    2013-01-01

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

  11. Hierarchical Discrete Event Supervisory Control of Aircraft Propulsion Systems

    NASA Technical Reports Server (NTRS)

    Yasar, Murat; Tolani, Devendra; Ray, Asok; Shah, Neerav; Litt, Jonathan S.

    2004-01-01

    This paper presents a hierarchical application of Discrete Event Supervisory (DES) control theory for intelligent decision and control of a twin-engine aircraft propulsion system. A dual layer hierarchical DES controller is designed to supervise and coordinate the operation of two engines of the propulsion system. The two engines are individually controlled to achieve enhanced performance and reliability, necessary for fulfilling the mission objectives. Each engine is operated under a continuously varying control system that maintains the specified performance and a local discrete-event supervisor for condition monitoring and life extending control. A global upper level DES controller is designed for load balancing and overall health management of the propulsion system.

  12. CAISSON: Interconnect Network Simulator

    NASA Technical Reports Server (NTRS)

    Springer, Paul L.

    2006-01-01

    Cray response to HPCS initiative. Model future petaflop computer interconnect. Parallel discrete event simulation techniques for large scale network simulation. Built on WarpIV engine. Run on laptop and Altix 3000. Can be sized up to 1000 simulated nodes per host node. Good parallel scaling characteristics. Flexible: multiple injectors, arbitration strategies, queue iterators, network topologies.

  13. Data parallel sorting for particle simulation

    NASA Technical Reports Server (NTRS)

    Dagum, Leonardo

    1992-01-01

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

  14. Xyce parallel electronic simulator : users' guide.

    SciTech Connect

    Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Warrender, Christina E.; Keiter, Eric Richard; Pawlowski, Roger Patrick

    2011-05-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers; (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only); and (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a unique electrical simulation capability, designed to meet the unique needs of the laboratory.

  15. Hierarchical, modular discrete-event modelling in an object-oriented environment

    SciTech Connect

    Zeigler, B.P.

    1987-11-01

    Hierarchical, modular specification of discrete-event models offers a basis for reusable model bases and hence for enhanced simulation of truly varied design alternatives. The authors describe an environment which realizes the DEVS formalism developed for hierarchical, modular models. It is implemented in PC-Scheme, a powerful Lisp dialect for microcomputers containing an object-oriented programming subsystem. Since both the implementation and the underlying language are accessible to the user, the result is a capable medium for combining simulation modelling and artificial intelligence techniques.

  16. Parallel Discrete Molecular Dynamics Simulation With Speculation and In-Order Commitment*†

    PubMed Central

    Khan, Md. Ashfaquzzaman; Herbordt, Martin C.

    2011-01-01

    Discrete molecular dynamics simulation (DMD) uses simplified and discretized models enabling simulations to advance by event rather than by timestep. DMD is an instance of discrete event simulation and so is difficult to scale: even in this multi-core era, all reported DMD codes are serial. In this paper we discuss the inherent difficulties of scaling DMD and present our method of parallelizing DMD through event-based decomposition. Our method is microarchitecture inspired: speculative processing of events exposes parallelism, while in-order commitment ensures correctness. We analyze the potential of this parallelization method for shared-memory multiprocessors. Achieving scalability required extensive experimentation with scheduling and synchronization methods to mitigate serialization. The speed-up achieved for a variety of system sizes and complexities is nearly 6× on an 8-core and over 9× on a 12-core processor. We present and verify analytical models that account for the achieved performance as a function of available concurrency and architectural limitations. PMID:21822327

  17. Stochastic Parallel PARticle Kinetic Simulator

    SciTech Connect

    Plimpton, Steve; Thompson, Aidan; Slepoy, Alex

    2008-07-01

    SPPARKS is a kinetic Monte Carlo simulator which implements kinetic and Metropolis Monte Carlo solvers in a general way so that they can be hooked to applications of various kinds. Specific applications are implemented in SPPARKS as physical models which generate events (e.g. a diffusive hop or chemical reaction) and execute them one-by-one. Applications can run in paralle so long as the simulation domain can be partitoned spatially so that multiple events can be invoked simultaneously. SPPARKS is used to model various kinds of mesoscale materials science scenarios such as grain growth, surface deposition and growth, and reaction kinetics. It can also be used to develop new Monte Carlo models that hook to the existing solver and paralle infrastructure provided by the code.

  18. Stochastic Parallel PARticle Kinetic Simulator

    Energy Science and Technology Software Center (ESTSC)

    2008-07-01

    SPPARKS is a kinetic Monte Carlo simulator which implements kinetic and Metropolis Monte Carlo solvers in a general way so that they can be hooked to applications of various kinds. Specific applications are implemented in SPPARKS as physical models which generate events (e.g. a diffusive hop or chemical reaction) and execute them one-by-one. Applications can run in paralle so long as the simulation domain can be partitoned spatially so that multiple events can be invokedmore » simultaneously. SPPARKS is used to model various kinds of mesoscale materials science scenarios such as grain growth, surface deposition and growth, and reaction kinetics. It can also be used to develop new Monte Carlo models that hook to the existing solver and paralle infrastructure provided by the code.« less

  19. Simulating the scheduling of parallel supercomputer applications

    SciTech Connect

    Seager, M.K.; Stichnoth, J.M.

    1989-09-19

    An Event Driven Simulator for Evaluating Multiprocessing Scheduling (EDSEMS) disciplines is presented. The simulator is made up of three components: machine model; parallel workload characterization ; and scheduling disciplines for mapping parallel applications (many processes cooperating on the same computation) onto processors. A detailed description of how the simulator is constructed, how to use it and how to interpret the output is also given. Initial results are presented from the simulation of parallel supercomputer workloads using Dog-Eat-Dog,'' Family'' and Gang'' scheduling disciplines. These results indicate that Gang scheduling is far better at giving the number of processors that a job requests than Dog-Eat-Dog or Family scheduling. In addition, the system throughput and turnaround time are not adversely affected by this strategy. 10 refs., 8 figs., 1 tab.

  20. Visualization and Tracking of Parallel CFD Simulations

    NASA Technical Reports Server (NTRS)

    Vaziri, Arsi; Kremenetsky, Mark

    1995-01-01

    We describe a system for interactive visualization and tracking of a 3-D unsteady computational fluid dynamics (CFD) simulation on a parallel computer. CM/AVS, a distributed, parallel implementation of a visualization environment (AVS) runs on the CM-5 parallel supercomputer. A CFD solver is run as a CM/AVS module on the CM-5. Data communication between the solver, other parallel visualization modules, and a graphics workstation, which is running AVS, are handled by CM/AVS. Partitioning of the visualization task, between CM-5 and the workstation, can be done interactively in the visual programming environment provided by AVS. Flow solver parameters can also be altered by programmable interactive widgets. This system partially removes the requirement of storing large solution files at frequent time steps, a characteristic of the traditional 'simulate (yields) store (yields) visualize' post-processing approach.

  1. Parallel processing of a rotating shaft simulation

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.

    1989-01-01

    A FORTRAN program describing the vibration modes of a rotor-bearing system is analyzed for parellelism in this simulation using a Pascal-like structured language. Potential vector operations are also identified. A critical path through the simulation is identified and used in conjunction with somewhat fictitious processor characteristics to determine the time to calculate the problem on a parallel processing system having those characteristics. A parallel processing overhead time is included as a parameter for proper evaluation of the gain over serial calculation. The serial calculation time is determined for the same fictitious system. An improvement of up to 640 percent is possible depending on the value of the overhead time. Based on the analysis, certain conclusions are drawn pertaining to the development needs of parallel processing technology, and to the specification of parallel processing systems to meet computational needs.

  2. Particle simulations on massively parallel machines

    SciTech Connect

    Plimpton, S.

    1993-06-01

    A wide variety of physical phenomena can be modeled with particles. Such simulations pose interesting challenges for parallel machines since the computations are often difficult to load-balance and can require irregular communication. We discuss the size of problems that can be simulated today, obstacles to higher performance, and areas where algorithmic improvements are need. The relevant issues are illustrated with two prototypical simulations: a Monte Carlo model of low-density fluid flow and molecular dynamics.

  3. The Xyce Parallel Electronic Simulator - An Overview

    SciTech Connect

    HUTCHINSON,SCOTT A.; KEITER,ERIC R.; HOEKSTRA,ROBERT J.; WATTS,HERMAN A.; WATERS,ARLON J.; SCHELLS,REGINA L.; WIX,STEVEN D.

    2000-12-08

    The Xyce{trademark} Parallel Electronic Simulator has been written to support the simulation needs of the Sandia National Laboratories electrical designers. As such, the development has focused on providing the capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). In addition, they are providing improved performance for numerical kernels using state-of-the-art algorithms, support for modeling circuit phenomena at a variety of abstraction levels and using object-oriented and modern coding-practices that ensure the code will be maintainable and extensible far into the future. The code is a parallel code in the most general sense of the phrase--a message passing parallel implementation--which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Furthermore, careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved even as the number of processors grows.

  4. Parallel and Distributed System Simulation

    NASA Technical Reports Server (NTRS)

    Dongarra, Jack

    1998-01-01

    This exploratory study initiated our research into the software infrastructure necessary to support the modeling and simulation techniques that are most appropriate for the Information Power Grid. Such computational power grids will use high-performance networking to connect hardware, software, instruments, databases, and people into a seamless web that supports a new generation of computation-rich problem solving environments for scientists and engineers. In this context we looked at evaluating the NetSolve software environment for network computing that leverages the potential of such systems while addressing their complexities. NetSolve's main purpose is to enable the creation of complex applications that harness the immense power of the grid, yet are simple to use and easy to deploy. NetSolve uses a modular, client-agent-server architecture to create a system that is very easy to use. Moreover, it is designed to be highly composable in that it readily permits new resources to be added by anyone willing to do so. In these respects NetSolve is to the Grid what the World Wide Web is to the Internet. But like the Web, the design that makes these wonderful features possible can also impose significant limitations on the performance and robustness of a NetSolve system. This project explored the design innovations that push the performance and robustness of the NetSolve paradigm as far as possible without sacrificing the Web-like ease of use and composability that make it so powerful.

  5. Xyce parallel electronic simulator release notes.

    SciTech Connect

    Keiter, Eric Richard; Hoekstra, Robert John; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Rankin, Eric Lamont; Coffey, Todd Stirling; Pawlowski, Roger Patrick; Santarelli, Keith R.

    2010-05-01

    The Xyce Parallel Electronic Simulator has been written to support, in a rigorous manner, the simulation needs of the Sandia National Laboratories electrical designers. Specific requirements include, among others, the ability to solve extremely large circuit problems by supporting large-scale parallel computing platforms, improved numerical performance and object-oriented code design and implementation. The Xyce release notes describe: Hardware and software requirements New features and enhancements Any defects fixed since the last release Current known defects and defect workarounds For up-to-date information not available at the time these notes were produced, please visit the Xyce web page at http://www.cs.sandia.gov/xyce.

  6. A parallel computational model for GATE simulations.

    PubMed

    Rannou, F R; Vega-Acevedo, N; El Bitar, Z

    2013-12-01

    GATE/Geant4 Monte Carlo simulations are computationally demanding applications, requiring thousands of processor hours to produce realistic results. The classical strategy of distributing the simulation of individual events does not apply efficiently for Positron Emission Tomography (PET) experiments, because it requires a centralized coincidence processing and large communication overheads. We propose a parallel computational model for GATE that handles event generation and coincidence processing in a simple and efficient way by decentralizing event generation and processing but maintaining a centralized event and time coordinator. The model is implemented with the inclusion of a new set of factory classes that can run the same executable in sequential or parallel mode. A Mann-Whitney test shows that the output produced by this parallel model in terms of number of tallies is equivalent (but not equal) to its sequential counterpart. Computational performance evaluation shows that the software is scalable and well balanced. PMID:24070545

  7. Parallel Performance of a Combustion Chemistry Simulation

    DOE PAGESBeta

    Skinner, Gregg; Eigenmann, Rudolf

    1995-01-01

    We used a description of a combustion simulation's mathematical and computational methods to develop a version for parallel execution. The result was a reasonable performance improvement on small numbers of processors. We applied several important programming techniques, which we describe, in optimizing the application. This work has implications for programming languages, compiler design, and software engineering.

  8. Parallel software simulation using PS-nets

    SciTech Connect

    Markov, N.G.; Miroshnichenko, E.A.; Saraikin, A.V.

    1995-09-01

    The requirements of techniques for parallel software simulation are discussed. According to these requirements, techniques on the basis of PS-nets are suggested. The fundamentals of program system modeling by PS-nets are given. The tools developed for modeling are described.

  9. Performance limitations in parallel processor simulations

    NASA Technical Reports Server (NTRS)

    O'Grady, E. Pearse; Wang, Chung-Hsien

    1987-01-01

    A jet-engine model is partitioned and simulated on a parallel processor system consisting of five 8086/8087 floating-point computers. The simulation uses Heun's integration method. A near-optimal parallel simulation (in the sense of minimum execution time) achieves speedup of only 2.13 and efficiency of 42.6 percent, in effect wasting 57.4 percent of the available processing power. A detailed analysis identifies and graphically demonstrates why the system fails to achieve ideal performance (viz., speedup of 5 and efficiency of 100 percent). Inherent characteristics of the problem equations and solution algorithm account for the loss of nearly half of the available processing power. Overheads associated with interprocessor communication and processor synchronization account for only a small fraction of the lost processing power. The effects of these and other factors which limit parallel processor performance are illustrated through real-time timing-analyzer tracers describing the run/idle status of the parallel processors during the simulation.

  10. Safety Discrete Event Models for Holonic Cyclic Manufacturing Systems

    NASA Astrophysics Data System (ADS)

    Ciufudean, Calin; Filote, Constantin

    In this paper the expression “holonic cyclic manufacturing systems” refers to complex assembly/disassembly systems or fork/join systems, kanban systems, and in general, to any discrete event system that transforms raw material and/or components into products. Such a system is said to be cyclic if it provides the same sequence of products indefinitely. This paper considers the scheduling of holonic cyclic manufacturing systems and describes a new approach using Petri nets formalism. We propose an approach to frame the optimum schedule of holonic cyclic manufacturing systems in order to maximize the throughput while minimize the work in process. We also propose an algorithm to verify the optimum schedule.

  11. Parallel Simulation of Unsteady Turbulent Flames

    NASA Technical Reports Server (NTRS)

    Menon, Suresh

    1996-01-01

    Time-accurate simulation of turbulent flames in high Reynolds number flows is a challenging task since both fluid dynamics and combustion must be modeled accurately. To numerically simulate this phenomenon, very large computer resources (both time and memory) are required. Although current vector supercomputers are capable of providing adequate resources for simulations of this nature, the high cost and their limited availability, makes practical use of such machines less than satisfactory. At the same time, the explicit time integration algorithms used in unsteady flow simulations often possess a very high degree of parallelism, making them very amenable to efficient implementation on large-scale parallel computers. Under these circumstances, distributed memory parallel computers offer an excellent near-term solution for greatly increased computational speed and memory, at a cost that may render the unsteady simulations of the type discussed above more feasible and affordable.This paper discusses the study of unsteady turbulent flames using a simulation algorithm that is capable of retaining high parallel efficiency on distributed memory parallel architectures. Numerical studies are carried out using large-eddy simulation (LES). In LES, the scales larger than the grid are computed using a time- and space-accurate scheme, while the unresolved small scales are modeled using eddy viscosity based subgrid models. This is acceptable for the moment/energy closure since the small scales primarily provide a dissipative mechanism for the energy transferred from the large scales. However, for combustion to occur, the species must first undergo mixing at the small scales and then come into molecular contact. Therefore, global models cannot be used. Recently, a new model for turbulent combustion was developed, in which the combustion is modeled, within the subgrid (small-scales) using a methodology that simulates the mixing and the molecular transport and the chemical kinetics within each LES grid cell. Finite-rate kinetics can be included without any closure and this approach actually provides a means to predict the turbulent rates and the turbulent flame speed. The subgrid combustion model requires resolution of the local time scales associated with small-scale mixing, molecular diffusion and chemical kinetics and, therefore, within each grid cell, a significant amount of computations must be carried out before the large-scale (LES resolved) effects are incorporated. Therefore, this approach is uniquely suited for parallel processing and has been implemented on various systems such as: Intel Paragon, IBM SP-2, Cray T3D and SGI Power Challenge (PC) using the system independent Message Passing Interface (MPI) compiler. In this paper, timing data on these machines is reported along with some characteristic results.

  12. Parallel algorithm strategies for circuit simulation.

    SciTech Connect

    Thornquist, Heidi K.; Schiek, Richard Louis; Keiter, Eric Richard

    2010-01-01

    Circuit simulation tools (e.g., SPICE) have become invaluable in the development and design of electronic circuits. However, they have been pushed to their performance limits in addressing circuit design challenges that come from the technology drivers of smaller feature scales and higher integration. Improving the performance of circuit simulation tools through exploiting new opportunities in widely-available multi-processor architectures is a logical next step. Unfortunately, not all traditional simulation applications are inherently parallel, and quickly adapting mature application codes (even codes designed to parallel applications) to new parallel paradigms can be prohibitively difficult. In general, performance is influenced by many choices: hardware platform, runtime environment, languages and compilers used, algorithm choice and implementation, and more. In this complicated environment, the use of mini-applications small self-contained proxies for real applications is an excellent approach for rapidly exploring the parameter space of all these choices. In this report we present a multi-core performance study of Xyce, a transistor-level circuit simulation tool, and describe the future development of a mini-application for circuit simulation.

  13. Parallel node placement method by bubble simulation

    NASA Astrophysics Data System (ADS)

    Nie, Yufeng; Zhang, Weiwei; Qi, Nan; Li, Yiqiang

    2014-03-01

    An efficient Parallel Node Placement method by Bubble Simulation (PNPBS), employing METIS-based domain decomposition (DD) for an arbitrary number of processors is introduced. In accordance with the desired nodal density and Newton’s Second Law of Motion, automatic generation of node sets by bubble simulation has been demonstrated in previous work. Since the interaction force between nodes is short-range, for two distant nodes, their positions and velocities can be updated simultaneously and independently during dynamic simulation, which indicates the inherent property of parallelism, it is quite suitable for parallel computing. In this PNPBS method, the METIS-based DD scheme has been investigated for uniform and non-uniform node sets, and dynamic load balancing is obtained by evenly distributing work among the processors. For the nodes near the common interface of two neighboring subdomains, there is no need for special treatment after dynamic simulation. These nodes have good geometrical properties and a smooth density distribution which is desirable in the numerical solution of partial differential equations (PDEs). The results of numerical examples show that quasi linear speedup in the number of processors and high efficiency are achieved.

  14. Xyce parallel electronic simulator : reference guide.

    SciTech Connect

    Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Warrender, Christina E.; Keiter, Eric Richard; Pawlowski, Roger Patrick

    2011-05-01

    This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide. The Xyce Parallel Electronic Simulator has been written to support, in a rigorous manner, the simulation needs of the Sandia National Laboratories electrical designers. It is targeted specifically to run on large-scale parallel computing platforms but also runs well on a variety of architectures including single processor workstations. It also aims to support a variety of devices and models specific to Sandia needs. This document is intended to complement the Xyce Users Guide. It contains comprehensive, detailed information about a number of topics pertinent to the usage of Xyce. Included in this document is a netlist reference for the input-file commands and elements supported within Xyce; a command line reference, which describes the available command line arguments for Xyce; and quick-references for users of other circuit codes, such as Orcad's PSpice and Sandia's ChileSPICE.

  15. Parallel-distributed mobile robot simulator

    NASA Astrophysics Data System (ADS)

    Okada, Hiroyuki; Sekiguchi, Minoru; Watanabe, Nobuo

    1996-06-01

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

  16. Efficient massively parallel simulation of dynamic channel assignment schemes for wireless cellular communications

    NASA Technical Reports Server (NTRS)

    Greenberg, Albert G.; Lubachevsky, Boris D.; Nicol, David M.; Wright, Paul E.

    1994-01-01

    Fast, efficient parallel algorithms are presented for discrete event simulations of dynamic channel assignment schemes for wireless cellular communication networks. The driving events are call arrivals and departures, in continuous time, to cells geographically distributed across the service area. A dynamic channel assignment scheme decides which call arrivals to accept, and which channels to allocate to the accepted calls, attempting to minimize call blocking while ensuring co-channel interference is tolerably low. Specifically, the scheme ensures that the same channel is used concurrently at different cells only if the pairwise distances between those cells are sufficiently large. Much of the complexity of the system comes from ensuring this separation. The network is modeled as a system of interacting continuous time automata, each corresponding to a cell. To simulate the model, conservative methods are used; i.e., methods in which no errors occur in the course of the simulation and so no rollback or relaxation is needed. Implemented on a 16K processor MasPar MP-1, an elegant and simple technique provides speedups of about 15 times over an optimized serial simulation running on a high speed workstation. A drawback of this technique, typical of conservative methods, is that processor utilization is rather low. To overcome this, new methods were developed that exploit slackness in event dependencies over short intervals of time, thereby raising the utilization to above 50 percent and the speedup over the optimized serial code to about 120 times.

  17. Xyce(™) Parallel Electronic Simulator

    Energy Science and Technology Software Center (ESTSC)

    2013-10-03

    The Xyce Parallel Electronic Simulator simulates electronic circuit behavior in DC, AC, HB, MPDE and transient mode using standard analog (DAE) and/or device (PDE) device models including several age and radiation aware devices. It supports a variety of computing platforms (both serial and parallel) computers. Lastly, it uses a variety of modern solution algorithms dynamic parallel load-balancing and iterative solvers.! ! Xyce is primarily used to simulate the voltage and current behavior of a circuitmore » network (a network of electronic devices connected via a conductive network). As a tool, it is mainly used for the design and analysis of electronic circuits.! ! Kirchoff's conservation laws are enforced over a network using modified nodal analysis. This results in a set of differential algebraic equations (DAEs). The resulting nonlinear problem is solved iteratively using a fully coupled Newton method, which in turn results in a linear system that is solved by either a standard sparse-direct solver or iteratively using Trilinos linear solver packages, also developed at Sandia National Laboratories.« less

  18. Xyce(™) Parallel Electronic Simulator

    SciTech Connect

    2013-10-03

    The Xyce Parallel Electronic Simulator simulates electronic circuit behavior in DC, AC, HB, MPDE and transient mode using standard analog (DAE) and/or device (PDE) device models including several age and radiation aware devices. It supports a variety of computing platforms (both serial and parallel) computers. Lastly, it uses a variety of modern solution algorithms dynamic parallel load-balancing and iterative solvers.! ! Xyce is primarily used to simulate the voltage and current behavior of a circuit network (a network of electronic devices connected via a conductive network). As a tool, it is mainly used for the design and analysis of electronic circuits.! ! Kirchoff's conservation laws are enforced over a network using modified nodal analysis. This results in a set of differential algebraic equations (DAEs). The resulting nonlinear problem is solved iteratively using a fully coupled Newton method, which in turn results in a linear system that is solved by either a standard sparse-direct solver or iteratively using Trilinos linear solver packages, also developed at Sandia National Laboratories.

  19. Parallelism extraction and program restructuring for parallel simulation of digital systems

    SciTech Connect

    Vellandi, B.L.

    1990-01-01

    Two topics currently of interest to the computer aided design (CADF) for the very-large-scale integrated circuit (VLSI) community are using the VHSIC Hardware Description Language (VHDL) effectively and decreasing simulation times of VLSI designs through parallel execution of the simulator. The goal of this research is to increase the degree of parallelism obtainable in VHDL simulation, and consequently to decrease simulation times. The research targets simulation on massively parallel architectures. Experimentation and instrumentation were done on the SIMD Connection Machine. The author discusses her method used to extract parallelism and restructure a VHDL program, experimental results using this method, and requirements for a parallel architecture for fast simulation.

  20. Fracture simulations via massively parallel molecular dynamics

    SciTech Connect

    Holian, B.L.; Abraham, F.F.; Ravelo, R.

    1993-09-01

    Fracture simulations at the atomistic level have heretofore been carried out for relatively small systems of particles, typically 10,000 or less. In order to study anything approaching a macroscopic system, massively parallel molecular dynamics (MD) must be employed. In two spatial dimensions (2D), it is feasible to simulate a sample that is 0.1 {mu}m on a side. We report on recent MD simulations of mode I crack extension under tensile loading at high strain rates. The method of uniaxial, homogeneously expanding periodic boundary conditions was employed to represent tensile stress conditions near the crack tip. The effects of strain rate, temperature, material properties (equation of state and defect energies), and system size were examined. We found that, in order to mimic a bulk sample, several tricks (in addition to expansion boundary conditions) need to be employed: (1) the sample must be pre-strained to nearly the condition at which the crack will spontaneously open; (2) to relieve the stresses at free surfaces, such as the initial notch, annealing by kinetic-energy quenching must be carried out to prevent unwanted rarefactions; (3) sound waves emitted as the crack tip opens and dislocations emitted from the crack tip during blunting must be absorbed by special reservoir regions. The tricks described briefly in this paper will be especially important to carrying out feasible massively parallel 3D simulations via MD.

  1. Parallel Strategies for Crash and Impact Simulations

    SciTech Connect

    Attaway, S.; Brown, K.; Hendrickson, B.; Plimpton, S.

    1998-12-07

    We describe a general strategy we have found effective for parallelizing solid mechanics simula- tions. Such simulations often have several computationally intensive parts, including finite element integration, detection of material contacts, and particle interaction if smoothed particle hydrody- namics is used to model highly deforming materials. The need to balance all of these computations simultaneously is a difficult challenge that has kept many commercial and government codes from being used effectively on parallel supercomputers with hundreds or thousands of processors. Our strategy is to load-balance each of the significant computations independently with whatever bal- ancing technique is most appropriate. The chief benefit is that each computation can be scalably paraIlelized. The drawback is the data exchange between processors and extra coding that must be written to maintain multiple decompositions in a single code. We discuss these trade-offs and give performance results showing this strategy has led to a parallel implementation of a widely-used solid mechanics code that can now be run efficiently on thousands of processors of the Pentium-based Sandia/Intel TFLOPS machine. We illustrate with several examples the kinds of high-resolution, million-element models that can now be simulated routinely. We also look to the future and dis- cuss what possibilities this new capabUity promises, as well as the new set of challenges it poses in material models, computational techniques, and computing infrastructure.

  2. Massively Parallel Direct Simulation of Multiphase Flow

    SciTech Connect

    COOK,BENJAMIN K.; PREECE,DALE S.; WILLIAMS,J.R.

    2000-08-10

    The authors understanding of multiphase physics and the associated predictive capability for multi-phase systems are severely limited by current continuum modeling methods and experimental approaches. This research will deliver an unprecedented modeling capability to directly simulate three-dimensional multi-phase systems at the particle-scale. The model solves the fully coupled equations of motion governing the fluid phase and the individual particles comprising the solid phase using a newly discovered, highly efficient coupled numerical method based on the discrete-element method and the Lattice-Boltzmann method. A massively parallel implementation will enable the solution of large, physically realistic systems.

  3. Optimal Parametric Discrete Event Control: Problem and Solution

    SciTech Connect

    Griffin, Christopher H

    2008-01-01

    We present a novel optimization problem for discrete event control, similar in spirit to the optimal parametric control problem common in statistical process control. In our problem, we assume a known finite state machine plant model $G$ defined over an event alphabet $\\Sigma$ so that the plant model language $L = \\LanM(G)$ is prefix closed. We further assume the existence of a \\textit{base control structure} $M_K$, which may be either a finite state machine or a deterministic pushdown machine. If $K = \\LanM(M_K)$, we assume $K$ is prefix closed and that $K \\subseteq L$. We associate each controllable transition of $M_K$ with a binary variable $X_1,\\dots,X_n$ indicating whether the transition is enabled or not. This leads to a function $M_K(X_1,\\dots,X_n)$, that returns a new control specification depending upon the values of $X_1,\\dots,X_n$. We exhibit a branch-and-bound algorithm to solve the optimization problem $\\min_{X_1,\\dots,X_n}\\max_{w \\in K} C(w)$ such that $M_K(X_1,\\dots,X_n) \\models \\Pi$ and $\\LanM(M_K(X_1,\\dots,X_n)) \\in \\Con(L)$. Here $\\Pi$ is a set of logical assertions on the structure of $M_K(X_1,\\dots,X_n)$, and $M_K(X_1,\\dots,X_n) \\models \\Pi$ indicates that $M_K(X_1,\\dots,X_n)$ satisfies the logical assertions; and, $\\Con(L)$ is the set of controllable sublanguages of $L$.

  4. Improving the Teaching of Discrete-Event Control Systems Using a LEGO Manufacturing Prototype

    ERIC Educational Resources Information Center

    Sanchez, A.; Bucio, J.

    2012-01-01

    This paper discusses the usefulness of employing LEGO as a teaching-learning aid in a post-graduate-level first course on the control of discrete-event systems (DESs). The final assignment of the course is presented, which asks students to design and implement a modular hierarchical discrete-event supervisor for the coordination layer of a…

  5. Improving the Teaching of Discrete-Event Control Systems Using a LEGO Manufacturing Prototype

    ERIC Educational Resources Information Center

    Sanchez, A.; Bucio, J.

    2012-01-01

    This paper discusses the usefulness of employing LEGO as a teaching-learning aid in a post-graduate-level first course on the control of discrete-event systems (DESs). The final assignment of the course is presented, which asks students to design and implement a modular hierarchical discrete-event supervisor for the coordination layer of a

  6. Parallel Numerical Simulations of Water Reservoirs

    NASA Astrophysics Data System (ADS)

    Torres, Pedro; Mangiavacchi, Norberto

    2010-11-01

    The study of the water flow and scalar transport in water reservoirs is important for the determination of the water quality during the initial stages of the reservoir filling and during the life of the reservoir. For this scope, a parallel 2D finite element code for solving the incompressible Navier-Stokes equations coupled with scalar transport was implemented using the message-passing programming model, in order to perform simulations of hidropower water reservoirs in a computer cluster environment. The spatial discretization is based on the MINI element that satisfies the Babuska-Brezzi (BB) condition, which provides sufficient conditions for a stable mixed formulation. All the distributed data structures needed in the different stages of the code, such as preprocessing, solving and post processing, were implemented using the PETSc library. The resulting linear systems for the velocity and the pressure fields were solved using the projection method, implemented by an approximate block LU factorization. In order to increase the parallel performance in the solution of the linear systems, we employ the static condensation method for solving the intermediate velocity at vertex and centroid nodes separately. We compare performance results of the static condensation method with the approach of solving the complete system. In our tests the static condensation method shows better performance for large problems, at the cost of an increased memory usage. Performance results for other intensive parts of the code in a computer cluster are also presented.

  7. Empirical study of parallel LRU simulation algorithms

    NASA Technical Reports Server (NTRS)

    Carr, Eric; Nicol, David M.

    1994-01-01

    This paper reports on the performance of five parallel algorithms for simulating a fully associative cache operating under the LRU (Least-Recently-Used) replacement policy. Three of the algorithms are SIMD, and are implemented on the MasPar MP-2 architecture. Two other algorithms are parallelizations of an efficient serial algorithm on the Intel Paragon. One SIMD algorithm is quite simple, but its cost is linear in the cache size. The two other SIMD algorithm are more complex, but have costs that are independent on the cache size. Both the second and third SIMD algorithms compute all stack distances; the second SIMD algorithm is completely general, whereas the third SIMD algorithm presumes and takes advantage of bounds on the range of reference tags. Both MIMD algorithm implemented on the Paragon are general and compute all stack distances; they differ in one step that may affect their respective scalability. We assess the strengths and weaknesses of these algorithms as a function of problem size and characteristics, and compare their performance on traces derived from execution of three SPEC benchmark programs.

  8. A polymorphic reconfigurable emulator for parallel simulation

    NASA Technical Reports Server (NTRS)

    Parrish, E. A., Jr.; Mcvey, E. S.; Cook, G.

    1980-01-01

    Microprocessor and arithmetic support chip technology was applied to the design of a reconfigurable emulator for real time flight simulation. The system developed consists of master control system to perform all man machine interactions and to configure the hardware to emulate a given aircraft, and numerous slave compute modules (SCM) which comprise the parallel computational units. It is shown that all parts of the state equations can be worked on simultaneously but that the algebraic equations cannot (unless they are slowly varying). Attempts to obtain algorithms that will allow parellel updates are reported. The word length and step size to be used in the SCM's is determined and the architecture of the hardware and software is described.

  9. Parallel Proximity Detection for Computer Simulations

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S. (Inventor); Wieland, Frederick P. (Inventor)

    1998-01-01

    The present invention discloses a system for performing proximity detection in computer simulations on parallel processing architectures utilizing a distribution list which includes movers and sensor coverages which check in and out of grids. Each mover maintains a list of sensors that detect the mover's motion as the mover and sensor coverages check in and out of the grids. Fuzzy grids are included by fuzzy resolution parameters to allow movers and sensor coverages to check in and out of grids without computing exact grid crossings. The movers check in and out of grids while moving sensors periodically inform the grids of their coverage. In addition, a lookahead function is also included for providing a generalized capability without making any limiting assumptions about the particular application to which it is applied. The lookahead function is initiated so that risk-free synchronization strategies never roll back grid events. The lookahead function adds fixed delays as events are scheduled for objects on other nodes.

  10. Parallel Proximity Detection for Computer Simulation

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S. (Inventor); Wieland, Frederick P. (Inventor)

    1997-01-01

    The present invention discloses a system for performing proximity detection in computer simulations on parallel processing architectures utilizing a distribution list which includes movers and sensor coverages which check in and out of grids. Each mover maintains a list of sensors that detect the mover's motion as the mover and sensor coverages check in and out of the grids. Fuzzy grids are includes by fuzzy resolution parameters to allow movers and sensor coverages to check in and out of grids without computing exact grid crossings. The movers check in and out of grids while moving sensors periodically inform the grids of their coverage. In addition, a lookahead function is also included for providing a generalized capability without making any limiting assumptions about the particular application to which it is applied. The lookahead function is initiated so that risk-free synchronization strategies never roll back grid events. The lookahead function adds fixed delays as events are scheduled for objects on other nodes.

  11. Parallel multiscale simulations of a brain aneurysm.

    PubMed

    Grinberg, Leopold; Fedosov, Dmitry A; Karniadakis, George Em

    2013-07-01

    Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr . The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work. PMID:23734066

  12. Parallel multiscale simulations of a brain aneurysm

    NASA Astrophysics Data System (ADS)

    Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

    2013-07-01

    Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver NɛκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NɛκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

  13. Parallel multiscale simulations of a brain aneurysm

    SciTech Connect

    Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

    2013-07-01

    Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

  14. A parallel algorithm for implicit depletant simulations

    NASA Astrophysics Data System (ADS)

    Glaser, Jens; Karas, Andrew S.; Glotzer, Sharon C.

    2015-11-01

    We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant particles are statistically independent and the depletion interaction is short-ranged, depletants are randomly inserted in parallel into the excluded volume surrounding a single translated and/or rotated colloid. A configurational bias scheme is used to enhance the acceptance rate. The method is validated and benchmarked both on multi-core processors and graphics processing units for the case of hard spheres, hemispheres, and discoids. With depletants, we report novel cluster phases in which hemispheres first assemble into spheres, which then form ordered hcp/fcc lattices. The method is significantly faster than any method without cluster moves and that tracks depletants explicitly, for systems of colloid packing fraction ϕc < 0.50, and additionally enables simulation of the fluid-solid transition.

  15. Parallelization of Rocket Engine Simulator Software (PRESS)

    NASA Technical Reports Server (NTRS)

    Cezzar, Ruknet

    1997-01-01

    Parallelization of Rocket Engine System Software (PRESS) project is part of a collaborative effort with Southern University at Baton Rouge (SUBR), University of West Florida (UWF), and Jackson State University (JSU). The second-year funding, which supports two graduate students enrolled in our new Master's program in Computer Science at Hampton University and the principal investigator, have been obtained for the period from October 19, 1996 through October 18, 1997. The key part of the interim report was new directions for the second year funding. This came about from discussions during Rocket Engine Numeric Simulator (RENS) project meeting in Pensacola on January 17-18, 1997. At that time, a software agreement between Hampton University and NASA Lewis Research Center had already been concluded. That agreement concerns off-NASA-site experimentation with PUMPDES/TURBDES software. Before this agreement, during the first year of the project, another large-scale FORTRAN-based software, Two-Dimensional Kinetics (TDK), was being used for translation to an object-oriented language and parallelization experiments. However, that package proved to be too complex and lacking sufficient documentation for effective translation effort to the object-oriented C + + source code. The focus, this time with better documented and more manageable PUMPDES/TURBDES package, was still on translation to C + + with design improvements. At the RENS Meeting, however, the new impetus for the RENS projects in general, and PRESS in particular, has shifted in two important ways. One was closer alignment with the work on Numerical Propulsion System Simulator (NPSS) through cooperation and collaboration with LERC ACLU organization. The other was to see whether and how NASA's various rocket design software can be run over local and intra nets without any radical efforts for redesign and translation into object-oriented source code. There were also suggestions that the Fortran based code be encapsulated in C + + code thereby facilitating reuse without undue development effort. The details are covered in the aforementioned section of the interim report filed on April 28, 1997.

  16. Improving the performance of molecular dynamics simulations on parallel clusters.

    PubMed

    Borstnik, Urban; Hodoscek, Milan; Janezic, Dusanka

    2004-01-01

    In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds. PMID:15032512

  17. Partitioning strategies for parallel KIVA-4 engine simulations

    SciTech Connect

    Torres, D J; Kong, S C

    2008-01-01

    Parallel KIVA-4 is described and simulated in four different engine geometries. The Message Passing-Interface (MPl) was used to parallelize KIVA-4. Par itioning strategies ar accesed in light of the fact that cells can become deactivated and activated during the course of an engine simulation which will affect the load balance between processors.

  18. Discrete event command and control for networked teams with multiple missions

    NASA Astrophysics Data System (ADS)

    Lewis, Frank L.; Hudas, Greg R.; Pang, Chee Khiang; Middleton, Matthew B.; McMurrough, Christopher

    2009-05-01

    During mission execution in military applications, the TRADOC Pamphlet 525-66 Battle Command and Battle Space Awareness capabilities prescribe expectations that networked teams will perform in a reliable manner under changing mission requirements, varying resource availability and reliability, and resource faults. In this paper, a Command and Control (C2) structure is presented that allows for computer-aided execution of the networked team decision-making process, control of force resources, shared resource dispatching, and adaptability to change based on battlefield conditions. A mathematically justified networked computing environment is provided called the Discrete Event Control (DEC) Framework. DEC has the ability to provide the logical connectivity among all team participants including mission planners, field commanders, war-fighters, and robotic platforms. The proposed data management tools are developed and demonstrated on a simulation study and an implementation on a distributed wireless sensor network. The results show that the tasks of multiple missions are correctly sequenced in real-time, and that shared resources are suitably assigned to competing tasks under dynamically changing conditions without conflicts and bottlenecks.

  19. Parallel methods for dynamic simulation of multiple manipulator systems

    NASA Technical Reports Server (NTRS)

    Mcmillan, Scott; Sadayappan, P.; Orin, David E.

    1993-01-01

    In this paper, efficient dynamic simulation algorithms for a system of m manipulators, cooperating to manipulate a large load, are developed; their performance, using two possible forms of parallelism on a general-purpose parallel computer, is investigated. One form, temporal parallelism, is obtained with the use of parallel numerical integration methods. A speedup of 3.78 on four processors of CRAY Y-MP8 was achieved with a parallel four-point block predictor-corrector method for the simulation of a four manipulator system. These multi-point methods suffer from reduced accuracy, and when comparing these runs with a serial integration method, the speedup can be as low as 1.83 for simulations with the same accuracy. To regain the performance lost due to accuracy problems, a second form of parallelism is employed. Spatial parallelism allows most of the dynamics of each manipulator chain to be computed simultaneously. Used exclusively in the four processor case, this form of parallelism in conjunction with a serial integration method results in a speedup of 3.1 on four processors over the best serial method. In cases where there are either more processors available or fewer chains in the system, the multi-point parallel integration methods are still advantageous despite the reduced accuracy because both forms of parallelism can then combine to generate more parallel tasks and achieve greater effective speedups. This paper also includes results for these cases.

  20. Aerodynamic simulation on massively parallel systems

    NASA Technical Reports Server (NTRS)

    Haeuser, Jochem; Simon, Horst D.

    1992-01-01

    This paper briefly addresses the computational requirements for the analysis of complete configurations of aircraft and spacecraft currently under design to be used for advanced transportation in commercial applications as well as in space flight. The discussion clearly shows that massively parallel systems are the only alternative which is both cost effective and on the other hand can provide the necessary TeraFlops, needed to satisfy the narrow design margins of modern vehicles. It is assumed that the solution of the governing physical equations, i.e., the Navier-Stokes equations which may be complemented by chemistry and turbulence models, is done on multiblock grids. This technique is situated between the fully structured approach of classical boundary fitted grids and the fully unstructured tetrahedra grids. A fully structured grid best represents the flow physics, while the unstructured grid gives best geometrical flexibility. The multiblock grid employed is structured within a block, but completely unstructured on the block level. While a completely unstructured grid is not straightforward to parallelize, the above mentioned multiblock grid is inherently parallel, in particular for multiple instruction multiple datastream (MIMD) machines. In this paper guidelines are provided for setting up or modifying an existing sequential code so that a direct parallelization on a massively parallel system is possible. Results are presented for three parallel systems, namely the Intel hypercube, the Ncube hypercube, and the FPS 500 system. Some preliminary results for an 8K CM2 machine will also be mentioned. The code run is the two dimensional grid generation module of Grid, which is a general two dimensional and three dimensional grid generation code for complex geometries. A system of nonlinear Poisson equations is solved. This code is also a good testcase for complex fluid dynamics codes, since the same datastructures are used. All systems provided good speedups, but message passing MIMD systems seem to be best suited for large miltiblock applications.

  1. Parallel-Processing Test Bed For Simulation Software

    NASA Technical Reports Server (NTRS)

    Blech, Richard; Cole, Gary; Townsend, Scott

    1996-01-01

    Second-generation Hypercluster computing system is multiprocessor test bed for research on parallel algorithms for simulation in fluid dynamics, electromagnetics, chemistry, and other fields with large computational requirements but relatively low input/output requirements. Built from standard, off-shelf hardware readily upgraded as improved technology becomes available. System used for experiments with such parallel-processing concepts as message-passing algorithms, debugging software tools, and computational steering. First-generation Hypercluster system described in "Hypercluster Parallel Processor" (LEW-15283).

  2. Parallel simulated annealing algorithms for cell placement on hypercube multiprocessors

    NASA Technical Reports Server (NTRS)

    Banerjee, Prithviraj; Jones, Mark Howard; Sargent, Jeff S.

    1990-01-01

    Two parallel algorithms for standard cell placement using simulated annealing are developed to run on distributed-memory message-passing hypercube multiprocessors. The cells can be mapped in a two-dimensional area of a chip onto processors in an n-dimensional hypercube in two ways, such that both small and large cell exchange and displacement moves can be applied. The computation of the cost function in parallel among all the processors in the hypercube is described, along with a distributed data structure that needs to be stored in the hypercube to support the parallel cost evaluation. A novel tree broadcasting strategy is used extensively for updating cell locations in the parallel environment. A dynamic parallel annealing schedule estimates the errors due to interacting parallel moves and adapts the rate of synchronization automatically. Two novel approaches in controlling error in parallel algorithms are described: heuristic cell coloring and adaptive sequence control.

  3. Parallel architecture for real-time simulation. Master's thesis

    SciTech Connect

    Cockrell, C.D.

    1989-01-01

    This thesis is concerned with the development of a very fast and highly efficient parallel computer architecture for real-time simulation of continuous systems. Currently, several parallel processing systems exist that may be capable of executing a complex simulation in real-time. These systems are examined and the pros and cons of each system discussed. The thesis then introduced a custom-designed parallel architecture based upon The University of Alabama's OPERA architecture. Each component of this system is discussed and rationale presented for its selection. The problem selected, real-time simulation of the Space Shuttle Main Engine for the test and evaluation of the proposed architecture, is explored, identifying the areas where parallelism can be exploited and parallel processing applied. Results from the test and evaluation phase are presented and compared with the results of the same problem that has been processed on a uniprocessor system.

  4. Xyce parallel electronic simulator : users' guide. Version 5.1.

    SciTech Connect

    Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick

    2009-11-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a unique electrical simulation capability, designed to meet the unique needs of the laboratory.

  5. Xyce Parallel Electronic Simulator : users' guide, version 4.1.

    SciTech Connect

    Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick

    2009-02-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a unique electrical simulation capability, designed to meet the unique needs of the laboratory.

  6. Large nonadiabatic quantum molecular dynamics simulations on parallel computers

    NASA Astrophysics Data System (ADS)

    Shimojo, Fuyuki; Ohmura, Satoshi; Mou, Weiwei; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2013-01-01

    We have implemented a quantum molecular dynamics simulation incorporating nonadiabatic electronic transitions on massively parallel computers to study photoexcitation dynamics of electrons and ions. The nonadiabatic quantum molecular dynamics (NAQMD) simulation is based on Casida's linear response time-dependent density functional theory to describe electronic excited states and Tully's fewest-switches surface hopping approach to describe nonadiabatic electron-ion dynamics. To enable large NAQMD simulations, a series of techniques are employed for efficiently calculating long-range exact exchange correction and excited-state forces. The simulation program is parallelized using hybrid spatial and band decomposition, and is tested for various materials.

  7. A conservative approach to parallelizing the Sharks World simulation

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Riffe, Scott E.

    1990-01-01

    Parallelizing a benchmark problem for parallel simulation, the Sharks World, is described. The described solution is conservative, in the sense that no state information is saved, and no 'rollbacks' occur. The used approach illustrates both the principal advantage and principal disadvantage of conservative parallel simulation. The advantage is that by exploiting lookahead an approach was found that dramatically improves the serial execution time, and also achieves excellent speedups. The disadvantage is that if the model rules are changed in such a way that the lookahead is destroyed, it is difficult to modify the solution to accommodate the changes.

  8. Traffic simulations on parallel computers using domain decomposition techniques

    SciTech Connect

    Hanebutte, U.R.; Tentner, A.M.

    1995-12-31

    Large scale simulations of Intelligent Transportation Systems (ITS) can only be achieved by using the computing resources offered by parallel computing architectures. Domain decomposition techniques are proposed which allow the performance of traffic simulations with the standard simulation package TRAF-NETSIM on a 128 nodes IBM SPx parallel supercomputer as well as on a cluster of SUN workstations. Whilst this particular parallel implementation is based on NETSIM, a microscopic traffic simulation model, the presented strategy is applicable to a broad class of traffic simulations. An outer iteration loop must be introduced in order to converge to a global solution. A performance study that utilizes a scalable test network that consist of square-grids is presented, which addresses the performance penalty introduced by the additional iteration loop.

  9. Parallel Signal Processing and System Simulation using aCe

    NASA Technical Reports Server (NTRS)

    Dorband, John E.; Aburdene, Maurice F.

    2003-01-01

    Recently, networked and cluster computation have become very popular for both signal processing and system simulation. A new language is ideally suited for parallel signal processing applications and system simulation since it allows the programmer to explicitly express the computations that can be performed concurrently. In addition, the new C based parallel language (ace C) for architecture-adaptive programming allows programmers to implement algorithms and system simulation applications on parallel architectures by providing them with the assurance that future parallel architectures will be able to run their applications with a minimum of modification. In this paper, we will focus on some fundamental features of ace C and present a signal processing application (FFT).

  10. The virtual marathon: parallel computing supports crowd simulations.

    PubMed

    Yilmaz, Erdal; Isler, Veysi; Cetin, Yasemin Yardimci

    2009-01-01

    To be realistic, an urban model must include appropriate numbers of pedestrians, vehicles, and other dynamic entities. Using a parallel-computing architecture, researchers simulated a marathon with more than a million participants. To simulate participant behavior, they used fuzzy logic on a GPU to perform millions of inferences in real time. PMID:19798860

  11. Parallelization of Rocket Engine Simulator Software (PRESS)

    NASA Technical Reports Server (NTRS)

    Cezzar, Ruknet

    1998-01-01

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

  12. Parallel Optimization with Large Eddy Simulations

    NASA Astrophysics Data System (ADS)

    Talnikar, Chaitanya; Blonigan, Patrick; Bodart, Julien; Wang, Qiqi; Alex Gorodetsky Collaboration; Jasper Snoek Collaboration

    2014-11-01

    For design optimization results to be useful, the model used must be trustworthy. For turbulent flows, Large Eddy Simulations (LES) can capture separation and other phenomena that traditional models such as RANS struggle with. However, optimization with LES can be challenging because of noisy objective function evaluations. This noise is a consequence of the sampling error of turbulent statistics, or long time averaged quantities of interest, such as the drag of an airfoil or heat transfer to a turbine blade. The sampling error causes the objective function to vary noisily with respect to design parameters for finite time simulations. Furthermore, the noise decays very slowly as computational time increases. Therefore, robustness with noisy objective functions is a crucial prerequisite to optimization candidates for LES. One way of dealing with noisy objective functions is to filter the noise using a surrogate model. Bayesian optimization, which uses Gaussian processes as surrogates, has shown promise in optimizing expensive objective functions. The following talk presents a new approach for optimization with LES incorporating these ideas. Applications to flow control of a turbulent channel and the design of a turbine blade trailing edge are also discussed.

  13. Improved task scheduling for parallel simulations. Master's thesis

    SciTech Connect

    McNear, A.E.

    1991-12-01

    The objective of this investigation is to design, analyze, and validate the generation of optimal schedules for simulation systems. Improved performance in simulation execution times can greatly improve the return rate of information provided by such simulations resulting in reduced development costs of future computer/electronic systems. Optimal schedule generation of precedence-constrained task systems including iterative feedback systems such as VHDL or war gaming simulations for execution on a parallel computer is known to be N P-hard. Efficiently parallelizing such problems takes full advantage of present computer technology to achieve a significant reduction in the search times required. Unfortunately, the extreme combinatoric 'explosion' of possible task assignments to processors creates an exponential search space prohibitive on any computer for search algorithms which maintain more than one branch of the search graph at any one time. This work develops various parallel modified backtracking (MBT) search algorithms for execution on an iPSC/2 hypercube that bound the space requirements and produce an optimally minimum schedule with linear speed-up. The parallel MBT search algorithm is validated using various feedback task simulation systems which are scheduled for execution on an iPSC/2 hypercube. The search time, size of the enumerated search space, and communications overhead required to ensure efficient utilization during the parallel search process are analyzed. The various applications indicated appreciable improvement in performance using this method.

  14. Parallel kinetic Monte Carlo simulation of Coulomb glasses

    NASA Astrophysics Data System (ADS)

    Ferrero, E. E.; Kolton, A. B.; Palassini, M.

    2014-08-01

    We develop a parallel rejection algorithm to tackle the problem of low acceptance in Monte Carlo methods, and apply it to the simulation of the hopping conduction in Coulomb glasses using Graphics Processing Units, for which we also parallelize the update of local energies. In two dimensions, our parallel code achieves speedups of up to two orders of magnitude in computing time over an equivalent serial code. We find numerical evidence of a scaling relation for the relaxation of the conductivity at different temperatures.

  15. Efficient parallel simulation of CO2 geologic sequestration insaline aquifers

    SciTech Connect

    Zhang, Keni; Doughty, Christine; Wu, Yu-Shu; Pruess, Karsten

    2007-01-01

    An efficient parallel simulator for large-scale, long-termCO2 geologic sequestration in saline aquifers has been developed. Theparallel simulator is a three-dimensional, fully implicit model thatsolves large, sparse linear systems arising from discretization of thepartial differential equations for mass and energy balance in porous andfractured media. The simulator is based on the ECO2N module of the TOUGH2code and inherits all the process capabilities of the single-CPU TOUGH2code, including a comprehensive description of the thermodynamics andthermophysical properties of H2O-NaCl- CO2 mixtures, modeling singleand/or two-phase isothermal or non-isothermal flow processes, two-phasemixtures, fluid phases appearing or disappearing, as well as saltprecipitation or dissolution. The new parallel simulator uses MPI forparallel implementation, the METIS software package for simulation domainpartitioning, and the iterative parallel linear solver package Aztec forsolving linear equations by multiple processors. In addition, theparallel simulator has been implemented with an efficient communicationscheme. Test examples show that a linear or super-linear speedup can beobtained on Linux clusters as well as on supercomputers. Because of thesignificant improvement in both simulation time and memory requirement,the new simulator provides a powerful tool for tackling larger scale andmore complex problems than can be solved by single-CPU codes. Ahigh-resolution simulation example is presented that models buoyantconvection, induced by a small increase in brine density caused bydissolution of CO2.

  16. Xyce Parallel Electronic Simulator : users' guide, version 2.0.

    SciTech Connect

    Hoekstra, Robert John; Waters, Lon J.; Rankin, Eric Lamont; Fixel, Deborah A.; Russo, Thomas V.; Keiter, Eric Richard; Hutchinson, Scott Alan; Pawlowski, Roger Patrick; Wix, Steven D.

    2004-06-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator capable of simulating electrical circuits at a variety of abstraction levels. Primarily, Xyce has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability the current state-of-the-art in the following areas: {sm_bullet} Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. {sm_bullet} Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. {sm_bullet} Device models which are specifically tailored to meet Sandia's needs, including many radiation-aware devices. {sm_bullet} A client-server or multi-tiered operating model wherein the numerical kernel can operate independently of the graphical user interface (GUI). {sm_bullet} Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing of computing platforms. These include serial, shared-memory and distributed-memory parallel implementation - which allows it to run efficiently on the widest possible number parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. One feature required by designers is the ability to add device models, many specific to the needs of Sandia, to the code. To this end, the device package in the Xyce These input formats include standard analytical models, behavioral models look-up Parallel Electronic Simulator is designed to support a variety of device model inputs. tables, and mesh-level PDE device models. Combined with this flexible interface is an architectural design that greatly simplifies the addition of circuit models. One of the most important feature of Xyce is in providing a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia now has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods) research and development can be performed. Ultimately, these capabilities are migrated to end users.

  17. A hybrid parallel framework for the cellular Potts model simulations

    SciTech Connect

    Jiang, Yi; He, Kejing; Dong, Shoubin

    2009-01-01

    The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).

  18. On the hierarchical parallelization of ab initio simulations

    NASA Astrophysics Data System (ADS)

    Ruiz-Barragan, Sergi; Ishimura, Kazuya; Shiga, Motoyuki

    2016-02-01

    A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.

  19. Parallel runway requirement analysis study. Volume 2: Simulation manual

    NASA Technical Reports Server (NTRS)

    Ebrahimi, Yaghoob S.; Chun, Ken S.

    1993-01-01

    This document is a user manual for operating the PLAND_BLUNDER (PLB) simulation program. This simulation is based on two aircraft approaching parallel runways independently and using parallel Instrument Landing System (ILS) equipment during Instrument Meteorological Conditions (IMC). If an aircraft should deviate from its assigned localizer course toward the opposite runway, this constitutes a blunder which could endanger the aircraft on the adjacent path. The worst case scenario would be if the blundering aircraft were unable to recover and continue toward the adjacent runway. PLAND_BLUNDER is a Monte Carlo-type simulation which employs the events and aircraft positioning during such a blunder situation. The model simulates two aircraft performing parallel ILS approaches using Instrument Flight Rules (IFR) or visual procedures. PLB uses a simple movement model and control law in three dimensions (X, Y, Z). The parameters of the simulation inputs and outputs are defined in this document along with a sample of the statistical analysis. This document is the second volume of a two volume set. Volume 1 is a description of the application of the PLB to the analysis of close parallel runway operations.

  20. Parallelization of a Monte Carlo particle transport simulation code

    NASA Astrophysics Data System (ADS)

    Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.

    2010-05-01

    We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.

  1. A network of discrete events for the representation and analysis of diffusion dynamics.

    PubMed

    Pintus, Alberto M; Pazzona, Federico G; Demontis, Pierfranco; Suffritti, Giuseppe B

    2015-11-14

    We developed a coarse-grained description of the phenomenology of diffusive processes, in terms of a space of discrete events and its representation as a network. Once a proper classification of the discrete events underlying the diffusive process is carried out, their transition matrix is calculated on the basis of molecular dynamics data. This matrix can be represented as a directed, weighted network where nodes represent discrete events, and the weight of edges is given by the probability that one follows the other. The structure of this network reflects dynamical properties of the process of interest in such features as its modularity and the entropy rate of nodes. As an example of the applicability of this conceptual framework, we discuss here the physics of diffusion of small non-polar molecules in a microporous material, in terms of the structure of the corresponding network of events, and explain on this basis the diffusivity trends observed. A quantitative account of these trends is obtained by considering the contribution of the various events to the displacement autocorrelation function. PMID:26567654

  2. A network of discrete events for the representation and analysis of diffusion dynamics

    NASA Astrophysics Data System (ADS)

    Pintus, Alberto M.; Pazzona, Federico G.; Demontis, Pierfranco; Suffritti, Giuseppe B.

    2015-11-01

    We developed a coarse-grained description of the phenomenology of diffusive processes, in terms of a space of discrete events and its representation as a network. Once a proper classification of the discrete events underlying the diffusive process is carried out, their transition matrix is calculated on the basis of molecular dynamics data. This matrix can be represented as a directed, weighted network where nodes represent discrete events, and the weight of edges is given by the probability that one follows the other. The structure of this network reflects dynamical properties of the process of interest in such features as its modularity and the entropy rate of nodes. As an example of the applicability of this conceptual framework, we discuss here the physics of diffusion of small non-polar molecules in a microporous material, in terms of the structure of the corresponding network of events, and explain on this basis the diffusivity trends observed. A quantitative account of these trends is obtained by considering the contribution of the various events to the displacement autocorrelation function.

  3. Efficient parallel CFD-DEM simulations using OpenMP

    NASA Astrophysics Data System (ADS)

    Amritkar, Amit; Deb, Surya; Tafti, Danesh

    2014-01-01

    The paper describes parallelization strategies for the Discrete Element Method (DEM) used for simulating dense particulate systems coupled to Computational Fluid Dynamics (CFD). While the field equations of CFD are best parallelized by spatial domain decomposition techniques, the N-body particulate phase is best parallelized over the number of particles. When the two are coupled together, both modes are needed for efficient parallelization. It is shown that under these requirements, OpenMP thread based parallelization has advantages over MPI processes. Two representative examples, fairly typical of dense fluid-particulate systems are investigated, including the validation of the DEM-CFD and thermal-DEM implementation with experiments. Fluidized bed calculations are performed on beds with uniform particle loading, parallelized with MPI and OpenMP. It is shown that as the number of processing cores and the number of particles increase, the communication overhead of building ghost particle lists at processor boundaries dominates time to solution, and OpenMP which does not require this step is about twice as fast as MPI. In rotary kiln heat transfer calculations, which are characterized by spatially non-uniform particle distributions, the low overhead of switching the parallelization mode in OpenMP eliminates the load imbalances, but introduces increased overheads in fetching non-local data. In spite of this, it is shown that OpenMP is between 50-90% faster than MPI.

  4. Dynamics and optimal number of replicas in parallel tempering simulations

    NASA Astrophysics Data System (ADS)

    Nadler, Walter; Hansmann, Ulrich H. E.

    2007-12-01

    We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the control parameter discretization allow a treatment independent of the system in question. By analyzing mean first passage times across the control parameter space, we find an expression for the optimal number of replicas in simulations covering a given temperature range. Our results suggest a particular protocol to optimize the number of replicas in actual simulations.

  5. Xyce Parallel Electronic Simulator : reference guide, version 4.1.

    SciTech Connect

    Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick

    2009-02-01

    This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide.

  6. Xyce parallel electronic simulator reference guide, version 6.0.

    SciTech Connect

    Keiter, Eric Richard; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Verley, Jason C.; Fixel, Deborah A.; Coffey, Todd Stirling; Pawlowski, Roger Patrick; Warrender, Christina E.; Baur, David G.

    2013-08-01

    This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1].

  7. Xyce parallel electronic simulator reference guide, version 6.1

    SciTech Connect

    Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Sholander, Peter E.; Thornquist, Heidi K.; Verley, Jason C.; Baur, David Gregory

    2014-03-01

    This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide [1] .

  8. Parallelization Strategies for Large Particle Simulations in Astrophysics

    NASA Astrophysics Data System (ADS)

    Pattabiraman, Bharath

    The modeling of collisional N-body stellar systems is a topic of great current interest in several branches of astrophysics and cosmology. These systems are dominated by the physics of relaxation, the collective effect of many weak, random gravitational encounters between stars. They connect directly to our understanding of star clusters, and to the formation of exotic objects such as X-ray binaries, pulsars, and massive black holes. As a prototypical multi-physics, multi-scale problem, the numerical simulation of such systems is computationally intensive, and can only be achieved through high-performance computing. The goal of this thesis is to present parallelization and optimization strategies that can be used to develop efficient computational tools for simulating collisional N-body systems. This leads to major advances: 1) From an astrophysics perspective, these tools enable the study of new physical regimes out of reach by previous simulations. They also lead to much more complete parameter space exploration, allowing direct comparison of numerical results to observational data. 2) On the high-performance computing front, efficient parallelization of a multi-component application requires the meticulous redesign of the various components, as well as innovative parallelization techniques. Many of the challenges faced in this process lie at the very heart of high-performance computing research, including achieving optimal load balancing, maximizing utilization of computational resources, and making effective use of different parallel platforms. For modeling collisional N-body systems, a Monte Carlo approach provides ideal balance between speed and accuracy, as opposed to the more accurate but less scalable direct N-body method. We describe the development of a new version of the Cluster Monte Carlo (CMC) code capable of simulating systems with a realistic number of stars, while accounting for all important physical processes. This efficient and scalable parallel version of CMC runs on both GPUs and distributed-memory architectures. We introduce various parallelization and optimization strategies that include the use of best-suited data structures, adaptive data partitioning schemes, parallel random number generation, parallel I/O, and optimized parallel algorithms, resulting in a very desirable scalability of the run-time with the processor number.

  9. The parallel subdomain-levelset deflation method in reservoir simulation

    NASA Astrophysics Data System (ADS)

    van der Linden, J. H.; Jönsthövel, T. B.; Lukyanov, A. A.; Vuik, C.

    2016-01-01

    Extreme and isolated eigenvalues are known to be harmful to the convergence of an iterative solver. These eigenvalues can be produced by strong heterogeneity in the underlying physics. We can improve the quality of the spectrum by 'deflating' the harmful eigenvalues. In this work, deflation is applied to linear systems in reservoir simulation. In particular, large, sudden differences in the permeability produce extreme eigenvalues. The number and magnitude of these eigenvalues is linked to the number and magnitude of the permeability jumps. Two deflation methods are discussed. Firstly, we state that harmonic Ritz eigenvector deflation, which computes the deflation vectors from the information produced by the linear solver, is unfeasible in modern reservoir simulation due to high costs and lack of parallelism. Secondly, we test a physics-based subdomain-levelset deflation algorithm that constructs the deflation vectors a priori. Numerical experiments show that both methods can improve the performance of the linear solver. We highlight the fact that subdomain-levelset deflation is particularly suitable for a parallel implementation. For cases with well-defined permeability jumps of a factor 104 or higher, parallel physics-based deflation has potential in commercial applications. In particular, the good scalability of parallel subdomain-levelset deflation combined with the robust parallel preconditioner for deflated system suggests the use of this method as an alternative for AMG.

  10. Random number generators for massively parallel simulations on GPU

    NASA Astrophysics Data System (ADS)

    Manssen, M.; Weigel, M.; Hartmann, A. K.

    2012-08-01

    High-performance streams of (pseudo) random numbers are crucial for the efficient implementation of countless stochastic algorithms, most importantly, Monte Carlo simulations and molecular dynamics simulations with stochastic thermostats. A number of implementations of random number generators has been discussed for GPU platforms before and some generators are even included in the CUDA supporting libraries. Nevertheless, not all of these generators are well suited for highly parallel applications where each thread requires its own generator instance. For this specific situation encountered, for instance, in simulations of lattice models, most of the high-quality generators with large states such as Mersenne twister cannot be used efficiently without substantial changes. We provide a broad review of existing CUDA variants of random-number generators and present the CUDA implementation of a new massively parallel high-quality, high-performance generator with a small memory load overhead.

  11. PRATHAM: Parallel Thermal Hydraulics Simulations using Advanced Mesoscopic Methods

    SciTech Connect

    Joshi, Abhijit S; Jain, Prashant K; Mudrich, Jaime A; Popov, Emilian L

    2012-01-01

    At the Oak Ridge National Laboratory, efforts are under way to develop a 3D, parallel LBM code called PRATHAM (PaRAllel Thermal Hydraulic simulations using Advanced Mesoscopic Methods) to demonstrate the accuracy and scalability of LBM for turbulent flow simulations in nuclear applications. The code has been developed using FORTRAN-90, and parallelized using the message passing interface MPI library. Silo library is used to compact and write the data files, and VisIt visualization software is used to post-process the simulation data in parallel. Both the single relaxation time (SRT) and multi relaxation time (MRT) LBM schemes have been implemented in PRATHAM. To capture turbulence without prohibitively increasing the grid resolution requirements, an LES approach [5] is adopted allowing large scale eddies to be numerically resolved while modeling the smaller (subgrid) eddies. In this work, a Smagorinsky model has been used, which modifies the fluid viscosity by an additional eddy viscosity depending on the magnitude of the rate-of-strain tensor. In LBM, this is achieved by locally varying the relaxation time of the fluid.

  12. Parallelization of Program to Optimize Simulated Trajectories (POST3D)

    NASA Technical Reports Server (NTRS)

    Hammond, Dana P.; Korte, John J. (Technical Monitor)

    2001-01-01

    This paper describes the parallelization of the Program to Optimize Simulated Trajectories (POST3D). POST3D uses a gradient-based optimization algorithm that reaches an optimum design point by moving from one design point to the next. The gradient calculations required to complete the optimization process, dominate the computational time and have been parallelized using a Single Program Multiple Data (SPMD) on a distributed memory NUMA (non-uniform memory access) architecture. The Origin2000 was used for the tests presented.

  13. Reusable component model development approach for parallel and distributed simulation.

    PubMed

    Zhu, Feng; Yao, Yiping; Chen, Huilong; Yao, Feng

    2014-01-01

    Model reuse is a key issue to be resolved in parallel and distributed simulation at present. However, component models built by different domain experts usually have diversiform interfaces, couple tightly, and bind with simulation platforms closely. As a result, they are difficult to be reused across different simulation platforms and applications. To address the problem, this paper first proposed a reusable component model framework. Based on this framework, then our reusable model development approach is elaborated, which contains two phases: (1) domain experts create simulation computational modules observing three principles to achieve their independence; (2) model developer encapsulates these simulation computational modules with six standard service interfaces to improve their reusability. The case study of a radar model indicates that the model developed using our approach has good reusability and it is easy to be used in different simulation platforms and applications. PMID:24729751

  14. Reusable Component Model Development Approach for Parallel and Distributed Simulation

    PubMed Central

    Zhu, Feng; Yao, Yiping; Chen, Huilong; Yao, Feng

    2014-01-01

    Model reuse is a key issue to be resolved in parallel and distributed simulation at present. However, component models built by different domain experts usually have diversiform interfaces, couple tightly, and bind with simulation platforms closely. As a result, they are difficult to be reused across different simulation platforms and applications. To address the problem, this paper first proposed a reusable component model framework. Based on this framework, then our reusable model development approach is elaborated, which contains two phases: (1) domain experts create simulation computational modules observing three principles to achieve their independence; (2) model developer encapsulates these simulation computational modules with six standard service interfaces to improve their reusability. The case study of a radar model indicates that the model developed using our approach has good reusability and it is easy to be used in different simulation platforms and applications. PMID:24729751

  15. Potts-model grain growth simulations: Parallel algorithms and applications

    SciTech Connect

    Wright, S.A.; Plimpton, S.J.; Swiler, T.P.

    1997-08-01

    Microstructural morphology and grain boundary properties often control the service properties of engineered materials. This report uses the Potts-model to simulate the development of microstructures in realistic materials. Three areas of microstructural morphology simulations were studied. They include the development of massively parallel algorithms for Potts-model grain grow simulations, modeling of mass transport via diffusion in these simulated microstructures, and the development of a gradient-dependent Hamiltonian to simulate columnar grain growth. Potts grain growth models for massively parallel supercomputers were developed for the conventional Potts-model in both two and three dimensions. Simulations using these parallel codes showed self similar grain growth and no finite size effects for previously unapproachable large scale problems. In addition, new enhancements to the conventional Metropolis algorithm used in the Potts-model were developed to accelerate the calculations. These techniques enable both the sequential and parallel algorithms to run faster and use essentially an infinite number of grain orientation values to avoid non-physical grain coalescence events. Mass transport phenomena in polycrystalline materials were studied in two dimensions using numerical diffusion techniques on microstructures generated using the Potts-model. The results of the mass transport modeling showed excellent quantitative agreement with one dimensional diffusion problems, however the results also suggest that transient multi-dimension diffusion effects cannot be parameterized as the product of the grain boundary diffusion coefficient and the grain boundary width. Instead, both properties are required. Gradient-dependent grain growth mechanisms were included in the Potts-model by adding an extra term to the Hamiltonian. Under normal grain growth, the primary driving term is the curvature of the grain boundary, which is included in the standard Potts-model Hamiltonian.

  16. Xyce Parallel Electronic Simulator Users Guide Version 6.2.

    SciTech Connect

    Keiter, Eric R.; Mei, Ting; Russo, Thomas V.; Schiek, Richard; Sholander, Peter E.; Thornquist, Heidi K.; Verley, Jason; Baur, David Gregory

    2014-09-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. Trademarks The information herein is subject to change without notice. Copyright c 2002-2014 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce%40sandia.gov (outside Sandia) xyce-sandia%40sandia.gov (Sandia only)

  17. Noise simulation in cone beam CT imaging with parallel computing

    PubMed Central

    Tu, Shu-Ju; Shaw, Chris C; Chen, Lingyun

    2007-01-01

    We developed a computer noise simulation model for cone beam computed tomography imaging using a general purpose PC cluster. This model uses a mono-energetic x-ray approximation and allows us to investigate three primary performance components, specifically quantum noise, detector blurring and additive system noise. A parallel random number generator based on the Weyl sequence was implemented in the noise simulation and a visualization technique was accordingly developed to validate the quality of the parallel random number generator. In our computer simulation model, three-dimensional (3D) phantoms were mathematically modelled and used to create 450 analytical projections, which were then sampled into digital image data. Quantum noise was simulated and added to the analytical projection image data, which were then filtered to incorporate flat panel detector blurring. Additive system noise was generated and added to form the final projection images. The Feldkamp algorithm was implemented and used to reconstruct the 3D images of the phantoms. A 24 dual-Xeon PC cluster was used to compute the projections and reconstructed images in parallel with each CPU processing 10 projection views for a total of 450 views. Based on this computer simulation system, simulated cone beam CT images were generated for various phantoms and technique settings. Noise power spectra for the flat panel x-ray detector and reconstructed images were then computed to characterize the noise properties. As an example among the potential applications of our noise simulation model, we showed that images of low contrast objects can be produced and used for image quality evaluation. PMID:16481694

  18. Determining the significance of associations between two series of discrete events : bootstrap methods /

    SciTech Connect

    Niehof, Jonathan T.; Morley, Steven K.

    2012-01-01

    We review and develop techniques to determine associations between series of discrete events. The bootstrap, a nonparametric statistical method, allows the determination of the significance of associations with minimal assumptions about the underlying processes. We find the key requirement for this method: one of the series must be widely spaced in time to guarantee the theoretical applicability of the bootstrap. If this condition is met, the calculated significance passes a reasonableness test. We conclude with some potential future extensions and caveats on the applicability of these methods. The techniques presented have been implemented in a Python-based software toolkit.

  19. Sequential Window Diagnoser for Discrete-Event Systems Under Unreliable Observations

    SciTech Connect

    Wen-Chiao Lin; Humberto E. Garcia; David Thorsley; Tae-Sic Yoo

    2009-09-01

    This paper addresses the issue of counting the occurrence of special events in the framework of partiallyobserved discrete-event dynamical systems (DEDS). Developed diagnosers referred to as sequential window diagnosers (SWDs) utilize the stochastic diagnoser probability transition matrices developed in [9] along with a resetting mechanism that allows on-line monitoring of special event occurrences. To illustrate their performance, the SWDs are applied to detect and count the occurrence of special events in a particular DEDS. Results show that SWDs are able to accurately track the number of times special events occur.

  20. Supervisor Localization: A Top-Down Approach to Distributed Control of Discrete-Event Systems

    NASA Astrophysics Data System (ADS)

    Cai, K.; Wonham, W. M.

    2009-03-01

    A purely distributed control paradigm is proposed for discrete-event systems (DES). In contrast to control by one or more external supervisors, distributed control aims to design built-in strategies for individual agents. First a distributed optimal nonblocking control problem is formulated. To solve it, a top-down localization procedure is developed which systematically decomposes an external supervisor into local controllers while preserving optimality and nonblockingness. An efficient localization algorithm is provided to carry out the computation, and an automated guided vehicles (AGV) example presented for illustration. Finally, the 'easiest' and 'hardest' boundary cases of localization are discussed.

  1. Scalability study of parallel spatial direct numerical simulation code on IBM SP1 parallel supercomputer

    NASA Technical Reports Server (NTRS)

    Hanebutte, Ulf R.; Joslin, Ronald D.; Zubair, Mohammad

    1994-01-01

    The implementation and the performance of a parallel spatial direct numerical simulation (PSDNS) code are reported for the IBM SP1 supercomputer. The spatially evolving disturbances that are associated with laminar-to-turbulent in three-dimensional boundary-layer flows are computed with the PS-DNS code. By remapping the distributed data structure during the course of the calculation, optimized serial library routines can be utilized that substantially increase the computational performance. Although the remapping incurs a high communication penalty, the parallel efficiency of the code remains above 40% for all performed calculations. By using appropriate compile options and optimized library routines, the serial code achieves 52-56 Mflops on a single node of the SP1 (45% of theoretical peak performance). The actual performance of the PSDNS code on the SP1 is evaluated with a 'real world' simulation that consists of 1.7 million grid points. One time step of this simulation is calculated on eight nodes of the SP1 in the same time as required by a Cray Y/MP for the same simulation. The scalability information provides estimated computational costs that match the actual costs relative to changes in the number of grid points.

  2. Parallel algorithms for simulating continuous time Markov chains

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Heidelberger, Philip

    1992-01-01

    We have previously shown that the mathematical technique of uniformization can serve as the basis of synchronization for the parallel simulation of continuous-time Markov chains. This paper reviews the basic method and compares five different methods based on uniformization, evaluating their strengths and weaknesses as a function of problem characteristics. The methods vary in their use of optimism, logical aggregation, communication management, and adaptivity. Performance evaluation is conducted on the Intel Touchstone Delta multiprocessor, using up to 256 processors.

  3. Time parallelization of advanced operation scenario simulations of ITER plasma

    SciTech Connect

    Samaddar, D.; Casper, T. A.; Kim, S. H.; Berry, Lee A; Elwasif, Wael R; Batchelor, Donald B; Houlberg, Wayne A

    2013-01-01

    This work demonstrates that simulations of advanced burning plasma operation scenarios can be successfully parallelized in time using the parareal algorithm. CORSICA - an advanced operation scenario code for tokamak plasmas is used as a test case. This is a unique application since the parareal algorithm has so far been applied to relatively much simpler systems except for the case of turbulence. In the present application, a computational gain of an order of magnitude has been achieved which is extremely promising. A successful implementation of the Parareal algorithm to codes like CORSICA ushers in the possibility of time efficient simulations of ITER plasmas.

  4. Xyce Parallel Electronic Simulator - Users' Guide Version 2.1.

    SciTech Connect

    Hutchinson, Scott A; Hoekstra, Robert J.; Russo, Thomas V.; Rankin, Eric; Pawlowski, Roger P.; Fixel, Deborah A; Schiek, Richard; Bogdan, Carolyn W.; Shirley, David N.; Campbell, Phillip M.; Keiter, Eric R.

    2005-06-01

    This manual describes the use of theXyceParallel Electronic Simulator.Xycehasbeen designed as a SPICE-compatible, high-performance analog circuit simulator, andhas been written to support the simulation needs of the Sandia National Laboratorieselectrical designers. This development has focused on improving capability over thecurrent state-of-the-art in the following areas:%04Capability to solve extremely large circuit problems by supporting large-scale par-allel computing platforms (up to thousands of processors). Note that this includessupport for most popular parallel and serial computers.%04Improved performance for all numerical kernels (e.g., time integrator, nonlinearand linear solvers) through state-of-the-art algorithms and novel techniques.%04Device models which are specifically tailored to meet Sandia's needs, includingmany radiation-aware devices.3 XyceTMUsers' Guide%04Object-oriented code design and implementation using modern coding practicesthat ensure that theXyceParallel Electronic Simulator will be maintainable andextensible far into the future.Xyceis a parallel code in the most general sense of the phrase - a message passingparallel implementation - which allows it to run efficiently on the widest possible numberof computing platforms. These include serial, shared-memory and distributed-memoryparallel as well as heterogeneous platforms. Careful attention has been paid to thespecific nature of circuit-simulation problems to ensure that optimal parallel efficiencyis achieved as the number of processors grows.The development ofXyceprovides a platform for computational research and de-velopment aimed specifically at the needs of the Laboratory. WithXyce, Sandia hasan %22in-house%22 capability with which both new electrical (e.g., device model develop-ment) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms)research and development can be performed. As a result,Xyceis a unique electricalsimulation capability, designed to meet the unique needs of the laboratory.4 XyceTMUsers' GuideAcknowledgementsThe authors would like to acknowledge the entire Sandia National Laboratories HPEMS(High Performance Electrical Modeling and Simulation) team, including Steve Wix, CarolynBogdan, Regina Schells, Ken Marx, Steve Brandon and Bill Ballard, for their support onthis project. We also appreciate very much the work of Jim Emery, Becky Arnold and MikeWilliamson for the help in reviewing this document.Lastly, a very special thanks to Hue Lai for typesetting this document with LATEX.TrademarksThe information herein is subject to change without notice.Copyrightc 2002-2003 Sandia Corporation. All rights reserved.XyceTMElectronic Simulator andXyceTMtrademarks of Sandia Corporation.Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence DesignSystems, Inc.Silicon Graphics, the Silicon Graphics logo and IRIX are registered trademarks of SiliconGraphics, Inc.Microsoft, Windows and Windows 2000 are registered trademark of Microsoft Corporation.Solaris and UltraSPARC are registered trademarks of Sun Microsystems Corporation.Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation.HP and Alpha are registered trademarks of Hewlett-Packard company.Amtec and TecPlot are trademarks of Amtec Engineering, Inc.Xyce's expression library is based on that inside Spice 3F5 developed by the EECS De-partment at the University of California.All other trademarks are property of their respective owners.ContactsBug Reportshttp://tvrusso.sandia.gov/bugzillaEmailxyce-support%40sandia.govWorld Wide Webhttp://www.cs.sandia.gov/xyce5 XyceTMUsers' GuideThis page is left intentionally blank6

  5. Dynamic Load Balancing Strategies for Parallel Reacting Flow Simulations

    NASA Astrophysics Data System (ADS)

    Pisciuneri, Patrick; Meneses, Esteban; Givi, Peyman

    2014-11-01

    Load balancing in parallel computing aims at distributing the work as evenly as possible among the processors. This is a critical issue in the performance of parallel, time accurate, flow simulators. The constraint of time accuracy requires that all processes must be finished with their calculation for a given time step before any process can begin calculation of the next time step. Thus, an irregularly balanced compute load will result in idle time for many processes for each iteration and thus increased walltimes for calculations. Two existing, dynamic load balancing approaches are applied to the simplified case of a partially stirred reactor for methane combustion. The first is Zoltan, a parallel partitioning, load balancing, and data management library developed at the Sandia National Laboratories. The second is Charm++, which is its own machine independent parallel programming system developed at the University of Illinois at Urbana-Champaign. The performance of these two approaches is compared, and the prospects for their application to full 3D, reacting flow solvers is assessed.

  6. Particle simulation of plasmas on the massively parallel processor

    NASA Technical Reports Server (NTRS)

    Gledhill, I. M. A.; Storey, L. R. O.

    1987-01-01

    Particle simulations, in which collective phenomena in plasmas are studied by following the self consistent motions of many discrete particles, involve several highly repetitive sets of calculations that are readily adaptable to SIMD parallel processing. A fully electromagnetic, relativistic plasma simulation for the massively parallel processor is described. The particle motions are followed in 2 1/2 dimensions on a 128 x 128 grid, with periodic boundary conditions. The two dimensional simulation space is mapped directly onto the processor network; a Fast Fourier Transform is used to solve the field equations. Particle data are stored according to an Eulerian scheme, i.e., the information associated with each particle is moved from one local memory to another as the particle moves across the spatial grid. The method is applied to the study of the nonlinear development of the whistler instability in a magnetospheric plasma model, with an anisotropic electron temperature. The wave distribution function is included as a new diagnostic to allow simulation results to be compared with satellite observations.

  7. A massively parallel cellular automaton for the simulation of recrystallization

    NASA Astrophysics Data System (ADS)

    Kühbach, M.; Barrales-Mora, L. A.; Gottstein, G.

    2014-10-01

    A new implementation of a cellular automaton for the simulation of primary recrystallization in 3D space is presented. In this new approach, a parallel computer architecture is utilized to partition the simulation domain into multiple computational subdomains that can be treated as coupled, gradually coupled or decoupled entities. This enabled us to identify the characteristic growth length associated with the space repartitioning during nucleus growth. In doing so, several communication strategies between the simulation domains were implemented and tested for accuracy and parallel performance. Specifically, the model was applied to investigate the effect of a gradual spatial decoupling on microstructure evolution during oriented growth of random texture components into a deformed Al single crystal. For a domain discretized into one billion cells, it was found that a particular decoupling strategy resulted in faster executions of about two orders of magnitude and highly accurate simulations. Further partition of the domain into isolated entities systematically and negatively impacts microstructure evolution. We investigated this effect quantitatively by geometrical considerations.

  8. Massively Parallel Processing for Fast and Accurate Stamping Simulations

    NASA Astrophysics Data System (ADS)

    Gress, Jeffrey J.; Xu, Siguang; Joshi, Ramesh; Wang, Chuan-tao; Paul, Sabu

    2005-08-01

    The competitive automotive market drives automotive manufacturers to speed up the vehicle development cycles and reduce the lead-time. Fast tooling development is one of the key areas to support fast and short vehicle development programs (VDP). In the past ten years, the stamping simulation has become the most effective validation tool in predicting and resolving all potential formability and quality problems before the dies are physically made. The stamping simulation and formability analysis has become an critical business segment in GM math-based die engineering process. As the simulation becomes as one of the major production tools in engineering factory, the simulation speed and accuracy are the two of the most important measures for stamping simulation technology. The speed and time-in-system of forming analysis becomes an even more critical to support the fast VDP and tooling readiness. Since 1997, General Motors Die Center has been working jointly with our software vendor to develop and implement a parallel version of simulation software for mass production analysis applications. By 2001, this technology was matured in the form of distributed memory processing (DMP) of draw die simulations in a networked distributed memory computing environment. In 2004, this technology was refined to massively parallel processing (MPP) and extended to line die forming analysis (draw, trim, flange, and associated spring-back) running on a dedicated computing environment. The evolution of this technology and the insight gained through the implementation of DM0P/MPP technology as well as performance benchmarks are discussed in this publication.

  9. Long-range interactions and parallel scalability in molecular simulations

    NASA Astrophysics Data System (ADS)

    Patra, Michael; Hyvönen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko

    2007-01-01

    Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes—we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.

  10. Mapping a battlefield simulation onto message-passing parallel architectures

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1987-01-01

    Perhaps the most critical problem in distributed simulation is that of mapping: without an effective mapping of workload to processors the speedup potential of parallel processing cannot be realized. Mapping a simulation onto a message-passing architecture is especially difficult when the computational workload dynamically changes as a function of time and space; this is exactly the situation faced by battlefield simulations. This paper studies an approach where the simulated battlefield domain is first partitioned into many regions of equal size; typically there are more regions than processors. The regions are then assigned to processors; a processor is responsible for performing all simulation activity associated with the regions. The assignment algorithm is quite simple and attempts to balance load by exploiting locality of workload intensity. The performance of this technique is studied on a simple battlefield simulation implemented on the Flex/32 multiprocessor. Measurements show that the proposed method achieves reasonable processor efficiencies. Furthermore, the method shows promise for use in dynamic remapping of the simulation.

  11. Conservative parallel simulation of priority class queueing networks

    NASA Technical Reports Server (NTRS)

    Nicol, David

    1992-01-01

    A conservative synchronization protocol is described for the parallel simulation of queueing networks having C job priority classes, where a job's class is fixed. This problem has long vexed designers of conservative synchronization protocols because of its seemingly poor ability to compute lookahead: the time of the next departure. For, a job in service having low priority can be preempted at any time by an arrival having higher priority and an arbitrarily small service time. The solution is to skew the event generation activity so that the events for higher priority jobs are generated farther ahead in simulated time than lower priority jobs. Thus, when a lower priority job enters service for the first time, all the higher priority jobs that may preempt it are already known and the job's departure time can be exactly predicted. Finally, the protocol was analyzed and it was demonstrated that good performance can be expected on the simulation of large queueing networks.

  12. Conservative parallel simulation of priority class queueing networks

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1990-01-01

    A conservative synchronization protocol is described for the parallel simulation of queueing networks having C job priority classes, where a job's class is fixed. This problem has long vexed designers of conservative synchronization protocols because of its seemingly poor ability to compute lookahead: the time of the next departure. For, a job in service having low priority can be preempted at any time by an arrival having higher priority and an arbitrarily small service time. The solution is to skew the event generation activity so that the events for higher priority jobs are generated farther ahead in simulated time than lower priority jobs. Thus, when a lower priority job enters service for the first time, all the higher priority jobs that may preempt it are already known and the job's departure time can be exactly predicted. Finally, the protocol was analyzed and it was demonstrated that good performance can be expected on the simulation of large queueing networks.

  13. Xyce Parallel Electronic Simulator Users Guide Version 6.4

    SciTech Connect

    Keiter, Eric R.; Mei, Ting; Russo, Thomas V.; Schiek, Richard; Sholander, Peter E.; Thornquist, Heidi K.; Verley, Jason; Baur, David Gregory

    2015-12-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. Trademarks The information herein is subject to change without notice. Copyright c 2002-2015 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)

  14. Development of magnetron sputtering simulator with GPU parallel computing

    NASA Astrophysics Data System (ADS)

    Sohn, Ilyoup; Kim, Jihun; Bae, Junkyeong; Lee, Jinpil

    2014-12-01

    Sputtering devices are widely used in the semiconductor and display panel manufacturing process. Currently, a number of surface treatment applications using magnetron sputtering techniques are being used to improve the efficiency of the sputtering process, through the installation of magnets outside the vacuum chamber. Within the internal space of the low pressure chamber, plasma generated from the combination of a rarefied gas and an electric field is influenced interactively. Since the quality of the sputtering and deposition rate on the substrate is strongly dependent on the multi-physical phenomena of the plasma regime, numerical simulations using PIC-MCC (Particle In Cell, Monte Carlo Collision) should be employed to develop an efficient sputtering device. In this paper, the development of a magnetron sputtering simulator based on the PIC-MCC method and the associated numerical techniques are discussed. To solve the electric field equations in the 2-D Cartesian domain, a Poisson equation solver based on the FDM (Finite Differencing Method) is developed and coupled with the Monte Carlo Collision method to simulate the motion of gas particles influenced by an electric field. The magnetic field created from the permanent magnet installed outside the vacuum chamber is also numerically calculated using Biot-Savart's Law. All numerical methods employed in the present PIC code are validated by comparison with analytical and well-known commercial engineering software results, with all of the results showing good agreement. Finally, the developed PIC-MCC code is parallelized to be suitable for general purpose computing on graphics processing unit (GPGPU) acceleration, so as to reduce the large computation time which is generally required for particle simulations. The efficiency and accuracy of the GPGPU parallelized magnetron sputtering simulator are examined by comparison with the calculated results and computation times from the original serial code. It is found that initially both simulations are in good agreement; however, differences develop over time due to statistical noise in the PIC-MCC GPGPU model.

  15. Numerical Simulation of Flow Field Within Parallel Plate Plastometer

    NASA Technical Reports Server (NTRS)

    Antar, Basil N.

    2002-01-01

    Parallel Plate Plastometer (PPP) is a device commonly used for measuring the viscosity of high polymers at low rates of shear in the range 10(exp 4) to 10(exp 9) poises. This device is being validated for use in measuring the viscosity of liquid glasses at high temperatures having similar ranges for the viscosity values. PPP instrument consists of two similar parallel plates, both in the range of 1 inch in diameter with the upper plate being movable while the lower one is kept stationary. Load is applied to the upper plate by means of a beam connected to shaft attached to the upper plate. The viscosity of the fluid is deduced from measuring the variation of the plate separation, h, as a function of time when a specified fixed load is applied on the beam. Operating plate speeds measured with the PPP is usually in the range of 10.3 cm/s or lower. The flow field within the PPP can be simulated using the equations of motion of fluid flow for this configuration. With flow speeds in the range quoted above the flow field between the two plates is certainly incompressible and laminar. Such flows can be easily simulated using numerical modeling with computational fluid dynamics (CFD) codes. We present below the mathematical model used to simulate this flow field and also the solutions obtained for the flow using a commercially available finite element CFD code.

  16. High Performance Parallel Methods for Space Weather Simulations

    NASA Technical Reports Server (NTRS)

    Hunter, Paul (Technical Monitor); Gombosi, Tamas I.

    2003-01-01

    This is the final report of our NASA AISRP grant entitled 'High Performance Parallel Methods for Space Weather Simulations'. The main thrust of the proposal was to achieve significant progress towards new high-performance methods which would greatly accelerate global MHD simulations and eventually make it possible to develop first-principles based space weather simulations which run much faster than real time. We are pleased to report that with the help of this award we made major progress in this direction and developed the first parallel implicit global MHD code with adaptive mesh refinement. The main limitation of all earlier global space physics MHD codes was the explicit time stepping algorithm. Explicit time steps are limited by the Courant-Friedrichs-Lewy (CFL) condition, which essentially ensures that no information travels more than a cell size during a time step. This condition represents a non-linear penalty for highly resolved calculations, since finer grid resolution (and consequently smaller computational cells) not only results in more computational cells, but also in smaller time steps.

  17. CHOLLA: A New Massively Parallel Hydrodynamics Code for Astrophysical Simulation

    NASA Astrophysics Data System (ADS)

    Schneider, Evan E.; Robertson, Brant E.

    2015-04-01

    We present Computational Hydrodynamics On ParaLLel Architectures (Cholla ), a new three-dimensional hydrodynamics code that harnesses the power of graphics processing units (GPUs) to accelerate astrophysical simulations. Cholla models the Euler equations on a static mesh using state-of-the-art techniques, including the unsplit Corner Transport Upwind algorithm, a variety of exact and approximate Riemann solvers, and multiple spatial reconstruction techniques including the piecewise parabolic method (PPM). Using GPUs, Cholla evolves the fluid properties of thousands of cells simultaneously and can update over 10 million cells per GPU-second while using an exact Riemann solver and PPM reconstruction. Owing to the massively parallel architecture of GPUs and the design of the Cholla code, astrophysical simulations with physically interesting grid resolutions (≳2563) can easily be computed on a single device. We use the Message Passing Interface library to extend calculations onto multiple devices and demonstrate nearly ideal scaling beyond 64 GPUs. A suite of test problems highlights the physical accuracy of our modeling and provides a useful comparison to other codes. We then use Cholla to simulate the interaction of a shock wave with a gas cloud in the interstellar medium, showing that the evolution of the cloud is highly dependent on its density structure. We reconcile the computed mixing time of a turbulent cloud with a realistic density distribution destroyed by a strong shock with the existing analytic theory for spherical cloud destruction by describing the system in terms of its median gas density.

  18. Massively parallel algorithms for trace-driven cache simulations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Greenberg, Albert G.; Lubachevsky, Boris D.

    1991-01-01

    Trace driven cache simulation is central to computer design. A trace is a very long sequence of reference lines from main memory. At the t(exp th) instant, reference x sub t is hashed into a set of cache locations, the contents of which are then compared with x sub t. If at the t sup th instant x sub t is not present in the cache, then it is said to be a miss, and is loaded into the cache set, possibly forcing the replacement of some other memory line, and making x sub t present for the (t+1) sup st instant. The problem of parallel simulation of a subtrace of N references directed to a C line cache set is considered, with the aim of determining which references are misses and related statistics. A simulation method is presented for the Least Recently Used (LRU) policy, which regradless of the set size C runs in time O(log N) using N processors on the exclusive read, exclusive write (EREW) parallel model. A simpler LRU simulation algorithm is given that runs in O(C log N) time using N/log N processors. Timings are presented of the second algorithm's implementation on the MasPar MP-1, a machine with 16384 processors. A broad class of reference based line replacement policies are considered, which includes LRU as well as the Least Frequently Used and Random replacement policies. A simulation method is presented for any such policy that on any trace of length N directed to a C line set runs in the O(C log N) time with high probability using N processors on the EREW model. The algorithms are simple, have very little space overhead, and are well suited for SIMD implementation.

  19. Exception handling controllers: An application of pushdown systems to discrete event control

    SciTech Connect

    Griffin, Christopher H

    2008-01-01

    Recent work by the author has extended the Supervisory Control Theory to include the class of control languages defined by pushdown machines. A pushdown machine is a finite state machine extended by an infinite stack memory. In this paper, we define a specific type of deterministic pushdown machine that is particularly useful as a discrete event controller. Checking controllability of pushdown machines requires computing the complement of the controller machine. We show that Exception Handling Controllers have the property that algorithms for taking their complements and determining their prefix closures are nearly identical to the algorithms available for finite state machines. Further, they exhibit an important property that makes checking for controllability extremely simple. Hence, they maintain the simplicity of the finite state machine, while providing the extra power associated with a pushdown stack memory. We provide an example of a useful control specification that cannot be implemented using a finite state machine, but can be implemented using an Exception Handling Controller.

  20. A Decision Tool that Combines Discrete Event Software Process Models with System Dynamics Pieces for Software Development Cost Estimation and Analysis

    NASA Technical Reports Server (NTRS)

    Mizell, Carolyn Barrett; Malone, Linda

    2007-01-01

    The development process for a large software development project is very complex and dependent on many variables that are dynamic and interrelated. Factors such as size, productivity and defect injection rates will have substantial impact on the project in terms of cost and schedule. These factors can be affected by the intricacies of the process itself as well as human behavior because the process is very labor intensive. The complex nature of the development process can be investigated with software development process models that utilize discrete event simulation to analyze the effects of process changes. The organizational environment and its effects on the workforce can be analyzed with system dynamics that utilizes continuous simulation. Each has unique strengths and the benefits of both types can be exploited by combining a system dynamics model and a discrete event process model. This paper will demonstrate how the two types of models can be combined to investigate the impacts of human resource interactions on productivity and ultimately on cost and schedule.

  1. Did a discrete event 200,000-100,000 years ago produce modern humans?

    PubMed

    Weaver, Timothy D

    2012-07-01

    Scenarios for modern human origins are often predicated on the assumption that modern humans arose 200,000-100,000 years ago in Africa. This assumption implies that something 'special' happened at this point in time in Africa, such as the speciation that produced Homo sapiens, a severe bottleneck in human population size, or a combination of the two. The common thread is that after the divergence of the modern human and Neandertal evolutionary lineages ∼400,000 years ago, there was another discrete event near in time to the Middle-Late Pleistocene boundary that produced modern humans. Alternatively, modern human origins could have been a lengthy process that lasted from the divergence of the modern human and Neandertal evolutionary lineages to the expansion of modern humans out of Africa, and nothing out of the ordinary happened 200,000-100,000 years ago in Africa. Three pieces of biological (fossil morphology and DNA sequences) evidence are typically cited in support of discrete event models. First, living human mitochondrial DNA haplotypes coalesce ∼200,000 years ago. Second, fossil specimens that are usually classified as 'anatomically modern' seem to appear shortly afterward in the African fossil record. Third, it is argued that these anatomically modern fossils are morphologically quite different from the fossils that preceded them. Here I use theory from population and quantitative genetics to show that lengthy process models are also consistent with current biological evidence. That this class of models is a viable option has implications for how modern human origins is conceptualized. PMID:22658331

  2. Molecular Dynamics Simulations from SNL's Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)

    DOE Data Explorer

    Plimpton, Steve; Thompson, Aidan; Crozier, Paul

    LAMMPS (http://lammps.sandia.gov/index.html) stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a code that can be used to model atoms or, as the LAMMPS website says, as a parallel particle simulator at the atomic, meso, or continuum scale. This Sandia-based website provides a long list of animations from large simulations. These were created using different visualization packages to read LAMMPS output, and each one provides the name of the PI and a brief description of the work done or visualization package used. See also the static images produced from simulations at http://lammps.sandia.gov/pictures.html The foundation paper for LAMMPS is: S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995), but the website also lists other papers describing contributions to LAMMPS over the years.

  3. Financial simulations on a massively parallel Connection Machine

    SciTech Connect

    Hutchinson, J.M.; Zenios, S.A. )

    1991-01-01

    This paper reports on the valuation of complex financial instruments that appear in the banking and insurance industries which requires simulations of their cashflow behavior in a volatile interest rate environment. These simulations are complex and computationally intensive. Their use, thus far, has been limited to intra-day analysis and planning. Researchers at the Wharton School and Thinking Machines Corporation have developed model formulations for massively parallel architectures, like the Connection Machine CM-2. A library of financial modeling primitives has been designed and used to implement a model for the valuation of mortgage-backed securities. Analyzing a portfolio of these securities-which would require 2 days on a large mainframe-is carried out in 1 hour on a CM-2a.

  4. Parallel Unsteady Turbopump Simulations for Liquid Rocket Engines

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin C.; Kwak, Dochan; Chan, William

    2000-01-01

    This paper reports the progress being made towards complete turbo-pump simulation capability for liquid rocket engines. Space Shuttle Main Engine (SSME) turbo-pump impeller is used as a test case for the performance evaluation of the MPI and hybrid MPI/Open-MP versions of the INS3D code. Then, a computational model of a turbo-pump has been developed for the shuttle upgrade program. Relative motion of the grid system for rotor-stator interaction was obtained by employing overset grid techniques. Time-accuracy of the scheme has been evaluated by using simple test cases. Unsteady computations for SSME turbo-pump, which contains 136 zones with 35 Million grid points, are currently underway on Origin 2000 systems at NASA Ames Research Center. Results from time-accurate simulations with moving boundary capability, and the performance of the parallel versions of the code will be presented in the final paper.

  5. Generating scenario trees: A parallel integrated simulation-optimization approach

    NASA Astrophysics Data System (ADS)

    Beraldi, Patrizia; de Simone, Francesco; Violi, Antonio

    2010-03-01

    A crucial issue for addressing decision-making problems under uncertainty is the approximate representation of multivariate stochastic processes in the form of scenario tree. This paper proposes a scenario generation approach based on the idea of integrating simulation and optimization techniques. In particular, simulation is used to generate outcomes associated with the nodes of the scenario tree which, in turn, provide the input parameters for an optimization model aimed at determining the scenarios' probabilities matching some prescribed targets. The approach relies on the moment-matching technique originally proposed in [K. Høyland, S.W. Wallace, Generating scenario trees for multistage decision problems, Manag. Sci. 47 (2001) 295-307] and further refined in [K. Høyland, M. Kaut, S.W. Wallace, A heuristic for moment-matching scenario generation, Comput. Optim. Appl. 24 (2003) 169-185]. By taking advantage of the iterative nature of our approach, a parallel implementation has been designed and extensively tested on financial data. Numerical results show the efficiency of the parallel algorithm and the improvement in accuracy and effectiveness.

  6. Roadmap for efficient parallelization of breast anatomy simulation

    NASA Astrophysics Data System (ADS)

    Chui, Joseph H.; Pokrajac, David D.; Maidment, Andrew D. A.; Bakic, Predrag R.

    2012-03-01

    A roadmap has been proposed to optimize the simulation of breast anatomy by parallel implementation, in order to reduce the time needed to generate software breast phantoms. The rapid generation of high resolution phantoms is needed to support virtual clinical trials of breast imaging systems. We have recently developed an octree-based recursive partitioning algorithm for breast anatomy simulation. The algorithm has good asymptotic complexity; however, its current MATLAB implementation cannot provide optimal execution times. The proposed roadmap for efficient parallelization includes the following steps: (i) migrate the current code to a C/C++ platform and optimize it for single-threaded implementation; (ii) modify the code to allow for multi-threaded CPU implementation; (iii) identify and migrate the code to a platform designed for multithreaded GPU implementation. In this paper, we describe our results in optimizing the C/C++ code for single-threaded and multi-threaded CPU implementations. As the first step of the proposed roadmap we have identified a bottleneck component in the MATLAB implementation using MATLAB's profiling tool, and created a single threaded CPU implementation of the algorithm using C/C++'s overloaded operators and standard template library. The C/C++ implementation has been compared to the MATLAB version in terms of accuracy and simulation time. A 520-fold reduction of the execution time was observed in a test of phantoms with 50- 400 μm voxels. In addition, we have identified several places in the code which will be modified to allow for the next roadmap milestone of the multithreaded CPU implementation.

  7. Massively Parallel Simulations of Diffusion in Dense Polymeric Structures

    SciTech Connect

    Faulon, Jean-Loup, Wilcox, R.T. , Hobbs, J.D. , Ford, D.M.

    1997-11-01

    An original computational technique to generate close-to-equilibrium dense polymeric structures is proposed. Diffusion of small gases are studied on the equilibrated structures using massively parallel molecular dynamics simulations running on the Intel Teraflops (9216 Pentium Pro processors) and Intel Paragon(1840 processors). Compared to the current state-of-the-art equilibration methods this new technique appears to be faster by some orders of magnitude.The main advantage of the technique is that one can circumvent the bottlenecks in configuration space that inhibit relaxation in molecular dynamics simulations. The technique is based on the fact that tetravalent atoms (such as carbon and silicon) fit in the center of a regular tetrahedron and that regular tetrahedrons can be used to mesh the three-dimensional space. Thus, the problem of polymer equilibration described by continuous equations in molecular dynamics is reduced to a discrete problem where solutions are approximated by simple algorithms. Practical modeling applications include the constructing of butyl rubber and ethylene-propylene-dimer-monomer (EPDM) models for oxygen and water diffusion calculations. Butyl and EPDM are used in O-ring systems and serve as sealing joints in many manufactured objects. Diffusion coefficients of small gases have been measured experimentally on both polymeric systems, and in general the diffusion coefficients in EPDM are an order of magnitude larger than in butyl. In order to better understand the diffusion phenomena, 10, 000 atoms models were generated and equilibrated for butyl and EPDM. The models were submitted to a massively parallel molecular dynamics simulation to monitor the trajectories of the diffusing species.

  8. Parallel Molecular Dynamics Stencil : a new parallel computing environment for a large-scale molecular dynamics simulation of solids

    NASA Astrophysics Data System (ADS)

    Shimizu, Futoshi; Kimizuka, Hajime; Kaburaki, Hideo

    2002-08-01

    A new parallel computing environment, called as ``Parallel Molecular Dynamics Stencil'', has been developed to carry out a large-scale short-range molecular dynamics simulation of solids. The stencil is written in C language using MPI for parallelization and designed successfully to separate and conceal parts of the programs describing cutoff schemes and parallel algorithms for data communication. This has been made possible by introducing the concept of image atoms. Therefore, only a sequential programming of the force calculation routine is required for executing the stencil in parallel environment. Typical molecular dynamics routines, such as various ensembles, time integration methods, and empirical potentials, have been implemented in the stencil. In the presentation, the performance of the stencil on parallel computers of Hitachi, IBM, SGI, and PC-cluster using the models of Lennard-Jones and the EAM type potentials for fracture problem will be reported.

  9. Parallel grid library for rapid and flexible simulation development

    NASA Astrophysics Data System (ADS)

    Honkonen, I.; von Alfthan, S.; Sandroos, A.; Janhunen, P.; Palmroth, M.

    2013-04-01

    We present an easy to use and flexible grid library for developing highly scalable parallel simulations. The distributed cartesian cell-refinable grid (dccrg) supports adaptive mesh refinement and allows an arbitrary C++ class to be used as cell data. The amount of data in grid cells can vary both in space and time allowing dccrg to be used in very different types of simulations, for example in fluid and particle codes. Dccrg transfers the data between neighboring cells on different processes transparently and asynchronously allowing one to overlap computation and communication. This enables excellent scalability at least up to 32 k cores in magnetohydrodynamic tests depending on the problem and hardware. In the version of dccrg presented here part of the mesh metadata is replicated between MPI processes reducing the scalability of adaptive mesh refinement (AMR) to between 200 and 600 processes. Dccrg is free software that anyone can use, study and modify and is available at https://gitorious.org/dccrg. Users are also kindly requested to cite this work when publishing results obtained with dccrg. Catalogue identifier: AEOM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOM_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU Lesser General Public License version 3 No. of lines in distributed program, including test data, etc.: 54975 No. of bytes in distributed program, including test data, etc.: 974015 Distribution format: tar.gz Programming language: C++. Computer: PC, cluster, supercomputer. Operating system: POSIX. The code has been parallelized using MPI and tested with 1-32768 processes RAM: 10 MB-10 GB per process Classification: 4.12, 4.14, 6.5, 19.3, 19.10, 20. External routines: MPI-2 [1], boost [2], Zoltan [3], sfc++ [4] Nature of problem: Grid library supporting arbitrary data in grid cells, parallel adaptive mesh refinement, transparent remote neighbor data updates and load balancing. Solution method: The simulation grid is represented by an adjacency list (graph) with vertices stored into a hash table and edges into contiguous arrays. Message Passing Interface standard is used for parallelization. Cell data is given as a template parameter when instantiating the grid. Restrictions: Logically cartesian grid. Running time: Running time depends on the hardware, problem and the solution method. Small problems can be solved in under a minute and very large problems can take weeks. The examples and tests provided with the package take less than about one minute using default options. In the version of dccrg presented here the speed of adaptive mesh refinement is at most of the order of 106 total created cells per second. http://www.mpi-forum.org/. http://www.boost.org/. K. Devine, E. Boman, R. Heaphy, B. Hendrickson, C. Vaughan, Zoltan data management services for parallel dynamic applications, Comput. Sci. Eng. 4 (2002) 90-97. http://dx.doi.org/10.1109/5992.988653. https://gitorious.org/sfc++.

  10. Parallel finite element simulation of large ram-air parachutes

    NASA Astrophysics Data System (ADS)

    Kalro, V.; Aliabadi, S.; Garrard, W.; Tezduyar, T.; Mittal, S.; Stein, K.

    1997-06-01

    In the near future, large ram-air parachutes are expected to provide the capability of delivering 21 ton payloads from altitudes as high as 25,000 ft. In development and test and evaluation of these parachutes the size of the parachute needed and the deployment stages involved make high-performance computing (HPC) simulations a desirable alternative to costly airdrop tests. Although computational simulations based on realistic, 3D, time-dependent models will continue to be a major computational challenge, advanced finite element simulation techniques recently developed for this purpose and the execution of these techniques on HPC platforms are significant steps in the direction to meet this challenge. In this paper, two approaches for analysis of the inflation and gliding of ram-air parachutes are presented. In one of the approaches the point mass flight mechanics equations are solved with the time-varying drag and lift areas obtained from empirical data. This approach is limited to parachutes with similar configurations to those for which data are available. The other approach is 3D finite element computations based on the Navier-Stokes equations governing the airflow around the parachute canopy and Newtons law of motion governing the 3D dynamics of the canopy, with the forces acting on the canopy calculated from the simulated flow field. At the earlier stages of canopy inflation the parachute is modelled as an expanding box, whereas at the later stages, as it expands, the box transforms to a parafoil and glides. These finite element computations are carried out on the massively parallel supercomputers CRAY T3D and Thinking Machines CM-5, typically with millions of coupled, non-linear finite element equations solved simultaneously at every time step or pseudo-time step of the simulation.

  11. A parallel algorithm for switch-level timing simulation on a hypercube multiprocessor

    NASA Technical Reports Server (NTRS)

    Rao, Hariprasad Nannapaneni

    1989-01-01

    The parallel approach to speeding up simulation is studied, specifically the simulation of digital LSI MOS circuitry on the Intel iPSC/2 hypercube. The simulation algorithm is based on RSIM, an event driven switch-level simulator that incorporates a linear transistor model for simulating digital MOS circuits. Parallel processing techniques based on the concepts of Virtual Time and rollback are utilized so that portions of the circuit may be simulated on separate processors, in parallel for as large an increase in speed as possible. A partitioning algorithm is also developed in order to subdivide the circuit for parallel processing.

  12. Sensor Configuration Selection for Discrete-Event Systems under Unreliable Observations

    SciTech Connect

    Wen-Chiao Lin; Tae-Sic Yoo; Humberto E. Garcia

    2010-08-01

    Algorithms for counting the occurrences of special events in the framework of partially-observed discrete event dynamical systems (DEDS) were developed in previous work. Their performances typically become better as the sensors providing the observations become more costly or increase in number. This paper addresses the problem of finding a sensor configuration that achieves an optimal balance between cost and the performance of the special event counting algorithm, while satisfying given observability requirements and constraints. Since this problem is generally computational hard in the framework considered, a sensor optimization algorithm is developed using two greedy heuristics, one myopic and the other based on projected performances of candidate sensors. The two heuristics are sequentially executed in order to find best sensor configurations. The developed algorithm is then applied to a sensor optimization problem for a multiunit- operation system. Results show that improved sensor configurations can be found that may significantly reduce the sensor configuration cost but still yield acceptable performance for counting the occurrences of special events.

  13. Parallel continuous simulated tempering and its applications in large-scale molecular simulations

    SciTech Connect

    Zang, Tianwu; Yu, Linglin; Zhang, Chong; Ma, Jianpeng

    2014-07-28

    In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys. 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2–3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.

  14. Parallel continuous simulated tempering and its applications in large-scale molecular simulations

    NASA Astrophysics Data System (ADS)

    Zang, Tianwu; Yu, Linglin; Zhang, Chong; Ma, Jianpeng

    2014-07-01

    In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys. 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2-3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.

  15. Parallel continuous simulated tempering and its applications in large-scale molecular simulations

    PubMed Central

    Zang, Tianwu; Yu, Linglin; Zhang, Chong; Ma, Jianpeng

    2014-01-01

    In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys.141, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys.141, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2–3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent. PMID:25084887

  16. A massively parallel solution strategy for efficient thermal radiation simulation

    NASA Astrophysics Data System (ADS)

    Nguyen, P. D.; Moureau, V.; Vervisch, L.; Perret, N.

    2012-06-01

    A novel and efficient methodology to solve the Radiative Transfer Equations (RTE) in thermal radiation is discussed. The BiCGStab(2) iterative solution method, as designed for the non-symmetric linear equation systems, is used to solve the discretized RTE. The numerical upwind and central schemes are blended to provide a stable numerical scheme (MUCS) for interpolation of the cell facial radiation intensities in finite volume formulation. The combination of the BiCGStab(2) and MUCS methods proved to be very efficient when coupling with the DOM approach to solve the RTE. A cost-effective tabulation technique for the gaseous radiative property model SNB-FSCK using 7-point Gauss-Labatto quadrature scheme is also introduced. The whole methodology is implemented into a massively parallel unstructured CFD code where the radiative and fluid flow solutions share the same domain decomposition, which is the bottleneck in current radiative solvers. The dual mesh decomposition at the cell groups level and processors level is adopted to optimize the CFD code for massively parallel computing. The whole method is applied to simulate the radiation heat-transfer in a 3D rectangular enclosure containing non-isothermal CO2 and H2O mixtures. Two test cases are studied for homogeneous and inhomogeneous distributions of CO2 and H2O in the enclosure. The result is reported for the heat flux and radiation energy source and the comparison is also made between the present methodology BiCGStab(2)/MUCS/tabulated SNB-FSCK, the benchmark method SNB-CK (implemented at 25cm-1 narrow-band) and some other methods available in the literature. The present method (BiCGStab(2)/MUCS/tabulated SNB-FSCK) yields more accurate predictions particularly for the radiation source term. When comparing with the benchmark solution, the relative error of the radiation source term is remarkably reduced to less than 4% and the CPU time is drastically diminished.

  17. Xyce Parallel Electronic Simulator Reference Guide Version 6.4

    SciTech Connect

    Keiter, Eric R.; Mei, Ting; Russo, Thomas V.; Schiek, Richard; Sholander, Peter E.; Thornquist, Heidi K.; Verley, Jason; Baur, David Gregory

    2015-12-01

    This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . Trademarks The information herein is subject to change without notice. Copyright c 2002-2015 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)

  18. Humans can integrate feedback of discrete events in their sensorimotor control of a robotic hand.

    PubMed

    Cipriani, Christian; Segil, Jacob L; Clemente, Francesco; ff Weir, Richard F; Edin, Benoni

    2014-11-01

    Providing functionally effective sensory feedback to users of prosthetics is a largely unsolved challenge. Traditional solutions require high band-widths for providing feedback for the control of manipulation and yet have been largely unsuccessful. In this study, we have explored a strategy that relies on temporally discrete sensory feedback that is technically simple to provide. According to the Discrete Event-driven Sensory feedback Control (DESC) policy, motor tasks in humans are organized in phases delimited by means of sensory encoded discrete mechanical events. To explore the applicability of DESC for control, we designed a paradigm in which healthy humans operated an artificial robot hand to lift and replace an instrumented object, a task that can readily be learned and mastered under visual control. Assuming that the central nervous system of humans naturally organizes motor tasks based on a strategy akin to DESC, we delivered short-lasting vibrotactile feedback related to events that are known to forcefully affect progression of the grasp-lift-and-hold task. After training, we determined whether the artificial feedback had been integrated with the sensorimotor control by introducing short delays and we indeed observed that the participants significantly delayed subsequent phases of the task. This study thus gives support to the DESC policy hypothesis. Moreover, it demonstrates that humans can integrate temporally discrete sensory feedback while controlling an artificial hand and invites further studies in which inexpensive, noninvasive technology could be used in clever ways to provide physiologically appropriate sensory feedback in upper limb prosthetics with much lower band-width requirements than with traditional solutions. PMID:24992899

  19. Particle/Continuum Hybrid Simulation in a Parallel Computing Environment

    NASA Technical Reports Server (NTRS)

    Baganoff, Donald

    1996-01-01

    The objective of this study was to modify an existing parallel particle code based on the direct simulation Monte Carlo (DSMC) method to include a Navier-Stokes (NS) calculation so that a hybrid solution could be developed. In carrying out this work, it was determined that the following five issues had to be addressed before extensive program development of a three dimensional capability was pursued: (1) find a set of one-sided kinetic fluxes that are fully compatible with the DSMC method, (2) develop a finite volume scheme to make use of these one-sided kinetic fluxes, (3) make use of the one-sided kinetic fluxes together with DSMC type boundary conditions at a material surface so that velocity slip and temperature slip arise naturally for near-continuum conditions, (4) find a suitable sampling scheme so that the values of the one-sided fluxes predicted by the NS solution at an interface between the two domains can be converted into the correct distribution of particles to be introduced into the DSMC domain, (5) carry out a suitable number of tests to confirm that the developed concepts are valid, individually and in concert for a hybrid scheme.

  20. Rasterizing geological models for parallel finite difference simulation using seismic simulation as an example

    NASA Astrophysics Data System (ADS)

    Zehner, Björn; Hellwig, Olaf; Linke, Maik; Görz, Ines; Buske, Stefan

    2016-01-01

    3D geological underground models are often presented by vector data, such as triangulated networks representing boundaries of geological bodies and geological structures. Since models are to be used for numerical simulations based on the finite difference method, they have to be converted into a representation discretizing the full volume of the model into hexahedral cells. Often the simulations require a high grid resolution and are done using parallel computing. The storage of such a high-resolution raster model would require a large amount of storage space and it is difficult to create such a model using the standard geomodelling packages. Since the raster representation is only required for the calculation, but not for the geometry description, we present an algorithm and concept for rasterizing geological models on the fly for the use in finite difference codes that are parallelized by domain decomposition. As a proof of concept we implemented a rasterizer library and integrated it into seismic simulation software that is run as parallel code on a UNIX cluster using the Message Passing Interface. We can thus run the simulation with realistic and complicated surface-based geological models that are created using 3D geomodelling software, instead of using a simplified representation of the geological subsurface using mathematical functions or geometric primitives. We tested this set-up using an example model that we provide along with the implemented library.

  1. Parallel processing for nonlinear dynamics simulations of structures including rotating bladed-disk assemblies

    NASA Technical Reports Server (NTRS)

    Hsieh, Shang-Hsien

    1993-01-01

    The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.

  2. A natural partitioning scheme for parallel simulation of multibody systems

    NASA Technical Reports Server (NTRS)

    Chiou, J. C.; Park, K. C.; Farhat, C.

    1993-01-01

    A parallel partitioning scheme based on physical-co-ordinate variables is presented to systematically eliminate system constraint forces and yield the equations of motion of multibody dynamics systems in terms of their independent coordinates. Key features of the present scheme include an explicit determination of the independent coordinates, a parallel construction of the null space matrix of the constraint Jacobian matrix, an easy incorporation of the previously developed two-stage staggered solution procedure and a Schur complement based parallel preconditioned conjugate gradient numerical algorithm.

  3. Parallel climate model (PCM) control and transient simulations

    NASA Astrophysics Data System (ADS)

    Washington, W. M.; Weatherly, J. W.; Meehl, G. A.; Semtner, A. J., Jr.; Bettge, T. W.; Craig, A. P.; Strand, W. G., Jr.; Arblaster, J.; Wayland, V. B.; James, R.; Zhang, Y.

    The Department of Energy (DOE) supported Parallel Climate Model (PCM) makes use of the NCAR Community Climate Model (CCM3) and Land Surface Model (LSM) for the atmospheric and land surface components, respectively, the DOE Los Alamos National Laboratory Parallel Ocean Program (POP) for the ocean component, and the Naval Postgraduate School sea-ice model. The PCM executes on several distributed and shared memory computer systems. The coupling method is similar to that used in the NCAR Climate System Model (CSM) in that a flux coupler ties the components together, with interpolations between the different grids of the component models. Flux adjustments are not used in the PCM. The ocean component has 2/3° average horizontal grid spacing with 32 vertical levels and a free surface that allows calculation of sea level changes. Near the equator, the grid spacing is approximately 1/2° in latitude to better capture the ocean equatorial dynamics. The North Pole is rotated over northern North America thus producing resolution smaller than 2/3° in the North Atlantic where the sinking part of the world conveyor circulation largely takes place. Because this ocean model component does not have a computational point at the North Pole, the Arctic Ocean circulation systems are more realistic and similar to the observed. The elastic viscous plastic sea ice model has a grid spacing of 27km to represent small-scale features such as ice transport through the Canadian Archipelago and the East Greenland current region. Results from a 300year present-day coupled climate control simulation are presented, as well as for a transient 1% per year compound CO2 increase experiment which shows a global warming of 1.27°C for a 10year average at the doubling point of CO2 and 2.89°C at the quadrupling point. There is a gradual warming beyond the doubling and quadrupling points with CO2 held constant. Globally averaged sea level rise at the time of CO2 doubling is approximately 7cm and at the time of quadrupling it is 23cm. Some of the regional sea level changes are larger and reflect the adjustments in the temperature, salinity, internal ocean dynamics, surface heat flux, and wind stress on the ocean. A 0.5% per year CO2 increase experiment also was performed showing a global warming of 1.5°C around the time of CO2 doubling and a similar warming pattern to the 1% CO2 per year increase experiment. El Niño and La Niña events in the tropical Pacific show approximately the observed frequency distribution and amplitude, which leads to near observed levels of variability on interannual time scales.

  4. Parallel Vehicular Traffic Simulation using Reverse Computation-based Optimistic Execution

    SciTech Connect

    Yoginath, Srikanth B; Perumalla, Kalyan S

    2008-01-01

    Vehicular traffic simulations are useful in applications such as emergency management and homeland security planning tools. High speed of traffic simulations translates directly to speed of response and level of resilience in those applications. Here, a parallel traffic simulation approach is presented that is aimed at reducing the time for simulating emergency vehicular traffic scenarios. Three unique aspects of this effort are: (1) exploration of optimistic simulation applied to vehicular traffic simulation (2) addressing reverse computation challenges specific to optimistic vehicular traffic simulation (3) achieving absolute (as opposed to self-relative) speedup with a sequential speed equal to that of a fast, de facto standard sequential simulator for emergency traffic. The design and development of the parallel simulation system is presented, along with a performance study that demonstrates excellent sequential performance as well as parallel performance.

  5. Large Scale Parallel 3D Simulation of Regional Wave Propagation Using the Earth Simulator

    NASA Astrophysics Data System (ADS)

    Furumura, T.

    2003-12-01

    This paper presents an efficient parallel code for seismic wave propagation in 3D heterogeneous structures developed for implementation on the Earth Simulator (5120 CPUs, 40 TFLOPS)_@at the JAMSTEC Yokohama Institute, a high-performance vector parallel system suitable for large-scale simulations. The equations of motion for the 3D wavefield are solved using a higher-order (8,16, 32 etc.) staggered-grid finite-difference method (FDM) in the horizontal (x,y) directions and a conventional fourth-order FDM in the vertical (z) direction. Compared to traditional Fourier pseudospectral method (PSM), the higher-order FDM achieves very good performance on vector processors as well as on the latest high-performance microprocessors (Intel Pentium 4, Itanium 2 etc.). The parallel computing is based on partition of the computational domain, with each subregion assigned to a node of the Earth Simulator. Message passing interface (MPI) inter-node communication is employed for data exchange between subregions. Small-scale heterogeneities such as low-velocity sedimentary basins are accounted for in large-scale models by adopting a multi-grid approach that combines a coarse mesh model with embedded finer mesh model. An accurate interpolation procedure, based on the fast Fourier transform (FFT), is used to combine the wavefield in the different grids. The results of application of the multi-grid, parallel FDM code on the Earth Simulator for modeling strong ground motions from recent large earthquakes are also presented. Events such as the 1993 Kushiro (Mj7.8) and 2000 Tottori-ken Seibu (Mj7.3) earthquakes were simulated using 3D structural models of northern and western Japan. The subsurface structures in Japan were derived by combining data from a number of reflection and refraction experiments, Bouguer anomaly data, and travel-time tomography studies of P and S waves. The scale of the 3D model is about 500 km by 1000 km by 350 km, which is divided into grid intervals of 0.5 to 1 km. The simulation required 128 to 364 Gb of computation memory, and computation took 1 to 2 h using 256 to 1408 processors of the Earth Simulator. Assuming a minimum shear wave velocity of Vs = 1.7 km/s, the modeling is capable of treating high-frequency seismic wave propagations of over 1 to 2 Hz. The volume rendering technique was employed to illuminate the 3D wavefield, and a set of snapshots was combined into a video sequence. The high-resolution 3D simulations for frequencies over 1 Hz provide a good representation of wave propagation in Japan during the large earthquakes. The computer simulation also matches the observations by the dense seismic array (K-Net and KiK-net, over 1700 stations) well, demonstrating the effectiveness of the simulation model. The combined studies of high-resolution computer simulation and dense seismic observation can therefore be expected to be highly valuable in understanding the complex seismic behavior associated with heterogeneities in the subsurface structure, and for predicting the pattern of ground motions expected for future earthquake scenarios.

  6. A sweep algorithm for massively parallel simulation of circuit-switched networks

    NASA Technical Reports Server (NTRS)

    Gaujal, Bruno; Greenberg, Albert G.; Nicol, David M.

    1992-01-01

    A new massively parallel algorithm is presented for simulating large asymmetric circuit-switched networks, controlled by a randomized-routing policy that includes trunk-reservation. A single instruction multiple data (SIMD) implementation is described, and corresponding experiments on a 16384 processor MasPar parallel computer are reported. A multiple instruction multiple data (MIMD) implementation is also described, and corresponding experiments on an Intel IPSC/860 parallel computer, using 16 processors, are reported. By exploiting parallelism, our algorithm increases the possible execution rate of such complex simulations by as much as an order of magnitude.

  7. ANNarchy: a code generation approach to neural simulations on parallel hardware

    PubMed Central

    Vitay, Julien; Dinkelbach, Helge Ü.; Hamker, Fred H.

    2015-01-01

    Many modern neural simulators focus on the simulation of networks of spiking neurons on parallel hardware. Another important framework in computational neuroscience, rate-coded neural networks, is mostly difficult or impossible to implement using these simulators. We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. This information is used to generate C++ code that will efficiently perform the simulation on the chosen parallel hardware (multi-core system or graphical processing unit). Several numerical methods are available to transform ordinary differential equations into an efficient C++code. We compare the parallel performance of the simulator to existing solutions. PMID:26283957

  8. ANNarchy: a code generation approach to neural simulations on parallel hardware.

    PubMed

    Vitay, Julien; Dinkelbach, Helge Ü; Hamker, Fred H

    2015-01-01

    Many modern neural simulators focus on the simulation of networks of spiking neurons on parallel hardware. Another important framework in computational neuroscience, rate-coded neural networks, is mostly difficult or impossible to implement using these simulators. We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. This information is used to generate C++ code that will efficiently perform the simulation on the chosen parallel hardware (multi-core system or graphical processing unit). Several numerical methods are available to transform ordinary differential equations into an efficient C++code. We compare the parallel performance of the simulator to existing solutions. PMID:26283957

  9. Comparison of serial and parallel simulations of a corridor fire using FDS

    NASA Astrophysics Data System (ADS)

    Valasek, L.

    2015-09-01

    Current fire simulators allow to model the course of fire in large areas and its impact on structure and equipment. This paper deals with a comparison of serial and parallel calculations of simulation of a corridor fire by the FDS (Fire Dynamics Simulator) system. In parallel case, the whole computational domain is divided into several computational meshes, the computation on each mesh is considered as a single MPI (Message Passing Interface) process realised on one computational core and communication between MPI processes is provided by MPI. The aim of this paper is to determine the size of error caused by parallelization of computation, which occurs at touches of computational meshes.

  10. amatos: Parallel adaptive mesh generator for atmospheric and oceanic simulation

    NASA Astrophysics Data System (ADS)

    Behrens, Jörn; Rakowsky, Natalja; Hiller, Wolfgang; Handorf, Dörthe; Läuter, Matthias; Päpke, Jürgen; Dethloff, Klaus

    The grid generator amatos has been developed for adaptive modeling of ocean and atmosphere circulation. It features adaptive control of planar, spherical, and volume grids with triangular or tetrahedral elements refined by bisection. The user interface (GRID API), a Fortran 90 module, shields the application programmer from the technical aspects of mesh adaptation like amatos' hierarchical data structure, the OpenMP parallelization, and the effective calculation of a domain decomposition by a space filling curve (SFC) approach. This article presents the basic structure and features of amatos, the powerful SFC ordering and decomposition of data, and two example applications, namely the modeling of tracer advection in the polar vortex and the development of the adaptive finite element atmosphere model PLASMA (parallel large scale model of the atmosphere).

  11. Parallel computing in enterprise modeling.

    SciTech Connect

    Goldsby, Michael E.; Armstrong, Robert C.; Shneider, Max S.; Vanderveen, Keith; Ray, Jaideep; Heath, Zach; Allan, Benjamin A.

    2008-08-01

    This report presents the results of our efforts to apply high-performance computing to entity-based simulations with a multi-use plugin for parallel computing. We use the term 'Entity-based simulation' to describe a class of simulation which includes both discrete event simulation and agent based simulation. What simulations of this class share, and what differs from more traditional models, is that the result sought is emergent from a large number of contributing entities. Logistic, economic and social simulations are members of this class where things or people are organized or self-organize to produce a solution. Entity-based problems never have an a priori ergodic principle that will greatly simplify calculations. Because the results of entity-based simulations can only be realized at scale, scalable computing is de rigueur for large problems. Having said that, the absence of a spatial organizing principal makes the decomposition of the problem onto processors problematic. In addition, practitioners in this domain commonly use the Java programming language which presents its own problems in a high-performance setting. The plugin we have developed, called the Parallel Particle Data Model, overcomes both of these obstacles and is now being used by two Sandia frameworks: the Decision Analysis Center, and the Seldon social simulation facility. While the ability to engage U.S.-sized problems is now available to the Decision Analysis Center, this plugin is central to the success of Seldon. Because Seldon relies on computationally intensive cognitive sub-models, this work is necessary to achieve the scale necessary for realistic results. With the recent upheavals in the financial markets, and the inscrutability of terrorist activity, this simulation domain will likely need a capability with ever greater fidelity. High-performance computing will play an important part in enabling that greater fidelity.

  12. Modelling and simulation of parallel triangular triple quantum dots (TTQD) by using SIMON 2.0

    NASA Astrophysics Data System (ADS)

    Fathany, Maulana Yusuf; Fuada, Syifaul; Lawu, Braham Lawas; Sulthoni, Muhammad Amin

    2016-04-01

    This research presents analysis of modeling on Parallel Triple Quantum Dots (TQD) by using SIMON (SIMulation Of Nano-structures). Single Electron Transistor (SET) is used as the basic concept of modeling. We design the structure of Parallel TQD by metal material with triangular geometry model, it is called by Triangular Triple Quantum Dots (TTQD). We simulate it with several scenarios using different parameters; such as different value of capacitance, various gate voltage, and different thermal condition.

  13. Parallel Unsteady Turbopump Flow Simulations for Reusable Launch Vehicles

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin; Kwak, Dochan

    2000-01-01

    An efficient solution procedure for time-accurate solutions of Incompressible Navier-Stokes equation is obtained. Artificial compressibility method requires a fast convergence scheme. Pressure projection method is efficient when small time-step is required. The number of sub-iteration is reduced significantly when Poisson solver employed with the continuity equation. Both computing time and memory usage are reduced (at least 3 times). Other work includes Multi Level Parallelism (MLP) of INS3D, overset connectivity for the validation case, experimental measurements, and computational model for boost pump.

  14. Parallelized modelling and solution scheme for hierarchically scaled simulations

    NASA Technical Reports Server (NTRS)

    Padovan, Joe

    1995-01-01

    This two-part paper presents the results of a benchmarked analytical-numerical investigation into the operational characteristics of a unified parallel processing strategy for implicit fluid mechanics formulations. This hierarchical poly tree (HPT) strategy is based on multilevel substructural decomposition. The Tree morphology is chosen to minimize memory, communications and computational effort. The methodology is general enough to apply to existing finite difference (FD), finite element (FEM), finite volume (FV) or spectral element (SE) based computer programs without an extensive rewrite of code. In addition to finding large reductions in memory, communications, and computational effort associated with a parallel computing environment, substantial reductions are generated in the sequential mode of application. Such improvements grow with increasing problem size. Along with a theoretical development of general 2-D and 3-D HPT, several techniques for expanding the problem size that the current generation of computers are capable of solving, are presented and discussed. Among these techniques are several interpolative reduction methods. It was found that by combining several of these techniques that a relatively small interpolative reduction resulted in substantial performance gains. Several other unique features/benefits are discussed in this paper. Along with Part 1's theoretical development, Part 2 presents a numerical approach to the HPT along with four prototype CFD applications. These demonstrate the potential of the HPT strategy.

  15. Parallel three-dimensional acoustic and elastic wave simulation methods with applications in nondestructive evaluation

    NASA Astrophysics Data System (ADS)

    Rudd, Kevin Edward

    In this dissertation, we present two parallelized 3D simulation techniques for three-dimensional acoustic and elastic wave propagation based on the finite integration technique. We demonstrate their usefulness in solving real-world problems with examples in the three very different areas of nondestructive evaluation, medical imaging, and security screening. More precisely, these include concealed weapons detection, periodontal ultrasography, and guided wave inspection of complex piping systems. We have employed these simulation methods to study complex wave phenomena and to develop and test a variety of signal processing and hardware configurations. Simulation results are compared to experimental measurements to confirm the accuracy of the parallel simulation methods.

  16. Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers

    SciTech Connect

    Vashishta, Priya; Kalia, Rajiv

    2005-02-24

    Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report.

  17. A high resolution finite volume method for efficient parallel simulation of casting processes on unstructured meshes

    SciTech Connect

    Kothe, D.B.; Turner, J.A.; Mosso, S.J.; Ferrell, R.C.

    1997-03-01

    We discuss selected aspects of a new parallel three-dimensional (3-D) computational tool for the unstructured mesh simulation of Los Alamos National Laboratory (LANL) casting processes. This tool, known as {bold Telluride}, draws upon on robust, high resolution finite volume solutions of metal alloy mass, momentum, and enthalpy conservation equations to model the filling, cooling, and solidification of LANL castings. We briefly describe the current {bold Telluride} physical models and solution methods, then detail our parallelization strategy as implemented with Fortran 90 (F90). This strategy has yielded straightforward and efficient parallelization on distributed and shared memory architectures, aided in large part by new parallel libraries {bold JTpack9O} for Krylov-subspace iterative solution methods and {bold PGSLib} for efficient gather/scatter operations. We illustrate our methodology and current capabilities with source code examples and parallel efficiency results for a LANL casting simulation.

  18. Xyce parallel electronic simulator users guide, version 6.1

    SciTech Connect

    Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Sholander, Peter E.; Thornquist, Heidi K.; Verley, Jason C.; Baur, David Gregory

    2014-03-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas; Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers; A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models; Device models that are specifically tailored to meet Sandia's needs, including some radiationaware devices (for Sandia users only); and Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase-a message passing parallel implementation-which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

  19. Xyce parallel electronic simulator users' guide, Version 6.0.1.

    SciTech Connect

    Keiter, Eric Richard; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Verley, Jason C.; Fixel, Deborah A.; Coffey, Todd Stirling; Pawlowski, Roger Patrick; Warrender, Christina E.; Baur, David Gregory.

    2014-01-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiationaware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

  20. Vector and parallel Monte Carlo radiative heat transfer simulation

    SciTech Connect

    Burns, P.J. . Dept. of Mechanical Engineering); Pryor, D.V. )

    1989-01-01

    A fully vectorized version of a Monte Carlo algorithm of radiative heat transfer in two-dimensional geometries is presented. This algorithm differs from previous applications in that its capabilities are more extensive, with arbitrary numbers of surfaces, arbitrary numbers of material properties, and surface characteristics that include transmission, specular reflection, and diffuse reflection (all of which may be functions of the angle of incidence). The algorithm is applied to an irregular, experimental geometry and implemented on a Cyber 205. A speedup factor of approximately 16, for this combination of geometry and material properties, is achieved for the vector version over the scalar code. Issues related to the details of vectorization, including heavy use of bit addressability, the maintaining of long vector lengths, and gather/scatter use, are discussed. The parallel application of this algorithm is straightforward and is discussed in light of architectural differences among several current supercomputers.

  1. Parallel performance optimizations on unstructured mesh-based simulations

    SciTech Connect

    Sarje, Abhinav; Song, Sukhyun; Jacobsen, Douglas; Huck, Kevin; Hollingsworth, Jeffrey; Malony, Allen; Williams, Samuel; Oliker, Leonid

    2015-06-01

    This paper addresses two key parallelization challenges the unstructured mesh-based ocean modeling code, MPAS-Ocean, which uses a mesh based on Voronoi tessellations: (1) load imbalance across processes, and (2) unstructured data access patterns, that inhibit intra- and inter-node performance. Our work analyzes the load imbalance due to naive partitioning of the mesh, and develops methods to generate mesh partitioning with better load balance and reduced communication. Furthermore, we present methods that minimize both inter- and intranode data movement and maximize data reuse. Our techniques include predictive ordering of data elements for higher cache efficiency, as well as communication reduction approaches. We present detailed performance data when running on thousands of cores using the Cray XC30 supercomputer and show that our optimization strategies can exceed the original performance by over 2×. Additionally, many of these solutions can be broadly applied to a wide variety of unstructured grid-based computations.

  2. Toward parallel, adaptive mesh refinement for chemically reacting flow simulations

    SciTech Connect

    Devine, K.D.; Shadid, J.N.; Salinger, A.G. Hutchinson, S.A.; Hennigan, G.L.

    1997-12-01

    Adaptive numerical methods offer greater efficiency than traditional numerical methods by concentrating computational effort in regions of the problem domain where the solution is difficult to obtain. In this paper, the authors describe progress toward adding mesh refinement to MPSalsa, a computer program developed at Sandia National laboratories to solve coupled three-dimensional fluid flow and detailed reaction chemistry systems for modeling chemically reacting flow on large-scale parallel computers. Data structures that support refinement and dynamic load-balancing are discussed. Results using uniform refinement with mesh sequencing to improve convergence to steady-state solutions are also presented. Three examples are presented: a lid driven cavity, a thermal convection flow, and a tilted chemical vapor deposition reactor.

  3. Virtual reality visualization of parallel molecular dynamics simulation

    SciTech Connect

    Disz, T.; Papka, M.; Stevens, R.; Pellegrino, M.; Taylor, V.

    1995-12-31

    When performing communications mapping experiments for massively parallel processors, it is important to be able to visualize the mappings and resulting communications. In a molecular dynamics model, visualization of the atom to atom interaction and the processor mappings provides insight into the effectiveness of the communications algorithms. The basic quantities available for visualization in a model of this type are the number of molecules per unit volume, the mass, and velocity of each molecule. The computational information available for visualization is the atom to atom interaction within each time step, the atom to processor mapping, and the energy resealing events. We use the CAVE (CAVE Automatic Virtual Environment) to provide interactive, immersive visualization experiences.

  4. Event Based Simulator for Parallel Computing over the Wide Area Network for Real Time Visualization

    NASA Astrophysics Data System (ADS)

    Sundararajan, Elankovan; Harwood, Aaron; Kotagiri, Ramamohanarao; Satria Prabuwono, Anton

    As the computational requirement of applications in computational science continues to grow tremendously, the use of computational resources distributed across the Wide Area Network (WAN) becomes advantageous. However, not all applications can be executed over the WAN due to communication overhead that can drastically slowdown the computation. In this paper, we introduce an event based simulator to investigate the performance of parallel algorithms executed over the WAN. The event based simulator known as SIMPAR (SIMulator for PARallel computation), simulates the actual computations and communications involved in parallel computation over the WAN using time stamps. Visualization of real time applications require steady stream of processed data flow for visualization purposes. Hence, SIMPAR may prove to be a valuable tool to investigate types of applications and computing resource requirements to provide uninterrupted flow of processed data for real time visualization purposes. The results obtained from the simulation show concurrence with the expected performance using the L-BSP model.

  5. Modular high-temperature gas-cooled reactor simulation using parallel processors

    SciTech Connect

    Ball, S.J.; Conklin, J.C.

    1989-01-01

    The MHPP (Modular HTGR Parallel Processor) code has been developed to simulate modular high-temperature gas-cooled reactor (MHTGR) transients and accidents. MHPP incorporates a very detailed model for predicting the dynamics of the reactor core, vessel, and cooling systems over a wide variety of scenarios ranging from expected transients to very-low-probability severe accidents. The simulation routines, which had originally been developed entirely as serial code, were readily adapted to parallel processing Fortran. The resulting parallelized simulation speed was enhanced significantly. Workstation interfaces are being developed to provide for user (''operator'') interaction. The benefits realized by adapting previous MHTGR codes to run on a parallel processor are discussed, along with results of typical accident analyses. 3 refs., 3 figs.

  6. Parallelization of a Molecular Dynamics Simulation of AN Ion-Surface Collision System:

    NASA Astrophysics Data System (ADS)

    Atiş, Murat; Özdoğan, Cem; Güvenç, Ziya B.

    Parallel molecular dynamics simulation study of the ion-surface collision system is reported. A sequential molecular dynamics simulation program is converted into a parallel code utilizing the concept of parallel virtual machine (PVM). An effective and favorable algorithm is developed. Our parallelization of the algorithm shows that it is more efficient because of the optimal pair listing, linear scaling, and constant behavior of the internode communications. The code is tested in a distributed memory system consisting of a cluster of eight PCs that run under Linux (Debian 2.4.20 kernel). Our results on the collision system are discussed based on the speed up, efficiency and the system size. Furthermore, the code is used for a full simulation of the Ar-Ni(100) collision system and calculated physical quantities are presented.

  7. An Optimization Algorithm for Multipath Parallel Allocation for Service Resource in the Simulation Task Workflow

    PubMed Central

    Zhang, Hongjun; Zhang, Rui; Li, Yong; Zhang, Xuliang

    2014-01-01

    Service oriented modeling and simulation are hot issues in the field of modeling and simulation, and there is need to call service resources when simulation task workflow is running. How to optimize the service resource allocation to ensure that the task is complete effectively is an important issue in this area. In military modeling and simulation field, it is important to improve the probability of success and timeliness in simulation task workflow. Therefore, this paper proposes an optimization algorithm for multipath service resource parallel allocation, in which multipath service resource parallel allocation model is built and multiple chains coding scheme quantum optimization algorithm is used for optimization and solution. The multiple chains coding scheme quantum optimization algorithm is to extend parallel search space to improve search efficiency. Through the simulation experiment, this paper investigates the effect for the probability of success in simulation task workflow from different optimization algorithm, service allocation strategy, and path number, and the simulation result shows that the optimization algorithm for multipath service resource parallel allocation is an effective method to improve the probability of success and timeliness in simulation task workflow. PMID:24963506

  8. Parallel kinetic Monte Carlo simulations of Ag(111) island coarsening using a large database.

    PubMed

    Nandipati, Giridhar; Shim, Yunsic; Amar, Jacques G; Karim, Altaf; Kara, Abdelkader; Rahman, Talat S; Trushin, Oleg

    2009-02-25

    The results of parallel kinetic Monte Carlo (KMC) simulations of the room-temperature coarsening of Ag(111) islands carried out using a very large database obtained via self-learning KMC simulations are presented. Our results indicate that, while cluster diffusion and coalescence play an important role for small clusters and at very early times, at late time the coarsening proceeds via Ostwald ripening, i.e. large clusters grow while small clusters evaporate. In addition, an asymptotic analysis of our results for the average island size S(t) as a function of time t leads to a coarsening exponent n = 1/3 (where S(t)?t(2n)), in good agreement with theoretical predictions. However, by comparing with simulations without concerted (multi-atom) moves, we also find that the inclusion of such moves significantly increases the average island size. Somewhat surprisingly we also find that, while the average island size increases during coarsening, the scaled island-size distribution does not change significantly. Our simulations were carried out both as a test of, and as an application of, a variety of different algorithms for parallel kinetic Monte Carlo including the recently developed optimistic synchronous relaxation (OSR) algorithm as well as the semi-rigorous synchronous sublattice (SL) algorithm. A variation of the OSR algorithm corresponding to optimistic synchronous relaxation with pseudo-rollback (OSRPR) is also proposed along with a method for improving the parallel efficiency and reducing the number of boundary events via dynamic boundary allocation (DBA). A variety of other methods for enhancing the efficiency of our simulations are also discussed. We note that, because of the relatively high temperature of our simulations, as well as the large range of energy barriers (ranging from 0.05 to 0.8eV), developing an efficient algorithm for parallel KMC and/or SLKMC simulations is particularly challenging. However, by using DBA to minimize the number of boundary events, we have achieved significantly improved parallel efficiencies for the OSRPR and SL algorithms. Finally, we note that, among the three parallel algorithms which we have tested here, the semi-rigorous SL algorithm with DBA led to the highest parallel efficiencies. As a result, we have obtained reasonable parallel efficiencies in our simulations of room-temperature Ag(111) island coarsening for a small number of processors (e.g.N(p) = 2 and 4). Since the SL algorithm scales with system size for fixed processor size, we expect that comparable and/or even larger parallel efficiencies should be possible for parallel KMC and/or SLKMC simulations of larger systems with larger numbers of processors. PMID:21817366

  9. A parallel finite element simulator for ion transport through three-dimensional ion channel systems.

    PubMed

    Tu, Bin; Chen, Minxin; Xie, Yan; Zhang, Linbo; Eisenberg, Bob; Lu, Benzhuo

    2013-09-15

    A parallel finite element simulator, ichannel, is developed for ion transport through three-dimensional ion channel systems that consist of protein and membrane. The coordinates of heavy atoms of the protein are taken from the Protein Data Bank and the membrane is represented as a slab. The simulator contains two components: a parallel adaptive finite element solver for a set of Poisson-Nernst-Planck (PNP) equations that describe the electrodiffusion process of ion transport, and a mesh generation tool chain for ion channel systems, which is an essential component for the finite element computations. The finite element method has advantages in modeling irregular geometries and complex boundary conditions. We have built a tool chain to get the surface and volume mesh for ion channel systems, which consists of a set of mesh generation tools. The adaptive finite element solver in our simulator is implemented using the parallel adaptive finite element package Parallel Hierarchical Grid (PHG) developed by one of the authors, which provides the capability of doing large scale parallel computations with high parallel efficiency and the flexibility of choosing high order elements to achieve high order accuracy. The simulator is applied to a real transmembrane protein, the gramicidin A (gA) channel protein, to calculate the electrostatic potential, ion concentrations and I - V curve, with which both primitive and transformed PNP equations are studied and their numerical performances are compared. To further validate the method, we also apply the simulator to two other ion channel systems, the voltage dependent anion channel (VDAC) and ?-Hemolysin (?-HL). The simulation results agree well with Brownian dynamics (BD) simulation results and experimental results. Moreover, because ionic finite size effects can be included in PNP model now, we also perform simulations using a size-modified PNP (SMPNP) model on VDAC and ?-HL. It is shown that the size effects in SMPNP can effectively lead to reduced current in the channel, and the results are closer to BD simulation results. PMID:23740647

  10. Parallel performance optimizations on unstructured mesh-based simulations

    DOE PAGESBeta

    Sarje, Abhinav; Song, Sukhyun; Jacobsen, Douglas; Huck, Kevin; Hollingsworth, Jeffrey; Malony, Allen; Williams, Samuel; Oliker, Leonid

    2015-06-01

    This paper addresses two key parallelization challenges the unstructured mesh-based ocean modeling code, MPAS-Ocean, which uses a mesh based on Voronoi tessellations: (1) load imbalance across processes, and (2) unstructured data access patterns, that inhibit intra- and inter-node performance. Our work analyzes the load imbalance due to naive partitioning of the mesh, and develops methods to generate mesh partitioning with better load balance and reduced communication. Furthermore, we present methods that minimize both inter- and intranode data movement and maximize data reuse. Our techniques include predictive ordering of data elements for higher cache efficiency, as well as communication reduction approaches.more » We present detailed performance data when running on thousands of cores using the Cray XC30 supercomputer and show that our optimization strategies can exceed the original performance by over 2×. Additionally, many of these solutions can be broadly applied to a wide variety of unstructured grid-based computations.« less

  11. Parallel finite element simulation of mooring forces on floating objects

    NASA Astrophysics Data System (ADS)

    Aliabadi, S.; Abedi, J.; Zellars, B.

    2003-03-01

    The coupling between the equations governing the free-surface flows, the six degrees of freedom non-linear rigid body dynamics, the linear elasticity equations for mesh-moving and the cables has resulted in a fluid-structure interaction technology capable of simulating mooring forces on floating objects. The finite element solution strategy is based on a combination approach derived from fixed-mesh and moving-mesh techniques. Here, the free-surface flow simulations are based on the Navier-Stokes equations written for two incompressible fluids where the impact of one fluid on the other one is extremely small. An interface function with two distinct values is used to locate the position of the free-surface. The stabilized finite element formulations are written and integrated in an arbitrary Lagrangian-Eulerian domain. This allows us to handle the motion of the time dependent geometries. Forces and momentums exerted on the floating object by both water and hawsers are calculated and used to update the position of the floating object in time. In the mesh moving scheme, we assume that the computational domain is made of elastic materials. The linear elasticity equations are solved to obtain the displacements for each computational node. The non-linear rigid body dynamics equations are coupled with the governing equations of fluid flow and are solved simultaneously to update the position of the floating object. The numerical examples includes a 3D simulation of water waves impacting on a moored floating box and a model boat and simulation of floating object under water constrained with a cable.

  12. Exploiting Quantum Parallelism to Simulate Quantum Random Many-Body Systems

    SciTech Connect

    Paredes, B.; Cirac, J.I.; Verstraete, F.

    2005-09-30

    We present an algorithm that exploits quantum parallelism to simulate randomness in a quantum system. In our scheme, all possible realizations of the random parameters are encoded quantum mechanically in a superposition state of an auxiliary system. We show how our algorithm allows for the efficient simulation of dynamics of quantum random spin chains with known numerical methods. We propose an experimental realization based on atoms in optical lattices in which disorder could be simulated in parallel and in a controlled way through the interaction with another atomic species.

  13. Acceleration of Radiance for Lighting Simulation by Using Parallel Computing with OpenCL

    SciTech Connect

    Zuo, Wangda; McNeil, Andrew; Wetter, Michael; Lee, Eleanor

    2011-09-06

    We report on the acceleration of annual daylighting simulations for fenestration systems in the Radiance ray-tracing program. The algorithm was optimized to reduce both the redundant data input/output operations and the floating-point operations. To further accelerate the simulation speed, the calculation for matrix multiplications was implemented using parallel computing on a graphics processing unit. We used OpenCL, which is a cross-platform parallel programming language. Numerical experiments show that the combination of the above measures can speed up the annual daylighting simulations 101.7 times or 28.6 times when the sky vector has 146 or 2306 elements, respectively.

  14. Parallel simulation of subsonic fluid dynamics on a cluster of workstations

    NASA Astrophysics Data System (ADS)

    Skordos, Panayotis A.

    1994-11-01

    An effective approach of simulating fluid dynamics on a cluster of non-dedicated workstations is presented. The approach uses local interaction algorithms, small communication capacity, and automatic migration of parallel processes from busy hosts to free hosts. The approach is well-suited for simulating subsonic flow problems which involve both hydrodynamics and acoustic waves, for example, the flow of air inside wind musical instruments. Typical simulations achieve 80% parallel efficiency (speedup/processors) using 20 HP-Apollo workstations. Detailed measurements of the parallel efficiency of 2D and 3D simulations are presented, and a theoretical model of efficiency is developed which fits closely the measurements. Two numerical methods of fluid dynamics are tested: explicit finite differences, and the lattice Boltzmann method.

  15. Parallel FEM Simulation of Electromechanics in the Heart

    NASA Astrophysics Data System (ADS)

    Xia, Henian; Wong, Kwai; Zhao, Xiaopeng

    2011-11-01

    Cardiovascular disease is the leading cause of death in America. Computer simulation of complicated dynamics of the heart could provide valuable quantitative guidance for diagnosis and treatment of heart problems. In this paper, we present an integrated numerical model which encompasses the interaction of cardiac electrophysiology, electromechanics, and mechanoelectrical feedback. The model is solved by finite element method on a Linux cluster and the Cray XT5 supercomputer, kraken. Dynamical influences between the effects of electromechanics coupling and mechanic-electric feedback are shown.

  16. Time-partitioning simulation models for calculation on parallel computers

    NASA Technical Reports Server (NTRS)

    Milner, Edward J.; Blech, Richard A.; Chima, Rodrick V.

    1987-01-01

    A technique allowing time-staggered solution of partial differential equations is presented in this report. Using this technique, called time-partitioning, simulation execution speedup is proportional to the number of processors used because all processors operate simultaneously, with each updating of the solution grid at a different time point. The technique is limited by neither the number of processors available nor by the dimension of the solution grid. Time-partitioning was used to obtain the flow pattern through a cascade of airfoils, modeled by the Euler partial differential equations. An execution speedup factor of 1.77 was achieved using a two processor Cray X-MP/24 computer.

  17. Partitioning and packing mathematical simulation models for calculation on parallel computers

    NASA Technical Reports Server (NTRS)

    Arpasi, D. J.; Milner, E. J.

    1986-01-01

    The development of multiprocessor simulations from a serial set of ordinary differential equations describing a physical system is described. Degrees of parallelism (i.e., coupling between the equations) and their impact on parallel processing are discussed. The problem of identifying computational parallelism within sets of closely coupled equations that require the exchange of current values of variables is described. A technique is presented for identifying this parallelism and for partitioning the equations for parallel solution on a multiprocessor. An algorithm which packs the equations into a minimum number of processors is also described. The results of the packing algorithm when applied to a turbojet engine model are presented in terms of processor utilization.

  18. LARGE-SCALE SIMULATION OF BEAM DYNAMICS IN HIGH INTENSITY ION LINACS USING PARALLEL SUPERCOMPUTERS

    SciTech Connect

    R. RYNE; J. QIANG

    2000-08-01

    In this paper we present results of using parallel supercomputers to simulate beam dynamics in next-generation high intensity ion linacs. Our approach uses a three-dimensional space charge calculation with six types of boundary conditions. The simulations use a hybrid approach involving transfer maps to treat externally applied fields (including rf cavities) and parallel particle-in-cell techniques to treat the space-charge fields. The large-scale simulation results presented here represent a three order of magnitude improvement in simulation capability, in terms of problem size and speed of execution, compared with typical two-dimensional serial simulations. Specific examples will be presented, including simulation of the spallation neutron source (SNS) linac and the Low Energy Demonstrator Accelerator (LEDA) beam halo experiment.

  19. Simulation of optically encoded multiplexing for parallel multipoint sensing.

    PubMed

    Babu Rao, C; Chelliah, Pandian; Sahoo, Trilochan

    2015-06-20

    Spectral emission/absorption-based sensors are commonly used to monitor explosives, narcotics, and other restricted materials in high-security zones such as airports. Monitoring a broad range of spectral wavelengths with high spectral resolution would increase the repertoire of chemicals that can be monitored. However, a portable unit will have limitations in meeting these requirements. Optical fibers can be employed for collecting and transmitting spectral signals from portable sensor heads (PSHs) to a sensitive central spectral analyzer. However, simultaneous detection by sensors in multiple PSHs needs to be differentiated for identifying individual PSHs. An optical encoding method is presented in this paper for use of a portable unit for highly sensitive measurement. The methodology is demonstrated through a simulation using MATLAB Simulink. PMID:26193007

  20. A parallel algorithm for transient solid dynamics simulations with contact detection

    SciTech Connect

    Attaway, S.; Hendrickson, B.; Plimpton, S.; Gardner, D.; Vaughan, C.; Heinstein, M.; Peery, J.

    1996-06-01

    Solid dynamics simulations with Lagrangian finite elements are used to model a wide variety of problems, such as the calculation of impact damage to shipping containers for nuclear waste and the analysis of vehicular crashes. Using parallel computers for these simulations has been hindered by the difficulty of searching efficiently for material surface contacts in parallel. A new parallel algorithm for calculation of arbitrary material contacts in finite element simulations has been developed and implemented in the PRONTO3D transient solid dynamics code. This paper will explore some of the issues involved in developing efficient, portable, parallel finite element models for nonlinear transient solid dynamics simulations. The contact-detection problem poses interesting challenges for efficient implementation of a solid dynamics simulation on a parallel computer. The finite element mesh is typically partitioned so that each processor owns a localized region of the finite element mesh. This mesh partitioning is optimal for the finite element portion of the calculation since each processor must communicate only with the few connected neighboring processors that share boundaries with the decomposed mesh. However, contacts can occur between surfaces that may be owned by any two arbitrary processors. Hence, a global search across all processors is required at every time step to search for these contacts. Load-imbalance can become a problem since the finite element decomposition divides the volumetric mesh evenly across processors but typically leaves the surface elements unevenly distributed. In practice, these complications have been limiting factors in the performance and scalability of transient solid dynamics on massively parallel computers. In this paper the authors present a new parallel algorithm for contact detection that overcomes many of these limitations.

  1. Robust large-scale parallel nonlinear solvers for simulations.

    SciTech Connect

    Bader, Brett William; Pawlowski, Roger Patrick; Kolda, Tamara Gibson

    2005-11-01

    This report documents research to develop robust and efficient solution techniques for solving large-scale systems of nonlinear equations. The most widely used method for solving systems of nonlinear equations is Newton's method. While much research has been devoted to augmenting Newton-based solvers (usually with globalization techniques), little has been devoted to exploring the application of different models. Our research has been directed at evaluating techniques using different models than Newton's method: a lower order model, Broyden's method, and a higher order model, the tensor method. We have developed large-scale versions of each of these models and have demonstrated their use in important applications at Sandia. Broyden's method replaces the Jacobian with an approximation, allowing codes that cannot evaluate a Jacobian or have an inaccurate Jacobian to converge to a solution. Limited-memory methods, which have been successful in optimization, allow us to extend this approach to large-scale problems. We compare the robustness and efficiency of Newton's method, modified Newton's method, Jacobian-free Newton-Krylov method, and our limited-memory Broyden method. Comparisons are carried out for large-scale applications of fluid flow simulations and electronic circuit simulations. Results show that, in cases where the Jacobian was inaccurate or could not be computed, Broyden's method converged in some cases where Newton's method failed to converge. We identify conditions where Broyden's method can be more efficient than Newton's method. We also present modifications to a large-scale tensor method, originally proposed by Bouaricha, for greater efficiency, better robustness, and wider applicability. Tensor methods are an alternative to Newton-based methods and are based on computing a step based on a local quadratic model rather than a linear model. The advantage of Bouaricha's method is that it can use any existing linear solver, which makes it simple to write and easily portable. However, the method usually takes twice as long to solve as Newton-GMRES on general problems because it solves two linear systems at each iteration. In this paper, we discuss modifications to Bouaricha's method for a practical implementation, including a special globalization technique and other modifications for greater efficiency. We present numerical results showing computational advantages over Newton-GMRES on some realistic problems. We further discuss a new approach for dealing with singular (or ill-conditioned) matrices. In particular, we modify an algorithm for identifying a turning point so that an increasingly ill-conditioned Jacobian does not prevent convergence.

  2. Influence of Parallel Dynamics and Electron Temperature Fluctuations on Collisional Drift-Wave Simulations of CSDX

    NASA Astrophysics Data System (ADS)

    Vaezi, Payam; Holland, Christopher; Tynan, George; Chakraborty Thakur, Saikat; Brandt, Christian

    2014-10-01

    Previous 2D numerical simulations of collisional drift-wave turbulence in the linear Controlled Shear Decorrelation Experiment (CSDX) device were unable to reproduce experimental observations at magnetic fields above 1.4 kG at either the quantitative or qualitative level. Experimental observations suggest that dynamics of previously neglected ion parallel velocity and associated parallel shear-flow driven instabilities become important at the higher fields. In this poster, we present comparisons of new 3D simulations performed with the BOUT++ framework which include parallel ion velocity dynamics, as well as self-consistent electron temperature fluctuations, to the CSDX observations at multiple magnetic field strengths. We compare the simulated scalings of density and potential fluctuation spectra with magnetic field, as well as radial particle flux and Reynolds stress to 2D results and experimental observations. The comparisons are made using synthetic probe and fast camera diagnostics that incorporate both the electron density and temperature dynamics.

  3. Satisfiability Test with Synchronous Simulated Annealing on the Fujitsu AP1000 Massively-Parallel Multiprocessor

    NASA Technical Reports Server (NTRS)

    Sohn, Andrew; Biswas, Rupak

    1996-01-01

    Solving the hard Satisfiability Problem is time consuming even for modest-sized problem instances. Solving the Random L-SAT Problem is especially difficult due to the ratio of clauses to variables. This report presents a parallel synchronous simulated annealing method for solving the Random L-SAT Problem on a large-scale distributed-memory multiprocessor. In particular, we use a parallel synchronous simulated annealing procedure, called Generalized Speculative Computation, which guarantees the same decision sequence as sequential simulated annealing. To demonstrate the performance of the parallel method, we have selected problem instances varying in size from 100-variables/425-clauses to 5000-variables/21,250-clauses. Experimental results on the AP1000 multiprocessor indicate that our approach can satisfy 99.9 percent of the clauses while giving almost a 70-fold speedup on 500 processors.

  4. Parallelization issues of a code for physically-based simulation of fabrics

    NASA Astrophysics Data System (ADS)

    Romero, Sergio; Gutiérrez, Eladio; Romero, Luis F.; Plata, Oscar; Zapata, Emilio L.

    2004-10-01

    The simulation of fabrics, clothes, and flexible materials is an essential topic in computer animation of realistic virtual humans and dynamic sceneries. New emerging technologies, as interactive digital TV and multimedia products, make necessary the development of powerful tools to perform real-time simulations. Parallelism is one of such tools. When analyzing computationally fabric simulations we found these codes belonging to the complex class of irregular applications. Frequently this kind of codes includes reduction operations in their core, so that an important fraction of the computational time is spent on such operations. In fabric simulators these operations appear when evaluating forces, giving rise to the equation system to be solved. For this reason, this paper discusses only this phase of the simulation. This paper analyzes and evaluates different irregular reduction parallelization techniques on ccNUMA shared memory machines, applied to a real, physically-based, fabric simulator we have developed. Several issues are taken into account in order to achieve high code performance, as exploitation of data access locality and parallelism, as well as careful use of memory resources (memory overhead). In this paper we use the concept of data affinity to develop various efficient algorithms for reduction parallelization exploiting data locality.

  5. Dependability analysis of parallel systems using a simulation-based approach. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Sawyer, Darren Charles

    1994-01-01

    The analysis of dependability in large, complex, parallel systems executing real applications or workloads is examined in this thesis. To effectively demonstrate the wide range of dependability problems that can be analyzed through simulation, the analysis of three case studies is presented. For each case, the organization of the simulation model used is outlined, and the results from simulated fault injection experiments are explained, showing the usefulness of this method in dependability modeling of large parallel systems. The simulation models are constructed using DEPEND and C++. Where possible, methods to increase dependability are derived from the experimental results. Another interesting facet of all three cases is the presence of some kind of workload of application executing in the simulation while faults are injected. This provides a completely new dimension to this type of study, not possible to model accurately with analytical approaches.

  6. Parallel computation for reservoir thermal simulation: An overlapping domain decomposition approach

    NASA Astrophysics Data System (ADS)

    Wang, Zhongxiao

    2005-11-01

    In this dissertation, we are involved in parallel computing for the thermal simulation of multicomponent, multiphase fluid flow in petroleum reservoirs. We report the development and applications of such a simulator. Unlike many efforts made to parallelize locally the solver of a linear equations system which affects the performance the most, this research takes a global parallelization strategy by decomposing the computational domain into smaller subdomains. This dissertation addresses the domain decomposition techniques and, based on the comparison, adopts an overlapping domain decomposition method. This global parallelization method hands over each subdomain to a single processor of the parallel computer to process. Communication is required when handling overlapping regions between subdomains. For this purpose, MPI (message passing interface) is used for data communication and communication control. A physical and mathematical model is introduced for the reservoir thermal simulation. Numerical tests on two sets of industrial data of practical oilfields indicate that this model and the parallel implementation match the history data accurately. Therefore, we expect to use both the model and the parallel code to predict oil production and guide the design, implementation and real-time fine tuning of new well operating schemes. A new adaptive mechanism to synchronize processes on different processors has been introduced, which not only ensures the computational accuracy but also improves the time performance. To accelerate the convergence rate of iterative solution of the large linear equations systems derived from the discretization of governing equations of our physical and mathematical model in space and time, we adopt the ORTHOMIN method in conjunction with an incomplete LU factorization preconditioning technique. Important improvements have been made in both ORTHOMIN method and incomplete LU factorization in order to enhance time performance without affecting the convergence rate of iterative solution. More importantly, the parallel implementation may serve as a working platform for any further research, for example, building and testing new physical and mathematical models, developing and testing new solver of pertinent linear equations system, etc.

  7. A conflict-free, path-level parallelization approach for sequential simulation algorithms

    NASA Astrophysics Data System (ADS)

    Rasera, Luiz Gustavo; Machado, Péricles Lopes; Costa, João Felipe C. L.

    2015-07-01

    Pixel-based simulation algorithms are the most widely used geostatistical technique for characterizing the spatial distribution of natural resources. However, sequential simulation does not scale well for stochastic simulation on very large grids, which are now commonly found in many petroleum, mining, and environmental studies. With the availability of multiple-processor computers, there is an opportunity to develop parallelization schemes for these algorithms to increase their performance and efficiency. Here we present a conflict-free, path-level parallelization strategy for sequential simulation. The method consists of partitioning the simulation grid into a set of groups of nodes and delegating all available processors for simulation of multiple groups of nodes concurrently. An automated classification procedure determines which groups are simulated in parallel according to their spatial arrangement in the simulation grid. The major advantage of this approach is that it does not require conflict resolution operations, and thus allows exact reproduction of results. Besides offering a large performance gain when compared to the traditional serial implementation, the method provides efficient use of computational resources and is generic enough to be adapted to several sequential algorithms.

  8. Application of integration algorithms in a parallel processing environment for the simulation of jet engines

    NASA Technical Reports Server (NTRS)

    Krosel, S. M.; Milner, E. J.

    1982-01-01

    The application of Predictor corrector integration algorithms developed for the digital parallel processing environment are investigated. The algorithms are implemented and evaluated through the use of a software simulator which provides an approximate representation of the parallel processing hardware. Test cases which focus on the use of the algorithms are presented and a specific application using a linear model of a turbofan engine is considered. Results are presented showing the effects of integration step size and the number of processors on simulation accuracy. Real time performance, interprocessor communication, and algorithm startup are also discussed.

  9. Parallel object oriented implementation of a 2D bounded electrostatic plasma PIC simulation

    SciTech Connect

    Norton, C.D.; Szymanski, B.K.; Decyk, V.K.

    1995-12-01

    We discuss the software development issues involved in designing parallel programs using object oriented techniques. Simulations involving 1D and 2D Particle In Cell plasma codes illustrate how C++ programs can effectively describe complex simulations while performing with reasonable efficiency when compared to the equivalent Fortran programs. The scalable object oriented modeling techniques closely match the physical view of the problem, thus supporting modifiability and portability of the code. Selection of a parallel programming paradigm must consider the important factors of efficiency of the computation and the programming implementation effort. C++ and Fortran implementation paradigms are compared and discussed from this point of view.

  10. A parallel finite volume algorithm for large-eddy simulation of turbulent flows

    NASA Astrophysics Data System (ADS)

    Bui, Trong Tri

    1998-11-01

    A parallel unstructured finite volume algorithm is developed for large-eddy simulation of compressible turbulent flows. Major components of the algorithm include piecewise linear least-square reconstruction of the unknown variables, trilinear finite element interpolation for the spatial coordinates, Roe flux difference splitting, and second-order MacCormack explicit time marching. The computer code is designed from the start to take full advantage of the additional computational capability provided by the current parallel computer systems. Parallel implementation is done using the message passing programming model and message passing libraries such as the Parallel Virtual Machine (PVM) and Message Passing Interface (MPI). The development of the numerical algorithm is presented in detail. The parallel strategy and issues regarding the implementation of a flow simulation code on the current generation of parallel machines are discussed. The results from parallel performance studies show that the algorithm is well suited for parallel computer systems that use the message passing programming model. Nearly perfect parallel speedup is obtained on MPP systems such as the Cray T3D and IBM SP2. Performance comparison with the older supercomputer systems such as the Cray YMP show that the simulations done on the parallel systems are approximately 10 to 30 times faster. The results of the accuracy and performance studies for the current algorithm are reported. To validate the flow simulation code, a number of Euler and Navier-Stokes simulations are done for internal duct flows. Inviscid Euler simulation of a very small amplitude acoustic wave interacting with a shock wave in a quasi-1D convergent-divergent nozzle shows that the algorithm is capable of simultaneously tracking the very small disturbances of the acoustic wave and capturing the shock wave. Navier-Stokes simulations are made for fully developed laminar flow in a square duct, developing laminar flow in a rectangular duct, and developing laminar flow in a 90-degree square bend. The Navier-Stokes solutions show good agreements with available analytical solutions and experimental data. To validate the flow simulation code for turbulence simulation, LES of fully-developed turbulent flow in a square duct is performed for a Reynolds number of 320 based on the average friction velocity and the hydraulic diameter of the duct. The accuracy of the above algorithm for turbulence simulations is evaluated by comparison with the DNS solution. The effects of grid resolution, upwind numerical dissipation, and subgrid scale dissipation on the accuracy of the LES are examined. Comparison with DNS results shows that the standard Roe flux difference splitting dissipation adversely affect the accuracy of the turbulence simulation. This problem is unique to the turbulence simulation, since it does not occur in the Euler and laminar Navier-Stokes simulations using the same code. For accurate turbulence simulation, it is found that only three to five percent of the standard Roe flux difference splitting dissipation is needed.

  11. Parallel simulation of tsunami inundation on a large-scale supercomputer

    NASA Astrophysics Data System (ADS)

    Oishi, Y.; Imamura, F.; Sugawara, D.

    2013-12-01

    An accurate prediction of tsunami inundation is important for disaster mitigation purposes. One approach is to approximate the tsunami wave source through an instant inversion analysis using real-time observation data (e.g., Tsushima et al., 2009) and then use the resulting wave source data in an instant tsunami inundation simulation. However, a bottleneck of this approach is the large computational cost of the non-linear inundation simulation and the computational power of recent massively parallel supercomputers is helpful to enable faster than real-time execution of a tsunami inundation simulation. Parallel computers have become approximately 1000 times faster in 10 years (www.top500.org), and so it is expected that very fast parallel computers will be more and more prevalent in the near future. Therefore, it is important to investigate how to efficiently conduct a tsunami simulation on parallel computers. In this study, we are targeting very fast tsunami inundation simulations on the K computer, currently the fastest Japanese supercomputer, which has a theoretical peak performance of 11.2 PFLOPS. One computing node of the K computer consists of 1 CPU with 8 cores that share memory, and the nodes are connected through a high-performance torus-mesh network. The K computer is designed for distributed-memory parallel computation, so we have developed a parallel tsunami model. Our model is based on TUNAMI-N2 model of Tohoku University, which is based on a leap-frog finite difference method. A grid nesting scheme is employed to apply high-resolution grids only at the coastal regions. To balance the computation load of each CPU in the parallelization, CPUs are first allocated to each nested layer in proportion to the number of grid points of the nested layer. Using CPUs allocated to each layer, 1-D domain decomposition is performed on each layer. In the parallel computation, three types of communication are necessary: (1) communication to adjacent neighbours for the finite difference calculation, (2) communication between adjacent layers for the calculations to connect each layer, and (3) global communication to obtain the time step which satisfies the CFL condition in the whole domain. A preliminary test on the K computer showed the parallel efficiency on 1024 cores was 57% relative to 64 cores. We estimate that the parallel efficiency will be considerably improved by applying a 2-D domain decomposition instead of the present 1-D domain decomposition in future work. The present parallel tsunami model was applied to the 2011 Great Tohoku tsunami. The coarsest resolution layer covers a 758 km × 1155 km region with a 405 m grid spacing. A nesting of five layers was used with the resolution ratio of 1/3 between nested layers. The finest resolution region has 5 m resolution and covers most of the coastal region of Sendai city. To complete 2 hours of simulation time, the serial (non-parallel) computation took approximately 4 days on a workstation. To complete the same simulation on 1024 cores of the K computer, it took 45 minutes which is more than two times faster than real-time. This presentation discusses the updated parallel computational performance and the efficient use of the K computer when considering the characteristics of the tsunami inundation simulation model in relation to the characteristics and capabilities of the K computer.

  12. Special purpose parallel computer architecture for real-time control and simulation in robotic applications

    NASA Technical Reports Server (NTRS)

    Fijany, Amir (Inventor); Bejczy, Antal K. (Inventor)

    1993-01-01

    This is a real-time robotic controller and simulator which is a MIMD-SIMD parallel architecture for interfacing with an external host computer and providing a high degree of parallelism in computations for robotic control and simulation. It includes a host processor for receiving instructions from the external host computer and for transmitting answers to the external host computer. There are a plurality of SIMD microprocessors, each SIMD processor being a SIMD parallel processor capable of exploiting fine grain parallelism and further being able to operate asynchronously to form a MIMD architecture. Each SIMD processor comprises a SIMD architecture capable of performing two matrix-vector operations in parallel while fully exploiting parallelism in each operation. There is a system bus connecting the host processor to the plurality of SIMD microprocessors and a common clock providing a continuous sequence of clock pulses. There is also a ring structure interconnecting the plurality of SIMD microprocessors and connected to the clock for providing the clock pulses to the SIMD microprocessors and for providing a path for the flow of data and instructions between the SIMD microprocessors. The host processor includes logic for controlling the RRCS by interpreting instructions sent by the external host computer, decomposing the instructions into a series of computations to be performed by the SIMD microprocessors, using the system bus to distribute associated data among the SIMD microprocessors, and initiating activity of the SIMD microprocessors to perform the computations on the data by procedure call.

  13. Virtual Simulator: An infrastructure for design and performance-prediction of massively parallel codes

    NASA Astrophysics Data System (ADS)

    Perumalla, K.; Fujimoto, R.; Pande, S.; Karimabadi, H.; Driscoll, J.; Omelchenko, Y.

    2005-12-01

    Large parallel/distributed scientific simulations are very complex, and their dynamic behavior is hard to predict. Efficient development of massively parallel codes remains a computational challenge. For example, almost none of the kinetic codes in use in space physics today have dynamic load balancing capability. Here we present a new infrastructure for design and prediction of parallel codes. Performance prediction is useful to analyze, understand and experiment with different partitioning schemes, multiple modeling alternatives and so on, without having to run the application on supercomputers. Instrumentation of the model (with least perturbance to performance) is useful to glean key metrics and understand application-level behavior. Unfortunately, traditional approaches to virtual execution and instrumentation are limited by either slow execution speed or low resolution or both. We present a new framework that provides a high-resolution framework that provides a virtual CPU abstraction (with a full thread context per CPU), yet scales to thousands of virtual CPUs. The tool, called PDES2, presents different levels of modeling interfaces, from general purpose parallel simulations to parallel grid-based particle-in-cell (PIC) codes. The tool itself runs on multiple processors in order to accommodate the high-resolution by distributing the virtual execution across processors. Validation experiments of PIC models in the framework using a 1-D hybrid shock application show close agreement of results from virtual executions with results from actual supercomputer runs. The utility of this tool is further illustrated through an application to a parallel global hybrid code.

  14. Transient dynamics simulations: Parallel algorithms for contact detection and smoothed particle hydrodynamics

    SciTech Connect

    Hendrickson, B.; Plimpton, S.; Attaway, S.; Swegle, J.

    1996-09-01

    Transient dynamics simulations are commonly used to model phenomena such as car crashes, underwater explosions, and the response of shipping containers to high-speed impacts. Physical objects in such a simulation are typically represented by Lagrangian meshes because the meshes can move and deform with the objects as they undergo stress. Fluids (gasoline, water) or fluid-like materials (earth) in the simulation can be modeled using the techniques of smoothed particle hydrodynamics. Implementing a hybrid mesh/particle model on a massively parallel computer poses several difficult challenges. One challenge is to simultaneously parallelize and load-balance both the mesh and particle portions of the computation. A second challenge is to efficiently detect the contacts that occur within the deforming mesh and between mesh elements and particles as the simulation proceeds. These contacts impart forces to the mesh elements and particles which must be computed at each timestep to accurately capture the physics of interest. In this paper we describe new parallel algorithms for smoothed particle hydrodynamics and contact detection which turn out to have several key features in common. Additionally, we describe how to join the new algorithms with traditional parallel finite element techniques to create an integrated particle/mesh transient dynamics simulation. Our approach to this problem differs from previous work in that we use three different parallel decompositions, a static one for the finite element analysis and dynamic ones for particles and for contact detection. We have implemented our ideas in a parallel version of the transient dynamics code PRONTO-3D and present results for the code running on a large Intel Paragon.

  15. Parallelization of ALICE simulation - a jump through the looking-glass

    NASA Astrophysics Data System (ADS)

    Tadel, Matevž; Carminati, Federico

    2010-04-01

    HEP computing is approaching the end of an era when simulation parallelization could be performed simply by running one instance of full simulation per core. The increasing number of cores and appearance of hardware-thread support both pose a severe limitation on memory and memory-bandwidth available to each execution unit. Typical simulation and reconstruction jobs of AliROOT (offline framework of the ALICE experiment at LHC) do not differ significantly in memory usage - but the input/output rate of reconstruction is approximately three times higher. This makes simulation a more natural candidate for parallelization, especially since the simulation code is relatively stable while the reconstruction code is not expected to settle until the detector is fully calibrated with real data and understood under stable running conditions. We have chosen to use multi-threading solution with one primary particle and all its secondaries being tracked by a given thread. This model corresponds well to Pb-Pb ion collision simulation where 60,000 primary particles need to be transported. After the MC processing of a primary particle is completed, the same thread also performs output serialization. Modifications of ROOT, AliROOT and GEANT3 that were required to perform this task are discussed. Performance of the parallelized version of simulation under varying running conditions is presented.

  16. Parallel implementation of molecular dynamics simulation for short-ranged interaction

    NASA Astrophysics Data System (ADS)

    Wu, Jong-Shinn; Hsu, Yu-Lin; Lee, Yun-Min

    2005-08-01

    A parallel molecular dynamics simulation method, designed for large-scale problems, employing dynamic spatial domain decomposition for short-ranged molecular interactions is proposed. In this parallel cellular molecular dynamics (PCMD) simulation method, the link-cell data structure is used to reduce the searching time required for forming the cut-off neighbor list as well as for domain decomposition, which utilizes the multi-level graph-partitioning technique. A simple threshold scheme (STS), in which workload imbalance is monitored and compared with some threshold value during the runtime, is proposed to decide the proper time for repartitioning the domain. The simulation code is implemented and tested on the memory-distributed parallel machine, e.g., PC-cluster system. Parallel performance is studied using approximately one million L-J atoms in the condensed, vaporized and supercritical states. Results show that fairly good parallel efficiency at 49 processors can be obtained for the condensed and supercritical states (˜60%), while it is comparably lower for the vaporized state (˜40%).

  17. A parallel simulated annealing algorithm for standard cell placement on a hypercube computer

    NASA Technical Reports Server (NTRS)

    Jones, Mark Howard

    1987-01-01

    A parallel version of a simulated annealing algorithm is presented which is targeted to run on a hypercube computer. A strategy for mapping the cells in a two dimensional area of a chip onto processors in an n-dimensional hypercube is proposed such that both small and large distance moves can be applied. Two types of moves are allowed: cell exchanges and cell displacements. The computation of the cost function in parallel among all the processors in the hypercube is described along with a distributed data structure that needs to be stored in the hypercube to support parallel cost evaluation. A novel tree broadcasting strategy is used extensively in the algorithm for updating cell locations in the parallel environment. Studies on the performance of the algorithm on example industrial circuits show that it is faster and gives better final placement results than the uniprocessor simulated annealing algorithms. An improved uniprocessor algorithm is proposed which is based on the improved results obtained from parallelization of the simulated annealing algorithm.

  18. Efficient parallel algorithm for statistical ion track simulations in crystalline materials

    NASA Astrophysics Data System (ADS)

    Jeon, Byoungseon; Grønbech-Jensen, Niels

    2009-02-01

    We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been successfully applied to studies of, e.g., ion implantation into crystalline semiconductor wafers. We discuss the strategies for parallelizing the method, and we settle on a host-client type polling scheme in which a multiple of asynchronous processors are continuously fed to the host, which, in turn, distributes the resulting feed-back information to the clients. This real-time feed-back consists of, e.g., cumulative damage information or statistics updates necessary for the cloning in the rare event algorithm. We finally demonstrate the algorithm for radiation effects in a nuclear oxide fuel, and we show the balanced parallel approach with high parallel efficiency in multiple processor configurations.

  19. Massively parallel Monte Carlo for many-particle simulations on GPUs

    NASA Astrophysics Data System (ADS)

    Glotzer, Sharon; Anderson, Joshua; Jankowski, Eric; Grubb, Thomas; Engel, Michael

    2013-03-01

    Current trends in parallel processors call for the design of efficient massively parallel algorithms for scientific computing. Parallel algorithms for Monte Carlo simulations of thermodynamic ensembles of particles have received little attention because of the inherent serial nature of the statistical sampling. We present a massively parallel method that obeys detailed balance and implement it for a system of hard disks on the GPU. We reproduce results of serial high-precision Monte Carlo runs to verify the method. This is a good test case because the hard disk equation of state over the range where the liquid transforms into the solid is particularly sensitive to small deviations away from the balance conditions. On a GeForce GTX 680, our GPU implementation executes 95 times faster than on a single Intel Xeon E5540 CPU core, enabling 17 times better performance per dollar and cutting energy usage by a factor of 10.

  20. Numerical simulation of compressible multiphase flows using the Parallel Adaptive Wavelet-Collocation Method

    NASA Astrophysics Data System (ADS)

    Aslani, Mohamad; Regele, Jonathan

    2015-11-01

    Numerical simulation of incompressible multiphase flows to describe fluid atomization is becoming more common. However, compressible multiphase flow simulations are mostly limited to shock-bubble interactions with only a few studies involving shock waves impacting liquid droplets. A methodology for simulating compressible multiphase flow is developed from existing approaches for the Parallel Adaptive Wavelet-Collocation Method. The method uses an interface capturing function with a steepening procedure for the fluid interface. Simulations of shock waves impacting liquid droplets illustrate the numerical capabilities.

  1. Research of control system stability in solar array simulator with continuous power amplifier of parallel type

    NASA Astrophysics Data System (ADS)

    Mizrah, E. A.; Tkachev, S. B.; Shtabel, N. V.

    2015-10-01

    Solar array simulators are nonlinear control systems designed to reproduce static and dynamic characteristics of solar array. Solar array characteristics depend on illumination, temperature, space environment and other causes. During on-earth testing of spacecraft power systems there is a problem reaching stable work of simulator with different impedance loads in wide range load regulation. In the article authors propose a research method for absolute process stability in solar array simulators and present results of absolute stability research for solar array simulator with continuous parallel type power amplifier.

  2. Wake Encounter Analysis for a Closely Spaced Parallel Runway Paired Approach Simulation

    NASA Technical Reports Server (NTRS)

    Mckissick,Burnell T.; Rico-Cusi, Fernando J.; Murdoch, Jennifer; Oseguera-Lohr, Rosa M.; Stough, Harry P, III; O'Connor, Cornelius J.; Syed, Hazari I.

    2009-01-01

    A Monte Carlo simulation of simultaneous approaches performed by two transport category aircraft from the final approach fix to a pair of closely spaced parallel runways was conducted to explore the aft boundary of the safe zone in which separation assurance and wake avoidance are provided. The simulation included variations in runway centerline separation, initial longitudinal spacing of the aircraft, crosswind speed, and aircraft speed during the approach. The data from the simulation showed that the majority of the wake encounters occurred near or over the runway and the aft boundaries of the safe zones were identified for all simulation conditions.

  3. IB: a Monte Carlo Simulation Tool for Neutron Scattering Instrument Design under Parallel Virtual Machine

    SciTech Connect

    Zhao, Jinkui

    2011-01-01

    IB is a Monte Carlo simulation tool for aiding neutron scattering instrument designs. It is written in C++ and implemented under Parallel Virtual Machine. The program has a few basic components, or modules, that can be used to build a virtual neutron scattering instrument. More complex components, such as neutron guides and multichannel beam benders, can be constructed using the grouping technique unique to IB. Users can specify a collection of modules as a group. For example, a neutron guide can be constructed by grouping four neutron mirrors together that make up the four sides of the guide. IB s simulation engine ensures that neutrons entering a group will be properly operated upon by all members of the group. For simulations that require higher computer speed, the program can be run in parallel mode under the PVM architecture. Initially, the program was written for designing instruments on pulsed neutron sources, it has since been used to simulate reactor based instruments as well.

  4. Overcoming Communication Latency Barriers in Massively Parallel Molecular Dynamics Simulations on Anton

    NASA Astrophysics Data System (ADS)

    Dror, Ron

    2013-03-01

    Strong scaling of scientific applications on parallel architectures is increasingly limited by communication latency. This talk will describe the techniques used to reduce latency and mitigate its effects on performance in Anton, a massively parallel special-purpose machine that accelerates molecular dynamics (MD) simulations by orders of magnitude compared with the previous state of the art. Achieving this speedup required both specialized hardware mechanisms and a restructuring of the application software to reduce network latency, sender and receiver overhead, and synchronization costs. Key elements of Anton's approach, in addition to tightly integrated communication hardware, include formulating data transfer in terms of counted remote writes and leveraging fine-grained communication. Anton delivers end-to-end inter-node latency significantly lower than any other large-scale parallel machine, and the total critical-path communication time for an Anton MD simulation is less than 3% that of the next-fastest MD platform.

  5. Xyce parallel electronic simulator reference guide, Version 6.0.1.

    SciTech Connect

    Keiter, Eric Richard; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Verley, Jason C.; Fixel, Deborah A.; Coffey, Todd Stirling; Pawlowski, Roger Patrick; Warrender, Christina E.; Baur, David Gregory.

    2014-01-01

    This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] .

  6. A Plane-Parallel Wind Solution for Testing Numerical Simulations of Photoevaporation

    NASA Astrophysics Data System (ADS)

    Hutchison, Mark A.; Laibe, Guillaume

    2016-04-01

    Here, we derive a Parker-wind-like solution for a stratified, plane-parallel atmosphere undergoing photoionisation. The difference compared to the standard Parker solar wind is that the sonic point is crossed only at infinity. The simplicity of the analytic solution makes it a convenient test problem for numerical simulations of photoevaporation in protoplanetary discs.

  7. A direct-execution parallel architecture for the Advanced Continuous Simulation Language (ACSL)

    NASA Technical Reports Server (NTRS)

    Carroll, Chester C.; Owen, Jeffrey E.

    1988-01-01

    A direct-execution parallel architecture for the Advanced Continuous Simulation Language (ACSL) is presented which overcomes the traditional disadvantages of simulations executed on a digital computer. The incorporation of parallel processing allows the mapping of simulations into a digital computer to be done in the same inherently parallel manner as they are currently mapped onto an analog computer. The direct-execution format maximizes the efficiency of the executed code since the need for a high level language compiler is eliminated. Resolution is greatly increased over that which is available with an analog computer without the sacrifice in execution speed normally expected with digitial computer simulations. Although this report covers all aspects of the new architecture, key emphasis is placed on the processing element configuration and the microprogramming of the ACLS constructs. The execution times for all ACLS constructs are computed using a model of a processing element based on the AMD 29000 CPU and the AMD 29027 FPU. The increase in execution speed provided by parallel processing is exemplified by comparing the derived execution times of two ACSL programs with the execution times for the same programs executed on a similar sequential architecture.

  8. Massively parallel simulation of flow and transport in variably saturated porous and fractured media

    SciTech Connect

    Wu, Yu-Shu; Zhang, Keni; Pruess, Karsten

    2002-01-15

    This paper describes a massively parallel simulation method and its application for modeling multiphase flow and multicomponent transport in porous and fractured reservoirs. The parallel-computing method has been implemented into the TOUGH2 code and its numerical performance is tested on a Cray T3E-900 and IBM SP. The efficiency and robustness of the parallel-computing algorithm are demonstrated by completing two simulations with more than one million gridblocks, using site-specific data obtained from a site-characterization study. The first application involves the development of a three-dimensional numerical model for flow in the unsaturated zone of Yucca Mountain, Nevada. The second application is the study of tracer/radionuclide transport through fracture-matrix rocks for the same site. The parallel-computing technique enhances modeling capabilities by achieving several-orders-of-magnitude speedup for large-scale and high resolution modeling studies. The resulting modeling results provide many new insights into flow and transport processes that could not be obtained from simulations using the single-CPU simulator.

  9. Parallel spatial direct numerical simulations on the Intel iPSC/860 hypercube

    NASA Technical Reports Server (NTRS)

    Joslin, Ronald D.; Zubair, Mohammad

    1993-01-01

    The implementation and performance of a parallel spatial direct numerical simulation (PSDNS) approach on the Intel iPSC/860 hypercube is documented. The direct numerical simulation approach is used to compute spatially evolving disturbances associated with the laminar-to-turbulent transition in boundary-layer flows. The feasibility of using the PSDNS on the hypercube to perform transition studies is examined. The results indicate that the direct numerical simulation approach can effectively be parallelized on a distributed-memory parallel machine. By increasing the number of processors nearly ideal linear speedups are achieved with nonoptimized routines; slower than linear speedups are achieved with optimized (machine dependent library) routines. This slower than linear speedup results because the Fast Fourier Transform (FFT) routine dominates the computational cost and because the routine indicates less than ideal speedups. However with the machine-dependent routines the total computational cost decreases by a factor of 4 to 5 compared with standard FORTRAN routines. The computational cost increases linearly with spanwise wall-normal and streamwise grid refinements. The hypercube with 32 processors was estimated to require approximately twice the amount of Cray supercomputer single processor time to complete a comparable simulation; however it is estimated that a subgrid-scale model which reduces the required number of grid points and becomes a large-eddy simulation (PSLES) would reduce the computational cost and memory requirements by a factor of 10 over the PSDNS. This PSLES implementation would enable transition simulations on the hypercube at a reasonable computational cost.

  10. Moldy: a portable molecular dynamics simulation program for serial and parallel computers

    NASA Astrophysics Data System (ADS)

    Refson, Keith

    2000-04-01

    Moldy is a highly portable C program for performing molecular-dynamics simulations of solids and liquids using periodic boundary conditions. It runs in serial mode on a conventional workstation or on a parallel system using an interface to a parallel communications library such as MPI or BSP. The "replicated data" parallelization strategy is used to achieve reasonable performance with a minimal difference between serial and parallel code. The code has been optimized for high performance in both serial and parallel cases. The model system is completely specified in a run-time input file and may contain atoms, molecules or ions in any mixture. Molecules or molecular ions are treated in the rigid-molecule approximation and their rotational motion is modeled using quaternion methods. The equations of motion are integrated using a modified form of the Beeman algorithm. Simulations may be performed in the usual NVE ensemble or in isobaric and/or isothermal ensembles. Potential functions of the Lennard-Jones, 6-exp and MCY forms are supported and the code is structured to give an straightforward interface to add a new functional form. The Ewald method is used to calculate long-ranged electrostatic forces.

  11. Parallel Simulation of Three-Dimensional Free Surface Fluid Flow Problems

    SciTech Connect

    BAER,THOMAS A.; SACKINGER,PHILIP A.; SUBIA,SAMUEL R.

    1999-10-14

    Simulation of viscous three-dimensional fluid flow typically involves a large number of unknowns. When free surfaces are included, the number of unknowns increases dramatically. Consequently, this class of problem is an obvious application of parallel high performance computing. We describe parallel computation of viscous, incompressible, free surface, Newtonian fluid flow problems that include dynamic contact fines. The Galerkin finite element method was used to discretize the fully-coupled governing conservation equations and a ''pseudo-solid'' mesh mapping approach was used to determine the shape of the free surface. In this approach, the finite element mesh is allowed to deform to satisfy quasi-static solid mechanics equations subject to geometric or kinematic constraints on the boundaries. As a result, nodal displacements must be included in the set of unknowns. Other issues discussed are the proper constraints appearing along the dynamic contact line in three dimensions. Issues affecting efficient parallel simulations include problem decomposition to equally distribute computational work among a SPMD computer and determination of robust, scalable preconditioners for the distributed matrix systems that must be solved. Solution continuation strategies important for serial simulations have an enhanced relevance in a parallel coquting environment due to the difficulty of solving large scale systems. Parallel computations will be demonstrated on an example taken from the coating flow industry: flow in the vicinity of a slot coater edge. This is a three dimensional free surface problem possessing a contact line that advances at the web speed in one region but transitions to static behavior in another region. As such, a significant fraction of the computational time is devoted to processing boundary data. Discussion focuses on parallel speed ups for fixed problem size, a class of problems of immediate practical importance.

  12. The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations.

    PubMed

    Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka

    2011-11-15

    Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. PMID:21793007

  13. Petascale turbulence simulation using a highly parallel fast multipole method on GPUs

    NASA Astrophysics Data System (ADS)

    Yokota, Rio; Barba, L. A.; Narumi, Tetsu; Yasuoka, Kenji

    2013-03-01

    This paper reports large-scale direct numerical simulations of homogeneous-isotropic fluid turbulence, achieving sustained performance of 1.08 petaflop/s on GPU hardware using single precision. The simulations use a vortex particle method to solve the Navier-Stokes equations, with a highly parallel fast multipole method (FMM) as numerical engine, and match the current record in mesh size for this application, a cube of 40963 computational points solved with a spectral method. The standard numerical approach used in this field is the pseudo-spectral method, relying on the FFT algorithm as the numerical engine. The particle-based simulations presented in this paper quantitatively match the kinetic energy spectrum obtained with a pseudo-spectral method, using a trusted code. In terms of parallel performance, weak scaling results show the FMM-based vortex method achieving 74% parallel efficiency on 4096 processes (one GPU per MPI process, 3 GPUs per node of the TSUBAME-2.0 system). The FFT-based spectral method is able to achieve just 14% parallel efficiency on the same number of MPI processes (using only CPU cores), due to the all-to-all communication pattern of the FFT algorithm. The calculation time for one time step was 108 s for the vortex method and 154 s for the spectral method, under these conditions. Computing with 69 billion particles, this work exceeds by an order of magnitude the largest vortex-method calculations to date.

  14. Parallel 3D Multi-Stage Simulation of a Turbofan Engine

    NASA Technical Reports Server (NTRS)

    Turner, Mark G.; Topp, David A.

    1998-01-01

    A 3D multistage simulation of each component of a modern GE Turbofan engine has been made. An axisymmetric view of this engine is presented in the document. This includes a fan, booster rig, high pressure compressor rig, high pressure turbine rig and a low pressure turbine rig. In the near future, all components will be run in a single calculation for a solution of 49 blade rows. The simulation exploits the use of parallel computations by using two levels of parallelism. Each blade row is run in parallel and each blade row grid is decomposed into several domains and run in parallel. 20 processors are used for the 4 blade row analysis. The average passage approach developed by John Adamczyk at NASA Lewis Research Center has been further developed and parallelized. This is APNASA Version A. It is a Navier-Stokes solver using a 4-stage explicit Runge-Kutta time marching scheme with variable time steps and residual smoothing for convergence acceleration. It has an implicit K-E turbulence model which uses an ADI solver to factor the matrix. Between 50 and 100 explicit time steps are solved before a blade row body force is calculated and exchanged with the other blade rows. This outer iteration has been coined a "flip." Efforts have been made to make the solver linearly scaleable with the number of blade rows. Enough flips are run (between 50 and 200) so the solution in the entire machine is not changing. The K-E equations are generally solved every other explicit time step. One of the key requirements in the development of the parallel code was to make the parallel solution exactly (bit for bit) match the serial solution. This has helped isolate many small parallel bugs and guarantee the parallelization was done correctly. The domain decomposition is done only in the axial direction since the number of points axially is much larger than the other two directions. This code uses MPI for message passing. The parallel speed up of the solver portion (no 1/0 or body force calculation) for a grid which has 227 points axially.

  15. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

    NASA Astrophysics Data System (ADS)

    Abraham, Mark James; Murtola, Teemu; Schulz, Roland; Páll, Szilárd; Smith, Jeremy C.; Hess, Berk; Lindahl, Erik

    2015-09-01

    GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU-GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.

  16. Parallel simulations of Grover's algorithm for closest match search in neutron monitor data

    NASA Astrophysics Data System (ADS)

    Kussainov, Arman; White, Yelena

    We are studying the parallel implementations of Grover's closest match search algorithm for neutron monitor data analysis. This includes data formatting, and matching quantum parameters to a conventional structure of a chosen programming language and selected experimental data type. We have employed several workload distribution models based on acquired data and search parameters. As a result of these simulations, we have an understanding of potential problems that may arise during configuration of real quantum computational devices and the way they could run tasks in parallel. The work was supported by the Science Committee of the Ministry of Science and Education of the Republic of Kazakhstan Grant #2532/GF3.

  17. Progress on the Multiphysics Capabilities of the Parallel Electromagnetic ACE3P Simulation Suite

    SciTech Connect

    Kononenko, Oleksiy

    2015-03-26

    ACE3P is a 3D parallel simulation suite that is being developed at SLAC National Accelerator Laboratory. Effectively utilizing supercomputer resources, ACE3P has become a key tool for the coupled electromagnetic, thermal and mechanical research and design of particle accelerators. Based on the existing finite-element infrastructure, a massively parallel eigensolver is developed for modal analysis of mechanical structures. It complements a set of the multiphysics tools in ACE3P and, in particular, can be used for the comprehensive study of microphonics in accelerating cavities ensuring the operational reliability of a particle accelerator.

  18. A method for data handling numerical results in parallel OpenFOAM simulations

    NASA Astrophysics Data System (ADS)

    Anton, Alin; Muntean, Sebastian

    2015-12-01

    Parallel computational fluid dynamics simulations produce vast amount of numerical result data. This paper introduces a method for reducing the size of the data by replaying the interprocessor traffic. The results are recovered only in certain regions of interest configured by the user. A known test case is used for several mesh partitioning scenarios using the OpenFOAM toolkit®[1]. The space savings obtained with classic algorithms remain constant for more than 60 Gb of floating point data. Our method is most efficient on large simulation meshes and is much better suited for compressing large scale simulation results than the regular algorithms.

  19. Adventures in Parallel Processing: Entry, Descent and Landing Simulation for the Genesis and Stardust Missions

    NASA Technical Reports Server (NTRS)

    Lyons, Daniel T.; Desai, Prasun N.

    2005-01-01

    This paper will describe the Entry, Descent and Landing simulation tradeoffs and techniques that were used to provide the Monte Carlo data required to approve entry during a critical period just before entry of the Genesis Sample Return Capsule. The same techniques will be used again when Stardust returns on January 15, 2006. Only one hour was available for the simulation which propagated 2000 dispersed entry states to the ground. Creative simulation tradeoffs combined with parallel processing were needed to provide the landing footprint statistics that were an essential part of the Go/NoGo decision that authorized release of the Sample Return Capsule a few hours before entry.

  20. Design of a real-time wind turbine simulator using a custom parallel architecture

    NASA Technical Reports Server (NTRS)

    Hoffman, John A.; Gluck, R.; Sridhar, S.

    1995-01-01

    The design of a new parallel-processing digital simulator is described. The new simulator has been developed specifically for analysis of wind energy systems in real time. The new processor has been named: the Wind Energy System Time-domain simulator, version 3 (WEST-3). Like previous WEST versions, WEST-3 performs many computations in parallel. The modules in WEST-3 are pure digital processors, however. These digital processors can be programmed individually and operated in concert to achieve real-time simulation of wind turbine systems. Because of this programmability, WEST-3 is very much more flexible and general than its two predecessors. The design features of WEST-3 are described to show how the system produces high-speed solutions of nonlinear time-domain equations. WEST-3 has two very fast Computational Units (CU's) that use minicomputer technology plus special architectural features that make them many times faster than a microcomputer. These CU's are needed to perform the complex computations associated with the wind turbine rotor system in real time. The parallel architecture of the CU causes several tasks to be done in each cycle, including an IO operation and the combination of a multiply, add, and store. The WEST-3 simulator can be expanded at any time for additional computational power. This is possible because the CU's interfaced to each other and to other portions of the simulation using special serial buses. These buses can be 'patched' together in essentially any configuration (in a manner very similar to the programming methods used in analog computation) to balance the input/ output requirements. CU's can be added in any number to share a given computational load. This flexible bus feature is very different from many other parallel processors which usually have a throughput limit because of rigid bus architecture.

  1. Application of parallel computing techniques to a large-scale reservoir simulation

    SciTech Connect

    Zhang, Keni; Wu, Yu-Shu; Ding, Chris; Pruess, Karsten

    2001-02-01

    Even with the continual advances made in both computational algorithms and computer hardware used in reservoir modeling studies, large-scale simulation of fluid and heat flow in heterogeneous reservoirs remains a challenge. The problem commonly arises from intensive computational requirement for detailed modeling investigations of real-world reservoirs. This paper presents the application of a massive parallel-computing version of the TOUGH2 code developed for performing large-scale field simulations. As an application example, the parallelized TOUGH2 code is applied to develop a three-dimensional unsaturated-zone numerical model simulating flow of moisture, gas, and heat in the unsaturated zone of Yucca Mountain, Nevada, a potential repository for high-level radioactive waste. The modeling approach employs refined spatial discretization to represent the heterogeneous fractured tuffs of the system, using more than a million 3-D gridblocks. The problem of two-phase flow and heat transfer within the model domain leads to a total of 3,226,566 linear equations to be solved per Newton iteration. The simulation is conducted on a Cray T3E-900, a distributed-memory massively parallel computer. Simulation results indicate that the parallel computing technique, as implemented in the TOUGH2 code, is very efficient. The reliability and accuracy of the model results have been demonstrated by comparing them to those of small-scale (coarse-grid) models. These comparisons show that simulation results obtained with the refined grid provide more detailed predictions of the future flow conditions at the site, aiding in the assessment of proposed repository performance.

  2. A Queue Simulation Tool for a High Performance Scientific Computing Center

    NASA Technical Reports Server (NTRS)

    Spear, Carrie; McGalliard, James

    2007-01-01

    The NASA Center for Computational Sciences (NCCS) at the Goddard Space Flight Center provides high performance highly parallel processors, mass storage, and supporting infrastructure to a community of computational Earth and space scientists. Long running (days) and highly parallel (hundreds of CPUs) jobs are common in the workload. NCCS management structures batch queues and allocates resources to optimize system use and prioritize workloads. NCCS technical staff use a locally developed discrete event simulation tool to model the impacts of evolving workloads, potential system upgrades, alternative queue structures and resource allocation policies.

  3. Massively parallel computing simulation of fluid flow in the unsaturated zone of Yucca Mountain, Nevada

    SciTech Connect

    Zhang, Keni; Wu, Yu-Shu; Bodvarsson, G.S.

    2001-08-31

    This paper presents the application of parallel computing techniques to large-scale modeling of fluid flow in the unsaturated zone (UZ) at Yucca Mountain, Nevada. In this study, parallel computing techniques, as implemented into the TOUGH2 code, are applied in large-scale numerical simulations on a distributed-memory parallel computer. The modeling study has been conducted using an over-one-million-cell three-dimensional numerical model, which incorporates a wide variety of field data for the highly heterogeneous fractured formation at Yucca Mountain. The objective of this study is to analyze the impact of various surface infiltration scenarios (under current and possible future climates) on flow through the UZ system, using various hydrogeological conceptual models with refined grids. The results indicate that the one-million-cell models produce better resolution results and reveal some flow patterns that cannot be obtained using coarse-grid modeling models.

  4. Parallel computing simulation of fluid flow in the unsaturated zone of Yucca Mountain, Nevada.

    PubMed

    Zhang, Keni; Wu, Yu-Shu; Bodvarsson, G S

    2003-01-01

    This paper presents the application of parallel computing techniques to large-scale modeling of fluid flow in the unsaturated zone (UZ) at Yucca Mountain, Nevada. In this study, parallel computing techniques, as implemented into the TOUGH2 code, are applied in large-scale numerical simulations on a distributed-memory parallel computer. The modeling study has been conducted using an over-1-million-cell three-dimensional numerical model, which incorporates a wide variety of field data for the highly heterogeneous fractured formation at Yucca Mountain. The objective of this study is to analyze the impact of various surface infiltration scenarios (under current and possible future climates) on flow through the UZ system, using various hydrogeological conceptual models with refined grids. The results indicate that the 1-million-cell models produce better resolution results and reveal some flow patterns that cannot be obtained using coarse-grid modeling models. PMID:12714301

  5. Evaluating the performance of parallel subsurface simulators: An illustrative example with PFLOTRAN

    NASA Astrophysics Data System (ADS)

    Hammond, G. E.; Lichtner, P. C.; Mills, R. T.

    2014-01-01

    To better inform the subsurface scientist on the expected performance of parallel simulators, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code PFLOTRAN as it is applied to several realistic modeling scenarios run on the Jaguar supercomputer. After a brief introduction to the code's parallel layout and code design, PFLOTRAN's parallel performance (measured through strong and weak scalability analyses) is evaluated in the context of conceptual model layout, software and algorithmic design, and known hardware limitations. PFLOTRAN scales well (with regard to strong scaling) for three realistic problem scenarios: (1) in situ leaching of copper from a mineral ore deposit within a 5-spot flow regime, (2) transient flow and solute transport within a regional doublet, and (3) a real-world problem involving uranium surface complexation within a heterogeneous and extremely dynamic variably saturated flow field. Weak scalability is discussed in detail for the regional doublet problem, and several difficulties with its interpretation are noted.

  6. Long-time atomistic simulations with the Parallel Replica Dynamics method

    NASA Astrophysics Data System (ADS)

    Perez, Danny

    Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

  7. Parallel-vector algorithms for particle simulations on shared-memory multiprocessors

    SciTech Connect

    Nishiura, Daisuke; Sakaguchi, Hide

    2011-03-01

    Over the last few decades, the computational demands of massive particle-based simulations for both scientific and industrial purposes have been continuously increasing. Hence, considerable efforts are being made to develop parallel computing techniques on various platforms. In such simulations, particles freely move within a given space, and so on a distributed-memory system, load balancing, i.e., assigning an equal number of particles to each processor, is not guaranteed. However, shared-memory systems achieve better load balancing for particle models, but suffer from the intrinsic drawback of memory access competition, particularly during (1) paring of contact candidates from among neighboring particles and (2) force summation for each particle. Here, novel algorithms are proposed to overcome these two problems. For the first problem, the key is a pre-conditioning process during which particle labels are sorted by a cell label in the domain to which the particles belong. Then, a list of contact candidates is constructed by pairing the sorted particle labels. For the latter problem, a table comprising the list indexes of the contact candidate pairs is created and used to sum the contact forces acting on each particle for all contacts according to Newton's third law. With just these methods, memory access competition is avoided without additional redundant procedures. The parallel efficiency and compatibility of these two algorithms were evaluated in discrete element method (DEM) simulations on four types of shared-memory parallel computers: a multicore multiprocessor computer, scalar supercomputer, vector supercomputer, and graphics processing unit. The computational efficiency of a DEM code was found to be drastically improved with our algorithms on all but the scalar supercomputer. Thus, the developed parallel algorithms are useful on shared-memory parallel computers with sufficient memory bandwidth.

  8. Parallel electric fields in a simulation of magnetotail reconnection and plasmoid evolution

    SciTech Connect

    Hesse, M.; Birn, J.

    1989-01-01

    We investigate properties of the electric field component parallel to the magnetic field (E/sub /parallel//) in a three-dimensional MHD simulation of plasmoid formation and evolution in the magnetotail in the presence of a net dawn-dusk magnetic field component. We emphasize particularly the spatial location of E/sub /parallel//, the concept of a diffusion zone and the role of E/sub /parallel// in accelerating electrons. We find a localization of the region of enhanced E/sub /parallel// in all space directions with a strong concentration in the z direction. We identify this region as the diffusion zone, which plays a crucial role in reconnection theory through the local break-down of magnetic flux conservation. The presence of B/sub y/ implies a north-south asymmetry of the injection of accelerated particles into the near-earth region, if the net B/sub y/ field is strong enough to force particles to follow field lines through the diffusion region. We estimate that for a typical net B/sub y/ field this should affect the injection of electrons into the near-earth dawn region, so that precipitation into the northern (southern) hemisphere should dominate for duskward (dawnward) net B/sub y/. In addition, we observe a spatial clottiness of the expected injection of adiabatic particles which could be related to the appearance bright spots in auroras. 12 refs., 9 figs.

  9. Vortex-induced vibration of two parallel risers: Experimental test and numerical simulation

    NASA Astrophysics Data System (ADS)

    Huang, Weiping; Zhou, Yang; Chen, Haiming

    2016-04-01

    The vortex-induced vibration of two identical rigidly mounted risers in a parallel arrangement was studied using Ansys- CFX and model tests. The vortex shedding and force were recorded to determine the effect of spacing on the two-degree-of-freedom oscillation of the risers. CFX was used to study the single riser and two parallel risers in 2-8 D spacing considering the coupling effect. Because of the limited width of water channel, only three different riser spacings, 2 D, 3 D, and 4 D, were tested to validate the characteristics of the two parallel risers by comparing to the numerical simulation. The results indicate that the lift force changes significantly with the increase in spacing, and in the case of 3 D spacing, the lift force of the two parallel risers reaches the maximum. The vortex shedding of the risers in 3 D spacing shows that a variable velocity field with the same frequency as the vortex shedding is generated in the overlapped area, thus equalizing the period of drag force to that of lift force. It can be concluded that the interaction between the two parallel risers is significant when the risers are brought to a small distance between them because the trajectory of riser changes from oval to curve 8 as the spacing is increased. The phase difference of lift force between the two risers is also different as the spacing changes.

  10. Parallel electric fields in a simulation of magnetotail reconnection and plasmoid evolution

    NASA Technical Reports Server (NTRS)

    Hesse, Michael; Birn, Joachim

    1989-01-01

    Properties of the electric field component parallel to the magnetic field (E sub parallel) in a three-dimensional MHD simulation of plasmoid formation and evolution in the magnetotail in the presence of a net dawn-dusk magnetic field component were observed. Particularly emphasized was the spatial location of E(sub parallel), the concept of a diffusion zone and the role of E(sub parallel) in accelerating electrons. A localization of the region of enhanced E(sub parallel) in all space directions with a strong concentration in the z direction was found. This region was identified as the diffusion zone, which plays a crucial role in reconnection theory through the local break-down of magnetic flux conservation. The presence of B(sub y) implies a north-south asymmetry of the injection of accelerated particles into the near-earth region, if the net B(sub y) field is strong enough to force particles to follow field lines through the diffusion region. It is estimated that for a typical net B(sub y) field this should affect the injection of electrons into the near-earth dawn region, so that precipitation into the Northern (Southern) Hemisphere should dominate for duskward (dawnward) net B(sub y). In addition, a spatial clottiness of the expected injection of adiabatic particles which could be related to the appearance bright spots in auroras was observed.

  11. Relevance of the parallel nonlinearity in gyrokinetic simulations of tokamak plasmas

    SciTech Connect

    Candy, J.; Waltz, R. E.; Parker, S. E.; Chen, Y.

    2006-07-15

    The influence of the parallel nonlinearity on transport in gyrokinetic simulations is assessed for values of {rho}{sub *} which are typical of current experiments. Here, {rho}{sub *}={rho}{sub s}/a is the ratio of gyroradius, {rho}{sub s}, to plasma minor radius, a. The conclusion, derived from simulations with both GYRO [J. Candy and R. E. Waltz, J. Comput. Phys., 186, 585 (2003)] and GEM [Y. Chen and S. E. Parker J. Comput. Phys., 189, 463 (2003)] is that no measurable effect of the parallel nonlinearity is apparent for {rho}{sub *}<0.012. This result is consistent with scaling arguments, which suggest that the parallel nonlinearity should be O({rho}{sub *}) smaller than the ExB nonlinearity. Indeed, for the plasma parameters under consideration, the magnitude of the parallel nonlinearity is a factor of 8{rho}{sub *} smaller (for 0.000 75<{rho}{sub *}<0.012) than the other retained terms in the nonlinear gyrokinetic equation.

  12. Parallel distributed, reciprocal Monte Carlo radiation in coupled, large eddy combustion simulations

    NASA Astrophysics Data System (ADS)

    Hunsaker, Isaac L.

    Radiation is the dominant mode of heat transfer in high temperature combustion environments. Radiative heat transfer affects the gas and particle phases, including all the associated combustion chemistry. The radiative properties are in turn affected by the turbulent flow field. This bi-directional coupling of radiation turbulence interactions poses a major challenge in creating parallel-capable, high-fidelity combustion simulations. In this work, a new model was developed in which reciprocal monte carlo radiation was coupled with a turbulent, large-eddy simulation combustion model. A technique wherein domain patches are stitched together was implemented to allow for scalable parallelism. The combustion model runs in parallel on a decomposed domain. The radiation model runs in parallel on a recomposed domain. The recomposed domain is stored on each processor after information sharing of the decomposed domain is handled via the message passing interface. Verification and validation testing of the new radiation model were favorable. Strong scaling analyses were performed on the Ember cluster and the Titan cluster for the CPU-radiation model and GPU-radiation model, respectively. The model demonstrated strong scaling to over 1,700 and 16,000 processing cores on Ember and Titan, respectively.

  13. A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nomura, Ken-ichi; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2008-01-01

    A scalable parallel algorithm has been designed to perform multimillion-atom molecular dynamics (MD) simulations, in which first principles-based reactive force fields (ReaxFF) describe chemical reactions. Environment-dependent bond orders associated with atomic pairs and their derivatives are reused extensively with the aid of linked-list cells to minimize the computation associated with atomic n-tuple interactions ( n⩽4 explicitly and ⩽6 due to chain-rule differentiation). These n-tuple computations are made modular, so that they can be reconfigured effectively with a multiple time-step integrator to further reduce the computation time. Atomic charges are updated dynamically with an electronegativity equalization method, by iteratively minimizing the electrostatic energy with the charge-neutrality constraint. The ReaxFF-MD simulation algorithm has been implemented on parallel computers based on a spatial decomposition scheme combined with distributed n-tuple data structures. The measured parallel efficiency of the parallel ReaxFF-MD algorithm is 0.998 on 131,072 IBM BlueGene/L processors for a 1.01 billion-atom RDX system.

  14. Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems

    PubMed Central

    D'Agostino, Daniele; Pasquale, Giulia; Clematis, Andrea; Maj, Carlo; Mosca, Ettore; Milanesi, Luciano; Merelli, Ivan

    2014-01-01

    There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort characterizing simulation approaches, coupled with the necessity to simulate the models several times to achieve statistically relevant information on the model behaviours, makes such kind of algorithms very time-consuming for studying real systems. So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms. In this work we discuss these aspects for the spatial TAU-leaping in crowded compartments (STAUCC) simulator, a voxel-based method for the stochastic simulation of reaction-diffusion processes which relies on the Sτ-DPP algorithm. In particular we present how the characteristics of the algorithm can be exploited for an effective parallelization on the present heterogeneous HPC architectures. PMID:25045716

  15. A Parallel, Finite-Volume Algorithm for Large-Eddy Simulation of Turbulent Flows

    NASA Technical Reports Server (NTRS)

    Bui, Trong T.

    1999-01-01

    A parallel, finite-volume algorithm has been developed for large-eddy simulation (LES) of compressible turbulent flows. This algorithm includes piecewise linear least-square reconstruction, trilinear finite-element interpolation, Roe flux-difference splitting, and second-order MacCormack time marching. Parallel implementation is done using the message-passing programming model. In this paper, the numerical algorithm is described. To validate the numerical method for turbulence simulation, LES of fully developed turbulent flow in a square duct is performed for a Reynolds number of 320 based on the average friction velocity and the hydraulic diameter of the duct. Direct numerical simulation (DNS) results are available for this test case, and the accuracy of this algorithm for turbulence simulations can be ascertained by comparing the LES solutions with the DNS results. The effects of grid resolution, upwind numerical dissipation, and subgrid-scale dissipation on the accuracy of the LES are examined. Comparison with DNS results shows that the standard Roe flux-difference splitting dissipation adversely affects the accuracy of the turbulence simulation. For accurate turbulence simulations, only 3-5 percent of the standard Roe flux-difference splitting dissipation is needed.

  16. Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators

    SciTech Connect

    Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.

    1999-11-13

    In this paper, we present an object-oriented three-dimensional parallel particle-in-cell code for beam dynamics simulation in linear accelerators. A two-dimensional parallel domain decomposition approach is employed within a message passing programming paradigm along with a dynamic load balancing. Implementing object-oriented software design provides the code with better maintainability, reusability, and extensibility compared with conventional structure based code. This also helps to encapsulate the details of communications syntax. Performance tests on SGI/Cray T3E-900 and SGI Origin 2000 machines show good scalability of the object-oriented code. Some important features of this code also include employing symplectic integration with linear maps of external focusing elements and using z as the independent variable, typical in accelerators. A successful application was done to simulate beam transport through three superconducting sections in the APT linac design.

  17. OSIRIS 2.0: an integrated framework for parallel PIC simulations

    NASA Astrophysics Data System (ADS)

    Fonseca, Ricardo; Tsung, Frank; Deng, Suzhi; Ren, Chuang

    2005-10-01

    We describe OSIRIS 2.0 framework, an integrated framework for particle-in-cell (PIC) simulations. This framework is based on a three-dimensional, fully relativistic, massively parallel, object oriented particle-in-cell code, that has successfully been applied to a number of problems, ranging from laser-plasma interaction and inertial fusion to plasma shell collisions in astrophysical scenarios. The OSIRIS 2.0 framework is the new version of the OSIRIS code. Developed in Fortran 95, the code runs on multiple platforms and can be easily ported to new ones. Details on the capabilities of the framework are given, focusing on the new capabilities introduced, such as bessel beams, binary collisions, tunnel (ADK) and impact ionization, and new diagnostics, and also dynamic load balancing and parallel I/O. This framework also includes a visualization and data-analysis infrastructure, tightly integrated into the framework, developed to post-process the scalar and vector results from our simulations.

  18. A Large Scale Simulation of Ultrasonic Wave Propagation in Concrete Using Parallelized EFIT

    NASA Astrophysics Data System (ADS)

    Nakahata, Kazuyuki; Tokunaga, Jyunichi; Kimoto, Kazushi; Hirose, Sohichi

    A time domain simulation tool for the ultrasonic propagation in concrete is developed using the elastodynamic finite integration technique (EFIT) and the image-based modeling. The EFIT is a grid-based time domain differential technique and easily treats the different boundary conditions in the inhomogeneous material such as concrete. Here, the geometry of concrete is determined by a scanned image of concrete and the processed color bitmap image is fed into the EFIT. Although the ultrasonic wave simulation in such a complex material requires much time to calculate, we here execute the EFIT by a parallel computing technique using a shared memory computer system. In this study, formulations of the EFIT and treatment of the different boundary conditions are briefly described and examples of shear horizontal wave propagations in reinforced concrete are demonstrated. The methodology and performance of parallelization for the EFIT are also discussed.

  19. Adaptive finite element simulation of flow and transport applications on parallel computers

    NASA Astrophysics Data System (ADS)

    Kirk, Benjamin Shelton

    The subject of this work is the adaptive finite element simulation of problems arising in flow and transport applications on parallel computers. Of particular interest are new contributions to adaptive mesh refinement (AMR) in this parallel high-performance context, including novel work on data structures, treatment of constraints in a parallel setting, generality and extensibility via object-oriented programming, and the design/implementation of a flexible software framework. This technology and software capability then enables more robust, reliable treatment of multiscale--multiphysics problems and specific studies of fine scale interaction such as those in biological chemotaxis (Chapter 4) and high-speed shock physics for compressible flows (Chapter 5). The work begins by presenting an overview of key concepts and data structures employed in AMR simulations. Of particular interest is how these concepts are applied in the physics-independent software framework which is developed here and is the basis for all the numerical simulations performed in this work. This open-source software framework has been adopted by a number of researchers in the U.S. and abroad for use in a wide range of applications. The dynamic nature of adaptive simulations pose particular issues for efficient implementation on distributed-memory parallel architectures. Communication cost, computational load balance, and memory requirements must all be considered when developing adaptive software for this class of machines. Specific extensions to the adaptive data structures to enable implementation on parallel computers is therefore considered in detail. The libMesh framework for performing adaptive finite element simulations on parallel computers is developed to provide a concrete implementation of the above ideas. This physics-independent framework is applied to two distinct flow and transport applications classes in the subsequent application studies to illustrate the flexibility of the design and to demonstrate the capability for resolving complex multiscale processes efficiently and reliably. The first application considered is the simulation of chemotactic biological systems such as colonies of Escherichia coli. This work appears to be the first application of AMR to chemotactic processes. These systems exhibit transient, highly localized features and are important in many biological processes, which make them ideal for simulation with adaptive techniques. A nonlinear reaction-diffusion model for such systems is described and a finite element formulation is developed. The solution methodology is described in detail. Several phenomenological studies are conducted to study chemotactic processes and resulting biological patterns which use the parallel adaptive refinement capability developed in this work. The other application study is much more extensive and deals with fine scale interactions for important hypersonic flows arising in aerospace applications. These flows are characterized by highly nonlinear, convection-dominated flowfields with very localized features such as shock waves and boundary layers. These localized features are well-suited to simulation with adaptive techniques. A novel treatment of the inviscid flux terms arising in a streamline-upwind Petrov-Galerkin finite element formulation of the compressible Navier-Stokes equations is also presented and is found to be superior to the traditional approach. The parallel adaptive finite element formulation is then applied to several complex flow studies, culminating in fully three-dimensional viscous flows about complex geometries such as the Space Shuttle Orbiter. Physical phenomena such as viscous/inviscid interaction, shock wave/boundary layer interaction, shock/shock interaction, and unsteady acoustic-driven flowfield response are considered in detail. A computational investigation of a 25°/55° double cone configuration details the complex multiscale flow features and investigates a potential source of experimentally-observed unsteady flowfield response.

  20. Construction of a parallel processor for simulating manipulators and other mechanical systems

    NASA Technical Reports Server (NTRS)

    Hannauer, George

    1991-01-01

    This report summarizes the results of NASA Contract NAS5-30905, awarded under phase 2 of the SBIR Program, for a demonstration of the feasibility of a new high-speed parallel simulation processor, called the Real-Time Accelerator (RTA). The principal goals were met, and EAI is now proceeding with phase 3: development of a commercial product. This product is scheduled for commercial introduction in the second quarter of 1992.

  1. SUPREM-DSMC: A New Scalable, Parallel, Reacting, Multidimensional Direct Simulation Monte Carlo Flow Code

    NASA Technical Reports Server (NTRS)

    Campbell, David; Wysong, Ingrid; Kaplan, Carolyn; Mott, David; Wadsworth, Dean; VanGilder, Douglas

    2000-01-01

    An AFRL/NRL team has recently been selected to develop a scalable, parallel, reacting, multidimensional (SUPREM) Direct Simulation Monte Carlo (DSMC) code for the DoD user community under the High Performance Computing Modernization Office (HPCMO) Common High Performance Computing Software Support Initiative (CHSSI). This paper will introduce the JANNAF Exhaust Plume community to this three-year development effort and present the overall goals, schedule, and current status of this new code.

  2. Scalable High Performance Computing: Direct and Large-Eddy Turbulent Flow Simulations Using Massively Parallel Computers

    NASA Technical Reports Server (NTRS)

    Morgan, Philip E.

    2004-01-01

    This final report contains reports of research related to the tasks "Scalable High Performance Computing: Direct and Lark-Eddy Turbulent FLow Simulations Using Massively Parallel Computers" and "Devleop High-Performance Time-Domain Computational Electromagnetics Capability for RCS Prediction, Wave Propagation in Dispersive Media, and Dual-Use Applications. The discussion of Scalable High Performance Computing reports on three objectives: validate, access scalability, and apply two parallel flow solvers for three-dimensional Navier-Stokes flows; develop and validate a high-order parallel solver for Direct Numerical Simulations (DNS) and Large Eddy Simulation (LES) problems; and Investigate and develop a high-order Reynolds averaged Navier-Stokes turbulence model. The discussion of High-Performance Time-Domain Computational Electromagnetics reports on five objectives: enhancement of an electromagnetics code (CHARGE) to be able to effectively model antenna problems; utilize lessons learned in high-order/spectral solution of swirling 3D jets to apply to solving electromagnetics project; transition a high-order fluids code, FDL3DI, to be able to solve Maxwell's Equations using compact-differencing; develop and demonstrate improved radiation absorbing boundary conditions for high-order CEM; and extend high-order CEM solver to address variable material properties. The report also contains a review of work done by the systems engineer.

  3. Efficient parallelization of short-range molecular dynamics simulations on many-core systems.

    PubMed

    Meyer, R

    2013-11-01

    This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly inhomogeneous systems like nanodevices or nanostructured materials. In the proposed scheme the calculation of the forces and the generation of neighbor lists are divided into small tasks. The tasks are then executed by a thread pool according to a dependent task schedule. This schedule is constructed in such a way that a particle is never accessed by two threads at the same time. Benchmark simulations on a typical 12-core machine show that the described algorithm achieves excellent parallel efficiencies above 80% for different kinds of systems and all numbers of cores. For inhomogeneous systems the speedups are strongly superior to those obtained with spatial decomposition. Further benchmarks were performed on an Intel Xeon Phi coprocessor. These simulations demonstrate that the algorithm scales well to large numbers of cores. PMID:24329381

  4. Efficient parallelization of short-range molecular dynamics simulations on many-core systems

    NASA Astrophysics Data System (ADS)

    Meyer, R.

    2013-11-01

    This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly inhomogeneous systems like nanodevices or nanostructured materials. In the proposed scheme the calculation of the forces and the generation of neighbor lists are divided into small tasks. The tasks are then executed by a thread pool according to a dependent task schedule. This schedule is constructed in such a way that a particle is never accessed by two threads at the same time. Benchmark simulations on a typical 12-core machine show that the described algorithm achieves excellent parallel efficiencies above 80% for different kinds of systems and all numbers of cores. For inhomogeneous systems the speedups are strongly superior to those obtained with spatial decomposition. Further benchmarks were performed on an Intel Xeon Phi coprocessor. These simulations demonstrate that the algorithm scales well to large numbers of cores.

  5. Spontaneous Hot Flow Anomalies at Quasi-Parallel Shocks: 2. Hybrid Simulations

    NASA Technical Reports Server (NTRS)

    Omidi, N.; Zhang, H.; Sibeck, D.; Turner, D.

    2013-01-01

    Motivated by recent THEMIS observations, this paper uses 2.5-D electromagnetic hybrid simulations to investigate the formation of Spontaneous Hot Flow Anomalies (SHFA) upstream of quasi-parallel bow shocks during steady solar wind conditions and in the absence of discontinuities. The results show the formation of a large number of structures along and upstream of the quasi-parallel bow shock. Their outer edges exhibit density and magnetic field enhancements, while their cores exhibit drops in density, magnetic field, solar wind velocity and enhancements in ion temperature. Using virtual spacecraft in the simulation, we show that the signatures of these structures in the time series data are very similar to those of SHFAs seen in THEMIS data and conclude that they correspond to SHFAs. Examination of the simulation data shows that SHFAs form as the result of foreshock cavitons interacting with the bow shock. Foreshock cavitons in turn form due to the nonlinear evolution of ULF waves generated by the interaction of the solar wind with the backstreaming ions. Because foreshock cavitons are an inherent part of the shock dissipation process, the formation of SHFAs is also an inherent part of the dissipation process leading to a highly non-uniform plasma in the quasi-parallel magnetosheath including large scale density and magnetic field cavities.

  6. Spontaneous hot flow anomalies at quasi-parallel shocks: 2. Hybrid simulations

    NASA Astrophysics Data System (ADS)

    Omidi, N.; Zhang, H.; Sibeck, D.; Turner, D.

    2013-01-01

    Abstract<p label="1">Motivated by recent THEMIS observations, this paper uses 2.5-D electromagnetic hybrid <span class="hlt">simulations</span> to investigate the formation of Spontaneous Hot Flow Anomalies (SHFAs) upstream of quasi-<span class="hlt">parallel</span> bow shocks during steady solar wind conditions and in the absence of discontinuities. The results show the formation of a large number of structures along and upstream of the quasi-<span class="hlt">parallel</span> bow shock. Their outer edges exhibit density and magnetic field enhancements, while their cores exhibit drops in density, magnetic field, solar wind velocity, and enhancements in ion temperature. Using virtual spacecraft in the <span class="hlt">simulation</span>, we show that the signatures of these structures in the time series data are very similar to those of SHFAs seen in THEMIS data and conclude that they correspond to SHFAs. Examination of the <span class="hlt">simulation</span> data shows that SHFAs form as the result of foreshock cavitons interacting with the bow shock. Foreshock cavitons in turn form due to the nonlinear evolution of ULF waves generated by the interaction of the solar wind with the backstreaming ions. Because foreshock cavitons are an inherent part of the shock dissipation process, the formation of SHFAs is also an inherent part of the dissipation process leading to a highly nonuniform plasma in the quasi-<span class="hlt">parallel</span> magnetosheath including large-scale density and magnetic field cavities.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1999APS..DPP.JP165L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1999APS..DPP.JP165L"><span id="translatedtitle"><span class="hlt">Parallel</span> PIC <span class="hlt">Simulations</span> of Ultra-High Intensity Laser Plasma Interactions.</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lasinski, B. F.; Still, C. H.; Langdon, A. B.; Wilks, S. C.; Hatchett, S. P.; Hinkel, D. E.</p> <p>1999-11-01</p> <p>We extend our previous <span class="hlt">simulations</span> of high intensity short pulse laser plasma interactionsfootnote B. F. Lasinski, A. B. Langdon, S. P. Hatchett, M. H. Key, and M. Tabak, Phys. Plasmas 6, 2041 (1999); S. C. Wilks and W. L. Kruer, IEEE Journal of Quantum Electronics 11, 1954 (1997). to 3D and to much larger systems in 2D using our new, modern, 3D, electromagnetic, fully relativistic, massively <span class="hlt">parallel</span> PIC code. Our <span class="hlt">simulation</span> parameters are guided by the recent Petawatt experiments at Livermore. We study the generation of hot electrons and energetic ions and the associated complex phenomena. Laser light filamentation and the formation of high static magnetic fields are described.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22218447','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22218447"><span id="translatedtitle"><span class="hlt">Parallel</span> implementation of three-dimensional molecular dynamic <span class="hlt">simulation</span> for laser-cluster interaction</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Holkundkar, Amol R.</p> <p>2013-11-15</p> <p>The objective of this article is to report the <span class="hlt">parallel</span> implementation of the 3D molecular dynamic <span class="hlt">simulation</span> code for laser-cluster interactions. The benchmarking of the code has been done by comparing the <span class="hlt">simulation</span> results with some of the experiments reported in the literature. Scaling laws for the computational time is established by varying the number of processor cores and number of macroparticles used. The capabilities of the code are highlighted by implementing various diagnostic tools. To study the dynamics of the laser-cluster interactions, the executable version of the code is available from the author.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2003PhDT........43K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2003PhDT........43K"><span id="translatedtitle"><span class="hlt">Parallel</span> octree-based multiresolution mesh method for large-scale earthquake ground motion <span class="hlt">simulation</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Kim, Eui Joong</p> <p></p> <p>Large scale ground motion <span class="hlt">simulation</span> requires supercomputing systems in order to obtain reliable and useful results within reasonable elapsed time. In this study, we develop a framework for terascale ground motion <span class="hlt">simulations</span> in highly heterogeneous basins. As part of the development, we present a <span class="hlt">parallel</span> octree-based multiresolution finite element methodology for the elastodynamic wave propagation problem. The octree-based multiresolution finite element method reduces memory use significantly and improves overall computational performance. The framework is comprised of three parts; (1) an octree-based mesh generator, Euclid developed by TV and O'Hallaron, (2) a <span class="hlt">parallel</span> mesh partitioner, ParMETIS developed by Karypis et al.[2], and (3) a <span class="hlt">parallel</span> octree-based multiresolution finite element solver, QUAKE developed in this study. Realistic earthquakes parameters, soil material properties, and sedimentary basins dimensions will produce extremely large meshes. The out-of-core versional octree-based mesh generator, Euclid overcomes the resulting severe memory limitations. By using a <span class="hlt">parallel</span>, distributed-memory graph partitioning algorithm, ParMETIS partitions large meshes, overcoming the memory and cost problem. Despite capability of the Octree-Based Multiresolution Mesh Method ( OBM3), large problem sizes necessitate <span class="hlt">parallelism</span> to handle large memory and work requirements. The <span class="hlt">parallel</span> OBM 3 elastic wave propagation code, QUAKE has been developed to address these issues. The numerical methodology and the framework have been used to <span class="hlt">simulate</span> the seismic response of both idealized systems and of the Greater Los Angeles basin to simple pulses and to a mainshock of the 1994 Northridge Earthquake, for frequencies of up to 1 Hz and domain size of 80 km x 80 km x 30 km. In the idealized models, QUAKE shows good agreement with the analytical Green's function solutions. In the realistic models for the Northridge earthquake mainshock, QUAKE qualitatively agrees, with at most a factor of 2.5, with the observational data. Through <span class="hlt">simulations</span> for several models, ranging in size from 400,000 to 300 million degrees of freedom on the 512-processors Cray T3E and the 3000-processors HP-Compaq AlphaServer Cluster at the Pittsburgh Supercomputing Center, we achieve excellent performance and scalability.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015GMD.....8..473H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015GMD.....8..473H"><span id="translatedtitle">A generic <span class="hlt">simulation</span> cell method for developing extensible, efficient and readable <span class="hlt">parallel</span> computational models</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Honkonen, I.</p> <p>2015-03-01</p> <p>I present a method for developing extensible and modular computational models without sacrificing serial or <span class="hlt">parallel</span> performance or source code readability. By using a generic <span class="hlt">simulation</span> cell method I show that it is possible to combine several distinct computational models to run in the same computational grid without requiring modification of existing code. This is an advantage for the development and testing of, e.g., geoscientific software as each submodel can be developed and tested independently and subsequently used without modification in a more complex coupled program. An implementation of the generic <span class="hlt">simulation</span> cell method presented here, generic <span class="hlt">simulation</span> cell class (gensimcell), also includes support for <span class="hlt">parallel</span> programming by allowing model developers to select which <span class="hlt">simulation</span> variables of, e.g., a domain-decomposed model to transfer between processes via a Message Passing Interface (MPI) library. This allows the communication strategy of a program to be formalized by explicitly stating which variables must be transferred between processes for the correct functionality of each submodel and the entire program. The generic <span class="hlt">simulation</span> cell class requires a C++ compiler that supports a version of the language standardized in 2011 (C++11). The code is available at <a href="https://github.com/nasailja/gensimcell"target="_blank">https://github.com/nasailja/gensimcell</a> for everyone to use, study, modify and redistribute; those who do are kindly requested to acknowledge and cite this work.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/957422','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/957422"><span id="translatedtitle">Wakefield <span class="hlt">Simulation</span> of CLIC PETS Structure Using <span class="hlt">Parallel</span> 3D Finite Element Time-Domain Solver T3P</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; Ko, K.; Syratchev, I.; /CERN</p> <p>2009-06-19</p> <p>In recent years, SLAC's Advanced Computations Department (ACD) has developed the <span class="hlt">parallel</span> 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively <span class="hlt">parallel</span> processing allow unprecedented <span class="hlt">simulation</span> accuracy for wakefield computations and <span class="hlt">simulations</span> of transient effects in realistic accelerator structures. Applications include <span class="hlt">simulation</span> of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22230824','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22230824"><span id="translatedtitle">Massively <span class="hlt">parallel</span> Monte Carlo for many-particle <span class="hlt">simulations</span> on GPUs</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Anderson, Joshua A.; Jankowski, Eric; Grubb, Thomas L.; Engel, Michael; Glotzer, Sharon C.</p> <p>2013-12-01</p> <p>Current trends in <span class="hlt">parallel</span> processors call for the design of efficient massively <span class="hlt">parallel</span> algorithms for scientific computing. <span class="hlt">Parallel</span> algorithms for Monte Carlo <span class="hlt">simulations</span> of thermodynamic ensembles of particles have received little attention because of the inherent serial nature of the statistical sampling. In this paper, we present a massively <span class="hlt">parallel</span> method that obeys detailed balance and implement it for a system of hard disks on the GPU. We reproduce results of serial high-precision Monte Carlo runs to verify the method. This is a good test case because the hard disk equation of state over the range where the liquid transforms into the solid is particularly sensitive to small deviations away from the balance conditions. On a Tesla K20, our GPU implementation executes over one billion trial moves per second, which is 148 times faster than on a single Intel Xeon E5540 CPU core, enables 27 times better performance per dollar, and cuts energy usage by a factor of 13. With this improved performance we are able to calculate the equation of state for systems of up to one million hard disks. These large system sizes are required in order to probe the nature of the melting transition, which has been debated for the last forty years. In this paper we present the details of our computational method, and discuss the thermodynamics of hard disks separately in a companion paper.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2001JChPh.114.9772S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2001JChPh.114.9772S"><span id="translatedtitle">A novel <span class="hlt">parallel</span>-rotation algorithm for atomistic Monte Carlo <span class="hlt">simulation</span> of dense polymer systems</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Santos, S.; Suter, U. W.; Mller, M.; Nievergelt, J.</p> <p>2001-06-01</p> <p>We develop and test a new elementary Monte Carlo move for use in the off-lattice <span class="hlt">simulation</span> of polymer systems. This novel <span class="hlt">Parallel</span>-Rotation algorithm (ParRot) permits moving very efficiently torsion angles that are deeply inside long chains in melts. The <span class="hlt">parallel</span>-rotation move is extremely simple and is also demonstrated to be computationally efficient and appropriate for Monte Carlo <span class="hlt">simulation</span>. The ParRot move does not affect the orientation of those parts of the chain outside the moving unit. The move consists of a concerted rotation around four adjacent skeletal bonds. No assumption is made concerning the backbone geometry other than that bond lengths and bond angles are held constant during the elementary move. Properly weighted sampling techniques are needed for ensuring detailed balance because the new move involves a correlated change in four degrees of freedom along the chain backbone. The ParRot move is supplemented with the classical Metropolis Monte Carlo, the Continuum-Configurational-Bias, and Reptation techniques in an isothermal-isobaric Monte Carlo <span class="hlt">simulation</span> of melts of short and long chains. Comparisons are made with the capabilities of other Monte Carlo techniques to move the torsion angles in the middle of the chains. We demonstrate that ParRot constitutes a highly promising Monte Carlo move for the treatment of long polymer chains in the off-lattice <span class="hlt">simulation</span> of realistic models of dense polymer systems.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010cosp...38..483V','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010cosp...38..483V"><span id="translatedtitle">Use of <span class="hlt">Parallel</span> Micro-Platform for the <span class="hlt">Simulation</span> the Space Exploration</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Velasco Herrera, Victor Manuel; Velasco Herrera, Graciela; Rosano, Felipe Lara; Rodriguez Lozano, Salvador; Lucero Roldan Serrato, Karen</p> <p></p> <p>The purpose of this work is to create a <span class="hlt">parallel</span> micro-platform, that <span class="hlt">simulates</span> the virtual movements of a space exploration in 3D. One of the innovations presented in this design consists of the application of a lever mechanism for the transmission of the movement. The development of such a robot is a challenging task very different of the industrial manipulators due to a totally different target system of requirements. This work presents the study and <span class="hlt">simulation</span>, aided by computer, of the movement of this <span class="hlt">parallel</span> manipulator. The development of this model has been developed using the platform of computer aided design Unigraphics, in which it was done the geometric modeled of each one of the components and end assembly (CAD), the generation of files for the computer aided manufacture (CAM) of each one of the pieces and the kinematics <span class="hlt">simulation</span> of the system evaluating different driving schemes. We used the toolbox (MATLAB) of aerospace and create an adaptive control module to <span class="hlt">simulate</span> the system.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/968614','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/968614"><span id="translatedtitle">Switching to High Gear: Opportunities for Grand-scale Real-time <span class="hlt">Parallel</span> <span class="hlt">Simulations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Perumalla, Kalyan S</p> <p>2009-01-01</p> <p>The recent emergence of dramatically large computational power, spanning desktops with multi-core processors and multiple graphics cards to supercomputers with 10^5 processor cores, has suddenly resulted in <span class="hlt">simulation</span>-based solutions trailing behind in the ability to fully tap the new computational capacity. Here, we motivate the need for switching the <span class="hlt">parallel</span> <span class="hlt">simulation</span> research to a higher gear to exploit the new, immense levels of computational power. The potential for grand-scale real-time solutions is illustrated using preliminary results from prototypes in four example application areas: (a) state- or regional-scale vehicular mobility modeling, (b) very large-scale epidemic modeling, (c) modeling the propagation of wireless network signals in very large, cluttered terrains, and, (d) country- or world-scale social behavioral modeling. We believe the stage is perfectly poised for the <span class="hlt">parallel</span>/distributed <span class="hlt">simulation</span> community to envision and formulate similar grand-scale, real-time <span class="hlt">simulation</span>-based solutions in many application areas.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014AdSpR..54.1581A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014AdSpR..54.1581A"><span id="translatedtitle"><span class="hlt">Parallel</span>, adaptive, multi-object trajectory integrator for space <span class="hlt">simulation</span> applications</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Atanassov, Atanas Marinov</p> <p>2014-10-01</p> <p>Computer <span class="hlt">simulation</span> is a very helpful approach for improving results from space born experiments. Initial-value problems (IVPs) can be applied for modeling dynamics of different objects - artificial Earth satellites, charged particles in magnetic and electric fields, charged or non-charged dust particles, space debris. An ordinary differential equations systems (ODESs) integrator based on applying different order embedded Runge-Kutta-Fehlberg methods is developed. These methods enable evaluation of the local error. Instead of step-size control based on local error evaluation, an optimal integration method is selected. Integration while meeting the required local error proceeds with constant-sized steps. This optimal scheme selection reduces the amount of calculation needed for solving the IVPs. In addition, for an implementation on a multi core processor and <span class="hlt">parallelization</span> based on threads application, we describe how to solve multiple systems of IVPs efficiently in <span class="hlt">parallel</span>. The proposed integrator allows the application of a different force model for every object in multi-satellite <span class="hlt">simulation</span> models. Simultaneous application of the integrator toward different kinds of problems in the frames of one combined <span class="hlt">simulation</span> model is possible too. The basic application of the integrator is solving mechanical IVPs in the context of <span class="hlt">simulation</span> models and their application in complex multi-satellite space missions and as a design tool for experiments.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010APS..DPPTP9006S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010APS..DPPTP9006S"><span id="translatedtitle"><span class="hlt">Parallelization</span> in time of numerical <span class="hlt">simulations</span> of drift-wave turbulence using the parareal algorithm</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sanchez, Raul; Samaddar, Debasmita; Newman, David</p> <p>2010-11-01</p> <p>The <span class="hlt">simulation</span> of turbulent fusion plasmas is very computationally intensive due to the large disparity of timescales that play a role in the dynamics. It is widely accepted that first principles <span class="hlt">simulations</span> of ITER-relevant plasmas are currently unfeasible, and will remain so for quite sometime unless some important algorithmic advances are made. Even shorter <span class="hlt">simulations</span> of a more restricted range of timescales, such as those based on gyrokinetics, are usually limited to tens of thousands of CPUs due to interprocessor communication, not scaling up to the 100,000+ CPUs that current supercomputers offer. In this contribution we test successfully a recently proposed scheme to <span class="hlt">parallelize</span> in time the integration of systems of PDEs on a drift-wave turbulence code [1]. The lessons learnt from this exercise suggest that an additional <span class="hlt">parallelization</span> path exists to enable longer <span class="hlt">simulations</span>, more complete physics models and a better utilization of existing computational resources. [4pt] [1] D. Samaddar, D.E. Newman and R. Sanchez, J. Comput. Phys. 229, 6558 (2010)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012JChPh.137r4703M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012JChPh.137r4703M"><span id="translatedtitle"><span class="hlt">Simulations</span> of structural and dynamic anisotropy in nano-confined water between <span class="hlt">parallel</span> graphite plates</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Mosaddeghi, Hamid; Alavi, Saman; Kowsari, M. H.; Najafi, Bijan</p> <p>2012-11-01</p> <p>We use molecular dynamics <span class="hlt">simulations</span> to study the structure, dynamics, and transport properties of nano-confined water between <span class="hlt">parallel</span> graphite plates with separation distances (H) from 7 to 20 Å at different water densities with an emphasis on anisotropies generated by confinement. The behavior of the confined water phase is compared to non-confined bulk water under similar pressure and temperature conditions. Our <span class="hlt">simulations</span> show anisotropic structure and dynamics of the confined water phase in directions <span class="hlt">parallel</span> and perpendicular to the graphite plate. The magnitude of these anisotropies depends on the slit width H. Confined water shows "solid-like" structure and slow dynamics for the water layers near the plates. The mean square displacements (MSDs) and velocity autocorrelation functions (VACFs) for directions <span class="hlt">parallel</span> and perpendicular to the graphite plates are calculated. By increasing the confinement distance from H = 7 Å to H = 20 Å, the MSD increases and the behavior of the VACF indicates that the confined water changes from solid-like to liquid-like dynamics. If the initial density of the water phase is set up using geometric criteria (i.e., distance between the graphite plates), large pressures (in the order of ˜10 katm), and large pressure anisotropies are established within the water. By decreasing the density of the water between the confined plates to about 0.9 g cm-3, bubble formation and restructuring of the water layers are observed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/974630','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/974630"><span id="translatedtitle"><span class="hlt">Parallel</span> Agent-Based <span class="hlt">Simulations</span> on Clusters of GPUs and Multi-Core Processors</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Aaby, Brandon G; Perumalla, Kalyan S; Seal, Sudip K</p> <p>2010-01-01</p> <p>An effective latency-hiding mechanism is presented in the <span class="hlt">parallelization</span> of agent-based model <span class="hlt">simulations</span> (ABMS) with millions of agents. The mechanism is designed to accommodate the hierarchical organization as well as heterogeneity of current state-of-the-art <span class="hlt">parallel</span> computing platforms. We use it to explore the computation vs. communication trade-off continuum available with the deep computational and memory hierarchies of extant platforms and present a novel analytical model of the tradeoff. We describe our implementation and report preliminary performance results on two distinct <span class="hlt">parallel</span> platforms suitable for ABMS: CUDA threads on multiple, networked graphical processing units (GPUs), and pthreads on multi-core processors. Message Passing Interface (MPI) is used for inter-GPU as well as inter-socket communication on a cluster of multiple GPUs and multi-core processors. Results indicate the benefits of our latency-hiding scheme, delivering as much as over 100-fold improvement in runtime for certain benchmark ABMS application scenarios with several million agents. This speed improvement is obtained on our system that is already two to three orders of magnitude faster on one GPU than an equivalent CPU-based execution in a popular <span class="hlt">simulator</span> in Java. Thus, the overall execution of our current work is over four orders of magnitude faster when executed on multiple GPUs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015CoPhC.194...18N','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015CoPhC.194...18N"><span id="translatedtitle">Computational performance of a smoothed particle hydrodynamics <span class="hlt">simulation</span> for shared-memory <span class="hlt">parallel</span> computing</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Nishiura, Daisuke; Furuichi, Mikito; Sakaguchi, Hide</p> <p>2015-09-01</p> <p>The computational performance of a smoothed particle hydrodynamics (SPH) <span class="hlt">simulation</span> is investigated for three types of current shared-memory <span class="hlt">parallel</span> computer devices: many integrated core (MIC) processors, graphics processing units (GPUs), and multi-core CPUs. We are especially interested in efficient shared-memory allocation methods for each chipset, because the efficient data access patterns differ between compute unified device architecture (CUDA) programming for GPUs and OpenMP programming for MIC processors and multi-core CPUs. We first introduce several <span class="hlt">parallel</span> implementation techniques for the SPH code, and then examine these on our target computer architectures to determine the most effective algorithms for each processor unit. In addition, we evaluate the effective computing performance and power efficiency of the SPH <span class="hlt">simulation</span> on each architecture, as these are critical metrics for overall performance in a multi-device environment. In our benchmark test, the GPU is found to produce the best arithmetic performance as a standalone device unit, and gives the most efficient power consumption. The multi-core CPU obtains the most effective computing performance. The computational speed of the MIC processor on Xeon Phi approached that of two Xeon CPUs. This indicates that using MICs is an attractive choice for existing SPH codes on multi-core CPUs <span class="hlt">parallelized</span> by OpenMP, as it gains computational acceleration without the need for significant changes to the source code.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li class="active"><span>17</span></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_17 --> <div id="page_18" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="341"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/974641','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/974641"><span id="translatedtitle">: A Scalable and Transparent System for <span class="hlt">Simulating</span> MPI Programs</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Perumalla, Kalyan S</p> <p>2010-01-01</p> <p>is a scalable, transparent system for experimenting with the execution of <span class="hlt">parallel</span> programs on <span class="hlt">simulated</span> computing platforms. The level of <span class="hlt">simulated</span> detail can be varied for application behavior as well as for machine characteristics. Unique features of are repeatability of execution, scalability to millions of <span class="hlt">simulated</span> (virtual) MPI ranks, scalability to hundreds of thousands of host (real) MPI ranks, portability of the system to a variety of host supercomputing platforms, and the ability to experiment with scientific applications whose source-code is available. The set of source-code interfaces supported by is being expanded to support a wider set of applications, and MPI-based scientific computing benchmarks are being ported. In proof-of-concept experiments, has been successfully exercised to spawn and sustain very large-scale executions of an MPI test program given in source code form. Low slowdowns are observed, due to its use of purely <span class="hlt">discrete</span> <span class="hlt">event</span> style of execution, and due to the scalability and efficiency of the underlying <span class="hlt">parallel</span> <span class="hlt">discrete</span> <span class="hlt">event</span> <span class="hlt">simulation</span> engine, sik. In the largest runs, has been executed on up to 216,000 cores of a Cray XT5 supercomputer, successfully <span class="hlt">simulating</span> over 27 million virtual MPI ranks, each virtual rank containing its own thread context, and all ranks fully synchronized by virtual time.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3605599','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3605599"><span id="translatedtitle">GROMACS 4.5: a high-throughput and highly <span class="hlt">parallel</span> open source molecular <span class="hlt">simulation</span> toolkit</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R.; Smith, Jeremy C.; Kasson, Peter M.; van der Spoel, David; Hess, Berk; Lindahl, Erik</p> <p>2013-01-01</p> <p>Motivation: Molecular <span class="hlt">simulation</span> has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated <span class="hlt">simulation</span> of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new <span class="hlt">simulation</span> algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient <span class="hlt">parallelization</span> even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art <span class="hlt">parallelization</span>, this provides extremely high performance and cost efficiency for high-throughput as well as massively <span class="hlt">parallel</span> <span class="hlt">simulations</span>. Availability: GROMACS is an open source and free software available from http://www.gromacs.org. Contact: erik.lindahl@scilifelab.se Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23407358</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/936704','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/936704"><span id="translatedtitle">De Novo Ultrascale Atomistic <span class="hlt">Simulations</span> On High-End <span class="hlt">Parallel</span> Supercomputers</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Nakano, A; Kalia, R K; Nomura, K; Sharma, A; Vashishta, P; Shimojo, F; van Duin, A; Goddard, III, W A; Biswas, R; Srivastava, D; Yang, L H</p> <p>2006-09-04</p> <p>We present a de novo hierarchical <span class="hlt">simulation</span> framework for first-principles based predictive <span class="hlt">simulations</span> of materials and their validation on high-end <span class="hlt">parallel</span> supercomputers and geographically distributed clusters. In this framework, high-end chemically reactive and non-reactive molecular dynamics (MD) <span class="hlt">simulations</span> explore a wide solution space to discover microscopic mechanisms that govern macroscopic material properties, into which highly accurate quantum mechanical (QM) <span class="hlt">simulations</span> are embedded to validate the discovered mechanisms and quantify the uncertainty of the solution. The framework includes an embedded divide-and-conquer (EDC) algorithmic framework for the design of linear-scaling <span class="hlt">simulation</span> algorithms with minimal bandwidth complexity and tight error control. The EDC framework also enables adaptive hierarchical <span class="hlt">simulation</span> with automated model transitioning assisted by graph-based event tracking. A tunable hierarchical cellular decomposition <span class="hlt">parallelization</span> framework then maps the O(N) EDC algorithms onto Petaflops computers, while achieving performance tunability through a hierarchy of parameterized cell data/computation structures, as well as its implementation using hybrid Grid remote procedure call + message passing + threads programming. High-end computing platforms such as IBM BlueGene/L, SGI Altix 3000 and the NSF TeraGrid provide an excellent test grounds for the framework. On these platforms, we have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic <span class="hlt">simulations</span>--1.06 billion-atom fast reactive force-field MD and 11.8 million-atom (1.04 trillion grid points) quantum-mechanical MD in the framework of the EDC density functional theory on adaptive multigrids--in addition to 134 billion-atom non-reactive space-time multiresolution MD, with the <span class="hlt">parallel</span> efficiency as high as 0.998 on 65,536 dual-processor BlueGene/L nodes. We have also achieved an automated execution of hierarchical QM/MD <span class="hlt">simulation</span> on a Grid consisting of 6 supercomputer centers in the US and Japan (in total of 150 thousand processor-hours), in which the number of processors change dynamically on demand and resources are allocated and migrated dynamically in response to faults. Furthermore, performance portability has been demonstrated on a wide range of platforms such as BlueGene/L, Altix 3000, and AMD Opteron-based Linux clusters.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/928005','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/928005"><span id="translatedtitle">LUsim: A Framework for <span class="hlt">Simulation</span>-Based Performance Modelingand Prediction of <span class="hlt">Parallel</span> Sparse LU Factorization</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Univ. of California, San Diego; Li, Xiaoye Sherry; Cicotti, Pietro; Li, Xiaoye Sherry; Baden, Scott B.</p> <p>2008-04-15</p> <p>Sparse <span class="hlt">parallel</span> factorization is among the most complicated and irregular algorithms to analyze and optimize. Performance depends both on system characteristics such as the floating point rate, the memory hierarchy, and the interconnect performance, as well as input matrix characteristics such as such as the number and location of nonzeros. We present LUsim, a <span class="hlt">simulation</span> framework for modeling the performance of sparse LU factorization. Our framework uses micro-benchmarks to calibrate the parameters of machine characteristics and additional tools to facilitate real-time performance modeling. We are using LUsim to analyze an existing <span class="hlt">parallel</span> sparse LU factorization code, and to explore a latency tolerant variant. We developed and validated a model of the factorization in SuperLU_DIST, then we modeled and implemented a new variant of slud, replacing a blocking collective communication phase with a non-blocking asynchronous point-to-point one. Our strategy realized a mean improvement of 11percent over a suite of test matrices.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016JSP...162..701U','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016JSP...162..701U"><span id="translatedtitle"><span class="hlt">Parallel</span> Tempering Monte Carlo <span class="hlt">Simulations</span> of Spherical Fixed-Connectivity Model for Polymerized Membranes</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Usui, Satoshi; Koibuchi, Hiroshi</p> <p>2016-02-01</p> <p>We study the first order phase transition of the fixed-connectivity triangulated surface model using the <span class="hlt">Parallel</span> Tempering Monte Carlo (PTMC) technique on relatively large lattices. From the PTMC results, we find that the transition is considerably stronger than the reported ones predicted by the conventional Metropolis MC (MMC) technique and the flat histogram MC technique. We also confirm that the results of the PTMC on relatively smaller lattices are in good agreement with those known results. This implies that the PTMC is successfully used to <span class="hlt">simulate</span> the first order phase transitions. The <span class="hlt">parallel</span> computation in the PTMC is implemented by OpenMP, where the speed of the PTMC on multi-core CPUs is considerably faster than that on the single-core CPUs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012SPIE.8454E..1FC','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012SPIE.8454E..1FC"><span id="translatedtitle">A study of the <span class="hlt">parallel</span> algorithm for large-scale DC <span class="hlt">simulation</span> of nonlinear systems</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Cortés Udave, Diego Ernesto; Ogrodzki, Jan; Gutiérrez de Anda, Miguel Angel</p> <p></p> <p>Newton-Raphson DC analysis of large-scale nonlinear circuits may be an extremely time consuming process even if sparse matrix techniques and bypassing of nonlinear models calculation are used. A slight decrease in the time required for this task may be enabled on multi-core, multithread computers if the calculation of the mathematical models for the nonlinear elements as well as the stamp management of the sparse matrix entries are managed through concurrent processes. This numerical complexity can be further reduced via the circuit decomposition and <span class="hlt">parallel</span> solution of blocks taking as a departure point the BBD matrix structure. This block-<span class="hlt">parallel</span> approach may give a considerable profit though it is strongly dependent on the system topology and, of course, on the processor type. This contribution presents the easy-parallelizable decomposition-based algorithm for DC <span class="hlt">simulation</span> and provides a detailed study of its effectiveness.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015GMDD....8.2369H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015GMDD....8.2369H"><span id="translatedtitle">A <span class="hlt">parallelization</span> scheme to <span class="hlt">simulate</span> reactive transport in the subsurface environment with OGS#IPhreeqc</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>He, W.; Beyer, C.; Fleckenstein, J. H.; Jang, E.; Kolditz, O.; Naumov, D.; Kalbacher, T.</p> <p>2015-03-01</p> <p>This technical paper presents an efficient and performance-oriented method to model reactive mass transport processes in environmental and geotechnical subsurface systems. The open source scientific software packages OpenGeoSys and IPhreeqc have been coupled, to combine their individual strengths and features to <span class="hlt">simulate</span> thermo-hydro-mechanical-chemical coupled processes in porous and fractured media with simultaneous consideration of aqueous geochemical reactions. Furthermore, a flexible <span class="hlt">parallelization</span> scheme using MPI (Message Passing Interface) grouping techniques has been implemented, which allows an optimized allocation of computer resources for the node-wise calculation of chemical reactions on the one hand, and the underlying processes such as for groundwater flow or solute transport on the other hand. The coupling interface and <span class="hlt">parallelization</span> scheme have been tested and verified in terms of precision and performance.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/21499769','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/21499769"><span id="translatedtitle">Billion-atom synchronous <span class="hlt">parallel</span> kinetic Monte Carlo <span class="hlt">simulations</span> of critical 3D Ising systems</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Martinez, E.; Monasterio, P.R.; Marian, J.</p> <p>2011-02-20</p> <p>An extension of the synchronous <span class="hlt">parallel</span> kinetic Monte Carlo (spkMC) algorithm developed by Martinez et al. [J. Comp. Phys. 227 (2008) 3804] to discrete lattices is presented. The method solves the master equation synchronously by recourse to null events that keep all processors' time clocks current in a global sense. Boundary conflicts are resolved by adopting a chessboard decomposition into non-interacting sublattices. We find that the bias introduced by the spatial correlations attendant to the sublattice decomposition is within the standard deviation of serial calculations, which confirms the statistical validity of our algorithm. We have analyzed the <span class="hlt">parallel</span> efficiency of spkMC and find that it scales consistently with problem size and sublattice partition. We apply the method to the calculation of scale-dependent critical exponents in billion-atom 3D Ising systems, with very good agreement with state-of-the-art multispin <span class="hlt">simulations</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/957421','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/957421"><span id="translatedtitle"><span class="hlt">Parallel</span> 3D Finite Element Particle-in-Cell <span class="hlt">Simulations</span> with Pic3P</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; Ko, K.; Ben-Zvi, I.; Kewisch, J.; /Brookhaven</p> <p>2009-06-19</p> <p>SLAC's Advanced Computations Department (ACD) has developed the <span class="hlt">parallel</span> 3D Finite Element electromagnetic Particle-In-Cell code Pic3P. Designed for <span class="hlt">simulations</span> of beam-cavity interactions dominated by space charge effects, Pic3P solves the complete set of Maxwell-Lorentz equations self-consistently and includes space-charge, retardation and boundary effects from first principles. Higher-order Finite Element methods with adaptive refinement on conformal unstructured meshes lead to highly efficient use of computational resources. Massively <span class="hlt">parallel</span> processing with dynamic load balancing enables large-scale modeling of photoinjectors with unprecedented accuracy, aiding the design and operation of next-generation accelerator facilities. Applications include the LCLS RF gun and the BNL polarized SRF gun.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/21333914','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/21333914"><span id="translatedtitle">A fast <span class="hlt">parallel</span> Poisson solver on irregular domains applied to beam dynamics <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Adelmann, A. Arbenz, P. Ineichen, Y.</p> <p>2010-06-20</p> <p>We discuss the scalable <span class="hlt">parallel</span> solution of the Poisson equation within a Particle-In-Cell (PIC) code for the <span class="hlt">simulation</span> of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences. Depending on the treatment of the Dirichlet boundary the resulting system of equations is symmetric or 'mildly' nonsymmetric positive definite. In all cases, the system is solved by the preconditioned conjugate gradient algorithm with smoothed aggregation (SA) based algebraic multigrid (AMG) preconditioning. We investigate variants of the implementation of SA-AMG that lead to considerable improvements in the execution times. We demonstrate good scalability of the solver on distributed memory <span class="hlt">parallel</span> processor with up to 2048 processors. We also compare our iterative solver with an FFT-based solver that is more commonly used for applications in beam dynamics.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016IAUS..312..260W','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016IAUS..312..260W"><span id="translatedtitle">Acceleration of hybrid MPI <span class="hlt">parallel</span> NBODY6++ for large N-body globular cluster <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Wang, Long; Spurzem, Rainer; Aarseth, Sverre; Nitadori, Keigo; Berczik, Peter; Kouwenhoven, M. B. N.; Naab, Thorsten</p> <p>2016-02-01</p> <p>Previous research on globular clusters (GCs) dynamics is mostly based on semi-analytic, Fokker-Planck, Monte-Carlo methods and on direct N-body (NB) <span class="hlt">simulations</span>. These works have great advantages but also limits since GCs are massive and compact and close encounters and binaries play very important roles in their dynamics. The former three methods make approximations and assumptions, while expensive computing time and number of stars limit the latter method. The current largest direct NB <span class="hlt">simulation</span> has ~ 500k stars (Heggie 2014). Here, we accelerate the direct NB code NBODY6++ (which extends NBODY6 to supercomputers by using MPI) with new <span class="hlt">parallel</span> computing technologies (GPU, OpenMP + SSE/AVX). Our aim is to handle large N (up to 106) direct NB <span class="hlt">simulations</span> to obtain better understanding of the dynamical evolution of GCs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/919137','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/919137"><span id="translatedtitle">Xyce <span class="hlt">parallel</span> electronic <span class="hlt">simulator</span> design : mathematical formulation, version 2.0.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Hoekstra, Robert John; Waters, Lon J.; Hutchinson, Scott Alan; Keiter, Eric Richard; Russo, Thomas V.</p> <p>2004-06-01</p> <p>This document is intended to contain a detailed description of the mathematical formulation of Xyce, a massively <span class="hlt">parallel</span> SPICE-style circuit <span class="hlt">simulator</span> developed at Sandia National Laboratories. The target audience of this document are people in the role of 'service provider'. An example of such a person would be a linear solver expert who is spending a small fraction of his time developing solver algorithms for Xyce. Such a person probably is not an expert in circuit <span class="hlt">simulation</span>, and would benefit from an description of the equations solved by Xyce. In this document, modified nodal analysis (MNA) is described in detail, with a number of examples. Issues that are unique to circuit <span class="hlt">simulation</span>, such as voltage limiting, are also described in detail.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1998ApOpt..37.6105G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1998ApOpt..37.6105G"><span id="translatedtitle">Hardware Description Language for Optical Processing ( hadlop ): a <span class="hlt">Simulation</span> Environment for <span class="hlt">Parallel</span> Optoelectronic Architectures</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Grimm, Guido; Fey, Dietmar; Degenkolb, Marko; Erhart, Werner</p> <p>1998-09-01</p> <p>We present a <span class="hlt">simulation</span> environment for <span class="hlt">parallel</span> optoelectronic data-processing systems, and we especially consider the fusion of optoelectronic integrated circuits and optical interconnection modules. hadlop , which stands for hardware description language for optical processing, is a <span class="hlt">simulator</span> that works at the digital design level. So far, hadlop has allowed algorithm and architecture studies for smart-pixel systems. We have just begun to extend the capabilities of hadlop toward an automatic synthesis tool for three-dimensional optoelectronic VLSI circuits. A hadlop architecture will then be the basis for the automatic generation of detailed construction plans that consider the interaction between optical interconnection modules and optoelectronic integrated circuits. The <span class="hlt">simulation</span> system is freeware and is available through the Internet at http: www2.informatik.uni-jena.de pope HADLOP hadlop.html.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1997CG.....23..771N','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1997CG.....23..771N"><span id="translatedtitle">The use of a <span class="hlt">parallel</span> virtual machine (PVM) for finite-difference wave <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Niccanna, Clodagh; Bean, Christopher J.</p> <p>1997-08-01</p> <p>Computer modelling is now applied routinely throughout the geosciences in an attempt to create synthetic data for comparison with real data. At present, in seismology, there is no analytical solution to the wave equation which allows wave <span class="hlt">simulations</span> in "geologically realistic" (complex) media. Consequently, computationally expensive numerical solutions are required. Using a finite-difference solution to the wave equation provides a suitable means of modelling seismic waves in a heterogeneous medium. However, when applying this method the grid sizes and the number of time steps required (to ensure numerical stability and sufficiently long wave propagation distances) are limited because of their demand on computer time and memory. Supercomputers represent an obvious solution to these limitations. This paper presents an alternative which is inexpensive, convenient and portable. By clustering a set of processors, for example PCs or workstations, a <span class="hlt">parallel</span> configuration can be obtained by using the processors available on each machine to perform sections of the calculations simultaneously. By using <span class="hlt">Parallel</span> Virtual Machine (PVM) — a public domain software package which allows a programmer to create and access a concurrent computing system made from networks of loosely coupled processing elements (Geist and others, 1994) — we have reduced wall-clock times and increased array sizes for a finite-difference solution to the acoustic, elastic and viscoelastic wave equations. In this paper we present methods of <span class="hlt">parallelizing</span> a serial code and load-balancing this <span class="hlt">parallelized</span> code. A comparison of serial and <span class="hlt">parallel</span> wall-clock times, a comparison of wall-clock times on a variety of clusters of machines and the role of communication in this application are presented for a finite-difference solution to the acoustic wave equation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2003CoPhC.155..159A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2003CoPhC.155..159A"><span id="translatedtitle">FLY. A <span class="hlt">parallel</span> tree N-body code for cosmological <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Antonuccio-Delogu, V.; Becciani, U.; Ferro, D.</p> <p>2003-10-01</p> <p>FLY is a <span class="hlt">parallel</span> treecode which makes heavy use of the one-sided communication paradigm to handle the management of the tree structure. In its public version the code implements the equations for cosmological evolution, and can be run for different cosmological models. This reference guide describes the actual implementation of the algorithms of the public version of FLY, and suggests how to modify them to implement other types of equations (for instance, the Newtonian ones). Program summary Title of program: FLY Catalogue identifier: ADSC Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADSC Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Cray T3E, Sgi Origin 3000, IBM SP Operating systems or monitors under which the program has been tested: Unicos 2.0.5.40, Irix 6.5.14, Aix 4.3.3 Programming language used: Fortran 90, C Memory required to execute with typical data: about 100 Mwords with 2 million-particles Number of bits in a word: 32 Number of processors used: <span class="hlt">parallel</span> program. The user can select the number of processors >=1 Has the code been vectorized or <span class="hlt">parallelized</span>?: <span class="hlt">parallelized</span> Number of bytes in distributed program, including test data, etc.: 4615604 Distribution format: tar gzip file Keywords: <span class="hlt">Parallel</span> tree N-body code for cosmological <span class="hlt">simulations</span> Nature of physical problem: FLY is a <span class="hlt">parallel</span> collisionless N-body code for the calculation of the gravitational force. Method of solution: It is based on the hierarchical oct-tree domain decomposition introduced by Barnes and Hut (1986). Restrictions on the complexity of the program: The program uses the leapfrog integrator schema, but could be changed by the user. Typical running time: 50 seconds for each time-step, running a 2-million-particles <span class="hlt">simulation</span> on an Sgi Origin 3800 system with 8 processors having 512 Mbytes RAM for each processor. Unusual features of the program: FLY uses the one-side communications libraries: the SHMEM library on the Cray T3E system and Sgi Origin system, and the LAPI library on IBM SP system</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014GMDD....7.4577H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014GMDD....7.4577H"><span id="translatedtitle">The generic <span class="hlt">simulation</span> cell method for developing extensible, efficient and readable <span class="hlt">parallel</span> computational models</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Honkonen, I.</p> <p>2014-07-01</p> <p>I present a method for developing extensible and modular computational models without sacrificing serial or <span class="hlt">parallel</span> performance or source code readability. By using a generic <span class="hlt">simulation</span> cell method I show that it is possible to combine several distinct computational models to run in the same computational grid without requiring any modification of existing code. This is an advantage for the development and testing of computational modeling software as each submodel can be developed and tested independently and subsequently used without modification in a more complex coupled program. Support for <span class="hlt">parallel</span> programming is also provided by allowing users to select which <span class="hlt">simulation</span> variables to transfer between processes via a Message Passing Interface library. This allows the communication strategy of a program to be formalized by explicitly stating which variables must be transferred between processes for the correct functionality of each submodel and the entire program. The generic <span class="hlt">simulation</span> cell class presented here requires a C++ compiler that supports variadic templates which were standardized in 2011 (C++11). The code is available at: <a href="https://github.com/nasailja/gensimcell">https://github.com/nasailja/gensimcell</a> for everyone to use, study, modify and redistribute; those that do are kindly requested to cite this work.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2007APS..DFD.GB003S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2007APS..DFD.GB003S"><span id="translatedtitle">Adaptive Flow <span class="hlt">Simulation</span> of Turbulence in Subject-Specific Abdominal Aortic Aneurysm on Massively <span class="hlt">Parallel</span> Computers</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sahni, Onkar; Jansen, Kenneth; Shephard, Mark; Taylor, Charles</p> <p>2007-11-01</p> <p>Flow within the healthy human vascular system is typically laminar but diseased conditions can alter the geometry sufficiently to produce transitional/turbulent flows in regions focal (and immediately downstream) of the diseased section. The mean unsteadiness (pulsatile or respiratory cycle) further complicates the situation making traditional turbulence <span class="hlt">simulation</span> techniques (e.g., Reynolds-averaged Navier-Stokes <span class="hlt">simulations</span> (RANSS)) suspect. At the other extreme, direct numerical <span class="hlt">simulation</span> (DNS) while fully appropriate can lead to large computational expense, particularly when the <span class="hlt">simulations</span> must be done quickly since they are intended to affect the outcome of a medical treatment (e.g., virtual surgical planning). To produce <span class="hlt">simulations</span> in a clinically relevant time frame requires; 1) adaptive meshing technique that closely matches the desired local mesh resolution in all three directions to the highly anisotropic physical length scales in the flow, 2) efficient solution algorithms, and 3) excellent scaling on massively <span class="hlt">parallel</span> computers. In this presentation we will demonstrate results for a subject-specific <span class="hlt">simulation</span> of an abdominal aortic aneurysm using stabilized finite element method on anisotropically adapted meshes consisting of O(10^8) elements over O(10^4) processors.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=20020010587&hterms=Weeratunga&qs=N%3D0%26Ntk%3DAll%26Ntx%3Dmode%2Bmatchall%26Ntt%3DWeeratunga','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=20020010587&hterms=Weeratunga&qs=N%3D0%26Ntk%3DAll%26Ntx%3Dmode%2Bmatchall%26Ntt%3DWeeratunga"><span id="translatedtitle"><span class="hlt">Simulation</span> of Unsteady Combustion in a Ramjet Engine Using a Highly <span class="hlt">Parallel</span> Computer</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Menon, Suresh; Weeratunga, Sisira; Cooper, D. M. (Technical Monitor)</p> <p>1994-01-01</p> <p>Combustion instability in ramjets is a complex phenomenon that involve nonlinear interaction between acoustic waves, vortex motion and unsteady heat release in the combustor. To numerically <span class="hlt">simulate</span> this 3-D, transient phenomenon, enormous computer resources (time, memory and disk storage) are required. Although current generation vector supercomputers are capable of providing adequate resources for <span class="hlt">simulations</span> of this nature, their high cost and limited availability, makes such machines less than satisfactory for routine use. The primary focus of this study is to assess the feasibility of using highly <span class="hlt">parallel</span> computer systems as a cost-effective alternative for conducting such unsteady flow <span class="hlt">simulations</span>. Towards this end, a large-eddy <span class="hlt">simulation</span> model for combustion instability was implemented on the Intel iPSC/860 and a careful study was conducted to determine the benefits and the problems associated with the use of such machines for transient <span class="hlt">simulations</span>. Details of this study along with the results obtained from the unsteady combustion <span class="hlt">simulations</span> carried out on the iPSC/860 are discussed in this paper.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010CG.....36..953M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010CG.....36..953M"><span id="translatedtitle">A general <span class="hlt">parallelization</span> strategy for random path based geostatistical <span class="hlt">simulation</span> methods</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Mariethoz, Grégoire</p> <p>2010-07-01</p> <p>The size of <span class="hlt">simulation</span> grids used for numerical models has increased by many orders of magnitude in the past years, and this trend is likely to continue. Efficient pixel-based geostatistical <span class="hlt">simulation</span> algorithms have been developed, but for very large grids and complex spatial models, the computational burden remains heavy. As cluster computers become widely available, using <span class="hlt">parallel</span> strategies is a natural step for increasing the usable grid size and the complexity of the models. These strategies must profit from of the possibilities offered by machines with a large number of processors. On such machines, the bottleneck is often the communication time between processors. We present a strategy distributing grid nodes among all available processors while minimizing communication and latency times. It consists in centralizing the <span class="hlt">simulation</span> on a master processor that calls other slave processors as if they were functions <span class="hlt">simulating</span> one node every time. The key is to decouple the sending and the receiving operations to avoid synchronization. Centralization allows having a conflict management system ensuring that nodes being <span class="hlt">simulated</span> simultaneously do not interfere in terms of neighborhood. The strategy is computationally efficient and is versatile enough to be applicable to all random path based <span class="hlt">simulation</span> methods.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23600445','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23600445"><span id="translatedtitle">Accelerating groundwater flow <span class="hlt">simulation</span> in MODFLOW using JASMIN-based <span class="hlt">parallel</span> computing.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Cheng, Tangpei; Mo, Zeyao; Shao, Jingli</p> <p>2014-01-01</p> <p>To accelerate the groundwater flow <span class="hlt">simulation</span> process, this paper reports our work on developing an efficient <span class="hlt">parallel</span> <span class="hlt">simulator</span> through rebuilding the well-known software MODFLOW on JASMIN (J Adaptive Structured Meshes applications Infrastructure). The rebuilding process is achieved by designing patch-based data structure and <span class="hlt">parallel</span> algorithms as well as adding slight modifications to the compute flow and subroutines in MODFLOW. Both the memory requirements and computing efforts are distributed among all processors; and to reduce communication cost, data transfers are batched and conveniently handled by adding ghost nodes to each patch. To further improve performance, constant-head/inactive cells are tagged and neglected during the linear solving process and an efficient load balancing strategy is presented. The accuracy and efficiency are demonstrated through modeling three scenarios: The first application is a field flow problem located at Yanming Lake in China to help design reasonable quantity of groundwater exploitation. Desirable numerical accuracy and significant performance enhancement are obtained. Typically, the tagged program with load balancing strategy running on 40 cores is six times faster than the fastest MICCG-based MODFLOW program. The second test is <span class="hlt">simulating</span> flow in a highly heterogeneous aquifer. The AMG-based JASMIN program running on 40 cores is nine times faster than the GMG-based MODFLOW program. The third test is a simplified transient flow problem with the order of tens of millions of cells to examine the scalability. Compared to 32 cores, <span class="hlt">parallel</span> efficiency of 77 and 68% are obtained on 512 and 1024 cores, respectively, which indicates impressive scalability. PMID:23600445</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_18 --> <div id="page_19" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="361"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/427933','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/427933"><span id="translatedtitle">A three-phase series-<span class="hlt">parallel</span> resonant converter -- analysis, design, <span class="hlt">simulation</span> and experimental results</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Bhat, A.K.S.; Zheng, L.</p> <p>1995-12-31</p> <p>A three-phase dc-to-dc series-<span class="hlt">parallel</span> resonant converter is proposed and its operating modes for 180{degree} wide gating pulse scheme are explained. A detailed analysis of the converter using constant current model and Fourier series approach is presented. Based on the analysis, design curves are obtained and a design example of 1 kW converter is given. SPICE <span class="hlt">simulation</span> results for the designed converter and experimental results for a 500 W converter are presented to verify the performance of the proposed converter for varying load conditions. The converter operates in lagging PF mode for the entire load range and requires a narrow variation in switching frequency.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1035294','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1035294"><span id="translatedtitle">Understanding Performance of <span class="hlt">Parallel</span> Scientific <span class="hlt">Simulation</span> Codes using Open|SpeedShop</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Ghosh, K K</p> <p>2011-11-07</p> <p>Conclusions of this presentation are: (1) Open SpeedShop's (OSS) is convenient to use for large, <span class="hlt">parallel</span>, scientific <span class="hlt">simulation</span> codes; (2) Large codes benefit from uninstrumented execution; (3) Many experiments can be run in a short time - might need multiple shots e.g. usertime for caller-callee, hwcsamp for HW counters; (4) Decent idea of code's performance is easily obtained; (5) Statistical sampling calls for decent number of samples; and (6) HWC data is very useful for micro-analysis but can be tricky to analyze.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/5574659','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/5574659"><span id="translatedtitle">Forced-convection boiling tests performed in <span class="hlt">parallel</span> <span class="hlt">simulated</span> LMR fuel assemblies</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Rose, S.D.; Carbajo, J.J.; Levin, A.E.; Lloyd, D.B.; Montgomery, B.H.; Wantland, J.L.</p> <p>1985-04-21</p> <p>Forced-convection tests have been carried out using <span class="hlt">parallel</span> <span class="hlt">simulated</span> Liquid Metal Reactor fuel assemblies in an engineering-scale sodium loop, the Thermal-Hydraulic Out-of-Reactor Safety facility. The tests, performed under single- and two-phase conditions, have shown that for low forced-convection flow there is significant flow augmentation by thermal convection, an important phenomenon under degraded shutdown heat removal conditions in an LMR. The power and flows required for boiling and dryout to occur are much higher than decay heat levels. The experimental evidence supports analytical results that heat removal from an LMR is possible with a degraded shutdown heat removal system.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2001APS..DPPKP1112L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2001APS..DPPKP1112L"><span id="translatedtitle"><span class="hlt">Parallel</span> PIC <span class="hlt">Simulations</span> of Short-Pulse High Intensity Laser Plasma Interactions.</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lasinski, B. F.; Still, C. H.; Langdon, A. B.</p> <p>2001-10-01</p> <p>We extend our previous <span class="hlt">simulations</span> of high intensity short pulse laser plasma interactions footnote B. F. Lasinski, A. B. Langdon, S. P. Hatchett, M. H. Key, and M. Tabak, Phys. Plasmas 6, 2041 (1999); S. C. Wilks and W. L. Kruer, IEEE Journal of Quantum Electronics 11, 1954 (1997). to 3D and to much larger systems in 2D using our new, modern, 3D, electromagnetic, fully relativistic, massively <span class="hlt">parallel</span> PIC code. We study the generation of hot electrons and energetic ions and the associated complex phenomena. Laser light filamentation and the formation of high static magnetic fields are described.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2005APS..MARD11012F','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2005APS..MARD11012F"><span id="translatedtitle">Massive <span class="hlt">parallel</span> <span class="hlt">simulation</span> of phenomena in condensed matter at high energy density</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Fortov, Vladimir</p> <p>2005-03-01</p> <p>This talk deals with computational hydrodynamics, advanced material properties and phenomena at high energy density. New results of massive <span class="hlt">parallel</span> 3D <span class="hlt">simulation</span> done with method of individual particles in cells have been obtained. The gas dynamic code includes advanced physical models of matter such as multi-phase equations of state, elastic-plastic, spallation, optic properties and ion-beams stopping. Investigated are the influence on hypervelocity impact processes effects of equation of state, elastic-plastic and spallation. We also report results of numerical modeling of the action of intense heavy ion beams on metallic targets in comparison with new experimental data.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19900007132','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19900007132"><span id="translatedtitle">Stochastic <span class="hlt">simulation</span> of charged particle transport on the massively <span class="hlt">parallel</span> processor</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Earl, James A.</p> <p>1988-01-01</p> <p>Computations of cosmic-ray transport based upon finite-difference methods are afflicted by instabilities, inaccuracies, and artifacts. To avoid these problems, researchers developed a Monte Carlo formulation which is closely related not only to the finite-difference formulation, but also to the underlying physics of transport phenomena. Implementations of this approach are currently running on the Massively <span class="hlt">Parallel</span> Processor at Goddard Space Flight Center, whose enormous computing power overcomes the poor statistical accuracy that usually limits the use of stochastic methods. These <span class="hlt">simulations</span> have progressed to a stage where they provide a useful and realistic picture of solar energetic particle propagation in interplanetary space.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2000PhDT.......208B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2000PhDT.......208B"><span id="translatedtitle"><span class="hlt">Parallel</span> direct numerical <span class="hlt">simulation</span> of wake vortex detection using monostatic and bistatic radio acoustic sounding systems</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Boluriaan Esfahaani, Said</p> <p></p> <p>A <span class="hlt">parallel</span> two-dimensional code is developed in this thesis to numerically <span class="hlt">simulate</span> wake vortex detection using a Radio Acoustic Sounding System (RASS). The Maxwell equations for media with non-uniform permittivity and the linearized Euler equations for media with non-uniform mean flow are the main framework for the <span class="hlt">simulations</span>. The code is written in Fortran 90 with the Message Passing Interface (MPI) for <span class="hlt">parallel</span> implementation. The main difficulty encountered with a time accurate <span class="hlt">simulation</span> of a RASS is the number of samples required to resolve the Doppler shift in the scattered electromagnetic signal. Even for a 1D <span class="hlt">simulation</span> with a typical scatterer size, the CPU time required to run the code is far beyond currently available computer resources. Two solutions that overcome this problem are described. In the first the actual electromagnetic wave propagation speed is replaced with a much lower value. This allows an explicit, time accurate numerical scheme to be used. In the second the governing differential equations are recast in order to remove the carrier frequency and solve only for the frequency shift using an implicit scheme with large time steps. The numerical stability characteristics of the resulting discretized equation with complex coefficients are examined. A number of cases for both the monostatic and bistatic configurations are considered. First, a uniform mean flow is considered and the RASS <span class="hlt">simulation</span> is performed for two different types of incident acoustic field, namely a short single frequency acoustic pulse and a continuous broadband acoustic source. Both the explicit and implicit schemes are examined and the mean flow velocity is determined from the spectrum of the backscattered electromagnetic signal with very good accuracy. Second, the Taylor and Oseen vortex models are considered and their velocity field along the incident electromagnetic beam is retrieved. The Abel transform is then applied to the velocity profiles determined by both explicit and implicit schemes, and the radial variation of the wake vortex velocity is reconstructed. The effect of the transmitter beam width on the results is also examined. The <span class="hlt">parallel</span> performance of the <span class="hlt">simulations</span> on several platforms is investigated. It is found that the code is nearly perfectly scalable on the tested platforms and for the number of processors considered.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4257577','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4257577"><span id="translatedtitle">Evaluating the performance of <span class="hlt">parallel</span> subsurface <span class="hlt">simulators</span>: An illustrative example with PFLOTRAN</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Hammond, G E; Lichtner, P C; Mills, R T</p> <p>2014-01-01</p> <p>[1] To better inform the subsurface scientist on the expected performance of <span class="hlt">parallel</span> <span class="hlt">simulators</span>, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code PFLOTRAN as it is applied to several realistic modeling scenarios run on the Jaguar supercomputer. After a brief introduction to the code's <span class="hlt">parallel</span> layout and code design, PFLOTRAN's <span class="hlt">parallel</span> performance (measured through strong and weak scalability analyses) is evaluated in the context of conceptual model layout, software and algorithmic design, and known hardware limitations. PFLOTRAN scales well (with regard to strong scaling) for three realistic problem scenarios: (1) in situ leaching of copper from a mineral ore deposit within a 5-spot flow regime, (2) transient flow and solute transport within a regional doublet, and (3) a real-world problem involving uranium surface complexation within a heterogeneous and extremely dynamic variably saturated flow field. Weak scalability is discussed in detail for the regional doublet problem, and several difficulties with its interpretation are noted. PMID:25506097</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2002A%26A...382..758M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2002A%26A...382..758M"><span id="translatedtitle">An efficient <span class="hlt">parallel</span> tree-code for the <span class="hlt">simulation</span> of self-gravitating systems</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Miocchi, P.; Capuzzo-Dolcetta, R.</p> <p>2002-02-01</p> <p>We describe a <span class="hlt">parallel</span> version of our tree-code for the <span class="hlt">simulation</span> of self-gravitating systems in Astrophysics. It is based on a dynamic and adaptive method for the domain decomposition, which exploits the hierarchical data arrangement used by the tree-code. It shows low computational costs for the <span class="hlt">parallelization</span> overhead - less than 4% of the total CPU-time in the tests done - because the domain decomposition is performed ``on the fly'' during the tree-construction and the portion of the tree that is local to each processor ``enriches'' itself of remote data only when they are actually needed. The performance of an implementation of the <span class="hlt">parallel</span> code on a Cray T3E is presented and discussed. They exhibit a very good behaviour of the speedup (=15 with 16 processors and 105 particles) and a rather low load unbalancing (<10% using up to 16 processors), achieving a high computation speed in the forces evaluation (>104 particles/sec with 8 processors). Supported by CINECA (http://www.cineca.it) and CNAA (http://cnaa.cineca.it) under Grant cnarm12a.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/750325','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/750325"><span id="translatedtitle"><span class="hlt">Parallel</span> <span class="hlt">Simulation</span> of Three-Dimensional Free-Surface Fluid Flow Problems</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>BAER,THOMAS A.; SUBIA,SAMUEL R.; SACKINGER,PHILIP A.</p> <p>2000-01-18</p> <p>We describe <span class="hlt">parallel</span> <span class="hlt">simulations</span> of viscous, incompressible, free surface, Newtonian fluid flow problems that include dynamic contact lines. The Galerlin finite element method was used to discretize the fully-coupled governing conservation equations and a ''pseudo-solid'' mesh mapping approach was used to determine the shape of the free surface. In this approach, the finite element mesh is allowed to deform to satisfy quasi-static solid mechanics equations subject to geometric or kinematic constraints on the boundaries. As a result, nodal displacements must be included in the set of problem unknowns. Issues concerning the proper constraints along the solid-fluid dynamic contact line in three dimensions are discussed. <span class="hlt">Parallel</span> computations are carried out for an example taken from the coating flow industry, flow in the vicinity of a slot coater edge. This is a three-dimensional free-surface problem possessing a contact line that advances at the web speed in one region but transitions to static behavior in another part of the flow domain. Discussion focuses on <span class="hlt">parallel</span> speedups for fixed problem size, a class of problems of immediate practical importance.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/18334421','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/18334421"><span id="translatedtitle">Gait <span class="hlt">simulation</span> via a 6-DOF <span class="hlt">parallel</span> robot with iterative learning control.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Aubin, Patrick M; Cowley, Matthew S; Ledoux, William R</p> <p>2008-03-01</p> <p>We have developed a robotic gait <span class="hlt">simulator</span> (RGS) by leveraging a 6-degree of freedom <span class="hlt">parallel</span> robot, with the goal of overcoming three significant challenges of gait <span class="hlt">simulation</span>, including: 1) operating at near physiologically correct velocities; 2) inputting full scale ground reaction forces; and 3) <span class="hlt">simulating</span> motion in all three planes (sagittal, coronal and transverse). The robot will eventually be employed with cadaveric specimens, but as a means of exploring the capability of the system, we have first used it with a prosthetic foot. Gait data were recorded from one transtibial amputee using a motion analysis system and force plate. Using the same prosthetic foot as the subject, the RGS accurately reproduced the recorded kinematics and kinetics and the appropriate vertical ground reaction force was realized with a proportional iterative learning controller. After six gait iterations the controller reduced the root mean square (RMS) error between the <span class="hlt">simulated</span> and in situ; vertical ground reaction force to 35 N during a 1.5 s <span class="hlt">simulation</span> of the stance phase of gait with a prosthetic foot. This paper addresses the design, methodology and validation of the novel RGS. PMID:18334421</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3876705','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3876705"><span id="translatedtitle">Large-Scale Modeling of Epileptic Seizures: Scaling Properties of Two <span class="hlt">Parallel</span> Neuronal Network <span class="hlt">Simulation</span> Algorithms</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Pesce, Lorenzo L.; Lee, Hyong C.; Stevens, Rick L.</p> <p>2013-01-01</p> <p>Our limited understanding of the relationship between the behavior of individual neurons and large neuronal networks is an important limitation in current epilepsy research and may be one of the main causes of our inadequate ability to treat it. Addressing this problem directly via experiments is impossibly complex; thus, we have been developing and studying medium-large-scale <span class="hlt">simulations</span> of detailed neuronal networks to guide us. Flexibility in the connection schemas and a complete description of the cortical tissue seem necessary for this purpose. In this paper we examine some of the basic issues encountered in these multiscale <span class="hlt">simulations</span>. We have determined the detailed behavior of two such <span class="hlt">simulators</span> on <span class="hlt">parallel</span> computer systems. The observed memory and computation-time scaling behavior for a distributed memory implementation were very good over the range studied, both in terms of network sizes (2,000 to 400,000 neurons) and processor pool sizes (1 to 256 processors). Our <span class="hlt">simulations</span> required between a few megabytes and about 150 gigabytes of RAM and lasted between a few minutes and about a week, well within the capability of most multinode clusters. Therefore, <span class="hlt">simulations</span> of epileptic seizures on networks with millions of cells should be feasible on current supercomputers. PMID:24416069</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2698777','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2698777"><span id="translatedtitle">PCSIM: A <span class="hlt">Parallel</span> <span class="hlt">Simulation</span> Environment for Neural Circuits Fully Integrated with Python</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Pecevski, Dejan; Natschläger, Thomas; Schuch, Klaus</p> <p>2008-01-01</p> <p>The <span class="hlt">Parallel</span> Circuit <span class="hlt">SIMulator</span> (PCSIM) is a software package for <span class="hlt">simulation</span> of neural circuits. It is primarily designed for distributed <span class="hlt">simulation</span> of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit <span class="hlt">simulator</span> with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural <span class="hlt">simulations</span>. PMID:19543450</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015A%26C....12..109H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015A%26C....12..109H"><span id="translatedtitle">L-PICOLA: A <span class="hlt">parallel</span> code for fast dark matter <span class="hlt">simulation</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Howlett, C.; Manera, M.; Percival, W. J.</p> <p>2015-09-01</p> <p>Robust measurements based on current large-scale structure surveys require precise knowledge of statistical and systematic errors. This can be obtained from large numbers of realistic mock galaxy catalogues that mimic the observed distribution of galaxies within the survey volume. To this end we present a fast, distributed-memory, planar-<span class="hlt">parallel</span> code, L-PICOLA, which can be used to generate and evolve a set of initial conditions into a dark matter field much faster than a full non-linear N-Body <span class="hlt">simulation</span>. Additionally, L-PICOLA has the ability to include primordial non-Gaussianity in the <span class="hlt">simulation</span> and <span class="hlt">simulate</span> the past lightcone at run-time, with optional replication of the <span class="hlt">simulation</span> volume. Through comparisons to fully non-linear N-Body <span class="hlt">simulations</span> we find that our code can reproduce the z = 0 power spectrum and reduced bispectrum of dark matter to within 2% and 5% respectively on all scales of interest to measurements of Baryon Acoustic Oscillations and Redshift Space Distortions, but 3 orders of magnitude faster. The accuracy, speed and scalability of this code, alongside the additional features we have implemented, make it extremely useful for both current and next generation large-scale structure surveys. L-PICOLA is publicly available at https://cullanhowlett.github.io/l-picola.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25570947','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25570947"><span id="translatedtitle"><span class="hlt">Parallel</span> computing <span class="hlt">simulation</span> of electrical excitation and conduction in the 3D human heart.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Di Yu; Dongping Du; Hui Yang; Yicheng Tu</p> <p>2014-01-01</p> <p>A correctly beating heart is important to ensure adequate circulation of blood throughout the body. Normal heart rhythm is produced by the orchestrated conduction of electrical signals throughout the heart. Cardiac electrical activity is the resulted function of a series of complex biochemical-mechanical reactions, which involves transportation and bio-distribution of ionic flows through a variety of biological ion channels. Cardiac arrhythmias are caused by the direct alteration of ion channel activity that results in changes in the AP waveform. In this work, we developed a whole-heart <span class="hlt">simulation</span> model with the use of massive <span class="hlt">parallel</span> computing with GPGPU and OpenGL. The <span class="hlt">simulation</span> algorithm was implemented under several different versions for the purpose of comparisons, including one conventional CPU version and two GPU versions based on Nvidia CUDA platform. OpenGL was utilized for the visualization / interaction platform because it is open source, light weight and universally supported by various operating systems. The experimental results show that the GPU-based <span class="hlt">simulation</span> outperforms the conventional CPU-based approach and significantly improves the speed of <span class="hlt">simulation</span>. By adopting modern computer architecture, this present investigation enables real-time <span class="hlt">simulation</span> and visualization of electrical excitation and conduction in the large and complicated 3D geometry of a real-world human heart. PMID:25570947</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22089677','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22089677"><span id="translatedtitle">A <span class="hlt">PARALLEL</span> MONTE CARLO CODE FOR <span class="hlt">SIMULATING</span> COLLISIONAL N-BODY SYSTEMS</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Pattabiraman, Bharath; Umbreit, Stefan; Liao, Wei-keng; Choudhary, Alok; Kalogera, Vassiliki; Memik, Gokhan; Rasio, Frederic A.</p> <p>2013-02-15</p> <p>We present a new <span class="hlt">parallel</span> code for computing the dynamical evolution of collisional N-body systems with up to N {approx} 10{sup 7} particles. Our code is based on the Henon Monte Carlo method for solving the Fokker-Planck equation, and makes assumptions of spherical symmetry and dynamical equilibrium. The principal algorithmic developments involve optimizing data structures and the introduction of a <span class="hlt">parallel</span> random number generation scheme as well as a <span class="hlt">parallel</span> sorting algorithm required to find nearest neighbors for interactions and to compute the gravitational potential. The new algorithms we introduce along with our choice of decomposition scheme minimize communication costs and ensure optimal distribution of data and workload among the processing units. Our implementation uses the Message Passing Interface library for communication, which makes it portable to many different supercomputing architectures. We validate the code by calculating the evolution of clusters with initial Plummer distribution functions up to core collapse with the number of stars, N, spanning three orders of magnitude from 10{sup 5} to 10{sup 7}. We find that our results are in good agreement with self-similar core-collapse solutions, and the core-collapse times generally agree with expectations from the literature. Also, we observe good total energy conservation, within {approx}< 0.04% throughout all <span class="hlt">simulations</span>. We analyze the performance of the code, and demonstrate near-linear scaling of the runtime with the number of processors up to 64 processors for N = 10{sup 5}, 128 for N = 10{sup 6} and 256 for N = 10{sup 7}. The runtime reaches saturation with the addition of processors beyond these limits, which is a characteristic of the <span class="hlt">parallel</span> sorting algorithm. The resulting maximum speedups we achieve are approximately 60 Multiplication-Sign , 100 Multiplication-Sign , and 220 Multiplication-Sign , respectively.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/91920','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/91920"><span id="translatedtitle">Numerical <span class="hlt">simulation</span> via <span class="hlt">parallel</span>-distributed computing of energy absorption by metal deformation</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Plaskacz, E.J.; Kulak, R.F.</p> <p>1995-07-01</p> <p>Collapsible steering column designs are credited with saving tens-of-thousands of lives since their introduction in the late 1960`s. The collapsible steering column is a safety feature designed to absorb energy and protect-the driver in a head-on collision. One of the most frequently used design concepts employs two telescoping metal tubes that slide over one another as the occupant impacts the steering wheel. Hardened steel ball bearings are embedded in a plastic sleeve located between the two tubes. There are two primary mechanisms for energy absorption during steering column collapse. One is the friction between the bearing and tube surfaces. Another is the gouging of the tubes` surfaces by the bearings. Current analytical models are unable to adequately capture the physics behind this process. In this paper we will present an overview of a <span class="hlt">parallel</span> finite element code, currently under development, that can be used to <span class="hlt">simulate</span> the highly nonlinear response of this energy absorbing mechanism. Our <span class="hlt">parallel</span> algorithms are constructed on a message-passing foundation. The actual message-passing implementation used was the Argonne-developed p4 package. However, other message-passing libraries can easily be accommodated as they are largely identical in function and differ only in syntax. Once the algorithm is restructured as a set of processes communicating through messages, the program can run on systems as diverse as a uniprocessor workstation, multiprocessors with and without shared memory, a group of workstations that communicate over a local network, or any combination of the above. Benchmarks of the <span class="hlt">parallel</span> code performance on networks of workstations and the IBM SP1 <span class="hlt">parallel</span> supercomputer will be discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013ApJS..204...15P','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013ApJS..204...15P"><span id="translatedtitle">A <span class="hlt">Parallel</span> Monte Carlo Code for <span class="hlt">Simulating</span> Collisional N-body Systems</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Pattabiraman, Bharath; Umbreit, Stefan; Liao, Wei-keng; Choudhary, Alok; Kalogera, Vassiliki; Memik, Gokhan; Rasio, Frederic A.</p> <p>2013-02-01</p> <p>We present a new <span class="hlt">parallel</span> code for computing the dynamical evolution of collisional N-body systems with up to N ~ 107 particles. Our code is based on the Hénon Monte Carlo method for solving the Fokker-Planck equation, and makes assumptions of spherical symmetry and dynamical equilibrium. The principal algorithmic developments involve optimizing data structures and the introduction of a <span class="hlt">parallel</span> random number generation scheme as well as a <span class="hlt">parallel</span> sorting algorithm required to find nearest neighbors for interactions and to compute the gravitational potential. The new algorithms we introduce along with our choice of decomposition scheme minimize communication costs and ensure optimal distribution of data and workload among the processing units. Our implementation uses the Message Passing Interface library for communication, which makes it portable to many different supercomputing architectures. We validate the code by calculating the evolution of clusters with initial Plummer distribution functions up to core collapse with the number of stars, N, spanning three orders of magnitude from 105 to 107. We find that our results are in good agreement with self-similar core-collapse solutions, and the core-collapse times generally agree with expectations from the literature. Also, we observe good total energy conservation, within <~ 0.04% throughout all <span class="hlt">simulations</span>. We analyze the performance of the code, and demonstrate near-linear scaling of the runtime with the number of processors up to 64 processors for N = 105, 128 for N = 106 and 256 for N = 107. The runtime reaches saturation with the addition of processors beyond these limits, which is a characteristic of the <span class="hlt">parallel</span> sorting algorithm. The resulting maximum speedups we achieve are approximately 60×, 100×, and 220×, respectively.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016JCoPh.307..321V','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016JCoPh.307..321V"><span id="translatedtitle">Massively <span class="hlt">parallel</span> kinetic Monte Carlo <span class="hlt">simulations</span> of charge carrier transport in organic semiconductors</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>van der Kaap, N. J.; Koster, L. J. A.</p> <p>2016-02-01</p> <p>A <span class="hlt">parallel</span>, lattice based Kinetic Monte Carlo <span class="hlt">simulation</span> is developed that runs on a GPGPU board and includes Coulomb like particle-particle interactions. The performance of this computationally expensive problem is improved by modifying the interaction potential due to nearby particle moves, instead of fully recalculating it. This modification is achieved by adding dipole correction terms that represent the particle move. Exact evaluation of these terms is guaranteed by representing all interactions as 32-bit floating numbers, where only the integers between -222 and 222 are used. We validate our method by modelling the charge transport in disordered organic semiconductors, including Coulomb interactions between charges. Performance is mainly governed by the particle density in the <span class="hlt">simulation</span> volume, and improves for increasing densities. Our method allows calculations on large volumes including particle-particle interactions, which is important in the field of organic semiconductors.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1093069','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1093069"><span id="translatedtitle"><span class="hlt">Parallel</span> adaptive fluid-structure interaction <span class="hlt">simulation</span> of explosions impacting on building structures</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Deiterding, Ralf; Wood, Stephen L</p> <p>2013-01-01</p> <p>We pursue a level set approach to couple an Eulerian shock-capturing fluid solver with space-time refinement to an explicit solid dynamics solver for large deformations and fracture. The coupling algorithms considering recursively finer fluid time steps as well as overlapping solver updates are discussed in detail. Our ideas are implemented in the AMROC adaptive fluid solver framework and are used for effective fluid-structure coupling to the general purpose solid dynamics code DYNA3D. Beside <span class="hlt">simulations</span> verifying the coupled fluid-structure solver and assessing its <span class="hlt">parallel</span> scalability, the detailed structural analysis of a reinforced concrete column under blast loading and the <span class="hlt">simulation</span> of a prototypical blast explosion in a realistic multistory building are presented.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_19 --> <div id="page_20" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="381"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20140009920','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20140009920"><span id="translatedtitle"><span class="hlt">Simulation</span>/Emulation Techniques: Compressing Schedules With <span class="hlt">Parallel</span> (HW/SW) Development</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Mangieri, Mark L.; Hoang, June</p> <p>2014-01-01</p> <p>NASA has always been in the business of balancing new technologies and techniques to achieve human space travel objectives. NASA's Kedalion engineering analysis lab has been validating and using many contemporary avionics HW/SW development and integration techniques, which represent new paradigms to NASA's heritage culture. Kedalion has validated many of the Orion HW/SW engineering techniques borrowed from the adjacent commercial aircraft avionics solution space, inserting new techniques and skills into the Multi - Purpose Crew Vehicle (MPCV) Orion program. Using contemporary agile techniques, Commercial-off-the-shelf (COTS) products, early rapid prototyping, in-house expertise and tools, and extensive use of <span class="hlt">simulators</span> and emulators, NASA has achieved cost effective paradigms that are currently serving the Orion program effectively. Elements of long lead custom hardware on the Orion program have necessitated early use of <span class="hlt">simulators</span> and emulators in advance of deliverable hardware to achieve <span class="hlt">parallel</span> design and development on a compressed schedule.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1096496','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1096496"><span id="translatedtitle">Xyce <span class="hlt">parallel</span> electronic <span class="hlt">simulator</span> users%3CU%2B2019%3E guide, version 6.0.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Keiter, Eric Richard; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Verley, Jason C.; Fixel, Deborah A.; Coffey, Todd Stirling; Pawlowski, Roger Patrick; Warrender, Christina E.; Baur, David G.</p> <p>2013-08-01</p> <p>This manual describes the use of the Xyce <span class="hlt">Parallel</span> Electronic <span class="hlt">Simulator</span>. Xyce has been designed as a SPICE-compatible, high-performance analog circuit <span class="hlt">simulator</span>, and has been written to support the <span class="hlt">simulation</span> needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale <span class="hlt">parallel</span> computing platforms (up to thousands of processors). This includes support for most popular <span class="hlt">parallel</span> and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiationaware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a <span class="hlt">parallel</span> code in the most general sense of the phrase - a message passing <span class="hlt">parallel</span> implementation - which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory <span class="hlt">parallel</span> platforms. Attention has been paid to the specific nature of circuit-<span class="hlt">simulation</span> problems to ensure that optimal <span class="hlt">parallel</span> efficiency is achieved as the number of processors grows.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1194329','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1194329"><span id="translatedtitle">A Many-Task <span class="hlt">Parallel</span> Approach for Multiscale <span class="hlt">Simulations</span> of Subsurface Flow and Reactive Transport</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Scheibe, Timothy D.; Yang, Xiaofan; Schuchardt, Karen L.; Agarwal, Khushbu; Chase, Jared M.; Palmer, Bruce J.; Tartakovsky, Alexandre M.</p> <p>2014-12-16</p> <p>Continuum-scale models have long been used to study subsurface flow, transport, and reactions but lack the ability to resolve processes that are governed by pore-scale mixing. Recently, pore-scale models, which explicitly resolve individual pores and soil grains, have been developed to more accurately model pore-scale phenomena, particularly reaction processes that are controlled by local mixing. However, pore-scale models are prohibitively expensive for modeling application-scale domains. This motivates the use of a hybrid multiscale approach in which continuum- and pore-scale codes are coupled either hierarchically or concurrently within an overall <span class="hlt">simulation</span> domain (time and space). This approach is naturally suited to an adaptive, loosely-coupled many-task methodology with three potential levels of concurrency. Each individual code (pore- and continuum-scale) can be implemented in <span class="hlt">parallel</span>; multiple semi-independent instances of the pore-scale code are required at each time step providing a second level of concurrency; and Monte Carlo <span class="hlt">simulations</span> of the overall system to represent uncertainty in material property distributions provide a third level of concurrency. We have developed a hybrid multiscale model of a mixing-controlled reaction in a porous medium wherein the reaction occurs only over a limited portion of the domain. Loose, minimally-invasive coupling of pre-existing <span class="hlt">parallel</span> continuum- and pore-scale codes has been accomplished by an adaptive script-based workflow implemented in the Swift workflow system. We describe here the methods used to create the model system, adaptively control multiple coupled instances of pore- and continuum-scale <span class="hlt">simulations</span>, and maximize the scalability of the overall system. We present results of numerical experiments conducted on NERSC supercomputing systems; our results demonstrate that loose many-task coupling provides a scalable solution for multiscale subsurface <span class="hlt">simulations</span> with minimal overhead.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016APS..MAR.T1021D','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016APS..MAR.T1021D"><span id="translatedtitle">Optimized <span class="hlt">simulations</span> of Olami-Feder-Christensen systems using <span class="hlt">parallel</span> algorithms</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Dominguez, Rachele; Necaise, Rance; Montag, Eric</p> <p></p> <p>The sequential nature of the Olami-Feder-Christensen (OFC) model for earthquake <span class="hlt">simulations</span> limits the benefits of <span class="hlt">parallel</span> computing approaches because of the frequent communication required between processors. We developed a <span class="hlt">parallel</span> version of the OFC algorithm for multi-core processors. Our data, even for relatively small system sizes and low numbers of processors, indicates that increasing the number of processors provides significantly faster <span class="hlt">simulations</span>; producing more efficient results than previous attempts that used network-based Beowulf clusters. Our algorithm optimizes performance by exploiting the multi-core processor architecture, minimizing communication time in contrast to the networked Beowulf-cluster approaches. Our multi-core algorithm is the basis for a new algorithm using GPUs that will drastically increase the number of processors available. Previous studies incorporating realistic structural features of faults into OFC models have revealed spatial and temporal patterns observed in real earthquake systems. The computational advances presented here will allow for studying interacting networks of faults, rather than individual faults, further enhancing our understanding of the relationship between the earth's structure and the triggering process. Support for this project comes from the Chenery Research Fund, the Rashkind Family Endowment, the Walter Williams Craigie Teaching Endowment, and the Schapiro Undergraduate Research Fellowship.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4755232','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4755232"><span id="translatedtitle">SDA 7: A modular and <span class="hlt">parallel</span> implementation of the <span class="hlt">simulation</span> of diffusional association software</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Martinez, Michael; Romanowska, Julia; Kokh, Daria B.; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan</p> <p>2015-01-01</p> <p>The <span class="hlt">simulation</span> of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to <span class="hlt">simulate</span> the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the <span class="hlt">parallelization</span> of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the <span class="hlt">parallel</span> performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26123630</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014ChPhB..23b8903W','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014ChPhB..23b8903W"><span id="translatedtitle">MDSLB: A new static load balancing method for <span class="hlt">parallel</span> molecular dynamics <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Wu, Yun-Long; Xu, Xin-Hai; Yang, Xue-Jun; Zou, Shun; Ren, Xiao-Guang</p> <p>2014-02-01</p> <p>Large-scale <span class="hlt">parallelization</span> of molecular dynamics <span class="hlt">simulations</span> is facing challenges which seriously affect the <span class="hlt">simulation</span> efficiency, among which the load imbalance problem is the most critical. In this paper, we propose, a new molecular dynamics static load balancing method (MDSLB). By analyzing the characteristics of the short-range force of molecular dynamics programs running in <span class="hlt">parallel</span>, we divide the short-range force into three kinds of force models, and then package the computations of each force model into many tiny computational units called “cell loads”, which provide the basic data structures for our load balancing method. In MDSLB, the spatial region is separated into sub-regions called “local domains”, and the cell loads of each local domain are allocated to every processor in turn. Compared with the dynamic load balancing method, MDSLB can guarantee load balance by executing the algorithm only once at program startup without migrating the loads dynamically. We implement MDSLB in OpenFOAM software and test it on TianHe-1A supercomputer with 16 to 512 processors. Experimental results show that MDSLB can save 34%-64% time for the load imbalanced cases.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26123630','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26123630"><span id="translatedtitle">SDA 7: A modular and <span class="hlt">parallel</span> implementation of the <span class="hlt">simulation</span> of diffusional association software.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Martinez, Michael; Bruce, Neil J; Romanowska, Julia; Kokh, Daria B; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan; Wade, Rebecca C</p> <p>2015-08-01</p> <p>The <span class="hlt">simulation</span> of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein-protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to <span class="hlt">simulate</span> the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration-dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the <span class="hlt">parallelization</span> of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object-oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the <span class="hlt">parallel</span> performance. PMID:26123630</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/447033','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/447033"><span id="translatedtitle">Scalar and <span class="hlt">parallel</span> optimized implementation of the direct <span class="hlt">simulation</span> Monte Carlo method</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Dietrich, S.; Boyd, I.D.</p> <p>1996-07-01</p> <p>This paper describes a new concept for the implementation of the direct <span class="hlt">simulation</span> Monte Carlo (DSMC) method. It uses a localized data structure based on a computational cell to achieve high performance, especially on workstation processors, which can also be used in <span class="hlt">parallel</span>. Since the data structure makes it possible to freely assign any cell to any processor, a domain decomposition can be found with equal calculation load on each processor while maintaining minimal communication among the nodes. Further, the new implementation strictly separates physical modeling, geometrical issues, and organizational tasks to achieve high maintainability and to simplify future enhancements. Three example flow configurations are calculated with the new implementation to demonstrate its generality and performance. They include a flow through a diverging channel using an adapted unstructured triangulated grid, a flow around a planetary probe, and an internal flow in a contactor used in plasma physics. The results are validated either by comparison with results obtained from other <span class="hlt">simulations</span> or by comparison with experimental data. High performance on an IBM SP2 system is achieved if problem size and number of <span class="hlt">parallel</span> processors are adapted accordingly. On 400 nodes, DSMC calculations with more than 100 million particles are possible. 19 refs., 18 figs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24732497','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24732497"><span id="translatedtitle">pWeb: A High-Performance, <span class="hlt">Parallel</span>-Computing Framework for Web-Browser-Based Medical <span class="hlt">Simulation</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Halic, Tansel; Ahn, Woojin; De, Suvranu</p> <p>2014-01-01</p> <p>This work presents a pWeb - a new language and compiler for <span class="hlt">parallelization</span> of client-side compute intensive web applications such as surgical <span class="hlt">simulations</span>. The recently introduced HTML5 standard has enabled creating unprecedented applications on the web. Low performance of the web browser, however, remains the bottleneck of computationally intensive applications including visualization of complex scenes, real time physical <span class="hlt">simulations</span> and image processing compared to native ones. The new proposed language is built upon web workers for multithreaded programming in HTML5. The language provides fundamental functionalities of <span class="hlt">parallel</span> programming languages as well as the fork/join <span class="hlt">parallel</span> model which is not supported by web workers. The language compiler automatically generates an equivalent <span class="hlt">parallel</span> script that complies with the HTML5 standard. A case study on realistic rendering for surgical <span class="hlt">simulations</span> demonstrates enhanced performance with a compact set of instructions. PMID:24732497</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016CoPhC.200..324N','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016CoPhC.200..324N"><span id="translatedtitle">MaMiCo: Software design for <span class="hlt">parallel</span> molecular-continuum flow <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Neumann, Philipp; Flohr, Hanno; Arora, Rahul; Jarmatz, Piet; Tchipev, Nikola; Bungartz, Hans-Joachim</p> <p>2016-03-01</p> <p>The macro-micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum <span class="hlt">simulations</span>, retaining sequential and <span class="hlt">parallel</span> performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementation SimpleMD, the node-level optimized software ls1 mardyn, and the community codes ESPResSo and LAMMPS. We detail interface implementations to connect each solver with MaMiCo. The coupling for each waLBerla-MD setup is validated in three-dimensional channel flow <span class="hlt">simulations</span> which are solved by means of a state-based coupling method. We provide sequential and strong scaling measurements for the four molecular-continuum <span class="hlt">simulations</span>. The overhead of MaMiCo is found to come at 10%-20% of the total (MD) runtime. The measurements further show that scalability of the hybrid <span class="hlt">simulations</span> is reached on up to 500 Intel SandyBridge, and more than 1000 AMD Bulldozer compute cores.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016CG.....89..174K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016CG.....89..174K"><span id="translatedtitle"><span class="hlt">Parallel</span> <span class="hlt">simulation</span> of particle transport in an advection field applied to volcanic explosive eruptions</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Künzli, Pierre; Tsunematsu, Kae; Albuquerque, Paul; Falcone, Jean-Luc; Chopard, Bastien; Bonadonna, Costanza</p> <p>2016-04-01</p> <p>Volcanic ash transport and dispersal models typically describe particle motion via a turbulent velocity field. Particles are advected inside this field from the moment they leave the vent of the volcano until they deposit on the ground. Several techniques exist to <span class="hlt">simulate</span> particles in an advection field such as finite difference Eulerian, Lagrangian-puff or pure Lagrangian techniques. In this paper, we present a new flexible <span class="hlt">simulation</span> tool called TETRAS (TEphra TRAnsport <span class="hlt">Simulator</span>) based on a hybrid Eulerian-Lagrangian model. This scheme offers the advantages of being numerically stable with no numerical diffusion and easily parallelizable. It also allows us to output particle atmospheric concentration or ground mass load at any given time. The model is validated using the advection-diffusion analytical equation. We also obtained a good agreement with field observations of the tephra deposit associated with the 2450 BP Pululagua (Ecuador) and the 1996 Ruapehu (New Zealand) eruptions. As this kind of model can lead to computationally intensive <span class="hlt">simulations</span>, a <span class="hlt">parallelization</span> on a distributed memory architecture was developed. A related performance model, taking into account load imbalance, is proposed and its accuracy tested.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2001AAS...198.4007K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2001AAS...198.4007K"><span id="translatedtitle">Application of a 3D, Adaptive, <span class="hlt">Parallel</span>, MHD Code to Supernova Remnant <span class="hlt">Simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Kominsky, P.; Drake, R. P.; Powell, K. G.</p> <p>2001-05-01</p> <p>We at Michigan have a computational model, BATS-R-US, which incorporates several modern features that make it suitable for calculations of supernova remnant evolution. In particular, it is a three-dimensional MHD model, using a method called the Multiscale Adaptive Upwind Scheme for MagnetoHydroDynamics (MAUS-MHD). It incorporates a data structure that allows for adaptive refinement of the mesh, even in massively <span class="hlt">parallel</span> calculations. Its advanced Godunov method, a solution-adaptive, upwind, high-resolution scheme, incorporates a new, flux-based approach to the Riemann solver with improved numerical properties. This code has been successfully applied to several problems, including the <span class="hlt">simulation</span> of comets and of planetary magnetospheres, in the 3D context of the Heliosphere. The code was developed under a NASA computational grand challenge grant to run very rapidly on <span class="hlt">parallel</span> platforms. It is also now being used to study time-dependent systems such as the transport of particles and energy from solar coronal mass ejections to the Earth. We are in the process of modifying this code so that it can accommodate the very strong shocks present in supernova remnants. Our test case <span class="hlt">simulates</span> the explosion of a star of 1.4 solar masses with an energy of 1 foe, in a uniform background medium. We have performed runs of 250,000 to 1 million cells on 8 nodes of an Origin 2000. These relatively coarse grids do not allow fine details of instabilities to become visible. Nevertheless, the macroscopic evolution of the shock is <span class="hlt">simulated</span> well, with the forward and reverse shocks visible in velocity profiles. We will show our work to date. This work was supported by NASA through its GSRP program.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013AGUFMIN23A1416G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013AGUFMIN23A1416G"><span id="translatedtitle">Accelerating Dust Storm <span class="hlt">Simulation</span> by Balancing Task Allocation in <span class="hlt">Parallel</span> Computing Environment</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Gui, Z.; Yang, C.; XIA, J.; Huang, Q.; YU, M.</p> <p>2013-12-01</p> <p>Dust storm has serious negative impacts on environment, human health, and assets. The continuing global climate change has increased the frequency and intensity of dust storm in the past decades. To better understand and predict the distribution, intensity and structure of dust storm, a series of dust storm models have been developed, such as Dust Regional Atmospheric Model (DREAM), the NMM meteorological module (NMM-dust) and Chinese Unified Atmospheric Chemistry Environment for Dust (CUACE/Dust). The developments and applications of these models have contributed significantly to both scientific research and our daily life. However, dust storm <span class="hlt">simulation</span> is a data and computing intensive process. Normally, a <span class="hlt">simulation</span> for a single dust storm event may take several days or hours to run. It seriously impacts the timeliness of prediction and potential applications. To speed up the process, high performance computing is widely adopted. By partitioning a large study area into small subdomains according to their geographic location and executing them on different computing nodes in a <span class="hlt">parallel</span> fashion, the computing performance can be significantly improved. Since spatiotemporal correlations exist in the geophysical process of dust storm <span class="hlt">simulation</span>, each subdomain allocated to a node need to communicate with other geographically adjacent subdomains to exchange data. Inappropriate allocations may introduce imbalance task loads and unnecessary communications among computing nodes. Therefore, task allocation method is the key factor, which may impact the feasibility of the <span class="hlt">paralleling</span>. The allocation algorithm needs to carefully leverage the computing cost and communication cost for each computing node to minimize total execution time and reduce overall communication cost for the entire system. This presentation introduces two algorithms for such allocation and compares them with evenly distributed allocation method. Specifically, 1) In order to get optimized solutions, a quadratic programming based modeling method is proposed. This algorithm performs well with small amount of computing tasks. However, its efficiency decreases significantly as the subdomain number and computing node number increase. 2) To compensate performance decreasing for large scale tasks, a K-Means clustering based algorithm is introduced. Instead of dedicating to get optimized solutions, this method can get relatively good feasible solutions within acceptable time. However, it may introduce imbalance communication for nodes or node-isolated subdomains. This research shows both two algorithms have their own strength and weakness for task allocation. A combination of the two algorithms is under study to obtain a better performance. Keywords: Scheduling; <span class="hlt">Parallel</span> Computing; Load Balance; Optimization; Cost Model</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1996gmu..rept.....W','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1996gmu..rept.....W"><span id="translatedtitle">Development of a Massively <span class="hlt">Parallel</span> Particle-Mesh Algorithm for <span class="hlt">Simulations</span> of Galaxy Dynamics and Plasmas</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Wallin, John</p> <p>1996-01-01</p> <p>Particle-mesh calculations treat forces and potentials as field quantities which are represented approximately on a mesh. A system of particles is mapped onto this mesh as a density distribution of mass or charge. The Fourier transform is used to convolve this distribution with the Green's function of the potential, and a finite difference scheme is used to calculate the forces acting on the particles. The computation time scales as the Ng log Ng, where Ng is the size of the computational grid. In contrast, the particle-particle method's computing time relies on direct summation, so the time for each calculation is given by Np2, where Np is the number of particles. The particle-mesh method is best suited for <span class="hlt">simulations</span> with a fixed minimum resolution and for collisionless systems, while hierarchical tree codes have proven to be superior for collisional systems where two-body interactions are important. Particle mesh methods still dominate in plasma physics where collisionless systems are modeled. The CM-200 Connection Machine produced by Thinking Machines Corp. is a data <span class="hlt">parallel</span> system. On this system, the front-end computer controls the timing and execution of the <span class="hlt">parallel</span> processing units. The programming paradigm is Single-Instruction, Multiple Data (SIMD). The processors on the CM-200 are connected in an N-dimensional hypercube; the largest number of links a message will ever have to make is N. As in all <span class="hlt">parallel</span> computing, the efficiency of an algorithm is primarily determined by the fraction of the time spent communicating compared to that spent computing. Because of the topology of the processors, nearest neighbor communication is more efficient than general communication.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013AGUSMIN23A..06M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013AGUSMIN23A..06M"><span id="translatedtitle">A <span class="hlt">parallelized</span> particle tracing code for massive 3D mantle flow <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Manea, V.; Manea, M.; Pomeran, M.; Besutiu, L.; Zlagnean, L.</p> <p>2013-05-01</p> <p>The problem of convective flows in a highly viscous fluid represents a common research direction in Earth Sciences. For tracing the convective motion of the fluid material, a source passive particles (or tracers) that flow at a local convection velocity and do not affect the pattern of flow it is commonly used. Here we present a <span class="hlt">parallelized</span> tracer code that uses passive and weightless particles with their position computed from their displacement during a small time interval at the velocity of flow previously calculated for a given point in space and time. The tracer code is integrated in the open source package CitcomS, which is widely used in the solid earth community (www.geodynamics.org). We benchmarked the tracer code on the state-of-the-art CyberDyn <span class="hlt">parallel</span> machine, a High Performance Computing (HPC) Cluster with 1344 computing cores available at the Institute of Geodynamics of the Romanian Academy. The benchmark tests are performed using a series of 3D geodynamic settings where we introduced various clusters of tracers at different places in the models. Using several millions of particles, the benchmark results show that the <span class="hlt">parallelized</span> tracer code performs well with an optimum number of computing cores between 32 and 64. Because of the large amount of communications among the computing cores, high-resolution CFD <span class="hlt">simulations</span> for geodynamic predictions that require tens of millions, or even billions of tracers to accurately track mantle flow, will greatly benefit from HPC systems based on low-latency high-speed interconnects. In this paper we will present several study cases regarding the 3D mantle flow as revealed by tracers in active subduction zones, as the subduction of Rivera and Cocos plates beneath North America plate as well as the subduction of Nazca plate beneath the South America plate.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/974699','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/974699"><span id="translatedtitle">Massively <span class="hlt">parallel</span> <span class="hlt">simulation</span> with DOE's ASCI supercomputers : an overview of the Los Alamos Crestone project</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Weaver, R. P.; Gittings, M. L.</p> <p>2004-01-01</p> <p>The Los Alamos Crestone Project is part of the Department of Energy's (DOE) Accelerated Strategic Computing Initiative, or ASCI Program. The main goal of this software development project is to investigate the use of continuous adaptive mesh refinement (CAMR) techniques for application to problems of interest to the Laboratory. There are many code development efforts in the Crestone Project, both unclassified and classified codes. In this overview I will discuss the unclassified SAGE and the RAGE codes. The SAGE (SAIC adaptive grid Eulerian) code is a one-, two-, and three-dimensional multimaterial Eulerian massively <span class="hlt">parallel</span> hydrodynamics code for use in solving a variety of high-deformation flow problems. The RAGE CAMR code is built from the SAGE code by adding various radiation packages, improved setup utilities and graphics packages and is used for problems in which radiation transport of energy is important. The goal of these massively-<span class="hlt">parallel</span> versions of the codes is to run extremely large problems in a reasonable amount of calendar time. Our target is scalable performance to {approx}10,000 processors on a 1 billion CAMR computational cell problem that requires hundreds of variables per cell, multiple physics packages (e.g. radiation and hydrodynamics), and implicit matrix solves for each cycle. A general description of the RAGE code has been published in [l],[ 2], [3] and [4]. Currently, the largest <span class="hlt">simulations</span> we do are three-dimensional, using around 500 million computation cells and running for literally months of calendar time using {approx}2000 processors. Current ASCI platforms range from several 3-teraOPS supercomputers to one 12-teraOPS machine at Lawrence Livermore National Laboratory, the White machine, and one 20-teraOPS machine installed at Los Alamos, the Q machine. Each machine is a system comprised of many component parts that must perform in unity for the successful run of these <span class="hlt">simulations</span>. Key features of any massively <span class="hlt">parallel</span> system include the processors, the disks, the interconnection between processors, the operating system, libraries for message passing and <span class="hlt">parallel</span> 1/0 and other fundamental units of the system. We will give an overview of the current status of the Crestone Project codes SAGE and RAGE. These codes are intended for general applications without tuning of algorithms or parameters. We have run a wide variety of physical applications from millimeter-scale laboratory laser experiments to the multikilometer-scale asteroid impacts into the Pacific Ocean to parsec-scale galaxy formation. Examples of these <span class="hlt">simulations</span> will be shown. The goal of our effort is to avoid ad hoc models and attempt to rely on first-principles physics. In addition to the large effort on developing <span class="hlt">parallel</span> code physics packages, a substantial effort in the project is devoted to improving the computer science and software quality engineering (SQE) of the Project codes as well as a sizable effort on the verification and validation (V&V) of the resulting codes. Examples of these efforts for our project will be discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014PhDT........13Z','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014PhDT........13Z"><span id="translatedtitle">Scalable <span class="hlt">parallel</span> programming for high performance seismic <span class="hlt">simulation</span> on petascale heterogeneous supercomputers</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Zhou, Jun</p> <p></p> <p>The 1994 Northridge earthquake in Los Angeles, California, killed 57 people, injured over 8,700 and caused an estimated $20 billion in damage. Petascale <span class="hlt">simulations</span> are needed in California and elsewhere to provide society with a better understanding of the rupture and wave dynamics of the largest earthquakes at shaking frequencies required to engineer safe structures. As the heterogeneous supercomputing infrastructures are becoming more common, numerical developments in earthquake system research are particularly challenged by the dependence on the accelerator elements to enable "the Big One" <span class="hlt">simulations</span> with higher frequency and finer resolution. Reducing time to solution and power consumption are two primary focus area today for the enabling technology of fault rupture dynamics and seismic wave propagation in realistic 3D models of the crust's heterogeneous structure. This dissertation presents scalable <span class="hlt">parallel</span> programming techniques for high performance seismic <span class="hlt">simulation</span> running on petascale heterogeneous supercomputers. A real world earthquake <span class="hlt">simulation</span> code, AWP-ODC, one of the most advanced earthquake codes to date, was chosen as the base code in this research, and the testbed is based on Titan at Oak Ridge National Laboraratory, the world's largest hetergeneous supercomputer. The research work is primarily related to architecture study, computation performance tuning and software system scalability. An earthquake <span class="hlt">simulation</span> workflow has also been developed to support the efficient production sets of <span class="hlt">simulations</span>. The highlights of the technical development are an aggressive performance optimization focusing on data locality and a notable data communication model that hides the data communication latency. This development results in the optimal computation efficiency and throughput for the 13-point stencil code on heterogeneous systems, which can be extended to general high-order stencil codes. Started from scratch, the hybrid CPU/GPU version of AWP-ODC code is ready now for real world petascale earthquake <span class="hlt">simulations</span>. This GPU-based code has demonstrated excellent weak scaling up to the full Titan scale and achieved 2.3 PetaFLOPs sustained computation performance in single precision. The production <span class="hlt">simulation</span> demonstrated the first 0-10Hz deterministic rough fault <span class="hlt">simulation</span>. Using the accelerated AWP-ODC, Southern California Earthquake Center (SCEC) has recently created the physics-based probablistic seismic hazard analysis model of the Los Angeles region, CyberShake 14.2, as of the time of the dissertation writing. The tensor-valued wavefield code based on this GPU research has dramatically reduced time-to-solution, making a statewide hazard model a goal reachable with existing heterogeneous supercomputers.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013PhDT.......119R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013PhDT.......119R"><span id="translatedtitle"><span class="hlt">Parallel</span> Algorithms for Monte Carlo Particle Transport <span class="hlt">Simulation</span> on Exascale Computing Architectures</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Romano, Paul Kollath</p> <p></p> <p>Monte Carlo particle transport methods are being considered as a viable option for high-fidelity <span class="hlt">simulation</span> of nuclear reactors. While Monte Carlo methods offer several potential advantages over deterministic methods, there are a number of algorithmic shortcomings that would prevent their immediate adoption for full-core analyses. In this thesis, algorithms are proposed both to ameliorate the degradation in <span class="hlt">parallel</span> efficiency typically observed for large numbers of processors and to offer a means of decomposing large tally data that will be needed for reactor analysis. A nearest-neighbor fission bank algorithm was proposed and subsequently implemented in the OpenMC Monte Carlo code. A theoretical analysis of the communication pattern shows that the expected cost is O( N ) whereas traditional fission bank algorithms are O(N) at best. The algorithm was tested on two supercomputers, the Intrepid Blue Gene/P and the Titan Cray XK7, and demonstrated nearly linear <span class="hlt">parallel</span> scaling up to 163,840 processor cores on a full-core benchmark problem. An algorithm for reducing network communication arising from tally reduction was analyzed and implemented in OpenMC. The proposed algorithm groups only particle histories on a single processor into batches for tally purposes---in doing so it prevents all network communication for tallies until the very end of the <span class="hlt">simulation</span>. The algorithm was tested, again on a full-core benchmark, and shown to reduce network communication substantially. A model was developed to predict the impact of load imbalances on the performance of domain decomposed <span class="hlt">simulations</span>. The analysis demonstrated that load imbalances in domain decomposed <span class="hlt">simulations</span> arise from two distinct phenomena: non-uniform particle densities and non-uniform spatial leakage. The dominant performance penalty for domain decomposition was shown to come from these physical effects rather than insufficient network bandwidth or high latency. The model predictions were verified with measured data from <span class="hlt">simulations</span> in OpenMC on a full-core benchmark problem. Finally, a novel algorithm for decomposing large tally data was proposed, analyzed, and implemented/tested in OpenMC. The algorithm relies on disjoint sets of compute processes and tally servers. The analysis showed that for a range of parameters relevant to LWR analysis, the tally server algorithm should perform with minimal overhead. Tests were performed on Intrepid and Titan and demonstrated that the algorithm did indeed perform well over a wide range of parameters. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012amos.confE..73H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012amos.confE..73H"><span id="translatedtitle">GPU-based Space Situational Awareness <span class="hlt">Simulation</span> utilising <span class="hlt">Parallelism</span> for Enhanced Multi-sensor Management</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Hobson, T.; Clarkson, V.</p> <p>2012-09-01</p> <p>As a result of continual space activity since the 1950s, there are now a large number of man-made Resident Space Objects (RSOs) orbiting the Earth. Because of the large number of items and their relative speeds, the possibility of destructive collisions involving important space assets is now of significant concern to users and operators of space-borne technologies. As a result, a growing number of international agencies are researching methods for improving techniques to maintain Space Situational Awareness (SSA). Computer <span class="hlt">simulation</span> is a method commonly used by many countries to validate competing methodologies prior to full scale adoption. The use of supercomputing and/or reduced scale testing is often necessary to effectively <span class="hlt">simulate</span> such a complex problem on todays computers. Recently the authors presented a <span class="hlt">simulation</span> aimed at reducing the computational burden by selecting the minimum level of fidelity necessary for contrasting methodologies and by utilising multi-core CPU <span class="hlt">parallelism</span> for increased computational efficiency. The resulting <span class="hlt">simulation</span> runs on a single PC while maintaining the ability to effectively evaluate competing methodologies. Nonetheless, the ability to control the scale and expand upon the computational demands of the sensor management system is limited. In this paper, we examine the advantages of increasing the <span class="hlt">parallelism</span> of the <span class="hlt">simulation</span> by means of General Purpose computing on Graphics Processing Units (GPGPU). As many sub-processes pertaining to SSA management are independent, we demonstrate how parallelisation via GPGPU has the potential to significantly enhance not only research into techniques for maintaining SSA, but also to enhance the level of sophistication of existing space surveillance sensors and sensor management systems. Nonetheless, the use of GPGPU imposes certain limitations and adds to the implementation complexity, both of which require consideration to achieve an effective system. We discuss these challenges and how they can be overcome. We further describe an application of the parallelised system where visibility prediction is used to enhance sensor management. This facilitates significant improvement in maximum catalogue error when RSOs become temporarily unobservable. The objective is to demonstrate the enhanced scalability and increased computational capability of the system.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2006CoPhC.175..440B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2006CoPhC.175..440B"><span id="translatedtitle">A package of Linux scripts for the <span class="hlt">parallelization</span> of Monte Carlo <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Badal, Andreu; Sempau, Josep</p> <p>2006-09-01</p> <p>Despite the fact that fast computers are nowadays available at low cost, there are many situations where obtaining a reasonably low statistical uncertainty in a Monte Carlo (MC) <span class="hlt">simulation</span> involves a prohibitively large amount of time. This limitation can be overcome by having recourse to <span class="hlt">parallel</span> computing. Most tools designed to facilitate this approach require modification of the source code and the installation of additional software, which may be inconvenient for some users. We present a set of tools, named clonEasy, that implement a <span class="hlt">parallelization</span> scheme of a MC <span class="hlt">simulation</span> that is free from these drawbacks. In clonEasy, which is designed to run under Linux, a set of "clone" CPUs is governed by a "master" computer by taking advantage of the capabilities of the Secure Shell (ssh) protocol. Any Linux computer on the Internet that can be ssh-accessed by the user can be used as a clone. A key ingredient for the <span class="hlt">parallel</span> calculation to be reliable is the availability of an independent string of random numbers for each CPU. Many generators—such as RANLUX, RANECU or the Mersenne Twister—can readily produce these strings by initializing them appropriately and, hence, they are suitable to be used with clonEasy. This work was primarily motivated by the need to find a straightforward way to <span class="hlt">parallelize</span> PENELOPE, a code for MC <span class="hlt">simulation</span> of radiation transport that (in its current 2005 version) employs the generator RANECU, which uses a combination of two multiplicative linear congruential generators (MLCGs). Thus, this paper is focused on this class of generators and, in particular, we briefly present an extension of RANECU that increases its period up to ˜5×10 and we introduce seedsMLCG, a tool that provides the information necessary to initialize disjoint sequences of an MLCG to feed different CPUs. This program, in combination with clonEasy, allows to run PENELOPE in <span class="hlt">parallel</span> easily, without requiring specific libraries or significant alterations of the sequential code. Program summary 1Title of program:clonEasy Catalogue identifier:ADYD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYD_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a Unix style shell (bash), support for the Secure Shell protocol and a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1) Compilers:GNU FORTRAN g77 (Linux); g95 (Linux); Intel Fortran Compiler 7.1 (Linux) Programming language used:Linux shell (bash) script, FORTRAN 77 No. of bits in a word:32 No. of lines in distributed program, including test data, etc.:1916 No. of bytes in distributed program, including test data, etc.:18 202 Distribution format:tar.gz Nature of the physical problem:There are many situations where a Monte Carlo <span class="hlt">simulation</span> involves a huge amount of CPU time. The <span class="hlt">parallelization</span> of such calculations is a simple way of obtaining a relatively low statistical uncertainty using a reasonable amount of time. Method of solution:The presented collection of Linux scripts and auxiliary FORTRAN programs implement Secure Shell-based communication between a "master" computer and a set of "clones". The aim of this communication is to execute a code that performs a Monte Carlo <span class="hlt">simulation</span> on all the clones simultaneously. The code is unique, but each clone is fed with a different set of random seeds. Hence, clonEasy effectively permits the <span class="hlt">parallelization</span> of the calculation. Restrictions on the complexity of the program:clonEasy can only be used with programs that produce statistically independent results using the same code, but with a different sequence of random numbers. Users must choose the initialization values for the random number generator on each computer and combine the output from the different executions. A FORTRAN program to combine the final results is also provided. Typical running time:The execution time of each script largely depends on the number of computers that are used, the actions that are to be performed and, to a lesser extent, on the network connexion bandwidth. Unusual features of the program:Any computer on the Internet with a Secure Shell client/server program installed can be used as a node of a virtual computer cluster for <span class="hlt">parallel</span> calculations with the sequential source code. The simplicity of the <span class="hlt">parallelization</span> scheme makes the use of this package a straightforward task, which does not require installing any additional libraries. Program summary 2Title of program:seedsMLCG Catalogue identifier:ADYE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYE_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1), MS Windows (2000, XP) Compilers:GNU FORTRAN g77 (Linux and Windows); g95 (Linux); Intel Fortran Compiler 7.1 (Linux); Compaq Visual Fortran 6.1 (Windows) Programming language used:FORTRAN 77 No. of bits in a word:32 Memory required to execute with typical data:500 kilobytes No. of lines in distributed program, including test data, etc.:492 No. of bytes in distributed program, including test data, etc.:5582 Distribution format:tar.gz Nature of the physical problem:Statistically independent results from different runs of a Monte Carlo code can be obtained using uncorrelated sequences of random numbers on each execution. Multiplicative linear congruential generators (MLCG), or other generators that are based on them such as RANECU, can be adapted to produce these sequences. Method of solution:For a given MLCG, the presented program calculates initialization values that produce disjoint, consecutive sequences of pseudo-random numbers. The calculated values initiate the generator in distant positions of the random number cycle and can be used, for instance, on a <span class="hlt">parallel</span> <span class="hlt">simulation</span>. The values are found using the formula S=(aS)MODm, which gives the random value that will be generated after J iterations of the MLCG. Restrictions on the complexity of the program:The 32-bit length restriction for the integer variables in standard FORTRAN 77 limits the produced seeds to be separated a distance smaller than 2 31, when the distance J is expressed as an integer value. The program allows the user to input the distance as a power of 10 for the purpose of efficiently splitting the sequence of generators with a very long period. Typical running time:The execution time depends on the parameters of the used MLCG and the distance between the generated seeds. The generation of 10 6 seeds separated 10 12 units in the sequential cycle, for one of the MLCGs found in the RANECU generator, takes 3 s on a 2.4 GHz Intel Pentium 4 using the g77 compiler.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_20 --> <div id="page_21" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="401"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1185588','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1185588"><span id="translatedtitle">Improving the Performance of the Extreme-scale <span class="hlt">Simulator</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Engelmann, Christian; Naughton III, Thomas J</p> <p>2014-01-01</p> <p>Investigating the performance of <span class="hlt">parallel</span> applications at scale on future high-performance computing (HPC) architectures and the performance impact of different architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale <span class="hlt">Simulator</span> (xSim) is a <span class="hlt">simulation</span>-based toolkit for investigating the performance of <span class="hlt">parallel</span> applications at scale. xSim scales to millions of <span class="hlt">simulated</span> Message Passing Interface (MPI) processes. The overhead introduced by a <span class="hlt">simulation</span> tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1) a new deadlock resolution protocol to reduce the <span class="hlt">parallel</span> <span class="hlt">discrete</span> <span class="hlt">event</span> <span class="hlt">simulation</span> management overhead and (2) a new <span class="hlt">simulated</span> MPI message matching algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement, such as by reducing the <span class="hlt">simulation</span> overhead for running the NAS <span class="hlt">Parallel</span> Benchmark suite inside the <span class="hlt">simulator</span> from 1,020\\% to 238% for the conjugate gradient (CG) benchmark and from 102% to 0% for the embarrassingly <span class="hlt">parallel</span> (EP) and benchmark, as well as, from 37,511% to 13,808% for CG and from 3,332% to 204% for EP with accurate process failure <span class="hlt">simulation</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015APS..DFD.M7005F','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015APS..DFD.M7005F"><span id="translatedtitle">FFeasibility of Amazon Cloud Computing Platform for <span class="hlt">Parallel</span> Multi-phase Flow <span class="hlt">Simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Freniere, Cole; Pathak, Ashish; Raessi, Mehdi; University of Massachusetts Dartmouth Team</p> <p>2015-11-01</p> <p>The feasibility of Amazon's Elastic Compute Cloud (EC2) service is evaluated as a resource for multi-phase flow <span class="hlt">simulations</span>. The results for two multi-phase flow solvers are presented: a 2D GPU-accelerated serial code and a 3D MPI-<span class="hlt">parallel</span> GPU-accelerated solver. In both cases, the interaction of two-fluid flow with a moving solid phase is captured, and a GPU pressure Poisson solver is used. A virtual cloud cluster is compared to a conventional high-performance computing cluster at the researchers' university in terms of performance and cost. The accuracy of the results obtained on Amazon's Cloud, where the GPUs are single-precision, is the same as those obtained on the university cluster with double-precision GPUs. The <span class="hlt">parallel</span> code is benchmarked on clusters of varying size, with strong and weak scaling curves. The steps necessary to outsource the data to the cloud, as well as acquiring the appropriate hardware and software stacks are outlined. Amazon's HPC cloud is competitive with the university cluster, but there are some performance limitations that will be discussed in the presentation. Funding from the National Science Foundation CBET - 1236462 and UMass Dartmouth OUR is gratefully acknowledged.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2003APS..DPPFP1114S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2003APS..DPPFP1114S"><span id="translatedtitle">MPI <span class="hlt">parallelization</span> of Vlasov codes for the <span class="hlt">simulation</span> of nonlinear laser-plasma interactions</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Savchenko, V.; Won, K.; Afeyan, B.; Decyk, V.; Albrecht-Marc, M.; Ghizzo, A.; Bertrand, P.</p> <p>2003-10-01</p> <p>The <span class="hlt">simulation</span> of optical mixing driven KEEN waves [1] and electron plasma waves [1] in laser-produced plasmas require nonlinear kinetic models and massive <span class="hlt">parallelization</span>. We use Massage Passing Interface (MPI) libraries and Appleseed [2] to solve the Vlasov Poisson system of equations on an 8 node dual processor MAC G4 cluster. We use the semi-Lagrangian time splitting method [3]. It requires only row-column exchanges in the global data redistribution, minimizing the total number of communications between processors. Recurrent communication patterns for 2D FFTs involves global transposition. In the Vlasov-Maxwell case, we use splitting into two 1D spatial advections and a 2D momentum advection [4]. Discretized momentum advection equations have a double loop structure with the outer index being assigned to different processors. We adhere to a code structure with separate routines for calculations and data management for <span class="hlt">parallel</span> computations. [1] B. Afeyan et al., IFSA 2003 Conference Proceedings, Monterey, CA [2] V. K. Decyk, Computers in Physics, 7, 418 (1993) [3] Sonnendrucker et al., JCP 149, 201 (1998) [4] Begue et al., JCP 151, 458 (1999)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015APS..DFDA12003Y','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015APS..DFDA12003Y"><span id="translatedtitle">Synchronized Molecular-Dynamics <span class="hlt">simulation</span> for thermal lubrication of a polymeric liquid between <span class="hlt">parallel</span> plates</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Yasuda, Shugo; Yamamoto, Ryoichi</p> <p>2015-11-01</p> <p>The Synchronized Molecular-Dynamics <span class="hlt">simulation</span> which was recently proposed by authors is applied to the analysis of polymer lubrication between <span class="hlt">parallel</span> plates. In the SMD method, the MD <span class="hlt">simulations</span> are assigned to small fluid elements to calculate the local stresses and temperatures and are synchronized at certain time intervals to satisfy the macroscopic heat- and momentum-transport equations.The rheological properties and conformation of the polymer chains coupled with local viscous heating are investigated with a non-dimensional parameter, the Nahme-Griffith number, which is defined as the ratio of the viscous heating to the thermal conduction at the characteristic temperature required to sufficiently change the viscosity. The present <span class="hlt">simulation</span> demonstrates that strong shear thinning and a transitional behavior of the conformation of the polymer chains are exhibited with a rapid temperature rise when the Nahme-Griffith number exceeds unity.The results also clarify that the reentrant transition of the linear stress-optical relation occurs for large shear stresses due to the coupling of the conformation of polymer chains with heat generation under shear flows. This study was financially supported by JSPS KAKENHI Grant Nos. 26790080 and 26247069.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20160006398','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20160006398"><span id="translatedtitle"><span class="hlt">Parallel</span> Adjective High-Order CFD <span class="hlt">Simulations</span> Characterizing SOFIA Cavity Acoustics</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Barad, Michael F.; Brehm, Christoph; Kiris, Cetin C.; Biswas, Rupak</p> <p>2016-01-01</p> <p>This paper presents large-scale MPI-<span class="hlt">parallel</span> computational uid dynamics <span class="hlt">simulations</span> for the Stratospheric Observatory for Infrared Astronomy (SOFIA). SOFIA is an airborne, 2.5-meter infrared telescope mounted in an open cavity in the aft fuselage of a Boeing 747SP. These <span class="hlt">simulations</span> focus on how the unsteady ow eld inside and over the cavity interferes with the optical path and mounting structure of the telescope. A temporally fourth-order accurate Runge-Kutta, and spatially fth-order accurate WENO- 5Z scheme was used to perform implicit large eddy <span class="hlt">simulations</span>. An immersed boundary method provides automated gridding for complex geometries and natural coupling to a block-structured Cartesian adaptive mesh re nement framework. Strong scaling studies using NASA's Pleiades supercomputer with up to 32k CPU cores and 4 billion compu- tational cells shows excellent scaling. Dynamic load balancing based on execution time on individual AMR blocks addresses irregular numerical cost associated with blocks con- taining boundaries. Limits to scaling beyond 32k cores are identi ed, and targeted code optimizations are discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19880008905','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19880008905"><span id="translatedtitle">Experiences with serial and <span class="hlt">parallel</span> algorithms for channel routing using <span class="hlt">simulated</span> annealing</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Brouwer, Randall Jay</p> <p>1988-01-01</p> <p>Two algorithms for channel routing using <span class="hlt">simulated</span> annealing are presented. <span class="hlt">Simulated</span> annealing is an optimization methodology which allows the solution process to back up out of local minima that may be encountered by inappropriate selections. By properly controlling the annealing process, it is very likely that the optimal solution to an NP-complete problem such as channel routing may be found. The algorithm presented proposes very relaxed restrictions on the types of allowable transformations, including overlapping nets. By freeing that restriction and controlling overlap situations with an appropriate cost function, the algorithm becomes very flexible and can be applied to many extensions of channel routing. The selection of the transformation utilizes a number of heuristics, still retaining the pseudorandom nature of <span class="hlt">simulated</span> annealing. The algorithm was implemented as a serial program for a workstation, and a <span class="hlt">parallel</span> program designed for a hypercube computer. The details of the serial implementation are presented, including many of the heuristics used and some of the resulting solutions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015APS..DFD.E9006P','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015APS..DFD.E9006P"><span id="translatedtitle">A 3D MPI-<span class="hlt">Parallel</span> GPU-accelerated framework for <span class="hlt">simulating</span> ocean wave energy converters</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Pathak, Ashish; Raessi, Mehdi</p> <p>2015-11-01</p> <p>We present an MPI-<span class="hlt">parallel</span> GPU-accelerated computational framework for studying the interaction between ocean waves and wave energy converters (WECs). The computational framework captures the viscous effects, nonlinear fluid-structure interaction (FSI), and breaking of waves around the structure, which cannot be captured in many potential flow solvers commonly used for WEC <span class="hlt">simulations</span>. The full Navier-Stokes equations are solved using the two-step projection method, which is accelerated by porting the pressure Poisson equation to GPUs. The FSI is captured using the numerically stable fictitious domain method. A novel three-phase interface reconstruction algorithm is used to resolve three phases in a VOF-PLIC context. A consistent mass and momentum transport approach enables <span class="hlt">simulations</span> at high density ratios. The accuracy of the overall framework is demonstrated via an array of test cases. Numerical <span class="hlt">simulations</span> of the interaction between ocean waves and WECs are presented. Funding from the National Science Foundation CBET-1236462 grant is gratefully acknowledged.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014APS..MARM27008W','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014APS..MARM27008W"><span id="translatedtitle">Large-scale massively <span class="hlt">parallel</span> atomistic <span class="hlt">simulations</span> of short pulse laser interaction with metals</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Wu, Chengping; Zhigilei, Leonid; Computational Materials Group Team</p> <p>2014-03-01</p> <p>Taking advantage of petascale supercomputing architectures, large-scale massively <span class="hlt">parallel</span> atomistic <span class="hlt">simulations</span> (108-109 atoms) are performed to study the microscopic mechanisms of short pulse laser interaction with metals. The results of the <span class="hlt">simulations</span> reveal a complex picture of highly non-equilibrium processes responsible for material modification and/or ejection. At low laser fluences below the ablation threshold, fast melting and resolidification occur under conditions of extreme heating and cooling rates resulting in surface microstructure modification. At higher laser fluences in the spallation regime, the material is ejected by the relaxation of laser-induced stresses and proceeds through the nucleation, growth and percolation of multiple voids in the sub-surface region of the irradiated target. At a fluence of ~ 2.5 times the spallation threshold, the top part of the target reaches the conditions for an explosive decomposition into vapor and small droplets, marking the transition to the phase explosion regime of laser ablation. The dynamics of plume formation and the characteristics of the ablation plume are obtained from the <span class="hlt">simulations</span> and compared with the results of time-resolved plume imaging experiments. Financial support for this work was provided by NSF (DMR-0907247 and CMMI-1301298) and AFOSR (FA9550-10-1-0541). Computational support was provided by the OLCF (MAT048) and XSEDE (TG-DMR110090).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22068805','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22068805"><span id="translatedtitle">Effect of <span class="hlt">parallel</span> currents on drift-interchange turbulence: Comparison of <span class="hlt">simulation</span> and experiment</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>D'Ippolito, D. A.; Russell, D. A.; Myra, J. R.; Thakur, S. C.; Tynan, G. R.; Holland, C.</p> <p>2012-10-15</p> <p>Two-dimensional (2D) turbulence <span class="hlt">simulations</span> are reported in which the balancing of the <span class="hlt">parallel</span> and perpendicular currents is modified by changing the axial boundary condition (BC) to vary the sheath conductivity. The <span class="hlt">simulations</span> are carried out using the 2D scrape-off-layer turbulence (SOLT) code. The results are compared with recent experiments on the controlled shear de-correlation experiment (CSDX) in which the axial BC was modified by changing the composition of the end plate. Reasonable qualitative agreement is found between the <span class="hlt">simulations</span> and the experiment. When an insulating axial BC is used, broadband turbulence is obtained and an inverse cascade occurs down to low frequencies and long spatial scales. Robust sheared flows are obtained. By contrast, employing a conducting BC at the plate resulted in coherent (drift wave) modes rather than broadband turbulence, with weaker inverse cascade, and smaller zonal flows. The dependence of the two instability mechanisms (rotationally driven interchange mode and drift waves) on the axial BC is also discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/372178','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/372178"><span id="translatedtitle">A three-phase series-<span class="hlt">parallel</span> resonant converter -- analysis, design, <span class="hlt">simulation</span>, and experimental results</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Bhat, A.K.S.; Zheng, R.L.</p> <p>1996-07-01</p> <p>A three-phase dc-to-dc series-<span class="hlt">parallel</span> resonant converter is proposed /and its operating modes for a 180{degree} wide gating pulse scheme are explained. A detailed analysis of the converter using a constant current model and the Fourier series approach is presented. Based on the analysis, design curves are obtained and a design example of a 1-kW converter is given. SPICE <span class="hlt">simulation</span> results for the designed converter and experimental results for a 500-W converter are presented to verify the performance of the proposed converter for varying load conditions. The converter operates in lagging power factor (PF) mode for the entire load range and requires a narrow variation in switching frequency, to adequately regulate the output power.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016IAUS..312...79V','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016IAUS..312...79V"><span id="translatedtitle"><span class="hlt">Simulation</span> of disc-bulge-halo galaxies using <span class="hlt">parallel</span> GPU based codes</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Veles, O.; Berczik, P.; Just, A.</p> <p>2016-02-01</p> <p>We compare the performance of the very popular Tree-GPU code BONSAI with the older Particle-(Multi)Mesh code SUPERBOX. Both code we run on a same hardware using the GPU acceleration for the force calculation. SUPERBOX is a particle-mesh code with high resolution sub-grid and a higher order NGP (nearest grid point) force-calculation scheme. In our research, we are aiming to demonstrate that the new <span class="hlt">parallel</span> version of SUPERBOX is capable to do the high resolution <span class="hlt">simulations</span> of the interaction of the system of disc-bulge-halo composed galaxy. We describe the improvement of performance and scalability of SUPERBOX particularly for the Kepler cluster (NVIDIA K20 GPU). A comparison was made with the very popular and publicly available Tree-GPU code BONSAI†.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013JCoPh.236..367T','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013JCoPh.236..367T"><span id="translatedtitle"><span class="hlt">Parallel</span> 3D-TLM algorithm for <span class="hlt">simulation</span> of the Earth-ionosphere cavity</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Toledo-Redondo, Sergio; Salinas, Alfonso; Morente-Molinera, Juan Antonio; Méndez, Antonio; Fornieles, Jesús; Portí, Jorge; Morente, Juan Antonio</p> <p>2013-03-01</p> <p>A <span class="hlt">parallel</span> 3D algorithm for solving time-domain electromagnetic problems with arbitrary geometries is presented. The technique employed is the Transmission Line Modeling (TLM) method implemented in Shared Memory (SM) environments. The benchmarking performed reveals that the maximum speedup depends on the memory size of the problem as well as multiple hardware factors, like the disposition of CPUs, cache, or memory. A maximum speedup of 15 has been measured for the largest problem. In certain circumstances of low memory requirements, superlinear speedup is achieved using our algorithm. The model is employed to model the Earth-ionosphere cavity, thus enabling a study of the natural electromagnetic phenomena that occur in it. The algorithm allows complete 3D <span class="hlt">simulations</span> of the cavity with a resolution of 10 km, within a reasonable timescale.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014EPJWC..6702098R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014EPJWC..6702098R"><span id="translatedtitle"><span class="hlt">Parallel</span> numerical <span class="hlt">simulation</span> of oscillating airfoil NACA0015 in the channel due to flutter instability</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>?idk, Vclav; idlof, Petr</p> <p>2014-03-01</p> <p>The work is devoted to 3D and 2D <span class="hlt">parallel</span> numerical computation of pressure and velocity fields around an elastically supported airfoil self-oscillating due to interaction with the airflow. Numerical solution is computed in the OpenFOAM package, an open-source software package based on finite volume method. Movement of airfoil is described by translation and rotation, identified from experimental data. A new boundary condition for the 2DOF motion of the airfoil was implemented. The results of numerical <span class="hlt">simulations</span> (velocity) are compared with data measured in a wind tunnel, where a physical model of NACA0015 airfoil was mounted and tuned to exhibit the flutter instability. The experimental results were obtained previously in the Institute of Thermomechanics by interferographic measurements in a subsonic wind tunnel in Nov Knn.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19051924','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19051924"><span id="translatedtitle">Non-equilibrium molecular dynamics <span class="hlt">simulation</span> of nanojet injection with adaptive-spatial decomposition <span class="hlt">parallel</span> algorithm.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Shin, Hyun-Ho; Yoon, Woong-Sup</p> <p>2008-07-01</p> <p>An Adaptive-Spatial Decomposition <span class="hlt">parallel</span> algorithm was developed to increase computation efficiency for molecular dynamics <span class="hlt">simulations</span> of nano-fluids. Injection of a liquid argon jet with a scale of 17.6 molecular diameters was investigated. A solid annular platinum injector was also solved simultaneously with the liquid injectant by adopting a solid modeling technique which incorporates phantom atoms. The viscous heat was naturally discharged through the solids so the liquid boiling problem was avoided with no separate use of temperature controlling methods. Parametric investigations of injection speed, wall temperature, and injector length were made. A sudden pressure drop at the orifice exit causes flash boiling of the liquid departing the nozzle exit with strong evaporation on the surface of the liquids, while rendering a slender jet. The elevation of the injection speed and the wall temperature causes an activation of the surface evaporation concurrent with reduction in the jet breakup length and the drop size. PMID:19051924</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22043417','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22043417"><span id="translatedtitle">The role of the electron convection term for the <span class="hlt">parallel</span> electric field and electron acceleration in MHD <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Matsuda, K.; Terada, N.; Katoh, Y.; Misawa, H.</p> <p>2011-08-15</p> <p>There has been a great concern about the origin of the <span class="hlt">parallel</span> electric field in the frame of fluid equations in the auroral acceleration region. This paper proposes a new method to <span class="hlt">simulate</span> magnetohydrodynamic (MHD) equations that include the electron convection term and shows its efficiency with <span class="hlt">simulation</span> results in one dimension. We apply a third-order semi-discrete central scheme to investigate the characteristics of the electron convection term including its nonlinearity. At a steady state discontinuity, the sum of the ion and electron convection terms balances with the ion pressure gradient. We find that the electron convection term works like the gradient of the negative pressure and reduces the ion sound speed or amplifies the sound mode when <span class="hlt">parallel</span> current flows. The electron convection term enables us to describe a situation in which a <span class="hlt">parallel</span> electric field and <span class="hlt">parallel</span> electron acceleration coexist, which is impossible for ideal or resistive MHD.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3306636','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3306636"><span id="translatedtitle">Macro-scale phenomena of arterial coupled cells: a massively <span class="hlt">parallel</span> <span class="hlt">simulation</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Shaikh, Mohsin Ahmed; Wall, David J. N.; David, Tim</p> <p>2012-01-01</p> <p>Impaired mass transfer characteristics of blood-borne vasoactive species such as adenosine triphosphate in regions such as an arterial bifurcation have been hypothesized as a prospective mechanism in the aetiology of atherosclerotic lesions. Arterial endothelial cells (ECs) and smooth muscle cells (SMCs) respond differentially to altered local haemodynamics and produce coordinated macro-scale responses via intercellular communication. Using a computationally designed arterial segment comprising large populations of mathematically modelled coupled ECs and SMCs, we investigate their response to spatial gradients of blood-borne agonist concentrations and the effect of micro-scale-driven perturbation on the macro-scale. Altering homocellular (between same cell type) and heterocellular (between different cell types) intercellular coupling, we <span class="hlt">simulated</span> four cases of normal and pathological arterial segments experiencing an identical gradient in the concentration of the agonist. Results show that the heterocellular calcium (Ca2+) coupling between ECs and SMCs is important in eliciting a rapid response when the vessel segment is stimulated by the agonist gradient. In the absence of heterocellular coupling, homocellular Ca2+ coupling between SMCs is necessary for propagation of Ca2+ waves from downstream to upstream cells axially. Desynchronized intracellular Ca2+ oscillations in coupled SMCs are mandatory for this propagation. Upon decoupling the heterocellular membrane potential, the arterial segment looses the inhibitory effect of ECs on the Ca2+ dynamics of the underlying SMCs. The full system comprises hundreds of thousands of coupled nonlinear ordinary differential equations <span class="hlt">simulated</span> on the massively <span class="hlt">parallel</span> Blue Gene architecture. The use of massively <span class="hlt">parallel</span> computational architectures shows the capability of this approach to address macro-scale phenomena driven by elementary micro-scale components of the system. PMID:21920960</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1165004','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1165004"><span id="translatedtitle">Acceleration of the matrix multiplication of Radiance three phase daylighting <span class="hlt">simulations</span> with <span class="hlt">parallel</span> computing on heterogeneous hardware of personal computer</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Zuo, Wangda; McNeil, Andrew; Wetter, Michael; Lee, Eleanor S.</p> <p>2013-05-23</p> <p>Building designers are increasingly relying on complex fenestration systems to reduce energy consumed for lighting and HVAC in low energy buildings. Radiance, a lighting <span class="hlt">simulation</span> program, has been used to conduct daylighting <span class="hlt">simulations</span> for complex fenestration systems. Depending on the configurations, the <span class="hlt">simulation</span> can take hours or even days using a personal computer. This paper describes how to accelerate the matrix multiplication portion of a Radiance three-phase daylight <span class="hlt">simulation</span> by conducting <span class="hlt">parallel</span> computing on heterogeneous hardware of a personal computer. The algorithm was optimized and the computational part was implemented in <span class="hlt">parallel</span> using OpenCL. The speed of new approach was evaluated using various daylighting <span class="hlt">simulation</span> cases on a multicore central processing unit and a graphics processing unit. Based on the measurements and analysis of the time usage for the Radiance daylighting <span class="hlt">simulation</span>, further speedups can be achieved by using fast I/O devices and storing the data in a binary format.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/979295','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/979295"><span id="translatedtitle"><span class="hlt">Parallel</span> Adaptive <span class="hlt">Simulation</span> of Weak and Strong Transverse-Wave Structures in H2-O2 Detonations</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Deiterding, Ralf</p> <p>2010-01-01</p> <p>Two- and three-dimensional <span class="hlt">simulation</span> results are presented that investigate at great detail the temporal evolution of Mach reflection sub-structure patterns intrinsic to gaseous detonation waves. High local resolution is achieved by utilizing a distributed memory <span class="hlt">parallel</span> shock-capturing finite volume code that employs block-structured dynamic mesh adaptation. The computational approach, the implemented <span class="hlt">parallelization</span> strategy, and the software design are discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/890856','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/890856"><span id="translatedtitle">A Multi-Bunch, Three-Dimensional, Strong-Strong Beam-Beam <span class="hlt">Simulation</span> Code for <span class="hlt">Parallel</span> Computers</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Cai, Y.; Kabel, A.C.; /SLAC</p> <p>2005-05-11</p> <p>For <span class="hlt">simulating</span> the strong-strong beam-beam effect, using Particle-In-Cell codes has become one of the methods of choice. While the two-dimensional problem is readily treatable using PC-class machines, the three-dimensional problem, i.e., a problem encompassing hourglass and phase-averaging effects, requires the use of <span class="hlt">parallel</span> processors. In this paper, we introduce a strong-strong code NIMZOVICH, which was specifically designed for <span class="hlt">parallel</span> processors and which is optimally used for many bunches and parasitic crossings. We describe the <span class="hlt">parallelization</span> scheme and give some benchmarking results.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010JGRB..11512101H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010JGRB..11512101H"><span id="translatedtitle">A <span class="hlt">parallel</span> 3-D staggered grid pseudospectral time domain method for ground-penetrating radar wave <span class="hlt">simulation</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Huang, Qinghua; Li, Zhanhui; Wang, Yanbin</p> <p>2010-12-01</p> <p>We presented a <span class="hlt">parallel</span> 3-D staggered grid pseudospectral time domain (PSTD) method for <span class="hlt">simulating</span> ground-penetrating radar (GPR) wave propagation. We took the staggered grid method to weaken the global effect in PSTD and developed a modified fast Fourier transform (FFT) spatial derivative operator to eliminate the wraparound effect due to the implicit periodical boundary condition in FFT operator. After the above improvements, we achieved the <span class="hlt">parallel</span> PSTD computation based on an overlap domain decomposition method without any absorbing condition for each subdomain, which can significantly reduce the required grids in each overlap subdomain comparing with other proposed algorithms. We test our <span class="hlt">parallel</span> technique for some numerical models and obtained consistent results with the analytical ones and/or those of the nonparallel PSTD method. The above numerical tests showed that our <span class="hlt">parallel</span> PSTD algorithm is effective in <span class="hlt">simulating</span> 3-D GPR wave propagation, with merits of saving computation time, as well as more flexibility in dealing with complicated models without losing the accuracy. The application of our <span class="hlt">parallel</span> PSTD method in applied geophysics and paleoseismology based on GPR data confirmed the efficiency of our algorithm and its potential applications in various subdisciplines of solid earth geophysics. This study would also provide a useful <span class="hlt">parallel</span> PSTD approach to the <span class="hlt">simulation</span> of other geophysical problems on distributed memory PC cluster.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_21 --> <div id="page_22" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li class="active"><span>22</span></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="421"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013JChPh.139v4706N','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013JChPh.139v4706N"><span id="translatedtitle"><span class="hlt">Parallel</span> kinetic Monte Carlo <span class="hlt">simulation</span> framework incorporating accurate models of adsorbate lateral interactions</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Nielsen, Jens; d'Avezac, Mayeul; Hetherington, James; Stamatakis, Michail</p> <p>2013-12-01</p> <p>Ab initio kinetic Monte Carlo (KMC) <span class="hlt">simulations</span> have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These <span class="hlt">simulations</span> necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. More recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for <span class="hlt">simulating</span> catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce <span class="hlt">parallelization</span> with OpenMP. We further benchmark our framework by <span class="hlt">simulating</span> a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016CoPhC.200...57J','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016CoPhC.200...57J"><span id="translatedtitle"><span class="hlt">Parallel</span> implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji</p> <p>2016-03-01</p> <p>Three-dimensional Fast Fourier Transform (3D FFT) plays an important role in a wide variety of computer <span class="hlt">simulations</span> and data analyses, including molecular dynamics (MD) <span class="hlt">simulations</span>. In this study, we develop hybrid (MPI+OpenMP) <span class="hlt">parallelization</span> schemes of 3D FFT based on two new volumetric decompositions, mainly for the particle mesh Ewald (PME) calculation in MD <span class="hlt">simulations</span>. In one scheme, (1d_Alltoall), five all-to-all communications in one dimension are carried out, and in the other, (2d_Alltoall), one two-dimensional all-to-all communication is combined with two all-to-all communications in one dimension. 2d_Alltoall is similar to the conventional volumetric decomposition scheme. We performed benchmark tests of 3D FFT for the systems with different grid sizes using a large number of processors on the K computer in RIKEN AICS. The two schemes show comparable performances, and are better than existing 3D FFTs. The performances of 1d_Alltoall and 2d_Alltoall depend on the supercomputer network system and number of processors in each dimension. There is enough leeway for users to optimize performance for their conditions. In the PME method, short-range real-space interactions as well as long-range reciprocal-space interactions are calculated. Our volumetric decomposition schemes are particularly useful when used in conjunction with the recently developed midpoint cell method for short-range interactions, due to the same decompositions of real and reciprocal spaces. The 1d_Alltoall scheme of 3D FFT takes 4.7 ms to <span class="hlt">simulate</span> one MD cycle for a virus system containing more than 1 million atoms using 32,768 cores on the K computer.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22253805','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22253805"><span id="translatedtitle"><span class="hlt">Parallel</span> kinetic Monte Carlo <span class="hlt">simulation</span> framework incorporating accurate models of adsorbate lateral interactions</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Nielsen, Jens; D’Avezac, Mayeul; Hetherington, James; Stamatakis, Michail</p> <p>2013-12-14</p> <p>Ab initio kinetic Monte Carlo (KMC) <span class="hlt">simulations</span> have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These <span class="hlt">simulations</span> necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. More recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for <span class="hlt">simulating</span> catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce <span class="hlt">parallelization</span> with OpenMP. We further benchmark our framework by <span class="hlt">simulating</span> a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=19910032090&hterms=computer+architecture&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3Dcomputer%2Barchitecture','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=19910032090&hterms=computer+architecture&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3Dcomputer%2Barchitecture"><span id="translatedtitle">Implementation of a blade element UH-60 helicopter <span class="hlt">simulation</span> on a <span class="hlt">parallel</span> computer architecture in real-time</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Moxon, Bruce C.; Green, John A.</p> <p>1990-01-01</p> <p>A high-performance platform for development of real-time helicopter flight <span class="hlt">simulations</span> based on a <span class="hlt">simulation</span> development and analysis platform combining a <span class="hlt">parallel</span> <span class="hlt">simulation</span> development and analysis environment with a scalable multiprocessor computer system is described. <span class="hlt">Simulation</span> functional decomposition is covered, including the sequencing and data dependency of <span class="hlt">simulation</span> modules and <span class="hlt">simulation</span> functional mapping to multiple processors. The multiprocessor-based implementation of a blade-element <span class="hlt">simulation</span> of the UH-60 helicopter is presented, and a prototype developed for a TC2000 computer is generalized in order to arrive at a portable multiprocessor software architecture. It is pointed out that the proposed approach coupled with a pilot's station creates a setting in which <span class="hlt">simulation</span> engineers, computer scientists, and pilots can work together in the design and evaluation of advanced real-time helicopter <span class="hlt">simulations</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/929325','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/929325"><span id="translatedtitle">Progress on H5Part: A Portable High Performance <span class="hlt">Parallel</span> DataInterface for Electromagnetics <span class="hlt">Simulations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Adelmann, Andreas; Gsell, Achim; Oswald, Benedikt; Schietinger,Thomas; Bethel, Wes; Shalf, John; Siegerist, Cristina; Stockinger, Kurt</p> <p>2007-06-22</p> <p>Significant problems facing all experimental andcomputationalsciences arise from growing data size and complexity. Commonto allthese problems is the need to perform efficient data I/O ondiversecomputer architectures. In our scientific application, thelargestparallel particle <span class="hlt">simulations</span> generate vast quantitiesofsix-dimensional data. Such a <span class="hlt">simulation</span> run produces data foranaggregate data size up to several TB per run. Motived by the needtoaddress data I/O and access challenges, we have implemented H5Part,anopen source data I/O API that simplifies the use of the HierarchicalDataFormat v5 library (HDF5). HDF5 is an industry standard forhighperformance, cross-platform data storage and retrieval that runsonall contemporary architectures from large <span class="hlt">parallel</span> supercomputerstolaptops. H5Part, which is oriented to the needs of the particlephysicsand cosmology communities, provides support for parallelstorage andretrieval of particles, structured and in the future unstructuredmeshes.In this paper, we describe recent work focusing on I/O supportforparticles and structured meshes and provide data showing performance onmodernsupercomputer architectures like the IBM POWER 5.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016NewA...43...49B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016NewA...43...49B"><span id="translatedtitle">Radiation hydrodynamics using characteristics on adaptive decomposed domains for massively <span class="hlt">parallel</span> star formation <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Buntemeyer, Lars; Banerjee, Robi; Peters, Thomas; Klassen, Mikhail; Pudritz, Ralph E.</p> <p>2016-02-01</p> <p>We present an algorithm for solving the radiative transfer problem on massively <span class="hlt">parallel</span> computers using adaptive mesh refinement and domain decomposition. The solver is based on the method of characteristics which requires an adaptive raytracer that integrates the equation of radiative transfer. The radiation field is split into local and global components which are handled separately to overcome the non-locality problem. The solver is implemented in the framework of the magneto-hydrodynamics code FLASH and is coupled by an operator splitting step. The goal is the study of radiation in the context of star formation <span class="hlt">simulations</span> with a focus on early disc formation and evolution. This requires a proper treatment of radiation physics that covers both the optically thin as well as the optically thick regimes and the transition region in particular. We successfully show the accuracy and feasibility of our method in a series of standard radiative transfer problems and two 3D collapse <span class="hlt">simulations</span> resembling the early stages of protostar and disc formation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20120014386','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20120014386"><span id="translatedtitle"><span class="hlt">Simulated</span> Wake Characteristics Data for Closely Spaced <span class="hlt">Parallel</span> Runway Operations Analysis</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Guerreiro, Nelson M.; Neitzke, Kurt W.</p> <p>2012-01-01</p> <p>A <span class="hlt">simulation</span> experiment was performed to generate and compile wake characteristics data relevant to the evaluation and feasibility analysis of closely spaced <span class="hlt">parallel</span> runway (CSPR) operational concepts. While the experiment in this work is not tailored to any particular operational concept, the generated data applies to the broader class of CSPR concepts, where a trailing aircraft on a CSPR approach is required to stay ahead of the wake vortices generated by a lead aircraft on an adjacent CSPR. Data for wake age, circulation strength, and wake altitude change, at various lateral offset distances from the wake-generating lead aircraft approach path were compiled for a set of nine aircraft spanning the full range of FAA and ICAO wake classifications. A total of 54 scenarios were <span class="hlt">simulated</span> to generate data related to key parameters that determine wake behavior. Of particular interest are wake age characteristics that can be used to evaluate both time- and distance- based in-trail separation concepts for all aircraft wake-class combinations. A simple first-order difference model was developed to enable the computation of wake parameter estimates for aircraft models having weight, wingspan and speed characteristics similar to those of the nine aircraft modeled in this work.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011AIPC.1333..348S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011AIPC.1333..348S"><span id="translatedtitle">DSMC <span class="hlt">Simulation</span> of Binary Rarefied Gas Flows between <span class="hlt">Parallel</span> Plates and Comparison to Other Methods</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Szalmas, L.</p> <p>2011-05-01</p> <p>The direct <span class="hlt">simulation</span> Monte-Carlo (DSMC) method has been developed to solve the Boltzmann equation for binary gas mixtures with hard-sphere molecules. The method is applied for pressure and concentration driven flows between two <span class="hlt">parallel</span> plates. The flow in both cases is maintained by external force, of which expression is derived from the linearized description of the flow. <span class="hlt">Simulations</span> have been performed in the low Mach number limit in order to test the method against the accurate solution of the linearzied Boltzmann equation (LBE) with hard-sphere molecules. Very good agreement is obtained between the two situations. The results provided by the present method have also been compared to the corresponding ones of the McCormack kinetic model. It is shown that the agreement between the results obtained from the DSMC method with hard-sphere molecules and the McCormack kinetic model is satisfactory. Hence, it is concluded that the McCormack kinetic model provides reliable results for isothermal flows in comparison to the linearized Boltzmann equation for hard-sphere gases.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3699968','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3699968"><span id="translatedtitle">A <span class="hlt">parallel</span> overset-curvilinear-immersed boundary framework for <span class="hlt">simulating</span> complex 3D incompressible flows</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Borazjani, Iman; Ge, Liang; Le, Trung; Sotiropoulos, Fotis</p> <p>2013-01-01</p> <p>We develop an overset-curvilinear immersed boundary (overset-CURVIB) method in a general non-inertial frame of reference to <span class="hlt">simulate</span> a wide range of challenging biological flow problems. The method incorporates overset-curvilinear grids to efficiently handle multi-connected geometries and increase the resolution locally near immersed boundaries. Complex bodies undergoing arbitrarily large deformations may be embedded within the overset-curvilinear background grid and treated as sharp interfaces using the curvilinear immersed boundary (CURVIB) method (Ge and Sotiropoulos, Journal of Computational Physics, 2007). The incompressible flow equations are formulated in a general non-inertial frame of reference to enhance the overall versatility and efficiency of the numerical approach. Efficient search algorithms to identify areas requiring blanking, donor cells, and interpolation coefficients for constructing the boundary conditions at grid interfaces of the overset grid are developed and implemented using efficient <span class="hlt">parallel</span> computing communication strategies to transfer information among sub-domains. The governing equations are discretized using a second-order accurate finite-volume approach and integrated in time via an efficient fractional-step method. Various strategies for ensuring globally conservative interpolation at grid interfaces suitable for incompressible flow fractional step methods are implemented and evaluated. The method is verified and validated against experimental data, and its capabilities are demonstrated by <span class="hlt">simulating</span> the flow past multiple aquatic swimmers and the systolic flow in an anatomic left ventricle with a mechanical heart valve implanted in the aortic position. PMID:23833331</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23833331','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23833331"><span id="translatedtitle">A <span class="hlt">parallel</span> overset-curvilinear-immersed boundary framework for <span class="hlt">simulating</span> complex 3D incompressible flows.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Borazjani, Iman; Ge, Liang; Le, Trung; Sotiropoulos, Fotis</p> <p>2013-04-01</p> <p>We develop an overset-curvilinear immersed boundary (overset-CURVIB) method in a general non-inertial frame of reference to <span class="hlt">simulate</span> a wide range of challenging biological flow problems. The method incorporates overset-curvilinear grids to efficiently handle multi-connected geometries and increase the resolution locally near immersed boundaries. Complex bodies undergoing arbitrarily large deformations may be embedded within the overset-curvilinear background grid and treated as sharp interfaces using the curvilinear immersed boundary (CURVIB) method (Ge and Sotiropoulos, Journal of Computational Physics, 2007). The incompressible flow equations are formulated in a general non-inertial frame of reference to enhance the overall versatility and efficiency of the numerical approach. Efficient search algorithms to identify areas requiring blanking, donor cells, and interpolation coefficients for constructing the boundary conditions at grid interfaces of the overset grid are developed and implemented using efficient <span class="hlt">parallel</span> computing communication strategies to transfer information among sub-domains. The governing equations are discretized using a second-order accurate finite-volume approach and integrated in time via an efficient fractional-step method. Various strategies for ensuring globally conservative interpolation at grid interfaces suitable for incompressible flow fractional step methods are implemented and evaluated. The method is verified and validated against experimental data, and its capabilities are demonstrated by <span class="hlt">simulating</span> the flow past multiple aquatic swimmers and the systolic flow in an anatomic left ventricle with a mechanical heart valve implanted in the aortic position. PMID:23833331</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/28186','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/28186"><span id="translatedtitle">Automated integration of genomic physical mapping data via <span class="hlt">parallel</span> <span class="hlt">simulated</span> annealing</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Slezak, T.</p> <p>1994-06-01</p> <p>The Human Genome Center at the Lawrence Livermore National Laboratory (LLNL) is nearing closure on a high-resolution physical map of human chromosome 19. We have build automated tools to assemble 15,000 fingerprinted cosmid clones into 800 contigs with minimal spanning paths identified. These islands are being ordered, oriented, and spanned by a variety of other techniques including: Fluorescence Insitu Hybridization (FISH) at 3 levels of resolution, ECO restriction fragment mapping across all contigs, and a multitude of different hybridization and PCR techniques to link cosmid, YAC, AC, PAC, and Pl clones. The FISH data provide us with partial order and distance data as well as orientation. We made the observation that map builders need a much rougher presentation of data than do map readers; the former wish to see raw data since these can expose errors or interesting biology. We further noted that by ignoring our length and distance data we could simplify our problem into one that could be readily attacked with optimization techniques. The data integration problem could then be seen as an M x N ordering of our N cosmid clones which ``intersect`` M larger objects by defining ``intersection`` to mean either contig/map membership or hybridization results. Clearly, the goal of making an integrated map is now to rearrange the N cosmid clone ``columns`` such that the number of gaps on the object ``rows`` are minimized. Our FISH partially-ordered cosmid clones provide us with a set of constraints that cannot be violated by the rearrangement process. We solved the optimization problem via <span class="hlt">simulated</span> annealing performed on a network of 40+ Unix machines in <span class="hlt">parallel</span>, using a server/client model built on explicit socket calls. For current maps we can create a map in about 4 hours on the <span class="hlt">parallel</span> net versus 4+ days on a single workstation. Our biologists are now using this software on a daily basis to guide their efforts toward final closure.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19930002341','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19930002341"><span id="translatedtitle">Direct numerical <span class="hlt">simulation</span> of instabilities in <span class="hlt">parallel</span> flow with spherical roughness elements</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Deanna, R. G.</p> <p>1992-01-01</p> <p>Results from a direct numerical <span class="hlt">simulation</span> of laminar flow over a flat surface with spherical roughness elements using a spectral-element method are given. The numerical <span class="hlt">simulation</span> approximates roughness as a cellular pattern of identical spheres protruding from a smooth wall. Periodic boundary conditions on the domain's horizontal faces <span class="hlt">simulate</span> an infinite array of roughness elements extending in the streamwise and spanwise directions, which implies the <span class="hlt">parallel</span>-flow assumption, and results in a closed domain. A body force, designed to yield the horizontal Blasius velocity in the absence of roughness, sustains the flow. Instabilities above a critical Reynolds number reveal negligible oscillations in the recirculation regions behind each sphere and in the free stream, high-amplitude oscillations in the layer directly above the spheres, and a mean profile with an inflection point near the sphere's crest. The inflection point yields an unstable layer above the roughness (where U''(y) is less than 0) and a stable region within the roughness (where U''(y) is greater than 0). Evidently, the instability begins when the low-momentum or wake region behind an element, being the region most affected by disturbances (purely numerical in this case), goes unstable and moves. In compressible flow with periodic boundaries, this motion sends disturbances to all regions of the domain. In the unstable layer just above the inflection point, the disturbances grow while being carried downstream with a propagation speed equal to the local mean velocity; they do not grow amid the low energy region near the roughness patch. The most amplified disturbance eventually arrives at the next roughness element downstream, perturbing its wake and inducing a global response at a frequency governed by the streamwise spacing between spheres and the mean velocity of the most amplified layer.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1995PhDT.......219M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1995PhDT.......219M"><span id="translatedtitle">Three-Dimensional <span class="hlt">Parallel</span> Lattice Boltzmann Hydrodynamic <span class="hlt">Simulations</span> of Turbulent Flows in Interstellar Dark Clouds</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Muders, Dirk</p> <p>1995-08-01</p> <p>Exploring the clumpy and filamentary structure of interstellar molecular clouds is one of the key problems of modern astrophysics. So far, we have little knowledge of the physical processes that cause the structure, but turbulence is suspected to be essential. In this thesis I study turbulent flows and how they contribute to the structure of interstellar dark clouds. To this end, three-dimensional numerical hydrodynamic <span class="hlt">simulations</span> are needed since the detailed turbulent spatial and velocity structure cannot be analytically calculated. I employ the ``Lattice Boltzmann Method'', a recently developed numerical method which solves the Boltzmann equation in a discretized phase space. Mesoscopic particle packets move with fixed velocities on a Cartesian lattice and at each time step they exchange mass according to given rules. Because of its mainly local operations the method is well suited for application on <span class="hlt">parallel</span> or clustered computers. As part of my thesis I have developed a <span class="hlt">parallelized</span> ``Lattice Boltzmann Method'' hydrodynamics code. I have improved the numerical stability for Reynolds numbers of up to 104.5 and Mach numbers of up to 0.9 and I have extended the method to include a second miscible fluid phase. The code has been used on the three currently most powerful workstations at the ``Max-Planck-Institut für Radioastronomie'' in Bonn and on the massively <span class="hlt">parallel</span> mainframe CM-5 at the ``Gesellschaft für Mathematik und Datenverarbeitung'' in St. Augustin. The <span class="hlt">simulations</span> consist of collimated shear flows and the motion of molecular clumps through an ambient medium. The dependence of the emerging structure on Reynolds and Mach numbers is studied. The main results are (1) that distinct clumps and filaments appear only at the transition between laminar and fully turbulent flow at Reynolds numbers between 500 and 5000 and (2) that subsonic viscous shear flows are capable of producing the dark cloud velocity structure. The unexpectedly low Reynolds numbers can be explained by the enlargement of the gas viscosity by magnetic fields of the order 10μ G and the strong coupling between ionized and neutral gas. The occurrence of well-defined structure between the highly ordered laminar and the chaotic turbulent flow regimes can be interpreted in the framework of the ``Edge of Chaos'', i.e. the tendency of complex systems to show self-organization only at the transition between phases. In order to compare the <span class="hlt">simulations</span> with observed data I have used the 100m radio telescope at Effelsberg to map the ground transition of sulphur monoxide toward the quiescent cold dark cloud L1512. The data show a clumpy structure that I interpret as a turbulent tail behind the dense central cloud. This thesis is available on the World Wide Web. The PostScript file including 15 full color figures can be obtained at: http://WWW.MPIfR-Bonn.MPG.de/iram/dmuders/dmuders.html</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/5289523','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/5289523"><span id="translatedtitle">Particle <span class="hlt">simulation</span> on radio frequency stabilization of flute modes in a tandem mirror. I. <span class="hlt">Parallel</span> antenna</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Kadoya, Y.; Abe, H.</p> <p>1988-04-01</p> <p>A two- and one-half-dimensional electromagnetic particle code (PS2M) (H. Abe and S. Nakajima, J. Phys. Soc. Jpn. 53, xxx (1987)) is used to study how an electric field applied <span class="hlt">parallel</span> to the magnetic field affects the radio frequency stabilization of flute modes in a tandem mirror plasma. The <span class="hlt">parallel</span> electric field E/sub <span class="hlt">parallel</span>/ perturbs the electron velocity v/sub <span class="hlt">parallel</span>/ <span class="hlt">parallel</span> to the magnetic field and also induces a perpendicular magnetic field perturbation B/sub perpendicular/. The unstable growth of the flute mode in the absence of such a radio frequency electric field is first studied as a basis for comparison. The ponderomotive force originating from the time-averaged product <v/sub <span class="hlt">parallel</span>/B/sub perpendicular/> is then shown to stabilize the flute modes. The stabilizing wave power threshold, the frequency dependency, and the dependence on delchemically bondE/sub <span class="hlt">parallel</span>/chemically bond all agree with the theoretical predictions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20040111318','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20040111318"><span id="translatedtitle">Scalability of <span class="hlt">Parallel</span> Spatial Direct Numerical <span class="hlt">Simulations</span> on Intel Hypercube and IBM SP1 and SP2</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Joslin, Ronald D.; Hanebutte, Ulf R.; Zubair, Mohammad</p> <p>1995-01-01</p> <p>The implementation and performance of a <span class="hlt">parallel</span> spatial direct numerical <span class="hlt">simulation</span> (PSDNS) approach on the Intel iPSC/860 hypercube and IBM SP1 and SP2 <span class="hlt">parallel</span> computers is documented. Spatially evolving disturbances associated with the laminar-to-turbulent transition in boundary-layer flows are computed with the PSDNS code. The feasibility of using the PSDNS to perform transition studies on these computers is examined. The results indicate that PSDNS approach can effectively be <span class="hlt">parallelized</span> on a distributed-memory <span class="hlt">parallel</span> machine by remapping the distributed data structure during the course of the calculation. Scalability information is provided to estimate computational costs to match the actual costs relative to changes in the number of grid points. By increasing the number of processors, slower than linear speedups are achieved with optimized (machine-dependent library) routines. This slower than linear speedup results because the computational cost is dominated by FFT routine, which yields less than ideal speedups. By using appropriate compile options and optimized library routines on the SP1, the serial code achieves 52-56 M ops on a single node of the SP1 (45 percent of theoretical peak performance). The actual performance of the PSDNS code on the SP1 is evaluated with a "real world" <span class="hlt">simulation</span> that consists of 1.7 million grid points. One time step of this <span class="hlt">simulation</span> is calculated on eight nodes of the SP1 in the same time as required by a Cray Y/MP supercomputer. For the same <span class="hlt">simulation</span>, 32-nodes of the SP1 and SP2 are required to reach the performance of a Cray C-90. A 32 node SP1 (SP2) configuration is 2.9 (4.6) times faster than a Cray Y/MP for this <span class="hlt">simulation</span>, while the hypercube is roughly 2 times slower than the Y/MP for this application. KEY WORDS: Spatial direct numerical <span class="hlt">simulations</span>; incompressible viscous flows; spectral methods; finite differences; <span class="hlt">parallel</span> computing.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/20674066','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/20674066"><span id="translatedtitle"><span class="hlt">Parallelized</span> computation for computer <span class="hlt">simulation</span> of electrocardiograms using personal computers with multi-core CPU and general-purpose GPU.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Shen, Wenfeng; Wei, Daming; Xu, Weimin; Zhu, Xin; Yuan, Shizhong</p> <p>2010-10-01</p> <p>Biological computations like electrocardiological modelling and <span class="hlt">simulation</span> usually require high-performance computing environments. This paper introduces an implementation of <span class="hlt">parallel</span> computation for computer <span class="hlt">simulation</span> of electrocardiograms (ECGs) in a personal computer environment with an Intel CPU of Core (TM) 2 Quad Q6600 and a GPU of Geforce 8800GT, with software support by OpenMP and CUDA. It was tested in three <span class="hlt">parallelization</span> device setups: (a) a four-core CPU without a general-purpose GPU, (b) a general-purpose GPU plus 1 core of CPU, and (c) a four-core CPU plus a general-purpose GPU. To effectively take advantage of a multi-core CPU and a general-purpose GPU, an algorithm based on load-prediction dynamic scheduling was developed and applied to setting (c). In the <span class="hlt">simulation</span> with 1600 time steps, the speedup of the <span class="hlt">parallel</span> computation as compared to the serial computation was 3.9 in setting (a), 16.8 in setting (b), and 20.0 in setting (c). This study demonstrates that a current PC with a multi-core CPU and a general-purpose GPU provides a good environment for <span class="hlt">parallel</span> computations in biological modelling and <span class="hlt">simulation</span> studies. PMID:20674066</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20020073408','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20020073408"><span id="translatedtitle">A Three-Dimensional <span class="hlt">Parallel</span> Time-Accurate Turbopump <span class="hlt">Simulation</span> Procedure Using Overset Grid System</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Kiris, Cetin; Chan, William; Kwak, Dochan</p> <p>2002-01-01</p> <p>The objective of the current effort is to provide a computational framework for design and analysis of the entire fuel supply system of a liquid rocket engine, including high-fidelity unsteady turbopump flow analysis. This capability is needed to support the design of pump sub-systems for advanced space transportation vehicles that are likely to involve liquid propulsion systems. To date, computational tools for design/analysis of turbopump flows are based on relatively lower fidelity methods. An unsteady, three-dimensional viscous flow analysis tool involving stationary and rotational components for the entire turbopump assembly has not been available for real-world engineering applications. The present effort provides developers with information such as transient flow phenomena at start up, and nonuniform inflows, and will eventually impact on system vibration and structures. In the proposed paper, the progress toward the capability of complete <span class="hlt">simulation</span> of the turbo-pump for a liquid rocket engine is reported. The Space Shuttle Main Engine (SSME) turbo-pump is used as a test case for evaluation of the hybrid MPI/Open-MP and MLP versions of the INS3D code. CAD to solution auto-scripting capability is being developed for turbopump applications. The relative motion of the grid systems for the rotor-stator interaction was obtained using overset grid techniques. Unsteady computations for the SSME turbo-pump, which contains 114 zones with 34.5 million grid points, are carried out on Origin 3000 systems at NASA Ames Research Center. Results from these time-accurate <span class="hlt">simulations</span> with moving boundary capability are presented along with the performance of <span class="hlt">parallel</span> versions of the code.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/988956','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/988956"><span id="translatedtitle">Mesoscale <span class="hlt">Simulations</span> of Particulate Flows with <span class="hlt">Parallel</span> Distributed Lagrange Multiplier Technique</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Kanarska, Y</p> <p>2010-03-24</p> <p>Fluid particulate flows are common phenomena in nature and industry. Modeling of such flows at micro and macro levels as well establishing relationships between these approaches are needed to understand properties of the particulate matter. We propose a computational technique based on the direct numerical <span class="hlt">simulation</span> of the particulate flows. The numerical method is based on the distributed Lagrange multiplier technique following the ideas of Glowinski et al. (1999). Each particle is explicitly resolved on an Eulerian grid as a separate domain, using solid volume fractions. The fluid equations are solved through the entire computational domain, however, Lagrange multiplier constrains are applied inside the particle domain such that the fluid within any volume associated with a solid particle moves as an incompressible rigid body. Mutual forces for the fluid-particle interactions are internal to the system. Particles interact with the fluid via fluid dynamic equations, resulting in implicit fluid-rigid-body coupling relations that produce realistic fluid flow around the particles (i.e., no-slip boundary conditions). The particle-particle interactions are implemented using explicit force-displacement interactions for frictional inelastic particles similar to the DEM method of Cundall et al. (1979) with some modifications using a volume of an overlapping region as an input to the contact forces. The method is flexible enough to handle arbitrary particle shapes and size distributions. A <span class="hlt">parallel</span> implementation of the method is based on the SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) library, which allows handling of large amounts of rigid particles and enables local grid refinement. Accuracy and convergence of the presented method has been tested against known solutions for a falling sphere as well as by examining fluid flows through stationary particle beds (periodic and cubic packing). To evaluate code performance and validate particle contact physics algorithm, we performed <span class="hlt">simulations</span> of a representative experiment conducted at the University of California at Berkley for pebble flow through a narrow opening.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20020060457','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20020060457"><span id="translatedtitle">A Three Dimensional <span class="hlt">Parallel</span> Time Accurate Turbopump <span class="hlt">Simulation</span> Procedure Using Overset Grid Systems</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Kiris, Cetin; Chan, William; Kwak, Dochan</p> <p>2001-01-01</p> <p>The objective of the current effort is to provide a computational framework for design and analysis of the entire fuel supply system of a liquid rocket engine, including high-fidelity unsteady turbopump flow analysis. This capability is needed to support the design of pump sub-systems for advanced space transportation vehicles that are likely to involve liquid propulsion systems. To date, computational tools for design/analysis of turbopump flows are based on relatively lower fidelity methods. An unsteady, three-dimensional viscous flow analysis tool involving stationary and rotational components for the entire turbopump assembly has not been available for real-world engineering applications. The present effort provides developers with information such as transient flow phenomena at start up, and non-uniform inflows, and will eventually impact on system vibration and structures. In the proposed paper, the progress toward the capability of complete <span class="hlt">simulation</span> of the turbo-pump for a liquid rocket engine is reported. The Space Shuttle Main Engine (SSME) turbo-pump is used as a test case for evaluation of the hybrid MPI/Open-MP and MLP versions of the INS3D code. CAD to solution auto-scripting capability is being developed for turbopump applications. The relative motion of the grid systems for the rotor-stator interaction was obtained using overset grid techniques. Unsteady computations for the SSME turbo-pump, which contains 114 zones with 34.5 million grid points, are carried out on Origin 3000 systems at NASA Ames Research Center. Results from these time-accurate <span class="hlt">simulations</span> with moving boundary capability will be presented along with the performance of <span class="hlt">parallel</span> versions of the code.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/957425','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/957425"><span id="translatedtitle"><span class="hlt">Parallel</span> Higher-order Finite Element Method for Accurate Field Computations in Wakefield and PIC <span class="hlt">Simulations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Prudencio, E.; Schussman, G.; Uplenchwar, R.; Ko, K.; /SLAC</p> <p>2009-06-19</p> <p>Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) <span class="hlt">parallel</span> higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale <span class="hlt">simulation</span> of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell) approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li class="active"><span>22</span></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_22 --> <div id="page_23" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li class="active"><span>23</span></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="441"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/876729','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/876729"><span id="translatedtitle">Performance Evaluation of Lattice-Boltzmann Magnetohydrodynamics<span class="hlt">Simulations</span> on Modern <span class="hlt">Parallel</span> Vector Systems</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Carter, Jonathan; Oliker, Leonid</p> <p>2006-01-09</p> <p>The last decade has witnessed a rapid proliferation of superscalarcache-based microprocessors to build high-end computing (HEC) platforms, primarily because of their generality, scalability, and cost effectiveness. However, the growing gap between sustained and peak performance for full-scale scientific applications on such platforms has become major concern in high performance computing. The latest generation of custom-built <span class="hlt">parallel</span> vector systems have the potential to address this concern for numerical algorithms with sufficient regularity in their computational structure. In this work, we explore two and three dimensional implementations of a lattice-Boltzmann magnetohydrodynamics (MHD) physics application, on some of today's most powerful supercomputing platforms. Results compare performance between the vector-based Cray X1, Earth <span class="hlt">Simulator</span>, and newly-released NEC SX-8, with the commodity-based superscalar platforms of the IBM Power3, IntelItanium2, and AMD Opteron. Overall results show that the SX-8 attains unprecedented aggregate performance across our evaluated applications.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2003JKAS...36..111K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2003JKAS...36..111K"><span id="translatedtitle">Cosmic Ray Acceleration at Cosmological Shocks: Numerical <span class="hlt">Simulations</span> of CR Modified Plane-<span class="hlt">Parallel</span> Shocks</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Kang, Hyesung</p> <p>2003-09-01</p> <p>In order to explore the cosmic ray acceleration at the cosmological shocks, we have performed numerical <span class="hlt">simulations</span> of one-dimensional, plane-<span class="hlt">parallel</span>, cosmic ray (CR) modified shocks with the newly developed CRASH (Cosmic Ray Amr SHock) numerical code. Based on the hypothesis that strong Alfvén waves are self-generated by streaming CRs, the Bohm diffusion model for CRs is adopted. The code includes a plasma-physics-based ``injection'' model that transfers a small proportion of the thermal proton flux through the shock into low energy CRs for acceleration there. We found that, for strong accretion shocks with Mach numbers greater than 10, CRs can absorb most of shock kinetic energy and the accretion shock speed is reduced up to 20 %, compared to pure gas dynamic shocks. Although the amount of kinetic energy passed through accretion shocks is small, since they propagate into the low density intergalactic medium, they might possibly provide acceleration sites for ultra-high energy cosmic rays of E>1018eV. For internal/merger shocks with Mach numbers less than 3, however, the energy transfer to CRs is only about 10-20 % and so nonlinear feedback due to the CR pressure is insignificant. Considering that intracluster medium (ICM) can be shocked repeatedly, however, the CRs generated by these weak shocks could be sufficient to explain the observed non-thermal signatures from clusters of galaxies.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015JThSc..24..140D','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015JThSc..24..140D"><span id="translatedtitle"><span class="hlt">Simulation</span> and instability investigation of the flow around a cylinder between two <span class="hlt">parallel</span> walls</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Dou, Hua-Shu; Ben, An-Qing</p> <p>2015-04-01</p> <p>The two-dimensional flows around a cylinder between two <span class="hlt">parallel</span> walls at Re=40 and Re=100 are <span class="hlt">simulated</span> with computational fluid dynamics (CFD). The governing equations are Navier-Stokes equations. They are discretized with finite volume method (FVM) and the solution is iterated with PISO Algorithm. Then, the calculating results are compared with the numerical results in literature, and good agreements are obtained. After that, the mechanism of the formation of Karman vortex street is investigated and the instability of the entire flow field is analyzed with the energy gradient theory. It is found that the two eddies attached at the rear of the cylinder have no effect on the flow instability for steady flow, i.e., they don't contribute to the formation of Karman vortex street. The formation of Karman vortex street originates from the combinations of the interaction of two shear layers at two lateral sides of the cylinder and the absolute instability in the cylinder wake. For the flow with Karman vortex street, the initial instability occurs at the region in a vortex downstream of the wake and the center of a vortex firstly loses its stability in a vortex. For pressure driven flow, it is confirmed that the inflection point on the time-averaged velocity profile leads to the instability. It is concluded that the energy gradient theory is potentially applicable to study the flow stability and to reveal the mechanism of turbulent transition.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/5256735','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/5256735"><span id="translatedtitle">Monte Carlo <span class="hlt">simulation</span> of photoelectron energization in <span class="hlt">parallel</span> electric fields: Electroglow on Uranus</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Singhal, R.P.; Bhardwaj, A. )</p> <p>1991-09-01</p> <p>A Monte Carlo <span class="hlt">simulation</span> of photoelectron energization and energy degradation in H{sub 2} gas in the presence of <span class="hlt">parallel</span> electric fields has been carried out. Numerical yield spectra which contain information about the electron energy degradation process and can be used to calculate the yield for any inelastic event are obtained. The variation of yield spectra with incident electron energy, electric field, pitch angle, and cutoff limit has been studied. The yield function is employed to determine the photoelectron fluxes. H{sub 2} Lyman and Werner band excitation rates and integrated column intensity are computed for three different electric field profiles taking various low-energy cutoff limits. It is found that an electric field profile with peak value of 4 mV/m at neutral number density of 3{times}10{sup 10} cm{sup {minus}3} produces enhanced volume emission rates of H{sub 2} bands ({lambda} < 1100 {angstrom}) explaining about 20% of the observed electroglow emission on Uranus. The effect of solar zenith angle and solar cycle variation on peak excitation rate is discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012AGUFM.H13G1442S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012AGUFM.H13G1442S"><span id="translatedtitle"><span class="hlt">Simulation</span> of hydraulic fracture networks in three dimensions utilizing massively <span class="hlt">parallel</span> computing platforms</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Settgast, R. R.; Johnson, S.; Fu, P.; Walsh, S. D.; Ryerson, F. J.; Antoun, T.</p> <p>2012-12-01</p> <p>Hydraulic fracturing has been an enabling technology for commercially stimulating fracture networks for over half of a century. It has become one of the most widespread technologies for engineering subsurface fracture systems. Despite the ubiquity of this technique in the field, understanding and prediction of the hydraulic induced propagation of the fracture network in realistic, heterogeneous reservoirs has been limited. A number of developments in multiscale modeling in recent years have allowed researchers in related fields to tackle the modeling of complex fracture propagation as well as the mechanics of heterogeneous materials. These developments, combined with advances in quantifying solution uncertainties, provide possibilities for the geologic modeling community to capture both the fracturing behavior and longer-term permeability evolution of rock masses under hydraulic loading across both dynamic and viscosity-dominated regimes. Here we will demonstrate the first phase of this effort through illustrations of fully three-dimensional, tightly coupled hydromechanical <span class="hlt">simulations</span> of hydraulically induced fracture network propagation run on massively <span class="hlt">parallel</span> computing scales, and discuss preliminary results regarding the mechanisms by which fracture interactions and the accompanying changes to the stress field can lead to deleterious or beneficial changes to the fracture network.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1131524','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1131524"><span id="translatedtitle">Supporting the Development of Resilient Message Passing Applications using <span class="hlt">Simulation</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Naughton, III, Thomas J; Engelmann, Christian; Vallee, Geoffroy R; Boehm, Swen</p> <p>2014-01-01</p> <p>An emerging aspect of high-performance computing (HPC) hardware/software co-design is investigating performance under failure. The work in this paper extends the Extreme-scale <span class="hlt">Simulator</span> (xSim), which was designed for evaluating the performance of message passing interface (MPI) applications on future HPC architectures, with fault-tolerant MPI extensions proposed by the MPI Fault Tolerance Working Group. xSim permits running MPI applications with millions of concurrent MPI ranks, while observing application performance in a <span class="hlt">simulated</span> extreme-scale system using a lightweight <span class="hlt">parallel</span> <span class="hlt">discrete</span> <span class="hlt">event</span> <span class="hlt">simulation</span>. The newly added features offer user-level failure mitigation (ULFM) extensions at the <span class="hlt">simulated</span> MPI layer to support algorithm-based fault tolerance (ABFT). The presented solution permits investigating performance under failure and failure handling of ABFT solutions. The newly enhanced xSim is the very first performance tool that supports ULFM and ABFT.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015EGUGA..17.6111S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015EGUGA..17.6111S"><span id="translatedtitle">A heterogeneous and <span class="hlt">parallel</span> computing framework for high-resolution hydrodynamic <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Smith, Luke; Liang, Qiuhua</p> <p>2015-04-01</p> <p>Shock-capturing hydrodynamic models are now widely applied in the context of flood risk assessment and forecasting, accurately capturing the behaviour of surface water over ground and within rivers. Such models are generally explicit in their numerical basis, and can be computationally expensive; this has prohibited full use of high-resolution topographic data for complex urban environments, now easily obtainable through airborne altimetric surveys (LiDAR). As processor clock speed advances have stagnated in recent years, further computational performance gains are largely dependent on the use of <span class="hlt">parallel</span> processing. Heterogeneous computing architectures (e.g. graphics processing units or compute accelerator cards) provide a cost-effective means of achieving high throughput in cases where the same calculation is performed with a large input dataset. In recent years this technique has been applied successfully for flood risk mapping, such as within the national surface water flood risk assessment for the United Kingdom. We present a flexible software framework for hydrodynamic <span class="hlt">simulations</span> across multiple processors of different architectures, within multiple computer systems, enabled using OpenCL and Message Passing Interface (MPI) libraries. A finite-volume Godunov-type scheme is implemented using the HLLC approach to solving the Riemann problem, with optional extension to second-order accuracy in space and time using the MUSCL-Hancock approach. The framework is successfully applied on personal computers and a small cluster to provide considerable improvements in performance. The most significant performance gains were achieved across two servers, each containing four NVIDIA GPUs, with a mix of K20, M2075 and C2050 devices. Advantages are found with respect to decreased parametric sensitivity, and thus in reducing uncertainty, for a major fluvial flood within a large catchment during 2005 in Carlisle, England. <span class="hlt">Simulations</span> for the three-day event could be performed on a 2m grid within a few hours. In the context of a rapid pluvial flood event in Newcastle upon Tyne during 2012, the technique allows <span class="hlt">simulation</span> of inundation for a 31km2 of the city centre in less than an hour on a 2m grid; however, further grid refinement is required to fully capture important smaller flow pathways. Good agreement between the model and observed inundation is achieved for a variety of dam failure, slow fluvial inundation, rapid pluvial inundation, and defence breach scenarios in the UK.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22303583','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22303583"><span id="translatedtitle">Extending molecular <span class="hlt">simulation</span> time scales: <span class="hlt">Parallel</span> in time integrations for high-level quantum chemistry and complex force representations</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.</p> <p>2013-08-21</p> <p><span class="hlt">Parallel</span> in time <span class="hlt">simulation</span> algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are <span class="hlt">parallelized</span> by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed <span class="hlt">parallel</span> in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD <span class="hlt">simulations</span>, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The <span class="hlt">parallel</span> in time algorithms developed are tested by applying them to MD and AIMD <span class="hlt">simulations</span> of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD <span class="hlt">simulation</span> using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD <span class="hlt">simulation</span> at the MP2 level. The maximum speedup ((serial execution time)/(<span class="hlt">parallel</span> execution time) ) obtained by <span class="hlt">parallelizing</span> the Stillinger-Weber MD <span class="hlt">simulation</span> was nearly 3.0. For the AIMD MP2 <span class="hlt">simulations</span>, the algorithms achieved speedups of up to 14.3. The <span class="hlt">parallel</span> in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD <span class="hlt">simulation</span> of HCl + 4H{sub 2}O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD <span class="hlt">simulations</span> at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already <span class="hlt">parallel</span>. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) <span class="hlt">simulation</span> that had reached its maximum possible speedup in the <span class="hlt">parallelization</span> of the electronic structure calculation from 32 s/time step to 6.9 s/time step.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013JChPh.139g4114B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013JChPh.139g4114B"><span id="translatedtitle">Extending molecular <span class="hlt">simulation</span> time scales: <span class="hlt">Parallel</span> in time integrations for high-level quantum chemistry and complex force representations</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.</p> <p>2013-08-01</p> <p><span class="hlt">Parallel</span> in time <span class="hlt">simulation</span> algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0…tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are <span class="hlt">parallelized</span> by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed <span class="hlt">parallel</span> in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD <span class="hlt">simulations</span>, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The <span class="hlt">parallel</span> in time algorithms developed are tested by applying them to MD and AIMD <span class="hlt">simulations</span> of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD <span class="hlt">simulation</span> using Stillinger-Weber potentials, and a HCl + 4H2O AIMD <span class="hlt">simulation</span> at the MP2 level. The maximum speedup (serial execution time/<span class="hlt">parallel</span> execution time) obtained by <span class="hlt">parallelizing</span> the Stillinger-Weber MD <span class="hlt">simulation</span> was nearly 3.0. For the AIMD MP2 <span class="hlt">simulations</span>, the algorithms achieved speedups of up to 14.3. The <span class="hlt">parallel</span> in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD <span class="hlt">simulation</span> of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD <span class="hlt">simulations</span> at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already <span class="hlt">parallel</span>. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) <span class="hlt">simulation</span> that had reached its maximum possible speedup in the <span class="hlt">parallelization</span> of the electronic structure calculation from 32 s/time step to 6.9 s/time step.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19910022757','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19910022757"><span id="translatedtitle">Comparisons of elastic and rigid blade-element rotor models using <span class="hlt">parallel</span> processing technology for piloted <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Hill, Gary; Duval, Ronald W.; Green, John A.; Huynh, Loc C.</p> <p>1991-01-01</p> <p>A piloted comparison of rigid and aeroelastic blade-element rotor models was conducted at the Crew Station Research and Development Facility (CSRDF) at Ames Research Center. A <span class="hlt">simulation</span> development and analysis tool, FLIGHTLAB, was used to implement these models in real time using <span class="hlt">parallel</span> processing technology. Pilot comments and quantitative analysis performed both on-line and off-line confirmed that elastic degrees of freedom significantly affect perceived handling qualities. Trim comparisons show improved correlation with flight test data when elastic modes are modeled. The results demonstrate the efficiency with which the mathematical modeling sophistication of existing <span class="hlt">simulation</span> facilities can be upgraded using <span class="hlt">parallel</span> processing, and the importance of these upgrades to <span class="hlt">simulation</span> fidelity.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/7295193','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/7295193"><span id="translatedtitle">Comparison of elastic and rigid blade-element rotor models using <span class="hlt">parallel</span> processing technology for piloted <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Hill, G.; Du Val, R.W.; Green, J.A.; Huynh, L.C. Advanced Rotorcraft Technology, Inc., Mountain View, CA )</p> <p>1991-09-01</p> <p>A piloted comparison of rigid and aeroelastic blade-element rotor models was conducted at the Crew Station Research and Development Facility (CSRDF) at Ames Research Center. A <span class="hlt">simulation</span> development and analysis tool, FLIGHTLAB, was used to implement these models in real time using <span class="hlt">parallel</span> processing technology. Pilot comments and qualitative analysis performed both on-line and off-line confirmed that elastic degrees of freedom significantly affect perceived handling qualities. Trim comparisons show improved correlation with flight test data when elastic modes are modeled. The results demonstrate the efficiency with which the mathematical modeling sophistication of existing <span class="hlt">simulation</span> facilities can be upgraded using <span class="hlt">parallel</span> processing, and the importance of these upgrades to <span class="hlt">simulation</span> fidelity. 8 refs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22230809','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22230809"><span id="translatedtitle">Obtaining identical results with double precision global accuracy on different numbers of processors in <span class="hlt">parallel</span> particle Monte Carlo <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Cleveland, Mathew A. Brunner, Thomas A.; Gentile, Nicholas A.; Keasler, Jeffrey A.</p> <p>2013-10-15</p> <p>We describe and compare different approaches for achieving numerical reproducibility in photon Monte Carlo <span class="hlt">simulations</span>. Reproducibility is desirable for code verification, testing, and debugging. <span class="hlt">Parallelism</span> creates a unique problem for achieving reproducibility in Monte Carlo <span class="hlt">simulations</span> because it changes the order in which values are summed. This is a numerical problem because double precision arithmetic is not associative. <span class="hlt">Parallel</span> Monte Carlo, both domain replicated and decomposed <span class="hlt">simulations</span>, will run their particles in a different order during different runs of the same <span class="hlt">simulation</span> because the non-reproducibility of communication between processors. In addition, runs of the same <span class="hlt">simulation</span> using different domain decompositions will also result in particles being <span class="hlt">simulated</span> in a different order. In [1], a way of eliminating non-associative accumulations using integer tallies was described. This approach successfully achieves reproducibility at the cost of lost accuracy by rounding double precision numbers to fewer significant digits. This integer approach, and other extended and reduced precision reproducibility techniques, are described and compared in this work. Increased precision alone is not enough to ensure reproducibility of photon Monte Carlo <span class="hlt">simulations</span>. Non-arbitrary precision approaches require a varying degree of rounding to achieve reproducibility. For the problems investigated in this work double precision global accuracy was achievable by using 100 bits of precision or greater on all unordered sums which where subsequently rounded to double precision at the end of every time-step.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1091975','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1091975"><span id="translatedtitle">Extending molecular <span class="hlt">simulation</span> time scales: <span class="hlt">Parallel</span> in time integrations for high-level quantum chemistry and complex force representations</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.</p> <p>2013-08-21</p> <p><span class="hlt">Parallel</span> in time <span class="hlt">simulation</span> algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f , (e.g. Verlet algorithm) is available to propagate the system from time ti (trajectory positions and velocities xi = (ri; vi)) to time ti+1 (xi+1) by xi+1 = fi(xi), the dynamics problem spanning an interval from t0 : : : tM can be transformed into a root finding problem, F(X) = [xi - f (x(i-1)]i=1;M = 0, for the trajectory variables. The root finding problem is solved using a variety of optimization techniques, including quasi-Newton and preconditioned quasi-Newton optimization schemes that are all unconditionally convergent. The algorithms are <span class="hlt">parallelized</span> by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed <span class="hlt">parallel</span> in time methods is discussed and the effectiveness of various approaches to solving the root finding problem are tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD <span class="hlt">simulations</span> such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The <span class="hlt">parallel</span> in time algorithms developed are tested by applying them to MD and AIMD <span class="hlt">simulations</span> of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD <span class="hlt">simulation</span> using Stillinger-Weber potentials, and a HCl+4H2O AIMD <span class="hlt">simulation</span> at the MP2 level. The maximum speedup obtained by <span class="hlt">parallelizing</span> the Stillinger-Weber MD <span class="hlt">simulation</span> was nearly 3.0. For the AIMD MP2 <span class="hlt">simulations</span> the algorithms achieved speedups of up to 14.3. The <span class="hlt">parallel</span> in time algorithms can be implemented in a distributed computing environment using very slow TCP/IP networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD <span class="hlt">simulation</span> of HCl+4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD <span class="hlt">simulations</span> at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already <span class="hlt">parallel</span>. By using these algorithms we are able to reduce the cost of a MP2/6-311++G(2d,2p) <span class="hlt">simulation</span> that had reached its maximum possible speedup in the <span class="hlt">parallelization</span> of the electronic structure calculation from 32 seconds per time step to 6.9 seconds per time step.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23968079','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23968079"><span id="translatedtitle">Extending molecular <span class="hlt">simulation</span> time scales: <span class="hlt">Parallel</span> in time integrations for high-level quantum chemistry and complex force representations.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Bylaska, Eric J; Weare, Jonathan Q; Weare, John H</p> <p>2013-08-21</p> <p><span class="hlt">Parallel</span> in time <span class="hlt">simulation</span> algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are <span class="hlt">parallelized</span> by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed <span class="hlt">parallel</span> in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD <span class="hlt">simulations</span>, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The <span class="hlt">parallel</span> in time algorithms developed are tested by applying them to MD and AIMD <span class="hlt">simulations</span> of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD <span class="hlt">simulation</span> using Stillinger-Weber potentials, and a HCl + 4H2O AIMD <span class="hlt">simulation</span> at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by <span class="hlt">parallelizing</span> the Stillinger-Weber MD <span class="hlt">simulation</span> was nearly 3.0. For the AIMD MP2 <span class="hlt">simulations</span>, the algorithms achieved speedups of up to 14.3. The <span class="hlt">parallel</span> in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD <span class="hlt">simulation</span> of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD <span class="hlt">simulations</span> at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already <span class="hlt">parallel</span>. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) <span class="hlt">simulation</span> that had reached its maximum possible speedup in the <span class="hlt">parallelization</span> of the electronic structure calculation from 32 s/time step to 6.9 s/time step. PMID:23968079</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014EGUGA..16.2584S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014EGUGA..16.2584S"><span id="translatedtitle"><span class="hlt">Parallel</span> Processing of Numerical Tsunami <span class="hlt">Simulations</span> on a High Performance Cluster based on the GDAL Library</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Schroeder, Matthias; Jankowski, Cedric; Hammitzsch, Martin; Wächter, Joachim</p> <p>2014-05-01</p> <p>Thousands of numerical tsunami <span class="hlt">simulations</span> allow the computation of inundation and run-up along the coast for vulnerable areas over the time. A so-called Matching Scenario Database (MSDB) [1] contains this large number of <span class="hlt">simulations</span> in text file format. In order to visualize these wave propagations the scenarios have to be reprocessed automatically. In the TRIDEC project funded by the seventh Framework Programme of the European Union a Virtual Scenario Database (VSDB) and a Matching Scenario Database (MSDB) were established amongst others by the working group of the University of Bologna (UniBo) [1]. One part of TRIDEC was the developing of a new generation of a Decision Support System (DSS) for tsunami Early Warning Systems (TEWS) [2]. A working group of the GFZ German Research Centre for Geosciences was responsible for developing the Command and Control User Interface (CCUI) as central software application which support operator activities, incident management and message disseminations. For the integration and visualization in the CCUI, the numerical tsunami <span class="hlt">simulations</span> from MSDB must be converted into the shapefiles format. The usage of shapefiles enables a much easier integration into standard Geographic Information Systems (GIS). Since also the CCUI is based on two widely used open source products (GeoTools library and uDig), whereby the integration of shapefiles is provided by these libraries a priori. In this case, for an example area around the Western Iberian margin several thousand tsunami variations were processed. Due to the mass of data only a program-controlled process was conceivable. In order to optimize the computing efforts and operating time the use of an existing GFZ High Performance Computing Cluster (HPC) had been chosen. Thus, a geospatial software was sought after that is capable for <span class="hlt">parallel</span> processing. The FOSS tool Geospatial Data Abstraction Library (GDAL/OGR) was used to match the coordinates with the wave heights and generates the different shapefiles for certain time steps. The shapefiles contain afterwards lines for visualizing the isochrones of the wave propagation and moreover, data about the maximum wave height and the Estimated Time of Arrival (ETA) at the coast. Our contribution shows the entire workflow and the visualizing results of the-processing for the example region Western Iberian ocean margin. [1] Armigliato A., Pagnoni G., Zaniboni F, Tinti S. (2013), Database of tsunami scenario <span class="hlt">simulations</span> for Western Iberia: a tool for the TRIDEC Project Decision Support System for tsunami early warning, Vol. 15, EGU2013-5567, EGU General Assembly 2013, Vienna (Austria). [2] Löwe, P., Wächter, J., Hammitzsch, M., Lendholt, M., Häner, R. (2013): The Evolution of Service-oriented Disaster Early Warning Systems in the TRIDEC Project, 23rd International Ocean and Polar Engineering Conference - ISOPE-2013, Anchorage (USA).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010EGUGA..12.7428P','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010EGUGA..12.7428P"><span id="translatedtitle">Efficient <span class="hlt">parallel</span> seismic <span class="hlt">simulations</span> including topography and 3-D material heterogeneities on locally refined composite grids</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Petersson, Anders; Rodgers, Arthur</p> <p>2010-05-01</p> <p>The finite difference method on a uniform Cartesian grid is a highly efficient and easy to implement technique for solving the elastic wave equation in seismic applications. However, the spacing in a uniform Cartesian grid is fixed throughout the computational domain, whereas the resolution requirements in realistic seismic <span class="hlt">simulations</span> usually are higher near the surface than at depth. This can be seen from the well-known formula h ≤ L-P which relates the grid spacing h to the wave length L, and the required number of grid points per wavelength P for obtaining an accurate solution. The compressional and shear wave lengths in the earth generally increase with depth and are often a factor of ten larger below the Moho discontinuity (at about 30 km depth), than in sedimentary basins near the surface. A uniform grid must have a grid spacing based on the small wave lengths near the surface, which results in over-resolving the solution at depth. As a result, the number of points in a uniform grid is unnecessarily large. In the wave propagation project (WPP) code, we address the over-resolution-at-depth issue by generalizing our previously developed single grid finite difference scheme to work on a composite grid consisting of a set of structured rectangular grids of different spacings, with hanging nodes on the grid refinement interfaces. The computational domain in a regional seismic <span class="hlt">simulation</span> often extends to depth 40-50 km. Hence, using a refinement ratio of two, we need about three grid refinements from the bottom of the computational domain to the surface, to keep the local grid size in approximate parity with the local wave lengths. The challenge of the composite grid approach is to find a stable and accurate method for coupling the solution across the grid refinement interface. Of particular importance is the treatment of the solution at the hanging nodes, i.e., the fine grid points which are located in between coarse grid points. WPP implements a new, energy conserving, coupling procedure for the elastic wave equation at grid refinement interfaces. When used together with our single grid finite difference scheme, it results in a method which is provably stable, without artificial dissipation, for arbitrary heterogeneous isotropic elastic materials. The new coupling procedure is based on satisfying the summation-by-parts principle across refinement interfaces. From a practical standpoint, an important advantage of the proposed method is the absence of tunable numerical parameters, which seldom are appreciated by application experts. In WPP, the composite grid discretization is combined with a curvilinear grid approach that enables accurate modeling of free surfaces on realistic (non-planar) topography. The overall method satisfies the summation-by-parts principle and is stable under a CFL time step restriction. A feature of great practical importance is that WPP automatically generates the composite grid based on the user provided topography and the depths of the grid refinement interfaces. The WPP code has been verified extensively, for example using the method of manufactured solutions, by solving Lamb's problem, by solving various layer over half- space problems and comparing to semi-analytic (FK) results, and by <span class="hlt">simulating</span> scenario earthquakes where results from other seismic <span class="hlt">simulation</span> codes are available. WPP has also been validated against seismographic recordings of moderate earthquakes. WPP performs well on large <span class="hlt">parallel</span> computers and has been run on up to 32,768 processors using about 26 Billion grid points (78 Billion DOF) and 41,000 time steps. WPP is an open source code that is available under the Gnu general public license.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4696414','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4696414"><span id="translatedtitle">GENESIS: a hybrid-<span class="hlt">parallel</span> and multi-scale molecular dynamics <span class="hlt">simulator</span> with enhanced sampling algorithms for biomolecular and cellular <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji</p> <p>2015-01-01</p> <p>GENESIS (Generalized-Ensemble <span class="hlt">Simulation</span> System) is a new software package for molecular dynamics (MD) <span class="hlt">simulations</span> of macromolecules. It has two MD <span class="hlt">simulators</span>, called ATDYN and SPDYN. ATDYN is <span class="hlt">parallelized</span> based on an atomic decomposition algorithm for the <span class="hlt">simulations</span> of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly <span class="hlt">parallelized</span> based on a domain decomposition scheme, allowing large-scale MD <span class="hlt">simulations</span> on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both <span class="hlt">simulators</span> to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly <span class="hlt">parallel</span> performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of <span class="hlt">parallel</span> input/output files, also contribute to the performance. We show the REMD <span class="hlt">simulation</span> results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 PMID:26753008</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1115367','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1115367"><span id="translatedtitle">SCORPIO: A Scalable Two-Phase <span class="hlt">Parallel</span> I/O Library With Application To A Large Scale Subsurface <span class="hlt">Simulator</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Sreepathi, Sarat; Sripathi, Vamsi; Mills, Richard T; Hammond, Glenn; Mahinthakumar, Kumar</p> <p>2013-01-01</p> <p>Inefficient <span class="hlt">parallel</span> I/O is known to be a major bottleneck among scientific applications employed on supercomputers as the number of processor cores grows into the thousands. Our prior experience indicated that <span class="hlt">parallel</span> I/O libraries such as HDF5 that rely on MPI-IO do not scale well beyond 10K processor cores, especially on <span class="hlt">parallel</span> file systems (like Lustre) with single point of resource contention. Our previous optimization efforts for a massively <span class="hlt">parallel</span> multi-phase and multi-component subsurface <span class="hlt">simulator</span> (PFLOTRAN) led to a two-phase I/O approach at the application level where a set of designated processes participate in the I/O process by splitting the I/O operation into a communication phase and a disk I/O phase. The designated I/O processes are created by splitting the MPI global communicator into multiple sub-communicators. The root process in each sub-communicator is responsible for performing the I/O operations for the entire group and then distributing the data to rest of the group. This approach resulted in over 25X speedup in HDF I/O read performance and 3X speedup in write performance for PFLOTRAN at over 100K processor cores on the ORNL Jaguar supercomputer. This research describes the design and development of a general purpose <span class="hlt">parallel</span> I/O library, SCORPIO (SCalable block-ORiented <span class="hlt">Parallel</span> I/O) that incorporates our optimized two-phase I/O approach. The library provides a simplified higher level abstraction to the user, sitting atop existing <span class="hlt">parallel</span> I/O libraries (such as HDF5) and implements optimized I/O access patterns that can scale on larger number of processors. Performance results with standard benchmark problems and PFLOTRAN indicate that our library is able to maintain the same speedups as before with the added flexibility of being applicable to a wider range of I/O intensive applications.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20090007630','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20090007630"><span id="translatedtitle">A Framework for <span class="hlt">Parallel</span> Unstructured Grid Generation for Complex Aerodynamic <span class="hlt">Simulations</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Zagaris, George; Pirzadeh, Shahyar Z.; Chrisochoides, Nikos</p> <p>2009-01-01</p> <p>A framework for <span class="hlt">parallel</span> unstructured grid generation targeting both shared memory multi-processors and distributed memory architectures is presented. The two fundamental building-blocks of the framework consist of: (1) the Advancing-Partition (AP) method used for domain decomposition and (2) the Advancing Front (AF) method used for mesh generation. Starting from the surface mesh of the computational domain, the AP method is applied recursively to generate a set of sub-domains. Next, the sub-domains are meshed in <span class="hlt">parallel</span> using the AF method. The recursive nature of domain decomposition naturally maps to a divide-and-conquer algorithm which exhibits inherent <span class="hlt">parallelism</span>. For the <span class="hlt">parallel</span> implementation, the Master/Worker pattern is employed to dynamically balance the varying workloads of each task on the set of available CPUs. Performance results by this approach are presented and discussed in detail as well as future work and improvements.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/585029','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/585029"><span id="translatedtitle">Infrastructure for distributed enterprise <span class="hlt">simulation</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Johnson, M.M.; Yoshimura, A.S.; Goldsby, M.E.</p> <p>1998-01-01</p> <p>Traditional <span class="hlt">discrete-event</span> <span class="hlt">simulations</span> employ an inherently sequential algorithm and are run on a single computer. However, the demands of many real-world problems exceed the capabilities of sequential <span class="hlt">simulation</span> systems. Often the capacity of a computer`s primary memory limits the size of the models that can be handled, and in some cases <span class="hlt">parallel</span> execution on multiple processors could significantly reduce the <span class="hlt">simulation</span> time. This paper describes the development of an Infrastructure for Distributed Enterprise <span class="hlt">Simulation</span> (IDES) - a large-scale portable <span class="hlt">parallel</span> <span class="hlt">simulation</span> framework developed to support Sandia National Laboratories` mission in stockpile stewardship. IDES is based on the Breathing-Time-Buckets synchronization protocol, and maps a message-based model of distributed computing onto an object-oriented programming model. IDES is portable across heterogeneous computing architectures, including single-processor systems, networks of workstations and multi-processor computers with shared or distributed memory. The system provides a simple and sufficient application programming interface that can be used by scientists to quickly model large-scale, complex enterprise systems. In the background and without involving the user, IDES is capable of making dynamic use of idle processing power available throughout the enterprise network. 16 refs., 14 figs.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li class="active"><span>23</span></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_23 --> <div id="page_24" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li class="active"><span>24</span></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="461"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27045833','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27045833"><span id="translatedtitle">Process <span class="hlt">Simulation</span> of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively <span class="hlt">Parallel</span> Computing Platforms.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ganesan, Narayan; Li, Jie; Sharma, Vishakha; Jiang, Hanyu; Compagnoni, Adriana</p> <p>2016-01-01</p> <p>Biological systems encompass complexity that far surpasses many artificial systems. Modeling and <span class="hlt">simulation</span> of large and complex biochemical pathways is a computationally intensive challenge. Traditional tools, such as ordinary differential equations, partial differential equations, stochastic master equations, and Gillespie type methods, are all limited either by their modeling fidelity or computational efficiency or both. In this work, we present a scalable computational framework based on modeling biochemical reactions in explicit 3D space, that is suitable for studying the behavior of large and complex biological pathways. The framework is designed to exploit <span class="hlt">parallelism</span> and scalability offered by commodity massively <span class="hlt">parallel</span> processors such as the graphics processing units (GPUs) and other <span class="hlt">parallel</span> computing platforms. The reaction modeling in 3D space is aimed at enhancing the realism of the model compared to traditional modeling tools and framework. We introduce the <span class="hlt">Parallel</span> Select algorithm that is key to breaking the sequential bottleneck limiting the performance of most other tools designed to study biochemical interactions. The algorithm is designed to be computationally tractable, handle hundreds of interacting chemical species and millions of independent agents by considering all-particle interactions within the system. We also present an implementation of the framework on the popular graphics processing units and apply it to the <span class="hlt">simulation</span> study of JAK-STAT Signal Transduction Pathway. The computational framework will offer a deeper insight into various biological processes within the cell and help us observe key events as they unfold in space and time. This will advance the current state-of-the-art in <span class="hlt">simulation</span> study of large scale biological systems and also enable the realistic <span class="hlt">simulation</span> study of macro-biological cultures, where inter-cellular interactions are prevalent. PMID:27045833</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2801163','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2801163"><span id="translatedtitle">A <span class="hlt">Parallel</span> Adaptive Finite Element Method for the <span class="hlt">Simulation</span> of Photon Migration with the Radiative-Transfer-Based Model</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Lu, Yujie; Chatziioannou, Arion F.</p> <p>2009-01-01</p> <p>Whole-body optical molecular imaging of mouse models in preclinical research is rapidly developing in recent years. In this context, it is essential and necessary to develop novel <span class="hlt">simulation</span> methods of light propagation for optical imaging, especially when a priori knowledge, large-volume domain and a wide-range of optical properties need to be considered in the reconstruction algorithm. In this paper, we propose a three dimensional <span class="hlt">parallel</span> adaptive finite element method with simplified spherical harmonics (SPN) approximation to <span class="hlt">simulate</span> optical photon propagation in large-volumes of heterogenous tissues. The <span class="hlt">simulation</span> speed is significantly improved by a posteriori <span class="hlt">parallel</span> adaptive mesh refinement and dynamic mesh repartitioning. Compared with the diffusion equation and the Monte Carlo methods, the SPN method shows improved performance and the necessity of high-order approximation in heterogeneous domains. Optimal solver selection and time-costing analysis in real mouse geometry further improve the performance of the proposed algorithm and show the superiority of the proposed <span class="hlt">parallel</span> adaptive framework for whole-body optical molecular imaging in murine models. PMID:20052300</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/86949','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/86949"><span id="translatedtitle">Large-eddy <span class="hlt">simulation</span> of the Rayleigh-Taylor instability on a massively <span class="hlt">parallel</span> computer</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Amala, P.A.K.</p> <p>1995-03-01</p> <p>A computational model for the solution of the three-dimensional Navier-Stokes equations is developed. This model includes a turbulence model: a modified Smagorinsky eddy-viscosity with a stochastic backscatter extension. The resultant equations are solved using finite difference techniques: the second-order explicit Lax-Wendroff schemes. This computational model is implemented on a massively <span class="hlt">parallel</span> computer. Programming models on massively <span class="hlt">parallel</span> computers are next studied. It is desired to determine the best programming model for the developed computational model. To this end, three different codes are tested on a current massively <span class="hlt">parallel</span> computer: the CM-5 at Los Alamos. Each code uses a different programming model: one is a data <span class="hlt">parallel</span> code; the other two are message passing codes. Timing studies are done to determine which method is the fastest. The data <span class="hlt">parallel</span> approach turns out to be the fastest method on the CM-5 by at least an order of magnitude. The resultant code is then used to study a current problem of interest to the computational fluid dynamics community. This is the Rayleigh-Taylor instability. The Lax-Wendroff methods handle shocks and sharp interfaces poorly. To this end, the Rayleigh-Taylor linear analysis is modified to include a smoothed interface. The linear growth rate problem is then investigated. Finally, the problem of the randomly perturbed interface is examined. Stochastic backscatter breaks the symmetry of the stationary unstable interface and generates a mixing layer growing at the experimentally observed rate. 115 refs., 51 figs., 19 tabs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26575558','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26575558"><span id="translatedtitle">Molecular <span class="hlt">simulation</span> workflows as <span class="hlt">parallel</span> algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesén, Björn; Kasson, Peter M; Lindahl, Erik</p> <p>2015-06-01</p> <p>Computational chemistry and other <span class="hlt">simulation</span> fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers-particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide more processing units rather than making individual units much faster, which <span class="hlt">simulation</span> applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple <span class="hlt">simulations</span> into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of <span class="hlt">simulations</span> and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally <span class="hlt">parallel</span>. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled <span class="hlt">simulations</span> using either distributed or <span class="hlt">parallel</span> resources with Copernicus. PMID:26575558</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19940010166','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19940010166"><span id="translatedtitle">Real-time dynamic <span class="hlt">simulation</span> of the Cassini spacecraft using DARTS. Part 2: <span class="hlt">Parallel</span>/vectorized real-time implementation</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Fijany, A.; Roberts, J. A.; Jain, A.; Man, G. K.</p> <p>1993-01-01</p> <p>Part 1 of this paper presented the requirements for the real-time <span class="hlt">simulation</span> of Cassini spacecraft along with some discussion of the DARTS algorithm. Here, in Part 2 we discuss the development and implementation of <span class="hlt">parallel</span>/vectorized DARTS algorithm and architecture for real-time <span class="hlt">simulation</span>. Development of the fast algorithms and architecture for real-time hardware-in-the-loop <span class="hlt">simulation</span> of spacecraft dynamics is motivated by the fact that it represents a hard real-time problem, in the sense that the correctness of the <span class="hlt">simulation</span> depends on both the numerical accuracy and the exact timing of the computation. For a given model fidelity, the computation should be computed within a predefined time period. Further reduction in computation time allows increasing the fidelity of the model (i.e., inclusion of more flexible modes) and the integration routine.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014SPIE.9145E..2PY','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014SPIE.9145E..2PY"><span id="translatedtitle">Modeling and <span class="hlt">simulation</span> of a 6-DOF <span class="hlt">parallel</span> platform for telescope secondary mirror</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Yue, Zhongyu; Ye, Yu; Gu, Bozhong</p> <p>2014-07-01</p> <p>The 6-DOF <span class="hlt">parallel</span> platform in this paper is a kind of Stewart platform. It can be used as supporting structure for telescope secondary mirror. In order to adapt the special dynamic environment of the telescope secondary mirror and to be installed in extremely narrow space, a unique <span class="hlt">parallel</span> platform is designed. PSS Stewart platform and SPS Stewart platform are analyzed and compared. Then the PSS Stewart platform is chosen for detailed design. The virtual prototyping model of the <span class="hlt">parallel</span> platform is built. The model is used for the analysis and calculation of multi-body dynamics. With the help of ANSYS, the finite element model of the platform is built and then the analysis is performed. According to the above analysis the experimental prototype of the platform is built.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1090857','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1090857"><span id="translatedtitle">Coupled models and <span class="hlt">parallel</span> <span class="hlt">simulations</span> for three-dimensional full-Stokes ice sheet modeling</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Zhang, Huai; Ju, Lili; Gunzburger, Max; Ringler, Todd; Price, Stephen</p> <p>2011-01-01</p> <p>A three-dimensional full-Stokes computational model is considered for determining the dynamics, temperature, and thickness of ice sheets. The governing thermomechanical equations consist of the three-dimensional full-Stokes system with nonlinear rheology for the momentum, an advective-diffusion energy equation for temperature evolution, and a mass conservation equation for icethickness changes. Here, we discuss the variable resolution meshes, the finite element discretizations, and the <span class="hlt">parallel</span> algorithms employed by the model components. The solvers are integrated through a well-designed coupler for the exchange of parametric data between components. The discretization utilizes high-quality, variable-resolution centroidal Voronoi Delaunay triangulation meshing and existing <span class="hlt">parallel</span> solvers. We demonstrate the gridding technology, discretization schemes, and the efficiency and scalability of the <span class="hlt">parallel</span> solvers through computational experiments using both simplified geometries arising from benchmark test problems and a realistic Greenland ice sheet geometry.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4334526','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4334526"><span id="translatedtitle">Neurite, a Finite Difference Large Scale <span class="hlt">Parallel</span> Program for the <span class="hlt">Simulation</span> of Electrical Signal Propagation in Neurites under Mechanical Loading</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>García-Grajales, Julián A.; Rucabado, Gabriel; García-Dopico, Antonio; Peña, José-María; Jérusalem, Antoine</p> <p>2015-01-01</p> <p>With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, functions of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells, Neurite, has only very recently been proposed. In this paper, we present the implementation details of this model: a finite difference <span class="hlt">parallel</span> program for <span class="hlt">simulating</span> electrical signal propagation along neurites under mechanical loading. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to <span class="hlt">simulate</span> the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The <span class="hlt">simulation</span> of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the <span class="hlt">simulated</span> cells grows. The solvers implemented in Neurite—explicit and implicit—were therefore <span class="hlt">parallelized</span> using graphics processing units in order to reduce the burden of the <span class="hlt">simulation</span> costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between electrophysiology and mechanics. This paper provides the details of the <span class="hlt">parallel</span> implementation of Neurite, along with three different application examples: a long myelinated axon, a segmented dendritic tree, and a damaged axon. The capabilities of the program to deal with large scale scenarios, segmented neuronal structures, and functional deficits under mechanical loading are specifically highlighted. PMID:25680098</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/10186983','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/10186983"><span id="translatedtitle">Embedded microclusters in zeolites and cluster beam sputtering -- <span class="hlt">simulation</span> on <span class="hlt">parallel</span> computers. Progress report, September 1993--September 1994</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Vashishta, P.; Kalia, R.K.; Greenwell, D.L.</p> <p>1994-09-01</p> <p>We have designed a time-space multiresolution approach for large-scale molecular-dynamics (MD) <span class="hlt">simulations</span> involving long-range Coulomb forces and three-body interactions. This approach has been implemented on various <span class="hlt">parallel</span> architectures including the 512-node Intel Touchstone Delta at Caltech and the 128-processor IBM SP1 at Argonne National Laboratory. <span class="hlt">Parallel</span> MD <span class="hlt">simulations</span> involving 1.12-million particles have been performed to investigate the pore interface growth and the roughness of fracture surfaces in porous silica. When the mass density is reduced to a critical value, pores grow catastrophically to cause fracture. The roughness exponent for internally fractured surfaces, {alpha} = 0.87 {+-} 0.02, supports experimental claims about the universality of {alpha}. A reliable interatomic potential has been developed for MD <span class="hlt">simulations</span> Of Si{sub 3}N{sub 4}. The nature of phonon densities-of-states due to low-energy floppy modes in crystalline and glassy states has been investigated. Floppy modes appear continuously in the glass as the connectivity of the system is reduced. In the crystal, they appear suddenly at 30% volume expansion. The density-of-states due to floppy modes varies linearly with energy, and the specific heat is significantly enhanced by these modes. Thermal conductivities of ceramic materials are calculated with a nonequilibrium MD method and the Kubo-Greenwood formula using a <span class="hlt">parallel</span> eigensolver and the <span class="hlt">parallel</span> MD approach. The calculations for amorphous silica agree well with experiments over a very wide range of temperatures above the plateau region. Currently, we are investigating thermal transport mechanisms in technologically important materials - porous glasses, nanophase ceramics, and zeolites.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2005JCoPh.207..493M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2005JCoPh.207..493M"><span id="translatedtitle">K-means clustering for optimal partitioning and dynamic load balancing of <span class="hlt">parallel</span> hierarchical N-body <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Marzouk, Youssef M.; Ghoniem, Ahmed F.</p> <p>2005-08-01</p> <p>A number of complex physical problems can be approached through N-body <span class="hlt">simulation</span>, from fluid flow at high Reynolds number to gravitational astrophysics and molecular dynamics. In all these applications, direct summation is prohibitively expensive for large N and thus hierarchical methods are employed for fast summation. This work introduces new algorithms, based on k-means clustering, for partitioning <span class="hlt">parallel</span> hierarchical N-body interactions. We demonstrate that the number of particle-cluster interactions and the order at which they are performed are directly affected by partition geometry. Weighted k-means partitions minimize the sum of clusters' second moments and create well-localized domains, and thus reduce the computational cost of N-body approximations by enabling the use of lower-order approximations and fewer cells. We also introduce compatible techniques for dynamic load balancing, including adaptive scaling of cluster volumes and adaptive redistribution of cluster centroids. We demonstrate the performance of these algorithms by constructing a <span class="hlt">parallel</span> treecode for vortex particle <span class="hlt">simulations</span>, based on the serial variable-order Cartesian code developed by Lindsay and Krasny [Journal of Computational Physics 172 (2) (2001) 879-907]. The method is applied to vortex <span class="hlt">simulations</span> of a transverse jet. Results show outstanding <span class="hlt">parallel</span> efficiencies even at high concurrencies, with velocity evaluation errors maintained at or below their serial values; on a realistic distribution of 1.2 million vortex particles, we observe a <span class="hlt">parallel</span> efficiency of 98% on 1024 processors. Excellent load balance is achieved even in the face of several obstacles, such as an irregular, time-evolving particle distribution containing a range of length scales and the continual introduction of new vortex particles throughout the domain. Moreover, results suggest that k-means yields a more efficient partition of the domain than a global oct-tree.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014APS..MAR.C1284S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014APS..MAR.C1284S"><span id="translatedtitle"><span class="hlt">Parallelized</span> Multi-Worm Algorithm for Large Scale Quantum Monte-Carlo <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Suzuki, Takafumi; Masaki-Kato, Akiko; Harada, Kenji; Todo, Synge; Kawashima, Naoki</p> <p>2014-03-01</p> <p>The quantum Monte Carlo (QMC) calculation is a powerful and accurate method for quantum many body interacting systems. In this study, we present a new algorithm for the worldline Monte Carlo method based on the Feynman path integral. While the worm algorithm (WA) has been used widely because of its broader range of applicability, the <span class="hlt">parallelization</span> of WA is not straightforward. We present a general QMC algorithm based on the directed-loop algorithm with the domain decomposition. This new algorithm is referred to as <span class="hlt">Parallelized</span> Multi-Worm Algorithm (PMWA). In PMWA, a large number of worms are introduced by controlling a fictitious transverse field. For a benchmark, we applied the PMWA to the hardcore Bose-Hubbard model on the square lattice, and computed the system-size dependence of the Bose-condensation order parameter up to L2 =102402 by using 3200 processors. The benchmark results showed high <span class="hlt">parallelization</span> efficiency. This indicates that the PMWA is suitable for <span class="hlt">parallelizing</span> on a distributed-memory computer.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012JPhCS.385a2009S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012JPhCS.385a2009S"><span id="translatedtitle">Convergence order vs. <span class="hlt">parallelism</span> in the numerical <span class="hlt">simulation</span> of the bidomain equations</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sharomi, Oluwaseun; Spiteri, Raymond J.</p> <p>2012-10-01</p> <p>The propagation of electrical activity in the human heart can be modelled mathematically by the bidomain equations. The bidomain equations represent a multi-scale reaction-diffusion model that consists of a set of ordinary differential equations governing the dynamics at the cellular level coupled with a set of partial differential equations governing the dynamics at the tissue level. Significant computation is generally required to generate clinically useful data from the bidomain equations. Contemporary developments in computer architecture, in particular multi- and many-core computers and graphics processing units, have made such computations feasible. However, the zeal to take advantage to <span class="hlt">parallel</span> architectures has typically caused another important aspect of numerical methods for the solution of differential equations to be overlooked, namely the convergence order. It is well known that higher-order methods are generally more efficient than lower-order ones when solutions are smooth and relatively high accuracy is desired. In these situations, serial implementations of high-order methods may remain surprisingly competitive with <span class="hlt">parallel</span> implementations of low-order methods. In this paper, we examine the effect of order on the numerical solution of the bidomain equations in <span class="hlt">parallel</span>. We find that high-order methods, in particular high-order time-integration methods with relatively better stability properties, tend to outperform their low-order counterparts, even when the latter are run in <span class="hlt">parallel</span>. In other words, increasing integration order often trumps increasing available computational resources, especially when relatively high accuracy is desired.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1226878','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1226878"><span id="translatedtitle">High Fidelity <span class="hlt">Simulations</span> of Large-Scale Wireless Networks</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Onunkwo, Uzoma; Benz, Zachary</p> <p>2015-11-01</p> <p>The worldwide proliferation of wireless connected devices continues to accelerate. There are 10s of billions of wireless links across the planet with an additional explosion of new wireless usage anticipated as the Internet of Things develops. Wireless technologies do not only provide convenience for mobile applications, but are also extremely cost-effective to deploy. Thus, this trend towards wireless connectivity will only continue and Sandia must develop the necessary <span class="hlt">simulation</span> technology to proactively analyze the associated emerging vulnerabilities. Wireless networks are marked by mobility and proximity-based connectivity. The de facto standard for exploratory studies of wireless networks is <span class="hlt">discrete</span> <span class="hlt">event</span> <span class="hlt">simulations</span> (DES). However, the <span class="hlt">simulation</span> of large-scale wireless networks is extremely difficult due to prohibitively large turnaround time. A path forward is to expedite <span class="hlt">simulations</span> with <span class="hlt">parallel</span> <span class="hlt">discrete</span> <span class="hlt">event</span> <span class="hlt">simulation</span> (PDES) techniques. The mobility and distance-based connectivity associated with wireless <span class="hlt">simulations</span>, however, typically doom PDES and fail to scale (e.g., OPNET and ns-3 <span class="hlt">simulators</span>). We propose a PDES-based tool aimed at reducing the communication overhead between processors. The proposed solution will use light-weight processes to dynamically distribute computation workload while mitigating communication overhead associated with synchronizations. This work is vital to the analytics and validation capabilities of <span class="hlt">simulation</span> and emulation at Sandia. We have years of experience in Sandia’s <span class="hlt">simulation</span> and emulation projects (e.g., MINIMEGA and FIREWHEEL). Sandia’s current highly-regarded capabilities in large-scale emulations have focused on wired networks, where two assumptions prevent scalable wireless studies: (a) the connections between objects are mostly static and (b) the nodes have fixed locations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2004MSAIS...4...46G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2004MSAIS...4...46G"><span id="translatedtitle"><span class="hlt">Parallelization</span> of a Smoothed Particle Hydrodynamic Code for <span class="hlt">Simulation</span> of Shocks in Accretion Disks</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Gerardi, G.; Molteni, D.</p> <p></p> <p>We present the <span class="hlt">parallelization</span> of a Serial Code that was designed to model shocks around black hole in accretion disks using the Smoothed Particles Hydrodynamics (SPH). The goal we obtained with our <span class="hlt">parallelization</span> is threefold: (1) Execution speed gain nearly proportional to the number of processors; (2) Processing a number of SPH particles so high that doesn't fit into a single computer; (3) Implementation of the <span class="hlt">parallel</span> code in such a way to make future additions of new physic ingredients easier. The paradigm we use to realize the <span class="hlt">parallelization</span> is the Multiple Instruction Multiple Data (MIMD) one. The three dimensional computational domain is decomposed into concentrically cylindrical sub domains. All the SPH particles, whose vector radius projection (in X,Y plane) lays between two consecutive cylinders, are assigned to the same process. A modified serial version of the code run on every sub domain. The interaction between particles in a sub domain with that owned by the two adjacent one is obtained defining "edge particles". All parameters of the "edge particles" are exchanged between two consecutive couple of process by, Message Passing Interface (MPI) standard. The sub-domain radius Rk are not fixed in order to ensure load balancing among processors. At each time step all internal SPH particles are processed and advanced after the density, pressure and gravitational forces are calculated considering the presence of the "edge particles". At the end of each time step particles migrating to the two consecutive sub domains are exchanged and the host particles are refreshed. The <span class="hlt">parallel</span> code we have realized has run in a cluster of bi processors workstations linked by a fast local Internet link and on the CINECA (Bologna) IBM PC Cluster.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015JCoPh.298..161W','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015JCoPh.298..161W"><span id="translatedtitle"><span class="hlt">Parallel</span> adaptive mesh refinement method based on WENO finite difference scheme for the <span class="hlt">simulation</span> of multi-dimensional detonation</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Wang, Cheng; Dong, XinZhuang; Shu, Chi-Wang</p> <p>2015-10-01</p> <p>For numerical <span class="hlt">simulation</span> of detonation, computational cost using uniform meshes is large due to the vast separation in both time and space scales. Adaptive mesh refinement (AMR) is advantageous for problems with vastly different scales. This paper aims to propose an AMR method with high order accuracy for numerical investigation of multi-dimensional detonation. A well-designed AMR method based on finite difference weighted essentially non-oscillatory (WENO) scheme, named as AMR&WENO is proposed. A new cell-based data structure is used to organize the adaptive meshes. The new data structure makes it possible for cells to communicate with each other quickly and easily. In order to develop an AMR method with high order accuracy, high order prolongations in both space and time are utilized in the data prolongation procedure. Based on the message passing interface (MPI) platform, we have developed a workload balancing <span class="hlt">parallel</span> AMR&WENO code using the Hilbert space-filling curve algorithm. Our numerical experiments with detonation <span class="hlt">simulations</span> indicate that the AMR&WENO is accurate and has a high resolution. Moreover, we evaluate and compare the performance of the uniform mesh WENO scheme and the <span class="hlt">parallel</span> AMR&WENO method. The comparison results provide us further insight into the high performance of the <span class="hlt">parallel</span> AMR&WENO method.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/21277303','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/21277303"><span id="translatedtitle">Influence of the <span class="hlt">parallel</span> nonlinearity on zonal flows and heat transport in global gyrokinetic particle-in-cell <span class="hlt">simulations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Jolliet, S.; McMillan, B. F.; Vernay, T.; Villard, L.; Hatzky, R.; Bottino, A.; Angelino, P.</p> <p>2009-07-15</p> <p>In this paper, the influence of the <span class="hlt">parallel</span> nonlinearity on zonal flows and heat transport in global particle-in-cell ion-temperature-gradient <span class="hlt">simulations</span> is studied. Although this term is in theory orders of magnitude smaller than the others, several authors [L. Villard, P. Angelino, A. Bottino et al., Plasma Phys. Contr. Fusion 46, B51 (2004); L. Villard, S. J. Allfrey, A. Bottino et al., Nucl. Fusion 44, 172 (2004); J. C. Kniep, J. N. G. Leboeuf, and V. C. Decyck, Comput. Phys. Commun. 164, 98 (2004); J. Candy, R. E. Waltz, S. E. Parker et al., Phys. Plasmas 13, 074501 (2006)] found different results on its role. The study is performed using the global gyrokinetic particle-in-cell codes TORB (theta-pinch) [R. Hatzky, T. M. Tran, A. Koenies et al., Phys. Plasmas 9, 898 (2002)] and ORB5 (tokamak geometry) [S. Jolliet, A. Bottino, P. Angelino et al., Comput. Phys. Commun. 177, 409 (2007)]. In particular, it is demonstrated that the <span class="hlt">parallel</span> nonlinearity, while important for energy conservation, affects the zonal electric field only if the <span class="hlt">simulation</span> is noise dominated. When a proper convergence is reached, the influence of <span class="hlt">parallel</span> nonlinearity on the zonal electric field, if any, is shown to be small for both the cases of decaying and driven turbulence.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/10165690','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/10165690"><span id="translatedtitle">Space-charge-dominated beam dynamics <span class="hlt">simulations</span> using the massively <span class="hlt">parallel</span> processors (MPPs) of the Cray T3D</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Liu, H.</p> <p>1996-10-01</p> <p>Computer <span class="hlt">simulations</span> using the multi-particle code PARMELA with a three-dimensional point-by-point space charge algorithm have turned out to be very helpful in supporting injector commissioning and operations at Thomas Jefferson National Accelerator Facility (Jefferson Lab, formerly called CEBAF). However, this algorithm, which defines a typical N{sup 2} problem in CPU time scaling, is very time-consuming when N, the number of macro-particles, is large. Therefore, it is attractive to use massively <span class="hlt">parallel</span> processors (MPPs) to speed up the <span class="hlt">simulations</span>. Motivated by this, the authors modified the space charge subroutine for using the MPPs of the Cray T3D. The techniques used to <span class="hlt">parallelize</span> and optimize the code on the T3D are discussed in this paper. The performance of the code on the T3D is examined in comparison with a <span class="hlt">Parallel</span> Vector Processing supercomputer of the Cray C90 and an HP 735/15 high-end workstation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/486013','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/486013"><span id="translatedtitle">High resolution finite volume <span class="hlt">parallel</span> <span class="hlt">simulations</span> of mould filling and binary alloy solidification on unstructured 3-D meshes</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Reddy, A.V.; Kothe, D.B.; Lam, K.L.</p> <p>1997-06-01</p> <p>The Los Alamos National Laboratory (LANL) is currently developing a new casting <span class="hlt">simulation</span> tool (known as Telluride) that employs robust, high-resolution finite volume algorithms for incompressible fluid flow, volume tracking of interfaces, and solidification physics on three-dimensional (3-D) unstructured meshes. Their finite volume algorithms are based on colocated cell-centered schemes that are formally second order in time and space. The flow algorithm is a 3-D extension of recent work on projection method solutions of the Navier-Stokes (NS) equations. Their volume tracking algorithm can accurately track topologically complex interfaces by approximating the interface geometry as piecewise planar. Coupled to their fluid flow algorithm is a comprehensive binary alloy solidification model that incorporates macroscopic descriptions of heat transfer, solute redistribution, and melt convection as well as a microscopic description of segregation. The finite volume algorithms, which are efficient, <span class="hlt">parallel</span>, and robust, can yield high-fidelity solutions on a variety of meshes, ranging from those that are structured orthogonal to fully unstructured (finite element). The authors discuss key computer science issues that have enabled them to efficiently <span class="hlt">parallelize</span> their unstructured mesh algorithms on both distributed and shared memory computing platforms. These include their functionally object-oriented use of Fortran 90 and new <span class="hlt">parallel</span> libraries for gather/scatter functions (PGSLib) and solutions of linear systems of equations (JTpack90). Examples of their current capabilities are illustrated with <span class="hlt">simulations</span> of mold filling and solidification of complex 3-D components currently being poured in LANL foundries.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25254255','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25254255"><span id="translatedtitle">Analysis and <span class="hlt">simulation</span> of the dynamic spectrum allocation based on <span class="hlt">parallel</span> immune optimization in cognitive wireless networks.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Huixin, Wu; Duo, Mo; He, Li</p> <p>2014-01-01</p> <p>Spectrum allocation is one of the key issues to improve spectrum efficiency and has become the hot topic in the research of cognitive wireless network. This paper discusses the real-time feature and efficiency of dynamic spectrum allocation and presents a new spectrum allocation algorithm based on the master-slave <span class="hlt">parallel</span> immune optimization model. The algorithm designs a new encoding scheme for the antibody based on the demand for convergence rate and population diversity. For improving the calculating efficiency, the antibody affinity in the population is calculated in multiple computing nodes at the same time. <span class="hlt">Simulation</span> results show that the algorithm reduces the total spectrum allocation time and can achieve higher network profits. Compared with traditional serial algorithms, the algorithm proposed in this paper has better speedup ratio and <span class="hlt">parallel</span> efficiency. PMID:25254255</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/10144429','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/10144429"><span id="translatedtitle">A massively <span class="hlt">parallel</span> algorithm for grand canonical Monte Carlo computer <span class="hlt">simulation</span> with the short-ranged Lennard-Jones potential</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Heffelfinger, G.S.; Lewitt, M.E.</p> <p>1994-05-01</p> <p>We present a new massively <span class="hlt">parallel</span> decomposition for grand canonical Monte Carlo computer <span class="hlt">simulation</span> (GCMC) suitable for short ranged fluids. Our spatial algorithm relies on the fact that for short-ranged fluids, molecules separated by a greater distance than the reach of the potential act independently, thus different processors can work concurrently in regions of the same system which are sufficiently far apart. Several <span class="hlt">parallelization</span> issues unique to GCMC are addressed such as the handling of the three different types of Monte Carlo move used in GCMC: the displacement of a molecule, the creation of a molecule, and the destruction of a molecule. The decomposition is shown to scale with system size, making it especially useful for systems where the physical problem dictates the system size, for example, fluid behavior in mesopores.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li class="active"><span>24</span></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_24 --> <div id="page_25" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li class="active"><span>25</span></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="481"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20110010844','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20110010844"><span id="translatedtitle">A Computer <span class="hlt">Simulation</span> of the System-Wide Effects of <span class="hlt">Parallel</span>-Offset Route Maneuvers</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Lauderdale, Todd A.; Santiago, Confesor; Pankok, Carl</p> <p>2010-01-01</p> <p>Most aircraft managed by air-traffic controllers in the National Airspace System are capable of flying <span class="hlt">parallel</span>-offset routes. This paper presents the results of two related studies on the effects of increased use of offset routes as a conflict resolution maneuver. The first study analyzes offset routes in the context of all standard resolution types which air-traffic controllers currently use. This study shows that by utilizing <span class="hlt">parallel</span>-offset route maneuvers, significant system-wide savings in delay due to conflict resolution of up to 30% are possible. It also shows that most offset resolutions replace horizontal-vectoring resolutions. The second study builds on the results of the first and directly compares offset resolutions and standard horizontal-vectoring maneuvers to determine that in-trail conflicts are often more efficiently resolved by offset maneuvers.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/11015901','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/11015901"><span id="translatedtitle">Dislocation emission at the Silicon/Silicon nitride interface: A million atom molecular dynamics <span class="hlt">simulation</span> on <span class="hlt">parallel</span> computers</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Bachlechner; Omeltchenko; Nakano; Kalia; Vashishta; Ebbsjo; Madhukar</p> <p>2000-01-10</p> <p>Mechanical behavior of the Si(111)/Si(3)N4(0001) interface is studied using million atom molecular dynamics <span class="hlt">simulations</span>. At a critical value of applied strain <span class="hlt">parallel</span> to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the (1; 1;1) plane of the silicon substrate with a speed of 500 (+/-100) m/s. Time evolution of the dislocation emission and nature of defects is studied. PMID:11015901</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014AGUFMSM51E4303F','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014AGUFMSM51E4303F"><span id="translatedtitle">Massively <span class="hlt">parallel</span> MHD <span class="hlt">simulation</span> of convection and auroral emissions in Saturn's magnetosphere driven by the observed solar wind</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Fukazawa, K.; Walker, R. J.; Eriksson, S.</p> <p>2014-12-01</p> <p>In a series of <span class="hlt">simulation</span> studies we have reported that vortices formed at Saturn's dawn magnetopause in <span class="hlt">simulations</span> when IMF was northward. We interpreted these vortices as resulting from the Kelvin Helmholtz (K-H) instability. Thanks to recent advances in computer performance, we have been able to perform high resolution global MHD <span class="hlt">simulations</span> of the Kronian magnetosphere with 0.1 Rs grid spacing. In these <span class="hlt">simulations</span> we obtained the signature of the field-aligned currents from the K-H vortices in Saturn's auroral ionosphere and found small patchy regions of upward field-aligned current which may be related to auroral emissions. These patchy aurorae resembling our results have been reported from Cassini observations. In our previous <span class="hlt">simulations</span> we have used the constant and simple solar wind conditions to understand the basic behavior of Kronian magnetosphere. In this study we have used Cassini observations of the solar wind upstream of Saturn to drive a massively <span class="hlt">parallel</span> <span class="hlt">simulation</span>. Using these solar wind data we <span class="hlt">simulated</span> the Kronian magnetosphere from 2008-02-12/14:00:31 to 2008-02-13/01:59:31 when the Hubble Space Telescope (HST) observed Kronian UV auroral emissions. For these solar wind conditions there are several enhancements of the solar wind dynamic pressure (shocks) and a polarity reversal in the IMF components. From these <span class="hlt">simulations</span> we obtained the dynamically changing shape and convection pattern of the Kronian magnetosphere in response to the variation of solar wind dynamic pressure and IMF direction. In particular, a layered convection pattern formed between the corotation region and magnetopause. The layers in this convection system interacted with each other, forming large vortices. We calculated the configuration of field aligned currents from the <span class="hlt">simulation</span> and found layered and patchy distributions in the ionosphere. The pattern of these upward field aligned currents in the dawn side ionosphere resembles the configuration of auroral emission observed by HST well.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AAS...22514029G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AAS...22514029G"><span id="translatedtitle">Supernova Emulators: Connecting Massively <span class="hlt">Parallel</span> SN Ia Radiative Transfer <span class="hlt">Simulations</span> to Data with Gaussian Processes</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Goldstein, Daniel; Thomas, Rollin; Kasen, Daniel</p> <p>2015-01-01</p> <p>Collaboration between the type Ia supernova (SN Ia) modeling and observation communities hinges on our ability to directly connect <span class="hlt">simulations</span> to data. Here we introduce supernova emulation, a method for facilitating such a connection. Emulation allows us to instantaneously predict the observables (light curves, spectra, spectral time series) generated by arbitrary SN Ia radiative transfer <span class="hlt">simulations</span>, with estimates of prediction error. Emulators learn the mapping between physically meaningful <span class="hlt">simulation</span> inputs and the resulting synthetic observables from a training set of <span class="hlt">simulation</span> input-output pairs. In our emulation framework, we model PCA-decomposed representations of <span class="hlt">simulated</span> observables as an ensemble of Gaussian Processes. As a proof of concept, we train a bolometric light curve (BLC) emulator on a grid of 400 <span class="hlt">simulation</span> inputs and BLCs synthesized with the publicly available, gray, time-dependent Monte Carlo expanding atmospheres code, SMOKE. We emulate SMOKE <span class="hlt">simulations</span> evaluated at a set of 100 out-of-sample input parameters, and achieve excellent agreement between the emulator predictions and the <span class="hlt">simulated</span> BLCs. In addition to predicting <span class="hlt">simulation</span> outputs, emulators allow us to infer the regions of <span class="hlt">simulation</span> input parameter space that correspond to observed SN Ia light curves and spectra. We present a Bayesian framework for solving this inverse problem using Markov Chain Monte Carlo sampling. We fit published bolometric light curves with our emulator and obtain reconstructed masses (nickel mass, total ejecta mass) in agreement with reconstructions from semi-analytic models. We discuss applications of emulation to supernova cosmology and physics, including how emulators can be used to identify and quantify astrophysical sources of systematic error affecting SNe Ia as distance indicators for cosmology.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/949977','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/949977"><span id="translatedtitle"><span class="hlt">Parallel</span>, Multigrid Finite Element <span class="hlt">Simulator</span> for Fractured/Faulted and Other Complex R