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At least 469 records · Page 26

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but the task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study,potentials of applying some of the techniques to realistic aerospace applications will be presented

Jin, Hao-Qiang↗

A transient FETI methodology for large-scale parallel implicit computations in structural mechanics, part 2

Explicit codes are often used to simulate the nonlinear dynamics of large-scale structural systems, even for low frequency response, because the storage and CPU requirements entailed by the repeated factorizations traditionally found in implicit codes rapidly overwhelm the available computing resources. With the advent of parallel processing, this trend is accelerating because explicit schemes are also easier to parallellize than implicit ones. However, the time step restriction imposed by the Courant stability condition on all explicit schemes cannot yet and perhaps will never be offset by the speed of parallel hardware. Therefore, it is essential to develop efficient and robust alternatives to direct methods that are also amenable to massively parallel processing because implicit codes using unconditionally stable time-integration algorithms are computationally more efficient than explicit codes when simulating low-frequency dynamics. Here we present a domain decomposition method for implicit schemes that requires significantly less storage than factorization algorithms, that is several times faster than other popular direct and iterative methods, that can be easily implemented on both shared and local memory parallel processors, and that is both computationally and communication-wise efficient. The proposed transient domain decomposition method is an extension of the method of Finite Element Tearing and Interconnecting (FETI) developed by Farhat and Roux for the solution of static problems. Serial and parallel performance results on the CRAY Y-MP/8 and the iPSC-860/128 systems are reported and analyzed for realistic structural dynamics problems. These results establish the superiority of the FETI method over both the serial/parallel conjugate gradient algorithm with diagonal scaling and the serial/parallel direct method, and contrast the computational power of the iPSC-860/128 parallel processor with that of the CRAY Y-MP/8 system.

Farhat, Charbel↗

A transient FETI methodology for large-scale parallel implicit computations in structural mechanics

Explicit codes are often used to simulate the nonlinear dynamics of large-scale structural systems, even for low frequency response, because the storage and CPU requirements entailed by the repeated factorizations traditionally found in implicit codes rapidly overwhelm the available computing resources. With the advent of parallel processing, this trend is accelerating because explicit schemes are also easier to parallelize than implicit ones. However, the time step restriction imposed by the Courant stability condition on all explicit schemes cannot yet -- and perhaps will never -- be offset by the speed of parallel hardware. Therefore, it is essential to develop efficient and robust alternatives to direct methods that are also amenable to massively parallel processing because implicit codes using unconditionally stable time-integration algorithms are computationally more efficient when simulating low-frequency dynamics. Here we present a domain decomposition method for implicit schemes that requires significantly less storage than factorization algorithms, that is several times faster than other popular direct and iterative methods, that can be easily implemented on both shared and local memory parallel processors, and that is both computationally and communication-wise efficient. The proposed transient domain decomposition method is an extension of the method of Finite Element Tearing and Interconnecting (FETI) developed by Farhat and Roux for the solution of static problems. Serial and parallel performance results on the CRAY Y-MP/8 and the iPSC-860/128 systems are reported and analyzed for realistic structural dynamics problems. These results establish the superiority of the FETI method over both the serial/parallel conjugate gradient algorithm with diagonal scaling and the serial/parallel direct method, and contrast the computational power of the iPSC-860/128 parallel processor with that of the CRAY Y-MP/8 system.

Farhat, Charbel↗

A Comparison of Automatic Parallelization Tools/Compilers on the SGI Origin 2000 Using the NAS Benchmarks

Porting applications to new high performance parallel and distributed computing platforms is a challenging task. Since writing parallel code by hand is extremely time consuming and costly, porting codes would ideally be automated by using some parallelization tools and compilers. In this paper, we compare the performance of the hand written NAB Parallel Benchmarks against three parallel versions generated with the help of tools and compilers: 1) CAPTools: an interactive computer aided parallelization too] that generates message passing code, 2) the Portland Group's HPF compiler and 3) using compiler directives with the native FORTAN77 compiler on the SGI Origin2000.

Saini, Subhash↗

Simulation and Optimizing Groundwater Investigations, Conceptual Design Analysis, Model Calibration and Remedial Design Using Parallel Numerical Methods: Theory and Application - 16578

Optimization of environmental restoration efforts at complex groundwater sites involves the development of a conceptual and often numerical flow and transport models. Typically, a limited number of simulations are done to assess the impact of parameter uncertainty, to evaluate remedial alternatives and develop a remedy, or to modify an existing remedy. A limited number of simulations are performed because each simulation can take upwards of several hours per simulation and until now the ability to conduct the 100's to 1000's of simulations needed to derive an optimal remedy was beyond the reach of the everyday practitioner. HGL has developed and implemented new parallel simulation and optimization methods in their software and has successfully deployed applications on high performance Cloud-based computing platforms. This advancement removes the impediment of burdensome and unpredictable runtime requirements these types of projects have typically exhibited using heuristic trial-and-error or even automated serial computation approaches. A parallel numerical solver has been added to the subsurface flow and transport simulator MODFLOW-SURFACT{sup TM} and has demonstrated reductions in solution time by as much as a factor of 9.8. This is accomplished by distributing the numerical computations of every time step over multiple processors. The integrated parallel simulation and optimization method uses the breadth and depth search approach; iteratively producing sets of tens or 100's of candidate solutions that are evaluated concurrently instead sequentially (i.e. one model evaluation at a time). Solutions within 80-100% of the globally optimal solution are regularly found expending only 5-10% of the usual computational effort using this new parallel optimization method (reducing computation effort by 10 to 20 times). Distributing optimal search runs across multiple processors additionally reduces calendar time to solutions. Practitioners evaluating multiple conceptual site models, model calibration by auto-calibration methods and remedial design by heuristics can enjoy significant reductions in model solution time by using the parallel numerical matrix solver in the physics-based simulator. Combining investigation and design analysis with breadth and depth parallel optimization methods, projects at the fringe of practical optimization, along with projects that were beyond the reach of formal optimization methods are now wholly feasible and tractable optimization problems. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Sub-microsecond-resolved multi-speckle X-ray photon correlation spectroscopy with a pixel array detector

Small-angle X-ray photon correlation spectroscopy (XPCS) measurements spanning delay times from 826 ns to 52.8 s were performed using a photon-counting pixel array detector with a dynamic range of 0–3 (2 bits). Fine resolution and a wide dynamic range of time scales was achieved by combining two modes of operation of the detector: (i) continuous mode, where data acquisition and data readout are performed in parallel with a frame acquisition time of 19.36 µs, and (ii) burst mode, where 12 frames are acquired with frame integration times of either 2.56 µs frame –1 or 826 ns frame –1 followed by 3.49 ms or 1.16 ms, respectively, for readout. The applicability of the detector for performing multi-speckle XPCS was demonstrated by measuring the Brownian dynamics of 10 nm-radius gold and 57 nm-radius silica colloids in water at room temperature. In addition, the capability of the detector to faithfully record one- and two-photon counts was examined by comparing the statistical distribution of photon counts with expected probabilities from the negative binomial distribution. In conclusion, it was found that in burst mode the ratio of 2s to 1s is markedly smaller than predicted and that this is attributable to pixel-response dead-time.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Aspherical particle models for molecular dynamics simulation

In traditional molecular dynamics (MD) simulations, atoms and coarse-grained particles are modeled as point masses interacting via isotropic potentials. For studies where particle shape plays a vital role, more complex models are required. Here, we describe a spectrum of approaches for modeling aspherical particles, all of which are now available (some recently) as options within the LAMMPS MD package. Broadly these include two classes of models. In the first, individual particles are aspherical, either via a pairwise anisotropic potential which implicitly assigns a simple geometric shape to each particle, or in a more general way where particles store internal state which can explicitly define a complex geometric shape. In the second class of models, individual particles are simple points or spheres, but rigid body constraints are used to create composite aspherical particles in a variety of complex shapes. This work discusses parallel algorithms and associated data structures for both kinds of models, which enable dynamics simulations of aspherical particle systems across a wide range of length and time scales. We also highlight parallel performance and scalability and give a few illustrative examples of aspherical models in different contexts.

74 ATOMIC AND MOLECULAR PHYSICS↗

The Updated DESGW Processing Pipeline for the Third LIGO/VIRGO Observing Run

The DESGW group seeks to identify electromagnetic counterparts of gravitational wave events seen by the LIGO-VIRGO network, such as those expected from binary neutron star mergers or neutron star- black hole mergers. DESGW was active throughout the first two LIGO observing seasons, following up several binary black hole mergers and the first binary neutron star merger, GW170817. We describe the modifications to the observing strategy generation and image processing pipeline between the second (ending in August 2017) and third (beginning in April 2019) LIGO observing seasons. The modifications include a more robust observing strategy generator, further parallelization of the image reduction software and difference imaging processing pipeline, data transfer streamlining, and a public webpage listing identified counterpart candidates that updates in real time. Taken together, the additional parallelization steps enable us to identify potential electromagnetic counterpa rts within fully calibrated search images in less than one hour, compared to the 3-5 hours it would typically take during the first two seasons. These performance improvements are critical to the entire EM followup community, as rapid identification (or rejection) of candidates enables detailed spectroscopic followup by multiple instruments as soon as possible, leading to more information about the environment immediately following such gravitational wave events.

79 ASTRONOMY AND ASTROPHYSICS↗

Implementation of an ultrasonic instrument for simultaneous mixture and flow analysis of binary gas systems

Precision ultrasonic measurements in binary gas systems provide continuous real-time monitoring of mixture composition and flow. Using custom micro-controller-based electronics, we have developed an ultrasonic instrument, with numerous potential applications, capable of making continuous high-precision sound velocity measurements. The instrument measures sound transit times along two opposite directions aligned parallel to - or obliquely crossing - the gas flow. The difference between the two measured times yields the gas flow rate while their average gives the sound velocity, which can be compared with a sound velocity vs. molar composition look-up table for the binary mixture at a given temperature and pressure. The look-up table may be generated from prior measurements in known mixtures of the two components, from theoretical calculations, or from a combination of the two. We describe the instrument and its performance within numerous applications in the ATLAS experiment at the CERN Large Hadron Collider (LHC). The instrument can be of interest in other areas where continuous in-situ binary gas analysis and flowmetry are required. (authors)

43 PARTICLE ACCELERATORS↗

The Continuous Readout Stream of the MicroBooNE Liquid Argon Time Projection Chamber for Detection of Supernova Neutrinos

The MicroBooNE Continuous Readout Stream is a parallel readout of the MicroBooNE liquid argon time projection chamber (LArTPC) which enables detection of non-beam events such as those from a supernova neutrino burst. The low energies of these neutrinos and the intense cosmic-ray flux due to the near-surface detector location makes triggering on these events very challenging. Instead, MicroBooNE has pioneered a novel approach for detecting supernova neutrinos relying on a delayed trigger generated by SNEWS (the Supernova Early Warning System). The continuous readout of the LArTPC is achieved through the use of real-time compression algorithms (zero suppression and Huffman compression) implemented in an FPGA (field-programmable gate array) in the readout electronics. We present the results of the optimization of the data reduction algorithms, and their operational performance. In order to demonstrate the capability of the continuous stream to detect low-energy electrons, a sample of Michel electrons from stopping cosmic-ray muons is reconstructed and compared to a similar sample from the lossless triggered readout stream.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Advancements in real-time engine simulation technology

The approaches used to develop real-time engine simulations are reviewed. Both digital and hybrid (analog and digital) techniques are discussed and specific examples of each are cited. These approaches are assessed from the standpoint of their usefulness for digital engine control development. A number of NASA-sponsored simulation research activities, aimed at exploring real-time simulation techniques, are described. These include the development of a microcomputer-based, parallel processor system for real-time engine simulation.

Szuch, J. R.↗

Efficient Optimization of Low-Thrust Spacecraft Trajectories

A paper describes a computationally efficient method of optimizing trajectories of spacecraft driven by propulsion systems that generate low thrusts and, hence, must be operated for long times. A common goal in trajectory-optimization problems is to find minimum-time, minimum-fuel, or Pareto-optimal trajectories (here, Pareto-optimality signifies that no other solutions are superior with respect to both flight time and fuel consumption). The present method utilizes genetic and simulated-annealing algorithms to search for globally Pareto-optimal solutions. These algorithms are implemented in parallel form to reduce computation time. These algorithms are coupled with either of two traditional trajectory- design approaches called "direct" and "indirect." In the direct approach, thrust control is discretized in either arc time or arc length, and the resulting discrete thrust vectors are optimized. The indirect approach involves the primer-vector theory (introduced in 1963), in which the thrust control problem is transformed into a co-state control problem and the initial values of the co-state vector are optimized. In application to two example orbit-transfer problems, this method was found to generate solutions comparable to those of other state-of-the-art trajectory-optimization methods while requiring much less computation time.

Lee, Seungwon↗

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

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

Fiebrich, Rolf-Dieter↗

Intelligent systems technology infrastructure for integrated systems

Significant advances have occurred during the last decade in intelligent systems technologies (a.k.a. knowledge-based systems, KBS) including research, feasibility demonstrations, and technology implementations in operational environments. Evaluation and simulation data obtained to date in real-time operational environments suggest that cost-effective utilization of intelligent systems technologies can be realized for Automated Rendezvous and Capture applications. The successful implementation of these technologies involve a complex system infrastructure integrating the requirements of transportation, vehicle checkout and health management, and communication systems without compromise to systems reliability and performance. The resources that must be invoked to accomplish these tasks include remote ground operations and control, built-in system fault management and control, and intelligent robotics. To ensure long-term evolution and integration of new validated technologies over the lifetime of the vehicle, system interfaces must also be addressed and integrated into the overall system interface requirements. An approach for defining and evaluating the system infrastructures including the testbed currently being used to support the on-going evaluations for the evolutionary Space Station Freedom Data Management System is presented and discussed. Intelligent system technologies discussed include artificial intelligence (real-time replanning and scheduling), high performance computational elements (parallel processors, photonic processors, and neural networks), real-time fault management and control, and system software development tools for rapid prototyping capabilities.

Lum, Henry, Jr.↗

A massively parallel computational approach to coupled thermoelastic/porous gas flow problems

A new computational scheme for coupled thermoelastic/porous gas flow problems is presented. Heat transfer, gas flow, and dynamic thermoelastic governing equations are expressed in fully explicit form, and solved on a massively parallel computer. The transpiration cooling problem is used as an example problem. The numerical solutions have been verified by comparison to available analytical solutions. Transient temperature, pressure, and stress distributions have been obtained. Small spatial oscillations in pressure and stress have been observed, which would be impractical to predict with previously available schemes. Comparisons between serial and massively parallel versions of the scheme have also been made. The results indicate that for small scale problems the serial and parallel versions use practically the same amount of CPU time. However, as the problem size increases the parallel version becomes more efficient than the serial version.

Shia, David↗

Nixie tube display unit employs time-shared logic

Cathodes of display tubes wired in parallel achieve input switching simplification of a Nixie tube display system. Use of time- shared logic energizes the appropriate anode and inhibits all unnecessary cathodes.

Gray, J.↗

Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions

Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn-glycero-3- phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.

Aoun, Bachir↗