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At least 1,657 records · Page 92

Femtosecond Compression Dynamics and Timing Jitter Suppression in a THz-driven Electron Bunch Compressor

Herein we present the first demonstration of THz driven bunch compression and timing stabilization of a relativistic electron beam. Quasi-single-cycle strong field THz radiation is used in a shorted parallel-plate structure to compress a few-fC beam with 2.5 MeV kinetic energy by a factor of 2.7, producing a 39 fs rms bunch length and a reduction in timing jitter by more than a factor of 2 to 31 fs rms. This THz driven technique offers a significant improvement to beam performance for applications like ultrafast electron diffraction, providing a critical step towards unprecedented timing resolution in ultrafast sciences, and other accelerator applications using femtosecond-scale electron beams.

43 PARTICLE ACCELERATORS↗

Adaptation of primate vestibuloocular reflex to altered peripheral vestibular inputs. II Spatiotemporal properties of the adapted slow-phase eye velocity

1. The ability of the vestibuloocular reflex (VOR) to undergo adaptive modification after selective changes in the peripheral vestibular system was investigated in rhesus monkeys by recording three-dimensional eye movements before and after inactivation of selective semicircular canals. In the preceding paper we showed that the horizontal VOR gain evoked by passive yaw oscillations after lateral semicircular canal inactivation recovers gradually over time in a frequency-specific manner. Here we present the spatial tuning of the adapted slow-phase eye velocity and describe its spatiotemporal properties as a function of time after canal inactivation. 2. The spatial organization of the VOR was investigated during oscillations at different head positions in the pitch, roll, and yaw planes, as well as in the right anterior/left posterior and left anterior/right posterior canal planes. Acutely after bilateral inactivation of the lateral semicircular canals, a small horizontal response could still be elicited that peaked during rotations in pitched head positions that would maximally stimulate vertical semicircular canals. In addition, the phase of horizontal slow-phase velocity abruptly reversed through 180 degrees at positions close to upright, similarly to torsional slow-phase velocity. These spatial response properties suggest that the small, residual horizontal response components that are present acutely after plugging of both lateral canals originate from vertical semicircular canal signals. 3. As the horizontal response amplitude increased over time, consistent changes were also observed in the spatiotemporal tuning of horizontal slow-phase velocity. 1) The spatiotemporal response properties of horizontal slow-phase velocity acquired noncosine tuning characteristics, primarily in the pitch plane, in the right anterior/left posterior and left anterior/right posterior canal planes. Accordingly, horizontal response amplitude was nonzero during rotation in any head position in these planes and response phase varied significantly as a function of head orientation. 2) The peak horizontal response amplitude shifted spatially over time, such that 5-10 mo after plugging it was maximal during rotations at head positions close to upright. 4. In parallel to these unique spatiotemporal response properties characterizing the adapted horizontal VOR, torsional slow-phase velocity also exhibited small spatiotemporal changes after lateral canal inactivation that tended to precede in time the changes associated with the horizontal response components. In contrast, vertical slow-phase velocity in the plugged animals was unaltered and continued to be characterized by cosine-tuned spatial properties in three dimensions. 5. Recovery of the horizontal response gain during yaw oscillations in upright position, as well as the unique, noncosine spatiotemporal characteristics of the adapted horizontal VOR, were also observed in an animal with all but one vertical semicircular canals inactivated. There was, however, no sign of VOR gain recovery up to 2 mo after all semicircular canals were inactivated. These results suggest that the observed recovery of horizontal VOR is at least partly due to signals originating from the remaining intact vertical canal(s). Even in the presence of a single intact vertical canal, the improvement in horizontal gaze stability is at least partly restored through spatiotemporal changes in the processing of vestibuloocular signals that improve the gain and spatial tuning of horizontal VOR at the expense of temporal response properties.

NASA Discipline Number 16-10↗

Linear complexity

We present factorization and solution phases for a new linear complexity direct solver designed for concurrent batch operations on fine-grained parallel architectures, for matrices amenable to hierarchical representation. We focus on the strong-admissibility-based $\mathscr{H}^{2}$ format, where strong recursive skeletonization factorization compresses remote interactions. We build upon previous implementations of $\mathscr{H}^{2}$ matrix construction for efficient factorization and solution algorithm design, which are illustrated graphically in stepwise detail. The algorithms are ‘blackbox’ in the sense that the only inputs are the matrix and right-hand side, without analytical or geometrical information about the origin of the system. We demonstrate linear complexity scaling in both time and memory on four representative families of dense matrices up to one million in size. Parallel scaling up to 16 threads is enabled by a multi-level matrix graph coloring and avoidance of dynamic memory allocations thanks to prefix-sum memory management. An experimental backward error analysis is included. We break down the timings of different phases, identify phases that are memory-bandwidth limited, and discuss alternatives for phases that may be sensitive to the trend to employ lower precisions for performance.

Boukaram, Wajih↗

Generation of Electron Suprathermal Tails in the Upper Solar Atmosphere: Implications for Coronal Heating

We present a mechanism for the generation of non-Maxwellian electron distribution function in the upper regions of the solar atmosphere in the presence of collisional damping. It is suggested that finite amplitude, low frequency, obliquely propagating electromagnetic waves can carry a substantial electric field component parallel to the mean magnetic field that can be significantly larger than the Dreicer electric field. This long wavelength electric fluctuation is capable of generating high frequency electron plasma oscillations and low frequency ion acoustic-like waves. The analysis has been performed using 1-1/2D Vlasov and PIC numerical simulations in which both electrons and ions are treated kinetically and self consistently. The simulation results indicate that high frequency electron plasma oscillations and low frequency ion acoustic-like waves are generated. The high frequency electron plasma oscillation drives electron plasma turbulence, which subsequently is damped out by the background electrons. The turbulence damping results in electron acceleration and the generation of non-Maxwellian suprathermal tails on time scales short compared to collisional damping. Bulk heating also occurs if the fluctuating parallel electric field is strong enough. This study suggests that finite amplitude, low frequency, obliquely propagating, electromagnetic waves can play a significant role in the acceleration and heating of the solar corona electrons and in the coupling of medium and small-scale phenomena.

Vinas, Adolfo F.↗

Generating unstructured nuclear reactor core meshes in parallel

Recent advances in supercomputers and parallel solver techniques have enabled users to run large simulations problems using millions of processors. Techniques for multiphysics nuclear reactor core simulations are under active development in several countries. Most of these techniques require large unstructured meshes that can be hard to generate in a standalone desktop computers because of high memory requirements, limited processing power, and other complexities. We have previously reported on a hierarchical lattice-based approach for generating reactor core meshes. Here, we describe efforts to exploit coarse-grained parallelism during reactor assembly and reactor core mesh generation processes. We highlight several reactor core examples including a very high temperature reactor, a full-core model of the Korean MONJU reactor, a ¼ pressurized water reactor core, the fast reactor Experimental Breeder Reactor-II core with a XX09 assembly, and an advanced breeder test reactor core. The times required to generate large mesh models, along with speedups obtained from running these problems in parallel, are reported. A graphical user interface to the tools described here has also been developed.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Concurrent processing adaptation of aeroplastic analysis of propfans

Discussed here is a study involving the adaptation of an advanced aeroelastic analysis program to run concurrently on a shared memory multiple processor computer. The program uses a three-dimensional compressible unsteady aerodynamic model and blade normal modes to calculate aeroelastic stability and response of propfan blades. The identification of the computational parallelism within the sequential code and the scheduling of the concurrent subtasks to minimize processor idle time are discussed. Processor idle time in the calculation of the unsteady aerodynamic coefficients was reduced by the simple strategy of appropriately ordering the computations. Speedup and efficiency results are presented for the calculation of the matched flutter point of an experimental propfan model. The results show that efficiencies above 70 percent can be obtained using the present implementation with 7 processors. The parallel computational strategy described here is also applicable to other aeroelastic analysis procedures based on panel methods.

Janetzke, David C.↗

Concurrent processing adaptation of aeroelastic analysis of propfans

This paper reports on a study involving the adaptation of an advanced aeroelastic analysis program to run concurrently on a shared memory multiple processor computer. The program uses a three-dimensional compressible unsteady aerodynamic model and blade normal modes to calculate aeroelastic stability and response of propfan blades. The identification of the computational parallelism within the sequential code and the scheduling of the concurrent subtasks to minimize processor idle time are discussed. Processor idle time in the calculation of the unsteady aerodynamic coefficients was reduced by the simple strategy of appropriately ordering the computations. Speedup and efficiency results are presented for the calculation of the matched flutter point of an experimental propfan model. The results show that efficiencies above 70 percent can be obtained using the present implementation with 7 processors. The parallel computational strategy described here is also applicable to other aeroelastic analysis procedures based on parallel methods.

Murthy, Durbha V.↗

Concurrent processing adaptation of aeroelastic analysis of propfans

Discussed here is a study involving the adaptation of an advanced aeroelastic analysis program to run concurrently on a shared memory multiple processor computer. The program uses a three-dimensional compressible unsteady aerodynamic model and blade normal modes to calculate aeroelastic stability and response of propfan blades. The identification of the computational parallelism within the sequential code and the scheduling of the concurrent subtasks to minimize processor idle time are discussed. Processor idle time in the calculation of the unsteady aerodynamic coefficients was reduced by the simple strategy of appropriately ordering the computations. Speedup and efficiency results are presented for the calculation of the matched flutter point of an experimental propfan model. The results show that efficiencies above 70 percent can be obtained using the present implementation with 7 processors. The parallel computational strategy described here is also applicable to other aeroelastic analysis procedures based on panel methods.

Murthy, D. V.↗

Real-time multi-EC-actuator MHD control on TCV

Real-time control of multiple plasma actuators is a requirement in advanced tokamaks; for example for burn control, plasma current profile control and MHD stabilization - EC wave absorption is ideally suited especially for the latter. For example, on ITER 24 EC sources can be switched between 54 inputs at the torus. In the torus, 5 launchers direct the power to various locations across the plasma profile via 11 steerable mirrors. For optimal usage of the available power, the aiming and polarization of the beams must be adapted to the plasma configuration and the needs of the scenario. Since the EC system performs many competing tasks, present day systems should demonstrate the ability of an EC plant to deal with several targets in parallel and/or to switch smoothly between goals to attain overall satisfaction. Recently TCV has taken a first step towards such a demonstration. Several EC launchers are used simultaneously to regulate the sawtooth period and to preempt m/n = 3/2 NTMs, by controlling the power levels. In parallel, a second algorithm stabilizes any NTM that saturates [1]. These and real-time MHD control experiments on ELMs [2] are presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores

Background: There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. Results: This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. Conclusions: In this paper, we presented a highly scalable and efficient genome assembly software, SWAPAssembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler

59 BASIC BIOLOGICAL SCIENCES↗

Automated high-throughput flow-through real-time diagnostic system

An automated real-time flow-through system capable of processing multiple samples in an asynchronous, simultaneous, and parallel fashion for nucleic acid extraction and purification, followed by assay assembly, genetic amplification, multiplex detection, analysis, and decontamination. The system is able to hold and access an unlimited number of fluorescent reagents that may be used to screen samples for the presence of specific sequences. The apparatus works by associating extracted and purified sample with a series of reagent plugs that have been formed in a flow channel and delivered to a flow-through real-time amplification detector that has a multiplicity of optical windows, to which the sample-reagent plugs are placed in an operative position. The diagnostic apparatus includes sample multi-position valves, a master sample multi-position valve, a master reagent multi-position valve, reagent multi-position valves, and an optical amplification/detection system.

47 OTHER INSTRUMENTATION↗

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times and memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.

59 BASIC BIOLOGICAL SCIENCES↗

Automata-based Debugging for Dissimilar Parallel Tasks

AutomaDeD is a tool that automatically diagnoses performance and correctness faults in MPI applications. It creates time and control-flow models of processes in an MPI program, and when a failure occus, these models are analyzed probabilistically to find the origin of the failure. The output of the tool is MPI processes ranked by the abnormality degree and regions of code where faults are first manifested. The granularity of code region is an MPI call or a computation region between two MPI calls.

Source record↗

Real-Time Reed-Solomon Decoder

RS decoder uses dedicated hardware and data pipelining for high-speed operation. Parallel processing techniques provide equivalent of over one billion operations per second at one step in decoding. Decoder finds commercial application in data encoding/decoding, telemetry, and radio communications.

Lahmeyer, C. R.↗

Automata-based Debugging for Dissimilar Parallel Tasks

AutomaDeD is a tool that automatically diagnoses performance and correctness faults in MPI applications. It creates time and control-flow models of processes in an MPI program, and when a failure occus, these models are analyzed probabilistically to find the origin of the failure. The output of the tool is MPI processes ranked by the abnormality degree and regions of code where faults are first manifested. The granularity of code region is an MPI call or a computation region between two MPI calls.

Source record↗

A Faster-Than-Real-Time Framework for Reliability-Oriented Simulation of PV Inverters

Physics-of-Failure (PoF) based reliability assessment for photovoltaic (PV) inverters requires long-duration electrical and electrothermal stress histories, yet generating such stress histories with high-fidelity switching models over year long mission profiles is computationally prohibitive. Conventional methods either sacrifice modeling fidelity for speed or require runtimes that are impractical for design iteration and uncertainty studies. To address this bottleneck, this paper presents a High-Performance Computing (HPC) based simulation frame work for faster-than-real-time reliability-oriented simulation. The proposed framework integrates the Average-to-Switching (A2S) method with parallel computing techniques to accelerate switching-level waveform reconstruction. We further introduce optimization strategies, including cluster merging and sensitivity based mission profile screening, to reduce the computational burden. Evaluated using real-world mission profile inputs and a MATLAB/Simulink switching-model reference, the framework reduces the simulation time for a one-year mission from an intractable multi-year duration to approximately 7.3 minutes while maintaining low waveform error. This acceleration provides a practical reliability-oriented simulation engine that can be coupled with component-specific aging models for subsequent PV inverter PoF assessment.

High-performance Computing↗

Moving target, distributed, real-time simulation using Ada

Research on a precompiler solution is described for the moving target compiler problem encountered when trying to run parallel simulation algorithms on several microcomputers. The precompiler is under development at NASA-Lewis for simulating jet engines. Since the behavior of any component of a jet engine, e.g., the fan inlet, rear duct, forward sensor, etc., depends on the previous behaviors and not the current behaviors of other components, the behaviors can be modeled on different processors provided the outputs of the processors reach other processors in appropriate time intervals. The simulator works in compute and transfer modes. The Ada procedure sets for the behaviors of different components are divided up and routed by the precompiler, which essentially receives a multitasking program. The subroutines are synchronized after each computation cycle.

Collins, W. R.↗