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At least 523 records · Page 29

Performance Potential of Mixed Data Management Modes for Heterogeneous Memory Systems

Many high-performance systems now include different types of memory devices within the same compute platform to meet strict performance and cost constraints. Such heterogeneous memory systems often include an upper-level tier with better performance, but limited capacity, and lower-level tiers with higher capacity, but less bandwidth and longer latencies for reads and writes. To utilize the different memory layers efficiently, current systems rely on hardware-directed, memory -side caching or they provide facilities in the operating system (OS) that allow applications to make their own data-tier assignments. Since these data management options each come with their own set of trade-offs, many systems also include mixed data management configurations that allow applications to employ hardware- and software-directed management simultaneously, but for different portions of their address space. Despite the opportunity to address limitations of stand-alone data management options, such mixed management modes are under-utilized in practice, and have not been evaluated in prior studies of complex memory hardware. In this work, we develop custom program profiling, configurations, and policies to study the potential of mixed data management modes to outperform hardware- or software-based management schemes alone. Our experiments, conducted on an Intel ® Knights Landing platform with high-bandwidth memory, demonstrate that the mixed data management mode achieves the same or better performance than the best stand-alone option for five memory intensive benchmark applications (run separately and in isolation), resulting in an average speedup compared to the best stand-alone policy of over 10 %, on average.

Effler, Chad↗

Cryogenic measurements of aerojet GaAs n-JFETs

The spectral noise characteristics of Aerojet gallium arsenide (GaAs) junction field effect transistors (JFET's) have been investigated down to liquid-helium temperatures. Noise characterization was performed with the field effect transistor (FET) in the floating-gate mode, in the grounded-gate mode to determine the lowest noise readings possible, and with an extrinsic silicon photodetector at various detector bias voltages to determine optimum operating conditions. The measurements indicate that the Aerojet GaAs JFET is a quiet and stable device at liquid helium temperatures. Hence, it can be considered a readout line driver or infrared detector preamplifier as well as a host of other cryogenic applications. Its noise performance is superior to silicon (Si) metal oxide semiconductor field effect transistor (MOSFET's) operating at liquid helium temperatures, and is equal to the best Si n channel junction field effect transistor (n-JFET's) operating at 300 K.

Goebel, John H.↗

Readout of DSN Monitor Data

DSN Monitor Data Reader is a computer program that, as its name suggests, reads file of monitor data from the Deep Space Network (DSN). The monitor data constitute information on the status and performance of tracking, telemetry, command, and pointing equipment at the DSN antennas. The DSN has recently introduced a new, more advanced monitor data format, denoted 0158-Mon, that is based on the standard formatted data unit (SFDU) and compressed header data objects (CHDO) of the Consultative Committee for Space Data Systems (CCSDS). The 0158-Mon data format is a very flexible generic format that provides for specific variable-length formats and for self-identifying parameters that obviate the proprietary NASA Communications (NASCOM) bit-packed formats of the past. The monitor data SFDUs are also encapsulated in Standard DSN Blocks and routed to DSN customers for processing at their local mission control centers. This program helps a DSN customer to read and parse the monitor data to assess the statuses of the DSN stations in support of spacecraft flight operations.

Levister, Katherine↗

Collective operations in a file system based execution model

A mechanism is provided for group communications using a MULTI-PIPE synthetic file system. A master application creates a multi-pipe synthetic file in the MULTI-PIPE synthetic file system, the master application indicating a multi-pipe operation to be performed. The master application then writes a header-control block of the multi-pipe synthetic file specifying at least one of a multi-pipe synthetic file system name, a message type, a message size, a specific destination, or a specification of the multi-pipe operation. Any other application participating in the group communications then opens the same multi-pipe synthetic file. A MULTI-PIPE file system module then implements the multi-pipe operation as identified by the master application. The master application and the other applications then either read or write operation messages to the multi-pipe synthetic file and the MULTI-PIPE synthetic file system module performs appropriate actions.

97 MATHEMATICS AND COMPUTING↗

Collective operations in a file system based execution model

A mechanism is provided for group communications using a MULTI-PIPE synthetic file system. A master application creates a multi-pipe synthetic file in the MULTI-PIPE synthetic file system, the master application indicating a multi-pipe operation to be performed. The master application then writes a header-control block of the multi-pipe synthetic file specifying at least one of a multi-pipe synthetic file system name, a message type, a message size, a specific destination, or a specification of the multi-pipe operation. Any other application participating in the group communications then opens the same multi-pipe synthetic file. A MULTI-PIPE file system module then implements the multi-pipe operation as identified by the master application. The master application and the other applications then either read or write operation messages to the multi-pipe synthetic file and the MULTI-PIPE synthetic file system module performs appropriate actions.

97 MATHEMATICS AND COMPUTING↗

Accurate Holdup Calculations with Predictive Modeling & Data Integration

In facilities that process special nuclear material (SNM) it is important to account accurately for the fissile material that enters and leaves the plant. Although there are many stages and processes through which materials must be traced and measured, the focus of this project is material that is “held-up” in equipment, pipes, and ducts during normal operation and that can accumulate over time into significant quantities. Accurately estimating the holdup is essential for proper SNM accounting (vis-à-vis nuclear non-proliferation), criticality and radiation safety, waste management, and efficient plant operation. Usually it is not possible to directly measure the holdup quantity and location, so these must be inferred from measured radiation fields, primarily gamma and less frequently neutrons. Current methods to quantify holdup, i.e. Generalized Geometry Holdup (GGH), primarily rely on simple source configurations and crude radiation transport models aided by ad hoc correction factors. This project seeks an alternate method of performing measurement-based holdup calculations using a predictive model that employs state-of-the-art radiation transport codes capable of accurately simulating such situations. Inverse and data assimilation methods use the forward transport model to search for a source configuration that best matches the measured data and simultaneously provide an estimate of the level of confidence in the correctness of such configuration. In this work the holdup problem is re-interpreted as an inverse problem that is under-determined, hence may permit multiple solutions. A probabilistic approach is applied to solving the resulting inverse problem. This approach rates possible solutions according to their plausibility given the measurements and initial information. This is accomplished through the use of Bayes’ Theorem that resolves the issue of multiple solutions by giving an estimate of the probability of observing each possible solution. To use Bayes’ Theorem, one must have a model y(x) that maps the state variables x (the solution in this case) to the measurements y. In this case, the unknown state variables are the configuration and composition of the heldup SNM. The measurements are the detector readings. Thus, the natural model is neutral-particle radiation transport where a wealth of computational tools exists for performing these simulations accurately and efficiently. The combination of predictive model and Bayesian inference forms the Data Integration with Modeled Predictions (DIMP) method that serves as foundation for this project. The cost functional describing the model-to-data misfit is computed via a norm created by the inverse of the covariance matrix of the model parameters and responses. Since the model y(x) for the holdup problem is nonlinear, a nonlinear optimization on Q is conducted via Newton-type iterative methods to find the optimal values of the model parameters x. This project comprised a collaboration between NC State University (NCSU), the University of South Carolina (USC), and Oak Ridge National Laboratory (ORNL). The project was originally proposed in seven main tasks with an eighth contingency task to be performed if time and funding permitted; in fact time did not permit commencement of the contingency task and it was not performed. The remaining tasks involved holdup analysis with gamma detection strategies and separately with neutrons based on coincidence counting. Early in the project, and upon consultation with experts in coincidence counting it became evident that this approach is not viable for holdup applications and this task was replaced with an alternative, but valuable investigation that was carried out by the USC partner. Nevertheless, the experimental 4 measurements at ORNL of both gamma and neutron sources for the purpose of constructing Detector Response Functions (DRFs) with the associated uncertainties were indeed completed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A BrachyPhantom for verification of dose calculation of HDR brachytherapy planning system

Purpose: To develop a calibration phantom for {sup 192}Ir high dose rate (HDR) brachytherapy units that renders possible the direct measurement of absorbed dose to water and verification of treatment planning system.Methods: A phantom, herein designated BrachyPhantom, consists of a Solid Water™ 8-cm high cylinder with a diameter of 14 cm cavity in its axis that allows the positioning of an A1SL ionization chamber with its reference measuring point at the midheight of the cylinder's axis. Inside the BrachyPhantom, at a 3-cm radial distance from the chamber's reference measuring point, there is a circular channel connected to a cylindrical-guide cavity that allows the insertion of a 6-French flexible plastic catheter from the BrachyPhantom surface. The PENELOPE Monte Carlo code was used to calculate a factor, P{sub sw}{sup lw}, to correct the reading of the ionization chamber to a full scatter condition in liquid water. The verification of dose calculation of a HDR brachytherapy treatment planning system was performed by inserting a catheter with a dummy source in the phantom channel and scanning it with a CT. The CT scan was then transferred to the HDR computer program in which a multiple treatment plan was programmed to deliver a total dose of 150 cGy to the ionization chamber. The instrument reading was then converted to absorbed dose to water using the N{sub gas} formalism and the P{sub sw}{sup lw} factor. Likewise, the absorbed dose to water was calculated using the source strength, S{sub k}, values provided by 15 institutions visited in this work.Results: A value of 1.020 (0.09%, k= 2) was found for P{sub sw}{sup lw}. The expanded uncertainty in the absorbed dose assessed with the BrachyPhantom was found to be 2.12% (k= 1). To an associated S{sub k} of 27.8 cGy m{sup 2} h{sup −1}, the total irradiation time to deliver 150 cGy to the ionization chamber point of reference was 161.0 s. The deviation between the absorbed doses to water assessed with the BrachyPhantom and those calculated by the treatment plans and using the S{sub k} values did not exceed ±3% and ±1.6%, respectively.Conclusions: The BrachyPhantom may be conveniently used for quality assurance and/or verification of HDR planning system with a priori threshold level to spot problems of 2% and ±3%, respectively, and in the long run save time for the medical physicist.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Readout optimization of multi-amplifier sensing charge-coupled devices for single-quantum measurement

The non-destructive readout capability of the Skipper Charge Coupled Device (CCD) has been demonstrated to reduce the noise limitation of conventional silicon devices to levels that allow single-photon or single-electron counting. The noise reduction is achieved by taking multiple measurements of the charge in each pixel. These multiple measurements come at the cost of extra readout time, which has been a limitation for the broader adoption of this technology in particle physics, quantum imaging, and astronomy applications. This work presents recent results of a novel sensor architecture that uses multiple non-destructive floating-gate amplifiers in series to achieve sub-electron readout noise in a thick, fully-depleted silicon detector to overcome the readout time overhead of the Skipper-CCD. This sensor is called the Multiple-Amplifier Sensing Charge-Coupled Device (MAS-CCD) can perform multiple independent charge measurements with each amplifier, and the measurements from multiple amplifiers can be combined to further reduce the readout noise. We will show results obtained for sensors with 8 and 16 amplifiers per readout stage in new readout operations modes to optimize its readout speed. The noise reduction capability of the new techniques will be demonstrated in terms of its ability to reduce the noise by combining the information from the different amplifiers, and to resolve signals in the order of a single photon per pixel. The first readout operation explored here avoids the extra readout time needed in the MAS-CCD to read a line of the sensor associated with the extra extent of the serial register. The second technique explore the capability of the MAS-CCD device to perform a region of interest readout increasing the number of multiple samples per amplifier in a targeted region of the active area of the device.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Performance and characterization of the SPT-3G digital frequency-domain multiplexed readout system using an improved noise and crosstalk model

The third-generation South Pole Telescope camera (SPT-3G) improves upon its predecessor (SPTpol) by an order of magnitude increase in detectors on the focal plane. The technology used to read out and control these detectors, digital frequency-domain multiplexing (DfMUX), is conceptually the same as used for SPTpol, but extended to accommodate more detectors. A nearly 5× expansion in the readout operating bandwidth has enabled the use of this large focal plane, and SPT-3G performance meets the forecasting targets relevant to its science objectives. However, the electrical dynamics of the higher-bandwidth readout differ from predictions based on models of the SPTpol system due to the higher frequencies used and parasitic impedances associated with new cryogenic electronic architecture. To address this, we present an updated derivation for electrical crosstalk in higher-bandwidth DfMUX systems and identify two previously uncharacterized contributions to readout noise, which become dominant at high bias frequency. The updated crosstalk and noise models successfully describe the measured crosstalk and readout noise performance of SPT-3G. These results also suggest specific changes to warm electronics component values, wire-harness properties, and SQUID parameters, to improve the readout system for future experiments using DfMUX, such as the LiteBIRD space telescope.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Spatially uniform resistance switching of low current, high endurance titanium–niobium-oxide memristors

Here we analyzed micrometer-scale titanium-niobium-oxide prototype memristors, which exhibited low write-power (< 3 μW) and energy (< 200 fJ per bit per μm 2 ), low read-power (~nW), and high endurance ( > millions of cycles). To understand their physico-chemical operating mechanisms, we performed in operando synchrotron X-ray transmission nanoscale spectromicroscopy using an ultra-sensitive time-multiplexed technique. We observed only spatially uniform material changes during cell operation, in sharp contrast to the frequently detected formation of a localized conduction channel in transition-metal-oxide memristors. We also associated the response of assigned spectral features distinctly to non-volatile storage (resistance change) and writing of information (application of voltage and Joule heating). Lastly, these results provide critical insights into high-performance memristors that will aid in device design, scaling and predictive circuit-modeling, all of which are essential for the widespread deployment of successful memristor applications.

36 MATERIALS SCIENCE↗

Genotyping‐in‐Thousands by sequencing (GT‐seq): A cost effective SNP genotyping method based on custom amplicon sequencing

Abstract Genotyping‐in‐Thousands by sequencing ( GT ‐seq) is a method that uses next‐generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50–500) of targeted single‐nucleotide polymorphisms ( SNP s) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon‐specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout ( Oncorhynchus mykiss ) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan ™ genotypes at the same 192 loci, but call rates were slightly lower with GT ‐seq (96.4%) relative to Taqman (99.0%). Of the 192 SNP s, 187 were genotyped in ≥90% of the individual samples and only 3 SNP s were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT ‐seq greatly reduces the cost of genotyping hundreds of targeted SNP s relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.

Campbell, Nathan R.↗

P3DFFT: A Framework for Parallel Computations of Fourier Transforms in Three Dimensions

Fourier and related transforms are a family of algorithms widely employed in diverse areas of computational science, notoriously difficult to scale on high-performance parallel computers with a large number of processing elements (cores). This paper introduces a popular software package called P3DFFT which implements fast Fourier transforms (FFTs) in three dimensions in a highly efficient and scalable way. It overcomes a well-known scalability bottleneck of three-dimensional (3D) FFT implementations by using two-dimensional domain decomposition. Designed for portable performance, P3DFFT achieves excellent timings for a number of systems and problem sizes. On a Cray XT5 system P3DFFT attains 45% efficiency in weak scaling from 128 to 65,536 computational cores. Library features include Fourier and Chebyshev transforms, Fortran and C interfaces, in- and out-of-place transforms, uneven data grids, and single and double precision. P3DFFT is available as open source at http://code.google.com/p/p3dfft/. This paper discusses P3DFFT implementation and performance in a way that helps guide the user in making optimal choices for parameters of their runs. Read More: https://epubs.siam.org/doi/10.1137/11082748X

Mathematics↗

Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011: Phylogeny, Selection Pressure and Evolutionary Time-Scale Analysis

West Nile virus (WNV), an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03). We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006–2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999–2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006–2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.0661024 substitutions/site/year (s/s/y). The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naive environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific therapies.

59 BASIC BIOLOGICAL SCIENCES↗

Large-Constraint-Length, Fast Viterbi Decoder

Scheme for efficient interconnection makes VLSI design feasible. Concept for fast Viterbi decoder provides for processing of convolutional codes of constraint length K up to 15 and rates of 1/2 to 1/6. Fully parallel (but bit-serial) architecture developed for decoder of K = 7 implemented in single dedicated VLSI circuit chip. Contains six major functional blocks. VLSI circuits perform branch metric computations, add-compare-select operations, and then store decisions in traceback memory. Traceback processor reads appropriate memory locations and puts out decoded bits. Used as building block for decoders of larger K.

Collins, O.↗

The infrared spectrograph during the SIRTF pre-definition phase

A test facility was set up to evaluate back-illuminated impurity band detectors constructed for an infrared spectrograph to be used on the Space Infrared Telescope Facility (SIRTF). Equipment built to perform the tests on these arrays is described. Initial tests have been geared toward determining dark current and read noise for the array. Four prior progress reports are incorporated into this report. They describe the first efforts in the detector development and testing effort; testing details and a new spectrograph concept; a discussion of resolution issues raised by the new design; management activities; a review of computer software and testing facility hardware; and a review of the preamplifier constructed as well as a revised schematic of the detector evaluation facility.

Houck, James R.↗

InSb DRO array characteristics

Researchers tested 58 x 62 low-doped InSb diode arrays bonded to MOSFET readouts for their performance potential in a low background space environment. Of primary concern were the quantum efficiency, dark current and read noise. The quantum efficiency (45 percent at 3.3 microns) and dark current (less than 2.4e(-)/s) were found to be adequate for the Space Infrared Telescope Facility (SIRTF) experiments, while the read noise (200 e(-) RMS) was found to be wanting. More subtle concerns, such as image quality, linearity/calibratibility and flat fielding were also investigated. In these respects the arrays appear to be well suited for the high sensitivity, photometric accuracy, and image clarity demanded by the SIRTF experiments.

Forrest, W. J.↗

A model-based approach to the symbolic control of space subsystems

A multilayered approach to the symbolic control of complex electromechanical assemblies, such as spaceborne thermal, power, and life subsystems, is discussed. An example of this approach is given in some recent tests of the Thermal Expert System (TEXSYS) in control of the Boeing Aerospace Thermal Bus System (BATBS), a prototype two-phase Space Station Freedom thermal bus. The BATBS hardware requires read-update-act cycles of under a minute, and it is subject to dynamic reconfiguration while operating. These performance requirements are addressed by layering model-based expert system software on a conventional numerical data acquisition and control system. TEXSYS test results demonstrate both nominal control and fault recovery actions with the BATBS. Dynamic modification of the symbolic model used in this approach is compared to that of a classical numerical adaptive controller.

Glass, B. J.↗

A Simulator Study of the Effectiveness of a Pilot's Indicator which Combined Angle of Attack and Rate of Change of Total Pressure as Applied to the Take-Off Rotation and Climbout of a Supersonic Transport

A simulator study has been made to determine the effectiveness of a single instrument presentation as an aid to the pilot in controlling both rotation and climbout path in take-off. The instrument was basically an angle-of-attack indicator, biased with a total-pressure-rate input as a means of suppressing the phugoid oscillation. Linearized six-degree-of-freedom equations of motion were utilized in simulating a hypothetical supersonic transport as the test vehicle. Each of several experienced pilots performed a number of simulated take-offs, using conventional flight instruments and either an angle-of-attack instrument or the combined angle-of-attack and total-pressure-rate instrument. The pilots were able to rotate the airplane, with satisfactory precision, to the 15 deg. angle of attack required for lift-off when using either an angle-of-attack instrument or the instrument which combined total-pressure-rate with angle of attack. At least 4 to 6 second-S appeared to be required for rotation to prevent overshoot, particularly with the latter instrument. The flight paths resulting from take-offs with simulated engine failures were relatively smooth and repeatable within a reasonably narrow band when the combined angle-of-attack and total-pressure-rate instrument presentation was used. Some of the flight paths resulting from take-offs with the same engine-failure conditions were very oscillatory when conventional instruments and an angle-of-attack instrument were used. The pilots considered the combined angle-of-attack and total- pressure-rate instrument a very effective aid. Even though they could, with sufficient practice, perform satisfactory climbouts after simulated engine failure by monitoring the conventional instruments and making correction based on their readings, it was much easier to maintain a smooth flight path with the single combined angle-of-attack and total-pressure-rate instrument.

Hall, Albert W.↗