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At least 181 records · Page 10

Xavier: High-Performance X-Drop Adaptive Banded Pairwise Alignment (Xavier) v1.0

Pairwise sequence alignment is one of the most compute-intense challenges for the analysis of genomics data and it can account for more than 90% of the runtime depending on the application. Despite the effort to reduce the computational cost introducing heuristics such as banded and x-drop alignment, the performance of state-of-the-art software is often unsatisfactory for long sequences. Recent advances in single-molecule sequencing technologies keep increasing the length of the sequences to align at the cost of higher error rates b ranging from 5% to 15% b, emphasizing the need for fast and accurate software. Our long-read alignment software, named Xavier, computes high-performance x-drop adaptive banded pairwise alignment exploiting instruction-level parallelism via Single-Instruction-Multiple-Data (SIMD) operations. Xavier uses a narrow bandwidth that appreciably improves performance reducing the search space for the optimal alignment. In our experiment, the adaptive mechanism enables Xavier to find the optimal alignment between related sequences even when the error rate is as high as 50%. Xavier achieves speed-up up to 5X over competitor software when enabling the x-drop termination and up to 415X when disabling it, with negligible accuracy loss.

Guidi, Giulia↗

Performance study of a data flow architecture

Teams of scientists studied data flow concepts, static data flow machine architecture, and the VAL language. Each team mapped its application onto the machine and coded it in VAL. The principal findings of the study were: (1) Five of the seven applications used the full power of the target machine. The galactic simulation and multigrid fluid flow teams found that a significantly smaller version of the machine (16 processing elements) would suffice. (2) A number of machine design parameters including processing element (PE) function unit numbers, array memory size and bandwidth, and routing network capability were found to be crucial for optimal machine performance. (3) The study participants readily acquired VAL programming skills. (4) Participants learned that application-based performance evaluation is a sound method of evaluating new computer architectures, even those that are not fully specified. During the course of the study, participants developed models for using computers to solve numerical problems and for evaluating new architectures. These models form the bases for future evaluation studies.

Adams, George↗

Optimization of an optically implemented on-board FDMA demultiplexer

Performance of a 30 GHz frequency division multiple access (FDMA) uplink to a processing satellite is modelled for the case where the onboard demultiplexer is implemented optically. Included in the performance model are the effects of adjacent channel interference, intersymbol interference, and spurious signals associated with the optical implementation. Demultiplexer parameters are optimized to provide the minimum bit error probability at a given bandwidth efficiency when filtered QPSK modulation is employed.

Fargnoli, J.↗

Multiabsorber Transition-Edge Sensors for X-Ray Astronomy

We are developing arrays of position-sensitive microcalorimeters for future x-ray astronomy applications. These position-sensitive devices commonly referred to as hydras consist of multiple x-ray absorbers, each with a different thermal coupling to a single-transition-edge sensor microcalorimeter. Their development is motivated by a desire to achieve very large pixel arrays with some modest compromise in performance. We report on the design, optimization, and first results from devices with small pitch pixels (<75 μm) being developed for a high-angular and energy resolution imaging spectrometer for Lynx. The Lynx x-ray space telescope is a flagship mission concept under study for the National Academy of Science 2020 decadal survey. Broadband full-width-half-maximum (FWHM) resolution measurements on a 9-pixel hydra have demonstrated ΔE(FWHM) = 2.23 ± 0.14 eV at Al-Kα, ΔE(FWHM) = 2.44 ± 0.29 eV at Mn-Kα, and ΔE(FWHM) = 3.39 ± 0.23 eV at Cu-Kα. Position discrimination is demonstrated to energies below <1 keV and the device performance is well-described by a finite-element model. Results from a prototype 20-pixel hydra with absorbers on a 50-μm pitch have shown ΔE(FWHM) = 3.38 ± 0.20 eV at Cr-Kα1. We are now optimizing designs specifically for Lynx and extending the number of absorbers up to 25/hydra. Numerical simulation suggests optimized designs could achieve ∼3 eV while being compatible with the bandwidth requirements of the state-of-the art multiplexed readout schemes, thus making a 100,000 pixel microcalorimeter instrument a realistic goal.

Smith, Stephen J.↗

Dual-mode coaxial feed with low crosspolarisation

Design data for optimized TE(11)-TM(11) dual-mode coaxial prime focus feeds is presented. The optimized feeds have a crosspolarization below -30 dB, an input reflection coefficient below 0.1 and very little phase error in their radiation patterns, over a 5 percent bandwidth. Experimental patterns are also given that show that the theoretically derived design data can be relied upon. The optimized feeds are useful for paraboloidal reflectors with focal-length/diameter ratios in the range 0.3 to 0.5, and will give overall efficiencies as high as 70 percent or more with sidelobes below -30 dB.

Collin, R. E.↗

Parametric optimization of fiber to waveguide coupler using Bragg gratings

The uniform grating coupler which consists of two pairs of reflector layers in the substrate region has been proposed to couple the optical power from single mode fiber to standard 220 nm silicon-on-insulator waveguide. The efficiency of ≈ 79% in a broadband 3 dB bandwidth of ≈ 150 nm is achieved for uniform Bragg grating coupler devices. Further, by making a sequence of chirped and uniform grating, the power coupling efficiency of ≈ 98% at 1550 nm wavelength and 3 dB bandwidth of 35 nm is achieved. The importance and benefits of reflector layers along with its parametric optimization is thoroughly investigated for the calculation of optimum coupling efficiency. This research mainly focus on fiber-to-waveguide/waveguide-to-fiber coupling design. The major contribution of the research focuses on compact and efficient optical interconnection of coupler devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

High Momentum Transfer Nucleon Elastic Electromagnetic Form Factor Measurements Using Super BigBite Spectrometer at Jefferson Lab

The nucleons - protons and neutrons - are the basic building blocks of atomic nuclei. We now know that the nucleon consists of fundamental particles called quarks and gluons. The quarks interact with each other by exchanging gluons via the strong interaction. Understanding the quark-gluon structure of the nucleon, especially the confinement of quarks within the nucleon in its ground state, remains one of the main unsolved puzzles of particle physics. The nucleon electromagnetic form factors are directly related to the internal structure of the nucleon. A new generation of high precision experiments, GEp-V, GEn-II, GEn-RP, and GMn, measuring the ground state nucleon space-like electro-magnetic form factor at high momentum transfer is underway at Jefferson Lab experimental Hall-A as part of the Super Bigbite Spectrometer (SBS) program. This series of experiments will provide a new level of understanding of the nucleon structure. These experiments are highly demanding due to the extremely fast drop off of the elastic cross section with the increasing four-momentum transfer squared(Q2). This thesis provides an overview of the SBS physics program and reports on the extensive R&D program carried out to achieve the high rate running conditions essential for carrying out the SBS experiments. SBS will provide an intermediate solid angle of approximately 35 msr, which is significantly larger than the solid angle of other dipole based spectrometers at Jefferson lab. Of course, there are much larger acceptance spectrometers at Jefferson Lab, CLAS12 for example. What is special about SBS is that it provides a sizable acceptance while operating at the highest possible luminosity at Jefferson Lab. With this combination of medium acceptance and the highest available luminosity, SBS provides an unparalleled opportunity to explore the nucleon in its ground state with unprecedented resolution. The relatively large acceptance of SBS is achieved by using a large gap dipole magnet and placing it close to the target. An unavoidable consequence of this is that the SBS GEM trackers and other detectors have a clear line-of-sight view of the target and a portion of the beam-line. As a result, the background hit rate in the SBS front GEM trackers is expected to be up to 500 kHz/cm2, over the entire active area of 6000 cm2. To the best of our knowledge, this extremely high rate over such a large area is unprecedented in any particle tracking system used anywhere in the world before. Correctly reconstructing the particle tracks of interest in this very high background environment is achieved by using especially adapted high rate techniques at every step of the tracking process: optimizing the GEM module and tracker design at the hardware level, using high bandwidth electronics and real time Field Programmable Gate Array (FPGA) based background suppression techniques at the Data Acquisition (DAQ) level, and developing highly specialized tracking algorithms to pick out the signal hits from among the vast amount of background hits. In order to ensure a smooth start and running of the SBS experiments, it is extremely crucial that these techniques are developed, implemented, and tested under realistic conditions well before the actual start of the SBS experimental program. A detailed Geant4 simulation of the experiment was combined with a digitization package to generate the detector level pseudodata similar to what is expected in the actual experiments. The digitization procedures were calibrated against actual GEM data from cosmic-ray runs, X-ray tests, beam test runs in experimental Hall-A, and the PRad experiment in Hall B. Then, optimized tracking algorithms were developed and implemented in an analysis program used to analyze these pseudo-data and to extract expected high-level parameters. These extracted quantities were then compared with the input parameters from the simulation to verify and determine the performance characteristics for the SBS tracker. From this work, a final tracking efficiency of 69% at 25% occupancy was achieved, with the required reconstruction accuracy, for the GMn experiment, the first experiment in the SBS program, with background level at 100 kHz/cm2. These demonstrated parameters are adequate for the successful running of not only the GMn experiment but as well as for GEn-RP and GEn-II experiments, the second and third experiments in the program. This work builds the solid ground to further improve the tracking performance for these experiments and achieve similar conditions for the running of the GEp-V experiment, the most demanding experiment in the SBS program, with an expected background level at 500 kHz/cm2.

Di, Danning↗

Efficient on-chip terahertz generation and detection with GaN photoconductive emitters

Photoconductive emitters for terahertz generation hold promise for highly efficient down-conversion of optical photons because it is not constrained by the Manley-Rowe relation. Existing terahertz photoconductive devices, however, faces limits in efficiency due to the semiconductor properties of commonly used GaAs materials. Here, we demonstrate that large bandgap semiconductor GaN, characterized by its high breakdown electric field, facilitates the highly efficient generation of terahertz waves in a coplanar stripline waveguide. Towards this goal, we investigated the excitonic contribution to the electro-optic response of GaN under static electric field both through experiments and first-principles calculations, revealing a robust excitonic Stark shift. Using this electro-optic effect, we developed a novel ultraviolet pump-probe spectroscopy for in-situ characterization of the terahertz electric field strength generated by the GaN photoconductive emitter. Our findings show that terahertz power scales quadratically with optical excitation power and applied electric field over a broad parameter range. We achieved an optical-to-terahertz conversion efficiency approaching 100% within the 0.03–1 THz bandwidth at the highest bias field (116 kV/cm) in our experiment. Further optimization of GaN-based terahertz generation devices could achieve even greater optical-to-terahertz conversion efficiencies.

Uzundal, Can B↗

A High Performance Block Eigensolver for Nuclear Configuration Interaction Calculations

As on-node parallelism increases and the performance gap between the processor and the memory system widens, achieving high performance in large-scale scientific applications requires an architecture-aware design of algorithms and solvers. We focus on the eigenvalue problem arising in nuclear Configuration Interaction (CI) calculations, where a few extreme eigenpairs of a sparse symmetric matrix are needed. Here, we consider a block iterative eigensolver whose main computational kernels are the multiplication of a sparse matrix with multiple vectors (SpMM), and tall-skinny matrix operations. We then present techniques to significantly improve the SpMM and the transpose operation SpMM T by using the compressed sparse blocks (CSB) format. We achieve 3-4× speedup on the requisite operations over good implementations with the commonly used compressed sparse row (CSR) format. We develop a performance model that allows us to correctly estimate the performance of our SpMM kernel implementations, and we identify cache bandwidth as a potential performance bottleneck beyond DRAM. We also analyze and optimize the performance of LOBPCG kernels (inner product and linear combinations on multiple vectors) and show up to 15× speedup over using high performance BLAS libraries for these operations. The resulting high performance LOBPCG solver achieves 1.4× to 1.8× speedup over the existing Lanczos solver on a series of CI computations on high-end multicore architectures (Intel Xeons). We also analyze the performance of our techniques on an Intel Xeon Phi Knights Corner (KNC) processor.

97 MATHEMATICS AND COMPUTING↗

Evaluation of the Single-precision Floatingpoint Vector Add Kernel Using the Intel FPGA SDK for OpenCL

Open Computing Language (OpenCL) is a high-level language that enables software programmers to explore Field Programmable Gate Arrays (FPGAs) for application acceleration. The Intel FPGA software development kit (SDK) for OpenCL allows a user to specify applications at a high level and explore the performance of low-level hardware acceleration. In this report, we present the FPGA performance and power consumption results of the single-precision floating-point vector add OpenCL kernel using the Intel FPGA SDK for OpenCL on the Nallatech 385A FPGA board. The board features an Arria 10 FPGA. We evaluate the FPGA implementations using the compute unit duplication and kernel vectorization optimization techniques. On the Nallatech 385A FPGA board, the maximum compute kernel bandwidth we achieve is 25.8 GB/s, approximately 76% of the peak memory bandwidth. The power consumption of the FPGA device when running the kernels ranges from 29W to 42W.

97 MATHEMATICS AND COMPUTING↗

Rate 3/4 convolutional coding of 16-PSK - Code design and performance study

Convolutional coding coupled with 16-PSK modulation is investigated for bandwidth efficient transmission. Rate 3/4, small memory codes are found which are optimized in the free-distance sense on the Gaussian channel. These codes provide up to 4.8 dB of coding gain with 32 states over uncoded 8-PSK, a scheme having the same spectral efficiency as the codes described. The performance is compared with earlier findings of Ungerboeck and some recent results on R = 2/3 coded 8-PSK. In addition, results of a channel transmission study to assess the performance of the four-state code on the band-limited nonlinear channel are presented, and it is found that performance of the coded scheme degrades comparably with uncoded 8-PSK, i.e., coding gain is roughly preserved.

Wilson, S. G.↗

An Atmospheric General Circulation Model with Chemistry for the CRAY T3E: Design, Performance Optimization and Coupling to an Ocean Model

The design, implementation and performance optimization on the CRAY T3E of an atmospheric general circulation model (AGCM) which includes the transport of, and chemical reactions among, an arbitrary number of constituents is reviewed. The parallel implementation is based on a two-dimensional (longitude and latitude) data domain decomposition. Initial optimization efforts centered on minimizing the impact of substantial static and weakly-dynamic load imbalances among processors through load redistribution schemes. Recent optimization efforts have centered on single-node optimization. Strategies employed include loop unrolling, both manually and through the compiler, the use of an optimized assembler-code library for special function calls, and restructuring of parts of the code to improve data locality. Data exchanges and synchronizations involved in coupling different data-distributed models can account for a significant fraction of the running time. Therefore, the required scattering and gathering of data must be optimized. In systems such as the T3E, there is much more aggregate bandwidth in the total system than in any particular processor. This suggests a distributed design. The design and implementation of a such distributed 'Data Broker' as a means to efficiently couple the components of our climate system model is described.

Farrara, John D.↗

Achievable Performance and Effective Interrogator Design for SAW RFID Sensor Tags

For many NASA missions, remote sensing is a critical application that supports activities such as environmental monitoring, planetary science, structural shape and health monitoring, non-destructive evaluation, etc. The utility of the remote sensing devices themselves is greatly increased if they are passive that is, they do not require any on-board power supply such as batteries and if they can be identified uniquely during the sensor interrogation process. Additional passive sensor characteristics that enable greater utilization in space applications are small size and weight, long read ranges with low interrogator power, ruggedness, and operability in extreme environments (vacuum, extreme high/low temperature, high radiation, etc.) In this paper, we consider one very promising passive sensor technology, called surface acoustic wave (SAW) radio-frequency identification (RFID), that satisfies all of these criteria. Although SAW RFID tags have great potential for use in numerous space-based remote sensing applications, the limited collision resolution capability of current generation tags limits the performance in a cluttered sensing environment. That is, as more SAW-based sensors are added to the environment, numerous tag responses are superimposed at the receiver and decoding all or even a subset of the telemetry becomes increasingly difficult. Background clutter generated by reflectors other than the sensors themselves is also a problem, as is multipath interference and signal distortion, but the limiting factor in many remote sensing applications can be expected to be tag mutual interference. This problem may be greatly mitigated by proper design of the SAW tag waveform, but that remains an open research problem, and in the meantime, several other related questions remain to be answered including: What are the fundamental relationships between tag parameters such as bit-rate, time-bandwidth-product, SNR, and achievable collision resolution? What are the differences in optimal or near-optimal interrogator designs between noise-limited environments and interference-limited environments? What are the performance characteristics of different interrogator designs in term of parameters such as transmitter power level, range, and number of interfering tags? In this paper, we present the results of a research effort aimed at providing at least partial answers to all of these questions.

Barton, Richard J.↗

Study Results and Plans for Future Improvement of the NSLS-II FOFB System

Currently, the fast orbit feedback (FOFB) system correct the transverse orbit in both planes via air coil magnets installed over low conductivity sections of vacuum chamber (stainless steel bellows) with a fast acquisition (FA) that samples at 10kHz. Bandwidth of a few kHz has been achieved (power-supply + corrector + vacuum chamber) for the purpose that the FOFB bandwidth limitation is not anymore limited by the correctors. The bandwidths of the FOFB system in both planes have been experimentally characterized in the open-loop condition via sinwave excitation method. They are significantly lower than the measurements (2.5kHz in x) done by Weixing Chen et al when the control system was largely bypassed, only from PSI to fast correctors, final to BPM. The estimated dI/dt as a function of the frequency from the beam noise spectrum has been compared to the slew rate of the power supply. The most recent study evidences: after the optimization of fast corrector compensation circuit, the power supply system along shows the 3dB bandwidth of 5.6kHz in the horizontal plane and 3.5kHz in the vertical plane. Preliminary beam studies indicate the potential increase of the system bandwidth and the gain within the FOFB bandwidth. Finally, the plan for combing the FOFB and SOFB systems to correct down to DC has been discussed.

36 MATERIALS SCIENCE↗

Circular Corrugated Miter Bend and Gap Losses for Broadband Frequency Applications

Circular corrugated waveguides are often used in fusion applications at single, multiple, or broadband millimeter frequencies due to their low ohmic loss, expected large frequency bandwidth, and direct coupling to free-space Gaussian modes. For single-frequency corrugated waveguide systems, transmission line components can be optimized to the desired frequency. For broadband or multiple-frequency applications, this is not possible. The goal of this paper is to demonstrate that the frequency bandwidth of circular corrugated waveguides can be compromised by diffraction losses to miter bends and gaps. It is shown that if the corrugation depth differs significantly from λ /4, a theory can substantially underpredict the gap and miter bend losses. The simulations are also shown to compare favorably to experimental measurements. To improve the transmission line performance in large frequency bandwidth systems, such as 33–165 GHz reflectometry, reducing the number of miter bends may, therefore, be necessary. For the improvement of performance in narrower frequency bandwidth or multiple-frequency systems, especially high-powered systems, wavelength-dependent techniques may be applicable. Furthermore, one such application is shown for a Bragg reflection technique to reduce the thermal load to insulating ceramic rings in a dc break component for multiple-frequency ITER electron cyclotron heating transmission lines.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Slow light engineering in a photonic crystal slab waveguide through optofluidic infiltration and geometric modulation

In this paper, a new type of flat-band slow light structure with high group index (n{sub g}) and large normalized delay-bandwidth product (NDBP) in a silicon on insulator (SOI) based photonic crystal (PC) slab waveguide with a triangular lattice of circular holes is demonstrated. The dispersion engineering is performed by infiltrating optical fluids with different refractive indices n{sub f} in the first row and shifting the second row of air holes adjacent to the PC waveguide (PCW) in the longitudinal direction. In the optimized case, a high NDBP of 0.32 with a group index of 54.55 and a bandwidth of 9.13 nm could be obtained. Furthermore, an ultra-low group velocity dispersion (GVD) in the range of 10{sup –20} s{sup 2}/m is achieved in all of the structures. These results are obtained by numerical simulations based on three-dimensional (3D) plane wave expansion (PWE) method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Notes on SAW Tag Interrogation Techniques

We consider the problem of interrogating a single SAW RFID tag with a known ID and known range in the presence of multiple interfering tags under the following assumptions: (1) The RF propagation environment is well approximated as a simple delay channel with geometric power-decay constant alpha >/= 2. (2) The interfering tag IDs are unknown but well approximated as independent, identically distributed random samples from a probability distribution of tag ID waveforms with known second-order properties, and the tag of interest is drawn independently from the same distribution. (3) The ranges of the interfering tags are unknown but well approximated as independent, identically distributed realizations of a random variable rho with a known probability distribution f(sub rho) , and the tag ranges are independent of the tag ID waveforms. In particular, we model the tag waveforms as random impulse responses from a wide-sense-stationary, uncorrelated-scattering (WSSUS) fading channel with known bandwidth and scattering function. A brief discussion of the properties of such channels and the notation used to describe them in this document is given in the Appendix. Under these assumptions, we derive the expression for the output signal-to-noise ratio (SNR) for an arbitrary combination of transmitted interrogation signal and linear receiver filter. Based on this expression, we derive the optimal interrogator configuration (i.e., transmitted signal/receiver filter combination) in the two extreme noise/interference regimes, i.e., noise-limited and interference-limited, under the additional assumption that the coherence bandwidth of the tags is much smaller than the total tag bandwidth. Finally, we evaluate the performance of both optimal interrogators over a broad range of operating scenarios using both numerical simulation based on the assumed model and Monte Carlo simulation based on a small sample of measured tag waveforms. The performance evaluation results not only provide guidelines for proper interrogator design, but also provide some insight on the validity of the assumed signal model. It should be noted that the assumption that the impulse response of the tag of interest is known precisely implies that the temperature and range of the tag are also known precisely, which is generally not the case in practice. However, analyzing interrogator performance under this simplifying assumption is much more straightforward and still provides a great deal of insight into the nature of the problem.

Barton, Richard J.↗

An Efficient, Highly Flexible Multi-Channel Digital Downconverter Architecture

In this innovation, a digital downconverter has been created that produces a large (16 or greater) number of output channels of smaller bandwidths. Additionally, this design has the flexibility to tune each channel independently to anywhere in the input bandwidth to cover a wide range of output bandwidths (from 32 MHz down to 1 kHz). Both the flexibility in channel frequency selection and the more than four orders of magnitude range in output bandwidths (decimation rates from 32 to 640,000) presented significant challenges to be solved. The solution involved breaking the digital downconversion process into a two-stage process. The first stage is a 2 oversampled filter bank that divides the whole input bandwidth as a real input signal into seven overlapping, contiguous channels represented with complex samples. Using the symmetry of the sine and cosine functions in a similar way to that of an FFT (fast Fourier transform), this downconversion is very efficient and gives seven channels fixed in frequency. An arbitrary number of smaller bandwidth channels can be formed from second-stage downconverters placed after the first stage of downconversion. Because of the overlapping of the first stage, there is no gap in coverage of the entire input bandwidth. The input to any of the second-stage downconverting channels has a multiplexer that chooses one of the seven wideband channels from the first stage. These second-stage downconverters take up fewer resources because they operate at lower bandwidths than doing the entire downconversion process from the input bandwidth for each independent channel. These second-stage downconverters are each independent with fine frequency control tuning, providing extreme flexibility in positioning the center frequency of a downconverted channel. Finally, these second-stage downconverters have flexible decimation factors over four orders of magnitude The algorithm was developed to run in an FPGA (field programmable gate array) at input data sampling rates of up to 1,280 MHz. The current implementation takes a 1,280-MHz real input, and first breaks it up into seven 160-MHz complex channels, each spaced 80 MHz apart. The eighth channel at baseband was not required for this implementation, and led to more optimization. Afterwards, 16 second stage narrow band channels with independently tunable center frequencies and bandwidth settings are implemented A future implementation in a larger Xilinx FPGA will hold up to 32 independent second-stage channels.

Goodhart, Charles E.↗