Electrostatically focused addressable field emission array chips (AFEA's) for high-speed massively parallel maskless digital E-beam direct write lithography and scanning electron microscopy

DOEpatents

Thomas, Clarence E.; Baylor, Larry R.; Voelkl, Edgar; Simpson, Michael L.; Paulus, Michael J.; Lowndes, Douglas H.; Whealton, John H.; Whitson, John C.; Wilgen, John B.

2002-12-24

Systems and methods are described for addressable field emission array (AFEA) chips. A method of operating an addressable field-emission array, includes: generating a plurality of electron beams from a pluralitly of emitters that compose the addressable field-emission array; and focusing at least one of the plurality of electron beams with an on-chip electrostatic focusing stack. The systems and methods provide advantages including the avoidance of space-charge blow-up.

Signal processing applications of massively parallel charge domain computing devices

NASA Technical Reports Server (NTRS)

Fijany, Amir (Inventor); Barhen, Jacob (Inventor); Toomarian, Nikzad (Inventor)

1999-01-01

The present invention is embodied in a charge coupled device (CCD)/charge injection device (CID) architecture capable of performing a Fourier transform by simultaneous matrix vector multiplication (MVM) operations in respective plural CCD/CID arrays in parallel in O(1) steps. For example, in one embodiment, a first CCD/CID array stores charge packets representing a first matrix operator based upon permutations of a Hartley transform and computes the Fourier transform of an incoming vector. A second CCD/CID array stores charge packets representing a second matrix operator based upon different permutations of a Hartley transform and computes the Fourier transform of an incoming vector. The incoming vector is applied to the inputs of the two CCD/CID arrays simultaneously, and the real and imaginary parts of the Fourier transform are produced simultaneously in the time required to perform a single MVM operation in a CCD/CID array.

Experience in highly parallel processing using DAP

NASA Technical Reports Server (NTRS)

Parkinson, D.

1987-01-01

Distributed Array Processors (DAP) have been in day to day use for ten years and a large amount of user experience has been gained. The profile of user applications is similar to that of the Massively Parallel Processor (MPP) working group. Experience has shown that contrary to expectations, highly parallel systems provide excellent performance on so-called dirty problems such as the physics part of meteorological codes. The reasons for this observation are discussed. The arguments against replacing bit processors with floating point processors are also discussed.

3-D readout-electronics packaging for high-bandwidth massively paralleled imager

DOEpatents

Kwiatkowski, Kris; Lyke, James

2007-12-18

Dense, massively parallel signal processing electronics are co-packaged behind associated sensor pixels. Microchips containing a linear or bilinear arrangement of photo-sensors, together with associated complex electronics, are integrated into a simple 3-D structure (a "mirror cube"). An array of photo-sensitive cells are disposed on a stacked CMOS chip's surface at a 45.degree. angle from light reflecting mirror surfaces formed on a neighboring CMOS chip surface. Image processing electronics are held within the stacked CMOS chip layers. Electrical connections couple each of said stacked CMOS chip layers and a distribution grid, the connections for distributing power and signals to components associated with each stacked CSMO chip layer.

Quantitative analysis of RNA-protein interactions on a massively parallel array for mapping biophysical and evolutionary landscapes

PubMed Central

Buenrostro, Jason D.; Chircus, Lauren M.; Araya, Carlos L.; Layton, Curtis J.; Chang, Howard Y.; Snyder, Michael P.; Greenleaf, William J.

2015-01-01

RNA-protein interactions drive fundamental biological processes and are targets for molecular engineering, yet quantitative and comprehensive understanding of the sequence determinants of affinity remains limited. Here we repurpose a high-throughput sequencing instrument to quantitatively measure binding and dissociation of MS2 coat protein to >107 RNA targets generated on a flow-cell surface by in situ transcription and inter-molecular tethering of RNA to DNA. We decompose the binding energy contributions from primary and secondary RNA structure, finding that differences in affinity are often driven by sequence-specific changes in association rates. By analyzing the biophysical constraints and modeling mutational paths describing the molecular evolution of MS2 from low- to high-affinity hairpins, we quantify widespread molecular epistasis, and a long-hypothesized structure-dependent preference for G:U base pairs over C:A intermediates in evolutionary trajectories. Our results suggest that quantitative analysis of RNA on a massively parallel array (RNAMaP) relationships across molecular variants. PMID:24727714

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2016-12-01

Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

Nanoelectrode array for electrochemical analysis

DOEpatents

Yelton, William G [Sandia Park, NM; Siegal, Michael P [Albuquerque, NM

2009-12-01

A nanoelectrode array comprises a plurality of nanoelectrodes wherein the geometric dimensions of the electrode controls the electrochemical response, and the current density is independent of time. By combining a massive array of nanoelectrodes in parallel, the current signal can be amplified while still retaining the beneficial geometric advantages of nanoelectrodes. Such nanoelectrode arrays can be used in a sensor system for rapid, non-contaminating field analysis. For example, an array of suitably functionalized nanoelectrodes can be incorporated into a small, integrated sensor system that can identify many species rapidly and simultaneously under field conditions in high-resistivity water, without the need for chemical addition to increase conductivity.

Development and characterization of hollow microprobe array as a potential tool for versatile and massively parallel manipulation of single cells.

PubMed

Nagai, Moeto; Oohara, Kiyotaka; Kato, Keita; Kawashima, Takahiro; Shibata, Takayuki

2015-04-01

Parallel manipulation of single cells is important for reconstructing in vivo cellular microenvironments and studying cell functions. To manipulate single cells and reconstruct their environments, development of a versatile manipulation tool is necessary. In this study, we developed an array of hollow probes using microelectromechanical systems fabrication technology and demonstrated the manipulation of single cells. We conducted a cell aspiration experiment with a glass pipette and modeled a cell using a standard linear solid model, which provided information for designing hollow stepped probes for minimally invasive single-cell manipulation. We etched a silicon wafer on both sides and formed through holes with stepped structures. The inner diameters of the holes were reduced by SiO2 deposition of plasma-enhanced chemical vapor deposition to trap cells on the tips. This fabrication process makes it possible to control the wall thickness, inner diameter, and outer diameter of the probes. With the fabricated probes, single cells were manipulated and placed in microwells at a single-cell level in a parallel manner. We studied the capture, release, and survival rates of cells at different suction and release pressures and found that the cell trapping rate was directly proportional to the suction pressure, whereas the release rate and viability decreased with increasing the suction pressure. The proposed manipulation system makes it possible to place cells in a well array and observe the adherence, spreading, culture, and death of the cells. This system has potential as a tool for massively parallel manipulation and for three-dimensional hetero cellular assays.

Massively Parallel Assimilation of TOGA/TAO and Topex/Poseidon Measurements into a Quasi Isopycnal Ocean General Circulation Model Using an Ensemble Kalman Filter

NASA Technical Reports Server (NTRS)

Keppenne, Christian L.; Rienecker, Michele; Borovikov, Anna Y.; Suarez, Max

1999-01-01

A massively parallel ensemble Kalman filter (EnKF)is used to assimilate temperature data from the TOGA/TAO array and altimetry from TOPEX/POSEIDON into a Pacific basin version of the NASA Seasonal to Interannual Prediction Project (NSIPP)ls quasi-isopycnal ocean general circulation model. The EnKF is an approximate Kalman filter in which the error-covariance propagation step is modeled by the integration of multiple instances of a numerical model. An estimate of the true error covariances is then inferred from the distribution of the ensemble of model state vectors. This inplementation of the filter takes advantage of the inherent parallelism in the EnKF algorithm by running all the model instances concurrently. The Kalman filter update step also occurs in parallel by having each processor process the observations that occur in the region of physical space for which it is responsible. The massively parallel data assimilation system is validated by withholding some of the data and then quantifying the extent to which the withheld information can be inferred from the assimilation of the remaining data. The distributions of the forecast and analysis error covariances predicted by the ENKF are also examined.

Nanopore arrays in a silicon membrane for parallel single-molecule detection: DNA translocation

NASA Astrophysics Data System (ADS)

Zhang, Miao; Schmidt, Torsten; Jemt, Anders; Sahlén, Pelin; Sychugov, Ilya; Lundeberg, Joakim; Linnros, Jan

2015-08-01

Optical nanopore sensing offers great potential in single-molecule detection, genotyping, or DNA sequencing for high-throughput applications. However, one of the bottle-necks for fluorophore-based biomolecule sensing is the lack of an optically optimized membrane with a large array of nanopores, which has large pore-to-pore distance, small variation in pore size and low background photoluminescence (PL). Here, we demonstrate parallel detection of single-fluorophore-labeled DNA strands (450 bps) translocating through an array of silicon nanopores that fulfills the above-mentioned requirements for optical sensing. The nanopore array was fabricated using electron beam lithography and anisotropic etching followed by electrochemical etching resulting in pore diameters down to ∼7 nm. The DNA translocation measurements were performed in a conventional wide-field microscope tailored for effective background PL control. The individual nanopore diameter was found to have a substantial effect on the translocation velocity, where smaller openings slow the translocation enough for the event to be clearly detectable in the fluorescence. Our results demonstrate that a uniform silicon nanopore array combined with wide-field optical detection is a promising alternative with which to realize massively-parallel single-molecule detection.

Spectral X-Ray Diffraction using a 6 Megapixel Photon Counting Array Detector.

PubMed

Muir, Ryan D; Pogranichniy, Nicholas R; Muir, J Lewis; Sullivan, Shane Z; Battaile, Kevin P; Mulichak, Anne M; Toth, Scott J; Keefe, Lisa J; Simpson, Garth J

2015-03-12

Pixel-array array detectors allow single-photon counting to be performed on a massively parallel scale, with several million counting circuits and detectors in the array. Because the number of photoelectrons produced at the detector surface depends on the photon energy, these detectors offer the possibility of spectral imaging. In this work, a statistical model of the instrument response is used to calibrate the detector on a per-pixel basis. In turn, the calibrated sensor was used to perform separation of dual-energy diffraction measurements into two monochromatic images. Targeting applications include multi-wavelength diffraction to aid in protein structure determination and X-ray diffraction imaging.

Spectral x-ray diffraction using a 6 megapixel photon counting array detector

NASA Astrophysics Data System (ADS)

Muir, Ryan D.; Pogranichniy, Nicholas R.; Muir, J. Lewis; Sullivan, Shane Z.; Battaile, Kevin P.; Mulichak, Anne M.; Toth, Scott J.; Keefe, Lisa J.; Simpson, Garth J.

2015-03-01

Pixel-array array detectors allow single-photon counting to be performed on a massively parallel scale, with several million counting circuits and detectors in the array. Because the number of photoelectrons produced at the detector surface depends on the photon energy, these detectors offer the possibility of spectral imaging. In this work, a statistical model of the instrument response is used to calibrate the detector on a per-pixel basis. In turn, the calibrated sensor was used to perform separation of dual-energy diffraction measurements into two monochromatic images. Targeting applications include multi-wavelength diffraction to aid in protein structure determination and X-ray diffraction imaging.

Function algorithms for MPP scientific subroutines, volume 1

NASA Technical Reports Server (NTRS)

Gouch, J. G.

1984-01-01

Design documentation and user documentation for function algorithms for the Massively Parallel Processor (MPP) are presented. The contract specifies development of MPP assembler instructions to perform the following functions: natural logarithm; exponential (e to the x power); square root; sine; cosine; and arctangent. To fulfill the requirements of the contract, parallel array and solar implementations for these functions were developed on the PDP11/34 Program Development and Management Unit (PDMU) that is resident at the MPP testbed installation located at the NASA Goddard facility.

Wideband aperture array using RF channelizers and massively parallel digital 2D IIR filterbank

NASA Astrophysics Data System (ADS)

Sengupta, Arindam; Madanayake, Arjuna; Gómez-García, Roberto; Engeberg, Erik D.

2014-05-01

Wideband receive-mode beamforming applications in wireless location, electronically-scanned antennas for radar, RF sensing, microwave imaging and wireless communications require digital aperture arrays that offer a relatively constant far-field beam over several octaves of bandwidth. Several beamforming schemes including the well-known true time-delay and the phased array beamformers have been realized using either finite impulse response (FIR) or fast Fourier transform (FFT) digital filter-sum based techniques. These beamforming algorithms offer the desired selectivity at the cost of a high computational complexity and frequency-dependant far-field array patterns. A novel approach to receiver beamforming is the use of massively parallel 2-D infinite impulse response (IIR) fan filterbanks for the synthesis of relatively frequency independent RF beams at an order of magnitude lower multiplier complexity compared to FFT or FIR filter based conventional algorithms. The 2-D IIR filterbanks demand fast digital processing that can support several octaves of RF bandwidth, fast analog-to-digital converters (ADCs) for RF-to-bits type direct conversion of wideband antenna element signals. Fast digital implementation platforms that can realize high-precision recursive filter structures necessary for real-time beamforming, at RF radio bandwidths, are also desired. We propose a novel technique that combines a passive RF channelizer, multichannel ADC technology, and single-phase massively parallel 2-D IIR digital fan filterbanks, realized at low complexity using FPGA and/or ASIC technology. There exists native support for a larger bandwidth than the maximum clock frequency of the digital implementation technology. We also strive to achieve More-than-Moore throughput by processing a wideband RF signal having content with N-fold (B = N Fclk/2) bandwidth compared to the maximum clock frequency Fclk Hz of the digital VLSI platform under consideration. Such increase in bandwidth is achieved without use of polyphase signal processing or time-interleaved ADC methods. That is, all digital processors operate at the same Fclk clock frequency without phasing, while wideband operation is achieved by sub-sampling of narrower sub-bands at the the RF channelizer outputs.

Energy-efficient STDP-based learning circuits with memristor synapses

NASA Astrophysics Data System (ADS)

Wu, Xinyu; Saxena, Vishal; Campbell, Kristy A.

2014-05-01

It is now accepted that the traditional von Neumann architecture, with processor and memory separation, is ill suited to process parallel data streams which a mammalian brain can efficiently handle. Moreover, researchers now envision computing architectures which enable cognitive processing of massive amounts of data by identifying spatio-temporal relationships in real-time and solving complex pattern recognition problems. Memristor cross-point arrays, integrated with standard CMOS technology, are expected to result in massively parallel and low-power Neuromorphic computing architectures. Recently, significant progress has been made in spiking neural networks (SNN) which emulate data processing in the cortical brain. These architectures comprise of a dense network of neurons and the synapses formed between the axons and dendrites. Further, unsupervised or supervised competitive learning schemes are being investigated for global training of the network. In contrast to a software implementation, hardware realization of these networks requires massive circuit overhead for addressing and individually updating network weights. Instead, we employ bio-inspired learning rules such as the spike-timing-dependent plasticity (STDP) to efficiently update the network weights locally. To realize SNNs on a chip, we propose to use densely integrating mixed-signal integrate-andfire neurons (IFNs) and cross-point arrays of memristors in back-end-of-the-line (BEOL) of CMOS chips. Novel IFN circuits have been designed to drive memristive synapses in parallel while maintaining overall power efficiency (<1 pJ/spike/synapse), even at spike rate greater than 10 MHz. We present circuit design details and simulation results of the IFN with memristor synapses, its response to incoming spike trains and STDP learning characterization.

Phase space simulation of collisionless stellar systems on the massively parallel processor

NASA Technical Reports Server (NTRS)

White, Richard L.

1987-01-01

A numerical technique for solving the collisionless Boltzmann equation describing the time evolution of a self gravitating fluid in phase space was implemented on the Massively Parallel Processor (MPP). The code performs calculations for a two dimensional phase space grid (with one space and one velocity dimension). Some results from calculations are presented. The execution speed of the code is comparable to the speed of a single processor of a Cray-XMP. Advantages and disadvantages of the MPP architecture for this type of problem are discussed. The nearest neighbor connectivity of the MPP array does not pose a significant obstacle. Future MPP-like machines should have much more local memory and easier access to staging memory and disks in order to be effective for this type of problem.

APRON: A Cellular Processor Array Simulation and Hardware Design Tool

NASA Astrophysics Data System (ADS)

Barr, David R. W.; Dudek, Piotr

2009-12-01

We present a software environment for the efficient simulation of cellular processor arrays (CPAs). This software (APRON) is used to explore algorithms that are designed for massively parallel fine-grained processor arrays, topographic multilayer neural networks, vision chips with SIMD processor arrays, and related architectures. The software uses a highly optimised core combined with a flexible compiler to provide the user with tools for the design of new processor array hardware architectures and the emulation of existing devices. We present performance benchmarks for the software processor array implemented on standard commodity microprocessors. APRON can be configured to use additional processing hardware if necessary and can be used as a complete graphical user interface and development environment for new or existing CPA systems, allowing more users to develop algorithms for CPA systems.

Transmissive Nanohole Arrays for Massively-Parallel Optical Biosensing

PubMed Central

2015-01-01

A high-throughput optical biosensing technique is proposed and demonstrated. This hybrid technique combines optical transmission of nanoholes with colorimetric silver staining. The size and spacing of the nanoholes are chosen so that individual nanoholes can be independently resolved in massive parallel using an ordinary transmission optical microscope, and, in place of determining a spectral shift, the brightness of each nanohole is recorded to greatly simplify the readout. Each nanohole then acts as an independent sensor, and the blocking of nanohole optical transmission by enzymatic silver staining defines the specific detection of a biological agent. Nearly 10000 nanoholes can be simultaneously monitored under the field of view of a typical microscope. As an initial proof of concept, biotinylated lysozyme (biotin-HEL) was used as a model analyte, giving a detection limit as low as 0.1 ng/mL. PMID:25530982

Silicon nanodisk array with a fin field-effect transistor for time-domain weighted sum calculation toward massively parallel spiking neural networks

NASA Astrophysics Data System (ADS)

Tohara, Takashi; Liang, Haichao; Tanaka, Hirofumi; Igarashi, Makoto; Samukawa, Seiji; Endo, Kazuhiko; Takahashi, Yasuo; Morie, Takashi

2016-03-01

A nanodisk array connected with a fin field-effect transistor is fabricated and analyzed for spiking neural network applications. This nanodevice performs weighted sums in the time domain using rising slopes of responses triggered by input spike pulses. The nanodisk arrays, which act as a resistance of several giga-ohms, are fabricated using a self-assembly bio-nano-template technique. Weighted sums are achieved with an energy dissipation on the order of 1 fJ, where the number of inputs can be more than one hundred. This amount of energy is several orders of magnitude lower than that of conventional digital processors.

Computations on the massively parallel processor at the Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Strong, James P.

1991-01-01

Described are four significant algorithms implemented on the massively parallel processor (MPP) at the Goddard Space Flight Center. Two are in the area of image analysis. Of the other two, one is a mathematical simulation experiment and the other deals with the efficient transfer of data between distantly separated processors in the MPP array. The first algorithm presented is the automatic determination of elevations from stereo pairs. The second algorithm solves mathematical logistic equations capable of producing both ordered and chaotic (or random) solutions. This work can potentially lead to the simulation of artificial life processes. The third algorithm is the automatic segmentation of images into reasonable regions based on some similarity criterion, while the fourth is an implementation of a bitonic sort of data which significantly overcomes the nearest neighbor interconnection constraints on the MPP for transferring data between distant processors.

Polar exponential sensor arrays unify iconic and Hough space representation

NASA Technical Reports Server (NTRS)

Weiman, Carl F. R.

1990-01-01

The log-polar coordinate system, inherent in both polar exponential sensor arrays and log-polar remapped video imagery, is identical to the coordinate system of its corresponding Hough transform parameter space. The resulting unification of iconic and Hough domains simplifies computation for line recognition and eliminates the slope quantization problems inherent in the classical Cartesian Hough transform. The geometric organization of the algorithm is more amenable to massively parallel architectures than that of the Cartesian version. The neural architecture of the human visual cortex meets the geometric requirements to execute 'in-place' log-Hough algorithms of the kind described here.

Commodity cluster and hardware-based massively parallel implementations of hyperspectral imaging algorithms

NASA Astrophysics Data System (ADS)

Plaza, Antonio; Chang, Chein-I.; Plaza, Javier; Valencia, David

2006-05-01

The incorporation of hyperspectral sensors aboard airborne/satellite platforms is currently producing a nearly continual stream of multidimensional image data, and this high data volume has soon introduced new processing challenges. The price paid for the wealth spatial and spectral information available from hyperspectral sensors is the enormous amounts of data that they generate. Several applications exist, however, where having the desired information calculated quickly enough for practical use is highly desirable. High computing performance of algorithm analysis is particularly important in homeland defense and security applications, in which swift decisions often involve detection of (sub-pixel) military targets (including hostile weaponry, camouflage, concealment, and decoys) or chemical/biological agents. In order to speed-up computational performance of hyperspectral imaging algorithms, this paper develops several fast parallel data processing techniques. Techniques include four classes of algorithms: (1) unsupervised classification, (2) spectral unmixing, and (3) automatic target recognition, and (4) onboard data compression. A massively parallel Beowulf cluster (Thunderhead) at NASA's Goddard Space Flight Center in Maryland is used to measure parallel performance of the proposed algorithms. In order to explore the viability of developing onboard, real-time hyperspectral data compression algorithms, a Xilinx Virtex-II field programmable gate array (FPGA) is also used in experiments. Our quantitative and comparative assessment of parallel techniques and strategies may help image analysts in selection of parallel hyperspectral algorithms for specific applications.

Direct write of microlens array using digital projection photopolymerization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu Yi; Chen Shaochen

Microlens array is a key element in the field of information processing, optoelectronics, and integrated optics. Many existing fabrication processes remain expensive and complicated even though relatively low-cost replication processes have been developed. Here, we demonstrate the fabrication of microlens arrays through projection photopolymerization using a digital micromirror device (DMD) as a dynamic photomask. The DMD projects grayscale images, which are designed in a computer, onto a photocurable resin. The resin is then solidified with its thickness determined by a grayscale ultraviolet light and exposure time. Therefore, various geometries can be formed in a single-step, massively parallel fashion. We presentmore » microlens arrays made of acrylate-based polymer precursor. The physical and optical characteristics of the resulting lenses suggest that this fabrication technique is potentially suitable for applications in integrated optics.« less

Parallel design patterns for a low-power, software-defined compressed video encoder

NASA Astrophysics Data System (ADS)

Bruns, Michael W.; Hunt, Martin A.; Prasad, Durga; Gunupudi, Nageswara R.; Sonachalam, Sekar

2011-06-01

Video compression algorithms such as H.264 offer much potential for parallel processing that is not always exploited by the technology of a particular implementation. Consumer mobile encoding devices often achieve real-time performance and low power consumption through parallel processing in Application Specific Integrated Circuit (ASIC) technology, but many other applications require a software-defined encoder. High quality compression features needed for some applications such as 10-bit sample depth or 4:2:2 chroma format often go beyond the capability of a typical consumer electronics device. An application may also need to efficiently combine compression with other functions such as noise reduction, image stabilization, real time clocks, GPS data, mission/ESD/user data or software-defined radio in a low power, field upgradable implementation. Low power, software-defined encoders may be implemented using a massively parallel memory-network processor array with 100 or more cores and distributed memory. The large number of processor elements allow the silicon device to operate more efficiently than conventional DSP or CPU technology. A dataflow programming methodology may be used to express all of the encoding processes including motion compensation, transform and quantization, and entropy coding. This is a declarative programming model in which the parallelism of the compression algorithm is expressed as a hierarchical graph of tasks with message communication. Data parallel and task parallel design patterns are supported without the need for explicit global synchronization control. An example is described of an H.264 encoder developed for a commercially available, massively parallel memorynetwork processor device.

Massively parallel sequencing and the emergence of forensic genomics: Defining the policy and legal issues for law enforcement.

PubMed

Scudder, Nathan; McNevin, Dennis; Kelty, Sally F; Walsh, Simon J; Robertson, James

2018-03-01

Use of DNA in forensic science will be significantly influenced by new technology in coming years. Massively parallel sequencing and forensic genomics will hasten the broadening of forensic DNA analysis beyond short tandem repeats for identity towards a wider array of genetic markers, in applications as diverse as predictive phenotyping, ancestry assignment, and full mitochondrial genome analysis. With these new applications come a range of legal and policy implications, as forensic science touches on areas as diverse as 'big data', privacy and protected health information. Although these applications have the potential to make a more immediate and decisive forensic intelligence contribution to criminal investigations, they raise policy issues that will require detailed consideration if this potential is to be realised. The purpose of this paper is to identify the scope of the issues that will confront forensic and user communities. Copyright © 2017 The Chartered Society of Forensic Sciences. All rights reserved.

Identification of the Bovine Arachnomelia Mutation by Massively Parallel Sequencing Implicates Sulfite Oxidase (SUOX) in Bone Development

PubMed Central

Drögemüller, Cord; Tetens, Jens; Sigurdsson, Snaevar; Gentile, Arcangelo; Testoni, Stefania; Lindblad-Toh, Kerstin; Leeb, Tosso

2010-01-01

Arachnomelia is a monogenic recessive defect of skeletal development in cattle. The causative mutation was previously mapped to a ∼7 Mb interval on chromosome 5. Here we show that array-based sequence capture and massively parallel sequencing technology, combined with the typical family structure in livestock populations, facilitates the identification of the causative mutation. We re-sequenced the entire critical interval in a healthy partially inbred cow carrying one copy of the critical chromosome segment in its ancestral state and one copy of the same segment with the arachnomelia mutation, and we detected a single heterozygous position. The genetic makeup of several partially inbred cattle provides extremely strong support for the causality of this mutation. The mutation represents a single base insertion leading to a premature stop codon in the coding sequence of the SUOX gene and is perfectly associated with the arachnomelia phenotype. Our findings suggest an important role for sulfite oxidase in bone development. PMID:20865119

Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

DTIC Science & Technology

2015-08-01

Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten and James P Larentzos Approved for...Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten Weapons and Materials Research Directorate, ARL James P Larentzos Engility...Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software 5a. CONTRACT NUMBER 5b

SAR processing on the MPP

NASA Technical Reports Server (NTRS)

Batcher, K. E.; Eddey, E. E.; Faiss, R. O.; Gilmore, P. A.

1981-01-01

The processing of synthetic aperture radar (SAR) signals using the massively parallel processor (MPP) is discussed. The fast Fourier transform convolution procedures employed in the algorithms are described. The MPP architecture comprises an array unit (ARU) which processes arrays of data; an array control unit which controls the operation of the ARU and performs scalar arithmetic; a program and data management unit which controls the flow of data; and a unique staging memory (SM) which buffers and permutes data. The ARU contains a 128 by 128 array of bit-serial processing elements (PE). Two-by-four surarrays of PE's are packaged in a custom VLSI HCMOS chip. The staging memory is a large multidimensional-access memory which buffers and permutes data flowing with the system. Efficient SAR processing is achieved via ARU communication paths and SM data manipulation. Real time processing capability can be realized via a multiple ARU, multiple SM configuration.

Parallel processing architecture for H.264 deblocking filter on multi-core platforms

NASA Astrophysics Data System (ADS)

Prasad, Durga P.; Sonachalam, Sekar; Kunchamwar, Mangesh K.; Gunupudi, Nageswara Rao

2012-03-01

Massively parallel computing (multi-core) chips offer outstanding new solutions that satisfy the increasing demand for high resolution and high quality video compression technologies such as H.264. Such solutions not only provide exceptional quality but also efficiency, low power, and low latency, previously unattainable in software based designs. While custom hardware and Application Specific Integrated Circuit (ASIC) technologies may achieve lowlatency, low power, and real-time performance in some consumer devices, many applications require a flexible and scalable software-defined solution. The deblocking filter in H.264 encoder/decoder poses difficult implementation challenges because of heavy data dependencies and the conditional nature of the computations. Deblocking filter implementations tend to be fixed and difficult to reconfigure for different needs. The ability to scale up for higher quality requirements such as 10-bit pixel depth or a 4:2:2 chroma format often reduces the throughput of a parallel architecture designed for lower feature set. A scalable architecture for deblocking filtering, created with a massively parallel processor based solution, means that the same encoder or decoder will be deployed in a variety of applications, at different video resolutions, for different power requirements, and at higher bit-depths and better color sub sampling patterns like YUV, 4:2:2, or 4:4:4 formats. Low power, software-defined encoders/decoders may be implemented using a massively parallel processor array, like that found in HyperX technology, with 100 or more cores and distributed memory. The large number of processor elements allows the silicon device to operate more efficiently than conventional DSP or CPU technology. This software programing model for massively parallel processors offers a flexible implementation and a power efficiency close to that of ASIC solutions. This work describes a scalable parallel architecture for an H.264 compliant deblocking filter for multi core platforms such as HyperX technology. Parallel techniques such as parallel processing of independent macroblocks, sub blocks, and pixel row level are examined in this work. The deblocking architecture consists of a basic cell called deblocking filter unit (DFU) and dependent data buffer manager (DFM). The DFU can be used in several instances, catering to different performance needs the DFM serves the data required for the different number of DFUs, and also manages all the neighboring data required for future data processing of DFUs. This approach achieves the scalability, flexibility, and performance excellence required in deblocking filters.

Algorithmic commonalities in the parallel environment

NASA Technical Reports Server (NTRS)

Mcanulty, Michael A.; Wainer, Michael S.

1987-01-01

The ultimate aim of this project was to analyze procedures from substantially different application areas to discover what is either common or peculiar in the process of conversion to the Massively Parallel Processor (MPP). Three areas were identified: molecular dynamic simulation, production systems (rule systems), and various graphics and vision algorithms. To date, only selected graphics procedures have been investigated. They are the most readily available, and produce the most visible results. These include simple polygon patch rendering, raycasting against a constructive solid geometric model, and stochastic or fractal based textured surface algorithms. Only the simplest of conversion strategies, mapping a major loop to the array, has been investigated so far. It is not entirely satisfactory.

Mn-silicide nanostructures aligned on massively parallel silicon nano-ribbons

NASA Astrophysics Data System (ADS)

De Padova, Paola; Ottaviani, Carlo; Ronci, Fabio; Colonna, Stefano; Olivieri, Bruno; Quaresima, Claudio; Cricenti, Antonio; Dávila, Maria E.; Hennies, Franz; Pietzsch, Annette; Shariati, Nina; Le Lay, Guy

2013-01-01

The growth of Mn nanostructures on a 1D grating of silicon nano-ribbons is investigated at atomic scale by means of scanning tunneling microscopy, low energy electron diffraction and core level photoelectron spectroscopy. The grating of silicon nano-ribbons represents an atomic scale template that can be used in a surface-driven route to control the combination of Si with Mn in the development of novel materials for spintronics devices. The Mn atoms show a preferential adsorption site on silicon atoms, forming one-dimensional nanostructures. They are parallel oriented with respect to the surface Si array, which probably predetermines the diffusion pathways of the Mn atoms during the process of nanostructure formation.

Mn-silicide nanostructures aligned on massively parallel silicon nano-ribbons.

PubMed

De Padova, Paola; Ottaviani, Carlo; Ronci, Fabio; Colonna, Stefano; Olivieri, Bruno; Quaresima, Claudio; Cricenti, Antonio; Dávila, Maria E; Hennies, Franz; Pietzsch, Annette; Shariati, Nina; Le Lay, Guy

2013-01-09

The growth of Mn nanostructures on a 1D grating of silicon nano-ribbons is investigated at atomic scale by means of scanning tunneling microscopy, low energy electron diffraction and core level photoelectron spectroscopy. The grating of silicon nano-ribbons represents an atomic scale template that can be used in a surface-driven route to control the combination of Si with Mn in the development of novel materials for spintronics devices. The Mn atoms show a preferential adsorption site on silicon atoms, forming one-dimensional nanostructures. They are parallel oriented with respect to the surface Si array, which probably predetermines the diffusion pathways of the Mn atoms during the process of nanostructure formation.

Wafer-scale, massively parallel carbon nanotube arrays for realizing field effect transistors with current density exceeding silicon and gallium arsenide

NASA Astrophysics Data System (ADS)

Arnold, Michael

Calculations have indicated that aligned arrays of semiconducting carbon nanotubes (CNTs) promise to outperform conventional semiconducting materials in short-channel, aggressively scaled field effect transistors (FETs) like those used in semiconductor logic and high frequency amplifier technologies. These calculations have been based on extrapolation of measurements of FETs based on one CNT, in which ballistic transport approaching the quantum conductance limit of 2Go = 4e2/h has been achieved. However, constraints in CNT sorting, processing, alignment, and contacts give rise to non-idealities when CNTs are implemented in densely-packed parallel arrays, which has resulted in a conductance per CNT far from 2Go. The consequence has been that it has been very difficult to create high performance CNT array FETs, and CNT array FETs have not outperformed but rather underperformed channel materials such as Si by 6 x or more. Here, we report nearly ballistic CNT array FETs at a density of 50 CNTs um-1, created via CNT sorting, wafer-scale alignment and assembly, and treatment. The on-state conductance in the arrays is as high as 0.46 Go per CNT, and the conductance of the arrays reaches 1.7 mS um-1, which is 7 x higher than previous state-of-the-art CNT array FETs made by other methods. The saturated on-state current density reaches 900 uA um-1 and is similar to or exceeds that of Si FETs when compared at equivalent gate oxide thickness, off-state current density, and channel length. The on-state current density exceeds that of GaAs FETs, as well. This leap in CNT FET array performance is a significant advance towards the exploitation of CNTs in high-performance semiconductor electronics technologies.

Parallel VLSI architecture emulation and the organization of APSA/MPP

NASA Technical Reports Server (NTRS)

Odonnell, John T.

1987-01-01

The Applicative Programming System Architecture (APSA) combines an applicative language interpreter with a novel parallel computer architecture that is well suited for Very Large Scale Integration (VLSI) implementation. The Massively Parallel Processor (MPP) can simulate VLSI circuits by allocating one processing element in its square array to an area on a square VLSI chip. As long as there are not too many long data paths, the MPP can simulate a VLSI clock cycle very rapidly. The APSA circuit contains a binary tree with a few long paths and many short ones. A skewed H-tree layout allows every processing element to simulate a leaf cell and up to four tree nodes, with no loss in parallelism. Emulation of a key APSA algorithm on the MPP resulted in performance 16,000 times faster than a Vax. This speed will make it possible for the APSA language interpreter to run fast enough to support research in parallel list processing algorithms.

The 2nd Symposium on the Frontiers of Massively Parallel Computations

NASA Technical Reports Server (NTRS)

Mills, Ronnie (Editor)

1988-01-01

Programming languages, computer graphics, neural networks, massively parallel computers, SIMD architecture, algorithms, digital terrain models, sort computation, simulation of charged particle transport on the massively parallel processor and image processing are among the topics discussed.

High-speed massively parallel scanning

DOEpatents

Decker, Derek E [Byron, CA

2010-07-06

A new technique for recording a series of images of a high-speed event (such as, but not limited to: ballistics, explosives, laser induced changes in materials, etc.) is presented. Such technique(s) makes use of a lenslet array to take image picture elements (pixels) and concentrate light from each pixel into a spot that is much smaller than the pixel. This array of spots illuminates a detector region (e.g., film, as one embodiment) which is scanned transverse to the light, creating tracks of exposed regions. Each track is a time history of the light intensity for a single pixel. By appropriately configuring the array of concentrated spots with respect to the scanning direction of the detection material, different tracks fit between pixels and sufficient lengths are possible which can be of interest in several high-speed imaging applications.

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.

PubMed

Gierahn, Todd M; Wadsworth, Marc H; Hughes, Travis K; Bryson, Bryan D; Butler, Andrew; Satija, Rahul; Fortune, Sarah; Love, J Christopher; Shalek, Alex K

2017-04-01

Single-cell RNA-seq can precisely resolve cellular states, but applying this method to low-input samples is challenging. Here, we present Seq-Well, a portable, low-cost platform for massively parallel single-cell RNA-seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture. We use Seq-Well to profile thousands of primary human macrophages exposed to Mycobacterium tuberculosis.

Neuromorphic Hardware Architecture Using the Neural Engineering Framework for Pattern Recognition.

PubMed

Wang, Runchun; Thakur, Chetan Singh; Cohen, Gregory; Hamilton, Tara Julia; Tapson, Jonathan; van Schaik, Andre

2017-06-01

We present a hardware architecture that uses the neural engineering framework (NEF) to implement large-scale neural networks on field programmable gate arrays (FPGAs) for performing massively parallel real-time pattern recognition. NEF is a framework that is capable of synthesising large-scale cognitive systems from subnetworks and we have previously presented an FPGA implementation of the NEF that successfully performs nonlinear mathematical computations. That work was developed based on a compact digital neural core, which consists of 64 neurons that are instantiated by a single physical neuron using a time-multiplexing approach. We have now scaled this approach up to build a pattern recognition system by combining identical neural cores together. As a proof of concept, we have developed a handwritten digit recognition system using the MNIST database and achieved a recognition rate of 96.55%. The system is implemented on a state-of-the-art FPGA and can process 5.12 million digits per second. The architecture and hardware optimisations presented offer high-speed and resource-efficient means for performing high-speed, neuromorphic, and massively parallel pattern recognition and classification tasks.

ArrayBridge: Interweaving declarative array processing with high-performance computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xing, Haoyuan; Floratos, Sofoklis; Blanas, Spyros

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aimsmore » to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.« less

GPU-Based Real-Time Volumetric Ultrasound Image Reconstruction for a Ring Array

PubMed Central

Choe, Jung Woo; Nikoozadeh, Amin; Oralkan, Ömer; Khuri-Yakub, Butrus T.

2014-01-01

Synthetic phased array (SPA) beamforming with Hadamard coding and aperture weighting is an optimal option for real-time volumetric imaging with a ring array, a particularly attractive geometry in intracardiac and intravascular applications. However, the imaging frame rate of this method is limited by the immense computational load required in synthetic beamforming. For fast imaging with a ring array, we developed graphics processing unit (GPU)-based, real-time image reconstruction software that exploits massive data-level parallelism in beamforming operations. The GPU-based software reconstructs and displays three cross-sectional images at 45 frames per second (fps). This frame rate is 4.5 times higher than that for our previously-developed multi-core CPU-based software. In an alternative imaging mode, it shows one B-mode image rotating about the axis and its maximum intensity projection (MIP), processed at a rate of 104 fps. This paper describes the image reconstruction procedure on the GPU platform and presents the experimental images obtained using this software. PMID:23529080

Parallel Processing of Large Scale Microphone Arrays for Sound Capture

NASA Astrophysics Data System (ADS)

Jan, Ea-Ee.

1995-01-01

Performance of microphone sound pick up is degraded by deleterious properties of the acoustic environment, such as multipath distortion (reverberation) and ambient noise. The degradation becomes more prominent in a teleconferencing environment in which the microphone is positioned far away from the speaker. Besides, the ideal teleconference should feel as easy and natural as face-to-face communication with another person. This suggests hands-free sound capture with no tether or encumbrance by hand-held or body-worn sound equipment. Microphone arrays for this application represent an appropriate approach. This research develops new microphone array and signal processing techniques for high quality hands-free sound capture in noisy, reverberant enclosures. The new techniques combine matched-filtering of individual sensors and parallel processing to provide acute spatial volume selectivity which is capable of mitigating the deleterious effects of noise interference and multipath distortion. The new method outperforms traditional delay-and-sum beamformers which provide only directional spatial selectivity. The research additionally explores truncated matched-filtering and random distribution of transducers to reduce complexity and improve sound capture quality. All designs are first established by computer simulation of array performance in reverberant enclosures. The simulation is achieved by a room model which can efficiently calculate the acoustic multipath in a rectangular enclosure up to a prescribed order of images. It also calculates the incident angle of the arriving signal. Experimental arrays were constructed and their performance was measured in real rooms. Real room data were collected in a hard-walled laboratory and a controllable variable acoustics enclosure of similar size, approximately 6 x 6 x 3 m. An extensive speech database was also collected in these two enclosures for future research on microphone arrays. The simulation results are shown to be consistent with the real room data. Localization of sound sources has been explored using cross-power spectrum time delay estimation and has been evaluated using real room data under slightly, moderately and highly reverberant conditions. To improve the accuracy and reliability of the source localization, an outlier detector that removes incorrect time delay estimation has been invented. To provide speaker selectivity for microphone array systems, a hands-free speaker identification system has been studied. A recently invented feature using selected spectrum information outperforms traditional recognition methods. Measured results demonstrate the capabilities of speaker selectivity from a matched-filtered array. In addition, simulation utilities, including matched -filtering processing of the array and hands-free speaker identification, have been implemented on the massively -parallel nCube super-computer. This parallel computation highlights the requirements for real-time processing of array signals.

A Real-Time Capable Software-Defined Receiver Using GPU for Adaptive Anti-Jam GPS Sensors

PubMed Central

Seo, Jiwon; Chen, Yu-Hsuan; De Lorenzo, David S.; Lo, Sherman; Enge, Per; Akos, Dennis; Lee, Jiyun

2011-01-01

Due to their weak received signal power, Global Positioning System (GPS) signals are vulnerable to radio frequency interference. Adaptive beam and null steering of the gain pattern of a GPS antenna array can significantly increase the resistance of GPS sensors to signal interference and jamming. Since adaptive array processing requires intensive computational power, beamsteering GPS receivers were usually implemented using hardware such as field-programmable gate arrays (FPGAs). However, a software implementation using general-purpose processors is much more desirable because of its flexibility and cost effectiveness. This paper presents a GPS software-defined radio (SDR) with adaptive beamsteering capability for anti-jam applications. The GPS SDR design is based on an optimized desktop parallel processing architecture using a quad-core Central Processing Unit (CPU) coupled with a new generation Graphics Processing Unit (GPU) having massively parallel processors. This GPS SDR demonstrates sufficient computational capability to support a four-element antenna array and future GPS L5 signal processing in real time. After providing the details of our design and optimization schemes for future GPU-based GPS SDR developments, the jamming resistance of our GPS SDR under synthetic wideband jamming is presented. Since the GPS SDR uses commercial-off-the-shelf hardware and processors, it can be easily adopted in civil GPS applications requiring anti-jam capabilities. PMID:22164116

Scientific Data Services -- A High-Performance I/O System with Array Semantics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Kesheng; Byna, Surendra; Rotem, Doron

2011-09-21

As high-performance computing approaches exascale, the existing I/O system design is having trouble keeping pace in both performance and scalability. We propose to address this challenge by adopting database principles and techniques in parallel I/O systems. First, we propose to adopt an array data model because many scientific applications represent their data in arrays. This strategy follows a cardinal principle from database research, which separates the logical view from the physical layout of data. This high-level data model gives the underlying implementation more freedom to optimize the physical layout and to choose the most effective way of accessing the data.more » For example, knowing that a set of write operations is working on a single multi-dimensional array makes it possible to keep the subarrays in a log structure during the write operations and reassemble them later into another physical layout as resources permit. While maintaining the high-level view, the storage system could compress the user data to reduce the physical storage requirement, collocate data records that are frequently used together, or replicate data to increase availability and fault-tolerance. Additionally, the system could generate secondary data structures such as database indexes and summary statistics. We expect the proposed Scientific Data Services approach to create a “live” storage system that dynamically adjusts to user demands and evolves with the massively parallel storage hardware.« less

A real-time capable software-defined receiver using GPU for adaptive anti-jam GPS sensors.

PubMed

Seo, Jiwon; Chen, Yu-Hsuan; De Lorenzo, David S; Lo, Sherman; Enge, Per; Akos, Dennis; Lee, Jiyun

2011-01-01

Due to their weak received signal power, Global Positioning System (GPS) signals are vulnerable to radio frequency interference. Adaptive beam and null steering of the gain pattern of a GPS antenna array can significantly increase the resistance of GPS sensors to signal interference and jamming. Since adaptive array processing requires intensive computational power, beamsteering GPS receivers were usually implemented using hardware such as field-programmable gate arrays (FPGAs). However, a software implementation using general-purpose processors is much more desirable because of its flexibility and cost effectiveness. This paper presents a GPS software-defined radio (SDR) with adaptive beamsteering capability for anti-jam applications. The GPS SDR design is based on an optimized desktop parallel processing architecture using a quad-core Central Processing Unit (CPU) coupled with a new generation Graphics Processing Unit (GPU) having massively parallel processors. This GPS SDR demonstrates sufficient computational capability to support a four-element antenna array and future GPS L5 signal processing in real time. After providing the details of our design and optimization schemes for future GPU-based GPS SDR developments, the jamming resistance of our GPS SDR under synthetic wideband jamming is presented. Since the GPS SDR uses commercial-off-the-shelf hardware and processors, it can be easily adopted in civil GPS applications requiring anti-jam capabilities.

Dynamic Programming and Transitive Closure on Linear Pipelines.

DTIC Science & Technology

1984-05-01

four partitions. 2.0 - 1.9 1.0t N. N 3N N -8 4 24 Figure41 An ideal solution to small problem sizes is to design an algorithm on an array where the...12 References [1] A.V. Aho, J. Hopcroft, and J.D. Ullman. The Design and Analysis of Computer Algorithms, Addison-Wesley, (1974). - " [2] R. Aubusson...K.E. Batcher, " Design of a Massively Parallel Processor," IEEE-TC, Vol. C-9, No. 9, (September, 1980), pp. 83-840. [4] K.Q. Brown, "Dynamic Programming

Array Databases: Agile Analytics (not just) for the Earth Sciences

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2015-12-01

Gridded data, such as images, image timeseries, and climate datacubes, today are managed separately from the metadata, and with different, restricted retrieval capabilities. While databases are good at metadata modelled in tables, XML hierarchies, or RDF graphs, they traditionally do not support multi-dimensional arrays.This gap is being closed by Array Databases, pioneered by the scalable rasdaman ("raster data manager") array engine. Its declarative query language, rasql, extends SQL with array operators which are optimized and parallelized on server side. Installations can easily be mashed up securely, thereby enabling large-scale location-transparent query processing in federations. Domain experts value the integration with their commonly used tools leading to a quick learning curve.Earth, Space, and Life sciences, but also Social sciences as well as business have massive amounts of data and complex analysis challenges that are answered by rasdaman. As of today, rasdaman is mature and in operational use on hundreds of Terabytes of timeseries datacubes, with transparent query distribution across more than 1,000 nodes. Additionally, its concepts have shaped international Big Data standards in the field, including the forthcoming array extension to ISO SQL, many of which are supported by both open-source and commercial systems meantime. In the geo field, rasdaman is reference implementation for the Open Geospatial Consortium (OGC) Big Data standard, WCS, now also under adoption by ISO. Further, rasdaman is in the final stage of OSGeo incubation.In this contribution we present array queries a la rasdaman, describe the architecture and novel optimization and parallelization techniques introduced in 2015, and put this in context of the intercontinental EarthServer initiative which utilizes rasdaman for enabling agile analytics on Petascale datacubes.

Particle Based Simulations of Complex Systems with MP2C : Hydrodynamics and Electrostatics

NASA Astrophysics Data System (ADS)

Sutmann, Godehard; Westphal, Lidia; Bolten, Matthias

2010-09-01

Particle based simulation methods are well established paths to explore system behavior on microscopic to mesoscopic time and length scales. With the development of new computer architectures it becomes more and more important to concentrate on local algorithms which do not need global data transfer or reorganisation of large arrays of data across processors. This requirement strongly addresses long-range interactions in particle systems, i.e. mainly hydrodynamic and electrostatic contributions. In this article, emphasis is given to the implementation and parallelization of the Multi-Particle Collision Dynamics method for hydrodynamic contributions and a splitting scheme based on Multigrid for electrostatic contributions. Implementations are done for massively parallel architectures and are demonstrated for the IBM Blue Gene/P architecture Jugene in Jülich.

Smart photodetector arrays for error control in page-oriented optical memory

NASA Astrophysics Data System (ADS)

Schaffer, Maureen Elizabeth

1998-12-01

Page-oriented optical memories (POMs) have been proposed to meet high speed, high capacity storage requirements for input/output intensive computer applications. This technology offers the capability for storage and retrieval of optical data in two-dimensional pages resulting in high throughput data rates. Since currently measured raw bit error rates for these systems fall several orders of magnitude short of industry requirements for binary data storage, powerful error control codes must be adopted. These codes must be designed to take advantage of the two-dimensional memory output. In addition, POMs require an optoelectronic interface to transfer the optical data pages to one or more electronic host systems. Conventional charge coupled device (CCD) arrays can receive optical data in parallel, but the relatively slow serial electronic output of these devices creates a system bottleneck thereby eliminating the POM advantage of high transfer rates. Also, CCD arrays are "unintelligent" interfaces in that they offer little data processing capabilities. The optical data page can be received by two-dimensional arrays of "smart" photo-detector elements that replace conventional CCD arrays. These smart photodetector arrays (SPAs) can perform fast parallel data decoding and error control, thereby providing an efficient optoelectronic interface between the memory and the electronic computer. This approach optimizes the computer memory system by combining the massive parallelism and high speed of optics with the diverse functionality, low cost, and local interconnection efficiency of electronics. In this dissertation we examine the design of smart photodetector arrays for use as the optoelectronic interface for page-oriented optical memory. We review options and technologies for SPA fabrication, develop SPA requirements, and determine SPA scalability constraints with respect to pixel complexity, electrical power dissipation, and optical power limits. Next, we examine data modulation and error correction coding for the purpose of error control in the POM system. These techniques are adapted, where possible, for 2D data and evaluated as to their suitability for a SPA implementation in terms of BER, code rate, decoder time and pixel complexity. Our analysis shows that differential data modulation combined with relatively simple block codes known as array codes provide a powerful means to achieve the desired data transfer rates while reducing error rates to industry requirements. Finally, we demonstrate the first smart photodetector array designed to perform parallel error correction on an entire page of data and satisfy the sustained data rates of page-oriented optical memories. Our implementation integrates a monolithic PN photodiode array and differential input receiver for optoelectronic signal conversion with a cluster error correction code using 0.35-mum CMOS. This approach provides high sensitivity, low electrical power dissipation, and fast parallel correction of 2 x 2-bit cluster errors in an 8 x 8 bit code block to achieve corrected output data rates scalable to 102 Gbps in the current technology increasing to 1.88 Tbps in 0.1-mum CMOS.

Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma

PubMed Central

Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

2017-01-01

Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations. PMID:28533481

Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma.

PubMed

Wu, Ren-Chin; Chao, An-Shine; Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

2017-07-18

Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations.

Feasibility of using the Massively Parallel Processor for large eddy simulations and other Computational Fluid Dynamics applications

NASA Technical Reports Server (NTRS)

Bruno, John

1984-01-01

The results of an investigation into the feasibility of using the MPP for direct and large eddy simulations of the Navier-Stokes equations is presented. A major part of this study was devoted to the implementation of two of the standard numerical algorithms for CFD. These implementations were not run on the Massively Parallel Processor (MPP) since the machine delivered to NASA Goddard does not have sufficient capacity. Instead, a detailed implementation plan was designed and from these were derived estimates of the time and space requirements of the algorithms on a suitably configured MPP. In addition, other issues related to the practical implementation of these algorithms on an MPP-like architecture were considered; namely, adaptive grid generation, zonal boundary conditions, the table lookup problem, and the software interface. Performance estimates show that the architectural components of the MPP, the Staging Memory and the Array Unit, appear to be well suited to the numerical algorithms of CFD. This combined with the prospect of building a faster and larger MMP-like machine holds the promise of achieving sustained gigaflop rates that are required for the numerical simulations in CFD.

A micromachined silicon parallel acoustic delay line (PADL) array for real-time photoacoustic tomography (PAT)

NASA Astrophysics Data System (ADS)

Cho, Young Y.; Chang, Cheng-Chung; Wang, Lihong V.; Zou, Jun

2015-03-01

To achieve real-time photoacoustic tomography (PAT), massive transducer arrays and data acquisition (DAQ) electronics are needed to receive the PA signals simultaneously, which results in complex and high-cost ultrasound receiver systems. To address this issue, we have developed a new PA data acquisition approach using acoustic time delay. Optical fibers were used as parallel acoustic delay lines (PADLs) to create different time delays in multiple channels of PA signals. This makes the PA signals reach a single-element transducer at different times. As a result, they can be properly received by single-channel DAQ electronics. However, due to their small diameter and fragility, using optical fiber as acoustic delay lines poses a number of challenges in the design, construction and packaging of the PADLs, thereby limiting their performances and use in real imaging applications. In this paper, we report the development of new silicon PADLs, which are directly made from silicon wafers using advanced micromachining technologies. The silicon PADLs have very low acoustic attenuation and distortion. A linear array of 16 silicon PADLs were assembled into a handheld package with one common input port and one common output port. To demonstrate its real-time PAT capability, the silicon PADL array (with its output port interfaced with a single-element transducer) was used to receive 16 channels of PA signals simultaneously from a tissue-mimicking optical phantom sample. The reconstructed PA image matches well with the imaging target. Therefore, the silicon PADL array can provide a 16× reduction in the ultrasound DAQ channels for real-time PAT.

Massively parallel algorithms for real-time wavefront control of a dense adaptive optics system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fijany, A.; Milman, M.; Redding, D.

1994-12-31

In this paper massively parallel algorithms and architectures for real-time wavefront control of a dense adaptive optic system (SELENE) are presented. The authors have already shown that the computation of a near optimal control algorithm for SELENE can be reduced to the solution of a discrete Poisson equation on a regular domain. Although, this represents an optimal computation, due the large size of the system and the high sampling rate requirement, the implementation of this control algorithm poses a computationally challenging problem since it demands a sustained computational throughput of the order of 10 GFlops. They develop a novel algorithm,more » designated as Fast Invariant Imbedding algorithm, which offers a massive degree of parallelism with simple communication and synchronization requirements. Due to these features, this algorithm is significantly more efficient than other Fast Poisson Solvers for implementation on massively parallel architectures. The authors also discuss two massively parallel, algorithmically specialized, architectures for low-cost and optimal implementation of the Fast Invariant Imbedding algorithm.« less

RAMA: A file system for massively parallel computers

NASA Technical Reports Server (NTRS)

Miller, Ethan L.; Katz, Randy H.

1993-01-01

This paper describes a file system design for massively parallel computers which makes very efficient use of a few disks per processor. This overcomes the traditional I/O bottleneck of massively parallel machines by storing the data on disks within the high-speed interconnection network. In addition, the file system, called RAMA, requires little inter-node synchronization, removing another common bottleneck in parallel processor file systems. Support for a large tertiary storage system can easily be integrated in lo the file system; in fact, RAMA runs most efficiently when tertiary storage is used.

Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots

PubMed Central

Scholma, Jetse; Fuhler, Gwenny M.; Joore, Jos; Hulsman, Marc; Schivo, Stefano; List, Alan F.; Reinders, Marcel J. T.; Peppelenbosch, Maikel P.; Post, Janine N.

2016-01-01

Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of “housekeeping” kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling. PMID:27225531

Radio Synthesis Imaging - A High Performance Computing and Communications Project

NASA Astrophysics Data System (ADS)

Crutcher, Richard M.

The National Science Foundation has funded a five-year High Performance Computing and Communications project at the National Center for Supercomputing Applications (NCSA) for the direct implementation of several of the computing recommendations of the Astronomy and Astrophysics Survey Committee (the "Bahcall report"). This paper is a summary of the project goals and a progress report. The project will implement a prototype of the next generation of astronomical telescope systems - remotely located telescopes connected by high-speed networks to very high performance, scalable architecture computers and on-line data archives, which are accessed by astronomers over Gbit/sec networks. Specifically, a data link has been installed between the BIMA millimeter-wave synthesis array at Hat Creek, California and NCSA at Urbana, Illinois for real-time transmission of data to NCSA. Data are automatically archived, and may be browsed and retrieved by astronomers using the NCSA Mosaic software. In addition, an on-line digital library of processed images will be established. BIMA data will be processed on a very high performance distributed computing system, with I/O, user interface, and most of the software system running on the NCSA Convex C3880 supercomputer or Silicon Graphics Onyx workstations connected by HiPPI to the high performance, massively parallel Thinking Machines Corporation CM-5. The very computationally intensive algorithms for calibration and imaging of radio synthesis array observations will be optimized for the CM-5 and new algorithms which utilize the massively parallel architecture will be developed. Code running simultaneously on the distributed computers will communicate using the Data Transport Mechanism developed by NCSA. The project will also use the BLANCA Gbit/s testbed network between Urbana and Madison, Wisconsin to connect an Onyx workstation in the University of Wisconsin Astronomy Department to the NCSA CM-5, for development of long-distance distributed computing. Finally, the project is developing 2D and 3D visualization software as part of the international AIPS++ project. This research and development project is being carried out by a team of experts in radio astronomy, algorithm development for massively parallel architectures, high-speed networking, database management, and Thinking Machines Corporation personnel. The development of this complete software, distributed computing, and data archive and library solution to the radio astronomy computing problem will advance our expertise in high performance computing and communications technology and the application of these techniques to astronomical data processing.

NeuroSeek dual-color image processing infrared focal plane array

NASA Astrophysics Data System (ADS)

McCarley, Paul L.; Massie, Mark A.; Baxter, Christopher R.; Huynh, Buu L.

1998-09-01

Several technologies have been developed in recent years to advance the state of the art of IR sensor systems including dual color affordable focal planes, on-focal plane array biologically inspired image and signal processing techniques and spectral sensing techniques. Pacific Advanced Technology (PAT) and the Air Force Research Lab Munitions Directorate have developed a system which incorporates the best of these capabilities into a single device. The 'NeuroSeek' device integrates these technologies into an IR focal plane array (FPA) which combines multicolor Midwave IR/Longwave IR radiometric response with on-focal plane 'smart' neuromorphic analog image processing. The readout and processing integrated circuit very large scale integration chip which was developed under this effort will be hybridized to a dual color detector array to produce the NeuroSeek FPA, which will have the capability to fuse multiple pixel-based sensor inputs directly on the focal plane. Great advantages are afforded by application of massively parallel processing algorithms to image data in the analog domain; the high speed and low power consumption of this device mimic operations performed in the human retina.

Bioinspired architecture approach for a one-billion transistor smart CMOS camera chip

NASA Astrophysics Data System (ADS)

Fey, Dietmar; Komann, Marcus

2007-05-01

In the paper we present a massively parallel VLSI architecture for future smart CMOS camera chips with up to one billion transistors. To exploit efficiently the potential offered by future micro- or nanoelectronic devices traditional on central structures oriented parallel architectures based on MIMD or SIMD approaches will fail. They require too long and too many global interconnects for the distribution of code or the access to common memory. On the other hand nature developed self-organising and emergent principles to manage successfully complex structures based on lots of interacting simple elements. Therefore we developed a new as Marching Pixels denoted emergent computing paradigm based on a mixture of bio-inspired computing models like cellular automaton and artificial ants. In the paper we present different Marching Pixels algorithms and the corresponding VLSI array architecture. A detailed synthesis result for a 0.18 μm CMOS process shows that a 256×256 pixel image is processed in less than 10 ms assuming a moderate 100 MHz clock rate for the processor array. Future higher integration densities and a 3D chip stacking technology will allow the integration and processing of Mega pixels within the same time since our architecture is fully scalable.

Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

PubMed

Gu, Liangcai; Li, Chao; Aach, John; Hill, David E; Vidal, Marc; Church, George M

2014-11-27

In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.

Multiplex single-molecule interaction profiling of DNA barcoded proteins

PubMed Central

Gu, Liangcai; Li, Chao; Aach, John; Hill, David E.; Vidal, Marc; Church, George M.

2014-01-01

In contrast with advances in massively parallel DNA sequencing1, high-throughput protein analyses2-4 are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule (SM) protein detection achieved using optical methods5 is limited by the number of spectrally nonoverlapping chromophores. Here, we introduce a single molecular interaction-sequencing (SMI-Seq) technology for parallel protein interaction profiling leveraging SM advantages. DNA barcodes are attached to proteins collectively via ribosome display6 or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide (PAA) thin film to construct a random SM array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies)7 and analyzed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimeter. Furthermore, protein interactions can be measured based on the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor (GPCR) and antibody binding profiling, were demonstrated. SMI-Seq enables “library vs. library” screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity. PMID:25252978

Parallel Logic Programming and Parallel Systems Software and Hardware

DTIC Science & Technology

1989-07-29

Conference, Dallas TX. January 1985. (55) [Rous75] Roussel, P., "PROLOG: Manuel de Reference et d’Uilisation", Group d’ Intelligence Artificielle , Universite d...completed. Tools were provided for software development using artificial intelligence techniques. Al software for massively parallel architectures was...using artificial intelligence tech- niques. Al software for massively parallel architectures was started. 1. Introduction We describe research conducted

Design of a massively parallel computer using bit serial processing elements

NASA Technical Reports Server (NTRS)

Aburdene, Maurice F.; Khouri, Kamal S.; Piatt, Jason E.; Zheng, Jianqing

1995-01-01

A 1-bit serial processor designed for a parallel computer architecture is described. This processor is used to develop a massively parallel computational engine, with a single instruction-multiple data (SIMD) architecture. The computer is simulated and tested to verify its operation and to measure its performance for further development.

SciSpark: Highly Interactive and Scalable Model Evaluation and Climate Metrics

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Palamuttam, R. S.; Mogrovejo, R. M.; Whitehall, K. D.; Mattmann, C. A.; Verma, R.; Waliser, D. E.; Lee, H.

2015-12-01

Remote sensing data and climate model output are multi-dimensional arrays of massive sizes locked away in heterogeneous file formats (HDF5/4, NetCDF 3/4) and metadata models (HDF-EOS, CF) making it difficult to perform multi-stage, iterative science processing since each stage requires writing and reading data to and from disk. We are developing a lightning fast Big Data technology called SciSpark based on ApacheTM Spark under a NASA AIST grant (PI Mattmann). Spark implements the map-reduce paradigm for parallel computing on a cluster, but emphasizes in-memory computation, "spilling" to disk only as needed, and so outperforms the disk-based ApacheTM Hadoop by 100x in memory and by 10x on disk. SciSpark will enable scalable model evaluation by executing large-scale comparisons of A-Train satellite observations to model grids on a cluster of 10 to 1000 compute nodes. This 2nd generation capability for NASA's Regional Climate Model Evaluation System (RCMES) will compute simple climate metrics at interactive speeds, and extend to quite sophisticated iterative algorithms such as machine-learning based clustering of temperature PDFs, and even graph-based algorithms for searching for Mesocale Convective Complexes. We have implemented a parallel data ingest capability in which the user specifies desired variables (arrays) as several time-sorted lists of URL's (i.e. using OPeNDAP model.nc?varname, or local files). The specified variables are partitioned by time/space and then each Spark node pulls its bundle of arrays into memory to begin a computation pipeline. We also investigated the performance of several N-dim. array libraries (scala breeze, java jblas & netlib-java, and ND4J). We are currently developing science codes using ND4J and studying memory behavior on the JVM. On the pyspark side, many of our science codes already use the numpy and SciPy ecosystems. The talk will cover: the architecture of SciSpark, the design of the scientific RDD (sRDD) data structure, our efforts to integrate climate science algorithms in Python and Scala, parallel ingest and partitioning of A-Train satellite observations from HDF files and model grids from netCDF files, first parallel runs to compute comparison statistics and PDF's, and first metrics quantifying parallel speedups and memory & disk usage.

Progress on complementary patterning using plasmon-excited electron beamlets (Conference Presentation)

NASA Astrophysics Data System (ADS)

Du, Zhidong; Chen, Chen; Pan, Liang

2017-04-01

Maskless lithography using parallel electron beamlets is a promising solution for next generation scalable maskless nanolithography. Researchers have focused on this goal but have been unable to find a robust technology to generate and control high-quality electron beamlets with satisfactory brightness and uniformity. In this work, we will aim to address this challenge by developing a revolutionary surface-plasmon-enhanced-photoemission (SPEP) technology to generate massively-parallel electron beamlets for maskless nanolithography. The new technology is built upon our recent breakthroughs in plasmonic lenses, which will be used to excite and focus surface plasmons to generate massively-parallel electron beamlets through photoemission. Specifically, the proposed SPEP device consists of an array of plasmonic lens and electrostatic micro-lens pairs, each pair independently producing an electron beamlet. During lithography, a spatial optical modulator will dynamically project light onto individual plasmonic lenses to control the switching and brightness of electron beamlets. The photons incident onto each plasmonic lens are concentrated into a diffraction-unlimited spot as localized surface plasmons to excite the local electrons to near their vacuum levels. Meanwhile, the electrostatic micro-lens extracts the excited electrons to form a focused beamlet, which can be rastered across a wafer to perform lithography. Studies showed that surface plasmons can enhance the photoemission by orders of magnitudes. This SPEP technology can scale up the maskless lithography process to write at wafers per hour. In this talk, we will report the mechanism of the strong electron-photon couplings and the locally enhanced photoexcitation, design of a SPEP device, overview of our proof-of-concept study, and demonstrated parallel lithography of 20-50 nm features.

Digital and optical shape representation and pattern recognition; Proceedings of the Meeting, Orlando, FL, Apr. 4-6, 1988

NASA Technical Reports Server (NTRS)

Juday, Richard D. (Editor)

1988-01-01

The present conference discusses topics in pattern-recognition correlator architectures, digital stereo systems, geometric image transformations and their applications, topics in pattern recognition, filter algorithms, object detection and classification, shape representation techniques, and model-based object recognition methods. Attention is given to edge-enhancement preprocessing using liquid crystal TVs, massively-parallel optical data base management, three-dimensional sensing with polar exponential sensor arrays, the optical processing of imaging spectrometer data, hybrid associative memories and metric data models, the representation of shape primitives in neural networks, and the Monte Carlo estimation of moment invariants for pattern recognition.

Binary synaptic connections based on memory switching in a-Si:H for artificial neural networks

NASA Technical Reports Server (NTRS)

Thakoor, A. P.; Lamb, J. L.; Moopenn, A.; Khanna, S. K.

1987-01-01

A scheme for nonvolatile associative electronic memory storage with high information storage density is proposed which is based on neural network models and which uses a matrix of two-terminal passive interconnections (synapses). It is noted that the massive parallelism in the architecture would require the ON state of a synaptic connection to be unusually weak (highly resistive). Memory switching using a-Si:H along with ballast resistors patterned from amorphous Ge-metal alloys is investigated for a binary programmable read only memory matrix. The fabrication of a 1600 synapse test array of uniform connection strengths and a-Si:H switching elements is discussed.

FPGA-based real time processing of the Plenoptic Wavefront Sensor

NASA Astrophysics Data System (ADS)

Rodríguez-Ramos, L. F.; Marín, Y.; Díaz, J. J.; Piqueras, J.; García-Jiménez, J.; Rodríguez-Ramos, J. M.

The plenoptic wavefront sensor combines measurements at pupil and image planes in order to obtain simultaneously wavefront information from different points of view, being capable to sample the volume above the telescope to extract the tomographic information of the atmospheric turbulence. The advantages of this sensor are presented elsewhere at this conference (José M. Rodríguez-Ramos et al). This paper will concentrate in the processing required for pupil plane phase recovery, and its computation in real time using FPGAs (Field Programmable Gate Arrays). This technology eases the implementation of massive parallel processing and allows tailoring the system to the requirements, maintaining flexibility, speed and cost figures.

The EMCC / DARPA Massively Parallel Electromagnetic Scattering Project

NASA Technical Reports Server (NTRS)

Woo, Alex C.; Hill, Kueichien C.

1996-01-01

The Electromagnetic Code Consortium (EMCC) was sponsored by the Advanced Research Program Agency (ARPA) to demonstrate the effectiveness of massively parallel computing in large scale radar signature predictions. The EMCC/ARPA project consisted of three parts.

High precision computing with charge domain devices and a pseudo-spectral method therefor

NASA Technical Reports Server (NTRS)

Barhen, Jacob (Inventor); Toomarian, Nikzad (Inventor); Fijany, Amir (Inventor); Zak, Michail (Inventor)

1997-01-01

The present invention enhances the bit resolution of a CCD/CID MVM processor by storing each bit of each matrix element as a separate CCD charge packet. The bits of each input vector are separately multiplied by each bit of each matrix element in massive parallelism and the resulting products are combined appropriately to synthesize the correct product. In another aspect of the invention, such arrays are employed in a pseudo-spectral method of the invention, in which partial differential equations are solved by expressing each derivative analytically as matrices, and the state function is updated at each computation cycle by multiplying it by the matrices. The matrices are treated as synaptic arrays of a neural network and the state function vector elements are treated as neurons. In a further aspect of the invention, moving target detection is performed by driving the soliton equation with a vector of detector outputs. The neural architecture consists of two synaptic arrays corresponding to the two differential terms of the soliton-equation and an adder connected to the output thereof and to the output of the detector array to drive the soliton equation.

Topical perspective on massive threading and parallelism.

PubMed

Farber, Robert M

2011-09-01

Unquestionably computer architectures have undergone a recent and noteworthy paradigm shift that now delivers multi- and many-core systems with tens to many thousands of concurrent hardware processing elements per workstation or supercomputer node. GPGPU (General Purpose Graphics Processor Unit) technology in particular has attracted significant attention as new software development capabilities, namely CUDA (Compute Unified Device Architecture) and OpenCL™, have made it possible for students as well as small and large research organizations to achieve excellent speedup for many applications over more conventional computing architectures. The current scientific literature reflects this shift with numerous examples of GPGPU applications that have achieved one, two, and in some special cases, three-orders of magnitude increased computational performance through the use of massive threading to exploit parallelism. Multi-core architectures are also evolving quickly to exploit both massive-threading and massive-parallelism such as the 1.3 million threads Blue Waters supercomputer. The challenge confronting scientists in planning future experimental and theoretical research efforts--be they individual efforts with one computer or collaborative efforts proposing to use the largest supercomputers in the world is how to capitalize on these new massively threaded computational architectures--especially as not all computational problems will scale to massive parallelism. In particular, the costs associated with restructuring software (and potentially redesigning algorithms) to exploit the parallelism of these multi- and many-threaded machines must be considered along with application scalability and lifespan. This perspective is an overview of the current state of threading and parallelize with some insight into the future. Published by Elsevier Inc.

Microresonator-based solitons for massively parallel coherent optical communications

NASA Astrophysics Data System (ADS)

Marin-Palomo, Pablo; Kemal, Juned N.; Karpov, Maxim; Kordts, Arne; Pfeifle, Joerg; Pfeiffer, Martin H. P.; Trocha, Philipp; Wolf, Stefan; Brasch, Victor; Anderson, Miles H.; Rosenberger, Ralf; Vijayan, Kovendhan; Freude, Wolfgang; Kippenberg, Tobias J.; Koos, Christian

2017-06-01

Solitons are waveforms that preserve their shape while propagating, as a result of a balance of dispersion and nonlinearity. Soliton-based data transmission schemes were investigated in the 1980s and showed promise as a way of overcoming the limitations imposed by dispersion of optical fibres. However, these approaches were later abandoned in favour of wavelength-division multiplexing schemes, which are easier to implement and offer improved scalability to higher data rates. Here we show that solitons could make a comeback in optical communications, not as a competitor but as a key element of massively parallel wavelength-division multiplexing. Instead of encoding data on the soliton pulse train itself, we use continuous-wave tones of the associated frequency comb as carriers for communication. Dissipative Kerr solitons (DKSs) (solitons that rely on a double balance of parametric gain and cavity loss, as well as dispersion and nonlinearity) are generated as continuously circulating pulses in an integrated silicon nitride microresonator via four-photon interactions mediated by the Kerr nonlinearity, leading to low-noise, spectrally smooth, broadband optical frequency combs. We use two interleaved DKS frequency combs to transmit a data stream of more than 50 terabits per second on 179 individual optical carriers that span the entire telecommunication C and L bands (centred around infrared telecommunication wavelengths of 1.55 micrometres). We also demonstrate coherent detection of a wavelength-division multiplexing data stream by using a pair of DKS frequency combs—one as a multi-wavelength light source at the transmitter and the other as the corresponding local oscillator at the receiver. This approach exploits the scalability of microresonator-based DKS frequency comb sources for massively parallel optical communications at both the transmitter and the receiver. Our results demonstrate the potential of these sources to replace the arrays of continuous-wave lasers that are currently used in high-speed communications. In combination with advanced spatial multiplexing schemes and highly integrated silicon photonic circuits, DKS frequency combs could bring chip-scale petabit-per-second transceivers into reach.

A novel VLSI processor architecture for supercomputing arrays

NASA Technical Reports Server (NTRS)

Venkateswaran, N.; Pattabiraman, S.; Devanathan, R.; Ahmed, Ashaf; Venkataraman, S.; Ganesh, N.

1993-01-01

Design of the processor element for general purpose massively parallel supercomputing arrays is highly complex and cost ineffective. To overcome this, the architecture and organization of the functional units of the processor element should be such as to suit the diverse computational structures and simplify mapping of complex communication structures of different classes of algorithms. This demands that the computation and communication structures of different class of algorithms be unified. While unifying the different communication structures is a difficult process, analysis of a wide class of algorithms reveals that their computation structures can be expressed in terms of basic IP,IP,OP,CM,R,SM, and MAA operations. The execution of these operations is unified on the PAcube macro-cell array. Based on this PAcube macro-cell array, we present a novel processor element called the GIPOP processor, which has dedicated functional units to perform the above operations. The architecture and organization of these functional units are such to satisfy the two important criteria mentioned above. The structure of the macro-cell and the unification process has led to a very regular and simpler design of the GIPOP processor. The production cost of the GIPOP processor is drastically reduced as it is designed on high performance mask programmable PAcube arrays.

Box schemes and their implementation on the iPSC/860

NASA Technical Reports Server (NTRS)

Chattot, J. J.; Merriam, M. L.

1991-01-01

Research on algoriths for efficiently solving fluid flow problems on massively parallel computers is continued in the present paper. Attention is given to the implementation of a box scheme on the iPSC/860, a massively parallel computer with a peak speed of 10 Gflops and a memory of 128 Mwords. A domain decomposition approach to parallelism is used.

Scan line graphics generation on the massively parallel processor

NASA Technical Reports Server (NTRS)

Dorband, John E.

1988-01-01

Described here is how researchers implemented a scan line graphics generation algorithm on the Massively Parallel Processor (MPP). Pixels are computed in parallel and their results are applied to the Z buffer in large groups. To perform pixel value calculations, facilitate load balancing across the processors and apply the results to the Z buffer efficiently in parallel requires special virtual routing (sort computation) techniques developed by the author especially for use on single-instruction multiple-data (SIMD) architectures.

Magnetic Fields in the Massive Dense Cores of the DR21 Filament: Weakly Magnetized Cores in a Strongly Magnetized Filament

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ching, Tao-Chung; Lai, Shih-Ping; Zhang, Qizhou

We present Submillimeter Array 880 μ m dust polarization observations of six massive dense cores in the DR21 filament. The dust polarization shows complex magnetic field structures in the massive dense cores with sizes of 0.1 pc, in contrast to the ordered magnetic fields of the parsec-scale filament. The major axes of the massive dense cores appear to be aligned either parallel or perpendicular to the magnetic fields of the filament, indicating that the parsec-scale magnetic fields play an important role in the formation of the massive dense cores. However, the correlation between the major axes of the cores andmore » the magnetic fields of the cores is less significant, suggesting that during the core formation, the magnetic fields below 0.1 pc scales become less important than the magnetic fields above 0.1 pc scales in supporting a core against gravity. Our analysis of the angular dispersion functions of the observed polarization segments yields a plane-of-sky magnetic field strength of 0.4–1.7 mG for the massive dense cores. We estimate the kinematic, magnetic, and gravitational virial parameters of the filament and the cores. The virial parameters show that the gravitational energy in the filament dominates magnetic and kinematic energies, while the kinematic energy dominates in the cores. Our work suggests that although magnetic fields may play an important role in a collapsing filament, the kinematics arising from gravitational collapse must become more important than magnetic fields during the evolution from filaments to massive dense cores.« less

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

NASA Technical Reports Server (NTRS)

Shia, David; Mcmanus, Hugh L.

1995-01-01

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.

Bit-parallel arithmetic in a massively-parallel associative processor

NASA Technical Reports Server (NTRS)

Scherson, Isaac D.; Kramer, David A.; Alleyne, Brian D.

1992-01-01

A simple but powerful new architecture based on a classical associative processor model is presented. Algorithms for performing the four basic arithmetic operations both for integer and floating point operands are described. For m-bit operands, the proposed architecture makes it possible to execute complex operations in O(m) cycles as opposed to O(m exp 2) for bit-serial machines. A word-parallel, bit-parallel, massively-parallel computing system can be constructed using this architecture with VLSI technology. The operation of this system is demonstrated for the fast Fourier transform and matrix multiplication.

An object-oriented approach for parallel self adaptive mesh refinement on block structured grids

NASA Technical Reports Server (NTRS)

Lemke, Max; Witsch, Kristian; Quinlan, Daniel

1993-01-01

Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.

Increasing the reach of forensic genetics with massively parallel sequencing.

PubMed

Budowle, Bruce; Schmedes, Sarah E; Wendt, Frank R

2017-09-01

The field of forensic genetics has made great strides in the analysis of biological evidence related to criminal and civil matters. More so, the discipline has set a standard of performance and quality in the forensic sciences. The advent of massively parallel sequencing will allow the field to expand its capabilities substantially. This review describes the salient features of massively parallel sequencing and how it can impact forensic genetics. The features of this technology offer increased number and types of genetic markers that can be analyzed, higher throughput of samples, and the capability of targeting different organisms, all by one unifying methodology. While there are many applications, three are described where massively parallel sequencing will have immediate impact: molecular autopsy, microbial forensics and differentiation of monozygotic twins. The intent of this review is to expose the forensic science community to the potential enhancements that have or are soon to arrive and demonstrate the continued expansion the field of forensic genetics and its service in the investigation of legal matters.

Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT.

PubMed

Maruyama, Yutaka; Yoshida, Norio; Tadano, Hiroto; Takahashi, Daisuke; Sato, Mitsuhisa; Hirata, Fumio

2014-07-05

A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically. We tested the 3D-RISM calculation on the large and fine calculation cell (2048(3) grid points) on 16,384 nodes, each having eight CPU cores. The new 3D-RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D-RISM program is effective to analyze the hydration properties of the large biomolecular systems. Copyright © 2014 Wiley Periodicals, Inc.

Parallel computing of a climate model on the dawn 1000 by domain decomposition method

NASA Astrophysics Data System (ADS)

Bi, Xunqiang

1997-12-01

In this paper the parallel computing of a grid-point nine-level atmospheric general circulation model on the Dawn 1000 is introduced. The model was developed by the Institute of Atmospheric Physics (IAP), Chinese Academy of Sciences (CAS). The Dawn 1000 is a MIMD massive parallel computer made by National Research Center for Intelligent Computer (NCIC), CAS. A two-dimensional domain decomposition method is adopted to perform the parallel computing. The potential ways to increase the speed-up ratio and exploit more resources of future massively parallel supercomputation are also discussed.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Multi-threading: A new dimension to massively parallel scientific computation

NASA Astrophysics Data System (ADS)

Nielsen, Ida M. B.; Janssen, Curtis L.

2000-06-01

Multi-threading is becoming widely available for Unix-like operating systems, and the application of multi-threading opens new ways for performing parallel computations with greater efficiency. We here briefly discuss the principles of multi-threading and illustrate the application of multi-threading for a massively parallel direct four-index transformation of electron repulsion integrals. Finally, other potential applications of multi-threading in scientific computing are outlined.

Neural Parallel Engine: A toolbox for massively parallel neural signal processing.

PubMed

Tam, Wing-Kin; Yang, Zhi

2018-05-01

Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings. In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs). It offers a selection of the most commonly used routines in neural signal processing such as spike detection and spike sorting, including advanced algorithms such as exponential-component-power-component (EC-PC) spike detection and binary pursuit spike sorting. We also propose a new method for detecting peaks in parallel through a parallel compact operation. Our toolbox is able to offer a 5× to 110× speedup compared with its CPU counterparts depending on the algorithms. A user-friendly MATLAB interface is provided to allow easy integration of the toolbox into existing workflows. Previous efforts on GPU neural signal processing only focus on a few rudimentary algorithms, are not well-optimized and often do not provide a user-friendly programming interface to fit into existing workflows. There is a strong need for a comprehensive toolbox for massively parallel neural signal processing. A new toolbox for massively parallel neural signal processing has been created. It can offer significant speedup in processing signals from large-scale recordings up to thousands of channels. Copyright © 2018 Elsevier B.V. All rights reserved.

Integrated nanoscale tools for interrogating living cells

NASA Astrophysics Data System (ADS)

Jorgolli, Marsela

The development of next-generation, nanoscale technologies that interface biological systems will pave the way towards new understanding of such complex systems. Nanowires -- one-dimensional nanoscale structures -- have shown unique potential as an ideal physical interface to biological systems. Herein, we focus on the development of nanowire-based devices that can enable a wide variety of biological studies. First, we built upon standard nanofabrication techniques to optimize nanowire devices, resulting in perfectly ordered arrays of both opaque (Silicon) and transparent (Silicon dioxide) nanowires with user defined structural profile, densities, and overall patterns, as well as high sample consistency and large scale production. The high-precision and well-controlled fabrication method in conjunction with additional technologies laid the foundation for the generation of highly specialized platforms for imaging, electrochemical interrogation, and molecular biology. Next, we utilized nanowires as the fundamental structure in the development of integrated nanoelectronic platforms to directly interrogate the electrical activity of biological systems. Initially, we generated a scalable intracellular electrode platform based on vertical nanowires that allows for parallel electrical interfacing to multiple mammalian neurons. Our prototype device consisted of 16 individually addressable stimulation/recording sites, each containing an array of 9 electrically active silicon nanowires. We showed that these vertical nanowire electrode arrays could intracellularly record and stimulate neuronal activity in dissociated cultures of rat cortical neurons similar to patch clamp electrodes. In addition, we used our intracellular electrode platform to measure multiple individual synaptic connections, which enables the reconstruction of the functional connectivity maps of neuronal circuits. In order to expand and improve the capability of this functional prototype device we designed and fabricated a new hybrid chip that combines a front-side nanowire-based interface for neuronal recording with backside complementary metal oxide semiconductor (CMOS) circuits for on-chip multiplexing, voltage control for stimulation, signal amplification, and signal processing. Individual chips contain 1024 stimulation/recording sites enabling large-scale interfacing of neuronal networks with single cell resolution. Through electrical and electrochemical characterization of the devices, we demonstrated their enhanced functionality at a massively parallel scale. In our initial cell experiments, we achieved intracellular stimulations and recordings of changes in the membrane potential in a variety of cells including: HEK293T, cardiomyocytes, and rat cortical neurons. This demonstrated the device capability for single-cell-resolution recording/stimulation which when extended to a large number of neurons in a massively parallel fashion will enable the functional mapping of a complex neuronal network.

Rasdaman for Big Spatial Raster Data

NASA Astrophysics Data System (ADS)

Hu, F.; Huang, Q.; Scheele, C. J.; Yang, C. P.; Yu, M.; Liu, K.

2015-12-01

Spatial raster data have grown exponentially over the past decade. Recent advancements on data acquisition technology, such as remote sensing, have allowed us to collect massive observation data of various spatial resolution and domain coverage. The volume, velocity, and variety of such spatial data, along with the computational intensive nature of spatial queries, pose grand challenge to the storage technologies for effective big data management. While high performance computing platforms (e.g., cloud computing) can be used to solve the computing-intensive issues in big data analysis, data has to be managed in a way that is suitable for distributed parallel processing. Recently, rasdaman (raster data manager) has emerged as a scalable and cost-effective database solution to store and retrieve massive multi-dimensional arrays, such as sensor, image, and statistics data. Within this paper, the pros and cons of using rasdaman to manage and query spatial raster data will be examined and compared with other common approaches, including file-based systems, relational databases (e.g., PostgreSQL/PostGIS), and NoSQL databases (e.g., MongoDB and Hive). Earth Observing System (EOS) data collected from NASA's Atmospheric Scientific Data Center (ASDC) will be used and stored in these selected database systems, and a set of spatial and non-spatial queries will be designed to benchmark their performance on retrieving large-scale, multi-dimensional arrays of EOS data. Lessons learnt from using rasdaman will be discussed as well.

Optimizing Nanoelectrode Arrays for Scalable Intracellular Electrophysiology.

PubMed

Abbott, Jeffrey; Ye, Tianyang; Ham, Donhee; Park, Hongkun

2018-03-20

Electrode technology for electrophysiology has a long history of innovation, with some decisive steps including the development of the voltage-clamp measurement technique by Hodgkin and Huxley in the 1940s and the invention of the patch clamp electrode by Neher and Sakmann in the 1970s. The high-precision intracellular recording enabled by the patch clamp electrode has since been a gold standard in studying the fundamental cellular processes underlying the electrical activities of neurons and other excitable cells. One logical next step would then be to parallelize these intracellular electrodes, since simultaneous intracellular recording from a large number of cells will benefit the study of complex neuronal networks and will increase the throughput of electrophysiological screening from basic neurobiology laboratories to the pharmaceutical industry. Patch clamp electrodes, however, are not built for parallelization; as for now, only ∼10 patch measurements in parallel are possible. It has long been envisioned that nanoscale electrodes may help meet this challenge. First, nanoscale electrodes were shown to enable intracellular access. Second, because their size scale is within the normal reach of the standard top-down fabrication, the nanoelectrodes can be scaled into a large array for parallelization. Third, such a nanoelectrode array can be monolithically integrated with complementary metal-oxide semiconductor (CMOS) electronics to facilitate the large array operation and the recording of the signals from a massive number of cells. These are some of the central ideas that have motivated the research activity into nanoelectrode electrophysiology, and these past years have seen fruitful developments. This Account aims to synthesize these findings so as to provide a useful reference. Summing up from the recent studies, we will first elucidate the morphology and associated electrical properties of the interface between a nanoelectrode and a cellular membrane, clarifying how the nanoelectrode attains intracellular access. This understanding will be translated into a circuit model for the nanobio interface, which we will then use to lay out the strategies for improving the interface. The intracellular interface of the nanoelectrode is currently inferior to that of the patch clamp electrode; reaching this benchmark will be an exciting challenge that involves optimization of electrode geometries, materials, chemical modifications, electroporation protocols, and recording/stimulation electronics, as we describe in the Account. Another important theme of this Account, beyond the optimization of the individual nanoelectrode-cell interface, is the scalability of the nanoscale electrodes. We will discuss this theme using a recent development from our groups as an example, where an array of ca. 1000 nanoelectrode pixels fabricated on a CMOS integrated circuit chip performs parallel intracellular recording from a few hundreds of cardiomyocytes, which marks a new milestone in electrophysiology.

The language parallel Pascal and other aspects of the massively parallel processor

NASA Technical Reports Server (NTRS)

Reeves, A. P.; Bruner, J. D.

1982-01-01

A high level language for the Massively Parallel Processor (MPP) was designed. This language, called Parallel Pascal, is described in detail. A description of the language design, a description of the intermediate language, Parallel P-Code, and details for the MPP implementation are included. Formal descriptions of Parallel Pascal and Parallel P-Code are given. A compiler was developed which converts programs in Parallel Pascal into the intermediate Parallel P-Code language. The code generator to complete the compiler for the MPP is being developed independently. A Parallel Pascal to Pascal translator was also developed. The architecture design for a VLSI version of the MPP was completed with a description of fault tolerant interconnection networks. The memory arrangement aspects of the MPP are discussed and a survey of other high level languages is given.

Guided growth of horizontal GaN nanowires on quartz and their transfer to other substrates.

PubMed

Goren-Ruck, Lior; Tsivion, David; Schvartzman, Mark; Popovitz-Biro, Ronit; Joselevich, Ernesto

2014-03-25

The guided growth of horizontal nanowires has so far been demonstrated on a limited number of substrates. In most cases, the nanowires are covalently bonded to the substrate where they grow and cannot be transferred to other substrates. Here we demonstrate the guided growth of well-aligned horizontal GaN nanowires on quartz and their subsequent transfer to silicon wafers by selective etching of the quartz while maintaining their alignment. The guided growth was observed on different planes of quartz with varying degrees of alignment. We characterized the crystallographic orientations of the nanowires and proposed a new mechanism of "dynamic graphoepitaxy" for their guided growth on quartz. The transfer of the guided nanowires enabled the fabrication of back-gated field-effect transistors from aligned nanowire arrays on oxidized silicon wafers and the production of crossbar arrays. The guided growth of transferrable nanowires opens up the possibility of massively parallel integration of nanowires into functional systems on virtually any desired substrate.

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Treesearch

Matthew Parks; Richard Cronn; Aaron Liston

2009-01-01

We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. We found that 30/33 ingroup nodes resolved wlth > 95-percent bootstrap support; this is a substantial improvement relative...

Implementing Access to Data Distributed on Many Processors

NASA Technical Reports Server (NTRS)

James, Mark

2006-01-01

A reference architecture is defined for an object-oriented implementation of domains, arrays, and distributions written in the programming language Chapel. This technology primarily addresses domains that contain arrays that have regular index sets with the low-level implementation details being beyond the scope of this discussion. What is defined is a complete set of object-oriented operators that allows one to perform data distributions for domain arrays involving regular arithmetic index sets. What is unique is that these operators allow for the arbitrary regions of the arrays to be fragmented and distributed across multiple processors with a single point of access giving the programmer the illusion that all the elements are collocated on a single processor. Today's massively parallel High Productivity Computing Systems (HPCS) are characterized by a modular structure, with a large number of processing and memory units connected by a high-speed network. Locality of access as well as load balancing are primary concerns in these systems that are typically used for high-performance scientific computation. Data distributions address these issues by providing a range of methods for spreading large data sets across the components of a system. Over the past two decades, many languages, systems, tools, and libraries have been developed for the support of distributions. Since the performance of data parallel applications is directly influenced by the distribution strategy, users often resort to low-level programming models that allow fine-tuning of the distribution aspects affecting performance, but, at the same time, are tedious and error-prone. This technology presents a reusable design of a data-distribution framework for data parallel high-performance applications. Distributions are a means to express locality in systems composed of large numbers of processor and memory components connected by a network. Since distributions have a great effect on the performance of applications, it is important that the distribution strategy is flexible, so its behavior can change depending on the needs of the application. At the same time, high productivity concerns require that the user be shielded from error-prone, tedious details such as communication and synchronization.

Massively Parallel Solution of Poisson Equation on Coarse Grain MIMD Architectures

NASA Technical Reports Server (NTRS)

Fijany, A.; Weinberger, D.; Roosta, R.; Gulati, S.

1998-01-01

In this paper a new algorithm, designated as Fast Invariant Imbedding algorithm, for solution of Poisson equation on vector and massively parallel MIMD architectures is presented. This algorithm achieves the same optimal computational efficiency as other Fast Poisson solvers while offering a much better structure for vector and parallel implementation. Our implementation on the Intel Delta and Paragon shows that a speedup of over two orders of magnitude can be achieved even for moderate size problems.

Modular and efficient ozone systems based on massively parallel chemical processing in microchannel plasma arrays: performance and commercialization

NASA Astrophysics Data System (ADS)

Kim, M.-H.; Cho, J. H.; Park, S.-J.; Eden, J. G.

2017-08-01

Plasmachemical systems based on the production of a specific molecule (O3) in literally thousands of microchannel plasmas simultaneously have been demonstrated, developed and engineered over the past seven years, and commercialized. At the heart of this new plasma technology is the plasma chip, a flat aluminum strip fabricated by photolithographic and wet chemical processes and comprising 24-48 channels, micromachined into nanoporous aluminum oxide, with embedded electrodes. By integrating 4-6 chips into a module, the mass output of an ozone microplasma system is scaled linearly with the number of modules operating in parallel. A 115 g/hr (2.7 kg/day) ozone system, for example, is realized by the combined output of 18 modules comprising 72 chips and 1,800 microchannels. The implications of this plasma processing architecture for scaling ozone production capability, and reducing capital and service costs when introducing redundancy into the system, are profound. In contrast to conventional ozone generator technology, microplasma systems operate reliably (albeit with reduced output) in ambient air and humidity levels up to 90%, a characteristic attributable to the water adsorption/desorption properties and electrical breakdown strength of nanoporous alumina. Extensive testing has documented chip and system lifetimes (MTBF) beyond 5,000 hours, and efficiencies >130 g/kWh when oxygen is the feedstock gas. Furthermore, the weight and volume of microplasma systems are a factor of 3-10 lower than those for conventional ozone systems of comparable output. Massively-parallel plasmachemical processing offers functionality, performance, and commercial value beyond that afforded by conventional technology, and is currently in operation in more than 30 countries worldwide.

Toward 4D Nanoprinting with Tip-Induced Organic Surface Reactions.

PubMed

Carbonell, Carlos; Braunschweig, Adam B

2017-02-21

Future nanomanufacturing tools will prepare organic materials with complex four-dimensional (4D) structure, where the position (x, y, z) and chemical composition within a volume is controlled with sub-1 μm spatial resolution. Such tools could produce substrates that mimic biological interfaces, like the cell surface or the extracellular matrix, whose topology and chemical complexity combine to direct some of the most sophisticated biological events. The control of organic materials at the nanoscale-level of spatial resolution could revolutionize the assembly of next generation optical and electronic devices or substrates for tissue engineering or enable fundamental biological or material science investigations. Organic chemistry provides the requisite control over the orientation and position of matter within a nanoscale reference frame through the formation of new covalent bonds. Several challenges however preclude the integration of organic chemistry with conventional nanomanufacturing approaches, namely most nanolithography platforms would denature or destroy delicate organic and biologically active matter, confirming covalent bond formation at interfaces remains difficult, and finally, only a small handful of the reactions used to transform molecules in solution have been validated on surfaces. Thus, entirely new approaches, where organic transformations and spatial control are considered equally important contributors, are needed to create 4D organic nanoprinting platforms. This Account describes efforts from our group to reconcile nanolithography, and specifically massively parallel scanning probe lithography (SPL), with organic chemistry to further the goal of 4D organic nanoprinting. Massively parallel SPL involves arrays of elastomeric pyramids mounted onto piezoelectric actuators, and creates patterns with feature diameters below 50 nm by using the pyramidal tips for either the direct deposition of ink or the localized delivery of energy to a surface. While other groups have focused on tip and array architetctures, our efforts have been on exploring their use for localizing organic chemistry on surfaces with nanoscale spatial resolution in 3D. Herein we describe the use of massively parallel SPL to create covalently immobilized patterns of organic materials using thermal, catalytic, photochemical, and force-accelerated reactions. In doing so, we have developed a high-throughput protocol for confirming interfacial bond formation. These efforts have resulted in new opportunities for the preparation of glycan arrays, novel approaches for covalently patterning graphene, and a 3D nanoprinter by combining photochemical brush polymerizations with SPL. Achieving true 4D nanoprinting involves advances in surface chemistry and instrumentation development, and to this end 4D micropatterns were produced in a microfluidic photoreactor that can position polymers composed of different monomers within micrometer proximity. A substantial gap remains, however, between these current technologies and the future's 4D nanomanufacturing tools, but the marriage of SPL with organic chemistry is an important step toward this goal. As this field continues to mature we can expect bottom-up 4D nanomanufacturing to begin supplanting conventional top-down strategies for preparing electronics, bioarrays, and functional substrates. In addition, these new printing technologies may enable the preparation of synthetic targets, such as artificial biological interfaces, with a level of organic sophistication that is entirely unachievable using existing technologies.

SIAM Conference on Parallel Processing for Scientific Computing, 4th, Chicago, IL, Dec. 11-13, 1989, Proceedings

NASA Technical Reports Server (NTRS)

Dongarra, Jack (Editor); Messina, Paul (Editor); Sorensen, Danny C. (Editor); Voigt, Robert G. (Editor)

1990-01-01

Attention is given to such topics as an evaluation of block algorithm variants in LAPACK and presents a large-grain parallel sparse system solver, a multiprocessor method for the solution of the generalized Eigenvalue problem on an interval, and a parallel QR algorithm for iterative subspace methods on the CM2. A discussion of numerical methods includes the topics of asynchronous numerical solutions of PDEs on parallel computers, parallel homotopy curve tracking on a hypercube, and solving Navier-Stokes equations on the Cedar Multi-Cluster system. A section on differential equations includes a discussion of a six-color procedure for the parallel solution of elliptic systems using the finite quadtree structure, data parallel algorithms for the finite element method, and domain decomposition methods in aerodynamics. Topics dealing with massively parallel computing include hypercube vs. 2-dimensional meshes and massively parallel computation of conservation laws. Performance and tools are also discussed.

A Compact VLSI System for Bio-Inspired Visual Motion Estimation.

PubMed

Shi, Cong; Luo, Gang

2018-04-01

This paper proposes a bio-inspired visual motion estimation algorithm based on motion energy, along with its compact very-large-scale integration (VLSI) architecture using low-cost embedded systems. The algorithm mimics motion perception functions of retina, V1, and MT neurons in a primate visual system. It involves operations of ternary edge extraction, spatiotemporal filtering, motion energy extraction, and velocity integration. Moreover, we propose the concept of confidence map to indicate the reliability of estimation results on each probing location. Our algorithm involves only additions and multiplications during runtime, which is suitable for low-cost hardware implementation. The proposed VLSI architecture employs multiple (frame, pixel, and operation) levels of pipeline and massively parallel processing arrays to boost the system performance. The array unit circuits are optimized to minimize hardware resource consumption. We have prototyped the proposed architecture on a low-cost field-programmable gate array platform (Zynq 7020) running at 53-MHz clock frequency. It achieved 30-frame/s real-time performance for velocity estimation on 160 × 120 probing locations. A comprehensive evaluation experiment showed that the estimated velocity by our prototype has relatively small errors (average endpoint error < 0.5 pixel and angular error < 10°) for most motion cases.

Cooled particle accelerator target

DOEpatents

Degtiarenko, Pavel V.

2005-06-14

A novel particle beam target comprising: a rotating target disc mounted on a retainer and thermally coupled to a first array of spaced-apart parallel plate fins that extend radially inwardly from the retainer and mesh without physical contact with a second array of spaced-apart parallel plate fins that extend radially outwardly from and are thermally coupled to a cooling mechanism capable of removing heat from said second array of spaced-apart fins and located within the first array of spaced-apart parallel fins. Radiant thermal exchange between the two arrays of parallel plate fins provides removal of heat from the rotating disc. A method of cooling the rotating target is also described.

Proxy-equation paradigm: A strategy for massively parallel asynchronous computations

NASA Astrophysics Data System (ADS)

Mittal, Ankita; Girimaji, Sharath

2017-09-01

Massively parallel simulations of transport equation systems call for a paradigm change in algorithm development to achieve efficient scalability. Traditional approaches require time synchronization of processing elements (PEs), which severely restricts scalability. Relaxing synchronization requirement introduces error and slows down convergence. In this paper, we propose and develop a novel "proxy equation" concept for a general transport equation that (i) tolerates asynchrony with minimal added error, (ii) preserves convergence order and thus, (iii) expected to scale efficiently on massively parallel machines. The central idea is to modify a priori the transport equation at the PE boundaries to offset asynchrony errors. Proof-of-concept computations are performed using a one-dimensional advection (convection) diffusion equation. The results demonstrate the promise and advantages of the present strategy.

Microfabricated ion trap array

DOEpatents

Blain, Matthew G [Albuquerque, NM; Fleming, James G [Albuquerque, NM

2006-12-26

A microfabricated ion trap array, comprising a plurality of ion traps having an inner radius of order one micron, can be fabricated using surface micromachining techniques and materials known to the integrated circuits manufacturing and microelectromechanical systems industries. Micromachining methods enable batch fabrication, reduced manufacturing costs, dimensional and positional precision, and monolithic integration of massive arrays of ion traps with microscale ion generation and detection devices. Massive arraying enables the microscale ion traps to retain the resolution, sensitivity, and mass range advantages necessary for high chemical selectivity. The reduced electrode voltage enables integration of the microfabricated ion trap array with on-chip circuit-based rf operation and detection electronics (i.e., cell phone electronics). Therefore, the full performance advantages of the microfabricated ion trap array can be realized in truly field portable, handheld microanalysis systems.

MEMS fluidic actuator

DOEpatents

Kholwadwala, Deepesh K [Albuquerque, NM; Johnston, Gabriel A [Trophy Club, TX; Rohrer, Brandon R [Albuquerque, NM; Galambos, Paul C [Albuquerque, NM; Okandan, Murat [Albuquerque, NM

2007-07-24

The present invention comprises a novel, lightweight, massively parallel device comprising microelectromechanical (MEMS) fluidic actuators, to reconfigure the profile, of a surface. Each microfluidic actuator comprises an independent bladder that can act as both a sensor and an actuator. A MEMS sensor, and a MEMS valve within each microfluidic actuator, operate cooperatively to monitor the fluid within each bladder, and regulate the flow of the fluid entering and exiting each bladder. When adjacently spaced in a array, microfluidic actuators can create arbitrary surface profiles in response to a change in the operating environment of the surface. In an embodiment of the invention, the profile of an airfoil is controlled by independent extension and contraction of a plurality of actuators, that operate to displace a compliant cover.

Performance improvements of MOEMS-based diffractive arrays: address isolation and optical switching

NASA Astrophysics Data System (ADS)

Panaman, Ganesh; Madison, Seth; Sano, Michael; Castracane, James

2005-01-01

Micro-Opto-Electro-Mechanical Systems (MOEMS) have found a variety of applications in fields such as telecommunications, spectroscopy and display technology. MOEMS-based optical switching is currently under investigation for the increased flexibility that such devices provide for reconfiguration of the I/O network for inter-chip communication applications. This potential not only adds an additional degree of freedom for adjustment of transmitter/receiver links but also allows for fine alignment of individual channels in the network link. Further, this use of diffractive arrays for specific applications combines beam steering/adjustment capabilities with the inherent wavelength dependence of the diffractive approach for channel separation and de-multiplexing. Research and development has been concentrated on the progression from single MOEMS components to parallel arrays integrated with optical source arrays for a successful feasibility demonstration. Successful development of such an approach will have a major impact of the next generation communication protocols. This paper will focus on the current status of the MOEMS research program for Free Space Optical inter-chip communication at the College of NanoScale Science and Engineering, University at Albany-SUNY (CNSE). New versions of diffractive arrays stemming from the basic MEMS Compound Grating (MCG; patent #5,999,319) have been produced through various fabrication methods including the MUMPs process1. Most MEMS components relying on electrostatic actuation tend to require high actuation voltages (>20V) compared to the typical 5V levels prevalent in conventional integrated circuits. The specific goal is to yield improved performance while minimizing the power consumption of the components. Structural modifications through the variation in the ruling/electrode spacing distance and array wiring layout through individually addressable gratings have been studied to understand effects on the actuation voltage and cross talk, respectively. A detailed overview of the optical and mechanical properties will be included. Modeling results along with the mechanical and optical testing results have been detailed and compared with previously obtained results. Future work focuses on alternate material sets for a reduction in operational voltage, improvements in optical efficiency and technology demonstrators for verification of massively parallel I/O performance.

A class of parallel algorithms for computation of the manipulator inertia matrix

NASA Technical Reports Server (NTRS)

Fijany, Amir; Bejczy, Antal K.

1989-01-01

Parallel and parallel/pipeline algorithms for computation of the manipulator inertia matrix are presented. An algorithm based on composite rigid-body spatial inertia method, which provides better features for parallelization, is used for the computation of the inertia matrix. Two parallel algorithms are developed which achieve the time lower bound in computation. Also described is the mapping of these algorithms with topological variation on a two-dimensional processor array, with nearest-neighbor connection, and with cardinality variation on a linear processor array. An efficient parallel/pipeline algorithm for the linear array was also developed, but at significantly higher efficiency.

Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Simulations of the Molecular Crystal alphaRDX

DTIC Science & Technology

2013-08-01

potential for HMX / RDX (3, 9). ...................................................................................8 1 1. Purpose This work...6 dispersion and electrostatic interactions. Constants for the SB potential are given in table 1. 8 Table 1. SB potential for HMX / RDX (3, 9...modeling dislocations in the energetic molecular crystal RDX using the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular

Algorithms and programming tools for image processing on the MPP

NASA Technical Reports Server (NTRS)

Reeves, A. P.

1985-01-01

Topics addressed include: data mapping and rotational algorithms for the Massively Parallel Processor (MPP); Parallel Pascal language; documentation for the Parallel Pascal Development system; and a description of the Parallel Pascal language used on the MPP.

Parallelized direct execution simulation of message-passing parallel programs

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

The architecture of tomorrow's massively parallel computer

NASA Technical Reports Server (NTRS)

Batcher, Ken

1987-01-01

Goodyear Aerospace delivered the Massively Parallel Processor (MPP) to NASA/Goddard in May 1983, over three years ago. Ever since then, Goodyear has tried to look in a forward direction. There is always some debate as to which way is forward when it comes to supercomputer architecture. Improvements to the MPP's massively parallel architecture are discussed in the areas of data I/O, memory capacity, connectivity, and indirect (or local) addressing. In I/O, transfer rates up to 640 megabytes per second can be achieved. There are devices that can supply the data and accept it at this rate. The memory capacity can be increased up to 128 megabytes in the ARU and over a gigabyte in the staging memory. For connectivity, there are several different kinds of multistage networks that should be considered.

Parallel computational fluid dynamics '91; Conference Proceedings, Stuttgart, Germany, Jun. 10-12, 1991

NASA Technical Reports Server (NTRS)

Reinsch, K. G. (Editor); Schmidt, W. (Editor); Ecer, A. (Editor); Haeuser, Jochem (Editor); Periaux, J. (Editor)

1992-01-01

A conference was held on parallel computational fluid dynamics and produced related papers. Topics discussed in these papers include: parallel implicit and explicit solvers for compressible flow, parallel computational techniques for Euler and Navier-Stokes equations, grid generation techniques for parallel computers, and aerodynamic simulation om massively parallel systems.

Overcoming rule-based rigidity and connectionist limitations through massively-parallel case-based reasoning

NASA Technical Reports Server (NTRS)

Barnden, John; Srinivas, Kankanahalli

1990-01-01

Symbol manipulation as used in traditional Artificial Intelligence has been criticized by neural net researchers for being excessively inflexible and sequential. On the other hand, the application of neural net techniques to the types of high-level cognitive processing studied in traditional artificial intelligence presents major problems as well. A promising way out of this impasse is to build neural net models that accomplish massively parallel case-based reasoning. Case-based reasoning, which has received much attention recently, is essentially the same as analogy-based reasoning, and avoids many of the problems leveled at traditional artificial intelligence. Further problems are avoided by doing many strands of case-based reasoning in parallel, and by implementing the whole system as a neural net. In addition, such a system provides an approach to some aspects of the problems of noise, uncertainty and novelty in reasoning systems. The current neural net system (Conposit), which performs standard rule-based reasoning, is being modified into a massively parallel case-based reasoning version.

Heat exchange apparatus

DOEpatents

Degtiarenko, Pavel V.

2003-08-12

A heat exchange apparatus comprising a coolant conduit or heat sink having attached to its surface a first radial array of spaced-apart parallel plate fins or needles and a second radial array of spaced-apart parallel plate fins or needles thermally coupled to a body to be cooled and meshed with, but not contacting the first radial array of spaced-apart parallel plate fins or needles.

Research in Parallel Algorithms and Software for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Domel, Neal D.

1996-01-01

Phase I is complete for the development of a Computational Fluid Dynamics parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

Research in Parallel Algorithms and Software for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Domel, Neal D.

1996-01-01

Phase 1 is complete for the development of a computational fluid dynamics CFD) parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

Performance of the Heavy Flavor Tracker (HFT) detector in star experiment at RHIC

NASA Astrophysics Data System (ADS)

Alruwaili, Manal

With the growing technology, the number of the processors is becoming massive. Current supercomputer processing will be available on desktops in the next decade. For mass scale application software development on massive parallel computing available on desktops, existing popular languages with large libraries have to be augmented with new constructs and paradigms that exploit massive parallel computing and distributed memory models while retaining the user-friendliness. Currently, available object oriented languages for massive parallel computing such as Chapel, X10 and UPC++ exploit distributed computing, data parallel computing and thread-parallelism at the process level in the PGAS (Partitioned Global Address Space) memory model. However, they do not incorporate: 1) any extension at for object distribution to exploit PGAS model; 2) the programs lack the flexibility of migrating or cloning an object between places to exploit load balancing; and 3) lack the programming paradigms that will result from the integration of data and thread-level parallelism and object distribution. In the proposed thesis, I compare different languages in PGAS model; propose new constructs that extend C++ with object distribution and object migration; and integrate PGAS based process constructs with these extensions on distributed objects. Object cloning and object migration. Also a new paradigm MIDD (Multiple Invocation Distributed Data) is presented when different copies of the same class can be invoked, and work on different elements of a distributed data concurrently using remote method invocations. I present new constructs, their grammar and their behavior. The new constructs have been explained using simple programs utilizing these constructs.

Role of APOE Isoforms in the Pathogenesis of TBI induced Alzheimer’s Disease

DTIC Science & Technology

2016-10-01

deletion, APOE targeted replacement, complex breeding, CCI model optimization, mRNA library generation, high throughput massive parallel sequencing...demonstrate that the lack of Abca1 increases amyloid plaques and decreased APOE protein levels in AD-model mice. In this proposal we will test the hypothesis...injury, inflammatory reaction, transcriptome, high throughput massive parallel sequencing, mRNA-seq., behavioral testing, memory impairment, recovery 3

High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing

DTIC Science & Technology

2010-10-14

High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing...Venezuelan equine encephalitis virus (VEEV) genome. We initially used a capillary electrophoresis method to gain insight into the role of the VEEV...Smith JM, Schmaljohn CS (2010) High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and

Efficient, massively parallel eigenvalue computation

NASA Technical Reports Server (NTRS)

Huo, Yan; Schreiber, Robert

1993-01-01

In numerical simulations of disordered electronic systems, one of the most common approaches is to diagonalize random Hamiltonian matrices and to study the eigenvalues and eigenfunctions of a single electron in the presence of a random potential. An effort to implement a matrix diagonalization routine for real symmetric dense matrices on massively parallel SIMD computers, the Maspar MP-1 and MP-2 systems, is described. Results of numerical tests and timings are also presented.

Exploring the Ability of a Coarse-grained Potential to Describe the Stress-strain Response of Glassy Polystyrene

DTIC Science & Technology

2012-10-01

using the open-source code Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) (http://lammps.sandia.gov) (23). The commercial...parameters are proprietary and cannot be ported to the LAMMPS 4 simulation code. In our molecular dynamics simulations at the atomistic resolution, we...IBI iterative Boltzmann inversion LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator MAPS Materials Processes and Simulations MS

Molecular profiling of single circulating tumor cells from lung cancer patients.

PubMed

Park, Seung-Min; Wong, Dawson J; Ooi, Chin Chun; Kurtz, David M; Vermesh, Ophir; Aalipour, Amin; Suh, Susie; Pian, Kelsey L; Chabon, Jacob J; Lee, Sang Hun; Jamali, Mehran; Say, Carmen; Carter, Justin N; Lee, Luke P; Kuschner, Ware G; Schwartz, Erich J; Shrager, Joseph B; Neal, Joel W; Wakelee, Heather A; Diehn, Maximilian; Nair, Viswam S; Wang, Shan X; Gambhir, Sanjiv S

2016-12-27

Circulating tumor cells (CTCs) are established cancer biomarkers for the "liquid biopsy" of tumors. Molecular analysis of single CTCs, which recapitulate primary and metastatic tumor biology, remains challenging because current platforms have limited throughput, are expensive, and are not easily translatable to the clinic. Here, we report a massively parallel, multigene-profiling nanoplatform to compartmentalize and analyze hundreds of single CTCs. After high-efficiency magnetic collection of CTC from blood, a single-cell nanowell array performs CTC mutation profiling using modular gene panels. Using this approach, we demonstrated multigene expression profiling of individual CTCs from non-small-cell lung cancer (NSCLC) patients with remarkable sensitivity. Thus, we report a high-throughput, multiplexed strategy for single-cell mutation profiling of individual lung cancer CTCs toward minimally invasive cancer therapy prediction and disease monitoring.

Python Winding Itself Around Datacubes: How to Access Massive Multi-Dimensional Arrays in a Pythonic Way

NASA Astrophysics Data System (ADS)

Merticariu, Vlad; Misev, Dimitar; Baumann, Peter

2017-04-01

While python has developed into the lingua franca in Data Science there is often a paradigm break when accessing specialized tools. In particular for one of the core data categories in science and engineering, massive multi-dimensional arrays, out-of-memory solutions typically employ their own, different models. We discuss this situation on the example of the scalable open-source array engine, rasdaman ("raster data manager") which offers access to and processing of Petascale multi-dimensional arrays through an SQL-style array query language, rasql. Such queries are executed in the server on a storage engine utilizing adaptive array partitioning and based on a processing engine implementing a "tile streaming" paradigm to allow processing of arrays massively larger than server RAM. The rasdaman QL has acted as blueprint for forthcoming ISO Array SQL and the Open Geospatial Consortium (OGC) geo analytics language, Web Coverage Processing Service, adopted in 2008. Not surprisingly, rasdaman is OGC and INSPIRE Reference Implementation for their "Big Earth Data" standards suite. Recently, rasdaman has been augmented with a python interface which allows to transparently interact with the database (credits go to Siddharth Shukla's Master Thesis at Jacobs University). Programmers do not need to know the rasdaman query language, as the operators are silently transformed, through lazy evaluation, into queries. Arrays delivered are likewise automatically transformed into their python representation. In the talk, the rasdaman concept will be illustrated with the help of large-scale real-life examples of operational satellite image and weather data services, and sample python code.

Massively parallel GPU-accelerated minimization of classical density functional theory

NASA Astrophysics Data System (ADS)

Stopper, Daniel; Roth, Roland

2017-08-01

In this paper, we discuss the ability to numerically minimize the grand potential of hard disks in two-dimensional and of hard spheres in three-dimensional space within the framework of classical density functional and fundamental measure theory on modern graphics cards. Our main finding is that a massively parallel minimization leads to an enormous performance gain in comparison to standard sequential minimization schemes. Furthermore, the results indicate that in complex multi-dimensional situations, a heavy parallel minimization of the grand potential seems to be mandatory in order to reach a reasonable balance between accuracy and computational cost.

Embedded Implementation of VHR Satellite Image Segmentation

PubMed Central

Li, Chao; Balla-Arabé, Souleymane; Ginhac, Dominique; Yang, Fan

2016-01-01

Processing and analysis of Very High Resolution (VHR) satellite images provide a mass of crucial information, which can be used for urban planning, security issues or environmental monitoring. However, they are computationally expensive and, thus, time consuming, while some of the applications, such as natural disaster monitoring and prevention, require high efficiency performance. Fortunately, parallel computing techniques and embedded systems have made great progress in recent years, and a series of massively parallel image processing devices, such as digital signal processors or Field Programmable Gate Arrays (FPGAs), have been made available to engineers at a very convenient price and demonstrate significant advantages in terms of running-cost, embeddability, power consumption flexibility, etc. In this work, we designed a texture region segmentation method for very high resolution satellite images by using the level set algorithm and the multi-kernel theory in a high-abstraction C environment and realize its register-transfer level implementation with the help of a new proposed high-level synthesis-based design flow. The evaluation experiments demonstrate that the proposed design can produce high quality image segmentation with a significant running-cost advantage. PMID:27240370

An integrated semiconductor device enabling non-optical genome sequencing.

PubMed

Rothberg, Jonathan M; Hinz, Wolfgang; Rearick, Todd M; Schultz, Jonathan; Mileski, William; Davey, Mel; Leamon, John H; Johnson, Kim; Milgrew, Mark J; Edwards, Matthew; Hoon, Jeremy; Simons, Jan F; Marran, David; Myers, Jason W; Davidson, John F; Branting, Annika; Nobile, John R; Puc, Bernard P; Light, David; Clark, Travis A; Huber, Martin; Branciforte, Jeffrey T; Stoner, Isaac B; Cawley, Simon E; Lyons, Michael; Fu, Yutao; Homer, Nils; Sedova, Marina; Miao, Xin; Reed, Brian; Sabina, Jeffrey; Feierstein, Erika; Schorn, Michelle; Alanjary, Mohammad; Dimalanta, Eileen; Dressman, Devin; Kasinskas, Rachel; Sokolsky, Tanya; Fidanza, Jacqueline A; Namsaraev, Eugeni; McKernan, Kevin J; Williams, Alan; Roth, G Thomas; Bustillo, James

2011-07-20

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.

A new parallel-vector finite element analysis software on distributed-memory computers

NASA Technical Reports Server (NTRS)

Qin, Jiangning; Nguyen, Duc T.

1993-01-01

A new parallel-vector finite element analysis software package MPFEA (Massively Parallel-vector Finite Element Analysis) is developed for large-scale structural analysis on massively parallel computers with distributed-memory. MPFEA is designed for parallel generation and assembly of the global finite element stiffness matrices as well as parallel solution of the simultaneous linear equations, since these are often the major time-consuming parts of a finite element analysis. Block-skyline storage scheme along with vector-unrolling techniques are used to enhance the vector performance. Communications among processors are carried out concurrently with arithmetic operations to reduce the total execution time. Numerical results on the Intel iPSC/860 computers (such as the Intel Gamma with 128 processors and the Intel Touchstone Delta with 512 processors) are presented, including an aircraft structure and some very large truss structures, to demonstrate the efficiency and accuracy of MPFEA.

Template based parallel checkpointing in a massively parallel computer system

DOEpatents

Archer, Charles Jens [Rochester, MN; Inglett, Todd Alan [Rochester, MN

2009-01-13

A method and apparatus for a template based parallel checkpoint save for a massively parallel super computer system using a parallel variation of the rsync protocol, and network broadcast. In preferred embodiments, the checkpoint data for each node is compared to a template checkpoint file that resides in the storage and that was previously produced. Embodiments herein greatly decrease the amount of data that must be transmitted and stored for faster checkpointing and increased efficiency of the computer system. Embodiments are directed to a parallel computer system with nodes arranged in a cluster with a high speed interconnect that can perform broadcast communication. The checkpoint contains a set of actual small data blocks with their corresponding checksums from all nodes in the system. The data blocks may be compressed using conventional non-lossy data compression algorithms to further reduce the overall checkpoint size.

Parallel computing works

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

An account of the Caltech Concurrent Computation Program (C{sup 3}P), a five year project that focused on answering the question: Can parallel computers be used to do large-scale scientific computations '' As the title indicates, the question is answered in the affirmative, by implementing numerous scientific applications on real parallel computers and doing computations that produced new scientific results. In the process of doing so, C{sup 3}P helped design and build several new computers, designed and implemented basic system software, developed algorithms for frequently used mathematical computations on massively parallel machines, devised performance models and measured the performance of manymore » computers, and created a high performance computing facility based exclusively on parallel computers. While the initial focus of C{sup 3}P was the hypercube architecture developed by C. Seitz, many of the methods developed and lessons learned have been applied successfully on other massively parallel architectures.« less

Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays

NASA Astrophysics Data System (ADS)

Laborde, C.; Pittino, F.; Verhoeven, H. A.; Lemay, S. G.; Selmi, L.; Jongsma, M. A.; Widdershoven, F. P.

2015-09-01

Platforms that offer massively parallel, label-free biosensing can, in principle, be created by combining all-electrical detection with low-cost integrated circuits. Examples include field-effect transistor arrays, which are used for mapping neuronal signals and sequencing DNA. Despite these successes, however, bioelectronics has so far failed to deliver a broadly applicable biosensing platform. This is due, in part, to the fact that d.c. or low-frequency signals cannot be used to probe beyond the electrical double layer formed by screening salt ions, which means that under physiological conditions the sensing of a target analyte located even a short distance from the sensor (∼1 nm) is severely hampered. Here, we show that high-frequency impedance spectroscopy can be used to detect and image microparticles and living cells under physiological salt conditions. Our assay employs a large-scale, high-density array of nanoelectrodes integrated with CMOS electronics on a single chip and the sensor response depends on the electrical properties of the analyte, allowing impedance-based fingerprinting. With our platform, we image the dynamic attachment and micromotion of BEAS, THP1 and MCF7 cancer cell lines in real time at submicrometre resolution in growth medium, demonstrating the potential of the platform for label/tracer-free high-throughput screening of anti-tumour drug candidates.

Reconstructing evolutionary trees in parallel for massive sequences.

PubMed

Zou, Quan; Wan, Shixiang; Zeng, Xiangxiang; Ma, Zhanshan Sam

2017-12-14

Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment is also challenging and time/space consuming. Hadoop and Spark are developed recently, which bring spring light for the classical computational biology problems. In this paper, we tried to solve the multiple sequence alignment and evolutionary reconstruction in parallel. HPTree, which is developed in this paper, can deal with big DNA sequence files quickly. It works well on the >1GB files, and gets better performance than other evolutionary reconstruction tools. Users could use HPTree for reonstructing evolutioanry trees on the computer clusters or cloud platform (eg. Amazon Cloud). HPTree could help on population evolution research and metagenomics analysis. In this paper, we employ the Hadoop and Spark platform and design an evolutionary tree reconstruction software tool for unaligned massive DNA sequences. Clustering and multiple sequence alignment are done in parallel. Neighbour-joining model was employed for the evolutionary tree building. We opened our software together with source codes via http://lab.malab.cn/soft/HPtree/ .

A compact linear accelerator based on a scalable microelectromechanical-system RF-structure

DOE PAGES

Persaud, A.; Ji, Q.; Feinberg, E.; ...

2017-06-08

Here, a new approach for a compact radio-frequency (RF) accelerator structure is presented. The new accelerator architecture is based on the Multiple Electrostatic Quadrupole Array Linear Accelerator (MEQALAC) structure that was first developed in the 1980s. The MEQALAC utilized RF resonators producing the accelerating fields and providing for higher beam currents through parallel beamlets focused using arrays of electrostatic quadrupoles (ESQs). While the early work obtained ESQs with lateral dimensions on the order of a few centimeters, using a printed circuit board (PCB), we reduce the characteristic dimension to the millimeter regime, while massively scaling up the potential number ofmore » parallel beamlets. Using Microelectromechanical systems scalable fabrication approaches, we are working on further red ucing the characteristic dimension to the sub-millimeter regime. The technology is based on RF-acceleration components and ESQs implemented in the PCB or silicon wafers where each beamlet passes through beam apertures in the wafer. The complete accelerator is then assembled by stacking these wafers. This approach has the potential for fast and inexpensive batch fabrication of the components and flexibility in system design for application specific beam energies and currents. For prototyping the accelerator architecture, the components have been fabricated using the PCB. In this paper, we present proof of concept results of the principal components using the PCB: RF acceleration and ESQ focusing. Finally, ongoing developments on implementing components in silicon and scaling of the accelerator technology to high currents and beam energies are discussed.« less

A compact linear accelerator based on a scalable microelectromechanical-system RF-structure

NASA Astrophysics Data System (ADS)

Persaud, A.; Ji, Q.; Feinberg, E.; Seidl, P. A.; Waldron, W. L.; Schenkel, T.; Lal, A.; Vinayakumar, K. B.; Ardanuc, S.; Hammer, D. A.

2017-06-01

A new approach for a compact radio-frequency (RF) accelerator structure is presented. The new accelerator architecture is based on the Multiple Electrostatic Quadrupole Array Linear Accelerator (MEQALAC) structure that was first developed in the 1980s. The MEQALAC utilized RF resonators producing the accelerating fields and providing for higher beam currents through parallel beamlets focused using arrays of electrostatic quadrupoles (ESQs). While the early work obtained ESQs with lateral dimensions on the order of a few centimeters, using a printed circuit board (PCB), we reduce the characteristic dimension to the millimeter regime, while massively scaling up the potential number of parallel beamlets. Using Microelectromechanical systems scalable fabrication approaches, we are working on further reducing the characteristic dimension to the sub-millimeter regime. The technology is based on RF-acceleration components and ESQs implemented in the PCB or silicon wafers where each beamlet passes through beam apertures in the wafer. The complete accelerator is then assembled by stacking these wafers. This approach has the potential for fast and inexpensive batch fabrication of the components and flexibility in system design for application specific beam energies and currents. For prototyping the accelerator architecture, the components have been fabricated using the PCB. In this paper, we present proof of concept results of the principal components using the PCB: RF acceleration and ESQ focusing. Ongoing developments on implementing components in silicon and scaling of the accelerator technology to high currents and beam energies are discussed.

A compact linear accelerator based on a scalable microelectromechanical-system RF-structure.

PubMed

Persaud, A; Ji, Q; Feinberg, E; Seidl, P A; Waldron, W L; Schenkel, T; Lal, A; Vinayakumar, K B; Ardanuc, S; Hammer, D A

2017-06-01

A new approach for a compact radio-frequency (RF) accelerator structure is presented. The new accelerator architecture is based on the Multiple Electrostatic Quadrupole Array Linear Accelerator (MEQALAC) structure that was first developed in the 1980s. The MEQALAC utilized RF resonators producing the accelerating fields and providing for higher beam currents through parallel beamlets focused using arrays of electrostatic quadrupoles (ESQs). While the early work obtained ESQs with lateral dimensions on the order of a few centimeters, using a printed circuit board (PCB), we reduce the characteristic dimension to the millimeter regime, while massively scaling up the potential number of parallel beamlets. Using Microelectromechanical systems scalable fabrication approaches, we are working on further reducing the characteristic dimension to the sub-millimeter regime. The technology is based on RF-acceleration components and ESQs implemented in the PCB or silicon wafers where each beamlet passes through beam apertures in the wafer. The complete accelerator is then assembled by stacking these wafers. This approach has the potential for fast and inexpensive batch fabrication of the components and flexibility in system design for application specific beam energies and currents. For prototyping the accelerator architecture, the components have been fabricated using the PCB. In this paper, we present proof of concept results of the principal components using the PCB: RF acceleration and ESQ focusing. Ongoing developments on implementing components in silicon and scaling of the accelerator technology to high currents and beam energies are discussed.

Load balancing for massively-parallel soft-real-time systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hailperin, M.

1988-09-01

Global load balancing, if practical, would allow the effective use of massively-parallel ensemble architectures for large soft-real-problems. The challenge is to replace quick global communications, which is impractical in a massively-parallel system, with statistical techniques. In this vein, the author proposes a novel approach to decentralized load balancing based on statistical time-series analysis. Each site estimates the system-wide average load using information about past loads of individual sites and attempts to equal that average. This estimation process is practical because the soft-real-time systems of interest naturally exhibit loads that are periodic, in a statistical sense akin to seasonality in econometrics.more » It is shown how this load-characterization technique can be the foundation for a load-balancing system in an architecture employing cut-through routing and an efficient multicast protocol.« less

Evaluation of massively parallel sequencing for forensic DNA methylation profiling.

PubMed

Richards, Rebecca; Patel, Jayshree; Stevenson, Kate; Harbison, SallyAnn

2018-05-11

Epigenetics is an emerging area of interest in forensic science. DNA methylation, a type of epigenetic modification, can be applied to chronological age estimation, identical twin differentiation and body fluid identification. However, there is not yet an agreed, established methodology for targeted detection and analysis of DNA methylation markers in forensic research. Recently a massively parallel sequencing-based approach has been suggested. The use of massively parallel sequencing is well established in clinical epigenetics and is emerging as a new technology in the forensic field. This review investigates the potential benefits, limitations and considerations of this technique for the analysis of DNA methylation in a forensic context. The importance of a robust protocol, regardless of the methodology used, that minimises potential sources of bias is highlighted. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Performance analysis of three dimensional integral equation computations on a massively parallel computer. M.S. Thesis

NASA Technical Reports Server (NTRS)

Logan, Terry G.

1994-01-01

The purpose of this study is to investigate the performance of the integral equation computations using numerical source field-panel method in a massively parallel processing (MPP) environment. A comparative study of computational performance of the MPP CM-5 computer and conventional Cray-YMP supercomputer for a three-dimensional flow problem is made. A serial FORTRAN code is converted into a parallel CM-FORTRAN code. Some performance results are obtained on CM-5 with 32, 62, 128 nodes along with those on Cray-YMP with a single processor. The comparison of the performance indicates that the parallel CM-FORTRAN code near or out-performs the equivalent serial FORTRAN code for some cases.

Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding

DOE PAGES

Zhang, Hong; Zapol, Peter; Dixon, David A.; ...

2015-11-17

The Shift-and-invert parallel spectral transformations (SIPs), a computational approach to solve sparse eigenvalue problems, is developed for massively parallel architectures with exceptional parallel scalability and robustness. The capabilities of SIPs are demonstrated by diagonalization of density-functional based tight-binding (DFTB) Hamiltonian and overlap matrices for single-wall metallic carbon nanotubes, diamond nanowires, and bulk diamond crystals. The largest (smallest) example studied is a 128,000 (2000) atom nanotube for which ~330,000 (~5600) eigenvalues and eigenfunctions are obtained in ~190 (~5) seconds when parallelized over 266,144 (16,384) Blue Gene/Q cores. Weak scaling and strong scaling of SIPs are analyzed and the performance of SIPsmore » is compared with other novel methods. Different matrix ordering methods are investigated to reduce the cost of the factorization step, which dominates the time-to-solution at the strong scaling limit. As a result, a parallel implementation of assembling the density matrix from the distributed eigenvectors is demonstrated.« less

Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hong; Zapol, Peter; Dixon, David A.

The Shift-and-invert parallel spectral transformations (SIPs), a computational approach to solve sparse eigenvalue problems, is developed for massively parallel architectures with exceptional parallel scalability and robustness. The capabilities of SIPs are demonstrated by diagonalization of density-functional based tight-binding (DFTB) Hamiltonian and overlap matrices for single-wall metallic carbon nanotubes, diamond nanowires, and bulk diamond crystals. The largest (smallest) example studied is a 128,000 (2000) atom nanotube for which ~330,000 (~5600) eigenvalues and eigenfunctions are obtained in ~190 (~5) seconds when parallelized over 266,144 (16,384) Blue Gene/Q cores. Weak scaling and strong scaling of SIPs are analyzed and the performance of SIPsmore » is compared with other novel methods. Different matrix ordering methods are investigated to reduce the cost of the factorization step, which dominates the time-to-solution at the strong scaling limit. As a result, a parallel implementation of assembling the density matrix from the distributed eigenvectors is demonstrated.« less

A Novel Implementation of Massively Parallel Three Dimensional Monte Carlo Radiation Transport

NASA Astrophysics Data System (ADS)

Robinson, P. B.; Peterson, J. D. L.

2005-12-01

The goal of our summer project was to implement the difference formulation for radiation transport into Cosmos++, a multidimensional, massively parallel, magneto hydrodynamics code for astrophysical applications (Peter Anninos - AX). The difference formulation is a new method for Symbolic Implicit Monte Carlo thermal transport (Brooks and Szöke - PAT). Formerly, simultaneous implementation of fully implicit Monte Carlo radiation transport in multiple dimensions on multiple processors had not been convincingly demonstrated. We found that a combination of the difference formulation and the inherent structure of Cosmos++ makes such an implementation both accurate and straightforward. We developed a "nearly nearest neighbor physics" technique to allow each processor to work independently, even with a fully implicit code. This technique coupled with the increased accuracy of an implicit Monte Carlo solution and the efficiency of parallel computing systems allows us to demonstrate the possibility of massively parallel thermal transport. This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48

TMVOC-MP: a parallel numerical simulator for Three-PhaseNon-isothermal Flows of Multicomponent Hydrocarbon Mixtures inporous/fractured media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Keni; Yamamoto, Hajime; Pruess, Karsten

2008-02-15

TMVOC-MP is a massively parallel version of the TMVOC code (Pruess and Battistelli, 2002), a numerical simulator for three-phase non-isothermal flow of water, gas, and a multicomponent mixture of volatile organic chemicals (VOCs) in multidimensional heterogeneous porous/fractured media. TMVOC-MP was developed by introducing massively parallel computing techniques into TMVOC. It retains the physical process model of TMVOC, designed for applications to contamination problems that involve hydrocarbon fuels or organic solvents in saturated and unsaturated zones. TMVOC-MP can model contaminant behavior under 'natural' environmental conditions, as well as for engineered systems, such as soil vapor extraction, groundwater pumping, or steam-assisted sourcemore » remediation. With its sophisticated parallel computing techniques, TMVOC-MP can handle much larger problems than TMVOC, and can be much more computationally efficient. TMVOC-MP models multiphase fluid systems containing variable proportions of water, non-condensible gases (NCGs), and water-soluble volatile organic chemicals (VOCs). The user can specify the number and nature of NCGs and VOCs. There are no intrinsic limitations to the number of NCGs or VOCs, although the arrays for fluid components are currently dimensioned as 20, accommodating water plus 19 components that may be either NCGs or VOCs. Among them, NCG arrays are dimensioned as 10. The user may select NCGs from a data bank provided in the software. The currently available choices include O{sub 2}, N{sub 2}, CO{sub 2}, CH{sub 4}, ethane, ethylene, acetylene, and air (a pseudo-component treated with properties averaged from N{sub 2} and O{sub 2}). Thermophysical property data of VOCs can be selected from a chemical data bank, included with TMVOC-MP, that provides parameters for 26 commonly encountered chemicals. Users also can input their own data for other fluids. The fluid components may partition (volatilize and/or dissolve) among gas, aqueous, and NAPL phases. Any combination of the three phases may present, and phases may appear and disappear in the course of a simulation. In addition, VOCs may be adsorbed by the porous medium, and may biodegrade according to a simple half-life model. Detailed discussion of physical processes, assumptions, and fluid properties used in TMVOC-MP can be found in the TMVOC user's guide (Pruess and Battistelli, 2002). TMVOC-MP was developed based on the parallel framework of the TOUGH2-MP code (Zhang et al. 2001, Wu et al. 2002). It uses the MPI (Message Passing Forum, 1994) for parallel implementation. A domain decomposition approach is adopted for the parallelization. The code partitions a simulation domain, defined by an unstructured grid, using partitioning algorithm from the METIS software package (Karypsis and Kumar, 1998). In parallel simulation, each processor is in charge of one part of the simulation domain for assembling mass and energy balance equations, solving linear equation systems, updating thermophysical properties, and performing other local computations. The local linear-equation systems are solved in parallel by multiple processors with the Aztec linear solver package (Tuminaro et al., 1999). Although each processor solves the linearized equations of subdomains independently, the entire linear equation system is solved together by all processors collaboratively via communication between neighboring processors during each iteration. Detailed discussion of the prototype of the data-exchange scheme can be found in Elmroth et al. (2001). In addition, FORTRAN 90 features are introduced to TMVOC-MP, such as dynamic memory allocation, array operation, matrix manipulation, and replacing 'common blocks' (used in the original TMVOC) with modules. All new subroutines are written in FORTRAN 90. Program units imported from the original TMVOC remain in standard FORTRAN 77. This report provides a quick starting guide for using the TMVOC-MP program. We suppose that the users have basic knowledge of using the original TMVOC code. The users can find the detailed technical description of the physical processes modeled, and the mathematical and numerical methods in the user's guide for TMVOC (Pruess and Battistelli, 2002).« less

The revised solar array synthesis computer program

NASA Technical Reports Server (NTRS)

1970-01-01

The Revised Solar Array Synthesis Computer Program is described. It is a general-purpose program which computes solar array output characteristics while accounting for the effects of temperature, incidence angle, charged-particle irradiation, and other degradation effects on various solar array configurations in either circular or elliptical orbits. Array configurations may consist of up to 75 solar cell panels arranged in any series-parallel combination not exceeding three series-connected panels in a parallel string and no more than 25 parallel strings in an array. Up to 100 separate solar array current-voltage characteristics, corresponding to 100 equal-time increments during the sunlight illuminated portion of an orbit or any 100 user-specified combinations of incidence angle and temperature, can be computed and printed out during one complete computer execution. Individual panel incidence angles may be computed and printed out at the user's option.

Parallel Spectral Acquisition with an Ion Cyclotron Resonance Cell Array.

PubMed

Park, Sung-Gun; Anderson, Gordon A; Navare, Arti T; Bruce, James E

2016-01-19

Mass measurement accuracy is a critical analytical figure-of-merit in most areas of mass spectrometry application. However, the time required for acquisition of high-resolution, high mass accuracy data limits many applications and is an aspect under continual pressure for development. Current efforts target implementation of higher electrostatic and magnetic fields because ion oscillatory frequencies increase linearly with field strength. As such, the time required for spectral acquisition of a given resolving power and mass accuracy decreases linearly with increasing fields. Mass spectrometer developments to include multiple high-resolution detectors that can be operated in parallel could further decrease the acquisition time by a factor of n, the number of detectors. Efforts described here resulted in development of an instrument with a set of Fourier transform ion cyclotron resonance (ICR) cells as detectors that constitute the first MS array capable of parallel high-resolution spectral acquisition. ICR cell array systems consisting of three or five cells were constructed with printed circuit boards and installed within a single superconducting magnet and vacuum system. Independent ion populations were injected and trapped within each cell in the array. Upon filling the array, all ions in all cells were simultaneously excited and ICR signals from each cell were independently amplified and recorded in parallel. Presented here are the initial results of successful parallel spectral acquisition, parallel mass spectrometry (MS) and MS/MS measurements, and parallel high-resolution acquisition with the MS array system.

Liquid-Nitrogen Test for Blocked Tubes

NASA Technical Reports Server (NTRS)

Wagner, W. R.

1984-01-01

Nondestructive test identifies obstructed tube in array of parallel tubes. Trickle of liquid nitrogen allowed to flow through tube array until array accumulates substantial formation of frost from moisture in air. Flow stopped and warm air introduced into inlet manifold to heat tubes in array. Tubes still frosted after others defrosted identified as obstructed tubes. Applications include inspection of flow systems having parallel legs.

Ion manipulation method and device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Gordon A.; Baker, Erin M.; Smith, Richard D.

2017-11-07

An ion manipulation method and device is disclosed. The device includes a pair of substantially parallel surfaces. An array of inner electrodes is contained within, and extends substantially along the length of, each parallel surface. The device includes a first outer array of electrodes and a second outer array of electrodes. Each outer array of electrodes is positioned on either side of the inner electrodes, and is contained within and extends substantially along the length of each parallel surface. A DC voltage is applied to the first and second outer array of electrodes. A RF voltage, with a superimposed electricmore » field, is applied to the inner electrodes by applying the DC voltages to each electrode. Ions either move between the parallel surfaces within an ion confinement area or along paths in the direction of the electric field, or can be trapped in the ion confinement area.« less

Ion manipulation device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Gordon A.; Baker, Erin M.; Smith, Richard D.

2018-05-08

An ion manipulation method and device is disclosed. The device includes a pair of substantially parallel surfaces. An array of inner electrodes is contained within, and extends substantially along the length of, each parallel surface. The device includes a first outer array of electrodes and a second outer array of electrodes. Each outer array of electrodes is positioned on either side of the inner electrodes, and is contained within and extends substantially along the length of each parallel surface. A DC voltage is applied to the first and second outer array of electrodes. A RF voltage, with a superimposed electricmore » field, is applied to the inner electrodes by applying the DC voltages to each electrode. Ions either move between the parallel surfaces within an ion confinement area or along paths in the direction of the electric field, or can be trapped in the ion confinement area.« less

Scalable and massively parallel Monte Carlo photon transport simulations for heterogeneous computing platforms

NASA Astrophysics Data System (ADS)

Yu, Leiming; Nina-Paravecino, Fanny; Kaeli, David; Fang, Qianqian

2018-01-01

We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing Language framework, this research extends our existing graphics processing unit (GPU)-accelerated MC technique to a highly scalable vendor-independent heterogeneous computing environment, achieving significantly improved performance and software portability. A number of parallel computing techniques are investigated to achieve portable performance over a wide range of computing hardware. Furthermore, multiple thread-level and device-level load-balancing strategies are developed to obtain efficient simulations using multiple central processing units and GPUs.

A fully coupled method for massively parallel simulation of hydraulically driven fractures in 3-dimensions: FULLY COUPLED PARALLEL SIMULATION OF HYDRAULIC FRACTURES IN 3-D

DOE PAGES

Settgast, Randolph R.; Fu, Pengcheng; Walsh, Stuart D. C.; ...

2016-09-18

This study describes a fully coupled finite element/finite volume approach for simulating field-scale hydraulically driven fractures in three dimensions, using massively parallel computing platforms. The proposed method is capable of capturing realistic representations of local heterogeneities, layering and natural fracture networks in a reservoir. A detailed description of the numerical implementation is provided, along with numerical studies comparing the model with both analytical solutions and experimental results. The results demonstrate the effectiveness of the proposed method for modeling large-scale problems involving hydraulically driven fractures in three dimensions.

A fully coupled method for massively parallel simulation of hydraulically driven fractures in 3-dimensions: FULLY COUPLED PARALLEL SIMULATION OF HYDRAULIC FRACTURES IN 3-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Settgast, Randolph R.; Fu, Pengcheng; Walsh, Stuart D. C.

This study describes a fully coupled finite element/finite volume approach for simulating field-scale hydraulically driven fractures in three dimensions, using massively parallel computing platforms. The proposed method is capable of capturing realistic representations of local heterogeneities, layering and natural fracture networks in a reservoir. A detailed description of the numerical implementation is provided, along with numerical studies comparing the model with both analytical solutions and experimental results. The results demonstrate the effectiveness of the proposed method for modeling large-scale problems involving hydraulically driven fractures in three dimensions.

Three-dimensional vectorial multifocal arrays created by pseudo-period encoding

NASA Astrophysics Data System (ADS)

Zeng, Tingting; Chang, Chenliang; Chen, Zhaozhong; Wang, Hui-Tian; Ding, Jianping

2018-06-01

Multifocal arrays have been attracting considerable attention recently owing to their potential applications in parallel optical tweezers, parallel single-molecule orientation determination, parallel recording and multifocal multiphoton microscopy. However, the generation of vectorial multifocal arrays with a tailorable structure and polarization state remains a great challenge, and reports on multifocal arrays have hitherto been restricted either to scalar focal spots without polarization versatility or to regular arrays with fixed spacing. In this work, we propose a specific pseudo-period encoding technique to create three-dimensional (3D) vectorial multifocal arrays with the ability to manipulate the position, polarization state and intensity of each focal spot. We experimentally validated the flexibility of our approach in the generation of 3D vectorial multiple spots with polarization multiplicity and position tunability.

An FPGA-based High Speed Parallel Signal Processing System for Adaptive Optics Testbed

NASA Astrophysics Data System (ADS)

Kim, H.; Choi, Y.; Yang, Y.

In this paper a state-of-the-art FPGA (Field Programmable Gate Array) based high speed parallel signal processing system (SPS) for adaptive optics (AO) testbed with 1 kHz wavefront error (WFE) correction frequency is reported. The AO system consists of Shack-Hartmann sensor (SHS) and deformable mirror (DM), tip-tilt sensor (TTS), tip-tilt mirror (TTM) and an FPGA-based high performance SPS to correct wavefront aberrations. The SHS is composed of 400 subapertures and the DM 277 actuators with Fried geometry, requiring high speed parallel computing capability SPS. In this study, the target WFE correction speed is 1 kHz; therefore, it requires massive parallel computing capabilities as well as strict hard real time constraints on measurements from sensors, matrix computation latency for correction algorithms, and output of control signals for actuators. In order to meet them, an FPGA based real-time SPS with parallel computing capabilities is proposed. In particular, the SPS is made up of a National Instrument's (NI's) real time computer and five FPGA boards based on state-of-the-art Xilinx Kintex 7 FPGA. Programming is done with NI's LabView environment, providing flexibility when applying different algorithms for WFE correction. It also facilitates faster programming and debugging environment as compared to conventional ones. One of the five FPGA's is assigned to measure TTS and calculate control signals for TTM, while the rest four are used to receive SHS signal, calculate slops for each subaperture and correction signal for DM. With this parallel processing capabilities of the SPS the overall closed-loop WFE correction speed of 1 kHz has been achieved. System requirements, architecture and implementation issues are described; furthermore, experimental results are also given.

Using CLIPS in the domain of knowledge-based massively parallel programming

NASA Technical Reports Server (NTRS)

Dvorak, Jiri J.

1994-01-01

The Program Development Environment (PDE) is a tool for massively parallel programming of distributed-memory architectures. Adopting a knowledge-based approach, the PDE eliminates the complexity introduced by parallel hardware with distributed memory and offers complete transparency in respect of parallelism exploitation. The knowledge-based part of the PDE is realized in CLIPS. Its principal task is to find an efficient parallel realization of the application specified by the user in a comfortable, abstract, domain-oriented formalism. A large collection of fine-grain parallel algorithmic skeletons, represented as COOL objects in a tree hierarchy, contains the algorithmic knowledge. A hybrid knowledge base with rule modules and procedural parts, encoding expertise about application domain, parallel programming, software engineering, and parallel hardware, enables a high degree of automation in the software development process. In this paper, important aspects of the implementation of the PDE using CLIPS and COOL are shown, including the embedding of CLIPS with C++-based parts of the PDE. The appropriateness of the chosen approach and of the CLIPS language for knowledge-based software engineering are discussed.

Enabling inspection solutions for future mask technologies through the development of massively parallel E-Beam inspection

NASA Astrophysics Data System (ADS)

Malloy, Matt; Thiel, Brad; Bunday, Benjamin D.; Wurm, Stefan; Jindal, Vibhu; Mukhtar, Maseeh; Quoi, Kathy; Kemen, Thomas; Zeidler, Dirk; Eberle, Anna Lena; Garbowski, Tomasz; Dellemann, Gregor; Peters, Jan Hendrik

2015-09-01

The new device architectures and materials being introduced for sub-10nm manufacturing, combined with the complexity of multiple patterning and the need for improved hotspot detection strategies, have pushed current wafer inspection technologies to their limits. In parallel, gaps in mask inspection capability are growing as new generations of mask technologies are developed to support these sub-10nm wafer manufacturing requirements. In particular, the challenges associated with nanoimprint and extreme ultraviolet (EUV) mask inspection require new strategies that enable fast inspection at high sensitivity. The tradeoffs between sensitivity and throughput for optical and e-beam inspection are well understood. Optical inspection offers the highest throughput and is the current workhorse of the industry for both wafer and mask inspection. E-beam inspection offers the highest sensitivity but has historically lacked the throughput required for widespread adoption in the manufacturing environment. It is unlikely that continued incremental improvements to either technology will meet tomorrow's requirements, and therefore a new inspection technology approach is required; one that combines the high-throughput performance of optical with the high-sensitivity capabilities of e-beam inspection. To support the industry in meeting these challenges SUNY Poly SEMATECH has evaluated disruptive technologies that can meet the requirements for high volume manufacturing (HVM), for both the wafer fab [1] and the mask shop. Highspeed massively parallel e-beam defect inspection has been identified as the leading candidate for addressing the key gaps limiting today's patterned defect inspection techniques. As of late 2014 SUNY Poly SEMATECH completed a review, system analysis, and proof of concept evaluation of multiple e-beam technologies for defect inspection. A champion approach has been identified based on a multibeam technology from Carl Zeiss. This paper includes a discussion on the need for high-speed e-beam inspection and then provides initial imaging results from EUV masks and wafers from 61 and 91 beam demonstration systems. Progress towards high resolution and consistent intentional defect arrays (IDA) is also shown.

Exploiting fluorescence for multiplex immunoassays on protein microarrays

NASA Astrophysics Data System (ADS)

Herbáth, Melinda; Papp, Krisztián; Balogh, Andrea; Matkó, János; Prechl, József

2014-09-01

Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications.

Integrated parallel reception, excitation, and shimming (iPRES).

PubMed

Han, Hui; Song, Allen W; Truong, Trong-Kha

2013-07-01

To develop a new concept for a hardware platform that enables integrated parallel reception, excitation, and shimming. This concept uses a single coil array rather than separate arrays for parallel excitation/reception and B0 shimming. It relies on a novel design that allows a radiofrequency current (for excitation/reception) and a direct current (for B0 shimming) to coexist independently in the same coil. Proof-of-concept B0 shimming experiments were performed with a two-coil array in a phantom, whereas B0 shimming simulations were performed with a 48-coil array in the human brain. Our experiments show that individually optimized direct currents applied in each coil can reduce the B0 root-mean-square error by 62-81% and minimize distortions in echo-planar images. The simulations show that dynamic shimming with the 48-coil integrated parallel reception, excitation, and shimming array can reduce the B0 root-mean-square error in the prefrontal and temporal regions by 66-79% as compared with static second-order spherical harmonic shimming and by 12-23% as compared with dynamic shimming with a 48-coil conventional shim array. Our results demonstrate the feasibility of the integrated parallel reception, excitation, and shimming concept to perform parallel excitation/reception and B0 shimming with a unified coil system as well as its promise for in vivo applications. Copyright © 2013 Wiley Periodicals, Inc.

Massively parallel sparse matrix function calculations with NTPoly

NASA Astrophysics Data System (ADS)

Dawson, William; Nakajima, Takahito

2018-04-01

We present NTPoly, a massively parallel library for computing the functions of sparse, symmetric matrices. The theory of matrix functions is a well developed framework with a wide range of applications including differential equations, graph theory, and electronic structure calculations. One particularly important application area is diagonalization free methods in quantum chemistry. When the input and output of the matrix function are sparse, methods based on polynomial expansions can be used to compute matrix functions in linear time. We present a library based on these methods that can compute a variety of matrix functions. Distributed memory parallelization is based on a communication avoiding sparse matrix multiplication algorithm. OpenMP task parallellization is utilized to implement hybrid parallelization. We describe NTPoly's interface and show how it can be integrated with programs written in many different programming languages. We demonstrate the merits of NTPoly by performing large scale calculations on the K computer.

Detection of Sagittarius A* at 330 MHz With the Very Large Array

DTIC Science & Technology

2004-01-20

our Galaxy’s central massive black hole , at 330 MHz with the Very Large Array. Implications for the spectrum and emission processes of Sgr A * are... A East, the Sgr A West H ii region, and Sgr A *, recently established as our Galaxy’s central massive black hole (e.g., Ghez et al. 2000; Eckart et al...toward Sgr A *. This could be explained by a localized clearing of the ambient gas accomplished either through the direct influence of the black hole

Compact modeling of CRS devices based on ECM cells for memory, logic and neuromorphic applications.

PubMed

Linn, E; Menzel, S; Ferch, S; Waser, R

2013-09-27

Dynamic physics-based models of resistive switching devices are of great interest for the realization of complex circuits required for memory, logic and neuromorphic applications. Here, we apply such a model of an electrochemical metallization (ECM) cell to complementary resistive switches (CRSs), which are favorable devices to realize ultra-dense passive crossbar arrays. Since a CRS consists of two resistive switching devices, it is straightforward to apply the dynamic ECM model for CRS simulation with MATLAB and SPICE, enabling study of the device behavior in terms of sweep rate and series resistance variations. Furthermore, typical memory access operations as well as basic implication logic operations can be analyzed, revealing requirements for proper spike and level read operations. This basic understanding facilitates applications of massively parallel computing paradigms required for neuromorphic applications.

Large-Scale, Parallel, Multi-Sensor Data Fusion in the Cloud

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Manipon, G.; Hua, H.

2012-12-01

NASA's Earth Observing System (EOS) is an ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the "A-Train" platforms (AIRS, AMSR-E, MODIS, MISR, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over periods of years to decades. However, moving from predominantly single-instrument studies to a multi-sensor, measurement-based model for long-duration analysis of important climate variables presents serious challenges for large-scale data mining and data fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another instrument (MODIS), and to a model (ECMWF), stratify the comparisons using a classification of the "cloud scenes" from CloudSat, and repeat the entire analysis over years of AIRS data. To perform such an analysis, one must discover & access multiple datasets from remote sites, find the space/time "matchups" between instruments swaths and model grids, understand the quality flags and uncertainties for retrieved physical variables, assemble merged datasets, and compute fused products for further scientific and statistical analysis. To efficiently assemble such decade-scale datasets in a timely manner, we are utilizing Elastic Computing in the Cloud and parallel map/reduce-based algorithms. "SciReduce" is a Hadoop-like parallel analysis system, programmed in parallel python, that is designed from the ground up for Earth science. SciReduce executes inside VMWare images and scales to any number of nodes in the Cloud. Unlike Hadoop, in which simple tuples (keys & values) are passed between the map and reduce functions, SciReduce operates on bundles of named numeric arrays, which can be passed in memory or serialized to disk in netCDF4 or HDF5. Thus, SciReduce uses the native datatypes (geolocated grids, swaths, and points) that geo-scientists are familiar with. We are deploying within SciReduce a versatile set of python operators for data lookup, access, subsetting, co-registration, mining, fusion, and statistical analysis. All operators take in sets of geo-located arrays and generate more arrays. Large, multi-year satellite and model datasets are automatically "sharded" by time and space across a cluster of nodes so that years of data (millions of granules) can be compared or fused in a massively parallel way. Input variables (arrays) are pulled on-demand into the Cloud using OPeNDAP or webification URLs, thereby minimizing the size of the stored input and intermediate datasets. A typical map function might assemble and quality control AIRS Level-2 water vapor profiles for a year of data in parallel, then a reduce function would average the profiles in lat/lon bins (again, in parallel), and a final reduce would aggregate the climatology and write it to output files. We are using SciReduce to automate the production of multiple versions of a multi-year water vapor climatology (AIRS & MODIS), stratified by Cloudsat cloud classification, and compare it to models (ECMWF & MERRA reanalysis). We will present the architecture of SciReduce, describe the achieved "clock time" speedups in fusing huge datasets on our own nodes and in the Amazon Cloud, and discuss the Cloud cost tradeoffs for storage, compute, and data transfer.

Large-Scale, Parallel, Multi-Sensor Data Fusion in the Cloud

NASA Astrophysics Data System (ADS)

Wilson, B.; Manipon, G.; Hua, H.

2012-04-01

NASA's Earth Observing System (EOS) is an ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the "A-Train" platforms (AIRS, AMSR-E, MODIS, MISR, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over periods of years to decades. However, moving from predominantly single-instrument studies to a multi-sensor, measurement-based model for long-duration analysis of important climate variables presents serious challenges for large-scale data mining and data fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another instrument (MODIS), and to a model (ECMWF), stratify the comparisons using a classification of the "cloud scenes" from CloudSat, and repeat the entire analysis over years of AIRS data. To perform such an analysis, one must discover & access multiple datasets from remote sites, find the space/time "matchups" between instruments swaths and model grids, understand the quality flags and uncertainties for retrieved physical variables, assemble merged datasets, and compute fused products for further scientific and statistical analysis. To efficiently assemble such decade-scale datasets in a timely manner, we are utilizing Elastic Computing in the Cloud and parallel map/reduce-based algorithms. "SciReduce" is a Hadoop-like parallel analysis system, programmed in parallel python, that is designed from the ground up for Earth science. SciReduce executes inside VMWare images and scales to any number of nodes in the Cloud. Unlike Hadoop, in which simple tuples (keys & values) are passed between the map and reduce functions, SciReduce operates on bundles of named numeric arrays, which can be passed in memory or serialized to disk in netCDF4 or HDF5. Thus, SciReduce uses the native datatypes (geolocated grids, swaths, and points) that geo-scientists are familiar with. We are deploying within SciReduce a versatile set of python operators for data lookup, access, subsetting, co-registration, mining, fusion, and statistical analysis. All operators take in sets of geo-arrays and generate more arrays. Large, multi-year satellite and model datasets are automatically "sharded" by time and space across a cluster of nodes so that years of data (millions of granules) can be compared or fused in a massively parallel way. Input variables (arrays) are pulled on-demand into the Cloud using OPeNDAP or webification URLs, thereby minimizing the size of the stored input and intermediate datasets. A typical map function might assemble and quality control AIRS Level-2 water vapor profiles for a year of data in parallel, then a reduce function would average the profiles in bins (again, in parallel), and a final reduce would aggregate the climatology and write it to output files. We are using SciReduce to automate the production of multiple versions of a multi-year water vapor climatology (AIRS & MODIS), stratified by Cloudsat cloud classification, and compare it to models (ECMWF & MERRA reanalysis). We will present the architecture of SciReduce, describe the achieved "clock time" speedups in fusing huge datasets on our own nodes and in the Amazon Cloud, and discuss the Cloud cost tradeoffs for storage, compute, and data transfer.

A fast ultrasonic simulation tool based on massively parallel implementations

NASA Astrophysics Data System (ADS)

Lambert, Jason; Rougeron, Gilles; Lacassagne, Lionel; Chatillon, Sylvain

2014-02-01

This paper presents a CIVA optimized ultrasonic inspection simulation tool, which takes benefit of the power of massively parallel architectures: graphical processing units (GPU) and multi-core general purpose processors (GPP). This tool is based on the classical approach used in CIVA: the interaction model is based on Kirchoff, and the ultrasonic field around the defect is computed by the pencil method. The model has been adapted and parallelized for both architectures. At this stage, the configurations addressed by the tool are : multi and mono-element probes, planar specimens made of simple isotropic materials, planar rectangular defects or side drilled holes of small diameter. Validations on the model accuracy and performances measurements are presented.

Ordered fast Fourier transforms on a massively parallel hypercube multiprocessor

NASA Technical Reports Server (NTRS)

Tong, Charles; Swarztrauber, Paul N.

1991-01-01

The present evaluation of alternative, massively parallel hypercube processor-applicable designs for ordered radix-2 decimation-in-frequency FFT algorithms gives attention to the reduction of computation time-dominating communication. A combination of the order and computational phases of the FFT is accordingly employed, in conjunction with sequence-to-processor maps which reduce communication. Two orderings, 'standard' and 'cyclic', in which the order of the transform is the same as that of the input sequence, can be implemented with ease on the Connection Machine (where orderings are determined by geometries and priorities. A parallel method for trigonometric coefficient computation is presented which does not employ trigonometric functions or interprocessor communication.

Investigation of multichannel phased array performance for fetal MR imaging on 1.5T clinical MR system

PubMed Central

Li, Ye; Pang, Yong; Vigneron, Daniel; Glenn, Orit; Xu, Duan; Zhang, Xiaoliang

2011-01-01

Fetal MRI on 1.5T clinical scanner has been increasingly becoming a powerful imaging tool for studying fetal brain abnormalities in vivo. Due to limited availability of dedicated fetal phased arrays, commercial torso or cardiac phased arrays are routinely used for fetal scans, which are unable to provide optimized SNR and parallel imaging performance with a small number coil elements, and insufficient coverage and filling factor. This poses a demand for the investigation and development of dedicated and efficient radiofrequency (RF) hardware to improve fetal imaging. In this work, an investigational approach to simulate the performance of multichannel flexible phased arrays is proposed to find a better solution to fetal MR imaging. A 32 channel fetal array is presented to increase coil sensitivity, coverage and parallel imaging performance. The electromagnetic field distribution of each element of the fetal array is numerically simulated by using finite-difference time-domain (FDTD) method. The array performance, including B1 coverage, parallel reconstructed images and artifact power, is then theoretically calculated and compared with the torso array. Study results show that the proposed array is capable of increasing B1 field strength as well as sensitivity homogeneity in the entire area of uterus. This would ensure high quality imaging regardless of the location of the fetus in the uterus. In addition, the paralleling imaging performance of the proposed fetal array is validated by using artifact power comparison with torso array. These results demonstrate the feasibility of the 32 channel flexible array for fetal MR imaging at 1.5T. PMID:22408747

The Fortran-P Translator: Towards Automatic Translation of Fortran 77 Programs for Massively Parallel Processors

DOE PAGES

O'keefe, Matthew; Parr, Terence; Edgar, B. Kevin; ...

1995-01-01

Massively parallel processors (MPPs) hold the promise of extremely high performance that, if realized, could be used to study problems of unprecedented size and complexity. One of the primary stumbling blocks to this promise has been the lack of tools to translate application codes to MPP form. In this article we show how applications codes written in a subset of Fortran 77, called Fortran-P, can be translated to achieve good performance on several massively parallel machines. This subset can express codes that are self-similar, where the algorithm applied to the global data domain is also applied to each subdomain. Wemore » have found many codes that match the Fortran-P programming style and have converted them using our tools. We believe a self-similar coding style will accomplish what a vectorizable style has accomplished for vector machines by allowing the construction of robust, user-friendly, automatic translation systems that increase programmer productivity and generate fast, efficient code for MPPs.« less

Template-directed atomically precise self-organization of perfectly ordered parallel cerium silicide nanowire arrays on Si(110)-16 × 2 surfaces.

PubMed

Hong, Ie-Hong; Liao, Yung-Cheng; Tsai, Yung-Feng

2013-11-05

The perfectly ordered parallel arrays of periodic Ce silicide nanowires can self-organize with atomic precision on single-domain Si(110)-16 × 2 surfaces. The growth evolution of self-ordered parallel Ce silicide nanowire arrays is investigated over a broad range of Ce coverages on single-domain Si(110)-16 × 2 surfaces by scanning tunneling microscopy (STM). Three different types of well-ordered parallel arrays, consisting of uniformly spaced and atomically identical Ce silicide nanowires, are self-organized through the heteroepitaxial growth of Ce silicides on a long-range grating-like 16 × 2 reconstruction at the deposition of various Ce coverages. Each atomically precise Ce silicide nanowire consists of a bundle of chains and rows with different atomic structures. The atomic-resolution dual-polarity STM images reveal that the interchain coupling leads to the formation of the registry-aligned chain bundles within individual Ce silicide nanowire. The nanowire width and the interchain coupling can be adjusted systematically by varying the Ce coverage on a Si(110) surface. This natural template-directed self-organization of perfectly regular parallel nanowire arrays allows for the precise control of the feature size and positions within ±0.2 nm over a large area. Thus, it is a promising route to produce parallel nanowire arrays in a straightforward, low-cost, high-throughput process.

Template-directed atomically precise self-organization of perfectly ordered parallel cerium silicide nanowire arrays on Si(110)-16 × 2 surfaces

PubMed Central

2013-01-01

The perfectly ordered parallel arrays of periodic Ce silicide nanowires can self-organize with atomic precision on single-domain Si(110)-16 × 2 surfaces. The growth evolution of self-ordered parallel Ce silicide nanowire arrays is investigated over a broad range of Ce coverages on single-domain Si(110)-16 × 2 surfaces by scanning tunneling microscopy (STM). Three different types of well-ordered parallel arrays, consisting of uniformly spaced and atomically identical Ce silicide nanowires, are self-organized through the heteroepitaxial growth of Ce silicides on a long-range grating-like 16 × 2 reconstruction at the deposition of various Ce coverages. Each atomically precise Ce silicide nanowire consists of a bundle of chains and rows with different atomic structures. The atomic-resolution dual-polarity STM images reveal that the interchain coupling leads to the formation of the registry-aligned chain bundles within individual Ce silicide nanowire. The nanowire width and the interchain coupling can be adjusted systematically by varying the Ce coverage on a Si(110) surface. This natural template-directed self-organization of perfectly regular parallel nanowire arrays allows for the precise control of the feature size and positions within ±0.2 nm over a large area. Thus, it is a promising route to produce parallel nanowire arrays in a straightforward, low-cost, high-throughput process. PMID:24188092

Vacuum chamber for ion manipulation device

DOEpatents

Chen, Tsung-Chi; Tang, Keqi; Ibrahim, Yehia M; Smith, Richard D; Anderson, Gordon A; Baker, Erin M

2014-12-09

An ion manipulation method and device is disclosed. The device includes a pair of substantially parallel surfaces. An array of inner electrodes is contained within, and extends substantially along the length of, each parallel surface. The device includes a first outer array of electrodes and a second outer array of electrodes. Each outer array of electrodes is positioned on either side of the inner electrodes, and is contained within and extends substantially along the length of each parallel surface. A DC voltage is applied to the first and second outer array of electrodes. A RF voltage, with a superimposed electric field, is applied to the inner electrodes by applying the DC voltages to each electrode. Ions either move between the parallel surfaces within an ion confinement area or along paths in the direction of the electric field, or can be trapped in the ion confinement area. A predetermined number of pairs of surfaces are disposed in one or more chambers, forming a multiple-layer ion mobility cyclotron device.

On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods

PubMed Central

Lee, Anthony; Yau, Christopher; Giles, Michael B.; Doucet, Arnaud; Holmes, Christopher C.

2011-01-01

We present a case-study on the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods. Graphics cards, containing multiple Graphics Processing Units (GPUs), are self-contained parallel computational devices that can be housed in conventional desktop and laptop computers and can be thought of as prototypes of the next generation of many-core processors. For certain classes of population-based Monte Carlo algorithms they offer massively parallel simulation, with the added advantage over conventional distributed multi-core processors that they are cheap, easily accessible, easy to maintain, easy to code, dedicated local devices with low power consumption. On a canonical set of stochastic simulation examples including population-based Markov chain Monte Carlo methods and Sequential Monte Carlo methods, we nd speedups from 35 to 500 fold over conventional single-threaded computer code. Our findings suggest that GPUs have the potential to facilitate the growth of statistical modelling into complex data rich domains through the availability of cheap and accessible many-core computation. We believe the speedup we observe should motivate wider use of parallelizable simulation methods and greater methodological attention to their design. PMID:22003276

Analysis of multigrid methods on massively parallel computers: Architectural implications

NASA Technical Reports Server (NTRS)

Matheson, Lesley R.; Tarjan, Robert E.

1993-01-01

We study the potential performance of multigrid algorithms running on massively parallel computers with the intent of discovering whether presently envisioned machines will provide an efficient platform for such algorithms. We consider the domain parallel version of the standard V cycle algorithm on model problems, discretized using finite difference techniques in two and three dimensions on block structured grids of size 10(exp 6) and 10(exp 9), respectively. Our models of parallel computation were developed to reflect the computing characteristics of the current generation of massively parallel multicomputers. These models are based on an interconnection network of 256 to 16,384 message passing, 'workstation size' processors executing in an SPMD mode. The first model accomplishes interprocessor communications through a multistage permutation network. The communication cost is a logarithmic function which is similar to the costs in a variety of different topologies. The second model allows single stage communication costs only. Both models were designed with information provided by machine developers and utilize implementation derived parameters. With the medium grain parallelism of the current generation and the high fixed cost of an interprocessor communication, our analysis suggests an efficient implementation requires the machine to support the efficient transmission of long messages, (up to 1000 words) or the high initiation cost of a communication must be significantly reduced through an alternative optimization technique. Furthermore, with variable length message capability, our analysis suggests the low diameter multistage networks provide little or no advantage over a simple single stage communications network.

Method and structure for skewed block-cyclic distribution of lower-dimensional data arrays in higher-dimensional processor grids

DOEpatents

Chatterjee, Siddhartha [Yorktown Heights, NY; Gunnels, John A [Brewster, NY

2011-11-08

A method and structure of distributing elements of an array of data in a computer memory to a specific processor of a multi-dimensional mesh of parallel processors includes designating a distribution of elements of at least a portion of the array to be executed by specific processors in the multi-dimensional mesh of parallel processors. The pattern of the designating includes a cyclical repetitive pattern of the parallel processor mesh, as modified to have a skew in at least one dimension so that both a row of data in the array and a column of data in the array map to respective contiguous groupings of the processors such that a dimension of the contiguous groupings is greater than one.

Parallel image-acquisition in continuous-wave electron paramagnetic resonance imaging with a surface coil array: Proof-of-concept experiments

NASA Astrophysics Data System (ADS)

Enomoto, Ayano; Hirata, Hiroshi

2014-02-01

This article describes a feasibility study of parallel image-acquisition using a two-channel surface coil array in continuous-wave electron paramagnetic resonance (CW-EPR) imaging. Parallel EPR imaging was performed by multiplexing of EPR detection in the frequency domain. The parallel acquisition system consists of two surface coil resonators and radiofrequency (RF) bridges for EPR detection. To demonstrate the feasibility of this method of parallel image-acquisition with a surface coil array, three-dimensional EPR imaging was carried out using a tube phantom. Technical issues in the multiplexing method of EPR detection were also clarified. We found that degradation in the signal-to-noise ratio due to the interference of RF carriers is a key problem to be solved.

Towards the hand-held mass spectrometer: design considerations, simulation, and fabrication of micrometer-scaled cylindrical ion traps

NASA Astrophysics Data System (ADS)

Blain, Matthew G.; Riter, Leah S.; Cruz, Dolores; Austin, Daniel E.; Wu, Guangxiang; Plass, Wolfgang R.; Cooks, R. Graham

2004-08-01

Breakthrough improvements in simplicity and reductions in the size of mass spectrometers are needed for high-consequence fieldable applications, including error-free detection of chemical/biological warfare agents, medical diagnoses, and explosives and contraband discovery. These improvements are most likely to be realized with the reconceptualization of the mass spectrometer, rather than by incremental steps towards miniaturization. Microfabricated arrays of mass analyzers represent such a conceptual advance. A massively parallel array of micrometer-scaled mass analyzers on a chip has the potential to set the performance standard for hand-held sensors due to the inherit selectivity, sensitivity, and universal applicability of mass spectrometry as an analytical method. While the effort to develop a complete micro-MS system must include innovations in ultra-small-scale sample introduction, ion sources, mass analyzers, detectors, and vacuum and power subsystems, the first step towards radical miniaturization lies in the design, fabrication, and characterization of the mass analyzer itself. In this paper we discuss design considerations and results from simulations of ion trapping behavior for a micrometer scale cylindrical ion trap (CIT) mass analyzer (internal radius r0 = 1 [mu]m). We also present a description of the design and microfabrication of a 0.25 cm2 array of 106 one-micrometer CITs, including integrated ion detectors, constructed in tungsten on a silicon substrate.

High-performance computing — an overview

NASA Astrophysics Data System (ADS)

Marksteiner, Peter

1996-08-01

An overview of high-performance computing (HPC) is given. Different types of computer architectures used in HPC are discussed: vector supercomputers, high-performance RISC processors, various parallel computers like symmetric multiprocessors, workstation clusters, massively parallel processors. Software tools and programming techniques used in HPC are reviewed: vectorizing compilers, optimization and vector tuning, optimization for RISC processors; parallel programming techniques like shared-memory parallelism, message passing and data parallelism; and numerical libraries.

Performance Analysis and Optimization on the UCLA Parallel Atmospheric General Circulation Model Code

NASA Technical Reports Server (NTRS)

Lou, John; Ferraro, Robert; Farrara, John; Mechoso, Carlos

1996-01-01

An analysis is presented of several factors influencing the performance of a parallel implementation of the UCLA atmospheric general circulation model (AGCM) on massively parallel computer systems. Several modificaitons to the original parallel AGCM code aimed at improving its numerical efficiency, interprocessor communication cost, load-balance and issues affecting single-node code performance are discussed.

LDRD final report on massively-parallel linear programming : the parPCx system.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parekh, Ojas; Phillips, Cynthia Ann; Boman, Erik Gunnar

2005-02-01

This report summarizes the research and development performed from October 2002 to September 2004 at Sandia National Laboratories under the Laboratory-Directed Research and Development (LDRD) project ''Massively-Parallel Linear Programming''. We developed a linear programming (LP) solver designed to use a large number of processors. LP is the optimization of a linear objective function subject to linear constraints. Companies and universities have expended huge efforts over decades to produce fast, stable serial LP solvers. Previous parallel codes run on shared-memory systems and have little or no distribution of the constraint matrix. We have seen no reports of general LP solver runsmore » on large numbers of processors. Our parallel LP code is based on an efficient serial implementation of Mehrotra's interior-point predictor-corrector algorithm (PCx). The computational core of this algorithm is the assembly and solution of a sparse linear system. We have substantially rewritten the PCx code and based it on Trilinos, the parallel linear algebra library developed at Sandia. Our interior-point method can use either direct or iterative solvers for the linear system. To achieve a good parallel data distribution of the constraint matrix, we use a (pre-release) version of a hypergraph partitioner from the Zoltan partitioning library. We describe the design and implementation of our new LP solver called parPCx and give preliminary computational results. We summarize a number of issues related to efficient parallel solution of LPs with interior-point methods including data distribution, numerical stability, and solving the core linear system using both direct and iterative methods. We describe a number of applications of LP specific to US Department of Energy mission areas and we summarize our efforts to integrate parPCx (and parallel LP solvers in general) into Sandia's massively-parallel integer programming solver PICO (Parallel Interger and Combinatorial Optimizer). We conclude with directions for long-term future algorithmic research and for near-term development that could improve the performance of parPCx.« less

How to cluster in parallel with neural networks

NASA Technical Reports Server (NTRS)

Kamgar-Parsi, Behzad; Gualtieri, J. A.; Devaney, Judy E.; Kamgar-Parsi, Behrooz

1988-01-01

Partitioning a set of N patterns in a d-dimensional metric space into K clusters - in a way that those in a given cluster are more similar to each other than the rest - is a problem of interest in astrophysics, image analysis and other fields. As there are approximately K(N)/K (factorial) possible ways of partitioning the patterns among K clusters, finding the best solution is beyond exhaustive search when N is large. Researchers show that this problem can be formulated as an optimization problem for which very good, but not necessarily optimal solutions can be found by using a neural network. To do this the network must start from many randomly selected initial states. The network is simulated on the MPP (a 128 x 128 SIMD array machine), where researchers use the massive parallelism not only in solving the differential equations that govern the evolution of the network, but also by starting the network from many initial states at once, thus obtaining many solutions in one run. Researchers obtain speedups of two to three orders of magnitude over serial implementations and the promise through Analog VLSI implementations of speedups comensurate with human perceptual abilities.

Field programmable chemistry: integrated chemical and electronic processing of informational molecules towards electronic chemical cells.

PubMed

Wagler, Patrick F; Tangen, Uwe; Maeke, Thomas; McCaskill, John S

2012-07-01

The topic addressed is that of combining self-constructing chemical systems with electronic computation to form unconventional embedded computation systems performing complex nano-scale chemical tasks autonomously. The hybrid route to complex programmable chemistry, and ultimately to artificial cells based on novel chemistry, requires a solution of the two-way massively parallel coupling problem between digital electronics and chemical systems. We present a chemical microprocessor technology and show how it can provide a generic programmable platform for complex molecular processing tasks in Field Programmable Chemistry, including steps towards the grand challenge of constructing the first electronic chemical cells. Field programmable chemistry employs a massively parallel field of electrodes, under the control of latched voltages, which are used to modulate chemical activity. We implement such a field programmable chemistry which links to chemistry in rather generic, two-phase microfluidic channel networks that are separated into weakly coupled domains. Electric fields, produced by the high-density array of electrodes embedded in the channel floors, are used to control the transport of chemicals across the hydrodynamic barriers separating domains. In the absence of electric fields, separate microfluidic domains are essentially independent with only slow diffusional interchange of chemicals. Electronic chemical cells, based on chemical microprocessors, exploit a spatially resolved sandwich structure in which the electronic and chemical systems are locally coupled through homogeneous fine-grained actuation and sensor networks and play symmetric and complementary roles. We describe how these systems are fabricated, experimentally test their basic functionality, simulate their potential (e.g. for feed forward digital electrophoretic (FFDE) separation) and outline the application to building electronic chemical cells. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Fabrication of heterogeneous nanomaterial array by programmable heating and chemical supply within microfluidic platform towards multiplexed gas sensing application

PubMed Central

Yang, Daejong; Kang, Kyungnam; Kim, Donghwan; Li, Zhiyong; Park, Inkyu

2015-01-01

A facile top-down/bottom-up hybrid nanofabrication process based on programmable temperature control and parallel chemical supply within microfluidic platform has been developed for the all liquid-phase synthesis of heterogeneous nanomaterial arrays. The synthesized materials and locations can be controlled by local heating with integrated microheaters and guided liquid chemical flow within microfluidic platform. As proofs-of-concept, we have demonstrated the synthesis of two types of nanomaterial arrays: (i) parallel array of TiO2 nanotubes, CuO nanospikes and ZnO nanowires, and (ii) parallel array of ZnO nanowire/CuO nanospike hybrid nanostructures, CuO nanospikes and ZnO nanowires. The laminar flow with negligible ionic diffusion between different precursor solutions as well as localized heating was verified by numerical calculation and experimental result of nanomaterial array synthesis. The devices made of heterogeneous nanomaterial array were utilized as a multiplexed sensor for toxic gases such as NO2 and CO. This method would be very useful for the facile fabrication of functional nanodevices based on highly integrated arrays of heterogeneous nanomaterials. PMID:25634814

Block iterative restoration of astronomical images with the massively parallel processor

NASA Technical Reports Server (NTRS)

Heap, Sara R.; Lindler, Don J.

1987-01-01

A method is described for algebraic image restoration capable of treating astronomical images. For a typical 500 x 500 image, direct algebraic restoration would require the solution of a 250,000 x 250,000 linear system. The block iterative approach is used to reduce the problem to solving 4900 121 x 121 linear systems. The algorithm was implemented on the Goddard Massively Parallel Processor, which can solve a 121 x 121 system in approximately 0.06 seconds. Examples are shown of the results for various astronomical images.

A Massively Parallel Code for Polarization Calculations

NASA Astrophysics Data System (ADS)

Akiyama, Shizuka; Höflich, Peter

2001-03-01

We present an implementation of our Monte-Carlo radiation transport method for rapidly expanding, NLTE atmospheres for massively parallel computers which utilizes both the distributed and shared memory models. This allows us to take full advantage of the fast communication and low latency inherent to nodes with multiple CPUs, and to stretch the limits of scalability with the number of nodes compared to a version which is based on the shared memory model. Test calculations on a local 20-node Beowulf cluster with dual CPUs showed an improved scalability by about 40%.

Routing performance analysis and optimization within a massively parallel computer

DOEpatents

Archer, Charles Jens; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen

2013-04-16

An apparatus, program product and method optimize the operation of a massively parallel computer system by, in part, receiving actual performance data concerning an application executed by the plurality of interconnected nodes, and analyzing the actual performance data to identify an actual performance pattern. A desired performance pattern may be determined for the application, and an algorithm may be selected from among a plurality of algorithms stored within a memory, the algorithm being configured to achieve the desired performance pattern based on the actual performance data.

Progressive Vector Quantization on a massively parallel SIMD machine with application to multispectral image data

NASA Technical Reports Server (NTRS)

Manohar, Mareboyana; Tilton, James C.

1994-01-01

A progressive vector quantization (VQ) compression approach is discussed which decomposes image data into a number of levels using full search VQ. The final level is losslessly compressed, enabling lossless reconstruction. The computational difficulties are addressed by implementation on a massively parallel SIMD machine. We demonstrate progressive VQ on multispectral imagery obtained from the Advanced Very High Resolution Radiometer instrument and other Earth observation image data, and investigate the trade-offs in selecting the number of decomposition levels and codebook training method.

Regional-scale calculation of the LS factor using parallel processing

NASA Astrophysics Data System (ADS)

Liu, Kai; Tang, Guoan; Jiang, Ling; Zhu, A.-Xing; Yang, Jianyi; Song, Xiaodong

2015-05-01

With the increase of data resolution and the increasing application of USLE over large areas, the existing serial implementation of algorithms for computing the LS factor is becoming a bottleneck. In this paper, a parallel processing model based on message passing interface (MPI) is presented for the calculation of the LS factor, so that massive datasets at a regional scale can be processed efficiently. The parallel model contains algorithms for calculating flow direction, flow accumulation, drainage network, slope, slope length and the LS factor. According to the existence of data dependence, the algorithms are divided into local algorithms and global algorithms. Parallel strategy are designed according to the algorithm characters including the decomposition method for maintaining the integrity of the results, optimized workflow for reducing the time taken for exporting the unnecessary intermediate data and a buffer-communication-computation strategy for improving the communication efficiency. Experiments on a multi-node system show that the proposed parallel model allows efficient calculation of the LS factor at a regional scale with a massive dataset.

Tough2{_}MP: A parallel version of TOUGH2

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2003-04-09

TOUGH2{_}MP is a massively parallel version of TOUGH2. It was developed for running on distributed-memory parallel computers to simulate large simulation problems that may not be solved by the standard, single-CPU TOUGH2 code. The new code implements an efficient massively parallel scheme, while preserving the full capacity and flexibility of the original TOUGH2 code. The new software uses the METIS software package for grid partitioning and AZTEC software package for linear-equation solving. The standard message-passing interface is adopted for communication among processors. Numerical performance of the current version code has been tested on CRAY-T3E and IBM RS/6000 SP platforms. Inmore » addition, the parallel code has been successfully applied to real field problems of multi-million-cell simulations for three-dimensional multiphase and multicomponent fluid and heat flow, as well as solute transport. In this paper, we will review the development of the TOUGH2{_}MP, and discuss the basic features, modules, and their applications.« less

Compact holographic optical neural network system for real-time pattern recognition

NASA Astrophysics Data System (ADS)

Lu, Taiwei; Mintzer, David T.; Kostrzewski, Andrew A.; Lin, Freddie S.

1996-08-01

One of the important characteristics of artificial neural networks is their capability for massive interconnection and parallel processing. Recently, specialized electronic neural network processors and VLSI neural chips have been introduced in the commercial market. The number of parallel channels they can handle is limited because of the limited parallel interconnections that can be implemented with 1D electronic wires. High-resolution pattern recognition problems can require a large number of neurons for parallel processing of an image. This paper describes a holographic optical neural network (HONN) that is based on high- resolution volume holographic materials and is capable of performing massive 3D parallel interconnection of tens of thousands of neurons. A HONN with more than 16,000 neurons packaged in an attache case has been developed. Rotation- shift-scale-invariant pattern recognition operations have been demonstrated with this system. System parameters such as the signal-to-noise ratio, dynamic range, and processing speed are discussed.

Breast ultrasound tomography with two parallel transducer arrays: preliminary clinical results

NASA Astrophysics Data System (ADS)

Huang, Lianjie; Shin, Junseob; Chen, Ting; Lin, Youzuo; Intrator, Miranda; Hanson, Kenneth; Epstein, Katherine; Sandoval, Daniel; Williamson, Michael

2015-03-01

Ultrasound tomography has great potential to provide quantitative estimations of physical properties of breast tumors for accurate characterization of breast cancer. We design and manufacture a new synthetic-aperture breast ultrasound tomography system with two parallel transducer arrays. The distance of these two transducer arrays is adjustable for scanning breasts with different sizes. The ultrasound transducer arrays are translated vertically to scan the entire breast slice by slice and acquires ultrasound transmission and reflection data for whole-breast ultrasound imaging and tomographic reconstructions. We use the system to acquire patient data at the University of New Mexico Hospital for clinical studies. We present some preliminary imaging results of in vivo patient ultrasound data. Our preliminary clinical imaging results show promising of our breast ultrasound tomography system with two parallel transducer arrays for breast cancer imaging and characterization.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barrett, Brian; Brightwell, Ronald B.; Grant, Ryan

This report presents a specification for the Portals 4 networ k programming interface. Portals 4 is intended to allow scalable, high-performance network communication betwee n nodes of a parallel computing system. Portals 4 is well suited to massively parallel processing and embedded syste ms. Portals 4 represents an adaption of the data movement layer developed for massively parallel processing platfor ms, such as the 4500-node Intel TeraFLOPS machine. Sandia's Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4 is tarmore » geted to the next generation of machines employing advanced network interface architectures that support enh anced offload capabilities.« less

The Portals 4.0 network programming interface.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barrett, Brian W.; Brightwell, Ronald Brian; Pedretti, Kevin

2012-11-01

This report presents a specification for the Portals 4.0 network programming interface. Portals 4.0 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4.0 is well suited to massively parallel processing and embedded systems. Portals 4.0 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandias Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4.0 is targeted to the next generationmore » of machines employing advanced network interface architectures that support enhanced offload capabilities.« less

Scalable isosurface visualization of massive datasets on commodity off-the-shelf clusters

PubMed Central

Bajaj, Chandrajit

2009-01-01

Tomographic imaging and computer simulations are increasingly yielding massive datasets. Interactive and exploratory visualizations have rapidly become indispensable tools to study large volumetric imaging and simulation data. Our scalable isosurface visualization framework on commodity off-the-shelf clusters is an end-to-end parallel and progressive platform, from initial data access to the final display. Interactive browsing of extracted isosurfaces is made possible by using parallel isosurface extraction, and rendering in conjunction with a new specialized piece of image compositing hardware called Metabuffer. In this paper, we focus on the back end scalability by introducing a fully parallel and out-of-core isosurface extraction algorithm. It achieves scalability by using both parallel and out-of-core processing and parallel disks. It statically partitions the volume data to parallel disks with a balanced workload spectrum, and builds I/O-optimal external interval trees to minimize the number of I/O operations of loading large data from disk. We also describe an isosurface compression scheme that is efficient for progress extraction, transmission and storage of isosurfaces. PMID:19756231

3-D parallel program for numerical calculation of gas dynamics problems with heat conductivity on distributed memory computational systems (CS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sofronov, I.D.; Voronin, B.L.; Butnev, O.I.

1997-12-31

The aim of the work performed is to develop a 3D parallel program for numerical calculation of gas dynamics problem with heat conductivity on distributed memory computational systems (CS), satisfying the condition of numerical result independence from the number of processors involved. Two basically different approaches to the structure of massive parallel computations have been developed. The first approach uses the 3D data matrix decomposition reconstructed at temporal cycle and is a development of parallelization algorithms for multiprocessor CS with shareable memory. The second approach is based on using a 3D data matrix decomposition not reconstructed during a temporal cycle.more » The program was developed on 8-processor CS MP-3 made in VNIIEF and was adapted to a massive parallel CS Meiko-2 in LLNL by joint efforts of VNIIEF and LLNL staffs. A large number of numerical experiments has been carried out with different number of processors up to 256 and the efficiency of parallelization has been evaluated in dependence on processor number and their parameters.« less

Massively parallel multicanonical simulations

NASA Astrophysics Data System (ADS)

Gross, Jonathan; Zierenberg, Johannes; Weigel, Martin; Janke, Wolfhard

2018-03-01

Generalized-ensemble Monte Carlo simulations such as the multicanonical method and similar techniques are among the most efficient approaches for simulations of systems undergoing discontinuous phase transitions or with rugged free-energy landscapes. As Markov chain methods, they are inherently serial computationally. It was demonstrated recently, however, that a combination of independent simulations that communicate weight updates at variable intervals allows for the efficient utilization of parallel computational resources for multicanonical simulations. Implementing this approach for the many-thread architecture provided by current generations of graphics processing units (GPUs), we show how it can be efficiently employed with of the order of 104 parallel walkers and beyond, thus constituting a versatile tool for Monte Carlo simulations in the era of massively parallel computing. We provide the fully documented source code for the approach applied to the paradigmatic example of the two-dimensional Ising model as starting point and reference for practitioners in the field.

Massively parallel X-ray holography

NASA Astrophysics Data System (ADS)

Marchesini, Stefano; Boutet, Sébastien; Sakdinawat, Anne E.; Bogan, Michael J.; Bajt, Saša; Barty, Anton; Chapman, Henry N.; Frank, Matthias; Hau-Riege, Stefan P.; Szöke, Abraham; Cui, Congwu; Shapiro, David A.; Howells, Malcolm R.; Spence, John C. H.; Shaevitz, Joshua W.; Lee, Joanna Y.; Hajdu, Janos; Seibert, Marvin M.

2008-09-01

Advances in the development of free-electron lasers offer the realistic prospect of nanoscale imaging on the timescale of atomic motions. We identify X-ray Fourier-transform holography as a promising but, so far, inefficient scheme to do this. We show that a uniformly redundant array placed next to the sample, multiplies the efficiency of X-ray Fourier transform holography by more than three orders of magnitude, approaching that of a perfect lens, and provides holographic images with both amplitude- and phase-contrast information. The experiments reported here demonstrate this concept by imaging a nano-fabricated object at a synchrotron source, and a bacterial cell with a soft-X-ray free-electron laser, where illumination by a single 15-fs pulse was successfully used in producing the holographic image. As X-ray lasers move to shorter wavelengths we expect to obtain higher spatial resolution ultrafast movies of transient states of matter.

Large-scale recording of neuronal ensembles.

PubMed

Buzsáki, György

2004-05-01

How does the brain orchestrate perceptions, thoughts and actions from the spiking activity of its neurons? Early single-neuron recording research treated spike pattern variability as noise that needed to be averaged out to reveal the brain's representation of invariant input. Another view is that variability of spikes is centrally coordinated and that this brain-generated ensemble pattern in cortical structures is itself a potential source of cognition. Large-scale recordings from neuronal ensembles now offer the opportunity to test these competing theoretical frameworks. Currently, wire and micro-machined silicon electrode arrays can record from large numbers of neurons and monitor local neural circuits at work. Achieving the full potential of massively parallel neuronal recordings, however, will require further development of the neuron-electrode interface, automated and efficient spike-sorting algorithms for effective isolation and identification of single neurons, and new mathematical insights for the analysis of network properties.

Microfabricated linear Paul-Straubel ion trap

DOEpatents

Mangan, Michael A [Albuquerque, NM; Blain, Matthew G [Albuquerque, NM; Tigges, Chris P [Albuquerque, NM; Linker, Kevin L [Albuquerque, NM

2011-04-19

An array of microfabricated linear Paul-Straubel ion traps can be used for mass spectrometric applications. Each ion trap comprises two parallel inner RF electrodes and two parallel outer DC control electrodes symmetric about a central trap axis and suspended over an opening in a substrate. Neighboring ion traps in the array can share a common outer DC control electrode. The ions confined transversely by an RF quadrupole electric field potential well on the ion trap axis. The array can trap a wide array of ions.

An eight-channel T/R head coil for parallel transmit MRI at 3T using ultra-low output impedance amplifiers

PubMed Central

Moody, Katherine Lynn; Hollingsworth, Neal A.; Zhao, Feng; Nielsen, Jon-Fredrik; Noll, Douglas C.; Wright, Steven M.; McDougall, Mary Preston

2014-01-01

Parallel transmit is an emerging technology to address the technical challenges associated with MR imaging at high field strengths. When developing arrays for parallel transmit systems, one of the primary factors to be considered is the mechanism to manage coupling and create independently operating channels. Recent work has demonstrated the use of amplifiers to provide some or all of the channel-to-channel isolation, reducing the need for on-coil decoupling networks in a manner analogous to the use of isolation preamplifiers with receive coils. This paper discusses an eight-channel transmit/receive head array for use with an ultra-low output impedance (ULOI) parallel transmit system. The ULOI amplifiers eliminated the need for a complex lumped element network to decouple the eight rung array. The design and construction details of the array are discussed in addition to the measurement considerations required for appropriately characterizing an array when using ULOI amplifiers. B1 maps and coupling matrices are used to verify the performance of the system. PMID:25072190

Ion manipulation device with electrical breakdown protection

DOEpatents

Chen, Tsung-Chi; Tang, Keqi; Ibrahim, Yehia M; Smith, Richard D; Anderson, Gordon A; Baker, Erin M

2014-12-02

An ion manipulation method and device is disclosed. The device includes a pair of substantially parallel surfaces. An array of inner electrodes is contained within, and extends substantially along the length of, each parallel surface. The device includes a first outer array of electrodes and a second outer array of electrodes. Each outer array of electrodes is positioned on either side of the inner electrodes, and is contained within and extends substantially along the length of each parallel surface. A DC voltage is applied to the first and second outer array of electrodes. A RF voltage, with a superimposed electric field, is applied to the inner electrodes by applying the DC voltages to each electrode. Ions either move between the parallel surfaces within an ion confinement area or along paths in the direction of the electric field, or can be trapped in the ion confinement area. The surfaces are housed in a chamber, and at least one electrically insulative shield is coupled to an inner surface of the chamber for increasing a mean-free-path between two adjacent electrodes in the chamber.

An eight-channel T/R head coil for parallel transmit MRI at 3T using ultra-low output impedance amplifiers

NASA Astrophysics Data System (ADS)

Moody, Katherine Lynn; Hollingsworth, Neal A.; Zhao, Feng; Nielsen, Jon-Fredrik; Noll, Douglas C.; Wright, Steven M.; McDougall, Mary Preston

2014-09-01

Parallel transmit is an emerging technology to address the technical challenges associated with MR imaging at high field strengths. When developing arrays for parallel transmit systems, one of the primary factors to be considered is the mechanism to manage coupling and create independently operating channels. Recent work has demonstrated the use of amplifiers to provide some or all of the channel-to-channel isolation, reducing the need for on-coil decoupling networks in a manner analogous to the use of isolation preamplifiers with receive coils. This paper discusses an eight-channel transmit/receive head array for use with an ultra-low output impedance (ULOI) parallel transmit system. The ULOI amplifiers eliminated the need for a complex lumped element network to decouple the eight-rung array. The design and construction details of the array are discussed in addition to the measurement considerations required for appropriately characterizing an array when using ULOI amplifiers. B1 maps and coupling matrices are used to verify the performance of the system.

Investigating the temporal domain of massive ionized jets - I. A pilot study

NASA Astrophysics Data System (ADS)

Purser, S. J. D.; Lumsden, S. L.; Hoare, M. G.; Cunningham, N.

2018-03-01

We present sensitive (σ < 10 μJy beam- 1), radio continuum observations using the Australian Telescope Compact Array at frequencies of 6 and 9 GHz towards four massive young stellar objects (MYSOs). From a previous, less sensitive work, these objects are known to harbour ionized jets associated with radio lobes, which result from shock processes. In comparison with that work, further emission components are detected towards each MYSO. These include extended, direct, thermal emission from the ionized jet's stream, new radio lobes indicative of shocks close (<105 au) to the MYSO, three radio Herbig-Haro objects separated by up to 3.8 pc from the jet's launching site, and an IR-dark source coincident with CH3OH maser emission. No significant, integrated flux variability is detected towards any jets or shocked lobes, and only one proper motion is observed (1806± 596{{ km}{ s}^{-1}{ }} parallel to the jet axis of G310.1420+00.7583A). Evidence for precession is detected in all four MYSOs with precession periods and angles within the ranges 66-15 480 yr and 6°-36°, respectively. Should precession be the result of the influence from a binary companion, we infer orbital radii of 30-1800 au.

Thought Leaders during Crises in Massive Social Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corley, Courtney D.; Farber, Robert M.; Reynolds, William

The vast amount of social media data that can be gathered from the internet coupled with workflows that utilize both commodity systems and massively parallel supercomputers, such as the Cray XMT, open new vistas for research to support health, defense, and national security. Computer technology now enables the analysis of graph structures containing more than 4 billion vertices joined by 34 billion edges along with metrics and massively parallel algorithms that exhibit near-linear scalability according to number of processors. The challenge lies in making this massive data and analysis comprehensible to an analyst and end-users that require actionable knowledge tomore » carry out their duties. Simply stated, we have developed language and content agnostic techniques to reduce large graphs built from vast media corpora into forms people can understand. Specifically, our tools and metrics act as a survey tool to identify thought leaders' -- those members that lead or reflect the thoughts and opinions of an online community, independent of the source language.« less

Parallel-wire grid assembly with method and apparatus for construction thereof

DOEpatents

Lewandowski, E.F.; Vrabec, J.

1981-10-26

Disclosed is a parallel wire grid and an apparatus and method for making the same. The grid consists of a generally coplanar array of parallel spaced-apart wires secured between metallic frame members by an electrically conductive epoxy. The method consists of continuously winding a wire about a novel winding apparatus comprising a plurality of spaced-apart generally parallel spindles. Each spindle is threaded with a number of predeterminedly spaced-apart grooves which receive and accurately position the wire at predetermined positions along the spindle. Overlying frame members coated with electrically conductive epoxy are then placed on either side of the wire array and are drawn together. After the epoxy hardens, portions of the wire array lying outside the frame members are trimmed away.

Parallel-wire grid assembly with method and apparatus for construction thereof

DOEpatents

Lewandowski, Edward F.; Vrabec, John

1984-01-01

Disclosed is a parallel wire grid and an apparatus and method for making the same. The grid consists of a generally coplanar array of parallel spaced-apart wires secured between metallic frame members by an electrically conductive epoxy. The method consists of continuously winding a wire about a novel winding apparatus comprising a plurality of spaced-apart generally parallel spindles. Each spindle is threaded with a number of predeterminedly spaced-apart grooves which receive and accurately position the wire at predetermined positions along the spindle. Overlying frame members coated with electrically conductive epoxy are then placed on either side of the wire array and are drawn together. After the epoxy hardens, portions of the wire array lying outside the frame members are trimmed away.

FWT2D: A massively parallel program for frequency-domain full-waveform tomography of wide-aperture seismic data—Part 1: Algorithm

NASA Astrophysics Data System (ADS)

Sourbier, Florent; Operto, Stéphane; Virieux, Jean; Amestoy, Patrick; L'Excellent, Jean-Yves

2009-03-01

This is the first paper in a two-part series that describes a massively parallel code that performs 2D frequency-domain full-waveform inversion of wide-aperture seismic data for imaging complex structures. Full-waveform inversion methods, namely quantitative seismic imaging methods based on the resolution of the full wave equation, are computationally expensive. Therefore, designing efficient algorithms which take advantage of parallel computing facilities is critical for the appraisal of these approaches when applied to representative case studies and for further improvements. Full-waveform modelling requires the resolution of a large sparse system of linear equations which is performed with the massively parallel direct solver MUMPS for efficient multiple-shot simulations. Efficiency of the multiple-shot solution phase (forward/backward substitutions) is improved by using the BLAS3 library. The inverse problem relies on a classic local optimization approach implemented with a gradient method. The direct solver returns the multiple-shot wavefield solutions distributed over the processors according to a domain decomposition driven by the distribution of the LU factors. The domain decomposition of the wavefield solutions is used to compute in parallel the gradient of the objective function and the diagonal Hessian, this latter providing a suitable scaling of the gradient. The algorithm allows one to test different strategies for multiscale frequency inversion ranging from successive mono-frequency inversion to simultaneous multifrequency inversion. These different inversion strategies will be illustrated in the following companion paper. The parallel efficiency and the scalability of the code will also be quantified.

Improving Performance and Predictability of Storage Arrays

ERIC Educational Resources Information Center

Altiparmak, Nihat

2013-01-01

Massive amount of data is generated everyday through sensors, Internet transactions, social networks, video, and all other digital sources available. Many organizations store this data to enable breakthrough discoveries and innovation in science, engineering, medicine, and commerce. Such massive scale of data poses new research problems called big…

Wire Array Solar Cells: Fabrication and Photoelectrochemical Studies

NASA Astrophysics Data System (ADS)

Spurgeon, Joshua Michael

Despite demand for clean energy to reduce our addiction to fossil fuels, the price of these technologies relative to oil and coal has prevented their widespread implementation. Solar energy has enormous potential as a carbon-free resource but is several times the cost of coal-produced electricity, largely because photovoltaics of practical efficiency require high-quality, pure semiconductor materials. To produce current in a planar junction solar cell, an electron or hole generated deep within the material must travel all the way to the junction without recombining. Radial junction, wire array solar cells, however, have the potential to decouple the directions of light absorption and charge-carrier collection so that a semiconductor with a minority-carrier diffusion length shorter than its absorption depth (i.e., a lower quality, potentially cheaper material) can effectively produce current. The axial dimension of the wires is long enough for sufficient optical absorption while the charge-carriers are collected along the shorter radial dimension in a massively parallel array. This thesis explores the wire array solar cell design by developing potentially low-cost fabrication methods and investigating the energy-conversion properties of the arrays in photoelectrochemical cells. The concept was initially investigated with Cd(Se, Te) rod arrays; however, Si was the primary focus of wire array research because its semiconductor properties make low-quality Si an ideal candidate for improvement in a radial geometry. Fabrication routes for Si wire arrays were explored, including the vapor-liquid-solid growth of wires using SiCl4. Uniform, vertically aligned Si wires were demonstrated in a process that permits control of the wire radius, length, and spacing. A technique was developed to transfer these wire arrays into a low-cost, flexible polymer film, and grow multiple subsequent arrays using a single Si(111) substrate. Photoelectrochemical measurements on Si wire array/polymer composite films showed that their energy-conversion properties were comparable to those of an array attached to the growth substrate. High quantum efficiencies were observed relative to the packing density of the wires, particularly with illumination at high angles of incidence. The results indicate that an inexpensive, solid-state Si wire array solar cell is possible, and a plan is presented to develop one.

Automatic Parallelization of Numerical Python Applications using the Global Arrays Toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Jeffrey A.; Lewis, Robert R.

2011-11-30

Global Arrays is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared-memory programming interface to manipulate distributed dense arrays. The NumPy module is the de facto standard for numerical calculation in the Python programming language, a language whose use is growing rapidly in the scientific and engineering communities. NumPy provides a powerful N-dimensional array class as well as other scientific computing capabilities. However, like the majority of the core Python modules, NumPy is inherently serial. Using a combination of Global Arrays and NumPy, we have reimplemented NumPy as a distributed drop-in replacement calledmore » Global Arrays in NumPy (GAiN). Serial NumPy applications can become parallel, scalable GAiN applications with only minor source code changes. Scalability studies of several different GAiN applications will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.« less

Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

PubMed Central

Roever, Stefan

2012-01-01

A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wylie, Brian Neil; Moreland, Kenneth D.

Graphs are a vital way of organizing data with complex correlations. A good visualization of a graph can fundamentally change human understanding of the data. Consequently, there is a rich body of work on graph visualization. Although there are many techniques that are effective on small to medium sized graphs (tens of thousands of nodes), there is a void in the research for visualizing massive graphs containing millions of nodes. Sandia is one of the few entities in the world that has the means and motivation to handle data on such a massive scale. For example, homeland security generates graphsmore » from prolific media sources such as television, telephone, and the Internet. The purpose of this project is to provide the groundwork for visualizing such massive graphs. The research provides for two major feature gaps: a parallel, interactive visualization framework and scalable algorithms to make the framework usable to a practical application. Both the frameworks and algorithms are designed to run on distributed parallel computers, which are already available at Sandia. Some features are integrated into the ThreatView{trademark} application and future work will integrate further parallel algorithms.« less

Vibration energy harvesting using a piezoelectric circular diaphragm array.

PubMed

Wang, Wei; Yang, Tongqing; Chen, Xurui; Yao, Xi

2012-09-01

This paper presents a method for harvesting electric energy from mechanical vibration using a mechanically excited piezoelectric circular membrane array. The piezoelectric circular diaphragm array consists of four plates with series and parallel connection, and the electrical characteristics of the array are examined under dynamic conditions. With an optimal load resistor of 160 kΩ, an output power of 28 mW was generated from the array in series connection at 150 Hz under a prestress of 0.8 N and a vibration acceleration of 9.8 m/s(2), whereas a maximal output power of 27 mW can be obtained from the array in parallel connection through a resistive load of 11 kΩ under the same frequency, prestress, and acceleration conditions. The results show that using a piezoelectric circular diaphragm array can significantly increase the output of energy compared with the use of a single plate. By choosing an appropriate connection pattern (series or parallel connections) among the plates, the equivalent impedance of the energy harvesting devices can be tailored to meet the matched load of different applications for maximal power output.

Experimental implementation of array-compressed parallel transmission at 7 tesla.

PubMed

Yan, Xinqiang; Cao, Zhipeng; Grissom, William A

2016-06-01

To implement and validate a hardware-based array-compressed parallel transmission (acpTx) system. In array-compressed parallel transmission, a small number of transmit channels drive a larger number of transmit coils, which are connected via an array compression network that implements optimized coil-to-channel combinations. A two channel-to-eight coil array compression network was developed using power splitters, attenuators and phase shifters, and a simulation was performed to investigate the effects of coil coupling on power dissipation in a simplified network. An eight coil transmit array was constructed using induced current elimination decoupling, and the coil and network were validated in benchtop measurements, B1+ mapping scans, and an accelerated spiral excitation experiment. The developed attenuators came within 0.08 dB of the desired attenuations, and reflection coefficients were -22 dB or better. The simulation demonstrated that up to 3× more power was dissipated in the network when coils were poorly isolated (-9.6 dB), versus well-isolated (-31 dB). Compared to split circularly-polarized coil combinations, the additional degrees of freedom provided by the array compression network led to 54% lower squared excitation error in the spiral experiment. Array-compressed parallel transmission was successfully implemented in a hardware system. Further work is needed to develop remote network tuning and to minimize network power dissipation. Magn Reson Med 75:2545-2552, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Tutorial: Performance and reliability in redundant disk arrays

NASA Technical Reports Server (NTRS)

Gibson, Garth A.

1993-01-01

A disk array is a collection of physically small magnetic disks that is packaged as a single unit but operates in parallel. Disk arrays capitalize on the availability of small-diameter disks from a price-competitive market to provide the cost, volume, and capacity of current disk systems but many times their performance. Unfortunately, relative to current disk systems, the larger number of components in disk arrays leads to higher rates of failure. To tolerate failures, redundant disk arrays devote a fraction of their capacity to an encoding of their information. This redundant information enables the contents of a failed disk to be recovered from the contents of non-failed disks. The simplest and least expensive encoding for this redundancy, known as N+1 parity is highlighted. In addition to compensating for the higher failure rates of disk arrays, redundancy allows highly reliable secondary storage systems to be built much more cost-effectively than is now achieved in conventional duplicated disks. Disk arrays that combine redundancy with the parallelism of many small-diameter disks are often called Redundant Arrays of Inexpensive Disks (RAID). This combination promises improvements to both the performance and the reliability of secondary storage. For example, IBM's premier disk product, the IBM 3390, is compared to a redundant disk array constructed of 84 IBM 0661 3 1/2-inch disks. The redundant disk array has comparable or superior values for each of the metrics given and appears likely to cost less. In the first section of this tutorial, I explain how disk arrays exploit the emergence of high performance, small magnetic disks to provide cost-effective disk parallelism that combats the access and transfer gap problems. The flexibility of disk-array configurations benefits manufacturer and consumer alike. In contrast, I describe in this tutorial's second half how parallelism, achieved through increasing numbers of components, causes overall failure rates to rise. Redundant disk arrays overcome this threat to data reliability by ensuring that data remains available during and after component failures.

The portals 4.0.1 network programming interface.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barrett, Brian W.; Brightwell, Ronald Brian; Pedretti, Kevin

2013-04-01

This report presents a specification for the Portals 4.0 network programming interface. Portals 4.0 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4.0 is well suited to massively parallel processing and embedded systems. Portals 4.0 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandias Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4.0 is targeted to the next generationmore » of machines employing advanced network interface architectures that support enhanced offload capabilities. 3« less

Merlin - Massively parallel heterogeneous computing

NASA Technical Reports Server (NTRS)

Wittie, Larry; Maples, Creve

1989-01-01

Hardware and software for Merlin, a new kind of massively parallel computing system, are described. Eight computers are linked as a 300-MIPS prototype to develop system software for a larger Merlin network with 16 to 64 nodes, totaling 600 to 3000 MIPS. These working prototypes help refine a mapped reflective memory technique that offers a new, very general way of linking many types of computer to form supercomputers. Processors share data selectively and rapidly on a word-by-word basis. Fast firmware virtual circuits are reconfigured to match topological needs of individual application programs. Merlin's low-latency memory-sharing interfaces solve many problems in the design of high-performance computing systems. The Merlin prototypes are intended to run parallel programs for scientific applications and to determine hardware and software needs for a future Teraflops Merlin network.

Massively parallel quantum computer simulator

NASA Astrophysics Data System (ADS)

De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.

2007-01-01

We describe portable software to simulate universal quantum computers on massive parallel computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray X1E, a SGI Altix 3700 and clusters of PCs running Windows XP. We study the performance of the software by simulating quantum computers containing up to 36 qubits, using up to 4096 processors and up to 1 TB of memory. Our results demonstrate that the simulator exhibits nearly ideal scaling as a function of the number of processors and suggest that the simulation software described in this paper may also serve as benchmark for testing high-end parallel computers.

Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by dynamic global mapping of contended links

DOEpatents

Archer, Charles Jens [Rochester, MN; Musselman, Roy Glenn [Rochester, MN; Peters, Amanda [Rochester, MN; Pinnow, Kurt Walter [Rochester, MN; Swartz, Brent Allen [Chippewa Falls, WI; Wallenfelt, Brian Paul [Eden Prairie, MN

2011-10-04

A massively parallel nodal computer system periodically collects and broadcasts usage data for an internal communications network. A node sending data over the network makes a global routing determination using the network usage data. Preferably, network usage data comprises an N-bit usage value for each output buffer associated with a network link. An optimum routing is determined by summing the N-bit values associated with each link through which a data packet must pass, and comparing the sums associated with different possible routes.

Scalable Visual Analytics of Massive Textual Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnan, Manoj Kumar; Bohn, Shawn J.; Cowley, Wendy E.

2007-04-01

This paper describes the first scalable implementation of text processing engine used in Visual Analytics tools. These tools aid information analysts in interacting with and understanding large textual information content through visual interfaces. By developing parallel implementation of the text processing engine, we enabled visual analytics tools to exploit cluster architectures and handle massive dataset. The paper describes key elements of our parallelization approach and demonstrates virtually linear scaling when processing multi-gigabyte data sets such as Pubmed. This approach enables interactive analysis of large datasets beyond capabilities of existing state-of-the art visual analytics tools.

Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by dynamically adjusting local routing strategies

DOEpatents

Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

2010-03-16

A massively parallel computer system contains an inter-nodal communications network of node-to-node links. Each node implements a respective routing strategy for routing data through the network, the routing strategies not necessarily being the same in every node. The routing strategies implemented in the nodes are dynamically adjusted during application execution to shift network workload as required. Preferably, adjustment of routing policies in selective nodes is performed at synchronization points. The network may be dynamically monitored, and routing strategies adjusted according to detected network conditions.

Highly scalable parallel processing of extracellular recordings of Multielectrode Arrays.

PubMed

Gehring, Tiago V; Vasilaki, Eleni; Giugliano, Michele

2015-01-01

Technological advances of Multielectrode Arrays (MEAs) used for multisite, parallel electrophysiological recordings, lead to an ever increasing amount of raw data being generated. Arrays with hundreds up to a few thousands of electrodes are slowly seeing widespread use and the expectation is that more sophisticated arrays will become available in the near future. In order to process the large data volumes resulting from MEA recordings there is a pressing need for new software tools able to process many data channels in parallel. Here we present a new tool for processing MEA data recordings that makes use of new programming paradigms and recent technology developments to unleash the power of modern highly parallel hardware, such as multi-core CPUs with vector instruction sets or GPGPUs. Our tool builds on and complements existing MEA data analysis packages. It shows high scalability and can be used to speed up some performance critical pre-processing steps such as data filtering and spike detection, helping to make the analysis of larger data sets tractable.

Moving-Article X-Ray Imaging System and Method for 3-D Image Generation

NASA Technical Reports Server (NTRS)

Fernandez, Kenneth R. (Inventor)

2012-01-01

An x-ray imaging system and method for a moving article are provided for an article moved along a linear direction of travel while the article is exposed to non-overlapping x-ray beams. A plurality of parallel linear sensor arrays are disposed in the x-ray beams after they pass through the article. More specifically, a first half of the plurality are disposed in a first of the x-ray beams while a second half of the plurality are disposed in a second of the x-ray beams. Each of the parallel linear sensor arrays is oriented perpendicular to the linear direction of travel. Each of the parallel linear sensor arrays in the first half is matched to a corresponding one of the parallel linear sensor arrays in the second half in terms of an angular position in the first of the x-ray beams and the second of the x-ray beams, respectively.

Means and method for the focusing and acceleration of parallel beams of charged particles

DOEpatents

Maschke, Alfred W.

1983-07-05

A novel apparatus and method for focussing beams of charged particles comprising planar arrays of electrostatic quadrupoles. The quadrupole arrays may comprise electrodes which are shared by two or more quadrupoles. Such quadrupole arrays are particularly adapted to providing strong focussing forces for high current, high brightness, beams of charged particles, said beams further comprising a plurality of parallel beams, or beamlets, each such beamlet being focussed by one quadrupole of the array. Such arrays may be incorporated in various devices wherein beams of charged particles are accelerated or transported, such as linear accelerators, klystron tubes, beam transport lines, etc.

Serial multiplier arrays for parallel computation

NASA Technical Reports Server (NTRS)

Winters, Kel

1990-01-01

Arrays of systolic serial-parallel multiplier elements are proposed as an alternative to conventional SIMD mesh serial adder arrays for applications that are multiplication intensive and require few stored operands. The design and operation of a number of multiplier and array configurations featuring locality of connection, modularity, and regularity of structure are discussed. A design methodology combining top-down and bottom-up techniques is described to facilitate development of custom high-performance CMOS multiplier element arrays as well as rapid synthesis of simulation models and semicustom prototype CMOS components. Finally, a differential version of NORA dynamic circuits requiring a single-phase uncomplemented clock signal introduced for this application.

Massively parallel data processing for quantitative total flow imaging with optical coherence microscopy and tomography

NASA Astrophysics Data System (ADS)

Sylwestrzak, Marcin; Szlag, Daniel; Marchand, Paul J.; Kumar, Ashwin S.; Lasser, Theo

2017-08-01

We present an application of massively parallel processing of quantitative flow measurements data acquired using spectral optical coherence microscopy (SOCM). The need for massive signal processing of these particular datasets has been a major hurdle for many applications based on SOCM. In view of this difficulty, we implemented and adapted quantitative total flow estimation algorithms on graphics processing units (GPU) and achieved a 150 fold reduction in processing time when compared to a former CPU implementation. As SOCM constitutes the microscopy counterpart to spectral optical coherence tomography (SOCT), the developed processing procedure can be applied to both imaging modalities. We present the developed DLL library integrated in MATLAB (with an example) and have included the source code for adaptations and future improvements. Catalogue identifier: AFBT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFBT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 913552 No. of bytes in distributed program, including test data, etc.: 270876249 Distribution format: tar.gz Programming language: CUDA/C, MATLAB. Computer: Intel x64 CPU, GPU supporting CUDA technology. Operating system: 64-bit Windows 7 Professional. Has the code been vectorized or parallelized?: Yes, CPU code has been vectorized in MATLAB, CUDA code has been parallelized. RAM: Dependent on users parameters, typically between several gigabytes and several tens of gigabytes Classification: 6.5, 18. Nature of problem: Speed up of data processing in optical coherence microscopy Solution method: Utilization of GPU for massively parallel data processing Additional comments: Compiled DLL library with source code and documentation, example of utilization (MATLAB script with raw data) Running time: 1,8 s for one B-scan (150 × faster in comparison to the CPU data processing time)

10-channel fiber array fabrication technique for parallel optical coherence tomography system

NASA Astrophysics Data System (ADS)

Arauz, Lina J.; Luo, Yuan; Castillo, Jose E.; Kostuk, Raymond K.; Barton, Jennifer

2007-02-01

Optical Coherence Tomography (OCT) shows great promise for low intrusive biomedical imaging applications. A parallel OCT system is a novel technique that replaces mechanical transverse scanning with electronic scanning. This will reduce the time required to acquire image data. In this system an array of small diameter fibers is required to obtain an image in the transverse direction. Each fiber in the array is configured in an interferometer and is used to image one pixel in the transverse direction. In this paper we describe a technique to package 15μm diameter fibers on a siliconsilica substrate to be used in a 2mm endoscopic probe tip. Single mode fibers are etched to reduce the cladding diameter from 125μm to 15μm. Etched fibers are placed into a 4mm by 150μm trench in a silicon-silica substrate and secured with UV glue. Active alignment was used to simplify the lay out of the fibers and minimize unwanted horizontal displacement of the fibers. A 10-channel fiber array was built, tested and later incorporated into a parallel optical coherence system. This paper describes the packaging, testing, and operation of the array in a parallel OCT system.

Time-dependent density-functional theory in massively parallel computer architectures: the octopus project

NASA Astrophysics Data System (ADS)

Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A.; Oliveira, Micael J. T.; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G.; Aspuru-Guzik, Alán; Rubio, Angel; Marques, Miguel A. L.

2012-06-01

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project.

PubMed

Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A; Oliveira, Micael J T; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G; Aspuru-Guzik, Alán; Rubio, Angel; Marques, Miguel A L

2012-06-13

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

Parallel Tensor Compression for Large-Scale Scientific Data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolda, Tamara G.; Ballard, Grey; Austin, Woody Nathan

As parallel computing trends towards the exascale, scientific data produced by high-fidelity simulations are growing increasingly massive. For instance, a simulation on a three-dimensional spatial grid with 512 points per dimension that tracks 64 variables per grid point for 128 time steps yields 8 TB of data. By viewing the data as a dense five way tensor, we can compute a Tucker decomposition to find inherent low-dimensional multilinear structure, achieving compression ratios of up to 10000 on real-world data sets with negligible loss in accuracy. So that we can operate on such massive data, we present the first-ever distributed memorymore » parallel implementation for the Tucker decomposition, whose key computations correspond to parallel linear algebra operations, albeit with nonstandard data layouts. Our approach specifies a data distribution for tensors that avoids any tensor data redistribution, either locally or in parallel. We provide accompanying analysis of the computation and communication costs of the algorithms. To demonstrate the compression and accuracy of the method, we apply our approach to real-world data sets from combustion science simulations. We also provide detailed performance results, including parallel performance in both weak and strong scaling experiments.« less

Optical Symbolic Computing

NASA Astrophysics Data System (ADS)

Neff, John A.

1989-12-01

Experiments originating from Gestalt psychology have shown that representing information in a symbolic form provides a more effective means to understanding. Computer scientists have been struggling for the last two decades to determine how best to create, manipulate, and store collections of symbolic structures. In the past, much of this struggling led to software innovations because that was the path of least resistance. For example, the development of heuristics for organizing the searching through knowledge bases was much less expensive than building massively parallel machines that could search in parallel. That is now beginning to change with the emergence of parallel architectures which are showing the potential for handling symbolic structures. This paper will review the relationships between symbolic computing and parallel computing architectures, and will identify opportunities for optics to significantly impact the performance of such computing machines. Although neural networks are an exciting subset of massively parallel computing structures, this paper will not touch on this area since it is receiving a great deal of attention in the literature. That is, the concepts presented herein do not consider the distributed representation of knowledge.

Parallel processing in a host plus multiple array processor system for radar

NASA Technical Reports Server (NTRS)

Barkan, B. Z.

1983-01-01

Host plus multiple array processor architecture is demonstrated to yield a modular, fast, and cost-effective system for radar processing. Software methodology for programming such a system is developed. Parallel processing with pipelined data flow among the host, array processors, and discs is implemented. Theoretical analysis of performance is made and experimentally verified. The broad class of problems to which the architecture and methodology can be applied is indicated.

Massively Parallel DNA Sequencing Facilitates Diagnosis of Patients with Usher Syndrome Type 1

PubMed Central

Yoshimura, Hidekane; Iwasaki, Satoshi; Nishio, Shin-ya; Kumakawa, Kozo; Tono, Tetsuya; Kobayashi, Yumiko; Sato, Hiroaki; Nagai, Kyoko; Ishikawa, Kotaro; Ikezono, Tetsuo; Naito, Yasushi; Fukushima, Kunihiro; Oshikawa, Chie; Kimitsuki, Takashi; Nakanishi, Hiroshi; Usami, Shin-ichi

2014-01-01

Usher syndrome is an autosomal recessive disorder manifesting hearing loss, retinitis pigmentosa and vestibular dysfunction, and having three clinical subtypes. Usher syndrome type 1 is the most severe subtype due to its profound hearing loss, lack of vestibular responses, and retinitis pigmentosa that appears in prepuberty. Six of the corresponding genes have been identified, making early diagnosis through DNA testing possible, with many immediate and several long-term advantages for patients and their families. However, the conventional genetic techniques, such as direct sequence analysis, are both time-consuming and expensive. Targeted exon sequencing of selected genes using the massively parallel DNA sequencing technology will potentially enable us to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using this technique combined with direct sequence analysis, we screened 17 unrelated Usher syndrome type 1 patients and detected probable pathogenic variants in the 16 of them (94.1%) who carried at least one mutation. Seven patients had the MYO7A mutation (41.2%), which is the most common type in Japanese. Most of the mutations were detected by only the massively parallel DNA sequencing. We report here four patients, who had probable pathogenic mutations in two different Usher syndrome type 1 genes, and one case of MYO7A/PCDH15 digenic inheritance. This is the first report of Usher syndrome mutation analysis using massively parallel DNA sequencing and the frequency of Usher syndrome type 1 genes in Japanese. Mutation screening using this technique has the power to quickly identify mutations of many causative genes while maintaining cost-benefit performance. In addition, the simultaneous mutation analysis of large numbers of genes is useful for detecting mutations in different genes that are possibly disease modifiers or of digenic inheritance. PMID:24618850

Massively parallel DNA sequencing facilitates diagnosis of patients with Usher syndrome type 1.

PubMed

Yoshimura, Hidekane; Iwasaki, Satoshi; Nishio, Shin-Ya; Kumakawa, Kozo; Tono, Tetsuya; Kobayashi, Yumiko; Sato, Hiroaki; Nagai, Kyoko; Ishikawa, Kotaro; Ikezono, Tetsuo; Naito, Yasushi; Fukushima, Kunihiro; Oshikawa, Chie; Kimitsuki, Takashi; Nakanishi, Hiroshi; Usami, Shin-Ichi

2014-01-01

Usher syndrome is an autosomal recessive disorder manifesting hearing loss, retinitis pigmentosa and vestibular dysfunction, and having three clinical subtypes. Usher syndrome type 1 is the most severe subtype due to its profound hearing loss, lack of vestibular responses, and retinitis pigmentosa that appears in prepuberty. Six of the corresponding genes have been identified, making early diagnosis through DNA testing possible, with many immediate and several long-term advantages for patients and their families. However, the conventional genetic techniques, such as direct sequence analysis, are both time-consuming and expensive. Targeted exon sequencing of selected genes using the massively parallel DNA sequencing technology will potentially enable us to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using this technique combined with direct sequence analysis, we screened 17 unrelated Usher syndrome type 1 patients and detected probable pathogenic variants in the 16 of them (94.1%) who carried at least one mutation. Seven patients had the MYO7A mutation (41.2%), which is the most common type in Japanese. Most of the mutations were detected by only the massively parallel DNA sequencing. We report here four patients, who had probable pathogenic mutations in two different Usher syndrome type 1 genes, and one case of MYO7A/PCDH15 digenic inheritance. This is the first report of Usher syndrome mutation analysis using massively parallel DNA sequencing and the frequency of Usher syndrome type 1 genes in Japanese. Mutation screening using this technique has the power to quickly identify mutations of many causative genes while maintaining cost-benefit performance. In addition, the simultaneous mutation analysis of large numbers of genes is useful for detecting mutations in different genes that are possibly disease modifiers or of digenic inheritance.

Silicon-fiber blanket solar-cell array concept

NASA Technical Reports Server (NTRS)

Eliason, J. T.

1973-01-01

Proposed economical manufacture of solar-cell arrays involves parallel, planar weaving of filaments made of doped silicon fibers with diffused radial junction. Each filament is a solar cell connected either in series or parallel with others to form a blanket of deposited grids or attached electrode wire mesh screens.

Variable-delay Polarization Modulators for the CLASS Telescope

NASA Astrophysics Data System (ADS)

Harrington, Kathleen; Ali, A.; Amiri, M.; Appel, J. W.; Araujo, D.; Bennett, C. L.; Boone, F.; Chan, M.; Cho, H.; Chuss, D. T.; Colazo, F.; Crowe, E.; Denis, K.; Dünner, R.; Eimer, J.; Essinger-Hileman, T.; Gothe, D.; Halpern, M.; Hilton, G.; Hinshaw, G. F.; Huang, C.; Irwin, K.; Jones, G.; Karakla, J.; Kogut, A. J.; Larson, D.; Limon, M.; Lowry, L.; Marriage, T.; Mehrle, N.; Miller, A. D.; Miller, N.; Mirel, P.; Moseley, S. H.; Novak, G.; Reintsema, C.; Rostem, K.; Stevenson, T.; Towner, D.; U-Yen, K.; Wagner, E.; Watts, D.; Wollack, E.; Xu, Z.; Zeng, L.

2014-01-01

The challenges of measuring faint polarized signals at microwave wavelengths have motivated the development of rapid polarization modulators. One scalable technique, called a Variable-delay Polarization Modulator (VPM), consists of a stationary wire array in front of a movable mirror. The mirror motion creates a changing phase difference between the polarization modes parallel and orthogonal to the wire array. The Cosmology Large Angular Scale Surveyor (CLASS) will use a VPM as the first optical element in a telescope array that will search for the signature of inflation through the “B-mode” pattern in the polarization of the cosmic microwave background. In the CLASS VPMs, parallel transport of the mirror is maintained by a voice-coil actuated flexure system which will translate the mirror in a repeatable manner while holding tight parallelism constraints with respect to the wire array. The wire array will use 51 μm diameter copper-plated tungsten wire with 160 μm pitch over a 60 cm clear aperture. We present the status of the construction and testing of the mirror transport mechanism and wire arrays for the CLASS VPMs.

A hierarchical, automated target recognition algorithm for a parallel analog processor

NASA Technical Reports Server (NTRS)

Woodward, Gail; Padgett, Curtis

1997-01-01

A hierarchical approach is described for an automated target recognition (ATR) system, VIGILANTE, that uses a massively parallel, analog processor (3DANN). The 3DANN processor is capable of performing 64 concurrent inner products of size 1x4096 every 250 nanoseconds.

Real-time electron dynamics for massively parallel excited-state simulations

NASA Astrophysics Data System (ADS)

Andrade, Xavier

The simulation of the real-time dynamics of electrons, based on time dependent density functional theory (TDDFT), is a powerful approach to study electronic excited states in molecular and crystalline systems. What makes the method attractive is its flexibility to simulate different kinds of phenomena beyond the linear-response regime, including strongly-perturbed electronic systems and non-adiabatic electron-ion dynamics. Electron-dynamics simulations are also attractive from a computational point of view. They can run efficiently on massively parallel architectures due to the low communication requirements. Our implementations of electron dynamics, based on the codes Octopus (real-space) and Qball (plane-waves), allow us to simulate systems composed of thousands of atoms and to obtain good parallel scaling up to 1.6 million processor cores. Due to the versatility of real-time electron dynamics and its parallel performance, we expect it to become the method of choice to apply the capabilities of exascale supercomputers for the simulation of electronic excited states.

Pushing configuration-interaction to the limit: Towards massively parallel MCSCF calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogiatzis, Konstantinos D.; Ma, Dongxia; Olsen, Jeppe

A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed. Unprecedented CI calculations with an active space of 22 electrons in 22 orbitals formore » the pentacene systems were performed and a single CI iteration calculation with an active space of 24 electrons in 24 orbitals for the chromium tetramer was possible. In conclusion, the chromium tetramer corresponds to a CI expansion of one trillion Slater determinants (914 058 513 424) and is the largest conventional CI calculation attempted up to date.« less

Pushing configuration-interaction to the limit: Towards massively parallel MCSCF calculations

DOE PAGES

Vogiatzis, Konstantinos D.; Ma, Dongxia; Olsen, Jeppe; ...

2017-11-14

A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed. Unprecedented CI calculations with an active space of 22 electrons in 22 orbitals formore » the pentacene systems were performed and a single CI iteration calculation with an active space of 24 electrons in 24 orbitals for the chromium tetramer was possible. In conclusion, the chromium tetramer corresponds to a CI expansion of one trillion Slater determinants (914 058 513 424) and is the largest conventional CI calculation attempted up to date.« less

Pushing configuration-interaction to the limit: Towards massively parallel MCSCF calculations

NASA Astrophysics Data System (ADS)

Vogiatzis, Konstantinos D.; Ma, Dongxia; Olsen, Jeppe; Gagliardi, Laura; de Jong, Wibe A.

2017-11-01

A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed. Unprecedented CI calculations with an active space of 22 electrons in 22 orbitals for the pentacene systems were performed and a single CI iteration calculation with an active space of 24 electrons in 24 orbitals for the chromium tetramer was possible. The chromium tetramer corresponds to a CI expansion of one trillion Slater determinants (914 058 513 424) and is the largest conventional CI calculation attempted up to date.

Animated computer graphics models of space and earth sciences data generated via the massively parallel processor

NASA Technical Reports Server (NTRS)

Treinish, Lloyd A.; Gough, Michael L.; Wildenhain, W. David

1987-01-01

The capability was developed of rapidly producing visual representations of large, complex, multi-dimensional space and earth sciences data sets via the implementation of computer graphics modeling techniques on the Massively Parallel Processor (MPP) by employing techniques recently developed for typically non-scientific applications. Such capabilities can provide a new and valuable tool for the understanding of complex scientific data, and a new application of parallel computing via the MPP. A prototype system with such capabilities was developed and integrated into the National Space Science Data Center's (NSSDC) Pilot Climate Data System (PCDS) data-independent environment for computer graphics data display to provide easy access to users. While developing these capabilities, several problems had to be solved independently of the actual use of the MPP, all of which are outlined.

Quadrature transmit array design using single-feed circularly polarized patch antenna for parallel transmission in MR imaging.

PubMed

Pang, Yong; Yu, Baiying; Vigneron, Daniel B; Zhang, Xiaoliang

2014-02-01

Quadrature coils are often desired in MR applications because they can improve MR sensitivity and also reduce excitation power. In this work, we propose, for the first time, a quadrature array design strategy for parallel transmission at 298 MHz using single-feed circularly polarized (CP) patch antenna technique. Each array element is a nearly square ring microstrip antenna and is fed at a point on the diagonal of the antenna to generate quadrature magnetic fields. Compared with conventional quadrature coils, the single-feed structure is much simple and compact, making the quadrature coil array design practical. Numerical simulations demonstrate that the decoupling between elements is better than -35 dB for all the elements and the RF fields are homogeneous with deep penetration and quadrature behavior in the area of interest. Bloch equation simulation is also performed to simulate the excitation procedure by using an 8-element quadrature planar patch array to demonstrate its feasibility in parallel transmission at the ultrahigh field of 7 Tesla.

Multicoil resonance-based parallel array for smart wireless power delivery.

PubMed

Mirbozorgi, S A; Sawan, M; Gosselin, B

2013-01-01

This paper presents a novel resonance-based multicoil structure as a smart power surface to wirelessly power up apparatus like mobile, animal headstage, implanted devices, etc. The proposed powering system is based on a 4-coil resonance-based inductive link, the resonance coil of which is formed by an array of several paralleled coils as a smart power transmitter. The power transmitter employs simple circuit connections and includes only one power driver circuit per multicoil resonance-based array, which enables higher power transfer efficiency and power delivery to the load. The power transmitted by the driver circuit is proportional to the load seen by the individual coil in the array. Thus, the transmitted power scales with respect to the load of the electric/electronic system to power up, and does not divide equally over every parallel coils that form the array. Instead, only the loaded coils of the parallel array transmit significant part of total transmitted power to the receiver. Such adaptive behavior enables superior power, size and cost efficiency then other solutions since it does not need to use complex detection circuitry to find the location of the load. The performance of the proposed structure is verified by measurement results. Natural load detection and covering 4 times bigger area than conventional topologies with a power transfer efficiency of 55% are the novelties of presented paper.

Integrated Parallel Reception, Excitation, and Shimming (iPRES)

PubMed Central

Han, Hui; Song, Allen W.; Truong, Trong-Kha

2013-01-01

Purpose To develop a new concept for a hardware platform that enables integrated parallel reception, excitation, and shimming (iPRES). Theory This concept uses a single coil array rather than separate arrays for parallel excitation/reception and B0 shimming. It relies on a novel design that allows a radiofrequency current (for excitation/reception) and a direct current (for B0 shimming) to coexist independently in the same coil. Methods Proof-of-concept B0 shimming experiments were performed with a two-coil array in a phantom, whereas B0 shimming simulations were performed with a 48-coil array in the human brain. Results Our experiments show that individually optimized direct currents applied in each coil can reduce the B0 root-mean-square error by 62–81% and minimize distortions in echo-planar images. The simulations show that dynamic shimming with the 48-coil iPRES array can reduce the B0 root-mean-square error in the prefrontal and temporal regions by 66–79% as compared to static 2nd-order spherical harmonic shimming and by 12–23% as compared to dynamic shimming with a 48-coil conventional shim array. Conclusion Our results demonstrate the feasibility of the iPRES concept to perform parallel excitation/reception and B0 shimming with a unified coil system as well as its promise for in vivo applications. PMID:23629974

Self-leveling 2D DPN probe arrays

NASA Astrophysics Data System (ADS)

Haaheim, Jason R.; Val, Vadim; Solheim, Ed; Bussan, John; Fragala, J.; Nelson, Mike

2010-02-01

Dip Pen Nanolithography® (DPN®) is a direct write scanning probe-based technique which operates under ambient conditions, making it suitable to deposit a wide range of biological and inorganic materials. Precision nanoscale deposition is a fundamental requirement to advance nanoscale technology in commercial applications, and tailoring chemical composition and surface structure on the sub-100 nm scale benefits researchers in areas ranging from cell adhesion to cell-signaling and biomimetic membranes. These capabilities naturally suggest a "Desktop Nanofab" concept - a turnkey system that allows a non-expert user to rapidly create high resolution, scalable nanostructures drawing upon well-characterized ink and substrate pairings. In turn, this system is fundamentally supported by a portfolio of MEMS devices tailored for microfluidic ink delivery, directed placement of nanoscale materials, and cm2 tip arrays for high-throughput nanofabrication. Massively parallel two-dimensional nanopatterning is now commercially available via NanoInk's 2D nano PrintArray™, making DPN a high-throughput (>3×107 μm2 per hour), flexible and versatile method for precision nanoscale pattern formation. However, cm2 arrays of nanoscopic tips introduce the nontrivial problem of getting them all evenly touching the surface to ensure homogeneous deposition; this requires extremely precise leveling of the array. Herein, we describe how we have made the process simple by way of a selfleveling gimbal attachment, coupled with semi-automated software leveling routines which bring the cm^2 chip to within 0.002 degrees of co-planarity. This excellent co-planarity yields highly homogeneous features across a square centimeter, with <6% feature size standard deviation. We have engineered the devices to be easy to use, wire-free, and fully integrated with both of our patterning tools: the DPN 5000, and the NLP 2000.

Is there a cluster in the massive star forming region IRAS 20126+4104?

NASA Astrophysics Data System (ADS)

Montes, V. A.; Hofner, Peter; Anderson, C.; Rosero, V.

2017-03-01

A Chandra X-ray Observatory ACIS-I observation and a 6 cm continuum radio observation with the Karl G. Jansky Very Large Array (VLA) together with a multiwavelength study in infrared (2MASS and Spitzer) and optical (USNO-B1.0) shows an increasing surface density of X-ray sources toward the massive protostar. There are at least 43 YSOs within 1.2 pc distance from the massive protostar. This number is consistent with typical B-type stars clusters (Lada & Lada 2003).

A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm

PubMed Central

Guo, Xinyu; Wang, Hong; Devabhaktuni, Vijay

2012-01-01

A design of systolic array-based Field Programmable Gate Array (FPGA) parallel architecture for Basic Local Alignment Search Tool (BLAST) Algorithm is proposed. BLAST is a heuristic biological sequence alignment algorithm which has been used by bioinformatics experts. In contrast to other designs that detect at most one hit in one-clock-cycle, our design applies a Multiple Hits Detection Module which is a pipelining systolic array to search multiple hits in a single-clock-cycle. Further, we designed a Hits Combination Block which combines overlapping hits from systolic array into one hit. These implementations completed the first and second step of BLAST architecture and achieved significant speedup comparing with previously published architectures. PMID:25969747

Massively parallel haplotyping on microscopic beads for the high-throughput phase analysis of single molecules.

PubMed

Boulanger, Jérôme; Muresan, Leila; Tiemann-Boege, Irene

2012-01-01

In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1:10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases.

Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by employing bandwidth shells at areas of overutilization

DOEpatents

Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

2010-04-27

A massively parallel computer system contains an inter-nodal communications network of node-to-node links. An automated routing strategy routes packets through one or more intermediate nodes of the network to reach a final destination. The default routing strategy is altered responsive to detection of overutilization of a particular path of one or more links, and at least some traffic is re-routed by distributing the traffic among multiple paths (which may include the default path). An alternative path may require a greater number of link traversals to reach the destination node.

A Massively Parallel Bayesian Approach to Planetary Protection Trajectory Analysis and Design

NASA Technical Reports Server (NTRS)

Wallace, Mark S.

2015-01-01

The NASA Planetary Protection Office has levied a requirement that the upper stage of future planetary launches have a less than 10(exp -4) chance of impacting Mars within 50 years after launch. A brute-force approach requires a decade of computer time to demonstrate compliance. By using a Bayesian approach and taking advantage of the demonstrated reliability of the upper stage, the required number of fifty-year propagations can be massively reduced. By spreading the remaining embarrassingly parallel Monte Carlo simulations across multiple computers, compliance can be demonstrated in a reasonable time frame. The method used is described here.

Systems and methods for rapid processing and storage of data

DOEpatents

Stalzer, Mark A.

2017-01-24

Systems and methods of building massively parallel computing systems using low power computing complexes in accordance with embodiments of the invention are disclosed. A massively parallel computing system in accordance with one embodiment of the invention includes at least one Solid State Blade configured to communicate via a high performance network fabric. In addition, each Solid State Blade includes a processor configured to communicate with a plurality of low power computing complexes interconnected by a router, and each low power computing complex includes at least one general processing core, an accelerator, an I/O interface, and cache memory and is configured to communicate with non-volatile solid state memory.

Massively Parallel Sequencing Detected a Mutation in the MFN2 Gene Missed by Sanger Sequencing Due to a Primer Mismatch on an SNP Site.

PubMed

Neupauerová, Jana; Grečmalová, Dagmar; Seeman, Pavel; Laššuthová, Petra

2016-05-01

We describe a patient with early onset severe axonal Charcot-Marie-Tooth disease (CMT2) with dominant inheritance, in whom Sanger sequencing failed to detect a mutation in the mitofusin 2 (MFN2) gene because of a single nucleotide polymorphism (rs2236057) under the PCR primer sequence. The severe early onset phenotype and the family history with severely affected mother (died after delivery) was very suggestive of CMT2A and this suspicion was finally confirmed by a MFN2 mutation. The mutation p.His361Tyr was later detected in the patient by massively parallel sequencing with a gene panel for hereditary neuropathies. According to this information, new primers for amplification and sequencing were designed which bind away from the polymorphic sites of the patient's DNA. Sanger sequencing with these new primers then confirmed the heterozygous mutation in the MFN2 gene in this patient. This case report shows that massively parallel sequencing may in some rare cases be more sensitive than Sanger sequencing and highlights the importance of accurate primer design which requires special attention. © 2016 John Wiley & Sons Ltd/University College London.

Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics.

PubMed

Hosokawa, Masahito; Nishikawa, Yohei; Kogawa, Masato; Takeyama, Haruko

2017-07-12

Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.

Array signal recovery algorithm for a single-RF-channel DBF array

NASA Astrophysics Data System (ADS)

Zhang, Duo; Wu, Wen; Fang, Da Gang

2016-12-01

An array signal recovery algorithm based on sparse signal reconstruction theory is proposed for a single-RF-channel digital beamforming (DBF) array. A single-RF-channel antenna array is a low-cost antenna array in which signals are obtained from all antenna elements by only one microwave digital receiver. The spatially parallel array signals are converted into time-sequence signals, which are then sampled by the system. The proposed algorithm uses these time-sequence samples to recover the original parallel array signals by exploiting the second-order sparse structure of the array signals. Additionally, an optimization method based on the artificial bee colony (ABC) algorithm is proposed to improve the reconstruction performance. Using the proposed algorithm, the motion compensation problem for the single-RF-channel DBF array can be solved effectively, and the angle and Doppler information for the target can be simultaneously estimated. The effectiveness of the proposed algorithms is demonstrated by the results of numerical simulations.

Optimal expression evaluation for data parallel architectures

NASA Technical Reports Server (NTRS)

Gilbert, John R.; Schreiber, Robert

1990-01-01

A data parallel machine represents an array or other composite data structure by allocating one processor (at least conceptually) per data item. A pointwise operation can be performed between two such arrays in unit time, provided their corresponding elements are allocated in the same processors. If the arrays are not aligned in this fashion, the cost of moving one or both of them is part of the cost of the operation. The choice of where to perform the operation then affects this cost. If an expression with several operands is to be evaluated, there may be many choices of where to perform the intermediate operations. An efficient algorithm is given to find the minimum-cost way to evaluate an expression, for several different data parallel architectures. This algorithm applies to any architecture in which the metric describing the cost of moving an array is robust. This encompasses most of the common data parallel communication architectures, including meshes of arbitrary dimension and hypercubes. Remarks are made on several variations of the problem, some of which are solved and some of which remain open.

Aerodynamic simulation on massively parallel systems

NASA Technical Reports Server (NTRS)

Haeuser, Jochem; Simon, Horst D.

1992-01-01

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

High figure of merit ultra-compact 3-channel parallel-connected photonic crystal mini-hexagonal-H1 defect microcavity sensor array

NASA Astrophysics Data System (ADS)

Wang, Chunhong; Sun, Fujun; Fu, Zhongyuan; Ding, Zhaoxiang; Wang, Chao; Zhou, Jian; Wang, Jiawen; Tian, Huiping

2017-08-01

In this paper, a photonic crystal (PhC) butt-coupled mini-hexagonal-H1 defect (MHHD) microcavity sensor is proposed. The MHHD microcavity is designed by introducing six mini-holes into the initial H1 defect region. Further, based on a well-designed 1 ×3 PhC Beam Splitter and three optimal MHHD microcavity sensors with different lattice constants (a), a 3-channel parallel-connected PhC sensor array on monolithic silicon on insulator (SOI) is proposed. Finite-difference time-domain (FDTD) simulations method is performed to demonstrate the high performance of our structures. As statistics show, the quality factor (Q) of our optimal MHHD microcavity attains higher than 7×104, while the sensitivity (S) reaches up to 233 nm/RIU(RIU = refractive index unit). Thus, the figure of merit (FOM) >104 of the sensor is obtained, which is enhanced by two orders of magnitude compared to the previous butt-coupled sensors [1-4]. As for the 3-channel parallel-connected PhC MHHD microcavity sensor array, the FOMs of three independent MHHD microcavity sensors are 8071, 8250 and 8250, respectively. In addition, the total footprint of the proposed 3-channel parallel-connected PhC sensor array is ultra-compactness of 12.5 μm ×31 μm (width × length). Therefore, the proposed high FOM sensor array is an ideal platform for realizing ultra-compact highly parallel refractive index (RI) sensing.

Redundant disk arrays: Reliable, parallel secondary storage. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Gibson, Garth Alan

1990-01-01

During the past decade, advances in processor and memory technology have given rise to increases in computational performance that far outstrip increases in the performance of secondary storage technology. Coupled with emerging small-disk technology, disk arrays provide the cost, volume, and capacity of current disk subsystems, by leveraging parallelism, many times their performance. Unfortunately, arrays of small disks may have much higher failure rates than the single large disks they replace. Redundant arrays of inexpensive disks (RAID) use simple redundancy schemes to provide high data reliability. The data encoding, performance, and reliability of redundant disk arrays are investigated. Organizing redundant data into a disk array is treated as a coding problem. Among alternatives examined, codes as simple as parity are shown to effectively correct single, self-identifying disk failures.

Incremental Parallelization of Non-Data-Parallel Programs Using the Charon Message-Passing Library

NASA Technical Reports Server (NTRS)

VanderWijngaart, Rob F.

2000-01-01

Message passing is among the most popular techniques for parallelizing scientific programs on distributed-memory architectures. The reasons for its success are wide availability (MPI), efficiency, and full tuning control provided to the programmer. A major drawback, however, is that incremental parallelization, as offered by compiler directives, is not generally possible, because all data structures have to be changed throughout the program simultaneously. Charon remedies this situation through mappings between distributed and non-distributed data. It allows breaking up the parallelization into small steps, guaranteeing correctness at every stage. Several tools are available to help convert legacy codes into high-performance message-passing programs. They usually target data-parallel applications, whose loops carrying most of the work can be distributed among all processors without much dependency analysis. Others do a full dependency analysis and then convert the code virtually automatically. Even more toolkits are available that aid construction from scratch of message passing programs. None, however, allows piecemeal translation of codes with complex data dependencies (i.e. non-data-parallel programs) into message passing codes. The Charon library (available in both C and Fortran) provides incremental parallelization capabilities by linking legacy code arrays with distributed arrays. During the conversion process, non-distributed and distributed arrays exist side by side, and simple mapping functions allow the programmer to switch between the two in any location in the program. Charon also provides wrapper functions that leave the structure of the legacy code intact, but that allow execution on truly distributed data. Finally, the library provides a rich set of communication functions that support virtually all patterns of remote data demands in realistic structured grid scientific programs, including transposition, nearest-neighbor communication, pipelining, gather/scatter, and redistribution. At the end of the conversion process most intermediate Charon function calls will have been removed, the non-distributed arrays will have been deleted, and virtually the only remaining Charon functions calls are the high-level, highly optimized communications. Distribution of the data is under complete control of the programmer, although a wide range of useful distributions is easily available through predefined functions. A crucial aspect of the library is that it does not allocate space for distributed arrays, but accepts programmer-specified memory. This has two major consequences. First, codes parallelized using Charon do not suffer from encapsulation; user data is always directly accessible. This provides high efficiency, and also retains the possibility of using message passing directly for highly irregular communications. Second, non-distributed arrays can be interpreted as (trivial) distributions in the Charon sense, which allows them to be mapped to truly distributed arrays, and vice versa. This is the mechanism that enables incremental parallelization. In this paper we provide a brief introduction of the library and then focus on the actual steps in the parallelization process, using some representative examples from, among others, the NAS Parallel Benchmarks. We show how a complicated two-dimensional pipeline-the prototypical non-data-parallel algorithm- can be constructed with ease. To demonstrate the flexibility of the library, we give examples of the stepwise, efficient parallel implementation of nonlocal boundary conditions common in aircraft simulations, as well as the construction of the sequence of grids required for multigrid.

A Survey of Parallel Computing

DTIC Science & Technology

1988-07-01

Evaluating Two Massively Parallel Machines. Communications of the ACM .9, , , 176 BIBLIOGRAPHY 29, 8 (August), pp. 752-758. Gajski , D.D., Padua, D.A., Kuck...Computer Architecture, edited by Gajski , D. D., Milutinovic, V. M. Siegel, H. J. and Furht, B. P. IEEE Computer Society Press, Washington, D.C., pp. 387-407

Magnetic arrays

DOEpatents

Trumper, David L.; Kim, Won-jong; Williams, Mark E.

1997-05-20

Electromagnet arrays which can provide selected field patterns in either two or three dimensions, and in particular, which can provide single-sided field patterns in two or three dimensions. These features are achieved by providing arrays which have current densities that vary in the windings both parallel to the array and in the direction of array thickness.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Baddourah, Majdi; Qin, Jiangning

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigensolution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization search analysis and domain decomposition. The source code for many of these algorithms is available.

Parallel Preconditioning for CFD Problems on the CM-5

NASA Technical Reports Server (NTRS)

Simon, Horst D.; Kremenetsky, Mark D.; Richardson, John; Lasinski, T. A. (Technical Monitor)

1994-01-01

Up to today, preconditioning methods on massively parallel systems have faced a major difficulty. The most successful preconditioning methods in terms of accelerating the convergence of the iterative solver such as incomplete LU factorizations are notoriously difficult to implement on parallel machines for two reasons: (1) the actual computation of the preconditioner is not very floating-point intensive, but requires a large amount of unstructured communication, and (2) the application of the preconditioning matrix in the iteration phase (i.e. triangular solves) are difficult to parallelize because of the recursive nature of the computation. Here we present a new approach to preconditioning for very large, sparse, unsymmetric, linear systems, which avoids both difficulties. We explicitly compute an approximate inverse to our original matrix. This new preconditioning matrix can be applied most efficiently for iterative methods on massively parallel machines, since the preconditioning phase involves only a matrix-vector multiplication, with possibly a dense matrix. Furthermore the actual computation of the preconditioning matrix has natural parallelism. For a problem of size n, the preconditioning matrix can be computed by solving n independent small least squares problems. The algorithm and its implementation on the Connection Machine CM-5 are discussed in detail and supported by extensive timings obtained from real problem data.

Bi-sensory, striped representations: comparative insights from owl and platypus.

PubMed

Pettigrew, John D

2004-01-01

Bi-sensory striped arrays are described in owl and platypus that share some similarities with the other variant of bi-sensory striped array found in primate and carnivore striate cortex: ocular dominance columns. Like ocular dominance columns, the owl and platypus striped systems each involve two different topographic arrays that are cut into parallel stripes, and interdigitated, so that higher-order neurons can integrate across both arrays. Unlike ocular dominance stripes, which have a separate array for each eye, the striped array in the middle third of the owl tectum has a separate array for each cerebral hemisphere. Binocular neurons send outputs from both hemispheres to the striped array where they are segregated into parallel stripes according to hemisphere of origin. In platypus primary somatosensory cortex (S1), the two arrays of interdigitated stripes are derived from separate sensory systems in the bill, 40,000 electroreceptors and 60,000 mechanoreceptors. The stripes in platypus S1 cortex produce bimodal electrosensory-mechanosensory neurons with specificity for the time-of-arrival difference between the two systems. This "thunder-and-lightning" system would allow the platypus to estimate the distance of the prey using time disparities generated at the bill between the earlier electrical wave and the later mechanical wave caused by the motion of benthic prey. The functional significance of parallel, striped arrays is not clear, even for the highly-studied ocular dominance system, but a general strategy is proposed here that is based on the detection of temporal disparities between the two arrays that can be used to estimate distance.

A biconjugate gradient type algorithm on massively parallel architectures

NASA Technical Reports Server (NTRS)

Freund, Roland W.; Hochbruck, Marlis

1991-01-01

The biconjugate gradient (BCG) method is the natural generalization of the classical conjugate gradient algorithm for Hermitian positive definite matrices to general non-Hermitian linear systems. Unfortunately, the original BCG algorithm is susceptible to possible breakdowns and numerical instabilities. Recently, Freund and Nachtigal have proposed a novel BCG type approach, the quasi-minimal residual method (QMR), which overcomes the problems of BCG. Here, an implementation is presented of QMR based on an s-step version of the nonsymmetric look-ahead Lanczos algorithm. The main feature of the s-step Lanczos algorithm is that, in general, all inner products, except for one, can be computed in parallel at the end of each block; this is unlike the other standard Lanczos process where inner products are generated sequentially. The resulting implementation of QMR is particularly attractive on massively parallel SIMD architectures, such as the Connection Machine.

Massive parallelization of serial inference algorithms for a complex generalized linear model

PubMed Central

Suchard, Marc A.; Simpson, Shawn E.; Zorych, Ivan; Ryan, Patrick; Madigan, David

2014-01-01

Following a series of high-profile drug safety disasters in recent years, many countries are redoubling their efforts to ensure the safety of licensed medical products. Large-scale observational databases such as claims databases or electronic health record systems are attracting particular attention in this regard, but present significant methodological and computational concerns. In this paper we show how high-performance statistical computation, including graphics processing units, relatively inexpensive highly parallel computing devices, can enable complex methods in large databases. We focus on optimization and massive parallelization of cyclic coordinate descent approaches to fit a conditioned generalized linear model involving tens of millions of observations and thousands of predictors in a Bayesian context. We find orders-of-magnitude improvement in overall run-time. Coordinate descent approaches are ubiquitous in high-dimensional statistics and the algorithms we propose open up exciting new methodological possibilities with the potential to significantly improve drug safety. PMID:25328363

Implementation, capabilities, and benchmarking of Shift, a massively parallel Monte Carlo radiation transport code

DOE PAGES

Pandya, Tara M.; Johnson, Seth R.; Evans, Thomas M.; ...

2015-12-21

This paper discusses the implementation, capabilities, and validation of Shift, a massively parallel Monte Carlo radiation transport package developed and maintained at Oak Ridge National Laboratory. It has been developed to scale well from laptop to small computing clusters to advanced supercomputers. Special features of Shift include hybrid capabilities for variance reduction such as CADIS and FW-CADIS, and advanced parallel decomposition and tally methods optimized for scalability on supercomputing architectures. Shift has been validated and verified against various reactor physics benchmarks and compares well to other state-of-the-art Monte Carlo radiation transport codes such as MCNP5, CE KENO-VI, and OpenMC. Somemore » specific benchmarks used for verification and validation include the CASL VERA criticality test suite and several Westinghouse AP1000 ® problems. These benchmark and scaling studies show promising results.« less

Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure

NASA Astrophysics Data System (ADS)

Hu, Changjun; Bai, He; He, Xinfu; Zhang, Boyao; Nie, Ningming; Wang, Xianmeng; Ren, Yingwen

2017-02-01

Material irradiation effect is one of the most important keys to use nuclear power. However, the lack of high-throughput irradiation facility and knowledge of evolution process, lead to little understanding of the addressed issues. With the help of high-performance computing, we could make a further understanding of micro-level-material. In this paper, a new data structure is proposed for the massively parallel simulation of the evolution of metal materials under irradiation environment. Based on the proposed data structure, we developed the new molecular dynamics software named Crystal MD. The simulation with Crystal MD achieved over 90% parallel efficiency in test cases, and it takes more than 25% less memory on multi-core clusters than LAMMPS and IMD, which are two popular molecular dynamics simulation software. Using Crystal MD, a two trillion particles simulation has been performed on Tianhe-2 cluster.

Elliptically polarizing adjustable phase insertion device

DOEpatents

Carr, Roger

1995-01-01

An insertion device for extracting polarized electromagnetic energy from a beam of particles is disclosed. The insertion device includes four linear arrays of magnets which are aligned with the particle beam. The magnetic field strength to which the particles are subjected is adjusted by altering the relative alignment of the arrays in a direction parallel to that of the particle beam. Both the energy and polarization of the extracted energy may be varied by moving the relevant arrays parallel to the beam direction. The present invention requires a substantially simpler and more economical superstructure than insertion devices in which the magnetic field strength is altered by changing the gap between arrays of magnets.

Coherent Detector Arrays for Continuum and Spectral Line Applications

NASA Technical Reports Server (NTRS)

Gaier, Todd C.

2006-01-01

This viewgraph presentation reviews the requirements for improved coherent detector arrays for use in continuum and spectral line applications. With detectors approaching fundamental limits, large arrays offer the only path to sensitivity improvement. Monolithic Microwave Integrated Circuit (MMIC) technology offers a straightforward path to massive focal plane millimeter wave arrays: The technology will readily support continuum imagers, polarimeters and spectral line receivers from 30-110 GHz. Science programs, particularly large field blind surveys will benefit from simultaneous observations of hundreds or thousands of pixels 1000 element array is competitive with a cost less than $2M.

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.

PubMed

Lagardère, Louis; Lipparini, Filippo; Polack, Étienne; Stamm, Benjamin; Cancès, Éric; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip

2014-02-28

In this paper, we present a scalable and efficient implementation of point dipole-based polarizable force fields for molecular dynamics (MD) simulations with periodic boundary conditions (PBC). The Smooth Particle-Mesh Ewald technique is combined with two optimal iterative strategies, namely, a preconditioned conjugate gradient solver and a Jacobi solver in conjunction with the Direct Inversion in the Iterative Subspace for convergence acceleration, to solve the polarization equations. We show that both solvers exhibit very good parallel performances and overall very competitive timings in an energy-force computation needed to perform a MD step. Various tests on large systems are provided in the context of the polarizable AMOEBA force field as implemented in the newly developed Tinker-HP package which is the first implementation for a polarizable model making large scale experiments for massively parallel PBC point dipole models possible. We show that using a large number of cores offers a significant acceleration of the overall process involving the iterative methods within the context of spme and a noticeable improvement of the memory management giving access to very large systems (hundreds of thousands of atoms) as the algorithm naturally distributes the data on different cores. Coupled with advanced MD techniques, gains ranging from 2 to 3 orders of magnitude in time are now possible compared to non-optimized, sequential implementations giving new directions for polarizable molecular dynamics in periodic boundary conditions using massively parallel implementations.

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald

PubMed Central

Lagardère, Louis; Lipparini, Filippo; Polack, Étienne; Stamm, Benjamin; Cancès, Éric; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip

2015-01-01

In this paper, we present a scalable and efficient implementation of point dipole-based polarizable force fields for molecular dynamics (MD) simulations with periodic boundary conditions (PBC). The Smooth Particle-Mesh Ewald technique is combined with two optimal iterative strategies, namely, a preconditioned conjugate gradient solver and a Jacobi solver in conjunction with the Direct Inversion in the Iterative Subspace for convergence acceleration, to solve the polarization equations. We show that both solvers exhibit very good parallel performances and overall very competitive timings in an energy-force computation needed to perform a MD step. Various tests on large systems are provided in the context of the polarizable AMOEBA force field as implemented in the newly developed Tinker-HP package which is the first implementation for a polarizable model making large scale experiments for massively parallel PBC point dipole models possible. We show that using a large number of cores offers a significant acceleration of the overall process involving the iterative methods within the context of spme and a noticeable improvement of the memory management giving access to very large systems (hundreds of thousands of atoms) as the algorithm naturally distributes the data on different cores. Coupled with advanced MD techniques, gains ranging from 2 to 3 orders of magnitude in time are now possible compared to non-optimized, sequential implementations giving new directions for polarizable molecular dynamics in periodic boundary conditions using massively parallel implementations. PMID:26512230

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

Relationship Between Faults Oriented Parallel and Oblique to Bedding in Neogene Massive Siliceous Mudstones at The Horonobe Underground Research Laboratory, Japan

NASA Astrophysics Data System (ADS)

Hayano, Akira; Ishii, Eiichi

2016-10-01

This study investigates the mechanical relationship between bedding-parallel and bedding-oblique faults in a Neogene massive siliceous mudstone at the site of the Horonobe Underground Research Laboratory (URL) in Hokkaido, Japan, on the basis of observations of drill-core recovered from pilot boreholes and fracture mapping on shaft and gallery walls. Four bedding-parallel faults with visible fault gouge, named respectively the MM Fault, the Last MM Fault, the S1 Fault, and the S2 Fault (stratigraphically, from the highest to the lowest), were observed in two pilot boreholes (PB-V01 and SAB-1). The distribution of the bedding-parallel faults at 350 m depth in the Horonobe URL indicates that these faults are spread over at least several tens of meters in parallel along a bedding plane. The observation that the bedding-oblique fault displaces the Last MM fault is consistent with the previous interpretation that the bedding- oblique faults formed after the bedding-parallel faults. In addition, the bedding-parallel faults terminate near the MM and S1 faults, indicating that the bedding-parallel faults with visible fault gouge act to terminate the propagation of younger bedding-oblique faults. In particular, the MM and S1 faults, which have a relatively thick fault gouge, appear to have had a stronger control on the propagation of bedding-oblique faults than did the Last MM fault, which has a relatively thin fault gouge.

Studies in optical parallel processing. [All optical and electro-optic approaches

NASA Technical Reports Server (NTRS)

Lee, S. H.

1978-01-01

Threshold and A/D devices for converting a gray scale image into a binary one were investigated for all-optical and opto-electronic approaches to parallel processing. Integrated optical logic circuits (IOC) and optical parallel logic devices (OPA) were studied as an approach to processing optical binary signals. In the IOC logic scheme, a single row of an optical image is coupled into the IOC substrate at a time through an array of optical fibers. Parallel processing is carried out out, on each image element of these rows, in the IOC substrate and the resulting output exits via a second array of optical fibers. The OPAL system for parallel processing which uses a Fabry-Perot interferometer for image thresholding and analog-to-digital conversion, achieves a higher degree of parallel processing than is possible with IOC.

Scalable load balancing for massively parallel distributed Monte Carlo particle transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Brien, M. J.; Brantley, P. S.; Joy, K. I.

2013-07-01

In order to run computer simulations efficiently on massively parallel computers with hundreds of thousands or millions of processors, care must be taken that the calculation is load balanced across the processors. Examining the workload of every processor leads to an unscalable algorithm, with run time at least as large as O(N), where N is the number of processors. We present a scalable load balancing algorithm, with run time 0(log(N)), that involves iterated processor-pair-wise balancing steps, ultimately leading to a globally balanced workload. We demonstrate scalability of the algorithm up to 2 million processors on the Sequoia supercomputer at Lawrencemore » Livermore National Laboratory. (authors)« less

Method and apparatus for obtaining stack traceback data for multiple computing nodes of a massively parallel computer system

DOEpatents

Gooding, Thomas Michael; McCarthy, Patrick Joseph

2010-03-02

A data collector for a massively parallel computer system obtains call-return stack traceback data for multiple nodes by retrieving partial call-return stack traceback data from each node, grouping the nodes in subsets according to the partial traceback data, and obtaining further call-return stack traceback data from a representative node or nodes of each subset. Preferably, the partial data is a respective instruction address from each node, nodes having identical instruction address being grouped together in the same subset. Preferably, a single node of each subset is chosen and full stack traceback data is retrieved from the call-return stack within the chosen node.

Method and apparatus for analyzing error conditions in a massively parallel computer system by identifying anomalous nodes within a communicator set

DOEpatents

Gooding, Thomas Michael [Rochester, MN

2011-04-19

An analytical mechanism for a massively parallel computer system automatically analyzes data retrieved from the system, and identifies nodes which exhibit anomalous behavior in comparison to their immediate neighbors. Preferably, anomalous behavior is determined by comparing call-return stack tracebacks for each node, grouping like nodes together, and identifying neighboring nodes which do not themselves belong to the group. A node, not itself in the group, having a large number of neighbors in the group, is a likely locality of error. The analyzer preferably presents this information to the user by sorting the neighbors according to number of adjoining members of the group.

Estimating water flow through a hillslope using the massively parallel processor

NASA Technical Reports Server (NTRS)

Devaney, Judy E.; Camillo, P. J.; Gurney, R. J.

1988-01-01

A new two-dimensional model of water flow in a hillslope has been implemented on the Massively Parallel Processor at the Goddard Space Flight Center. Flow in the soil both in the saturated and unsaturated zones, evaporation and overland flow are all modelled, and the rainfall rates are allowed to vary spatially. Previous models of this type had always been very limited computationally. This model takes less than a minute to model all the components of the hillslope water flow for a day. The model can now be used in sensitivity studies to specify which measurements should be taken and how accurate they should be to describe such flows for environmental studies.

Recovery Act - CAREER: Sustainable Silicon -- Energy-Efficient VLSI Interconnect for Extreme-Scale Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiang, Patrick

2014-01-31

The research goal of this CAREER proposal is to develop energy-efficient, VLSI interconnect circuits and systems that will facilitate future massively-parallel, high-performance computing. Extreme-scale computing will exhibit massive parallelism on multiple vertical levels, from thou­ sands of computational units on a single processor to thousands of processors in a single data center. Unfortunately, the energy required to communicate between these units at every level (on­ chip, off-chip, off-rack) will be the critical limitation to energy efficiency. Therefore, the PI's career goal is to become a leading researcher in the design of energy-efficient VLSI interconnect for future computing systems.

De novo assembly of human genomes with massively parallel short read sequencing.

PubMed

Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue; Qian, Wubin; Fang, Xiaodong; Shi, Zhongbin; Li, Yingrui; Li, Shengting; Shan, Gao; Kristiansen, Karsten; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

2010-02-01

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.

An Efficient Pipeline Wavefront Phase Recovery for the CAFADIS Camera for Extremely Large Telescopes

PubMed Central

Magdaleno, Eduardo; Rodríguez, Manuel; Rodríguez-Ramos, José Manuel

2010-01-01

In this paper we show a fast, specialized hardware implementation of the wavefront phase recovery algorithm using the CAFADIS camera. The CAFADIS camera is a new plenoptic sensor patented by the Universidad de La Laguna (Canary Islands, Spain): international patent PCT/ES2007/000046 (WIPO publication number WO/2007/082975). It can simultaneously measure the wavefront phase and the distance to the light source in a real-time process. The pipeline algorithm is implemented using Field Programmable Gate Arrays (FPGA). These devices present architecture capable of handling the sensor output stream using a massively parallel approach and they are efficient enough to resolve several Adaptive Optics (AO) problems in Extremely Large Telescopes (ELTs) in terms of processing time requirements. The FPGA implementation of the wavefront phase recovery algorithm using the CAFADIS camera is based on the very fast computation of two dimensional fast Fourier Transforms (FFTs). Thus we have carried out a comparison between our very novel FPGA 2D-FFTa and other implementations. PMID:22315523

An efficient pipeline wavefront phase recovery for the CAFADIS camera for extremely large telescopes.

PubMed

Magdaleno, Eduardo; Rodríguez, Manuel; Rodríguez-Ramos, José Manuel

2010-01-01

In this paper we show a fast, specialized hardware implementation of the wavefront phase recovery algorithm using the CAFADIS camera. The CAFADIS camera is a new plenoptic sensor patented by the Universidad de La Laguna (Canary Islands, Spain): international patent PCT/ES2007/000046 (WIPO publication number WO/2007/082975). It can simultaneously measure the wavefront phase and the distance to the light source in a real-time process. The pipeline algorithm is implemented using Field Programmable Gate Arrays (FPGA). These devices present architecture capable of handling the sensor output stream using a massively parallel approach and they are efficient enough to resolve several Adaptive Optics (AO) problems in Extremely Large Telescopes (ELTs) in terms of processing time requirements. The FPGA implementation of the wavefront phase recovery algorithm using the CAFADIS camera is based on the very fast computation of two dimensional fast Fourier Transforms (FFTs). Thus we have carried out a comparison between our very novel FPGA 2D-FFTa and other implementations.

Component-based integration of chemistry and optimization software.

PubMed

Kenny, Joseph P; Benson, Steven J; Alexeev, Yuri; Sarich, Jason; Janssen, Curtis L; McInnes, Lois Curfman; Krishnan, Manojkumar; Nieplocha, Jarek; Jurrus, Elizabeth; Fahlstrom, Carl; Windus, Theresa L

2004-11-15

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

Signal and noise extraction from analog memory elements for neuromorphic computing.

PubMed

Gong, N; Idé, T; Kim, S; Boybat, I; Sebastian, A; Narayanan, V; Ando, T

2018-05-29

Dense crossbar arrays of non-volatile memory (NVM) can potentially enable massively parallel and highly energy-efficient neuromorphic computing systems. The key requirements for the NVM elements are continuous (analog-like) conductance tuning capability and switching symmetry with acceptable noise levels. However, most NVM devices show non-linear and asymmetric switching behaviors. Such non-linear behaviors render separation of signal and noise extremely difficult with conventional characterization techniques. In this study, we establish a practical methodology based on Gaussian process regression to address this issue. The methodology is agnostic to switching mechanisms and applicable to various NVM devices. We show tradeoff between switching symmetry and signal-to-noise ratio for HfO 2 -based resistive random access memory. Then, we characterize 1000 phase-change memory devices based on Ge 2 Sb 2 Te 5 and separate total variability into device-to-device variability and inherent randomness from individual devices. These results highlight the usefulness of our methodology to realize ideal NVM devices for neuromorphic computing.

Parallel computations and control of adaptive structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Alvin, Kenneth F.; Belvin, W. Keith; Chong, K. P. (Editor); Liu, S. C. (Editor); Li, J. C. (Editor)

1991-01-01

The equations of motion for structures with adaptive elements for vibration control are presented for parallel computations to be used as a software package for real-time control of flexible space structures. A brief introduction of the state-of-the-art parallel computational capability is also presented. Time marching strategies are developed for an effective use of massive parallel mapping, partitioning, and the necessary arithmetic operations. An example is offered for the simulation of control-structure interaction on a parallel computer and the impact of the approach presented for applications in other disciplines than aerospace industry is assessed.

Magnetic arrays

DOEpatents

Trumper, D.L.; Kim, W.; Williams, M.E.

1997-05-20

Electromagnet arrays are disclosed which can provide selected field patterns in either two or three dimensions, and in particular, which can provide single-sided field patterns in two or three dimensions. These features are achieved by providing arrays which have current densities that vary in the windings both parallel to the array and in the direction of array thickness. 12 figs.

A Generic Mesh Data Structure with Parallel Applications

ERIC Educational Resources Information Center

Cochran, William Kenneth, Jr.

2009-01-01

High performance, massively-parallel multi-physics simulations are built on efficient mesh data structures. Most data structures are designed from the bottom up, focusing on the implementation of linear algebra routines. In this thesis, we explore a top-down approach to design, evaluating the various needs of many aspects of simulation, not just…

Parallel computer vision

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uhr, L.

1987-01-01

This book is written by research scientists involved in the development of massively parallel, but hierarchically structured, algorithms, architectures, and programs for image processing, pattern recognition, and computer vision. The book gives an integrated picture of the programs and algorithms that are being developed, and also of the multi-computer hardware architectures for which these systems are designed.

DICE/ColDICE: 6D collisionless phase space hydrodynamics using a lagrangian tesselation

NASA Astrophysics Data System (ADS)

Sousbie, Thierry

2018-01-01

DICE is a C++ template library designed to solve collisionless fluid dynamics in 6D phase space using massively parallel supercomputers via an hybrid OpenMP/MPI parallelization. ColDICE, based on DICE, implements a cosmological and physical VLASOV-POISSON solver for cold systems such as dark matter (CDM) dynamics.

A Review of Lightweight Thread Approaches for High Performance Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castello, Adrian; Pena, Antonio J.; Seo, Sangmin

High-level, directive-based solutions are becoming the programming models (PMs) of the multi/many-core architectures. Several solutions relying on operating system (OS) threads perfectly work with a moderate number of cores. However, exascale systems will spawn hundreds of thousands of threads in order to exploit their massive parallel architectures and thus conventional OS threads are too heavy for that purpose. Several lightweight thread (LWT) libraries have recently appeared offering lighter mechanisms to tackle massive concurrency. In order to examine the suitability of LWTs in high-level runtimes, we develop a set of microbenchmarks consisting of commonlyfound patterns in current parallel codes. Moreover, wemore » study the semantics offered by some LWT libraries in order to expose the similarities between different LWT application programming interfaces. This study reveals that a reduced set of LWT functions can be sufficient to cover the common parallel code patterns and that those LWT libraries perform better than OS threads-based solutions in cases where task and nested parallelism are becoming more popular with new architectures.« less

Automated Handling of Garments for Pressing

DTIC Science & Technology

1991-09-30

Parallel Algorithms for 2D Kalman Filtering ................................. 47 DJ. Potter and M.P. Cline Hash Table and Sorted Array: A Case Study of... Kalman Filtering on the Connection Machine ............................ 55 MA. Palis and D.K. Krecker Parallel Sorting of Large Arrays on the MasPar...ALGORITHM’VS FOR SEAM SENSING. .. .. .. ... ... .... ..... 24 6.1 KarelTW Algorithms .. .. ... ... ... ... .... ... ...... 24 6.1.1 Image Filtering

Parallel traveling-wave MRI: a feasibility study.

PubMed

Pang, Yong; Vigneron, Daniel B; Zhang, Xiaoliang

2012-04-01

Traveling-wave magnetic resonance imaging utilizes far fields of a single-piece patch antenna in the magnet bore to generate radio frequency fields for imaging large-size samples, such as the human body. In this work, the feasibility of applying the "traveling-wave" technique to parallel imaging is studied using microstrip patch antenna arrays with both the numerical analysis and experimental tests. A specific patch array model is built and each array element is a microstrip patch antenna. Bench tests show that decoupling between two adjacent elements is better than -26-dB while matching of each element reaches -36-dB, demonstrating excellent isolation performance and impedance match capability. The sensitivity patterns are simulated and g-factors are calculated for both unloaded and loaded cases. The results on B 1- sensitivity patterns and g-factors demonstrate the feasibility of the traveling-wave parallel imaging. Simulations also suggest that different array configuration such as patch shape, position and orientation leads to different sensitivity patterns and g-factor maps, which provides a way to manipulate B(1) fields and improve the parallel imaging performance. The proposed method is also validated by using 7T MR imaging experiments. Copyright © 2011 Wiley-Liss, Inc.

Parallel image compression

NASA Technical Reports Server (NTRS)

Reif, John H.

1987-01-01

A parallel compression algorithm for the 16,384 processor MPP machine was developed. The serial version of the algorithm can be viewed as a combination of on-line dynamic lossless test compression techniques (which employ simple learning strategies) and vector quantization. These concepts are described. How these concepts are combined to form a new strategy for performing dynamic on-line lossy compression is discussed. Finally, the implementation of this algorithm in a massively parallel fashion on the MPP is discussed.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Nguyen, D. T.; Baddourah, M. A.; Qin, J.

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigen-solution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization algorithm and domain decomposition. The source code for many of these algorithms is available from NASA Langley.

Expression Profiling Smackdown: Human Transcriptome Array HTA 2.0 vs. RNA-Seq

PubMed Central

Palermo, Meghann; Driscoll, Heather; Tighe, Scott; Dragon, Julie; Bond, Jeff; Shukla, Arti; Vangala, Mahesh; Vincent, James; Hunter, Tim

2014-01-01

The advent of both microarray and massively parallel sequencing have revolutionized high-throughput analysis of the human transcriptome. Due to limitations in microarray technology, detecting and quantifying coding transcript isoforms, in addition to non-coding transcripts, has been challenging. As a result, RNA-Seq has been the preferred method for characterizing the full human transcriptome, until now. A new high-resolution array from Affymetrix, GeneChip Human Transcriptome Array 2.0 (HTA 2.0), has been designed to interrogate all transcript isoforms in the human transcriptome with >6 million probes targeting coding transcripts, exon-exon splice junctions, and non-coding transcripts. Here we compare expression results from GeneChip HTA 2.0 and RNA-Seq data using identical RNA extractions from three samples each of healthy human mesothelial cells in culture, LP9-C1, and healthy mesothelial cells treated with asbestos, LP9-A1. For GeneChip HTA 2.0 sample preparation, we chose to compare two target preparation methods, NuGEN Ovation Pico WTA V2 with the Encore Biotin Module versus Affymetrix's GeneChip WT PLUS with the WT Terminal Labeling Kit, on identical RNA extractions from both untreated and treated samples. These same RNA extractions were used for the RNA-Seq library preparation. All analyses were performed in Partek Genomics Suite 6.6. Expression profiles for control and asbestos-treated mesothelial cells prepared with NuGEN versus Affymetrix target preparation methods (GeneChip HTA 2.0) are compared to each other as well as to RNA-Seq results.

Camera Development for the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Moncada, Roberto Jose

2017-01-01

With the Cherenkov Telescope Array (CTA), the very-high-energy gamma-ray universe, between 30 GeV and 300 TeV, will be probed at an unprecedented resolution, allowing deeper studies of known gamma-ray emitters and the possible discovery of new ones. This exciting project could also confirm the particle nature of dark matter by looking for the gamma rays produced by self-annihilating weakly interacting massive particles (WIMPs). The telescopes will use the imaging atmospheric Cherenkov technique (IACT) to record Cherenkov photons that are produced by the gamma-ray induced extensive air shower. One telescope design features dual-mirror Schwarzschild-Couder (SC) optics that allows the light to be finely focused on the high-resolution silicon photomultipliers of the camera modules starting from a 9.5-meter primary mirror. Each camera module will consist of a focal plane module and front-end electronics, and will have four TeV Array Readout with GSa/s Sampling and Event Trigger (TARGET) chips, giving them 64 parallel input channels. The TARGET chip has a self-trigger functionality for readout that can be used in higher logic across camera modules as well as across individual telescopes, which will each have 177 camera modules. There will be two sites, one in the northern and the other in the southern hemisphere, for full sky coverage, each spanning at least one square kilometer. A prototype SC telescope is currently under construction at the Fred Lawrence Whipple Observatory in Arizona. This work was supported by the National Science Foundation's REU program through NSF award AST-1560016.

dc properties of series-parallel arrays of Josephson junctions in an external magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewandowski, S.J.

1991-04-01

A detailed dc theory of superconducting multijunction interferometers has previously been developed by several authors for the case of parallel junction arrays. The theory is now extended to cover the case of a loop containing several junctions connected in series. The problem is closely associated with high-{ital T}{sub {ital c}} superconductors and their clusters of intrinsic Josephson junctions. These materials exhibit spontaneous interferometric effects, and there is no reason to assume that the intrinsic junctions form only parallel arrays. A simple formalism of phase states is developed in order to express the superconducting phase differences across the junctions forming amore » series array as functions of the phase difference across the weakest junction of the system, and to relate the differences in critical currents of the junctions to gaps in the allowed ranges of their phase functions. This formalism is used to investigate the energy states of the array, which in the case of different junctions are split and separated by energy barriers of height depending on the phase gaps. Modifications of the washboard model of a single junction are shown. Next a superconducting inductive loop containing a series array of two junctions is considered, and this model is used to demonstrate the transitions between phase states and the associated instabilities. Finally, the critical current of a parallel connection of two series arrays is analyzed and shown to be a multivalued function of the externally applied magnetic flux. The instabilities caused by the presence of intrinsic serial junctions in granular high-{ital T}{sub {ital c}} materials are pointed out as a potential source of additional noise.« less

High Performance Distributed Computing in a Supercomputer Environment: Computational Services and Applications Issues

NASA Technical Reports Server (NTRS)

Kramer, Williams T. C.; Simon, Horst D.

1994-01-01

This tutorial proposes to be a practical guide for the uninitiated to the main topics and themes of high-performance computing (HPC), with particular emphasis to distributed computing. The intent is first to provide some guidance and directions in the rapidly increasing field of scientific computing using both massively parallel and traditional supercomputers. Because of their considerable potential computational power, loosely or tightly coupled clusters of workstations are increasingly considered as a third alternative to both the more conventional supercomputers based on a small number of powerful vector processors, as well as high massively parallel processors. Even though many research issues concerning the effective use of workstation clusters and their integration into a large scale production facility are still unresolved, such clusters are already used for production computing. In this tutorial we will utilize the unique experience made at the NAS facility at NASA Ames Research Center. Over the last five years at NAS massively parallel supercomputers such as the Connection Machines CM-2 and CM-5 from Thinking Machines Corporation and the iPSC/860 (Touchstone Gamma Machine) and Paragon Machines from Intel were used in a production supercomputer center alongside with traditional vector supercomputers such as the Cray Y-MP and C90.

Development of massive multilevel molecular dynamics simulation program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the elucidation of protein functions.

PubMed

Takano, Yu; Nakata, Kazuto; Yonezawa, Yasushige; Nakamura, Haruki

2016-05-05

A massively parallel program for quantum mechanical-molecular mechanical (QM/MM) molecular dynamics simulation, called Platypus (PLATform for dYnamic Protein Unified Simulation), was developed to elucidate protein functions. The speedup and the parallelization ratio of Platypus in the QM and QM/MM calculations were assessed for a bacteriochlorophyll dimer in the photosynthetic reaction center (DIMER) on the K computer, a massively parallel computer achieving 10 PetaFLOPs with 705,024 cores. Platypus exhibited the increase in speedup up to 20,000 core processors at the HF/cc-pVDZ and B3LYP/cc-pVDZ, and up to 10,000 core processors by the CASCI(16,16)/6-31G** calculations. We also performed excited QM/MM-MD simulations on the chromophore of Sirius (SIRIUS) in water. Sirius is a pH-insensitive and photo-stable ultramarine fluorescent protein. Platypus accelerated on-the-fly excited-state QM/MM-MD simulations for SIRIUS in water, using over 4000 core processors. In addition, it also succeeded in 50-ps (200,000-step) on-the-fly excited-state QM/MM-MD simulations for the SIRIUS in water. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Elliptically polarizing adjustable phase insertion device

DOEpatents

Carr, R.

1995-01-17

An insertion device for extracting polarized electromagnetic energy from a beam of particles is disclosed. The insertion device includes four linear arrays of magnets which are aligned with the particle beam. The magnetic field strength to which the particles are subjected is adjusted by altering the relative alignment of the arrays in a direction parallel to that of the particle beam. Both the energy and polarization of the extracted energy may be varied by moving the relevant arrays parallel to the beam direction. The present invention requires a substantially simpler and more economical superstructure than insertion devices in which the magnetic field strength is altered by changing the gap between arrays of magnets. 3 figures.

Array processor architecture

NASA Technical Reports Server (NTRS)

Barnes, George H. (Inventor); Lundstrom, Stephen F. (Inventor); Shafer, Philip E. (Inventor)

1983-01-01

A high speed parallel array data processing architecture fashioned under a computational envelope approach includes a data base memory for secondary storage of programs and data, and a plurality of memory modules interconnected to a plurality of processing modules by a connection network of the Omega gender. Programs and data are fed from the data base memory to the plurality of memory modules and from hence the programs are fed through the connection network to the array of processors (one copy of each program for each processor). Execution of the programs occur with the processors operating normally quite independently of each other in a multiprocessing fashion. For data dependent operations and other suitable operations, all processors are instructed to finish one given task or program branch before all are instructed to proceed in parallel processing fashion on the next instruction. Even when functioning in the parallel processing mode however, the processors are not locked-step but execute their own copy of the program individually unless or until another overall processor array synchronization instruction is issued.

Scaling bioinformatics applications on HPC.

PubMed

Mikailov, Mike; Luo, Fu-Jyh; Barkley, Stuart; Valleru, Lohit; Whitney, Stephen; Liu, Zhichao; Thakkar, Shraddha; Tong, Weida; Petrick, Nicholas

2017-12-28

Recent breakthroughs in molecular biology and next generation sequencing technologies have led to the expenential growh of the sequence databases. Researchrs use BLAST for processing these sequences. However traditional software parallelization techniques (threads, message passing interface) applied in newer versios of BLAST are not adequate for processing these sequences in timely manner. A new method for array job parallelization has been developed which offers O(T) theoretical speed-up in comparison to multi-threading and MPI techniques. Here T is the number of array job tasks. (The number of CPUs that will be used to complete the job equals the product of T multiplied by the number of CPUs used by a single task.) The approach is based on segmentation of both input datasets to the BLAST process, combining partial solutions published earlier (Dhanker and Gupta, Int J Comput Sci Inf Technol_5:4818-4820, 2014), (Grant et al., Bioinformatics_18:765-766, 2002), (Mathog, Bioinformatics_19:1865-1866, 2003). It is accordingly referred to as a "dual segmentation" method. In order to implement the new method, the BLAST source code was modified to allow the researcher to pass to the program the number of records (effective number of sequences) in the original database. The team also developed methods to manage and consolidate the large number of partial results that get produced. Dual segmentation allows for massive parallelization, which lifts the scaling ceiling in exciting ways. BLAST jobs that hitherto failed or slogged inefficiently to completion now finish with speeds that characteristically reduce wallclock time from 27 days on 40 CPUs to a single day using 4104 tasks, each task utilizing eight CPUs and taking less than 7 minutes to complete. The massive increase in the number of tasks when running an analysis job with dual segmentation reduces the size, scope and execution time of each task. Besides significant speed of completion, additional benefits include fine-grained checkpointing and increased flexibility of job submission. "Trickling in" a swarm of individual small tasks tempers competition for CPU time in the shared HPC environment, and jobs submitted during quiet periods can complete in extraordinarily short time frames. The smaller task size also allows the use of older and less powerful hardware. The CDRH workhorse cluster was commissioned in 2010, yet its eight-core CPUs with only 24GB RAM work well in 2017 for these dual segmentation jobs. Finally, these techniques are excitingly friendly to budget conscious scientific research organizations where probabilistic algorithms such as BLAST might discourage attempts at greater certainty because single runs represent a major resource drain. If a job that used to take 24 days can now be completed in less than an hour or on a space available basis (which is the case at CDRH), repeated runs for more exhaustive analyses can be usefully contemplated.

Efficient Parallel Levenberg-Marquardt Model Fitting towards Real-Time Automated Parametric Imaging Microscopy

PubMed Central

Zhu, Xiang; Zhang, Dianwen

2013-01-01

We present a fast, accurate and robust parallel Levenberg-Marquardt minimization optimizer, GPU-LMFit, which is implemented on graphics processing unit for high performance scalable parallel model fitting processing. GPU-LMFit can provide a dramatic speed-up in massive model fitting analyses to enable real-time automated pixel-wise parametric imaging microscopy. We demonstrate the performance of GPU-LMFit for the applications in superresolution localization microscopy and fluorescence lifetime imaging microscopy. PMID:24130785

A 32-channel lattice transmission line array for parallel transmit and receive MRI at 7 tesla.

PubMed

Adriany, Gregor; Auerbach, Edward J; Snyder, Carl J; Gözübüyük, Ark; Moeller, Steen; Ritter, Johannes; Van de Moortele, Pierre-François; Vaughan, Tommy; Uğurbil, Kâmil

2010-06-01

Transmit and receive RF coil arrays have proven to be particularly beneficial for ultra-high-field MR. Transmit coil arrays enable such techniques as B(1) (+) shimming to substantially improve transmit B(1) homogeneity compared to conventional volume coil designs, and receive coil arrays offer enhanced parallel imaging performance and SNR. Concentric coil arrangements hold promise for developing transceiver arrays incorporating large numbers of coil elements. At magnetic field strengths of 7 tesla and higher where the Larmor frequencies of interest can exceed 300 MHz, the coil array design must also overcome the problem of the coil conductor length approaching the RF wavelength. In this study, a novel concentric arrangement of resonance elements built from capacitively-shortened half-wavelength transmission lines is presented. This approach was utilized to construct an array with whole-brain coverage using 16 transceiver elements and 16 receive-only elements, resulting in a coil with a total of 16 transmit and 32 receive channels. (c) 2010 Wiley-Liss, Inc.

CMOS VLSI Layout and Verification of a SIMD Computer

NASA Technical Reports Server (NTRS)

Zheng, Jianqing

1996-01-01

A CMOS VLSI layout and verification of a 3 x 3 processor parallel computer has been completed. The layout was done using the MAGIC tool and the verification using HSPICE. Suggestions for expanding the computer into a million processor network are presented. Many problems that might be encountered when implementing a massively parallel computer are discussed.

Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by routing through transporter nodes

DOEpatents

Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

2010-11-16

A massively parallel computer system contains an inter-nodal communications network of node-to-node links. An automated routing strategy routes packets through one or more intermediate nodes of the network to reach a destination. Some packets are constrained to be routed through respective designated transporter nodes, the automated routing strategy determining a path from a respective source node to a respective transporter node, and from a respective transporter node to a respective destination node. Preferably, the source node chooses a routing policy from among multiple possible choices, and that policy is followed by all intermediate nodes. The use of transporter nodes allows greater flexibility in routing.

Ordered fast fourier transforms on a massively parallel hypercube multiprocessor

NASA Technical Reports Server (NTRS)

Tong, Charles; Swarztrauber, Paul N.

1989-01-01

Design alternatives for ordered Fast Fourier Transformation (FFT) algorithms were examined on massively parallel hypercube multiprocessors such as the Connection Machine. Particular emphasis is placed on reducing communication which is known to dominate the overall computing time. To this end, the order and computational phases of the FFT were combined, and the sequence to processor maps that reduce communication were used. The class of ordered transforms is expanded to include any FFT in which the order of the transform is the same as that of the input sequence. Two such orderings are examined, namely, standard-order and A-order which can be implemented with equal ease on the Connection Machine where orderings are determined by geometries and priorities. If the sequence has N = 2 exp r elements and the hypercube has P = 2 exp d processors, then a standard-order FFT can be implemented with d + r/2 + 1 parallel transmissions. An A-order sequence can be transformed with 2d - r/2 parallel transmissions which is r - d + 1 fewer than the standard order. A parallel method for computing the trigonometric coefficients is presented that does not use trigonometric functions or interprocessor communication. A performance of 0.9 GFLOPS was obtained for an A-order transform on the Connection Machine.

Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics

PubMed Central

Liwo, Adam; Ołdziej, Stanisław; Czaplewski, Cezary; Kleinerman, Dana S.; Blood, Philip; Scheraga, Harold A.

2010-01-01

We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarse-grained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica-exchange molecular dynamics. With IBM BlueGene/P, about 50 % efficiency and 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino-acid residues in days of wall-clock time. PMID:20305729

Optimisation of a parallel ocean general circulation model

NASA Astrophysics Data System (ADS)

Beare, M. I.; Stevens, D. P.

1997-10-01

This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by a number of factors, for which optimisations are discussed and implemented. The resulting ocean code is portable and, in particular, allows science to be achieved on local workstations that could otherwise only be undertaken on state-of-the-art supercomputers.

Light emission from silicon: Some perspectives and applications

NASA Astrophysics Data System (ADS)

Fiory, A. T.; Ravindra, N. M.

2003-10-01

Research on efficient light emission from silicon devices is moving toward leading-edge advances in components for nano-optoelectronics and related areas. A silicon laser is being eagerly sought and may be at hand soon. A key advantage is in the use of silicon-based materials and processing, thereby using high yield and low-cost fabrication techniques. Anticipated applications include an optical emitter for integrated optical circuits, logic, memory, and interconnects; electro-optic isolators; massively parallel optical interconnects and cross connects for integrated circuit chips; lightwave components; high-power discrete and array emitters; and optoelectronic nanocell arrays for detecting biological and chemical agents. The new technical approaches resolve a basic issue with native interband electro-optical emission from bulk Si, which competes with nonradiative phonon- and defect-mediated pathways for electron-hole recombination. Some of the new ways to enhance optical emission efficiency in Si diode devices rely on carrier confinement, including defect and strain engineering in the bulk material. Others use Si nanocrystallites, nanowires, and alloying with Ge and crystal strain methods to achieve the carrier confinement required to boost radiative recombination efficiency. Another approach draws on the considerable progress that has been made in high-efficiency, solar-cell design and uses the reciprocity between photo- and light-emitting diodes. Important advances are also being made with silicon-oxide materials containing optically active rare-earth impurities.

Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

PubMed

Ozer, Abdullah; Tome, Jacob M; Friedman, Robin C; Gheba, Dan; Schroth, Gary P; Lis, John T

2015-08-01

Because RNA-protein interactions have a central role in a wide array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay that couples sequencing on an Illumina GAIIx genome analyzer with the quantitative assessment of protein-RNA interactions. This assay is able to analyze interactions between one or possibly several proteins with millions of different RNAs in a single experiment. We have successfully used HiTS-RAP to analyze interactions of the EGFP and negative elongation factor subunit E (NELF-E) proteins with their corresponding canonical and mutant RNA aptamers. Here we provide a detailed protocol for HiTS-RAP that can be completed in about a month (8 d hands-on time). This includes the preparation and testing of recombinant proteins and DNA templates, clustering DNA templates on a flowcell, HiTS and protein binding with a GAIIx instrument, and finally data analysis. We also highlight aspects of HiTS-RAP that can be further improved and points of comparison between HiTS-RAP and two other recently developed methods, quantitative analysis of RNA on a massively parallel array (RNA-MaP) and RNA Bind-n-Seq (RBNS), for quantitative analysis of RNA-protein interactions.

Infrared technology for satellite power conversion. [antenna arrays and bolometers

NASA Technical Reports Server (NTRS)

Campbell, D. P.; Gouker, M. A.; Gallagher, J. J.

1984-01-01

Successful fabrication of bismuth bolometers led to the observation of antenna action rom array elements. Fabrication of the best antennas arrays was made more facile with finding that increased argon flow during the dc sputtering produced more uniform bismuth films and bonding to antennas must be done with the substrate temperaure below 100 C. Higher temperatures damaged the bolometers. During the testing of the antennas, it was found that the use of a quasi-optical system provided a uniform radiation field. Groups of antennas were bonded in series and in parallel with the parallel configuration showing the greater response.

Range and egomotion estimation from compound photodetector arrays with parallel optical axis using optical flow techniques.

PubMed

Chahl, J S

2014-01-20

This paper describes an application for arrays of narrow-field-of-view sensors with parallel optical axes. These devices exhibit some complementary characteristics with respect to conventional perspective projection or angular projection imaging devices. Conventional imaging devices measure rotational egomotion directly by measuring the angular velocity of the projected image. Translational egomotion cannot be measured directly by these devices because the induced image motion depends on the unknown range of the viewed object. On the other hand, a known translational motion generates image velocities which can be used to recover the ranges of objects and hence the three-dimensional (3D) structure of the environment. A new method is presented for computing egomotion and range using the properties of linear arrays of independent narrow-field-of-view optical sensors. An approximate parallel projection can be used to measure translational egomotion in terms of the velocity of the image. On the other hand, a known rotational motion of the paraxial sensor array generates image velocities, which can be used to recover the 3D structure of the environment. Results of tests of an experimental array confirm these properties.

Impact of the coupling effect and the configuration on a compact rectenna array

NASA Astrophysics Data System (ADS)

Rivière, J.; Douyere, A.; Luk, J. D. Lan Sun

2014-10-01

This paper proposes an experimental study of the coupling effect of a rectenna array. The rectifying antenna consists of a compact and efficient rectifying circuit in a series topology, coupled with a small metamaterial-inspired antenna. The measurements are investigated in the X plane on the rectenna array's behavior, with series and parallel DC- combining configuration of two and three spaced rectennas from 3 cm to 10 cm. This study shows that the maximum efficiency is reached for the series configuration, with a resistive load of 10 kQ. The optimal distance is not significant for series or parallel configuration. Then, a comparison between a rectenna array with non-optimal mutual coupling and a more traditional patch rectenna is performed. Finally, a practical application is tested to demonstrate the effectiveness of such small rectenna array.

Afterburner Performance of Circular V-Gutters and a Sector of Parallel V-Gutters for a Range of Inlet Temperatures to 1255 K (1800 F)

NASA Technical Reports Server (NTRS)

Brandstetter, J. Robert; Reck, Gregory M.

1973-01-01

Combustion tests of two V-gutter types were conducted in a 19.25-in. diameter duct using vitiated air. Fuel spraybars were mounted in line with the V-gutters. Combustor length was set by flame-quench water sprays which were part of a calorimeter for measuring combustion efficiency. Although the levels of performance of the parallel and circular array afterburners were different, the trends with geometry variations were consistent. Therefore, parallel arrays can be used for evaluating V-gutter geometry effects on combustion performance. For both arrays, the highest inlet temperature produced combustion efficiencies near 100 percent. A 5-in. spraybar - to - V-gutter spacing gave higher efficiency and better lean blowout performance than a spacing twice as large. Gutter durability was good.

Observation of layered antiferromagnetism in self-assembled parallel NiSi nanowire arrays on Si(110) by spin-polarized scanning tunneling spectromicroscopy

NASA Astrophysics Data System (ADS)

Hong, Ie-Hong; Hsu, Hsin-Zan

2018-03-01

The layered antiferromagnetism of parallel nanowire (NW) arrays self-assembled on Si(110) have been observed at room temperature by direct imaging of both the topographies and magnetic domains using spin-polarized scanning tunneling microscopy/spectroscopy (SP-STM/STS). The topographic STM images reveal that the self-assembled unidirectional and parallel NiSi NWs grow into the Si(110) substrate along the [\\bar{1}10] direction (i.e. the endotaxial growth) and exhibit multiple-layer growth. The spatially-resolved SP-STS maps show that these parallel NiSi NWs of different heights produce two opposite magnetic domains, depending on the heights of either even or odd layers in the layer stack of the NiSi NWs. This layer-wise antiferromagnetic structure can be attributed to an antiferromagnetic interlayer exchange coupling between the adjacent layers in the multiple-layer NiSi NW with a B2 (CsCl-type) crystal structure. Such an endotaxial heterostructure of parallel magnetic NiSi NW arrays with a layered antiferromagnetic ordering in Si(110) provides a new and important perspective for the development of novel Si-based spintronic nanodevices.

Imaging Stellar Surface with The CHARA Array

NASA Astrophysics Data System (ADS)

Schaefer, Gail

2018-04-01

I will provide an overview of results on imaging stellar surfaces with the CHARA Array. These include imaging gravity darkening on rapid rotators, starspots on magnetically active stars, convective cells on red supergiants, and stellar winds from massive stars. In binary systems, the CHARA Array has been used to observe tidal distortions from Roche lobe filling in interactive binaries, transiting companions as they move through eclipse, and the angular expansion of novae explosions. I will discuss the impact of these results in an astrophysical context.

Photovoltaic cell array

NASA Technical Reports Server (NTRS)

Eliason, J. T. (Inventor)

1976-01-01

A photovoltaic cell array consisting of parallel columns of silicon filaments is described. Each fiber is doped to produce an inner region of one polarity type and an outer region of an opposite polarity type to thereby form a continuous radial semi conductor junction. Spaced rows of electrical contacts alternately connect to the inner and outer regions to provide a plurality of electrical outputs which may be combined in parallel or in series.

Graphics Processing Unit Assisted Thermographic Compositing

NASA Technical Reports Server (NTRS)

Ragasa, Scott; McDougal, Matthew; Russell, Sam

2012-01-01

Objective: To develop a software application utilizing general purpose graphics processing units (GPUs) for the analysis of large sets of thermographic data. Background: Over the past few years, an increasing effort among scientists and engineers to utilize the GPU in a more general purpose fashion is allowing for supercomputer level results at individual workstations. As data sets grow, the methods to work them grow at an equal, and often great, pace. Certain common computations can take advantage of the massively parallel and optimized hardware constructs of the GPU to allow for throughput that was previously reserved for compute clusters. These common computations have high degrees of data parallelism, that is, they are the same computation applied to a large set of data where the result does not depend on other data elements. Signal (image) processing is one area were GPUs are being used to greatly increase the performance of certain algorithms and analysis techniques. Technical Methodology/Approach: Apply massively parallel algorithms and data structures to the specific analysis requirements presented when working with thermographic data sets.

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

PubMed

Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

2016-08-05

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Particle simulation of plasmas on the massively parallel processor

NASA Technical Reports Server (NTRS)

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

1987-01-01

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

A Massively Parallel Computational Method of Reading Index Files for SOAPsnv.

PubMed

Zhu, Xiaoqian; Peng, Shaoliang; Liu, Shaojie; Cui, Yingbo; Gu, Xiang; Gao, Ming; Fang, Lin; Fang, Xiaodong

2015-12-01

SOAPsnv is the software used for identifying the single nucleotide variation in cancer genes. However, its performance is yet to match the massive amount of data to be processed. Experiments reveal that the main performance bottleneck of SOAPsnv software is the pileup algorithm. The original pileup algorithm's I/O process is time-consuming and inefficient to read input files. Moreover, the scalability of the pileup algorithm is also poor. Therefore, we designed a new algorithm, named BamPileup, aiming to improve the performance of sequential read, and the new pileup algorithm implemented a parallel read mode based on index. Using this method, each thread can directly read the data start from a specific position. The results of experiments on the Tianhe-2 supercomputer show that, when reading data in a multi-threaded parallel I/O way, the processing time of algorithm is reduced to 3.9 s and the application program can achieve a speedup up to 100×. Moreover, the scalability of the new algorithm is also satisfying.

Quantum supercharger library: hyper-parallelism of the Hartree-Fock method.

PubMed

Fernandes, Kyle D; Renison, C Alicia; Naidoo, Kevin J

2015-07-05

We present here a set of algorithms that completely rewrites the Hartree-Fock (HF) computations common to many legacy electronic structure packages (such as GAMESS-US, GAMESS-UK, and NWChem) into a massively parallel compute scheme that takes advantage of hardware accelerators such as Graphical Processing Units (GPUs). The HF compute algorithm is core to a library of routines that we name the Quantum Supercharger Library (QSL). We briefly evaluate the QSL's performance and report that it accelerates a HF 6-31G Self-Consistent Field (SCF) computation by up to 20 times for medium sized molecules (such as a buckyball) when compared with mature Central Processing Unit algorithms available in the legacy codes in regular use by researchers. It achieves this acceleration by massive parallelization of the one- and two-electron integrals and optimization of the SCF and Direct Inversion in the Iterative Subspace routines through the use of GPU linear algebra libraries. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

The nightmare scenario: measuring the stochastic gravitational wave background from stalling massive black hole binaries with pulsar timing arrays

NASA Astrophysics Data System (ADS)

Dvorkin, Irina; Barausse, Enrico

2017-10-01

Massive black hole binaries, formed when galaxies merge, are among the primary sources of gravitational waves targeted by ongoing pulsar timing array (PTA) experiments and the upcoming space-based Laser Interferometer Space Antenna (LISA) interferometer. However, their formation and merger rates are still highly uncertain. Recent upper limits on the stochastic gravitational wave background obtained by PTAs are starting to be in marginal tension with theoretical models for the pairing and orbital evolution of these systems. This tension can be resolved by assuming that these binaries are more eccentric or interact more strongly with the environment (gas and stars) than expected, or by accounting for possible selection biases in the construction of the theoretical models. However, another (pessimistic) possibility is that these binaries do not merge at all, but stall at large (˜pc) separations. We explore this extreme scenario by using a semi-analytic galaxy formation model including massive black holes (isolated and in binaries), and show that future generations of PTAs will detect the stochastic gravitational wave background from the massive black hole binary population within 10-15 yr of observations, even in the `nightmare scenario' in which all binaries stall at the hardening radius. Moreover, we argue that this scenario is too pessimistic, because our model predicts the existence of a subpopulation of binaries with small mass ratios (q ≲ 10-3) that should merge within a Hubble time simply as a result of gravitational wave emission. This subpopulation will be observable with large signal-to-noise ratios by future PTAs thanks to next-generation radio telescopes such as Square Kilometre Array or Five-hundred-meter Aperture Spherical Telescope, and possibly by LISA.

Applications of Parallel Process HiMAP for Large Scale Multidisciplinary Problems

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.; Potsdam, Mark; Rodriguez, David; Kwak, Dochay (Technical Monitor)

2000-01-01

HiMAP is a three level parallel middleware that can be interfaced to a large scale global design environment for code independent, multidisciplinary analysis using high fidelity equations. Aerospace technology needs are rapidly changing. Computational tools compatible with the requirements of national programs such as space transportation are needed. Conventional computation tools are inadequate for modern aerospace design needs. Advanced, modular computational tools are needed, such as those that incorporate the technology of massively parallel processors (MPP).

Development and Applications of a Modular Parallel Process for Large Scale Fluid/Structures Problems

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.; Kwak, Dochan (Technical Monitor)

2002-01-01

A modular process that can efficiently solve large scale multidisciplinary problems using massively parallel supercomputers is presented. The process integrates disciplines with diverse physical characteristics by retaining the efficiency of individual disciplines. Computational domain independence of individual disciplines is maintained using a meta programming approach. The process integrates disciplines without affecting the combined performance. Results are demonstrated for large scale aerospace problems on several supercomputers. The super scalability and portability of the approach is demonstrated on several parallel computers.

Development and Applications of a Modular Parallel Process for Large Scale Fluid/Structures Problems

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.; Byun, Chansup; Kwak, Dochan (Technical Monitor)

2001-01-01

A modular process that can efficiently solve large scale multidisciplinary problems using massively parallel super computers is presented. The process integrates disciplines with diverse physical characteristics by retaining the efficiency of individual disciplines. Computational domain independence of individual disciplines is maintained using a meta programming approach. The process integrates disciplines without affecting the combined performance. Results are demonstrated for large scale aerospace problems on several supercomputers. The super scalability and portability of the approach is demonstrated on several parallel computers.

Adaptive parallel logic networks

NASA Technical Reports Server (NTRS)

Martinez, Tony R.; Vidal, Jacques J.

1988-01-01

Adaptive, self-organizing concurrent systems (ASOCS) that combine self-organization with massive parallelism for such applications as adaptive logic devices, robotics, process control, and system malfunction management, are presently discussed. In ASOCS, an adaptive network composed of many simple computing elements operating in combinational and asynchronous fashion is used and problems are specified by presenting if-then rules to the system in the form of Boolean conjunctions. During data processing, which is a different operational phase from adaptation, the network acts as a parallel hardware circuit.

Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

DOE Office of Scientific and Technical Information (OSTI.GOV)

Candel, A.; Kabel, A.; Lee, L.

In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

Excitation of a Parallel Plate Waveguide by an Array of Rectangular Waveguides

NASA Technical Reports Server (NTRS)

Rengarajan, Sembiam

2011-01-01

This work addresses the problem of excitation of a parallel plate waveguide by an array of rectangular waveguides that arises in applications such as the continuous transverse stub (CTS) antenna and dual-polarized parabolic cylindrical reflector antennas excited by a scanning line source. In order to design the junction region between the parallel plate waveguide and the linear array of rectangular waveguides, waveguide sizes have to be chosen so that the input match is adequate for the range of scan angles for both polarizations. Electromagnetic wave scattered by the junction of a parallel plate waveguide by an array of rectangular waveguides is analyzed by formulating coupled integral equations for the aperture electric field at the junction. The integral equations are solved by the method of moments. In order to make the computational process efficient and accurate, the method of weighted averaging was used to evaluate rapidly oscillating integrals encountered in the moment matrix. In addition, the real axis spectral integral is evaluated in a deformed contour for speed and accuracy. The MoM results for a large finite array have been validated by comparing its reflection coefficients with corresponding results for an infinite array generated by the commercial finite element code, HFSS. Once the aperture electric field is determined by MoM, the input reflection coefficients at each waveguide port, and coupling for each polarization over the range of useful scan angles, are easily obtained. Results for the input impedance and coupling characteristics for both the vertical and horizontal polarizations are presented over a range of scan angles. It is shown that the scan range is limited to about 35 for both polarizations and therefore the optimum waveguide is a square of size equal to about 0.62 free space wavelength.

Dynamic load balancing of applications

DOEpatents

Wheat, Stephen R.

1997-01-01

An application-level method for dynamically maintaining global load balance on a parallel computer, particularly on massively parallel MIMD computers. Global load balancing is achieved by overlapping neighborhoods of processors, where each neighborhood performs local load balancing. The method supports a large class of finite element and finite difference based applications and provides an automatic element management system to which applications are easily integrated.

Practical aspects of prestack depth migration with finite differences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ober, C.C.; Oldfield, R.A.; Womble, D.E.

1997-07-01

Finite-difference, prestack, depth migrations offers significant improvements over Kirchhoff methods in imaging near or under salt structures. The authors have implemented a finite-difference prestack depth migration algorithm for use on massively parallel computers which is discussed. The image quality of the finite-difference scheme has been investigated and suggested improvements are discussed. In this presentation, the authors discuss an implicit finite difference migration code, called Salvo, that has been developed through an ACTI (Advanced Computational Technology Initiative) joint project. This code is designed to be efficient on a variety of massively parallel computers. It takes advantage of both frequency and spatialmore » parallelism as well as the use of nodes dedicated to data input/output (I/O). Besides giving an overview of the finite-difference algorithm and some of the parallelism techniques used, migration results using both Kirchhoff and finite-difference migration will be presented and compared. The authors start out with a very simple Cartoon model where one can intuitively see the multiple travel paths and some of the potential problems that will be encountered with Kirchhoff migration. More complex synthetic models as well as results from actual seismic data from the Gulf of Mexico will be shown.« less

Massively Parallel Dantzig-Wolfe Decomposition Applied to Traffic Flow Scheduling

NASA Technical Reports Server (NTRS)

Rios, Joseph Lucio; Ross, Kevin

2009-01-01

Optimal scheduling of air traffic over the entire National Airspace System is a computationally difficult task. To speed computation, Dantzig-Wolfe decomposition is applied to a known linear integer programming approach for assigning delays to flights. The optimization model is proven to have the block-angular structure necessary for Dantzig-Wolfe decomposition. The subproblems for this decomposition are solved in parallel via independent computation threads. Experimental evidence suggests that as the number of subproblems/threads increases (and their respective sizes decrease), the solution quality, convergence, and runtime improve. A demonstration of this is provided by using one flight per subproblem, which is the finest possible decomposition. This results in thousands of subproblems and associated computation threads. This massively parallel approach is compared to one with few threads and to standard (non-decomposed) approaches in terms of solution quality and runtime. Since this method generally provides a non-integral (relaxed) solution to the original optimization problem, two heuristics are developed to generate an integral solution. Dantzig-Wolfe followed by these heuristics can provide a near-optimal (sometimes optimal) solution to the original problem hundreds of times faster than standard (non-decomposed) approaches. In addition, when massive decomposition is employed, the solution is shown to be more likely integral, which obviates the need for an integerization step. These results indicate that nationwide, real-time, high fidelity, optimal traffic flow scheduling is achievable for (at least) 3 hour planning horizons.

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madduri, Kamesh; Ediger, David; Jiang, Karl

2009-02-15

We present a new lock-free parallel algorithm for computing betweenness centralityof massive small-world networks. With minor changes to the data structures, ouralgorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in HPCS SSCA#2, a benchmark extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the Threadstorm processor, and a single-socket Sun multicore server with the UltraSPARC T2 processor. For a small-world network of 134 millionmore » vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.« less

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madduri, Kamesh; Ediger, David; Jiang, Karl

2009-05-29

We present a new lock-free parallel algorithm for computing betweenness centrality of massive small-world networks. With minor changes to the data structures, our algorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in the HPCS SSCA#2 Graph Analysis benchmark, which has been extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the ThreadStorm processor, and a single-socket Sun multicore server with the UltraSparc T2 processor.more » For a small-world network of 134 million vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.« less

Learning Quantitative Sequence-Function Relationships from Massively Parallel Experiments

NASA Astrophysics Data System (ADS)

Atwal, Gurinder S.; Kinney, Justin B.

2016-03-01

A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships—functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques for effectively measuring these relationships been developed. The advent of such "massively parallel" experiments presents an exciting opportunity for the concepts and methods of statistical physics to inform the study of biological systems. After reviewing these recent experimental advances, we focus on the problem of how to infer parametric models of sequence-function relationships from the data produced by these experiments. Specifically, we retrace and extend recent theoretical work showing that inference based on mutual information, not the standard likelihood-based approach, is often necessary for accurately learning the parameters of these models. Closely connected with this result is the emergence of "diffeomorphic modes"—directions in parameter space that are far less constrained by data than likelihood-based inference would suggest. Analogous to Goldstone modes in physics, diffeomorphic modes arise from an arbitrarily broken symmetry of the inference problem. An analytically tractable model of a massively parallel experiment is then described, providing an explicit demonstration of these fundamental aspects of statistical inference. This paper concludes with an outlook on the theoretical and computational challenges currently facing studies of quantitative sequence-function relationships.

Multifaceted free-space image distributor for optical interconnects in massively parrallel processing

NASA Astrophysics Data System (ADS)

Zhao, Feng; Frietman, Edward E. E.; Han, Zhong; Chen, Ray T.

1999-04-01

A characteristic feature of a conventional von Neumann computer is that computing power is delivered by a single processing unit. Although increasing the clock frequency improves the performance of the computer, the switching speed of the semiconductor devices and the finite speed at which electrical signals propagate along the bus set the boundaries. Architectures containing large numbers of nodes can solve this performance dilemma, with the comment that main obstacles in designing such systems are caused by difficulties to come up with solutions that guarantee efficient communications among the nodes. Exchanging data becomes really a bottleneck should al nodes be connected by a shared resource. Only optics, due to its inherent parallelism, could solve that bottleneck. Here, we explore a multi-faceted free space image distributor to be used in optical interconnects in massively parallel processing. In this paper, physical and optical models of the image distributor are focused on from diffraction theory of light wave to optical simulations. the general features and the performance of the image distributor are also described. The new structure of an image distributor and the simulations for it are discussed. From the digital simulation and experiment, it is found that the multi-faceted free space image distributing technique is quite suitable for free space optical interconnection in massively parallel processing and new structure of the multifaceted free space image distributor would perform better.

Computer Sciences and Data Systems, volume 2

NASA Technical Reports Server (NTRS)

1987-01-01

Topics addressed include: data storage; information network architecture; VHSIC technology; fiber optics; laser applications; distributed processing; spaceborne optical disk controller; massively parallel processors; and advanced digital SAR processors.

Digital Parallel Processor Array for Optimum Path Planning

NASA Technical Reports Server (NTRS)

Kremeny, Sabrina E. (Inventor); Fossum, Eric R. (Inventor); Nixon, Robert H. (Inventor)

1996-01-01

The invention computes the optimum path across a terrain or topology represented by an array of parallel processor cells interconnected between neighboring cells by links extending along different directions to the neighboring cells. Such an array is preferably implemented as a high-speed integrated circuit. The computation of the optimum path is accomplished by, in each cell, receiving stimulus signals from neighboring cells along corresponding directions, determining and storing the identity of a direction along which the first stimulus signal is received, broadcasting a subsequent stimulus signal to the neighboring cells after a predetermined delay time, whereby stimulus signals propagate throughout the array from a starting one of the cells. After propagation of the stimulus signal throughout the array, a master processor traces back from a selected destination cell to the starting cell along an optimum path of the cells in accordance with the identity of the directions stored in each of the cells.

Design considerations for parallel graphics libraries

NASA Technical Reports Server (NTRS)

Crockett, Thomas W.

1994-01-01

Applications which run on parallel supercomputers are often characterized by massive datasets. Converting these vast collections of numbers to visual form has proven to be a powerful aid to comprehension. For a variety of reasons, it may be desirable to provide this visual feedback at runtime. One way to accomplish this is to exploit the available parallelism to perform graphics operations in place. In order to do this, we need appropriate parallel rendering algorithms and library interfaces. This paper provides a tutorial introduction to some of the issues which arise in designing parallel graphics libraries and their underlying rendering algorithms. The focus is on polygon rendering for distributed memory message-passing systems. We illustrate our discussion with examples from PGL, a parallel graphics library which has been developed on the Intel family of parallel systems.

Directions in parallel programming: HPF, shared virtual memory and object parallelism in pC++

NASA Technical Reports Server (NTRS)

Bodin, Francois; Priol, Thierry; Mehrotra, Piyush; Gannon, Dennis

1994-01-01

Fortran and C++ are the dominant programming languages used in scientific computation. Consequently, extensions to these languages are the most popular for programming massively parallel computers. We discuss two such approaches to parallel Fortran and one approach to C++. The High Performance Fortran Forum has designed HPF with the intent of supporting data parallelism on Fortran 90 applications. HPF works by asking the user to help the compiler distribute and align the data structures with the distributed memory modules in the system. Fortran-S takes a different approach in which the data distribution is managed by the operating system and the user provides annotations to indicate parallel control regions. In the case of C++, we look at pC++ which is based on a concurrent aggregate parallel model.

Multifrequency Ultra-High Resolution Miniature Scanning Microscope Using Microchannel And Solid-State Sensor Technologies And Method For Scanning Samples

NASA Technical Reports Server (NTRS)

Wang, Yu (Inventor)

2006-01-01

A miniature, ultra-high resolution, and color scanning microscope using microchannel and solid-state technology that does not require focus adjustment. One embodiment includes a source of collimated radiant energy for illuminating a sample, a plurality of narrow angle filters comprising a microchannel structure to permit the passage of only unscattered radiant energy through the microchannels with some portion of the radiant energy entering the microchannels from the sample, a solid-state sensor array attached to the microchannel structure, the microchannels being aligned with an element of the solid-state sensor array, that portion of the radiant energy entering the microchannels parallel to the microchannel walls travels to the sensor element generating an electrical signal from which an image is reconstructed by an external device, and a moving element for movement of the microchannel structure relative to the sample. Discloses a method for scanning samples whereby the sensor array elements trace parallel paths that are arbitrarily close to the parallel paths traced by other elements of the array.

Low-cost silicon solar array project environmental hail model for assessing risk to solar collectors

NASA Technical Reports Server (NTRS)

Gonzalez, C.

1977-01-01

The probability of solar arrays being struck by hailstones of various sizes as a function of geographic location and service life was assessed. The study complements parallel studies of solar array sensitivity to hail damage, the final objective being an estimate of the most cost effective level for solar array hail protection.

Digitally programmable signal generator and method

DOEpatents

Priatko, G.J.; Kaskey, J.A.

1989-11-14

Disclosed is a digitally programmable waveform generator for generating completely arbitrary digital or analog waveforms from very low frequencies to frequencies in the gigasample per second range. A memory array with multiple parallel outputs is addressed; then the parallel output data is latched into buffer storage from which it is serially multiplexed out at a data rate many times faster than the access time of the memory array itself. While data is being multiplexed out serially, the memory array is accessed with the next required address and presents its data to the buffer storage before the serial multiplexing of the last group of data is completed, allowing this new data to then be latched into the buffer storage for smooth continuous serial data output. In a preferred implementation, a plurality of these serial data outputs are paralleled to form the input to a digital to analog converter, providing a programmable analog output. 6 figs.

Digitally programmable signal generator and method

DOEpatents

Priatko, Gordon J.; Kaskey, Jeffrey A.

1989-01-01

A digitally programmable waveform generator for generating completely arbitrary digital or analog waveforms from very low frequencies to frequencies in the gigasample per second range. A memory array with multiple parallel outputs is addressed; then the parallel output data is latched into buffer storage from which it is serially multiplexed out at a data rate many times faster than the access time of the memory array itself. While data is being multiplexed out serially, the memory array is accessed with the next required address and presents its data to the buffer storage before the serial multiplexing of the last group of data is completed, allowing this new data to then be latched into the buffer storage for smooth continuous serial data output. In a preferred implementation, a plurality of these serial data outputs are paralleled to form the input to a digital to analog converter, providing a programmable analog output.

SciSpark's SRDD : A Scientific Resilient Distributed Dataset for Multidimensional Data

NASA Astrophysics Data System (ADS)

Palamuttam, R. S.; Wilson, B. D.; Mogrovejo, R. M.; Whitehall, K. D.; Mattmann, C. A.; McGibbney, L. J.; Ramirez, P.

2015-12-01

Remote sensing data and climate model output are multi-dimensional arrays of massive sizes locked away in heterogeneous file formats (HDF5/4, NetCDF 3/4) and metadata models (HDF-EOS, CF) making it difficult to perform multi-stage, iterative science processing since each stage requires writing and reading data to and from disk. We have developed SciSpark, a robust Big Data framework, that extends ApacheTM Spark for scaling scientific computations. Apache Spark improves the map-reduce implementation in ApacheTM Hadoop for parallel computing on a cluster, by emphasizing in-memory computation, "spilling" to disk only as needed, and relying on lazy evaluation. Central to Spark is the Resilient Distributed Dataset (RDD), an in-memory distributed data structure that extends the functional paradigm provided by the Scala programming language. However, RDDs are ideal for tabular or unstructured data, and not for highly dimensional data. The SciSpark project introduces the Scientific Resilient Distributed Dataset (sRDD), a distributed-computing array structure which supports iterative scientific algorithms for multidimensional data. SciSpark processes data stored in NetCDF and HDF files by partitioning them across time or space and distributing the partitions among a cluster of compute nodes. We show usability and extensibility of SciSpark by implementing distributed algorithms for geospatial operations on large collections of multi-dimensional grids. In particular we address the problem of scaling an automated method for finding Mesoscale Convective Complexes. SciSpark provides a tensor interface to support the pluggability of different matrix libraries. We evaluate performance of the various matrix libraries in distributed pipelines, such as Nd4jTM and BreezeTM. We detail the architecture and design of SciSpark, our efforts to integrate climate science algorithms, parallel ingest and partitioning (sharding) of A-Train satellite observations from model grids. These solutions are encompassed in SciSpark, an open-source software framework for distributed computing on scientific data.

Progress of the Swedish-Australian research collaboration on uncooled smart IR sensors

NASA Astrophysics Data System (ADS)

Liddiard, Kevin C.; Ringh, Ulf; Jansson, Christer; Reinhold, Olaf

1998-10-01

Progress is reported on the development of uncooled microbolometer IR focal plane detector arrays (IRFPDA) under a research collaboration between the Swedish Defence Research Establishment (FOA), and the Defence Science and Technology Organization (DSTO), Australia. The paper describes current focal plane detector arrays designed by Electro-optic Sensor Design (EOSD) for readout circuits developed by FOA. The readouts are fabricated in 0.8 micrometer CMOS, and have a novel signal conditioning and 16 bit parallel ADC design. The arrays are post-processed at DSTO on wafers supplied by FOA. During the past year array processing has been carried out at a new microengineering facility at DSTO, Salisbury, South Australia. A number of small format 16 X 16 arrays have been delivered to FOA for evaluation, and imaging has been demonstrated with these arrays. A 320 X 240 readout with 320 parallel 16 bit ADCs has been developed and IRFPDAs for this readout have been fabricated and are currently being evaluated.

Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by semi-randomly varying routing policies for different packets

DOEpatents

Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

2010-11-23

A massively parallel computer system contains an inter-nodal communications network of node-to-node links. Nodes vary a choice of routing policy for routing data in the network in a semi-random manner, so that similarly situated packets are not always routed along the same path. Semi-random variation of the routing policy tends to avoid certain local hot spots of network activity, which might otherwise arise using more consistent routing determinations. Preferably, the originating node chooses a routing policy for a packet, and all intermediate nodes in the path route the packet according to that policy. Policies may be rotated on a round-robin basis, selected by generating a random number, or otherwise varied.

Applications of massively parallel computers in telemetry processing

NASA Technical Reports Server (NTRS)

El-Ghazawi, Tarek A.; Pritchard, Jim; Knoble, Gordon

1994-01-01

Telemetry processing refers to the reconstruction of full resolution raw instrumentation data with artifacts, of space and ground recording and transmission, removed. Being the first processing phase of satellite data, this process is also referred to as level-zero processing. This study is aimed at investigating the use of massively parallel computing technology in providing level-zero processing to spaceflights that adhere to the recommendations of the Consultative Committee on Space Data Systems (CCSDS). The workload characteristics, of level-zero processing, are used to identify processing requirements in high-performance computing systems. An example of level-zero functions on a SIMD MPP, such as the MasPar, is discussed. The requirements in this paper are based in part on the Earth Observing System (EOS) Data and Operation System (EDOS).

Genetic heterogeneity of RPMI-8402, a T-acute lymphoblastic leukemia cell line

PubMed Central

STOCZYNSKA-FIDELUS, EWELINA; PIASKOWSKI, SYLWESTER; PAWLOWSKA, ROZA; SZYBKA, MALGORZATA; PECIAK, JOANNA; HULAS-BIGOSZEWSKA, KRYSTYNA; WINIECKA-KLIMEK, MARTA; RIESKE, PIOTR

2016-01-01

Thorough examination of genetic heterogeneity of cell lines is uncommon. In order to address this issue, the present study analyzed the genetic heterogeneity of RPMI-8402, a T-acute lymphoblastic leukemia (T-ALL) cell line. For this purpose, traditional techniques such as fluorescence in situ hybridization and immunocytochemistry were used, in addition to more advanced techniques, including cell sorting, Sanger sequencing and massive parallel sequencing. The results indicated that the RPMI-8402 cell line consists of several genetically different cell subpopulations. Furthermore, massive parallel sequencing of RPMI-8402 provided insight into the evolution of T-ALL carcinogenesis, since this cell line exhibited the genetic heterogeneity typical of T-ALL. Therefore, the use of cell lines for drug testing in future studies may aid the progress of anticancer drug research. PMID:26870252

Big data mining analysis method based on cloud computing

NASA Astrophysics Data System (ADS)

Cai, Qing Qiu; Cui, Hong Gang; Tang, Hao

2017-08-01

Information explosion era, large data super-large, discrete and non-(semi) structured features have gone far beyond the traditional data management can carry the scope of the way. With the arrival of the cloud computing era, cloud computing provides a new technical way to analyze the massive data mining, which can effectively solve the problem that the traditional data mining method cannot adapt to massive data mining. This paper introduces the meaning and characteristics of cloud computing, analyzes the advantages of using cloud computing technology to realize data mining, designs the mining algorithm of association rules based on MapReduce parallel processing architecture, and carries out the experimental verification. The algorithm of parallel association rule mining based on cloud computing platform can greatly improve the execution speed of data mining.

Hybrid massively parallel fast sweeping method for static Hamilton-Jacobi equations

NASA Astrophysics Data System (ADS)

Detrixhe, Miles; Gibou, Frédéric

2016-10-01

The fast sweeping method is a popular algorithm for solving a variety of static Hamilton-Jacobi equations. Fast sweeping algorithms for parallel computing have been developed, but are severely limited. In this work, we present a multilevel, hybrid parallel algorithm that combines the desirable traits of two distinct parallel methods. The fine and coarse grained components of the algorithm take advantage of heterogeneous computer architecture common in high performance computing facilities. We present the algorithm and demonstrate its effectiveness on a set of example problems including optimal control, dynamic games, and seismic wave propagation. We give results for convergence, parallel scaling, and show state-of-the-art speedup values for the fast sweeping method.

PFLOTRAN User Manual: A Massively Parallel Reactive Flow and Transport Model for Describing Surface and Subsurface Processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lichtner, Peter C.; Hammond, Glenn E.; Lu, Chuan

PFLOTRAN solves a system of generally nonlinear partial differential equations describing multi-phase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops (e.g. Hammond et al., 2011). Parallelization is achieved through domain decomposition using the PETSc (Portable Extensible Toolkit for Scientific Computation) libraries for the parallelization framework (Balay et al., 1997). PFLOTRAN has been developed from the ground up for parallel scalability and has been run on up to 218 processor cores with problem sizes up to 2 billion degrees of freedom. Writtenmore » in object oriented Fortran 90, the code requires the latest compilers compatible with Fortran 2003. At the time of this writing this requires gcc 4.7.x, Intel 12.1.x and PGC compilers. As a requirement of running problems with a large number of degrees of freedom, PFLOTRAN allows reading input data that is too large to fit into memory allotted to a single processor core. The current limitation to the problem size PFLOTRAN can handle is the limitation of the HDF5 file format used for parallel IO to 32 bit integers. Noting that 2 32 = 4; 294; 967; 296, this gives an estimate of the maximum problem size that can be currently run with PFLOTRAN. Hopefully this limitation will be remedied in the near future.« less

Parallel manipulation of individual magnetic microbeads for lab-on-a-chip applications

NASA Astrophysics Data System (ADS)

Peng, Zhengchun

Many scientists and engineers are turning to lab-on-a-chip systems for faster and cheaper analysis of chemical reactions and biomolecular interactions. A common approach that facilitates the handling of reagents and biomolecules in these systems utilizes micro/nano beads as the solid carrier. Physical manipulation, such as assembly, transport, sorting, and tweezing, of beads on a chip represents an essential step for fully utilizing their potentials in a wide spectrum of bead-based analysis. Previous work demonstrated manipulation of either an ensemble of beads without individual control, or single beads but lacks the capability for parallel operation. Parallel manipulation of individual beads is required to meet the demand for high-throughput and location-specific analysis. In this work, we introduced two methods for parallel manipulation of individual magnetic microbeads, which can serve as effective lab-on-a-chip platforms and/or efficient analytic tools. The first method employs arrays of soft ferromagnetic patterns fabricated inside a microfluidic channel and subjected to an external magnetic field. We demonstrated that the system can be used to assemble individual beads (1-3 mum) from a flow of suspended beads into a regular array on the chip, hence improving the integrated electrochemical detection of biomolecules bound to the bead surface. By rotating the external field, the assembled microbeads can be remotely controlled with synchronized, high-speed circular motion around individual soft magnets on the chip. We employed this manipulation mode for efficient sample mixing in continuous microflow. Furthermore, we discovered a simple but effective way of transporting the microbeads on the chip by varying the strength of the local bias field within a revolution of the external field. In addition, selective transport of microbeads with different size was realized, providing a platform for effective on-chip sample separation and offering the potential for multiplexing capability. The second method integrates magnetic and dielectrophoretic manipulations of the same microbeads. The device combines tapered conducting wires and fingered electrodes to generate desirable magnetic and electric fields, respectively. By externally programming the magnetic attraction and dielectrophoretic repulsion forces, out-of-plane oscillation of the microbeads across the channel height was realized. This manipulation mode can facilitate the interaction between the beads with multiple layers of sample fluid inside the channel. We further demonstrated the tweezing of microbeads in liquid with high spatial resolutions, i.e., from submicrometer to nanometer range, by fine-tuning the net force from magnetic attraction and dielectrophoretic repulsion of the beads. The highresolution control of the out-of-plane motion of the microbeads led to the invention of massively parallel biomolecular tweezers. We believe the maturation of bead-based microtweezers will revolutionize the state-of-art tools currently used for single cell and single molecule studies.

Large-Scale, Parallel, Multi-Sensor Atmospheric Data Fusion Using Cloud Computing

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Manipon, G.; Hua, H.; Fetzer, E.

2013-05-01

NASA's Earth Observing System (EOS) is an ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the "A-Train" platforms (AIRS, AMSR-E, MODIS, MISR, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over decades. Moving to multi-sensor, long-duration analyses of important climate variables presents serious challenges for large-scale data mining and fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another (MODIS), and to a model (ECMWF), stratify the comparisons using a classification of the "cloud scenes" from CloudSat, and repeat the entire analysis over 10 years of data. To efficiently assemble such datasets, we are utilizing Elastic Computing in the Cloud and parallel map/reduce-based algorithms. However, these problems are Data Intensive computing so the data transfer times and storage costs (for caching) are key issues. SciReduce is a Hadoop-like parallel analysis system, programmed in parallel python, that is designed from the ground up for Earth science. SciReduce executes inside VMWare images and scales to any number of nodes in the Cloud. Unlike Hadoop, SciReduce operates on bundles of named numeric arrays, which can be passed in memory or serialized to disk in netCDF4 or HDF5. Figure 1 shows the architecture of the full computational system, with SciReduce at the core. Multi-year datasets are automatically "sharded" by time and space across a cluster of nodes so that years of data (millions of files) can be processed in a massively parallel way. Input variables (arrays) are pulled on-demand into the Cloud using OPeNDAP URLs or other subsetting services, thereby minimizing the size of the cached input and intermediate datasets. We are using SciReduce to automate the production of multiple versions of a ten-year A-Train water vapor climatology under a NASA MEASURES grant. We will present the architecture of SciReduce, describe the achieved "clock time" speedups in fusing datasets on our own nodes and in the Cloud, and discuss the Cloud cost tradeoffs for storage, compute, and data transfer. We will also present a concept/prototype for staging NASA's A-Train Atmospheric datasets (Levels 2 & 3) in the Amazon Cloud so that any number of compute jobs can be executed "near" the multi-sensor data. Given such a system, multi-sensor climate studies over 10-20 years of data could be performed in an efficient way, with the researcher paying only his own Cloud compute bill.; Figure 1 -- Architecture.

Large-Scale, Parallel, Multi-Sensor Atmospheric Data Fusion Using Cloud Computing

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Manipon, G.; Hua, H.; Fetzer, E. J.

2013-12-01

NASA's Earth Observing System (EOS) is an ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the 'A-Train' platforms (AIRS, AMSR-E, MODIS, MISR, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over decades. Moving to multi-sensor, long-duration analyses of important climate variables presents serious challenges for large-scale data mining and fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another (MODIS), and to a model (MERRA), stratify the comparisons using a classification of the 'cloud scenes' from CloudSat, and repeat the entire analysis over 10 years of data. To efficiently assemble such datasets, we are utilizing Elastic Computing in the Cloud and parallel map/reduce-based algorithms. However, these problems are Data Intensive computing so the data transfer times and storage costs (for caching) are key issues. SciReduce is a Hadoop-like parallel analysis system, programmed in parallel python, that is designed from the ground up for Earth science. SciReduce executes inside VMWare images and scales to any number of nodes in the Cloud. Unlike Hadoop, SciReduce operates on bundles of named numeric arrays, which can be passed in memory or serialized to disk in netCDF4 or HDF5. Figure 1 shows the architecture of the full computational system, with SciReduce at the core. Multi-year datasets are automatically 'sharded' by time and space across a cluster of nodes so that years of data (millions of files) can be processed in a massively parallel way. Input variables (arrays) are pulled on-demand into the Cloud using OPeNDAP URLs or other subsetting services, thereby minimizing the size of the cached input and intermediate datasets. We are using SciReduce to automate the production of multiple versions of a ten-year A-Train water vapor climatology under a NASA MEASURES grant. We will present the architecture of SciReduce, describe the achieved 'clock time' speedups in fusing datasets on our own compute nodes and in the public Cloud, and discuss the Cloud cost tradeoffs for storage, compute, and data transfer. We will also present a concept/prototype for staging NASA's A-Train Atmospheric datasets (Levels 2 & 3) in the Amazon Cloud so that any number of compute jobs can be executed 'near' the multi-sensor data. Given such a system, multi-sensor climate studies over 10-20 years of data could be performed in an efficient way, with the researcher paying only his own Cloud compute bill. SciReduce Architecture

Microchannel cross load array with dense parallel input

DOEpatents

Swierkowski, Stefan P.

2004-04-06

An architecture or layout for microchannel arrays using T or Cross (+) loading for electrophoresis or other injection and separation chemistry that are performed in microfluidic configurations. This architecture enables a very dense layout of arrays of functionally identical shaped channels and it also solves the problem of simultaneously enabling efficient parallel shapes and biasing of the input wells, waste wells, and bias wells at the input end of the separation columns. One T load architecture uses circular holes with common rows, but not columns, which allows the flow paths for each channel to be identical in shape, using multiple mirror image pieces. Another T load architecture enables the access hole array to be formed on a biaxial, collinear grid suitable for EDM micromachining (square holes), with common rows and columns.

High-resolution microcontact printing and transfer of massive arrays of microorganisms on planar and compartmentalized nanoporous aluminium oxide.

PubMed

Ingham, Colin; Bomer, Johan; Sprenkels, Ad; van den Berg, Albert; de Vos, Willem; van Hylckama Vlieg, Johan

2010-06-07

Handling microorganisms in high throughput and their deployment into miniaturized platforms presents significant challenges. Contact printing can be used to create dense arrays of viable microorganisms. Such "living arrays", potentially with multiple identical replicates, are useful in the selection of improved industrial microorganisms, screening antimicrobials, clinical diagnostics, strain storage, and for research into microbial genetics. A high throughput method to print microorganisms at high density was devised, employing a microscope and a stamp with a massive array of PDMS pins. Viable bacteria (Lactobacillus plantarum, Esherichia coli), yeast (Candida albicans) and fungal spores (Aspergillus fumigatus) were deposited onto porous aluminium oxide (PAO) using arrays of pins with areas from 5 x 5 to 20 x 20 microm. Printing onto PAO with up to 8100 pins of 20 x 20 microm area with 3 replicates was achieved. Printing with up to 200 pins onto PAO culture chips (divided into 40 x 40 microm culture areas) allowed inoculation followed by effective segregation of microcolonies during outgrowth. Additionally, it was possible to print mixtures of C. albicans and spores of A. fumigatus with a degree of selectivity by capture onto a chemically modified PAO surface. High resolution printing of microorganisms within segregated compartments and on functionalized PAO surfaces has significant advantages over what is possible on semi-solid surfaces such as agar.

Structure of a Yeast Dyn2-Nup159 Complex and Molecular Basis for Dynein Light Chain-Nuclear Pore Interaction*

PubMed Central

Romes, Erin M.; Tripathy, Ashutosh; Slep, Kevin C.

2012-01-01

The nuclear pore complex gates nucleocytoplasmic transport through a massive, eight-fold symmetric channel capped by a nucleoplasmic basket and structurally unique, cytoplasmic fibrils whose tentacles bind and regulate asymmetric traffic. The conserved Nup82 complex, composed of Nsp1, Nup82, and Nup159, forms the unique cytoplasmic fibrils that regulate mRNA nuclear export. Although the nuclear pore complex plays a fundamental, conserved role in nuclear trafficking, structural information about the cytoplasmic fibrils is limited. Here, we investigate the structural and biochemical interactions between Saccharomyces cerevisiae Nup159 and the nucleoporin, Dyn2. We find that Dyn2 is predominantly a homodimer and binds arrayed sites on Nup159, promoting the Nup159 parallel homodimerization. We present the first structure of Dyn2, determined at 1.85 Å resolution, complexed with a Nup159 target peptide. Dyn2 resembles homologous metazoan dynein light chains, forming homodimeric composite substrate binding sites that engage two independent 10-residue target motifs, imparting a β-strand structure to each peptide via antiparallel extension of the Dyn2 core β-sandwich. Dyn2 recognizes a highly conserved QT motif while allowing sequence plasticity in the flanking residues of the peptide. Isothermal titration calorimetric analysis of the comparative binding of Dyn2 to two Nup159 target sites shows similar affinities (18 and 13 μm), but divergent thermal binding modes. Dyn2 homodimers are arrayed in the crystal lattice, likely mimicking the arrayed architecture of Dyn2 on the Nup159 multivalent binding sites. Crystallographic interdimer interactions potentially reflect a cooperative basis for Dyn2-Nup159 complex formation. Our data highlight the determinants that mediate oligomerization of the Nup82 complex and promote a directed, elongated cytoplasmic fibril architecture. PMID:22411995

Accessing sparse arrays in parallel memories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banerjee, U.; Gajski, D.; Kuck, D.

The concept of dense and sparse execution of arrays is introduced. Arrays themselves can be stored in a dense or sparse manner in a parallel memory with m memory modules. The paper proposes hardware for speeding up the execution of array operations of the form c(c/sub 0/+ci)=a(a/sub 0/+ai) op b(b/sub 0/+bi), where a/sub 0/, a, b/sub 0/, b, c/sub 0/, c are integer constants and i is an index variable. The hardware handles 'sparse execution', in which the operation op is not executed for every value of i. The hardware also makes provision for 'sparse storage', in which memory spacemore » is not provided for every array element. It is shown how to access array elements of the above form without conflict in an efficient way. The efficiency is obtained by using some specialised units which are basically smart memories with priority detection, one's counting or associative searching. Generalisation to multidimensional arrays is shown possible under restrictions defined in the paper. 12 references.« less

Parallel synthesis of a series of potentially brain penetrant aminoalkyl benzoimidazoles.

PubMed

Micco, Iolanda; Nencini, Arianna; Quinn, Joanna; Bothmann, Hendrick; Ghiron, Chiara; Padova, Alessandro; Papini, Silvia

2008-03-01

Alpha7 agonists were identified via GOLD (CCDC) docking in the putative agonist binding site of an alpha7 homology model and a series of aminoalkyl benzoimidazoles was synthesised to obtain potentially brain penetrant drugs. The array was prepared starting from the reaction of ortho-fluoronitrobenzenes with a selection of diamines, followed by reduction of the nitro group to obtain a series of monoalkylated phenylene diamines. N,N'-Carbonyldiimidazole (CDI) mediated acylation, followed by a parallel automated work-up procedure, afforded the monoacylated phenylenediamines which were cyclised under acidic conditions. Parallel work-up and purification afforded the array products in good yields and purities with a robust parallel methodology which will be useful for other libraries. Screening for alpha7 activity revealed compounds with agonist activity for the receptor.

Large-Scale, Multi-Sensor Atmospheric Data Fusion Using Hybrid Cloud Computing

NASA Astrophysics Data System (ADS)

Wilson, Brian; Manipon, Gerald; Hua, Hook; Fetzer, Eric

2014-05-01

NASA's Earth Observing System (EOS) is an ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the "A-Train" platforms (AIRS, AMSR-E, MODIS, MISR, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over decades. Moving to multi-sensor, long-duration analyses of important climate variables presents serious challenges for large-scale data mining and fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another (MODIS), and to a model (ECMWF), stratify the comparisons using a classification of the "cloud scenes" from CloudSat, and repeat the entire analysis over 10 years of data. To efficiently assemble such datasets, we are utilizing Elastic Computing in the Cloud and parallel map-reduce-based algorithms. However, these problems are Data Intensive computing so the data transfer times and storage costs (for caching) are key issues. SciReduce is a Hadoop-like parallel analysis system, programmed in parallel python, that is designed from the ground up for Earth science. SciReduce executes inside VMWare images and scales to any number of nodes in a hybrid Cloud (private eucalyptus & public Amazon). Unlike Hadoop, SciReduce operates on bundles of named numeric arrays, which can be passed in memory or serialized to disk in netCDF4 or HDF5. Multi-year datasets are automatically "sharded" by time and space across a cluster of nodes so that years of data (millions of files) can be processed in a massively parallel way. Input variables (arrays) are pulled on-demand into the Cloud using OPeNDAP URLs or other subsetting services, thereby minimizing the size of the cached input and intermediate datasets. We are using SciReduce to automate the production of multiple versions of a ten-year A-Train water vapor climatology under a NASA MEASURES grant. We will present the architecture of SciReduce, describe the achieved "clock time" speedups in fusing datasets on our own nodes and in the Cloud, and discuss the Cloud cost tradeoffs for storage, compute, and data transfer. We will also present a concept and prototype for staging NASA's A-Train Atmospheric datasets (Levels 2 & 3) in the Amazon Cloud so that any number of compute jobs can be executed "near" the multi-sensor data. Given such a system, multi-sensor climate studies over 10-20 years of data could be perform

Dynamic Imbalance Would Counter Offcenter Thrust

NASA Technical Reports Server (NTRS)

Mccanna, Jason

1994-01-01

Dynamic imbalance generated by offcenter thrust on rotating body eliminated by shifting some of mass of body to generate opposing dynamic imbalance. Technique proposed originally for spacecraft including massive crew module connected via long, lightweight intermediate structure to massive engine module, such that artificial gravitation in crew module generated by rotating spacecraft around axis parallel to thrust generated by engine. Also applicable to dynamic balancing of rotating terrestrial equipment to which offcenter forces applied.

ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains

PubMed Central

Canova, Carlos; Denker, Michael; Gerstein, George; Helias, Moritz

2016-01-01

With the ability to observe the activity from large numbers of neurons simultaneously using modern recording technologies, the chance to identify sub-networks involved in coordinated processing increases. Sequences of synchronous spike events (SSEs) constitute one type of such coordinated spiking that propagates activity in a temporally precise manner. The synfire chain was proposed as one potential model for such network processing. Previous work introduced a method for visualization of SSEs in massively parallel spike trains, based on an intersection matrix that contains in each entry the degree of overlap of active neurons in two corresponding time bins. Repeated SSEs are reflected in the matrix as diagonal structures of high overlap values. The method as such, however, leaves the task of identifying these diagonal structures to visual inspection rather than to a quantitative analysis. Here we present ASSET (Analysis of Sequences of Synchronous EvenTs), an improved, fully automated method which determines diagonal structures in the intersection matrix by a robust mathematical procedure. The method consists of a sequence of steps that i) assess which entries in the matrix potentially belong to a diagonal structure, ii) cluster these entries into individual diagonal structures and iii) determine the neurons composing the associated SSEs. We employ parallel point processes generated by stochastic simulations as test data to demonstrate the performance of the method under a wide range of realistic scenarios, including different types of non-stationarity of the spiking activity and different correlation structures. Finally, the ability of the method to discover SSEs is demonstrated on complex data from large network simulations with embedded synfire chains. Thus, ASSET represents an effective and efficient tool to analyze massively parallel spike data for temporal sequences of synchronous activity. PMID:27420734

Airfoil-based electromagnetic energy harvester containing parallel array motion between moving coil and multi-pole magnets towards enhanced power density.

PubMed

Leung, Chung Ming; Wang, Ya; Chen, Wusi

2016-11-01

In this letter, the airfoil-based electromagnetic energy harvester containing parallel array motion between moving coil and trajectory matching multi-pole magnets was investigated. The magnets were aligned in an alternatively magnetized formation of 6 magnets to explore enhanced power density. In particular, the magnet array was positioned in parallel to the trajectory of the tip coil within its tip deflection span. The finite element simulations of the magnetic flux density and induced voltages at an open circuit condition were studied to find the maximum number of alternatively magnetized magnets that was required for the proposed energy harvester. Experimental results showed that the energy harvester with a pair of 6 alternatively magnetized linear magnet arrays was able to generate an induced voltage (V o ) of 20 V, with an open circuit condition, and 475 mW, under a 30 Ω optimal resistance load operating with the wind speed (U) at 7 m/s and a natural bending frequency of 3.54 Hz. Compared to the traditional electromagnetic energy harvester with a single magnet moving through a coil, the proposed energy harvester, containing multi-pole magnets and parallel array motion, enables the moving coil to accumulate a stronger magnetic flux in each period of the swinging motion. In addition to the comparison made with the airfoil-based piezoelectric energy harvester of the same size, our proposed electromagnetic energy harvester generates 11 times more power output, which is more suitable for high-power-density energy harvesting applications at regions with low environmental frequency.

Dynamic load balancing of applications

DOEpatents

Wheat, S.R.

1997-05-13

An application-level method for dynamically maintaining global load balance on a parallel computer, particularly on massively parallel MIMD computers is disclosed. Global load balancing is achieved by overlapping neighborhoods of processors, where each neighborhood performs local load balancing. The method supports a large class of finite element and finite difference based applications and provides an automatic element management system to which applications are easily integrated. 13 figs.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

Two key areas of crucial importance to the computer-based simulation of large space structures are discussed. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area involves massively parallel computers.

DGDFT: A massively parallel method for large scale density functional theory calculations.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-09-28

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10(-4) Hartree/atom in terms of the error of energy and 6.2 × 10(-4) Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

Capillary array scanner for time-resolved detection and identification of fluorescently labelled DNA fragments.

PubMed

Neumann, M; Herten, D P; Dietrich, A; Wolfrum, J; Sauer, M

2000-02-25

The first capillary array scanner for time-resolved fluorescence detection in parallel capillary electrophoresis based on semiconductor technology is described. The system consists essentially of a confocal fluorescence microscope and a x,y-microscope scanning stage. Fluorescence of the labelled probe molecules was excited using a short-pulse diode laser emitting at 640 nm with a repetition rate of 50 MHz. Using a single filter system the fluorescence decays of different labels were detected by an avalanche photodiode in combination with a PC plug-in card for time-correlated single-photon counting (TCSPC). The time-resolved fluorescence signals were analyzed and identified by a maximum likelihood estimator (MLE). The x,y-microscope scanning stage allows for discontinuous, bidirectional scanning of up to 16 capillaries in an array, resulting in longer fluorescence collection times per capillary compared to scanners working in a continuous mode. Synchronization of the alignment and measurement process were developed to allow for data acquisition without overhead. Detection limits in the subzeptomol range for different dye molecules separated in parallel capillaries have been achieved. In addition, we report on parallel time-resolved detection and separation of more than 400 bases of single base extension DNA fragments in capillary array electrophoresis. Using only semiconductor technology the presented technique represents a low-cost alternative for high throughput DNA sequencing in parallel capillaries.

Ocean Modeling and Visualization on Massively Parallel Computer

NASA Technical Reports Server (NTRS)

Chao, Yi; Li, P. Peggy; Wang, Ping; Katz, Daniel S.; Cheng, Benny N.

1997-01-01

Climate modeling is one of the grand challenges of computational science, and ocean modeling plays an important role in both understanding the current climatic conditions and predicting future climate change.

ILLIAC 4 systems characteristics and programming manual

NASA Technical Reports Server (NTRS)

1973-01-01

The latest edition is presented of the Systems Characteristics and Programming Manual of the ILLIAC 4 array and parallel disc memory system. The major aspects of the array described include: the array systems characteristics, programming characteristics, definition and flow charts, and timing. A glossary of terms, and an instruction index are included.

Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing.

PubMed

Moskalev, Evgeny A; Frohnauer, Judith; Merkelbach-Bruse, Sabine; Schildhaus, Hans-Ulrich; Dimmler, Arno; Schubert, Thomas; Boltze, Carsten; König, Helmut; Fuchs, Florian; Sirbu, Horia; Rieker, Ralf J; Agaimy, Abbas; Hartmann, Arndt; Haller, Florian

2014-06-01

Recurrent gene fusions of anaplastic lymphoma receptor tyrosine kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) have been recently identified in ∼5% of non-small cell lung cancers (NSCLCs) and are targets for selective tyrosine kinase inhibitors. While fluorescent in situ hybridization (FISH) is the current gold standard for detection of EML4-ALK rearrangements, several limitations exist including high costs, time-consuming evaluation and somewhat equivocal interpretation of results. In contrast, targeted massive parallel sequencing has been introduced as a powerful method for simultaneous and sensitive detection of multiple somatic mutations even in limited biopsies, and is currently evolving as the method of choice for molecular diagnostic work-up of NSCLCs. We developed a novel approach for indirect detection of EML4-ALK rearrangements based on 454 massive parallel sequencing after reverse transcription and subsequent multiplex amplification (multiplex ALK RNA-seq) which takes advantage of unbalanced expression of the 5' and 3' ALK mRNA regions. Two lung cancer cell lines and a selected series of 32 NSCLC samples including 11 cases with EML4-ALK rearrangement were analyzed with this novel approach in comparison to ALK FISH, ALK qRT-PCR and EML4-ALK RT-PCR. The H2228 cell line with known EML4-ALK rearrangement showed 171 and 729 reads for 5' and 3' ALK regions, respectively, demonstrating a clearly unbalanced expression pattern. In contrast, the H1299 cell line with ALK wildtype status displayed no reads for both ALK regions. Considering a threshold of 100 reads for 3' ALK region as indirect indicator of EML4-ALK rearrangement, there was 100% concordance between the novel multiplex ALK RNA-seq approach and ALK FISH among all 32 NSCLC samples. Multiplex ALK RNA-seq is a sensitive and specific method for indirect detection of EML4-ALK rearrangements, and can be easily implemented in panel based molecular diagnostic work-up of NSCLCs by massive parallel sequencing. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Speeding up parallel processing

NASA Technical Reports Server (NTRS)

Denning, Peter J.

1988-01-01

In 1967 Amdahl expressed doubts about the ultimate utility of multiprocessors. The formulation, now called Amdahl's law, became part of the computing folklore and has inspired much skepticism about the ability of the current generation of massively parallel processors to efficiently deliver all their computing power to programs. The widely publicized recent results of a group at Sandia National Laboratory, which showed speedup on a 1024 node hypercube of over 500 for three fixed size problems and over 1000 for three scalable problems, have convincingly challenged this bit of folklore and have given new impetus to parallel scientific computing.

Porting LAMMPS to GPUs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, William Michael; Plimpton, Steven James; Wang, Peng

2010-03-01

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

All Inkjet-Printed Amperometric Multiplexed Biosensors Based on Nanostructured Conductive Hydrogel Electrodes.

PubMed

Li, Lanlan; Pan, Lijia; Ma, Zhong; Yan, Ke; Cheng, Wen; Shi, Yi; Yu, Guihua

2018-06-13

Multiplexing, one of the main trends in biosensors, aims to detect several analytes simultaneously by integrating miniature sensors on a chip. However, precisely depositing electrode materials and selective enzymes on distinct microelectrode arrays remains an obstacle to massively produced multiplexed sensors. Here, we report on a "drop-on-demand" inkjet printing process to fabricate multiplexed biosensors based on nanostructured conductive hydrogels in which the electrode material and several kinds of enzymes were printed on the electrode arrays one by one by employing a multinozzle inkjet system. The whole inkjet printing process can be finished within three rounds of printing and only one round of alignment. For a page of sensor arrays containing 96 working electrodes, the printing process took merely ∼5 min. The multiplexed assays can detect glucose, lactate, and triglycerides in real time with good selectivity and high sensitivity, and the results in phosphate buffer solutions and calibration serum samples are comparable. The inkjet printing process exhibited advantages of high efficiency and accuracy, which opens substantial possibilities for massive fabrication of integrated multiplexed biosensors for human health monitoring.

AdiosStMan: Parallelizing Casacore Table Data System using Adaptive IO System

NASA Astrophysics Data System (ADS)

Wang, R.; Harris, C.; Wicenec, A.

2016-07-01

In this paper, we investigate the Casacore Table Data System (CTDS) used in the casacore and CASA libraries, and methods to parallelize it. CTDS provides a storage manager plugin mechanism for third-party developers to design and implement their own CTDS storage managers. Having this in mind, we looked into various storage backend techniques that can possibly enable parallel I/O for CTDS by implementing new storage managers. After carrying on benchmarks showing the excellent parallel I/O throughput of the Adaptive IO System (ADIOS), we implemented an ADIOS based parallel CTDS storage manager. We then applied the CASA MSTransform frequency split task to verify the ADIOS Storage Manager. We also ran a series of performance tests to examine the I/O throughput in a massively parallel scenario.

Dubinett - Targeted Sequencing 2012 — EDRN Public Portal

Cancer.gov

we propose to use targeted massively parallel DNA sequencing to identify somatic alterations within mutational hotspots in matched sets of primary lung tumors, premalignant lesions, and adjacent,histologically normal lung tissue.

Reconfigurable optical interconnection network for multimode optical fiber sensor arrays

NASA Technical Reports Server (NTRS)

Chen, R. T.; Robinson, D.; Lu, H.; Wang, M. R.; Jannson, T.; Baumbick, R.

1992-01-01

A single-source, single-detector architecture has been developed to implement a reconfigurable optical interconnection network multimode optical fiber sensor arrays. The network was realized by integrating LiNbO3 electrooptic (EO) gratings working at the Raman Na regime and a massive fan-out waveguide hologram (WH) working at the Bragg regime onto a multimode glass waveguide. The glass waveguide utilized the whole substrate as a guiding medium. A 1-to-59 massive waveguide fan-out was demonstrated using a WH operating at 514 nm. Measured diffraction efficiency of 59 percent was experimentally confirmed. Reconfigurability of the interconnection was carried out by generating an EO grating through an externally applied electric field. Unlike conventional single-mode integrated optical devices, the guided mode demonstrated has an azimuthal symmetry in mode profile which is the same as that of a fiber mode.

"Science SQL" as a Building Block for Flexible, Standards-based Data Infrastructures

NASA Astrophysics Data System (ADS)

Baumann, Peter

2016-04-01

We have learnt to live with the pain of separating data and metadata into non-interoperable silos. For metadata, we enjoy the flexibility of databases, be they relational, graph, or some other NoSQL. Contrasting this, users still "drown in files" as an unstructured, low-level archiving paradigm. It is time to bridge this chasm which once was technologically induced, but today can be overcome. One building block towards a common re-integrated information space is to support massive multi-dimensional spatio-temporal arrays. These "datacubes" appear as sensor, image, simulation, and statistics data in all science and engineering domains, and beyond. For example, 2-D satellilte imagery, 2-D x/y/t image timeseries and x/y/z geophysical voxel data, and 4-D x/y/z/t climate data contribute to today's data deluge in the Earth sciences. Virtual observatories in the Space sciences routinely generate Petabytes of such data. Life sciences deal with microarray data, confocal microscopy, human brain data, which all fall into the same category. The ISO SQL/MDA (Multi-Dimensional Arrays) candidate standard is extending SQL with modelling and query support for n-D arrays ("datacubes") in a flexible, domain-neutral way. This heralds a new generation of services with new quality parameters, such as flexibility, ease of access, embedding into well-known user tools, and scalability mechanisms that remain completely transparent to users. Technology like the EU rasdaman ("raster data manager") Array Database system can support all of the above examples simultaneously, with one technology. This is practically proven: As of today, rasdaman is in operational use on hundreds of Terabytes of satellite image timeseries datacubes, with transparent query distribution across more than 1,000 nodes. Therefore, Array Databases offering SQL/MDA constitute a natural common building block for next-generation data infrastructures. Being initiator and editor of the standard we present principles, implementation facets, and application examples as a basis for further discussion. Further, we highlight recent implementation progress in parallelization, data distribution, and query optimization showing their effects on real-life use cases.

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele; Biegel, Bryan (Technical Monitor)

2001-01-01

This viewgraph presentation provides information on the technical aspects of debugging computer code that has been automatically converted for use in a parallel computing system. Shared memory parallelization and distributed memory parallelization entail separate and distinct challenges for a debugging program. A prototype system has been developed which integrates various tools for the debugging of automatically parallelized programs including the CAPTools Database which provides variable definition information across subroutines as well as array distribution information.

Parallel language constructs for tensor product computations on loosely coupled architectures

NASA Technical Reports Server (NTRS)

Mehrotra, Piyush; Van Rosendale, John

1989-01-01

A set of language primitives designed to allow the specification of parallel numerical algorithms at a higher level is described. The authors focus on tensor product array computations, a simple but important class of numerical algorithms. They consider first the problem of programming one-dimensional kernel routines, such as parallel tridiagonal solvers, and then look at how such parallel kernels can be combined to form parallel tensor product algorithms.

Shift-, rotation-, and scale-invariant shape recognition system using an optical Hough transform

NASA Astrophysics Data System (ADS)

Schmid, Volker R.; Bader, Gerhard; Lueder, Ernst H.

1998-02-01

We present a hybrid shape recognition system with an optical Hough transform processor. The features of the Hough space offer a separate cancellation of distortions caused by translations and rotations. Scale invariance is also provided by suitable normalization. The proposed system extends the capabilities of Hough transform based detection from only straight lines to areas bounded by edges. A very compact optical design is achieved by a microlens array processor accepting incoherent light as direct optical input and realizing the computationally expensive connections massively parallel. Our newly developed algorithm extracts rotation and translation invariant normalized patterns of bright spots on a 2D grid. A neural network classifier maps the 2D features via a nonlinear hidden layer onto the classification output vector. We propose initialization of the connection weights according to regions of activity specifically assigned to each neuron in the hidden layer using a competitive network. The presented system is designed for industry inspection applications. Presently we have demonstrated detection of six different machined parts in real-time. Our method yields very promising detection results of more than 96% correctly classified parts.

Forces and dynamics in epithelial domes of controlled size and shape

NASA Astrophysics Data System (ADS)

Latorre-Ibars, Ernest; Casares, Laura; Gomez-Gonzalez, Manuel; Uroz, Marina; Arroyo, Marino; Trepat, Xavier

Mechanobiology of epithelia plays a central role in morphogenesis, wound healing, and tumor progression. Its current understanding relies on mechanical measurements on flat epithelial layers. However, most epithelia in vivo exhibit a curved 3D shape enclosing a pressurized lumen. Using soft micropatterned substrates we produce massive parallel arrays of epithelial domes with controlled size and basal shape. We measure epithelial traction, tension, and luminal pressure in epithelial domes. The local stress tensor on the freestanding epithelial membrane is then mapped by combining measured luminal pressure and local curvature. We show that tension and cell shape are highly anisotropic and vary along the meridional position of the domes. Finally, we establish constitutive relations between shape, tension, and pressure during perturbations of the contractile machinery, osmotic shocks, and spontaneous fluctuations of dome volume. Our findings contradict a description of the epithelium as a fluid capillary surface. Cells in the dome are unable to relax into a uniform and isotropic tensional state through sub- and supra-cellular rearrangements. Mapping epithelial shape, tension, and pressure will enable quantitative studies of mechanobiology in 3D epithelia of controlled size and shape.

3D highly oriented nanoparticulate and microparticulate array ofmetal oxide materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vayssieres, Lionel; Guo, Jinghua; Nordgren, Joseph

2006-09-15

Advanced nano and micro particulate thin films of 3d transition and post-transition metal oxides consisting of nanorods and microrods with parallel and perpendicular orientation with respect to the substrate normal, have been successfully grown onto various substrates by heteronucleation, without template and/or surfactant, from the aqueous condensation of solution of metal salts or metal complexes (aqueous chemical growth). Three-dimensional arrays of iron oxide nanorods and zinc oxide nanorods with parallel and perpendicular orientation are presented as well as the oxygen K-edge polarization dependent x-ray absorption spectroscopy (XAS) study of anisotropic perpendicularly oriented microrod array of ZnO performed at synchrotron radiationmore » source facility.« less

VCSELs for datacom applications

NASA Astrophysics Data System (ADS)

Wipiejewski, Torsten; Wolf, Hans-Dieter; Korte, Lutz; Huber, Wolfgang; Kristen, Guenter; Hoyler, Charlotte; Hedrich, Harald; Kleinbub, Oliver; Albrecht, Tony; Mueller, Juergen; Orth, Andreas; Spika, Zeljko; Lutgen, Stephan; Pflaeging, Hartwig; Harrasser, Joerg; Droegemueller, Karsten; Plickert, Volker; Kuhl, Detlef; Blank, Juergen; Pietsch, Doris; Stange, Herwig; Karstensen, Holger

1999-04-01

The use of oxide confined VCSELs in datacom applications is demonstrated. The devices exhibit low threshold currents of approximately 3 mA and low electrical series resistance of about 50 (Omega) . The emission wavelength is in the 850 nm range. Life times of the devices are several million hours under normal operating conditions. VCSEL arrays are employed in a high performance parallel optical link called PAROLITM. This optical ink provides 12 parallel channels with a total bandwidth exceeding 12 Gbit/s. The VCSELs optimized for the parallel optical link show excellent threshold current uniformity between channels of < 50 (mu) A. The array life time drops compared to a single device, but is still larger than 1 million hours.

Electroosmotic velocity in an array of parallel soft cylinders in a salt-free medium.

PubMed

Ohshima, Hiroyuki

2004-11-15

A theory of electroosmosis in an array of parallel soft cylinders (i.e. polyelectrolyte-coated cylinders) in a salt-free medium is presented. It is shown that there is a certain critical value of the particle charge and that if the particle charge is greater than the critical value, then the electroosmotic velocity becomes constant independent of the particle charge due to the counterion condensation effects, as in the case of other electrokinetic phenomena in salt-free media.

Massively parallel electrical conductivity imaging of the subsurface: Applications to hydrocarbon exploration

NASA Astrophysics Data System (ADS)

Newman, Gregory A.; Commer, Michael

2009-07-01

Three-dimensional (3D) geophysical imaging is now receiving considerable attention for electrical conductivity mapping of potential offshore oil and gas reservoirs. The imaging technology employs controlled source electromagnetic (CSEM) and magnetotelluric (MT) fields and treats geological media exhibiting transverse anisotropy. Moreover when combined with established seismic methods, direct imaging of reservoir fluids is possible. Because of the size of the 3D conductivity imaging problem, strategies are required exploiting computational parallelism and optimal meshing. The algorithm thus developed has been shown to scale to tens of thousands of processors. In one imaging experiment, 32,768 tasks/processors on the IBM Watson Research Blue Gene/L supercomputer were successfully utilized. Over a 24 hour period we were able to image a large scale field data set that previously required over four months of processing time on distributed clusters based on Intel or AMD processors utilizing 1024 tasks on an InfiniBand fabric. Electrical conductivity imaging using massively parallel computational resources produces results that cannot be obtained otherwise and are consistent with timeframes required for practical exploration problems.

Running ATLAS workloads within massively parallel distributed applications using Athena Multi-Process framework (AthenaMP)

NASA Astrophysics Data System (ADS)

Calafiura, Paolo; Leggett, Charles; Seuster, Rolf; Tsulaia, Vakhtang; Van Gemmeren, Peter

2015-12-01

AthenaMP is a multi-process version of the ATLAS reconstruction, simulation and data analysis framework Athena. By leveraging Linux fork and copy-on-write mechanisms, it allows for sharing of memory pages between event processors running on the same compute node with little to no change in the application code. Originally targeted to optimize the memory footprint of reconstruction jobs, AthenaMP has demonstrated that it can reduce the memory usage of certain configurations of ATLAS production jobs by a factor of 2. AthenaMP has also evolved to become the parallel event-processing core of the recently developed ATLAS infrastructure for fine-grained event processing (Event Service) which allows the running of AthenaMP inside massively parallel distributed applications on hundreds of compute nodes simultaneously. We present the architecture of AthenaMP, various strategies implemented by AthenaMP for scheduling workload to worker processes (for example: Shared Event Queue and Shared Distributor of Event Tokens) and the usage of AthenaMP in the diversity of ATLAS event processing workloads on various computing resources: Grid, opportunistic resources and HPC.

GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations

NASA Astrophysics Data System (ADS)

Nguyen, Trung Dac

2017-03-01

The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.

Progress report on PIXIE3D, a fully implicit 3D extended MHD solver

NASA Astrophysics Data System (ADS)

Chacon, Luis

2008-11-01

Recently, invited talk at DPP07 an optimal, massively parallel implicit algorithm for 3D resistive magnetohydrodynamics (PIXIE3D) was demonstrated. Excellent algorithmic and parallel results were obtained with up to 4096 processors and 138 million unknowns. While this is a remarkable result, further developments are still needed for PIXIE3D to become a 3D extended MHD production code in general geometries. In this poster, we present an update on the status of PIXIE3D on several fronts. On the physics side, we will describe our progress towards the full Braginskii model, including: electron Hall terms, anisotropic heat conduction, and gyroviscous corrections. Algorithmically, we will discuss progress towards a robust, optimal, nonlinear solver for arbitrary geometries, including preconditioning for the new physical effects described, the implementation of a coarse processor-grid solver (to maintain optimal algorithmic performance for an arbitrarily large number of processors in massively parallel computations), and of a multiblock capability to deal with complicated geometries. L. Chac'on, Phys. Plasmas 15, 056103 (2008);

Hybrid massively parallel fast sweeping method for static Hamilton–Jacobi equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Detrixhe, Miles, E-mail: mdetrixhe@engineering.ucsb.edu; University of California Santa Barbara, Santa Barbara, CA, 93106; Gibou, Frédéric, E-mail: fgibou@engineering.ucsb.edu

The fast sweeping method is a popular algorithm for solving a variety of static Hamilton–Jacobi equations. Fast sweeping algorithms for parallel computing have been developed, but are severely limited. In this work, we present a multilevel, hybrid parallel algorithm that combines the desirable traits of two distinct parallel methods. The fine and coarse grained components of the algorithm take advantage of heterogeneous computer architecture common in high performance computing facilities. We present the algorithm and demonstrate its effectiveness on a set of example problems including optimal control, dynamic games, and seismic wave propagation. We give results for convergence, parallel scaling,more » and show state-of-the-art speedup values for the fast sweeping method.« less

Large-eddy simulations of compressible convection on massively parallel computers. [stellar physics

NASA Technical Reports Server (NTRS)

Xie, Xin; Toomre, Juri

1993-01-01

We report preliminary implementation of the large-eddy simulation (LES) technique in 2D simulations of compressible convection carried out on the CM-2 massively parallel computer. The convective flow fields in our simulations possess structures similar to those found in a number of direct simulations, with roll-like flows coherent across the entire depth of the layer that spans several density scale heights. Our detailed assessment of the effects of various subgrid scale (SGS) terms reveals that they may affect the gross character of convection. Yet, somewhat surprisingly, we find that our LES solutions, and another in which the SGS terms are turned off, only show modest differences. The resulting 2D flows realized here are rather laminar in character, and achieving substantial turbulence may require stronger forcing and less dissipation.

Contextual classification on the massively parallel processor

NASA Technical Reports Server (NTRS)

Tilton, James C.

1987-01-01

Classifiers are often used to produce land cover maps from multispectral Earth observation imagery. Conventionally, these classifiers have been designed to exploit the spectral information contained in the imagery. Very few classifiers exploit the spatial information content of the imagery, and the few that do rarely exploit spatial information content in conjunction with spectral and/or temporal information. A contextual classifier that exploits spatial and spectral information in combination through a general statistical approach was studied. Early test results obtained from an implementation of the classifier on a VAX-11/780 minicomputer were encouraging, but they are of limited meaning because they were produced from small data sets. An implementation of the contextual classifier is presented on the Massively Parallel Processor (MPP) at Goddard that for the first time makes feasible the testing of the classifier on large data sets.

Massively Parallel Sequencing of Patients with Intellectual Disability, Congenital Anomalies and/or Autism Spectrum Disorders with a Targeted Gene Panel

PubMed Central

Brett, Maggie; McPherson, John; Zang, Zhi Jiang; Lai, Angeline; Tan, Ee-Shien; Ng, Ivy; Ong, Lai-Choo; Cham, Breana; Tan, Patrick; Rozen, Steve; Tan, Ene-Choo

2014-01-01

Developmental delay and/or intellectual disability (DD/ID) affects 1–3% of all children. At least half of these are thought to have a genetic etiology. Recent studies have shown that massively parallel sequencing (MPS) using a targeted gene panel is particularly suited for diagnostic testing for genetically heterogeneous conditions. We report on our experiences with using massively parallel sequencing of a targeted gene panel of 355 genes for investigating the genetic etiology of eight patients with a wide range of phenotypes including DD/ID, congenital anomalies and/or autism spectrum disorder. Targeted sequence enrichment was performed using the Agilent SureSelect Target Enrichment Kit and sequenced on the Illumina HiSeq2000 using paired-end reads. For all eight patients, 81–84% of the targeted regions achieved read depths of at least 20×, with average read depths overlapping targets ranging from 322× to 798×. Causative variants were successfully identified in two of the eight patients: a nonsense mutation in the ATRX gene and a canonical splice site mutation in the L1CAM gene. In a third patient, a canonical splice site variant in the USP9X gene could likely explain all or some of her clinical phenotypes. These results confirm the value of targeted MPS for investigating DD/ID in children for diagnostic purposes. However, targeted gene MPS was less likely to provide a genetic diagnosis for children whose phenotype includes autism. PMID:24690944

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

PubMed

Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

2016-07-01

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library.

PubMed

Waugh, Caryll; Cromer, Deborah; Grimm, Andrew; Chopra, Abha; Mallal, Simon; Davenport, Miles; Mak, Johnson

2015-04-09

Massive, parallel sequencing is a potent tool for dissecting the regulation of biological processes by revealing the dynamics of the cellular RNA profile under different conditions. Similarly, massive, parallel sequencing can be used to reveal the complexity of viral quasispecies that are often found in the RNA virus infected host. However, the production of cDNA libraries for next-generation sequencing (NGS) necessitates the reverse transcription of RNA into cDNA and the amplification of the cDNA template using PCR, which may introduce artefact in the form of phantom nucleic acids species that can bias the composition and interpretation of original RNA profiles. Using HIV as a model we have characterised the major sources of error during the conversion of viral RNA to cDNA, namely excess RNA template and the RNaseH activity of the polymerase enzyme, reverse transcriptase. In addition we have analysed the effect of PCR cycle on detection of recombinants and assessed the contribution of transfection of highly similar plasmid DNA to the formation of recombinant species during the production of our control viruses. We have identified RNA template concentrations, RNaseH activity of reverse transcriptase, and PCR conditions as key parameters that must be carefully optimised to minimise chimeric artefacts. Using our optimised RT-PCR conditions, in combination with our modified PCR amplification procedure, we have developed a reliable technique for accurate determination of RNA species using NGS technology.

Sierra Structural Dynamics User's Notes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reese, Garth M.

2015-10-19

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

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

NASA Technical Reports Server (NTRS)

Fiebrich, Rolf-Dieter

1987-01-01

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.

Massively-Parallel Architectures for Automatic Recognition of Visual Speech Signals

DTIC Science & Technology

1988-10-12

Secusrity Clamifieation, Nlassively-Parallel Architectures for Automa ic Recognitio of Visua, Speech Signals 12. PERSONAL AUTHOR(S) Terrence J...characteristics of speech from tJhe, visual speech signals. Neural networks have been trained on a database of vowels. The rqw images of faces , aligned and...images of faces , aligned and preprocessed, were used as input to these network which were trained to estimate the corresponding envelope of the

Solving Navier-Stokes equations on a massively parallel processor; The 1 GFLOP performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saati, A.; Biringen, S.; Farhat, C.

This paper reports on experience in solving large-scale fluid dynamics problems on the Connection Machine model CM-2. The authors have implemented a parallel version of the MacCormack scheme for the solution of the Navier-Stokes equations. By using triad floating point operations and reducing the number of interprocessor communications, they have achieved a sustained performance rate of 1.42 GFLOPS.

Sierra/SD User's Notes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munday, Lynn Brendon; Day, David M.; Bunting, Gregory

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

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

NASA Technical Reports Server (NTRS)

Morgan, Philip E.

2004-01-01

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

Representing and computing regular languages on massively parallel networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, M.I.; O'Sullivan, J.A.; Boysam, B.

1991-01-01

This paper proposes a general method for incorporating rule-based constraints corresponding to regular languages into stochastic inference problems, thereby allowing for a unified representation of stochastic and syntactic pattern constraints. The authors' approach first established the formal connection of rules to Chomsky grammars, and generalizes the original work of Shannon on the encoding of rule-based channel sequences to Markov chains of maximum entropy. This maximum entropy probabilistic view leads to Gibb's representations with potentials which have their number of minima growing at precisely the exponential rate that the language of deterministically constrained sequences grow. These representations are coupled to stochasticmore » diffusion algorithms, which sample the language-constrained sequences by visiting the energy minima according to the underlying Gibbs' probability law. The coupling to stochastic search methods yields the all-important practical result that fully parallel stochastic cellular automata may be derived to generate samples from the rule-based constraint sets. The production rules and neighborhood state structure of the language of sequences directly determines the necessary connection structures of the required parallel computing surface. Representations of this type have been mapped to the DAP-510 massively-parallel processor consisting of 1024 mesh-connected bit-serial processing elements for performing automated segmentation of electron-micrograph images.« less

SediFoam: A general-purpose, open-source CFD-DEM solver for particle-laden flow with emphasis on sediment transport

NASA Astrophysics Data System (ADS)

Sun, Rui; Xiao, Heng

2016-04-01

With the growth of available computational resource, CFD-DEM (computational fluid dynamics-discrete element method) becomes an increasingly promising and feasible approach for the study of sediment transport. Several existing CFD-DEM solvers are applied in chemical engineering and mining industry. However, a robust CFD-DEM solver for the simulation of sediment transport is still desirable. In this work, the development of a three-dimensional, massively parallel, and open-source CFD-DEM solver SediFoam is detailed. This solver is built based on open-source solvers OpenFOAM and LAMMPS. OpenFOAM is a CFD toolbox that can perform three-dimensional fluid flow simulations on unstructured meshes; LAMMPS is a massively parallel DEM solver for molecular dynamics. Several validation tests of SediFoam are performed using cases of a wide range of complexities. The results obtained in the present simulations are consistent with those in the literature, which demonstrates the capability of SediFoam for sediment transport applications. In addition to the validation test, the parallel efficiency of SediFoam is studied to test the performance of the code for large-scale and complex simulations. The parallel efficiency tests show that the scalability of SediFoam is satisfactory in the simulations using up to O(107) particles.

Parallel and series FED microstrip array with high efficiency and low cross polarization

NASA Technical Reports Server (NTRS)

Huang, John (Inventor)

1995-01-01

A microstrip array antenna for vertically polarized fan beam (approximately 2 deg x 50 deg) for C-band SAR applications with a physical area of 1.7 m by 0.17 m comprises two rows of patch elements and employs a parallel feed to left- and right-half sections of the rows. Each section is divided into two segments that are fed in parallel with the elements in each segment fed in series through matched transmission lines for high efficiency. The inboard section has half the number of patch elements of the outboard section, and the outboard sections, which have tapered distribution with identical transmission line sections, terminated with half wavelength long open-circuit stubs so that the remaining energy is reflected and radiated in phase. The elements of the two inboard segments of the two left- and right-half sections are provided with tapered transmission lines from element to element for uniform power distribution over the central third of the entire array antenna. The two rows of array elements are excited at opposite patch feed locations with opposite (180 deg difference) phases for reduced cross-polarization.

Parallel, confocal, and complete spectrum imager for fluorescent detection of high-density microarray

NASA Astrophysics Data System (ADS)

Bogdanov, Valery L.; Boyce-Jacino, Michael

1999-05-01

Confined arrays of biochemical probes deposited on a solid support surface (analytical microarray or 'chip') provide an opportunity to analysis multiple reactions simultaneously. Microarrays are increasingly used in genetics, medicine and environment scanning as research and analytical instruments. A power of microarray technology comes from its parallelism which grows with array miniaturization, minimization of reagent volume per reaction site and reaction multiplexing. An optical detector of microarray signals should combine high sensitivity, spatial and spectral resolution. Additionally, low-cost and a high processing rate are needed to transfer microarray technology into biomedical practice. We designed an imager that provides confocal and complete spectrum detection of entire fluorescently-labeled microarray in parallel. Imager uses microlens array, non-slit spectral decomposer, and high- sensitive detector (cooled CCD). Two imaging channels provide a simultaneous detection of localization, integrated and spectral intensities for each reaction site in microarray. A dimensional matching between microarray and imager's optics eliminates all in moving parts in instrumentation, enabling highly informative, fast and low-cost microarray detection. We report theory of confocal hyperspectral imaging with microlenses array and experimental data for implementation of developed imager to detect fluorescently labeled microarray with a density approximately 103 sites per cm2.

Analysis of Camera Arrays Applicable to the Internet of Things.

PubMed

Yang, Jiachen; Xu, Ru; Lv, Zhihan; Song, Houbing

2016-03-22

The Internet of Things is built based on various sensors and networks. Sensors for stereo capture are essential for acquiring information and have been applied in different fields. In this paper, we focus on the camera modeling and analysis, which is very important for stereo display and helps with viewing. We model two kinds of cameras, a parallel and a converged one, and analyze the difference between them in vertical and horizontal parallax. Even though different kinds of camera arrays are used in various applications and analyzed in the research work, there are few discussions on the comparison of them. Therefore, we make a detailed analysis about their performance over different shooting distances. From our analysis, we find that the threshold of shooting distance for converged cameras is 7 m. In addition, we design a camera array in our work that can be used as a parallel camera array, as well as a converged camera array and take some images and videos with it to identify the threshold.

Cost-effective GPU-grid for genome-wide epistasis calculations.

PubMed

Pütz, B; Kam-Thong, T; Karbalai, N; Altmann, A; Müller-Myhsok, B

2013-01-01

Until recently, genotype studies were limited to the investigation of single SNP effects due to the computational burden incurred when studying pairwise interactions of SNPs. However, some genetic effects as simple as coloring (in plants and animals) cannot be ascribed to a single locus but only understood when epistasis is taken into account [1]. It is expected that such effects are also found in complex diseases where many genes contribute to the clinical outcome of affected individuals. Only recently have such problems become feasible computationally. The inherently parallel structure of the problem makes it a perfect candidate for massive parallelization on either grid or cloud architectures. Since we are also dealing with confidential patient data, we were not able to consider a cloud-based solution but had to find a way to process the data in-house and aimed to build a local GPU-based grid structure. Sequential epistatsis calculations were ported to GPU using CUDA at various levels. Parallelization on the CPU was compared to corresponding GPU counterparts with regards to performance and cost. A cost-effective solution was created by combining custom-built nodes equipped with relatively inexpensive consumer-level graphics cards with highly parallel GPUs in a local grid. The GPU method outperforms current cluster-based systems on a price/performance criterion, as a single GPU shows speed performance comparable up to 200 CPU cores. The outlined approach will work for problems that easily lend themselves to massive parallelization. Code for various tasks has been made available and ongoing development of tools will further ease the transition from sequential to parallel algorithms.

The paradigm compiler: Mapping a functional language for the connection machine

NASA Technical Reports Server (NTRS)

Dennis, Jack B.

1989-01-01

The Paradigm Compiler implements a new approach to compiling programs written in high level languages for execution on highly parallel computers. The general approach is to identify the principal data structures constructed by the program and to map these structures onto the processing elements of the target machine. The mapping is chosen to maximize performance as determined through compile time global analysis of the source program. The source language is Sisal, a functional language designed for scientific computations, and the target language is Paris, the published low level interface to the Connection Machine. The data structures considered are multidimensional arrays whose dimensions are known at compile time. Computations that build such arrays usually offer opportunities for highly parallel execution; they are data parallel. The Connection Machine is an attractive target for these computations, and the parallel for construct of the Sisal language is a convenient high level notation for data parallel algorithms. The principles and organization of the Paradigm Compiler are discussed.

MEMS fabrication and frequency sweep for suspending beam and plate electrode in electrostatic capacitor

NASA Astrophysics Data System (ADS)

Zhu, Jianxiong; Song, Weixing

2018-01-01

We report a MEMS fabrication and frequency sweep for a high-order mode suspending beam and plate layer in electrostatic micro-gap semiconductor capacitor. This suspended beam and plate was designed with silicon oxide (SiO2) film which was fabricated using bulk silicon micromachining technology on both side of a silicon substrate. The designed semiconductor capacitors were driven by a bias direct current (DC) and a sweep frequency alternative current (AC) in a room temperature for an electrical response test. Finite element calculating software was used to evaluate the deformation mode around its high-order response frequency. Compared a single capacitor with a high-order response frequency (0.42 MHz) and a 1 × 2 array parallel capacitor, we found that the 1 × 2 array parallel capacitor had a broader high-order response range. And it concluded that a DC bias voltage can be used to modulate a high-order response frequency for both a single and 1 × 2 array parallel capacitors.

Iterative algorithms for large sparse linear systems on parallel computers

NASA Technical Reports Server (NTRS)

Adams, L. M.

1982-01-01

Algorithms for assembling in parallel the sparse system of linear equations that result from finite difference or finite element discretizations of elliptic partial differential equations, such as those that arise in structural engineering are developed. Parallel linear stationary iterative algorithms and parallel preconditioned conjugate gradient algorithms are developed for solving these systems. In addition, a model for comparing parallel algorithms on array architectures is developed and results of this model for the algorithms are given.

Air-cathode microbial fuel cell array: a device for identifying and characterizing electrochemically active microbes.

PubMed

Hou, Huijie; Li, Lei; de Figueiredo, Paul; Han, Arum

2011-01-15

Microbial fuel cells (MFCs) have generated excitement in environmental and bioenergy communities due to their potential for coupling wastewater treatment with energy generation and powering diverse devices. The pursuit of strategies such as improving microbial cultivation practices and optimizing MFC devices has increased power generating capacities of MFCs. However, surprisingly few microbial species with electrochemical activity in MFCs have been identified because current devices do not support parallel analyses or high throughput screening. We have recently demonstrated the feasibility of using advanced microfabrication methods to fabricate an MFC microarray. Here, we extend these studies by demonstrating a microfabricated air-cathode MFC array system. The system contains 24 individual air-cathode MFCs integrated onto a single chip. The device enables the direct and parallel comparison of different microbes loaded onto the array. Environmental samples were used to validate the utility of the air-cathode MFC array system and two previously identified isolates, 7Ca (Shewanella sp.) and 3C (Arthrobacter sp.), were shown to display enhanced electrochemical activities of 2.69 mW/m(2) and 1.86 mW/m(2), respectively. Experiments using a large scale conventional air-cathode MFC validated these findings. The parallel air-cathode MFC array system demonstrated here is expected to promote and accelerate the discovery and characterization of electrochemically active microbes. Copyright © 2010 Elsevier B.V. All rights reserved.

An Innovative Infrastructure with a Universal Geo-spatiotemporal Data Representation Supporting Cost-effective Integration of Diverse Earth Science Data

NASA Astrophysics Data System (ADS)

Kuo, K. S.; Rilee, M. L.

2017-12-01

Existing pathways for bringing together massive, diverse Earth Science datasets for integrated analyses burden end users with data packaging and management details irrelevant to their domain goals. The major data repositories focus on archival, discovery, and dissemination of products (files) in a standardized manner. End-users must download and then adapt these files using local resources and custom methods before analysis can proceed. This reduces scientific or other domain productivity, as scarce resources and expertise must be diverted to data processing. The Spatio-Temporal Adaptive Resolution Encoding (STARE) is a unifying scheme encoding geospatial and temporal information for organizing data on scalable computing/storage resources, minimizing expensive data transfers. STARE provides a compact representation that turns set-logic functions, e.g. conditional subsetting, into integer operations, that takes into account representative spatiotemporal resolutions of the data in the datasets, which is needed for data placement alignment of geo-spatiotemporally diverse data on massive parallel resources. Automating important scientific functions (e.g. regridding) and computational functions (e.g. data placement) allows scientists to focus on domain specific questions instead of expending their expertise on data processing. While STARE is not tied to any particular computing technology, we have used STARE for visualization and the SciDB array database to analyze Earth Science data on a 28-node compute cluster. STARE's automatic data placement and coupling of geometric and array indexing allows complicated data comparisons to be realized as straightforward database operations like "join." With STARE-enabled automation, SciDB+STARE provides a database interface, reducing costly data preparation, increasing the volume and variety of integrable data, and easing result sharing. Using SciDB+STARE as part of an integrated analysis infrastructure, we demonstrate the dramatic ease of combining diametrically different datasets, i.e. gridded (NMQ radar) vs. spacecraft swath (TRMM). SciDB+STARE is an important step towards a computational infrastructure for integrating and sharing diverse, complex Earth Science data and science products derived from them.

Use Massive Parallel Sequencing and Exome Capture Technology to Sequence the Exome of Fanconi Anemia Children and Their Patents

ClinicalTrials.gov

2013-11-21

Fanconi Anemia; Autosomal or Sex Linked Recessive Genetic Disease; Bone Marrow Hematopoiesis Failure, Multiple Congenital Abnormalities, and Susceptibility to Neoplastic Diseases.; Hematopoiesis Maintainance.

Utilizing Maximum Power Point Trackers in Parallel to Maximize the Power Output of a Solar (Photovoltaic) Array

DTIC Science & Technology

2012-12-01

photovoltaic (PV) system to use a maximum power point tracker ( MPPT ) to increase... photovoltaic (PV) system to use a maximum power point tracker ( MPPT ) to increase the power output of the solar array. Currently, most military... MPPT ) is an optimizing circuit that is used in conjunction with photovoltaic (PV) arrays to achieve the maximum delivery of power from the array

The Use of a Microcomputer Based Array Processor for Real Time Laser Velocimeter Data Processing

NASA Technical Reports Server (NTRS)

Meyers, James F.

1990-01-01

The application of an array processor to laser velocimeter data processing is presented. The hardware is described along with the method of parallel programming required by the array processor. A portion of the data processing program is described in detail. The increase in computational speed of a microcomputer equipped with an array processor is illustrated by comparative testing with a minicomputer.

Many-Body Subradiant Excitations in Metamaterial Arrays: Experiment and Theory.

PubMed

Jenkins, Stewart D; Ruostekoski, Janne; Papasimakis, Nikitas; Savo, Salvatore; Zheludev, Nikolay I

2017-08-04

Subradiant excitations, originally predicted by Dicke, have posed a long-standing challenge in physics owing to their weak radiative coupling to environment. Here we engineer massive coherently driven classical subradiance in planar metamaterial arrays as a spatially extended eigenmode comprising over 1000 metamolecules. By comparing the near- and far-field response in large-scale numerical simulations with those in experimental observations we identify strong evidence for classically correlated multimetamolecule subradiant states that dominate the total excitation energy. We show that similar spatially extended many-body subradiance can also exist in plasmonic metamaterial arrays at optical frequencies.

Optimum sensor placement for microphone arrays

NASA Astrophysics Data System (ADS)

Rabinkin, Daniel V.

Microphone arrays can be used for high-quality sound pickup in reverberant and noisy environments. Sound capture using conventional single microphone methods suffers severe degradation under these conditions. The beamforming capabilities of microphone array systems allow highly directional sound capture, providing enhanced signal-to-noise ratio (SNR) when compared to single microphone performance. The overall performance of an array system is governed by its ability to locate and track sound sources and its ability to capture sound from desired spatial volumes. These abilities are strongly affected by the spatial placement of microphone sensors. A method is needed to optimize placement for a specified number of sensors in a given acoustical environment. The objective of the optimization is to obtain the greatest average system SNR for sound capture in the region of interest. A two-step sound source location method is presented. In the first step, time delay of arrival (TDOA) estimates for select microphone pairs are determined using a modified version of the Omologo-Svaizer cross-power spectrum phase expression. In the second step, the TDOA estimates are used in a least-mean-squares gradient descent search algorithm to obtain a location estimate. Statistics for TDOA estimate error as a function of microphone pair/sound source geometry and acoustic environment are gathered from a set of experiments. These statistics are used to model position estimation accuracy for a given array geometry. The effectiveness of sound source capture is also dependent on array geometry and the acoustical environment. Simple beamforming and time delay compensation (TDC) methods provide spatial selectivity but suffer performance degradation in reverberant environments. Matched filter array (MFA) processing can mitigate the effects of reverberation. The shape and gain advantage of the capture region for these techniques is described and shown to be highly influenced by the placement of array sensors. A procedure is developed to evaluate a given array configuration based on the above-mentioned metrics. Constrained placement optimizations are performed that maximize SNR for both TDC and MFA capture methods. Results are compared for various acoustic environments and various enclosure sizes. General guidelines are presented for placement strategy and bandwidth dependence, as they relate to reverberation levels, ambient noise, and enclosure geometry. An overall performance function is described based on these metrics. Performance of the microphone array system is also constrained by the design limitations of the supporting hardware. Two newly developed hardware architectures are presented that support the described algorithms. A low- cost 8-channel system with off-the-shelf componentry was designed and its performance evaluated. A massively parallel 512-channel custom-built system is in development-its capabilities and the rationale for its design are described.

64 x 64 thresholding photodetector array for optical pattern recognition

NASA Astrophysics Data System (ADS)

Langenbacher, Harry; Chao, Tien-Hsin; Shaw, Timothy; Yu, Jeffrey W.

1993-10-01

A high performance 32 X 32 peak detector array is introduced. This detector consists of a 32 X 32 array of thresholding photo-transistor cells, manufactured with a standard MOSIS digital 2-micron CMOS process. A built-in thresholding function that is able to perform 1024 thresholding operations in parallel strongly distinguishes this chip from available CCD detectors. This high speed detector offers responses from one to 10 milliseconds that is much higher than the commercially available CCD detectors operating at a TV frame rate. The parallel multiple peaks thresholding detection capability makes it particularly suitable for optical correlator and optoelectronically implemented neural networks. The principle of operation, circuit design and the performance characteristics are described. Experimental demonstration of correlation peak detection is also provided. Recently, we have also designed and built an advanced version of a 64 X 64 thresholding photodetector array chip. Experimental investigation of using this chip for pattern recognition is ongoing.

THz wavefront manipulation based on metal waveguides

NASA Astrophysics Data System (ADS)

Wu, Mengru; Lang, Tingting; Shen, Changyu; Shi, Guohua; Han, Zhanghua

2018-07-01

In this paper, two waveguiding structures for arbitrary wavefront manipulation in the terahertz spectral region were proposed, designed and characterized. The first structure consists of parallel stack copper plates forming an array of parallel-plate waveguides (PPWGs). The second structure is three-dimensional metal rectangular waveguides array. The phase delay of the input wave after passing through the waveguide array is mainly determined by the effective index of the waveguides. Therefore, the waveguide array can be engineered using different core width distribution to generate any desired light beam. Examples, working at the frequency of 0.3 THz show that good focusing phenomenon with different focus lengths and spot sizes were observed, as well as arbitrarily tilted propagation of incident plane waves. The structure introduces a new method to perform wavefront manipulation, and can be utilized in many important applications in terahertz imaging and communication systems.

A model for the distributed storage and processing of large arrays

NASA Technical Reports Server (NTRS)

Mehrota, P.; Pratt, T. W.

1983-01-01

A conceptual model for parallel computations on large arrays is developed. The model provides a set of language concepts appropriate for processing arrays which are generally too large to fit in the primary memories of a multiprocessor system. The semantic model is used to represent arrays on a concurrent architecture in such a way that the performance realities inherent in the distributed storage and processing can be adequately represented. An implementation of the large array concept as an Ada package is also described.

A Tale of Two Comets: ISON

NASA Image and Video Library

2013-11-25

An optical color image of galaxies is seen here overlaid with X-ray data magenta from NASA Nuclear Spectroscopic Telescope Array NuSTAR. Both magenta blobs show X-rays from massive black holes buried at the hearts of galaxies.

The radiation asymmetry in MGI rapid shutdown on J-TEXT tokamak

NASA Astrophysics Data System (ADS)

Tong, Ruihai; Chen, Zhongyong; Huang, Duwei; Cheng, Zhifeng; Zhang, Xiaolong; Zhuang, Ge; J-TEXT Team

2017-10-01

Disruptions, the sudden termination of tokamak fusion plasmas by instabilities, have the potential to cause severe material wall damage to large tokamaks like ITER. The mitigation of disruption damage is an essential part of any fusion reactor system. Massive gas injection (MGI) rapid shutdown is a technique in which large amounts of noble gas are injected into the plasma in order to safely radiate the plasma energy evenly over the entire plasma-facing first wall. However, the radiated energy during the thermal quench (TQ) in massive gas injection (MGI) induced disruptions is found toroidal asymmetric, and the degrees of asymmetry correlate with the gas penetration and MGI induced magnetohydrodynamics (MHD) activities. A toroidal and poloidal array of ultraviolet photodiodes (AXUV) has been developed to investigate the radiation asymmetry on J-TEXT tokamak. Together with the upgraded mirnov probe arrays, the relation between MGI triggered MHD activities with radiation asymmetry is studied.

Taking the Measure of Massive Stars and their Environments with the CHARA Array Long-baseline Interferometer

NASA Astrophysics Data System (ADS)

Gies, Douglas R.

2017-11-01

Most massive stars are so distant that their angular diameters are too small for direct resolution. However, the observational situation is now much more favorable, thanks to new opportunities available with optical/IR long-baseline interferometry. The Georgia State University Center for High Angular Resolution Astronomy Array at Mount Wilson Observatory is a six-telescope instrument with a maximum baseline of 330 meters, which is capable of resolving stellar disks with diameters as small as 0.2 milliarcsec. The distant stars are no longer out of range, and many kinds of investigations are possible. Here we summarize a number of studies involving angular diameter measurements and effective temperature estimates for OB stars, binary and multiple stars (including the σ Orionis system), and outflows in Luminous Blue Variables. An enlarged visitors program will begin in 2017 that will open many opportunities for new programs in high angular resolution astronomy.

Gemini Follow-up of Two Massive H I Clouds Discovered with the Australian Square Kilometer Array Pathfinder

NASA Astrophysics Data System (ADS)

Madrid, Juan P.; Lee-Waddell, Karen; Serra, Paolo; Koribalski, Bärbel S.; Schirmer, Mischa; Spekkens, Kristine; Wang, Jing

2018-02-01

Using the Gemini Multi Object Spectrograph (GMOS) we search for optical counterparts of two massive (∼109 M ⊙) neutral hydrogen clouds near the spiral galaxy IC 5270, located in the outskirts of the IC 1459 group. These two H I clouds were recently discovered using the Australian Square Kilometer Array Pathfinder (ASKAP). Two low surface brightness optical counterparts to one of these H I clouds are identified in the new Gemini data that reaches down to magnitudes of ∼27.5 mag in the g-band. The observed H I mass-to-light ratio derived with these new data, {M}{{H}{{I}}}/{L}g=242, is among the highest reported to date. We are also able to rule out that the two H I clouds are dwarf companions of IC 5270. Tidal interactions and ram pressure stripping are plausible explanations for the physical origin of these two clouds.

A study of DC-DC converters with MCT's for arcjet power supplies

NASA Technical Reports Server (NTRS)

Stuart, Thomas A.

1994-01-01

Many arcjet DC power supplies use PWM full bridge converters with large arrays of parallel FET's. This report investigates an alternative supply using a variable frequency series resonant converter with small arrays of parallel MCT's (metal oxide semiconductor controlled thyristors). The reasons for this approach are to: increase reliability by reducing the number of switching devices; and decrease the surface mounting area of the switching arrays. The variable frequency series resonant approach is used because the relatively slow switching speed of the MCT precludes the use of PWM. The 10 kW converter operated satisfactorily with an efficiency of over 91 percent. Test results indicate this efficiency could be increased further by additional optimization of the series resonant inductor.

Role of APOE Isoforms in the Pathogenesis of TBI Induced Alzheimer’s Disease

DTIC Science & Technology

2015-10-01

global deletion, APOE targeted replacement, complex breeding, CCI model optimization, mRNA library generation, high throughput massive parallel ...ATP binding cassette transporter A1 (ABCA1) is a lipid transporter that controls the generation of HDL in plasma and ApoE-containing lipoproteins in... parallel sequencing, mRNA-seq, behavioral testing, mem- ory impairement, recovery. 3 Overall Project Summary During the reported period, we have been able

Application of lean manufacturing concepts to drug discovery: rapid analogue library synthesis.

PubMed

Weller, Harold N; Nirschl, David S; Petrillo, Edward W; Poss, Michael A; Andres, Charles J; Cavallaro, Cullen L; Echols, Martin M; Grant-Young, Katherine A; Houston, John G; Miller, Arthur V; Swann, R Thomas

2006-01-01

The application of parallel synthesis to lead optimization programs in drug discovery has been an ongoing challenge since the first reports of library synthesis. A number of approaches to the application of parallel array synthesis to lead optimization have been attempted over the years, ranging from widespread deployment by (and support of) individual medicinal chemists to centralization as a service by an expert core team. This manuscript describes our experience with the latter approach, which was undertaken as part of a larger initiative to optimize drug discovery. In particular, we highlight how concepts taken from the manufacturing sector can be applied to drug discovery and parallel synthesis to improve the timeliness and thus the impact of arrays on drug discovery.

Applications and accuracy of the parallel diagonal dominant algorithm

NASA Technical Reports Server (NTRS)

Sun, Xian-He

1993-01-01

The Parallel Diagonal Dominant (PDD) algorithm is a highly efficient, ideally scalable tridiagonal solver. In this paper, a detailed study of the PDD algorithm is given. First the PDD algorithm is introduced. Then the algorithm is extended to solve periodic tridiagonal systems. A variant, the reduced PDD algorithm, is also proposed. Accuracy analysis is provided for a class of tridiagonal systems, the symmetric, and anti-symmetric Toeplitz tridiagonal systems. Implementation results show that the analysis gives a good bound on the relative error, and the algorithm is a good candidate for the emerging massively parallel machines.

Scalability and Portability of Two Parallel Implementations of ADI

NASA Technical Reports Server (NTRS)

Phung, Thanh; VanderWijngaart, Rob F.

1994-01-01

Two domain decompositions for the implementation of the NAS Scalar Penta-diagonal Parallel Benchmark on MIMD systems are investigated, namely transposition and multi-partitioning. Hardware platforms considered are the Intel iPSC/860 and Paragon XP/S-15, and clusters of SGI workstations on ethernet, communicating through PVM. It is found that the multi-partitioning strategy offers the kind of coarse granularity that allows scaling up to hundreds of processors on a massively parallel machine. Moreover, efficiency is retained when the code is ported verbatim (save message passing syntax) to a PVM environment on a modest size cluster of workstations.

Nuclide Depletion Capabilities in the Shift Monte Carlo Code

DOE PAGES

Davidson, Gregory G.; Pandya, Tara M.; Johnson, Seth R.; ...

2017-12-21

A new depletion capability has been developed in the Exnihilo radiation transport code suite. This capability enables massively parallel domain-decomposed coupling between the Shift continuous-energy Monte Carlo solver and the nuclide depletion solvers in ORIGEN to perform high-performance Monte Carlo depletion calculations. This paper describes this new depletion capability and discusses its various features, including a multi-level parallel decomposition, high-order transport-depletion coupling, and energy-integrated power renormalization. Several test problems are presented to validate the new capability against other Monte Carlo depletion codes, and the parallel performance of the new capability is analyzed.

Crystal Orientation Controlled Photovoltaic Properties of Multilayer GaAs Nanowire Arrays.

PubMed

Han, Ning; Yang, Zai-Xing; Wang, Fengyun; Yip, SenPo; Li, Dapan; Hung, Tak Fu; Chen, Yunfa; Ho, Johnny C

2016-06-28

In recent years, despite significant progress in the synthesis, characterization, and integration of various nanowire (NW) material systems, crystal orientation controlled NW growth as well as real-time assessment of their growth-structure-property relationships still presents one of the major challenges in deploying NWs for practical large-scale applications. In this study, we propose, design, and develop a multilayer NW printing scheme for the determination of crystal orientation controlled photovoltaic properties of parallel GaAs NW arrays. By tuning the catalyst thickness and nucleation and growth temperatures in the two-step chemical vapor deposition, crystalline GaAs NWs with uniform, pure ⟨110⟩ and ⟨111⟩ orientations and other mixture ratios can be successfully prepared. Employing lift-off resists, three-layer NW parallel arrays can be easily attained for X-ray diffraction in order to evaluate their growth orientation along with the fabrication of NW parallel array based Schottky photovoltaic devices for the subsequent performance assessment. Notably, the open-circuit voltage of purely ⟨111⟩-oriented NW arrayed cells is far higher than that of ⟨110⟩-oriented NW arrayed counterparts, which can be interpreted by the different surface Fermi level pinning that exists on various NW crystal surface planes due to the different As dangling bond densities. All this indicates the profound effect of NW crystal orientation on physical and chemical properties of GaAs NWs, suggesting the careful NW design considerations for achieving optimal photovoltaic performances. The approach presented here could also serve as a versatile and powerful platform for in situ characterization of other NW materials.

The CAnadian NIRISS Unbiased Cluster Survey (CANUCS)

NASA Astrophysics Data System (ADS)

Ravindranath, Swara; NIRISS GTO Team

2017-06-01

CANUCS GTO program is a JWST spectroscopy and imaging survey of five massive galaxy clusters and ten parallel fields using the NIRISS low-resolution grisms, NIRCam imaging and NIRSpec multi-object spectroscopy. The primary goal is to understand the evolution of low mass galaxies across cosmic time. The resolved emission line maps and line ratios for many galaxies, with some at resolution of 100pc via the magnification by gravitational lensing will enable determining the spatial distribution of star formation, dust and metals. Other science goals include the detection and characterization of galaxies within the reionization epoch, using multiply-imaged lensed galaxies to constrain cluster mass distributions and dark matter substructure, and understanding star-formation suppression in the most massive galaxy clusters. In this talk I will describe the science goals of the CANUCS program. The proposed prime and parallel observations will be presented with details of the implementation of the observation strategy using JWST proposal planning tools.

Integration of targeted sequencing and NIPT into clinical practice in a Chinese family with maple syrup urine disease.

PubMed

You, Yanqin; Sun, Yan; Li, Xuchao; Li, Yali; Wei, Xiaoming; Chen, Fang; Ge, Huijuan; Lan, Zhangzhang; Zhu, Qian; Tang, Ying; Wang, Shujuan; Gao, Ya; Jiang, Fuman; Song, Jiaping; Shi, Quan; Zhu, Xuan; Mu, Feng; Dong, Wei; Gao, Vince; Jiang, Hui; Yi, Xin; Wang, Wei; Gao, Zhiying

2014-08-01

This article demonstrates a prominent noninvasive prenatal approach to assist the clinical diagnosis of a single-gene disorder disease, maple syrup urine disease, using targeted sequencing knowledge from the affected family. The method reported here combines novel mutant discovery in known genes by targeted massively parallel sequencing with noninvasive prenatal testing. By applying this new strategy, we successfully revealed novel mutations in the gene BCKDHA (Ex2_4dup and c.392A>G) in this Chinese family and developed a prenatal haplotype-assisted approach to noninvasively detect the genotype of the fetus (transmitted from both parents). This is the first report of integration of targeted sequencing and noninvasive prenatal testing into clinical practice. Our study has demonstrated that this massively parallel sequencing-based strategy can potentially be used for single-gene disorder diagnosis in the future.

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

PubMed

Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

2013-08-01

Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq.

PubMed

Hu, Peng; Fabyanic, Emily; Kwon, Deborah Y; Tang, Sheng; Zhou, Zhaolan; Wu, Hao

2017-12-07

Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-assisted purification of nuclei with droplet microfluidics to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ∼18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.

PubMed

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin

2014-10-14

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

PubMed Central

Gole, Jeff; Gore, Athurva; Richards, Andrew; Chiu, Yu-Jui; Fung, Ho-Lim; Bushman, Diane; Chiang, Hsin-I; Chun, Jerold; Lo, Yu-Hwa; Zhang, Kun

2013-01-01

Genome sequencing of single cells has a variety of applications, including characterizing difficult-to-culture microorganisms and identifying somatic mutations in single cells from mammalian tissues. A major hurdle in this process is the bias in amplifying the genetic material from a single cell, a procedure known as polymerase cloning. Here we describe the microwell displacement amplification system (MIDAS), a massively parallel polymerase cloning method in which single cells are randomly distributed into hundreds to thousands of nanoliter wells and simultaneously amplified for shotgun sequencing. MIDAS reduces amplification bias because polymerase cloning occurs in physically separated nanoliter-scale reactors, facilitating the de novo assembly of near-complete microbial genomes from single E. coli cells. In addition, MIDAS allowed us to detect single-copy number changes in primary human adult neurons at 1–2 Mb resolution. MIDAS will further the characterization of genomic diversity in many heterogeneous cell populations. PMID:24213699

Massive formation of square array junctions dramatically alters cell shape but does not cause lens opacity in the cav1-KO mice.

PubMed

Biswas, Sondip K; Brako, Lawrence; Lo, Woo-Kuen

2014-08-01

The wavy square array junctions are composed of truncated aquaporin-0 (AQP0) proteins typically distributed in the deep cortical and nuclear fibers in wild-type lenses. These junctions may help maintain the narrowed extracellular spaces between fiber cells to minimize light scattering. Herein, we investigate the impact of the cell shape changes, due to abnormal formation of extensive square array junctions, on the lens opacification in the caveolin-1 knockout mice. The cav1-KO and wild-type mice at age 1-22 months were used. By light microscopy examinations, cav1-KO lenses at age 1-18 months were transparent in both cortical and nuclear regions, whereas some lenses older than 18 months old exhibited nuclear cataracts. Scanning EM consistently observed the massive formation of ridge-and-valley membrane surfaces in young fibers at approximately 150 μm deep in all cav1-KO lenses studied. In contrast, the typical ridge-and-valleys were only seen in mature fibers deeper than 400 μm in wild-type lenses. The resulting extensive ridge-and-valleys dramatically altered the overall cell shape in cav1-KO lenses. Remarkably, despite dramatic shape changes, these deformed fiber cells remained intact and made close contact with their neighboring cells. By freeze-fracture TEM, ridge-and-valleys exhibited the typical orthogonal arrangement of 6.6 nm square array intramembrane particles and displayed the narrowed extracellular spaces. Immunofluorescence analysis showed that AQP0 C-terminus labeling was significantly decreased in outer cortical fibers in cav1-KO lenses. However, freeze-fracture immunogold labeling showed that the AQP0 C-terminus antibody was sparsely distributed on the wavy square array junctions, suggesting that the cleavage of AQP0 C-termini might not yet be complete. The cav1-KO lenses with nuclear cataracts showed complete cellular breakdown and large globule formation in the lens nucleus. This study suggests that despite dramatic cell shape changes, the massive formation of wavy square array junctions in intact fibers may provide additional adhesive support for maintaining the narrowed extracellular spaces that are crucial for the transparency of cav1-KO lenses. Copyright © 2014 Elsevier Ltd. All rights reserved.

Toward Wearable Energy Storage Devices: Paper-Based Biofuel Cells based on a Screen-Printing Array Structure.

PubMed

Shitanda, Isao; Momiyama, Misaki; Watanabe, Naoto; Tanaka, Tomohiro; Tsujimura, Seiya; Hoshi, Yoshinao; Itagaki, Masayuki

2017-10-01

A novel paper-based biofuel cell with a series/parallel array structure has been fabricated, in which the cell voltage and output power can easily be adjusted as required by printing. The output of the fabricated 4-series/4-parallel biofuel cell reached 0.97±0.02 mW at 1.4 V, which is the highest output power reported to date for a paper-based biofuel cell. This work contributes to the development of flexible, wearable energy storage device.

Inband radar cross section of phased arrays with parallel feeds

NASA Astrophysics Data System (ADS)

Flokas, Vassilios

1994-06-01

Approximate formulas for the inband radar cross section of arrays with parallel feeds are presented. To obtain the formulas, multiple reflections are neglected, and devices of the same type are assumed to have identical electrical performance. The approximate results were compared to the results obtained using a scattering matrix formulation. Both methods were in agreement in predicting RCS lobe positions, levels, and behavior with scanning. The advantages of the approximate method are its computational efficiency and its flexibility in handling an arbitrary number of coupler levels.

Controlled Growth of Parallel Oriented ZnO Nanostructural Arrays on Ga2O3 Nanowires

DTIC Science & Technology

2008-11-01

Controlled Growth of Parallel Oriented ZnO Nanostructural Arrays on Ga2O3 Nanowires Lena Mazeina,* Yoosuf N. Picard, and Sharka M. Prokes Electronics...Manuscript ReceiVed NoVember 6, 2008 ABSTRACT: Novel hierarchical ZnO- Ga2O3 nanostructures were fabricated via a two stage growth process. Nanowires of Ga2O3 ...nanobrushes (NBs) with Ga2O3 as the core and ZnO as the branches self-assembling symmetrically in six equiangular directions around the core

New Hybridized Surface Wave Approach for Geotechnical Modeling of Shear Wave Velocity at Strong Motion Recording Stations

NASA Astrophysics Data System (ADS)

Kayen, R.; Carkin, B.; Minasian, D.

2006-12-01

Strong motion recording (SMR) networks often have little or no shear wave velocity measurements at stations where characterization of site amplification and site period effects is needed. Using the active Spectral Analysis of Surface Waves (SASW) method, and passive H/V microtremor method we have investigated nearly two hundred SMR sites in California, Alaska, Japan, Australia, China and Taiwan. We are conducting these studies, in part, to develop a new hybridized method of site characterization that utilizes a parallel array of harmonic-wave sources for active-source SASW, and a single long period seismometer for passive-source microtremor measurement. Surface wave methods excel in their ability to non-invasively and rapidly characterize the variation of ground stiffness properties with depth below the surface. These methods are lightweight, inexpensive to deploy, and time-efficient. They have been shown to produce accurate and deep soil stiffness profiles. By placing and wiring shakers in a large parallel circuit, either side-by-side on the ground or in a trailer-mounted array, a strong in-phase harmonic wave can be produced. The effect of arraying many sources in parallel is to increase the amplitude of waves received at far-away spaced seismometers at low frequencies so as to extend the longest wavelengths of the captured dispersion curve. The USGS system for profiling uses this concept by arraying between two and eight electro-mechanical harmonic-wave shakers. With large parallel arrays of vibrators, a dynamic force in excess of 1000 lb can be produced to vibrate the ground and produce surface waves. We adjust the harmonic wave through a swept-sine procedure to profile surface wave dispersion down to a frequency of 1 Hz and out to surface wave-wavelengths of 200-1000 meters, depending on the site stiffness. The parallel-array SASW procedure is augmented using H/V microtremor data collected with the active source turned off. Passive array microtremor data reveal the natural and resonance characteristics of the ground by capturing persistent natural vibrations. These microtremors are the result of the interaction of surface waves arriving from distant sources and the stiffness structure of the site under investigation. As such, these resonance effects are effective in constraining the layer thicknesses of the SASW shear wave velocity structure and aid in determining the depth of the deepest layer. Together, the hybridized SASW and H/V procedure provides a complete data set for modeling the geotechnical aspects of ground amplification of earthquake motions. Data from these investigations are available at http://walrus.wr.usgs.gov/geotech.

Distributing coil elements in three dimensions enhances parallel transmission multiband RF performance: A simulation study in the human brain at 7 Tesla.

PubMed

Wu, Xiaoping; Tian, Jinfeng; Schmitter, Sebastian; Vaughan, J Tommy; Uğurbil, Kâmil; Van de Moortele, Pierre-François

2016-06-01

We explore the advantages of using a double-ring radiofrequency (RF) array and slice orientation to design parallel transmission (pTx) multiband (MB) pulses for simultaneous multislice (SMS) imaging with whole-brain coverage at 7 Tesla (T). A double-ring head array with 16 elements split evenly in two rings stacked in the z-direction was modeled and compared with two single-ring arrays consisting of 8 or 16 elements. The array performance was evaluated by designing band-specific pTx MB pulses with local specific absorption rate (SAR) control. The impact of slice orientations was also investigated. The double-ring array consistently and significantly outperformed the other two single-ring arrays, with peak local SAR reduced by up to 40% at a fixed excitation error of 0.024. For all three arrays, exciting sagittal or coronal slices yielded better RF performance than exciting axial or oblique slices. A double-ring RF array can be used to drastically improve SAR versus excitation fidelity tradeoff for pTx MB pulse design for brain imaging at 7 T; therefore, it is preferable against single-ring RF array designs when pursuing various biomedical applications of pTx SMS imaging. In comparing the stripline arrays, coronal and sagittal slices are more advantageous than axial and oblique slices for pTx MB pulses. Magn Reson Med 75:2464-2472, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

High Resolution Size Analysis of Fetal DNA in the Urine of Pregnant Women by Paired-End Massively Parallel Sequencing

PubMed Central

Tsui, Nancy B. Y.; Jiang, Peiyong; Chow, Katherine C. K.; Su, Xiaoxi; Leung, Tak Y.; Sun, Hao; Chan, K. C. Allen; Chiu, Rossa W. K.; Lo, Y. M. Dennis

2012-01-01

Background Fetal DNA in maternal urine, if present, would be a valuable source of fetal genetic material for noninvasive prenatal diagnosis. However, the existence of fetal DNA in maternal urine has remained controversial. The issue is due to the lack of appropriate technology to robustly detect the potentially highly degraded fetal DNA in maternal urine. Methodology We have used massively parallel paired-end sequencing to investigate cell-free DNA molecules in maternal urine. Catheterized urine samples were collected from seven pregnant women during the third trimester of pregnancies. We detected fetal DNA by identifying sequenced reads that contained fetal-specific alleles of the single nucleotide polymorphisms. The sizes of individual urinary DNA fragments were deduced from the alignment positions of the paired reads. We measured the fractional fetal DNA concentration as well as the size distributions of fetal and maternal DNA in maternal urine. Principal Findings Cell-free fetal DNA was detected in five of the seven maternal urine samples, with the fractional fetal DNA concentrations ranged from 1.92% to 4.73%. Fetal DNA became undetectable in maternal urine after delivery. The total urinary cell-free DNA molecules were less intact when compared with plasma DNA. Urinary fetal DNA fragments were very short, and the most dominant fetal sequences were between 29 bp and 45 bp in length. Conclusions With the use of massively parallel sequencing, we have confirmed the existence of transrenal fetal DNA in maternal urine, and have shown that urinary fetal DNA was heavily degraded. PMID:23118982

Massively parallel cis-regulatory analysis in the mammalian central nervous system

PubMed Central

Shen, Susan Q.; Myers, Connie A.; Hughes, Andrew E.O.; Byrne, Leah C.; Flannery, John G.; Corbo, Joseph C.

2016-01-01

Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell–derived organoids. PMID:26576614

Massively Parallel Simulations of Diffusion in Dense Polymeric Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faulon, Jean-Loup, Wilcox, R.T.

1997-11-01

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

FDD Massive MIMO Channel Estimation With Arbitrary 2D-Array Geometry

NASA Astrophysics Data System (ADS)

Dai, Jisheng; Liu, An; Lau, Vincent K. N.

2018-05-01

This paper addresses the problem of downlink channel estimation in frequency-division duplexing (FDD) massive multiple-input multiple-output (MIMO) systems. The existing methods usually exploit hidden sparsity under a discrete Fourier transform (DFT) basis to estimate the cdownlink channel. However, there are at least two shortcomings of these DFT-based methods: 1) they are applicable to uniform linear arrays (ULAs) only, since the DFT basis requires a special structure of ULAs, and 2) they always suffer from a performance loss due to the leakage of energy over some DFT bins. To deal with the above shortcomings, we introduce an off-grid model for downlink channel sparse representation with arbitrary 2D-array antenna geometry, and propose an efficient sparse Bayesian learning (SBL) approach for the sparse channel recovery and off-grid refinement. The main idea of the proposed off-grid method is to consider the sampled grid points as adjustable parameters. Utilizing an in-exact block majorization-minimization (MM) algorithm, the grid points are refined iteratively to minimize the off-grid gap. Finally, we further extend the solution to uplink-aided channel estimation by exploiting the angular reciprocity between downlink and uplink channels, which brings enhanced recovery performance.

Implementation of High Time Delay Accuracy of Ultrasonic Phased Array Based on Interpolation CIC Filter

PubMed Central

Liu, Peilu; Li, Xinghua; Li, Haopeng; Su, Zhikun; Zhang, Hongxu

2017-01-01

In order to improve the accuracy of ultrasonic phased array focusing time delay, analyzing the original interpolation Cascade-Integrator-Comb (CIC) filter, an 8× interpolation CIC filter parallel algorithm was proposed, so that interpolation and multichannel decomposition can simultaneously process. Moreover, we summarized the general formula of arbitrary multiple interpolation CIC filter parallel algorithm and established an ultrasonic phased array focusing time delay system based on 8× interpolation CIC filter parallel algorithm. Improving the algorithmic structure, 12.5% of addition and 29.2% of multiplication was reduced, meanwhile the speed of computation is still very fast. Considering the existing problems of the CIC filter, we compensated the CIC filter; the compensated CIC filter’s pass band is flatter, the transition band becomes steep, and the stop band attenuation increases. Finally, we verified the feasibility of this algorithm on Field Programming Gate Array (FPGA). In the case of system clock is 125 MHz, after 8× interpolation filtering and decomposition, time delay accuracy of the defect echo becomes 1 ns. Simulation and experimental results both show that the algorithm we proposed has strong feasibility. Because of the fast calculation, small computational amount and high resolution, this algorithm is especially suitable for applications with high time delay accuracy and fast detection. PMID:29023385

Implementation of High Time Delay Accuracy of Ultrasonic Phased Array Based on Interpolation CIC Filter.

PubMed

Liu, Peilu; Li, Xinghua; Li, Haopeng; Su, Zhikun; Zhang, Hongxu

2017-10-12

In order to improve the accuracy of ultrasonic phased array focusing time delay, analyzing the original interpolation Cascade-Integrator-Comb (CIC) filter, an 8× interpolation CIC filter parallel algorithm was proposed, so that interpolation and multichannel decomposition can simultaneously process. Moreover, we summarized the general formula of arbitrary multiple interpolation CIC filter parallel algorithm and established an ultrasonic phased array focusing time delay system based on 8× interpolation CIC filter parallel algorithm. Improving the algorithmic structure, 12.5% of addition and 29.2% of multiplication was reduced, meanwhile the speed of computation is still very fast. Considering the existing problems of the CIC filter, we compensated the CIC filter; the compensated CIC filter's pass band is flatter, the transition band becomes steep, and the stop band attenuation increases. Finally, we verified the feasibility of this algorithm on Field Programming Gate Array (FPGA). In the case of system clock is 125 MHz, after 8× interpolation filtering and decomposition, time delay accuracy of the defect echo becomes 1 ns. Simulation and experimental results both show that the algorithm we proposed has strong feasibility. Because of the fast calculation, small computational amount and high resolution, this algorithm is especially suitable for applications with high time delay accuracy and fast detection.

Electron temperature and heat load measurements in the COMPASS divertor using the new system of probes

NASA Astrophysics Data System (ADS)

Adamek, J.; Seidl, J.; Horacek, J.; Komm, M.; Eich, T.; Panek, R.; Cavalier, J.; Devitre, A.; Peterka, M.; Vondracek, P.; Stöckel, J.; Sestak, D.; Grover, O.; Bilkova, P.; Böhm, P.; Varju, J.; Havranek, A.; Weinzettl, V.; Lovell, J.; Dimitrova, M.; Mitosinkova, K.; Dejarnac, R.; Hron, M.; The COMPASS Team; The EUROfusion MST1 Team

2017-11-01

A new system of probes was recently installed in the divertor of tokamak COMPASS in order to investigate the ELM energy density with high spatial and temporal resolution. The new system consists of two arrays of rooftop-shaped Langmuir probes (LPs) used to measure the floating potential or the ion saturation current density and one array of Ball-pen probes (BPPs) used to measure the plasma potential with a spatial resolution of ~3.5 mm. The combination of floating BPPs and LPs yields the electron temperature with microsecond temporal resolution. We report on the design of the new divertor probe arrays and first results of electron temperature profile measurements in ELMy H-mode and L-mode. We also present comparative measurements of the parallel heat flux using the new probe arrays and fast infrared termography (IR) data during L-mode with excellent agreement between both techniques using a heat power transmission coefficient γ  =  7. The ELM energy density {{\\varepsilon }\\parallel } was measured during a set of NBI assisted ELMy H-mode discharges. The peak values of {{\\varepsilon }\\parallel } were compared with those predicted by model and with experimental data from JET, AUG and MAST with a good agreement.

Aberration compensation of an ultrasound imaging instrument with a reduced number of channels.

PubMed

Jiang, Wei; Astheimer, Jeffrey P; Waag, Robert C

2012-10-01

Focusing and imaging qualities of an ultrasound imaging system that uses aberration correction were experimentally investigated as functions of the number of parallel channels. Front-end electronics that consolidate signals from multiple physical elements can be used to lower hardware and computational costs by reducing the number of parallel channels. However, the signals from sparse arrays of synthetic elements yield poorer aberration estimates. In this study, aberration estimates derived from synthetic arrays of varying element sizes are evaluated by comparing compensated receive focuses, compensated transmit focuses, and compensated b-scan images of a point target and a cyst phantom. An array of 80 x 80 physical elements with a pitch of 0.6 x 0.6 mm was used for all of the experiments and the aberration was produced by a phantom selected to mimic propagation through abdominal wall. The results show that aberration correction derived from synthetic arrays with pitches that have a diagonal length smaller than 70% of the correlation length of the aberration yield focuses and images of approximately the same quality. This connection between correlation length of the aberration and synthetic element size provides a guideline for determining the number of parallel channels that are required when designing imaging systems that employ aberration correction.

General design approach and practical realization of decoupling matrices for parallel transmission coils.

PubMed

Mahmood, Zohaib; McDaniel, Patrick; Guérin, Bastien; Keil, Boris; Vester, Markus; Adalsteinsson, Elfar; Wald, Lawrence L; Daniel, Luca

2016-07-01

In a coupled parallel transmit (pTx) array, the power delivered to a channel is partially distributed to other channels because of coupling. This power is dissipated in circulators resulting in a significant reduction in power efficiency. In this study, a technique for designing robust decoupling matrices interfaced between the RF amplifiers and the coils is proposed. The decoupling matrices ensure that most forward power is delivered to the load without loss of encoding capabilities of the pTx array. The decoupling condition requires that the impedance matrix seen by the power amplifiers is a diagonal matrix whose entries match the characteristic impedance of the power amplifiers. In this work, the impedance matrix of the coupled coils is diagonalized by a successive multiplication by its eigenvectors. A general design procedure and software are developed to generate automatically the hardware that implements diagonalization using passive components. The general design method is demonstrated by decoupling two example parallel transmit arrays. Our decoupling matrices achieve better than -20 db decoupling in both cases. A robust framework for designing decoupling matrices for pTx arrays is presented and validated. The proposed decoupling strategy theoretically scales to any arbitrary number of channels. Magn Reson Med 76:329-339, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Laser illumination of multiple capillaries that form a waveguide

DOEpatents

Dhadwal, Harbans S.; Quesada, Mark A.; Studier, F. William

1998-08-04

A system and method are disclosed for efficient laser illumination of the interiors of multiple capillaries simultaneously, and collection of light emitted from them. Capillaries in a parallel array can form an optical waveguide wherein refraction at the cylindrical surfaces confines side-on illuminating light to the core of each successive capillary in the array. Methods are provided for determining conditions where capillaries will form a waveguide and for assessing and minimizing losses due to reflection. Light can be delivered to the arrayed capillaries through an integrated fiber optic transmitter or through a pair of such transmitters aligned coaxially at opposite sides of the array. Light emitted from materials within the capillaries can be carried to a detection system through optical fibers, each of which collects light from a single capillary, with little cross talk between the capillaries. The collection ends of the optical fibers can be in a parallel array with the same spacing as the capillary array, so that the collection fibers can all be aligned to the capillaries simultaneously. Applicability includes improving the efficiency of many analytical methods that use capillaries, including particularly high-throughput DNA sequencing and diagnostic methods based on capillary electrophoresis.

Laser illumination of multiple capillaries that form a waveguide

DOEpatents

Dhadwal, H.S.; Quesada, M.A.; Studier, F.W.

1998-08-04

A system and method are disclosed for efficient laser illumination of the interiors of multiple capillaries simultaneously, and collection of light emitted from them. Capillaries in a parallel array can form an optical waveguide wherein refraction at the cylindrical surfaces confines side-on illuminating light to the core of each successive capillary in the array. Methods are provided for determining conditions where capillaries will form a waveguide and for assessing and minimizing losses due to reflection. Light can be delivered to the arrayed capillaries through an integrated fiber optic transmitter or through a pair of such transmitters aligned coaxially at opposite sides of the array. Light emitted from materials within the capillaries can be carried to a detection system through optical fibers, each of which collects light from a single capillary, with little cross talk between the capillaries. The collection ends of the optical fibers can be in a parallel array with the same spacing as the capillary array, so that the collection fibers can all be aligned to the capillaries simultaneously. Applicability includes improving the efficiency of many analytical methods that use capillaries, including particularly high-throughput DNA sequencing and diagnostic methods based on capillary electrophoresis. 35 figs.

Fast disk array for image storage

NASA Astrophysics Data System (ADS)

Feng, Dan; Zhu, Zhichun; Jin, Hai; Zhang, Jiangling

1997-01-01

A fast disk array is designed for the large continuous image storage. It includes a high speed data architecture and the technology of data striping and organization on the disk array. The high speed data path which is constructed by two dual port RAM and some control circuit is configured to transfer data between a host system and a plurality of disk drives. The bandwidth can be more than 100 MB/s if the data path based on PCI (peripheral component interconnect). The organization of data stored on the disk array is similar to RAID 4. Data are striped on a plurality of disk, and each striping unit is equal to a track. I/O instructions are performed in parallel on the disk drives. An independent disk is used to store the parity information in the fast disk array architecture. By placing the parity generation circuit directly on the SCSI (or SCSI 2) bus, the parity information can be generated on the fly. It will affect little on the data writing in parallel on the other disks. The fast disk array architecture designed in the paper can meet the demands of the image storage.

Implementation and Characterization of Three-Dimensional Particle-in-Cell Codes on Multiple-Instruction-Multiple-Data Massively Parallel Supercomputers

NASA Technical Reports Server (NTRS)

Lyster, P. M.; Liewer, P. C.; Decyk, V. K.; Ferraro, R. D.

1995-01-01

A three-dimensional electrostatic particle-in-cell (PIC) plasma simulation code has been developed on coarse-grain distributed-memory massively parallel computers with message passing communications. Our implementation is the generalization to three-dimensions of the general concurrent particle-in-cell (GCPIC) algorithm. In the GCPIC algorithm, the particle computation is divided among the processors using a domain decomposition of the simulation domain. In a three-dimensional simulation, the domain can be partitioned into one-, two-, or three-dimensional subdomains ("slabs," "rods," or "cubes") and we investigate the efficiency of the parallel implementation of the push for all three choices. The present implementation runs on the Intel Touchstone Delta machine at Caltech; a multiple-instruction-multiple-data (MIMD) parallel computer with 512 nodes. We find that the parallel efficiency of the push is very high, with the ratio of communication to computation time in the range 0.3%-10.0%. The highest efficiency (> 99%) occurs for a large, scaled problem with 64(sup 3) particles per processing node (approximately 134 million particles of 512 nodes) which has a push time of about 250 ns per particle per time step. We have also developed expressions for the timing of the code which are a function of both code parameters (number of grid points, particles, etc.) and machine-dependent parameters (effective FLOP rate, and the effective interprocessor bandwidths for the communication of particles and grid points). These expressions can be used to estimate the performance of scaled problems--including those with inhomogeneous plasmas--to other parallel machines once the machine-dependent parameters are known.

Solving very large, sparse linear systems on mesh-connected parallel computers

NASA Technical Reports Server (NTRS)

Opsahl, Torstein; Reif, John

1987-01-01

The implementation of Pan and Reif's Parallel Nested Dissection (PND) algorithm on mesh connected parallel computers is described. This is the first known algorithm that allows very large, sparse linear systems of equations to be solved efficiently in polylog time using a small number of processors. How the processor bound of PND can be matched to the number of processors available on a given parallel computer by slowing down the algorithm by constant factors is described. Also, for the important class of problems where G(A) is a grid graph, a unique memory mapping that reduces the inter-processor communication requirements of PND to those that can be executed on mesh connected parallel machines is detailed. A description of an implementation on the Goodyear Massively Parallel Processor (MPP), located at Goddard is given. Also, a detailed discussion of data mappings and performance issues is given.

System and method for representing and manipulating three-dimensional objects on massively parallel architectures

DOEpatents

Karasick, Michael S.; Strip, David R.

1996-01-01

A parallel computing system is described that comprises a plurality of uniquely labeled, parallel processors, each processor capable of modelling a three-dimensional object that includes a plurality of vertices, faces and edges. The system comprises a front-end processor for issuing a modelling command to the parallel processors, relating to a three-dimensional object. Each parallel processor, in response to the command and through the use of its own unique label, creates a directed-edge (d-edge) data structure that uniquely relates an edge of the three-dimensional object to one face of the object. Each d-edge data structure at least includes vertex descriptions of the edge and a description of the one face. As a result, each processor, in response to the modelling command, operates upon a small component of the model and generates results, in parallel with all other processors, without the need for processor-to-processor intercommunication.

An Overview of Mesoscale Modeling Software for Energetic Materials Research

DTIC Science & Technology

2010-03-01

12 2.9 Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ...13 Table 10. LAMMPS summary...extensive reviews, lectures and workshops are available on multiscale modeling of materials applications (76-78). • Multi-phase mixtures of

Engineered plant biomass feedstock particles

DOEpatents

Dooley, James H [Federal Way, WA; Lanning, David N [Federal Way, WA; Broderick, Thomas F [Lake Forest Park, WA

2012-04-17

A new class of plant biomass feedstock particles characterized by consistent piece size and shape uniformity, high skeletal surface area, and good flow properties. The particles of plant biomass material having fibers aligned in a grain are characterized by a length dimension (L) aligned substantially parallel to the grain and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces. The L.times.W surfaces of particles with L/H dimension ratios of 4:1 or less are further elaborated by surface checking between longitudinally arrayed fibers. The length dimension L is preferably aligned within 30.degree. parallel to the grain, and more preferably within 10.degree. parallel to the grain. The plant biomass material is preferably selected from among wood, agricultural crop residues, plantation grasses, hemp, bagasse, and bamboo.

GPU computing in medical physics: a review.

PubMed

Pratx, Guillem; Xing, Lei

2011-05-01

The graphics processing unit (GPU) has emerged as a competitive platform for computing massively parallel problems. Many computing applications in medical physics can be formulated as data-parallel tasks that exploit the capabilities of the GPU for reducing processing times. The authors review the basic principles of GPU computing as well as the main performance optimization techniques, and survey existing applications in three areas of medical physics, namely image reconstruction, dose calculation and treatment plan optimization, and image processing.

Massively parallel and linear-scaling algorithm for second-order Møller-Plesset perturbation theory applied to the study of supramolecular wires

NASA Astrophysics Data System (ADS)

Kjærgaard, Thomas; Baudin, Pablo; Bykov, Dmytro; Eriksen, Janus Juul; Ettenhuber, Patrick; Kristensen, Kasper; Larkin, Jeff; Liakh, Dmitry; Pawłowski, Filip; Vose, Aaron; Wang, Yang Min; Jørgensen, Poul

2017-03-01

We present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide-Expand-Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide-Expand-Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, where X is either OpenMP or OpenACC. We demonstrate strong and weak scalability of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the "resolution of the identity second-order Møller-Plesset perturbation theory" (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24 440 basis functions and 91 280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods.

Parallel confocal detection of single biomolecules using diffractive optics and integrated detector units.

PubMed

Blom, H; Gösch, M

2004-04-01

The past few years we have witnessed a tremendous surge of interest in so-called array-based miniaturised analytical systems due to their value as extremely powerful tools for high-throughput sequence analysis, drug discovery and development, and diagnostic tests in medicine (see articles in Issue 1). Terminologies that have been used to describe these array-based bioscience systems include (but are not limited to): DNA-chip, microarrays, microchip, biochip, DNA-microarrays and genome chip. Potential technological benefits of introducing these miniaturised analytical systems include improved accuracy, multiplexing, lower sample and reagent consumption, disposability, and decreased analysis times, just to mention a few examples. Among the many alternative principles of detection-analysis (e.g.chemiluminescence, electroluminescence and conductivity), fluorescence-based techniques are widely used, examples being fluorescence resonance energy transfer, fluorescence quenching, fluorescence polarisation, time-resolved fluorescence, and fluorescence fluctuation spectroscopy (see articles in Issue 11). Time-dependent fluctuations of fluorescent biomolecules with different molecular properties, like molecular weight, translational and rotational diffusion time, colour and lifetime, potentially provide all the kinetic and thermodynamic information required in analysing complex interactions. In this mini-review article, we present recent extensions aimed to implement parallel laser excitation and parallel fluorescence detection that can lead to even further increase in throughput in miniaturised array-based analytical systems. We also report on developments and characterisations of multiplexing extension that allow multifocal laser excitation together with matched parallel fluorescence detection for parallel confocal dynamical fluorescence fluctuation studies at the single biomolecule level.

Massive parallel 3D PIC simulation of negative ion extraction

NASA Astrophysics Data System (ADS)

Revel, Adrien; Mochalskyy, Serhiy; Montellano, Ivar Mauricio; Wünderlich, Dirk; Fantz, Ursel; Minea, Tiberiu

2017-09-01

The 3D PIC-MCC code ONIX is dedicated to modeling Negative hydrogen/deuterium Ion (NI) extraction and co-extraction of electrons from radio-frequency driven, low pressure plasma sources. It provides valuable insight on the complex phenomena involved in the extraction process. In previous calculations, a mesh size larger than the Debye length was used, implying numerical electron heating. Important steps have been achieved in terms of computation performance and parallelization efficiency allowing successful massive parallel calculations (4096 cores), imperative to resolve the Debye length. In addition, the numerical algorithms have been improved in terms of grid treatment, i.e., the electric field near the complex geometry boundaries (plasma grid) is calculated more accurately. The revised model preserves the full 3D treatment, but can take advantage of a highly refined mesh. ONIX was used to investigate the role of the mesh size, the re-injection scheme for lost particles (extracted or wall absorbed), and the electron thermalization process on the calculated extracted current and plasma characteristics. It is demonstrated that all numerical schemes give the same NI current distribution for extracted ions. Concerning the electrons, the pair-injection technique is found well-adapted to simulate the sheath in front of the plasma grid.

GPAW - massively parallel electronic structure calculations with Python-based software.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Enkovaara, J.; Romero, N.; Shende, S.

2011-01-01

Electronic structure calculations are a widely used tool in materials science and large consumer of supercomputing resources. Traditionally, the software packages for these kind of simulations have been implemented in compiled languages, where Fortran in its different versions has been the most popular choice. While dynamic, interpreted languages, such as Python, can increase the effciency of programmer, they cannot compete directly with the raw performance of compiled languages. However, by using an interpreted language together with a compiled language, it is possible to have most of the productivity enhancing features together with a good numerical performance. We have used thismore » approach in implementing an electronic structure simulation software GPAW using the combination of Python and C programming languages. While the chosen approach works well in standard workstations and Unix environments, massively parallel supercomputing systems can present some challenges in porting, debugging and profiling the software. In this paper we describe some details of the implementation and discuss the advantages and challenges of the combined Python/C approach. We show that despite the challenges it is possible to obtain good numerical performance and good parallel scalability with Python based software.« less

Multidisciplinary Design Optimization (MDO) Methods: Their Synergy with Computer Technology in Design Process

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, Jaroslaw

1998-01-01

The paper identifies speed, agility, human interface, generation of sensitivity information, task decomposition, and data transmission (including storage) as important attributes for a computer environment to have in order to support engineering design effectively. It is argued that when examined in terms of these attributes the presently available environment can be shown to be inadequate a radical improvement is needed, and it may be achieved by combining new methods that have recently emerged from multidisciplinary design optimization (MDO) with massively parallel processing computer technology. The caveat is that, for successful use of that technology in engineering computing, new paradigms for computing will have to be developed - specifically, innovative algorithms that are intrinsically parallel so that their performance scales up linearly with the number of processors. It may be speculated that the idea of simulating a complex behavior by interaction of a large number of very simple models may be an inspiration for the above algorithms, the cellular automata are an example. Because of the long lead time needed to develop and mature new paradigms, development should be now, even though the widespread availability of massively parallel processing is still a few years away.

Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization

PubMed Central

Cazzaniga, Paolo; Nobile, Marco S.; Besozzi, Daniela; Bellini, Matteo; Mauri, Giancarlo

2014-01-01

The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations. PMID:25025072

Massively Multithreaded Maxflow for Image Segmentation on the Cray XMT-2

PubMed Central

Bokhari, Shahid H.; Çatalyürek, Ümit V.; Gurcan, Metin N.

2014-01-01

SUMMARY Image segmentation is a very important step in the computerized analysis of digital images. The maxflow mincut approach has been successfully used to obtain minimum energy segmentations of images in many fields. Classical algorithms for maxflow in networks do not directly lend themselves to efficient parallel implementations on contemporary parallel processors. We present the results of an implementation of Goldberg-Tarjan preflow-push algorithm on the Cray XMT-2 massively multithreaded supercomputer. This machine has hardware support for 128 threads in each physical processor, a uniformly accessible shared memory of up to 4 TB and hardware synchronization for each 64 bit word. It is thus well-suited to the parallelization of graph theoretic algorithms, such as preflow-push. We describe the implementation of the preflow-push code on the XMT-2 and present the results of timing experiments on a series of synthetically generated as well as real images. Our results indicate very good performance on large images and pave the way for practical applications of this machine architecture for image analysis in a production setting. The largest images we have run are 320002 pixels in size, which are well beyond the largest previously reported in the literature. PMID:25598745

Multidisciplinary Design Optimisation (MDO) Methods: Their Synergy with Computer Technology in the Design Process

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, Jaroslaw

1999-01-01

The paper identifies speed, agility, human interface, generation of sensitivity information, task decomposition, and data transmission (including storage) as important attributes for a computer environment to have in order to support engineering design effectively. It is argued that when examined in terms of these attributes the presently available environment can be shown to be inadequate. A radical improvement is needed, and it may be achieved by combining new methods that have recently emerged from multidisciplinary design optimisation (MDO) with massively parallel processing computer technology. The caveat is that, for successful use of that technology in engineering computing, new paradigms for computing will have to be developed - specifically, innovative algorithms that are intrinsically parallel so that their performance scales up linearly with the number of processors. It may be speculated that the idea of simulating a complex behaviour by interaction of a large number of very simple models may be an inspiration for the above algorithms; the cellular automata are an example. Because of the long lead time needed to develop and mature new paradigms, development should begin now, even though the widespread availability of massively parallel processing is still a few years away.

A massively asynchronous, parallel brain.

PubMed

Zeki, Semir

2015-05-19

Whether the visual brain uses a parallel or a serial, hierarchical, strategy to process visual signals, the end result appears to be that different attributes of the visual scene are perceived asynchronously--with colour leading form (orientation) by 40 ms and direction of motion by about 80 ms. Whatever the neural root of this asynchrony, it creates a problem that has not been properly addressed, namely how visual attributes that are perceived asynchronously over brief time windows after stimulus onset are bound together in the longer term to give us a unified experience of the visual world, in which all attributes are apparently seen in perfect registration. In this review, I suggest that there is no central neural clock in the (visual) brain that synchronizes the activity of different processing systems. More likely, activity in each of the parallel processing-perceptual systems of the visual brain is reset independently, making of the brain a massively asynchronous organ, just like the new generation of more efficient computers promise to be. Given the asynchronous operations of the brain, it is likely that the results of activities in the different processing-perceptual systems are not bound by physiological interactions between cells in the specialized visual areas, but post-perceptually, outside the visual brain.

Low-Speed Investigation of Upper-Surface Leading-Edge Blowing on a High-Speed Civil Transport Configuration

NASA Technical Reports Server (NTRS)

Banks, Daniel W.; Laflin, Brenda E. Gile; Kemmerly, Guy T.; Campbell, Bryan A.

1999-01-01

The paper identifies speed, agility, human interface, generation of sensitivity information, task decomposition, and data transmission (including storage) as important attributes for a computer environment to have in order to support engineering design effectively. It is argued that when examined in terms of these attributes the presently available environment can be shown to be inadequate. A radical improvement is needed, and it may be achieved by combining new methods that have recently emerged from multidisciplinary design optimisation (MDO) with massively parallel processing computer technology. The caveat is that, for successful use of that technology in engineering computing, new paradigms for computing will have to be developed - specifically, innovative algorithms that are intrinsically parallel so that their performance scales up linearly with the number of processors. It may be speculated that the idea of simulating a complex behaviour by interaction of a large number of very simple models may be an inspiration for the above algorithms; the cellular automata are an example. Because of the long lead time needed to develop and mature new paradigms, development should begin now, even though the widespread availability of massively parallel processing is still a few years away.

The galatic and LMC extreme line supergiants compared: IUE observations of the Henize-Carlson and Zoo star samples of massive supergiants. [Large Magellanic cloud (LMC)

NASA Technical Reports Server (NTRS)

Shore, S. N.; Sanduleak, N.; Brown, D. N.; Sonneborn, G.; Bopp, B. W.; Robinson, C. R.

1988-01-01

The Henize-Carlson sample of galactic massive supergiants, and a comparison between the Galactic and LMC samples are discussed. Several of the stars, notably He3-395 and S 127/LMC, have very similar shell characteristics. There appears to be little difference, other than luminosity, between the LMC and Galactic samples. One star, He3-1482, was detected with the Very Large Array at 6 cm. The UV data is combined with IRAS and optical information.

Suppressing correlations in massively parallel simulations of lattice models

NASA Astrophysics Data System (ADS)

Kelling, Jeffrey; Ódor, Géza; Gemming, Sibylle

2017-11-01

For lattice Monte Carlo simulations parallelization is crucial to make studies of large systems and long simulation time feasible, while sequential simulations remain the gold-standard for correlation-free dynamics. Here, various domain decomposition schemes are compared, concluding with one which delivers virtually correlation-free simulations on GPUs. Extensive simulations of the octahedron model for 2 + 1 dimensional Kardar-Parisi-Zhang surface growth, which is very sensitive to correlation in the site-selection dynamics, were performed to show self-consistency of the parallel runs and agreement with the sequential algorithm. We present a GPU implementation providing a speedup of about 30 × over a parallel CPU implementation on a single socket and at least 180 × with respect to the sequential reference.

The remote sensing image segmentation mean shift algorithm parallel processing based on MapReduce

NASA Astrophysics Data System (ADS)

Chen, Xi; Zhou, Liqing

2015-12-01

With the development of satellite remote sensing technology and the remote sensing image data, traditional remote sensing image segmentation technology cannot meet the massive remote sensing image processing and storage requirements. This article put cloud computing and parallel computing technology in remote sensing image segmentation process, and build a cheap and efficient computer cluster system that uses parallel processing to achieve MeanShift algorithm of remote sensing image segmentation based on the MapReduce model, not only to ensure the quality of remote sensing image segmentation, improved split speed, and better meet the real-time requirements. The remote sensing image segmentation MeanShift algorithm parallel processing algorithm based on MapReduce shows certain significance and a realization of value.

Line-drawing algorithms for parallel machines

NASA Technical Reports Server (NTRS)

Pang, Alex T.

1990-01-01

The fact that conventional line-drawing algorithms, when applied directly on parallel machines, can lead to very inefficient codes is addressed. It is suggested that instead of modifying an existing algorithm for a parallel machine, a more efficient implementation can be produced by going back to the invariants in the definition. Popular line-drawing algorithms are compared with two alternatives; distance to a line (a point is on the line if sufficiently close to it) and intersection with a line (a point on the line if an intersection point). For massively parallel single-instruction-multiple-data (SIMD) machines (with thousands of processors and up), the alternatives provide viable line-drawing algorithms. Because of the pixel-per-processor mapping, their performance is independent of the line length and orientation.

Building Educational Programs for the Australian Square Kilometre Array Pathfinder

NASA Astrophysics Data System (ADS)

Hollow, R.; Hobbs, G.

2010-08-01

The Australian Square Kilometre Array Pathfinder (ASKAP) will be an array of 36 antennas in Western Australia, each 12-m in diameter, and is due for operation in 2013. With a large instantaneous field-of-view ASKAP will survey the whole sky faster than existing radio telescopes, producing massive data sets. Government funding for ASKAP was contingent on it being available for education purposes, providing an exciting opportunity to develop innovative education projects for schools and citizen science. Building on the PULSE@Parkes program we plan to have a range of activities and resources, providing scope for student investigations. Challenges and educational opportunities are discussed.

Parallel scheduling of recursively defined arrays

NASA Technical Reports Server (NTRS)

Myers, T. J.; Gokhale, M. B.

1986-01-01

A new method of automatic generation of concurrent programs which constructs arrays defined by sets of recursive equations is described. It is assumed that the time of computation of an array element is a linear combination of its indices, and integer programming is used to seek a succession of hyperplanes along which array elements can be computed concurrently. The method can be used to schedule equations involving variable length dependency vectors and mutually recursive arrays. Portions of the work reported here have been implemented in the PS automatic program generation system.

Refractive multiple optical tweezers for parallel biochemical analysis in micro-fluidics

NASA Astrophysics Data System (ADS)

Merenda, Fabrice; Rohner, Johann; Pascoal, Pedro; Fournier, Jean-Marc; Vogel, Horst; Salathé, René-Paul

2007-02-01

We present a multiple laser tweezers system based on refractive optics. The system produces an array of 100 optical traps thanks to a refractive microlens array, whose focal plane is imaged into the focal plane of a high-NA microscope objective. This refractive multi-tweezers system is combined to micro-fluidics, aiming at performing simultaneous biochemical reactions on ensembles of free floating objects. Micro-fluidics allows both transporting the particles to the trapping area, and conveying biochemical reagents to the trapped particles. Parallel trapping in micro-fluidics is achieved with polystyrene beads as well as with native vesicles produced from mammalian cells. The traps can hold objects against fluid flows exceeding 100 micrometers per second. Parallel fluorescence excitation and detection on the ensemble of trapped particles is also demonstrated. Additionally, the system is capable of selectively and individually releasing particles from the tweezers array using a complementary steerable laser beam. Strategies for high-yield particle capture and individual particle release in a micro-fluidic environment are discussed. A comparison with diffractive optical tweezers enhances the pros and cons of refractive systems.

Evaluation of Orientation Performance of Attention Patterns for Blind Person.

PubMed

Fujisawa, Shoichiro; Ishibashi, Tatsuki; Sato, Katsuya; Ito, Sin-Ichi; Sueda, Osamu

2017-01-01

Tactile walking surface indicators (TWSIs) are installed on footpath to support independent travel for the blind. There are two types of TWSIs, attention patterns and guiding patterns. The attention pattern is usually installed at the crosswalk entrances. The direction of the crossing can be acquired by the row of the projection of the attention pattern through the soles of the shoes. In addition, truncated domes or cones of the attention pattern were arranged in a square grid, parallel or diagonal at 45 degrees to the principal direction of travel. However, the international standard organization (ISO) allows a wide-ranging size. In this research, the direction indicating performance was compared at the same intervals for the five diameters specified by the international standard. As a result of the experiment, the diagonal array does not indicate the direction of travel, but the projection row does indicate the direction of travel in the parallel array. When the attention pattern is installed at a crosswalk entrance, a parallel array should be installed in the direction of the crossing.

Integration of Si-CMOS embedded photo detector array and mixed signal processing system with embedded optical waveguide input

NASA Astrophysics Data System (ADS)

Kim, Daeik D.; Thomas, Mikkel A.; Brooke, Martin A.; Jokerst, Nan M.

2004-06-01

Arrays of embedded bipolar junction transistor (BJT) photo detectors (PD) and a parallel mixed-signal processing system were fabricated as a silicon complementary metal oxide semiconductor (Si-CMOS) circuit for the integration optical sensors on the surface of the chip. The circuit was fabricated with AMI 1.5um n-well CMOS process and the embedded PNP BJT PD has a pixel size of 8um by 8um. BJT PD was chosen to take advantage of its higher gain amplification of photo current than that of PiN type detectors since the target application is a low-speed and high-sensitivity sensor. The photo current generated by BJT PD is manipulated by mixed-signal processing system, which consists of parallel first order low-pass delta-sigma oversampling analog-to-digital converters (ADC). There are 8 parallel ADCs on the chip and a group of 8 BJT PDs are selected with CMOS switches. An array of PD is composed of three or six groups of PDs depending on the number of rows.

Two-dimensional radiant energy array computers and computing devices

NASA Technical Reports Server (NTRS)

Schaefer, D. H.; Strong, J. P., III (Inventor)

1976-01-01

Two dimensional digital computers and computer devices operate in parallel on rectangular arrays of digital radiant energy optical signal elements which are arranged in ordered rows and columns. Logic gate devices receive two input arrays and provide an output array having digital states dependent only on the digital states of the signal elements of the two input arrays at corresponding row and column positions. The logic devices include an array of photoconductors responsive to at least one of the input arrays for either selectively accelerating electrons to a phosphor output surface, applying potentials to an electroluminescent output layer, exciting an array of discrete radiant energy sources, or exciting a liquid crystal to influence crystal transparency or reflectivity.

An efficient parallel algorithm for matrix-vector multiplication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hendrickson, B.; Leland, R.; Plimpton, S.

The multiplication of a vector by a matrix is the kernel computation of many algorithms in scientific computation. A fast parallel algorithm for this calculation is therefore necessary if one is to make full use of the new generation of parallel supercomputers. This paper presents a high performance, parallel matrix-vector multiplication algorithm that is particularly well suited to hypercube multiprocessors. For an n x n matrix on p processors, the communication cost of this algorithm is O(n/[radical]p + log(p)), independent of the matrix sparsity pattern. The performance of the algorithm is demonstrated by employing it as the kernel in themore » well-known NAS conjugate gradient benchmark, where a run time of 6.09 seconds was observed. This is the best published performance on this benchmark achieved to date using a massively parallel supercomputer.« less

Beginning the Dialogue on the e-Transformation: Behavior Analysis' First Massive Open Online Course (MOOC).

PubMed

Rehfeldt, Ruth Anne; Jung, Heidi L; Aguirre, Angelica; Nichols, Jane L; Root, William B

2016-03-01

The e-Transformation in higher education, in which Massive Open Online Courses (MOOCs) are playing a pivotal role, has had an impact on the modality in which behavior analysis is taught. In this paper, we survey the history and implications of online education including MOOCs and describe the implementation and results for the discipline's first MOOC, delivered at Southern Illinois University in spring 2015. Implications for the globalization and free access of higher education are discussed, as well as the parallel between MOOCs and Skinner's teaching machines.

DC switching regulated power supply for driving an inductive load

DOEpatents

Dyer, George R.

1986-01-01

A power supply for driving an inductive load current from a dc power supply hrough a regulator circuit including a bridge arrangement of diodes and switching transistors controlled by a servo controller which regulates switching in response to the load current to maintain a selected load current. First and second opposite legs of the bridge are formed by first and second parallel-connected transistor arrays, respectively, while the third and fourth legs of the bridge are formed by appropriately connected first and second parallel connected diode arrays, respectively. The regulator may be operated in three "stages" or modes: (1) For current runup in the load, both first and second transistor switch arrays are turned "on" and current is supplied to the load through both transistor arrays. (2) When load current reaches the desired level, the first switch is turned "off", and load current "flywheels" through the second switch array and the fourth leg diode array connecting the second switch array in series with the load. Current is maintained by alternating between modes 1 and 2 at a suitable duty cycle and switching rate set by the controller. (3) Rapid current rundown is accomplished by turning both switch arrays "off", allowing load current to be dumped back into the source through the third and fourth diode arrays connecting the source in series opposition with the load to recover energy from the inductive load. The three operating states are controlled automatically by the controller.

DC switching regulated power supply for driving an inductive load

DOEpatents

Dyer, G.R.

1983-11-29

A dc switching regulated power supply for driving an inductive load is provided. The regulator basic circuit is a bridge arrangement of diodes and transistors. First and second opposite legs of the bridge are formed by first and second parallel-connected transistor arrays, respectively, while the third and fourth legs of the bridge are formed by appropriately connected first and second parallel connected diode arrays, respectively. A dc power supply is connected to the input of the bridge and the output is connected to the load. A servo controller is provided to control the switching rate of the transistors to maintain a desired current to the load. The regulator may be operated in three stages or modes: (1) for current runup in the load, both first and second transistor switch arrays are turned on and current is supplied to the load through both transistor arrays. (2) When load current reaches the desired level, the first switch is turned off, and load current flywheels through the second switch array and the fourth leg diode array connecting the second switch array in series with the load. Current is maintained by alternating between modes 1 and 2 at a suitable duty cycle and switching rate set by the controller. (3) Rapid current rundown is accomplished by turning both switch arrays off, allowing load current to be dumped back into the source through the third and fourth diode arrays connecting the source in series opposition with the load to recover energy from the inductive load.

A Pervasive Parallel Processing Framework for Data Visualization and Analysis at Extreme Scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moreland, Kenneth; Geveci, Berk

2014-11-01

The evolution of the computing world from teraflop to petaflop has been relatively effortless, with several of the existing programming models scaling effectively to the petascale. The migration to exascale, however, poses considerable challenges. All industry trends infer that the exascale machine will be built using processors containing hundreds to thousands of cores per chip. It can be inferred that efficient concurrency on exascale machines requires a massive amount of concurrent threads, each performing many operations on a localized piece of data. Currently, visualization libraries and applications are based off what is known as the visualization pipeline. In the pipelinemore » model, algorithms are encapsulated as filters with inputs and outputs. These filters are connected by setting the output of one component to the input of another. Parallelism in the visualization pipeline is achieved by replicating the pipeline for each processing thread. This works well for today’s distributed memory parallel computers but cannot be sustained when operating on processors with thousands of cores. Our project investigates a new visualization framework designed to exhibit the pervasive parallelism necessary for extreme scale machines. Our framework achieves this by defining algorithms in terms of worklets, which are localized stateless operations. Worklets are atomic operations that execute when invoked unlike filters, which execute when a pipeline request occurs. The worklet design allows execution on a massive amount of lightweight threads with minimal overhead. Only with such fine-grained parallelism can we hope to fill the billions of threads we expect will be necessary for efficient computation on an exascale machine.« less

A Fast Algorithm for Massively Parallel, Long-Term, Simulation of Complex Molecular Dynamics Systems

NASA Technical Reports Server (NTRS)

Jaramillo-Botero, Andres; Goddard, William A, III; Fijany, Amir

1997-01-01

The advances in theory and computing technology over the last decade have led to enormous progress in applying atomistic molecular dynamics (MD) methods to the characterization, prediction, and design of chemical, biological, and material systems,.