Science.gov

Sample records for massively parallel ligation

  1. Massively parallel visualization: Parallel rendering

    SciTech Connect

    Hansen, C.D.; Krogh, M.; White, W.

    1995-12-01

    This paper presents rendering algorithms, developed for massively parallel processors (MPPs), for polygonal, spheres, and volumetric data. The polygon algorithm uses a data parallel approach whereas the sphere and volume renderer use a MIMD approach. Implementations for these algorithms are presented for the Thinking Machines Corporation CM-5 MPP.

  2. Massively parallel mathematical sieves

    SciTech Connect

    Montry, G.R.

    1989-01-01

    The Sieve of Eratosthenes is a well-known algorithm for finding all prime numbers in a given subset of integers. A parallel version of the Sieve is described that produces computational speedups over 800 on a hypercube with 1,024 processing elements for problems of fixed size. Computational speedups as high as 980 are achieved when the problem size per processor is fixed. The method of parallelization generalizes to other sieves and will be efficient on any ensemble architecture. We investigate two highly parallel sieves using scattered decomposition and compare their performance on a hypercube multiprocessor. A comparison of different parallelization techniques for the sieve illustrates the trade-offs necessary in the design and implementation of massively parallel algorithms for large ensemble computers.

  3. Massively parallel processor computer

    NASA Technical Reports Server (NTRS)

    Fung, L. W. (Inventor)

    1983-01-01

    An apparatus for processing multidimensional data with strong spatial characteristics, such as raw image data, characterized by a large number of parallel data streams in an ordered array is described. It comprises a large number (e.g., 16,384 in a 128 x 128 array) of parallel processing elements operating simultaneously and independently on single bit slices of a corresponding array of incoming data streams under control of a single set of instructions. Each of the processing elements comprises a bidirectional data bus in communication with a register for storing single bit slices together with a random access memory unit and associated circuitry, including a binary counter/shift register device, for performing logical and arithmetical computations on the bit slices, and an I/O unit for interfacing the bidirectional data bus with the data stream source. The massively parallel processor architecture enables very high speed processing of large amounts of ordered parallel data, including spatial translation by shifting or sliding of bits vertically or horizontally to neighboring processing elements.

  4. Massively Parallel QCD

    SciTech Connect

    Soltz, R; Vranas, P; Blumrich, M; Chen, D; Gara, A; Giampap, M; Heidelberger, P; Salapura, V; Sexton, J; Bhanot, G

    2007-04-11

    The theory of the strong nuclear force, Quantum Chromodynamics (QCD), can be numerically simulated from first principles on massively-parallel supercomputers using the method of Lattice Gauge Theory. We describe the special programming requirements of lattice QCD (LQCD) as well as the optimal supercomputer hardware architectures that it suggests. We demonstrate these methods on the BlueGene massively-parallel supercomputer and argue that LQCD and the BlueGene architecture are a natural match. This can be traced to the simple fact that LQCD is a regular lattice discretization of space into lattice sites while the BlueGene supercomputer is a discretization of space into compute nodes, and that both are constrained by requirements of locality. This simple relation is both technologically important and theoretically intriguing. The main result of this paper is the speedup of LQCD using up to 131,072 CPUs on the largest BlueGene/L supercomputer. The speedup is perfect with sustained performance of about 20% of peak. This corresponds to a maximum of 70.5 sustained TFlop/s. At these speeds LQCD and BlueGene are poised to produce the next generation of strong interaction physics theoretical results.

  5. Parallel rendering techniques for massively parallel visualization

    SciTech Connect

    Hansen, C.; Krogh, M.; Painter, J.

    1995-07-01

    As the resolution of simulation models increases, scientific visualization algorithms which take advantage of the large memory. and parallelism of Massively Parallel Processors (MPPs) are becoming increasingly important. For large applications rendering on the MPP tends to be preferable to rendering on a graphics workstation due to the MPP`s abundant resources: memory, disk, and numerous processors. The challenge becomes developing algorithms that can exploit these resources while minimizing overhead, typically communication costs. This paper will describe recent efforts in parallel rendering for polygonal primitives as well as parallel volumetric techniques. This paper presents rendering algorithms, developed for massively parallel processors (MPPs), for polygonal, spheres, and volumetric data. The polygon algorithm uses a data parallel approach whereas the sphere and volume render use a MIMD approach. Implementations for these algorithms are presented for the Thinking Ma.chines Corporation CM-5 MPP.

  6. Massively Parallel MRI Detector Arrays

    PubMed Central

    Keil, Boris; Wald, Lawrence L

    2013-01-01

    Originally proposed as a method to increase sensitivity by extending the locally high-sensitivity of small surface coil elements to larger areas, the term parallel imaging now includes the use of array coils to perform image encoding. This methodology has impacted clinical imaging to the point where many examinations are performed with an array comprising multiple smaller surface coil elements as the detector of the MR signal. This article reviews the theoretical and experimental basis for the trend towards higher channel counts relying on insights gained from modeling and experimental studies as well as the theoretical analysis of the so-called “ultimate” SNR and g-factor. We also review the methods for optimally combining array data and changes in RF methodology needed to construct massively parallel MRI detector arrays and show some examples of state-of-the-art for highly accelerated imaging with the resulting highly parallel arrays. PMID:23453758

  7. 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.

  8. Massively parallel femtosecond laser processing.

    PubMed

    Hasegawa, Satoshi; Ito, Haruyasu; Toyoda, Haruyoshi; Hayasaki, Yoshio

    2016-08-01

    Massively parallel femtosecond laser processing with more than 1000 beams was demonstrated. Parallel beams were generated by a computer-generated hologram (CGH) displayed on a spatial light modulator (SLM). The key to this technique is to optimize the CGH in the laser processing system using a scheme called in-system optimization. It was analytically demonstrated that the number of beams is determined by the horizontal number of pixels in the SLM NSLM that is imaged at the pupil plane of an objective lens and a distance parameter pd obtained by dividing the distance between adjacent beams by the diffraction-limited beam diameter. A performance limitation of parallel laser processing in our system was estimated at NSLM of 250 and pd of 7.0. Based on these parameters, the maximum number of beams in a hexagonal close-packed structure was calculated to be 1189 by using an analytical equation. PMID:27505815

  9. 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. PMID:25823871

  10. Massively Parallel Computing: A Sandia Perspective

    SciTech Connect

    Dosanjh, Sudip S.; Greenberg, David S.; Hendrickson, Bruce; Heroux, Michael A.; Plimpton, Steve J.; Tomkins, James L.; Womble, David E.

    1999-05-06

    The computing power available to scientists and engineers has increased dramatically in the past decade, due in part to progress in making massively parallel computing practical and available. The expectation for these machines has been great. The reality is that progress has been slower than expected. Nevertheless, massively parallel computing is beginning to realize its potential for enabling significant break-throughs in science and engineering. This paper provides a perspective on the state of the field, colored by the authors' experiences using large scale parallel machines at Sandia National Laboratories. We address trends in hardware, system software and algorithms, and we also offer our view of the forces shaping the parallel computing industry.

  11. 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. PMID:21764615

  12. Massive parallelism in the future of science

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1988-01-01

    Massive parallelism appears in three domains of action of concern to scientists, where it produces collective action that is not possible from any individual agent's behavior. In the domain of data parallelism, computers comprising very large numbers of processing agents, one for each data item in the result will be designed. These agents collectively can solve problems thousands of times faster than current supercomputers. In the domain of distributed parallelism, computations comprising large numbers of resource attached to the world network will be designed. The network will support computations far beyond the power of any one machine. In the domain of people parallelism collaborations among large groups of scientists around the world who participate in projects that endure well past the sojourns of individuals within them will be designed. Computing and telecommunications technology will support the large, long projects that will characterize big science by the turn of the century. Scientists must become masters in these three domains during the coming decade.

  13. Template based parallel checkpointing in a massively parallel computer system

    DOEpatents

    Archer, Charles Jens; Inglett, Todd Alan

    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.

  14. Efficient communication in massively parallel computers

    SciTech Connect

    Cypher, R.E.

    1989-01-01

    A fundamental operation in parallel computation is sorting. Sorting is important not only because it is required by many algorithms, but also because it can be used to implement irregular, pointer-based communication. The author studies two algorithms for sorting in massively parallel computers. First, he examines Shellsort. Shellsort is a sorting algorithm that is based on a sequence of parameters called increments. Shellsort can be used to create a parallel sorting device known as a sorting network. Researchers have suggested that if the correct increment sequence is used, an optimal size sorting network can be obtained. All published increment sequences have been monotonically decreasing. He shows that no monotonically decreasing increment sequence will yield an optimal size sorting network. Second, he presents a sorting algorithm called Cubesort. Cubesort is the fastest known sorting algorithm for a variety of parallel computers aver a wide range of parameters. He also presents a paradigm for developing parallel algorithms that have efficient communication. The paradigm, called the data reduction paradigm, consists of using a divide-and-conquer strategy. Both the division and combination phases of the divide-and-conquer algorithm may require irregular, pointer-based communication between processors. However, the problem is divided so as to limit the amount of data that must be communicated. As a result the communication can be performed efficiently. He presents data reduction algorithms for the image component labeling problem, the closest pair problem and four versions of the parallel prefix problem.

  15. Time sharing massively parallel machines. Draft

    SciTech Connect

    Gorda, B.; Wolski, R.

    1995-03-01

    As part of the Massively Parallel Computing Initiative (MPCI) at the Lawrence Livermore National Laboratory, the authors have developed a simple, effective and portable time sharing mechanism by scheduling gangs of processes on tightly coupled parallel machines. By time-sharing the resources, the system interleaves production and interactive jobs. Immediate priority is given to interactive use, maintaining good response time. Production jobs are scheduled during idle periods, making use of the otherwise unused resources. In this paper the authors discuss their experience with gang scheduling over the 3 year life-time of the project. In section 2, they motivate the project and discuss some of its details. Section 3.0 describes the general scheduling problem and how gang scheduling addresses it. In section 4.0, they describe the implementation. Section 8.0 presents results culled over the lifetime of the project. They conclude this paper with some observations and possible future directions.

  16. Fracture simulations via massively parallel molecular dynamics

    SciTech Connect

    Holian, B.L.; Abraham, F.F.; Ravelo, R.

    1993-09-01

    Fracture simulations at the atomistic level have heretofore been carried out for relatively small systems of particles, typically 10,000 or less. In order to study anything approaching a macroscopic system, massively parallel molecular dynamics (MD) must be employed. In two spatial dimensions (2D), it is feasible to simulate a sample that is 0.1 {mu}m on a side. We report on recent MD simulations of mode I crack extension under tensile loading at high strain rates. The method of uniaxial, homogeneously expanding periodic boundary conditions was employed to represent tensile stress conditions near the crack tip. The effects of strain rate, temperature, material properties (equation of state and defect energies), and system size were examined. We found that, in order to mimic a bulk sample, several tricks (in addition to expansion boundary conditions) need to be employed: (1) the sample must be pre-strained to nearly the condition at which the crack will spontaneously open; (2) to relieve the stresses at free surfaces, such as the initial notch, annealing by kinetic-energy quenching must be carried out to prevent unwanted rarefactions; (3) sound waves emitted as the crack tip opens and dislocations emitted from the crack tip during blunting must be absorbed by special reservoir regions. The tricks described briefly in this paper will be especially important to carrying out feasible massively parallel 3D simulations via MD.

  17. Seismic imaging on massively parallel computers

    SciTech Connect

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

    1997-07-01

    A key to reducing the risks and costs associated with oil and gas exploration is the fast, accurate imaging of complex geologies, such as salt domes in the Gulf of Mexico and overthrust regions in US onshore regions. Pre-stack depth migration generally yields the most accurate images, and one approach to this is to solve the scalar-wave equation using finite differences. Current industry computational capabilities are insufficient for the application of finite-difference, 3-D, prestack, depth-migration algorithms. High performance computers and state-of-the-art algorithms and software are required to meet this need. As part of an ongoing ACTI project funded by the US Department of Energy, the authors have developed a finite-difference, 3-D prestack, depth-migration code for massively parallel computer systems. The goal of this work is to demonstrate that massively parallel computers (thousands of processors) can be used efficiently for seismic imaging, and that sufficient computing power exists (or soon will exist) to make finite-difference, prestack, depth migration practical for oil and gas exploration.

  18. MASSIVE HYBRID PARALLELISM FOR FULLY IMPLICIT MULTIPHYSICS

    SciTech Connect

    Cody J. Permann; David Andrs; John W. Peterson; Derek R. Gaston

    2013-05-01

    As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided.

  19. Massive hybrid parallelism for fully implicit multiphysics

    SciTech Connect

    Gaston, D. R.; Permann, C. J.; Andrs, D.; Peterson, J. W.

    2013-07-01

    As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided. (authors)

  20. A nanofluidic system for massively parallel PCR

    NASA Astrophysics Data System (ADS)

    Brenan, Colin; Morrison, Tom; Roberts, Douglas; Hurley, James

    2008-02-01

    Massively parallel nanofluidic systems are lab-on-a-chip devices where solution phase biochemical and biological analyses are implemented in high density arrays of nanoliter holes micro-machined in a thin platen. Polymer coatings make the interior surfaces of the holes hydrophilic and the exterior surface of the platen hydrophobic for precise and accurate self-metered loading of liquids into each hole without cross-contamination. We have created a "nanoplate" based on this concept, equivalent in performance to standard microtiter plates, having 3072 thirty-three nanoliter holes in a stainless steel platen the dimensions of a microscope slide. We report on the performance of this device for PCR-based single nucleotide polymorphism (SNP) genotyping or quantitative measurement of gene expression by real-time PCR in applications ranging from plant and animal diagnostics, agricultural genetics and human disease research.

  1. Multiplexed microsatellite recovery using massively parallel sequencing

    USGS Publications Warehouse

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  2. Fault tolerant massively parallel processing architecture

    SciTech Connect

    Balasubramanian, V.; Banerjee, P.

    1987-08-01

    This paper presents two massively parallel processing architectures suitable for solving a wide variety of algorithms of divide-and-conquer type for problems such as the discrete Fourier transform, production systems, design automation, and others. The first architecture, called the Chain-structured Butterfly ARchitecture (CBAR), consists of a two-dimensional array of N-L . (log/sub 2/(L)+1) processing elements (PE) organized as L levels of log/sub 2/(L)+1 stages, and which has the butterfly connection between PEs in consecutive stages with straight-through feedback between PEs in the last and first stages. This connection system has the desirable property of allowing thousands of PEs to be connected with O(N) connection cost, O(log/sub 2/(N/log/sub 2/N)) communication paths, and a small number (=4) of I/O ports per PE. However, this architecture is not fault tolerant. The authors, therefore, propose a second architecture, called the REconfigurable Chain-structured Butterfly ARchitecture (RECBAR), which is a modified version of the CBAR. The RECBAR possesses all the desirable features of the CBAR, with the number of I/O ports per PE increased to six, and uses O(log/sub 2/N)/N) overhead in PEs and approximately 50% overhead in links to achieve single-level fault tolerance. Reliability improvements of the RECBAR over the CBAR are studied. This paper also presents a distributed diagnostic and structuring algorithm for the RECBAR that enables the architecture to detect faults and structure itself accordingly within 2 . log/sub 2/(L)+1 time steps, thus making it a truly fault tolerant architecture.

  3. 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.

  4. Experimental free-space optical network for massively parallel computers

    NASA Astrophysics Data System (ADS)

    Araki, S.; Kajita, M.; Kasahara, K.; Kubota, K.; Kurihara, K.; Redmond, I.; Schenfeld, E.; Suzaki, T.

    1996-03-01

    A free-space optical interconnection scheme is described for massively parallel processors based on the interconnection-cached network architecture. The optical network operates in a circuit-switching mode. Combined with a packet-switching operation among the circuit-switched optical channels, a high-bandwidth, low-latency network for massively parallel processing results. The design and assembly of a 64-channel experimental prototype is discussed, and operational results are presented.

  5. 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.

  6. 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.

  7. EFFICIENT SCHEDULING OF PARALLEL JOBS ON MASSIVELY PARALLEL SYSTEMS

    SciTech Connect

    F. PETRINI; W. FENG

    1999-09-01

    We present buffered coscheduling, a new methodology to multitask parallel jobs in a message-passing environment and to develop parallel programs that can pave the way to the efficient implementation of a distributed operating system. Buffered coscheduling is based on three innovative techniques: communication buffering, strobing, and non-blocking communication. By leveraging these techniques, we can perform effective optimizations based on the global status of the parallel machine rather than on the limited knowledge available locally to each processor. The advantages of buffered coscheduling include higher resource utilization, reduced communication overhead, efficient implementation of low-control strategies and fault-tolerant protocols, accurate performance modeling, and a simplified yet still expressive parallel programming model. Preliminary experimental results show that buffered coscheduling is very effective in increasing the overall performance in the presence of load imbalance and communication-intensive workloads.

  8. Massively parallel neural encoding and decoding of visual stimuli.

    PubMed

    Lazar, Aurel A; Zhou, Yiyin

    2012-08-01

    The massively parallel nature of video Time Encoding Machines (TEMs) calls for scalable, massively parallel decoders that are implemented with neural components. The current generation of decoding algorithms is based on computing the pseudo-inverse of a matrix and does not satisfy these requirements. Here we consider video TEMs with an architecture built using Gabor receptive fields and a population of Integrate-and-Fire neurons. We show how to build a scalable architecture for video Time Decoding Machines using recurrent neural networks. Furthermore, we extend our architecture to handle the reconstruction of visual stimuli encoded with massively parallel video TEMs having neurons with random thresholds. Finally, we discuss in detail our algorithms and demonstrate their scalability and performance on a large scale GPU cluster. PMID:22397951

  9. Staging memory for massively parallel processor

    NASA Technical Reports Server (NTRS)

    Batcher, Kenneth E. (Inventor)

    1988-01-01

    The invention herein relates to a computer organization capable of rapidly processing extremely large volumes of data. A staging memory is provided having a main stager portion consisting of a large number of memory banks which are accessed in parallel to receive, store, and transfer data words simultaneous with each other. Substager portions interconnect with the main stager portion to match input and output data formats with the data format of the main stager portion. An address generator is coded for accessing the data banks for receiving or transferring the appropriate words. Input and output permutation networks arrange the lineal order of data into and out of the memory banks.

  10. Design and implementation of a massively parallel version of DIRECT

    SciTech Connect

    He, J.; Verstak, A.; Watson, L.; Sosonkina, M.

    2007-10-24

    This paper describes several massively parallel implementations for a global search algorithm DIRECT. Two parallel schemes take different approaches to address DIRECT's design challenges imposed by memory requirements and data dependency. Three design aspects in topology, data structures, and task allocation are compared in detail. The goal is to analytically investigate the strengths and weaknesses of these parallel schemes, identify several key sources of inefficiency, and experimentally evaluate a number of improvements in the latest parallel DIRECT implementation. The performance studies demonstrate improved data structure efficiency and load balancing on a 2200 processor cluster.

  11. Contact-impact simulations on massively parallel SIMD supercomputers

    SciTech Connect

    Plaskacz, E.J. ); Belytscko, T.; Chiang, H.Y. )

    1992-01-01

    The implementation of explicit finite element methods with contact-impact on massively parallel SIMD computers is described. The basic parallel finite element algorithm employs an exchange process which minimizes interprocessor communication at the expense of redundant computations and storage. The contact-impact algorithm is based on the pinball method in which compatibility is enforced by preventing interpenetration on spheres embedded in elements adjacent to surfaces. The enhancements to the pinball algorithm include a parallel assembled surface normal algorithm and a parallel detection of interpenetrating pairs. Some timings with and without contact-impact are given.

  12. Massively parallel solution of the assignment problem. Technical report

    SciTech Connect

    Wein, J.; Zenios, S.

    1990-12-01

    In this paper we discuss the design, implementation and effectiveness of massively parallel algorithms for the solution of large-scale assignment problems. In particular, we study the auction algorithms of Bertsekas, an algorithm based on the method of multipliers of Hestenes and Powell, and an algorithm based on the alternating direction method of multipliers of Eckstein. We discuss alternative approaches to the massively parallel implementation of the auction algorithm, including Jacobi, Gauss-Seidel and a hybrid scheme. The hybrid scheme, in particular, exploits two different levels of parallelism and an efficient way of communicating the data between them without the need to perform general router operations across the hypercube network. We then study the performance of massively parallel implementations of two methods of multipliers. Implementations are carried out on the Connection Machine CM-2, and the algorithms are evaluated empirically with the solution of large scale problems. The hybrid scheme significantly outperforms all of the other methods and gives the best computational results to date for a massively parallel solution to this problem.

  13. Shift: A Massively Parallel Monte Carlo Radiation Transport Package

    SciTech Connect

    Pandya, Tara M; Johnson, Seth R; Davidson, Gregory G; Evans, Thomas M; Hamilton, Steven P

    2015-01-01

    This paper discusses the massively-parallel Monte Carlo radiation transport package, Shift, developed at Oak Ridge National Laboratory. It reviews the capabilities, implementation, and parallel performance of this code package. Scaling results demonstrate very good strong and weak scaling behavior of the implemented algorithms. Benchmark results from various reactor problems show that Shift results compare well to other contemporary Monte Carlo codes and experimental results.

  14. Proposal for massively parallel data storage system

    NASA Technical Reports Server (NTRS)

    Mansuripur, M.

    1992-01-01

    An architecture for integrating large numbers of data storage units (drives) to form a distributed mass storage system is proposed. The network of interconnected units consists of nodes and links. At each node there resides a controller board, a data storage unit and, possibly, a local/remote user-terminal. The links (twisted-pair wires, coax cables, or fiber-optic channels) provide the communications backbone of the network. There is no central controller for the system as a whole; all decisions regarding allocation of resources, routing of messages and data-blocks, creation and distribution of redundant data-blocks throughout the system (for protection against possible failures), frequency of backup operations, etc., are made locally at individual nodes. The system can handle as many user-terminals as there are nodes in the network. Various users compete for resources by sending their requests to the local controller-board and receiving allocations of time and storage space. In principle, each user can have access to the entire system, and all drives can be running in parallel to service the requests for one or more users. The system is expandable up to a maximum number of nodes, determined by the number of routing-buffers built into the controller boards. Additional drives, controller-boards, user-terminals, and links can be simply plugged into an existing system in order to expand its capacity.

  15. Efficient parallel global garbage collection on massively parallel computers

    SciTech Connect

    Kamada, Tomio; Matsuoka, Satoshi; Yonezawa, Akinori

    1994-12-31

    On distributed-memory high-performance MPPs where processors are interconnected by an asynchronous network, efficient Garbage Collection (GC) becomes difficult due to inter-node references and references within pending, unprocessed messages. The parallel global GC algorithm (1) takes advantage of reference locality, (2) efficiently traverses references over nodes, (3) admits minimum pause time of ongoing computations, and (4) has been shown to scale up to 1024 node MPPs. The algorithm employs a global weight counting scheme to substantially reduce message traffic. The two methods for confirming the arrival of pending messages are used: one counts numbers of messages and the other uses network `bulldozing.` Performance evaluation in actual implementations on a multicomputer with 32-1024 nodes, Fujitsu AP1000, reveals various favorable properties of the algorithm.

  16. Solving unstructured grid problems on massively parallel computers

    NASA Technical Reports Server (NTRS)

    Hammond, Steven W.; Schreiber, Robert

    1990-01-01

    A highly parallel graph mapping technique that enables one to efficiently solve unstructured grid problems on massively parallel computers is presented. Many implicit and explicit methods for solving discretized partial differential equations require each point in the discretization to exchange data with its neighboring points every time step or iteration. The cost of this communication can negate the high performance promised by massively parallel computing. To eliminate this bottleneck, the graph of the irregular problem is mapped into the graph representing the interconnection topology of the computer such that the sum of the distances that the messages travel is minimized. It is shown that using the heuristic mapping algorithm significantly reduces the communication time compared to a naive assignment of processes to processors.

  17. 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.

  18. Supercomputing on massively parallel bit-serial architectures

    NASA Technical Reports Server (NTRS)

    Iobst, Ken

    1985-01-01

    Research on the Goodyear Massively Parallel Processor (MPP) suggests that high-level parallel languages are practical and can be designed with powerful new semantics that allow algorithms to be efficiently mapped to the real machines. For the MPP these semantics include parallel/associative array selection for both dense and sparse matrices, variable precision arithmetic to trade accuracy for speed, micro-pipelined train broadcast, and conditional branching at the processing element (PE) control unit level. The preliminary design of a FORTRAN-like parallel language for the MPP has been completed and is being used to write programs to perform sparse matrix array selection, min/max search, matrix multiplication, Gaussian elimination on single bit arrays and other generic algorithms. A description is given of the MPP design. Features of the system and its operation are illustrated in the form of charts and diagrams.

  19. 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.

  20. Development of massively parallel quantum chemistry program SMASH

    NASA Astrophysics Data System (ADS)

    Ishimura, Kazuya

    2015-12-01

    A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C150H30)2 with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer.

  1. Development of massively parallel quantum chemistry program SMASH

    SciTech Connect

    Ishimura, Kazuya

    2015-12-31

    A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C{sub 150}H{sub 30}){sub 2} with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer.

  2. Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

    PubMed Central

    Starita, Lea M.; Young, David L.; Islam, Muhtadi; Kitzman, Jacob O.; Gullingsrud, Justin; Hause, Ronald J.; Fowler, Douglas M.; Parvin, Jeffrey D.; Shendure, Jay; Fields, Stanley

    2015-01-01

    Interpreting variants of uncertain significance (VUS) is a central challenge in medical genetics. One approach is to experimentally measure the functional consequences of VUS, but to date this approach has been post hoc and low throughput. Here we use massively parallel assays to measure the effects of nearly 2000 missense substitutions in the RING domain of BRCA1 on its E3 ubiquitin ligase activity and its binding to the BARD1 RING domain. From the resulting scores, we generate a model to predict the capacities of full-length BRCA1 variants to support homology-directed DNA repair, the essential role of BRCA1 in tumor suppression, and show that it outperforms widely used biological-effect prediction algorithms. We envision that massively parallel functional assays may facilitate the prospective interpretation of variants observed in clinical sequencing. PMID:25823446

  3. Solving mazes with memristors: A massively parallel approach

    NASA Astrophysics Data System (ADS)

    Pershin, Yuriy V.; di Ventra, Massimiliano

    2011-10-01

    Solving mazes is not just a fun pastime: They are prototype models in several areas of science and technology. However, when maze complexity increases, their solution becomes cumbersome and very time consuming. Here, we show that a network of memristors—resistors with memory—can solve such a nontrivial problem quite easily. In particular, maze solving by the network of memristors occurs in a massively parallel fashion since all memristors in the network participate simultaneously in the calculation. The result of the calculation is then recorded into the memristors’ states and can be used and/or recovered at a later time. Furthermore, the network of memristors finds all possible solutions in multiple-solution mazes and sorts out the solution paths according to their length. Our results demonstrate not only the application of memristive networks to the field of massively parallel computing, but also an algorithm to solve mazes, which could find applications in different fields.

  4. Massively parallel sequencing, a new method for detecting adventitious agents.

    PubMed

    Onions, David; Kolman, John

    2010-05-01

    There has been an upsurge of interest in developing new veterinary and human vaccines and, in turn, this has involved the development of new mammalian and insect cell substrates. Excluding adventitious agents from these cells can be problematic, particularly for cells derived from species with limited virological investigation. Massively parallel sequencing is a powerful new method for the identification of viruses and other adventitious agents, without prior knowledge of the nature of the agent. We have developed methods using random priming to detect viruses in the supernatants from cell substrates or in virus seed stocks. Using these methods we have recently discovered a new parvovirus in bovine serum. When applied to sequencing the transcriptome, massively parallel sequencing can reveal latent or silent infections. Enormous amounts of data are developed in this process usually between 100 and 400 Mbp. Consequently, sophisticated bioinformatic algorithms are required to analyse and verify virus targets.

  5. TSE computers - A means for massively parallel computations

    NASA Technical Reports Server (NTRS)

    Strong, J. P., III

    1976-01-01

    A description is presented of hardware concepts for building a massively parallel processing system for two-dimensional data. The processing system is to use logic arrays of 128 x 128 elements which perform over 16 thousand operations simultaneously. Attention is given to image data, logic arrays, basic image logic functions, a prototype negator, an interleaver device, image logic circuits, and an image memory circuit.

  6. Computational fluid dynamics on a massively parallel computer

    NASA Technical Reports Server (NTRS)

    Jespersen, Dennis C.; Levit, Creon

    1989-01-01

    A finite difference code was implemented for the compressible Navier-Stokes equations on the Connection Machine, a massively parallel computer. The code is based on the ARC2D/ARC3D program and uses the implicit factored algorithm of Beam and Warming. The codes uses odd-even elimination to solve linear systems. Timings and computation rates are given for the code, and a comparison is made with a Cray XMP.

  7. Massively parallel Wang Landau sampling on multiple GPUs

    SciTech Connect

    Yin, Junqi; Landau, D. P.

    2012-01-01

    Wang Landau sampling is implemented on the Graphics Processing Unit (GPU) with the Compute Unified Device Architecture (CUDA). Performances on three different GPU cards, including the new generation Fermi architecture card, are compared with that on a Central Processing Unit (CPU). The parameters for massively parallel Wang Landau sampling are tuned in order to achieve fast convergence. For simulations of the water cluster systems, we obtain an average of over 50 times speedup for a given workload.

  8. MIMD massively parallel methods for engineering and science problems

    SciTech Connect

    Camp, W.J.; Plimpton, S.J.

    1993-08-01

    MIMD massively parallel computers promise unique power and flexibility for engineering and scientific simulations. In this paper we review the development of a number of software methods and algorithms for scientific and engineering problems which are helping to realize that promise. We discuss new domain decomposition, load balancing, data layout and communications methods applicable to simulations in a broad range of technical field including signal processing, multi-dimensional structural and fluid mechanics, materials science, and chemical and biological systems.

  9. 3D seismic imaging on massively parallel computers

    SciTech Connect

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

    1997-02-01

    The ability to image complex geologies such as salt domes in the Gulf of Mexico and thrusts in mountainous regions is a key to reducing the risk and cost associated with oil and gas exploration. Imaging these structures, however, is computationally expensive. Datasets can be terabytes in size, and the processing time required for the multiple iterations needed to produce a velocity model can take months, even with the massively parallel computers available today. Some algorithms, such as 3D, finite-difference, prestack, depth migration remain beyond the capacity of production seismic processing. Massively parallel processors (MPPs) and algorithms research are the tools that will enable this project to provide new seismic processing capabilities to the oil and gas industry. The goals of this work are to (1) develop finite-difference algorithms for 3D, prestack, depth migration; (2) develop efficient computational approaches for seismic imaging and for processing terabyte datasets on massively parallel computers; and (3) develop a modular, portable, seismic imaging code.

  10. Requirements for supercomputing in energy research: The transition to massively parallel computing

    SciTech Connect

    Not Available

    1993-02-01

    This report discusses: The emergence of a practical path to TeraFlop computing and beyond; requirements of energy research programs at DOE; implementation: supercomputer production computing environment on massively parallel computers; and implementation: user transition to massively parallel computing.

  11. 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.

  12. 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.

  13. 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.

  14. A massively parallel fractional step solver for incompressible flows

    SciTech Connect

    Houzeaux, G. Vazquez, M. Aubry, R. Cela, J.M.

    2009-09-20

    This paper presents a parallel implementation of fractional solvers for the incompressible Navier-Stokes equations using an algebraic approach. Under this framework, predictor-corrector and incremental projection schemes are seen as sub-classes of the same class, making apparent its differences and similarities. An additional advantage of this approach is to set a common basis for a parallelization strategy, which can be extended to other split techniques or to compressible flows. The predictor-corrector scheme consists in solving the momentum equation and a modified 'continuity' equation (namely a simple iteration for the pressure Schur complement) consecutively in order to converge to the monolithic solution, thus avoiding fractional errors. On the other hand, the incremental projection scheme solves only one iteration of the predictor-corrector per time step and adds a correction equation to fulfill the mass conservation. As shown in the paper, these two schemes are very well suited for massively parallel implementation. In fact, when compared with monolithic schemes, simpler solvers and preconditioners can be used to solve the non-symmetric momentum equations (GMRES, Bi-CGSTAB) and to solve the symmetric continuity equation (CG, Deflated CG). This gives good speedup properties of the algorithm. The implementation of the mesh partitioning technique is presented, as well as the parallel performances and speedups for thousands of processors.

  15. Numerical computation on massively parallel hypercubes. [Connection machine

    SciTech Connect

    McBryan, O.A.

    1986-01-01

    We describe numerical computations on the Connection Machine, a massively parallel hypercube architecture with 65,536 single-bit processors and 32 Mbytes of memory. A parallel extension of COMMON LISP, provides access to the processors and network. The rich software environment is further enhanced by a powerful virtual processor capability, which extends the degree of fine-grained parallelism beyond 1,000,000. We briefly describe the hardware and indicate the principal features of the parallel programming environment. We then present implementations of SOR, multigrid and pre-conditioned conjugate gradient algorithms for solving partial differential equations on the Connection Machine. Despite the lack of floating point hardware, computation rates above 100 megaflops have been achieved in PDE solution. Virtual processors prove to be a real advantage, easing the effort of software development while improving system performance significantly. The software development effort is also facilitated by the fact that hypercube communications prove to be fast and essentially independent of distance. 29 refs., 4 figs.

  16. Polymerase chain reaction preparation of template for massively parallel pyrosequencing.

    PubMed

    Whetten, Ross W; Sofía, Valenzuela A; Frampton, John

    2009-04-01

    Massively parallel pyrosequencing of DNA fragments immobilized on beads has been applied to genome survey sequencing and transcriptome analysis of a variety of eukaryotic organisms, including laboratory model species, agricultural crops and livestock, and species of interest to population biologists and ecologists. Preparation of sufficient high-quality template for sequencing has been an obstacle to sequence analysis of nucleic acids from tissues or cell types available in limited quantities. We report that the use of a biotinylated primer for polymerase chain reaction amplification allows removal of excess primer and poly(A) tract fragments from the sequencing templates, providing much higher yields of useful sequence information from pyrosequencing of amplified templates. This advance allows deep sequencing analysis of nucleic acids isolated from very small tissue samples. Massively parallel pyrosequencing is particularly useful for preliminary investigations of species that have not yet been the subject of significant genomic research, as genomic survey sequences and catalogs of expressed genes provide a means of linking the biology of less intensively studied species to that of more intensively studied model organisms. We obtained over 220 Mb of transcript DNA sequences from Abies fraseri (Pursh) Poir., a conifer species native to the southern Appalachian Mountains of eastern North America. Comparison of the resulting assembled putative transcripts with similar data obtained by other sequencing methods from other conifers demonstrates the utility of the improved sequencing template preparation. PMID:19503624

  17. The performance realities of massively parallel processors: A case study

    SciTech Connect

    Lubeck, O.M.; Simmons, M.L.; Wasserman, H.J.

    1992-07-01

    This paper presents the results of an architectural comparison of SIMD massive parallelism, as implemented in the Thinking Machines Corp. CM-2 computer, and vector or concurrent-vector processing, as implemented in the Cray Research Inc. Y-MP/8. The comparison is based primarily upon three application codes that represent Los Alamos production computing. Tests were run by porting optimized CM Fortran codes to the Y-MP, so that the same level of optimization was obtained on both machines. The results for fully-configured systems, using measured data rather than scaled data from smaller configurations, show that the Y-MP/8 is faster than the 64k CM-2 for all three codes. A simple model that accounts for the relative characteristic computational speeds of the two machines, and reduction in overall CM-2 performance due to communication or SIMD conditional execution, is included. The model predicts the performance of two codes well, but fails for the third code, because the proportion of communications in this code is very high. Other factors, such as memory bandwidth and compiler effects, are also discussed. Finally, the paper attempts to show the equivalence of the CM-2 and Y-MP programming models, and also comments on selected future massively parallel processor designs.

  18. Massively parallel density functional calculations for thousands of atoms: KKRnano

    NASA Astrophysics Data System (ADS)

    Thiess, A.; Zeller, R.; Bolten, M.; Dederichs, P. H.; Blügel, S.

    2012-06-01

    Applications of existing precise electronic-structure methods based on density functional theory are typically limited to the treatment of about 1000 inequivalent atoms, which leaves unresolved many open questions in material science, e.g., on complex defects, interfaces, dislocations, and nanostructures. KKRnano is a new massively parallel linear scaling all-electron density functional algorithm in the framework of the Korringa-Kohn-Rostoker (KKR) Green's-function method. We conceptualized, developed, and optimized KKRnano for large-scale applications of many thousands of atoms without compromising on the precision of a full-potential all-electron method, i.e., it is a method without any shape approximation of the charge density or potential. A key element of the new method is the iterative solution of the sparse linear Dyson equation, which we parallelized atom by atom, across energy points in the complex plane and for each spin degree of freedom using the message passing interface standard, followed by a lower-level OpenMP parallelization. This hybrid four-level parallelization allows for an efficient use of up to 100000 processors on the latest generation of supercomputers. The iterative solution of the Dyson equation is significantly accelerated, employing preconditioning techniques making use of coarse-graining principles expressed in a block-circulant preconditioner. In this paper, we will describe the important elements of this new algorithm, focusing on the parallelization and preconditioning and showing scaling results for NiPd alloys up to 8192 atoms and 65536 processors. At the end, we present an order-N algorithm for large-scale simulations of metallic systems, making use of the nearsighted principle of the KKR Green's-function approach by introducing a truncation of the electron scattering to a local cluster of atoms, the size of which is determined by the requested accuracy. By exploiting this algorithm, we show linear scaling calculations of more

  19. A Computational Fluid Dynamics Algorithm on a Massively Parallel Computer

    NASA Technical Reports Server (NTRS)

    Jespersen, Dennis C.; Levit, Creon

    1989-01-01

    The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. We investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicit time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. We find that the Connection Machine ran achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as today's most powerful conventional supercomputers.

  20. Optimal evaluation of array expressions on massively parallel machines

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert; Teng, Shang-Hua

    1992-01-01

    We investigate the problem of evaluating FORTRAN 90 style array expressions on massively parallel distributed-memory machines. On such machines, an elementwise operation can be performed in constant time for arrays whose corresponding elements are in the same processor. If the arrays are not aligned in this manner, the cost of aligning them is part of the cost of evaluating the expression. The choice of where to perform the operation then affects this cost. We present algorithms based on dynamic programming to solve this problem efficiently for a wide variety of interconnection schemes, including multidimensional grids and rings, hypercubes, and fat-trees. We also consider expressions containing operations that change the shape of the arrays, and show that our approach extends naturally to handle this case.

  1. Development of a massively parallel parachute performance prediction code

    SciTech Connect

    Peterson, C.W.; Strickland, J.H.; Wolfe, W.P.; Sundberg, W.D.; McBride, D.D.

    1997-04-01

    The Department of Energy has given Sandia full responsibility for the complete life cycle (cradle to grave) of all nuclear weapon parachutes. Sandia National Laboratories is initiating development of a complete numerical simulation of parachute performance, beginning with parachute deployment and continuing through inflation and steady state descent. The purpose of the parachute performance code is to predict the performance of stockpile weapon parachutes as these parachutes continue to age well beyond their intended service life. A new massively parallel computer will provide unprecedented speed and memory for solving this complex problem, and new software will be written to treat the coupled fluid, structure and trajectory calculations as part of a single code. Verification and validation experiments have been proposed to provide the necessary confidence in the computations.

  2. Massively parallel sequencing approaches for characterization of structural variation.

    PubMed

    Koboldt, Daniel C; Larson, David E; Chen, Ken; Ding, Li; Wilson, Richard K

    2012-01-01

    The emergence of next-generation sequencing (NGS) technologies offers an incredible opportunity to comprehensively study DNA sequence variation in human genomes. Commercially available platforms from Roche (454), Illumina (Genome Analyzer and Hiseq 2000), and Applied Biosystems (SOLiD) have the capability to completely sequence individual genomes to high levels of coverage. NGS data is particularly advantageous for the study of structural variation (SV) because it offers the sensitivity to detect variants of various sizes and types, as well as the precision to characterize their breakpoints at base pair resolution. In this chapter, we present methods and software algorithms that have been developed to detect SVs and copy number changes using massively parallel sequencing data. We describe visualization and de novo assembly strategies for characterizing SV breakpoints and removing false positives.

  3. Massively parallel high-order combinatorial genetics in human cells.

    PubMed

    Wong, Alan S L; Choi, Gigi C G; Cheng, Allen A; Purcell, Oliver; Lu, Timothy K

    2015-09-01

    The systematic functional analysis of combinatorial genetics has been limited by the throughput that can be achieved and the order of complexity that can be studied. To enable massively parallel characterization of genetic combinations in human cells, we developed a technology for rapid, scalable assembly of high-order barcoded combinatorial genetic libraries that can be quantified with high-throughput sequencing. We applied this technology, combinatorial genetics en masse (CombiGEM), to create high-coverage libraries of 1,521 two-wise and 51,770 three-wise barcoded combinations of 39 human microRNA (miRNA) precursors. We identified miRNA combinations that synergistically sensitize drug-resistant cancer cells to chemotherapy and/or inhibit cancer cell proliferation, providing insights into complex miRNA networks. More broadly, our method will enable high-throughput profiling of multifactorial genetic combinations that regulate phenotypes of relevance to biomedicine, biotechnology and basic science.

  4. Massively parallel high-order combinatorial genetics in human cells

    PubMed Central

    Wong, Alan S L; Choi, Gigi C G; Cheng, Allen A; Purcell, Oliver; Lu, Timothy K

    2016-01-01

    The systematic functional analysis of combinatorial genetics has been limited by the throughput that can be achieved and the order of complexity that can be studied. To enable massively parallel characterization of genetic combinations in human cells, we developed a technology for rapid, scalable assembly of high-order barcoded combinatorial genetic libraries that can be quantified with high-throughput sequencing. We applied this technology, combinatorial genetics en masse (CombiGEM), to create high-coverage libraries of 1,521 two-wise and 51,770 three-wise barcoded combinations of 39 human microRNA (miRNA) precursors. We identified miRNA combinations that synergistically sensitize drug-resistant cancer cells to chemotherapy and/or inhibit cancer cell proliferation, providing insights into complex miRNA networks. More broadly, our method will enable high-throughput profiling of multifactorial genetic combinations that regulate phenotypes of relevance to biomedicine, biotechnology and basic science. PMID:26280411

  5. Integration of IR focal plane arrays with massively parallel processor

    NASA Astrophysics Data System (ADS)

    Esfandiari, P.; Koskey, P.; Vaccaro, K.; Buchwald, W.; Clark, F.; Krejca, B.; Rekeczky, C.; Zarandy, A.

    2008-04-01

    The intent of this investigation is to replace the low fill factor visible sensor of a Cellular Neural Network (CNN) processor with an InGaAs Focal Plane Array (FPA) using both bump bonding and epitaxial layer transfer techniques for use in the Ballistic Missile Defense System (BMDS) interceptor seekers. The goal is to fabricate a massively parallel digital processor with a local as well as a global interconnect architecture. Currently, this unique CNN processor is capable of processing a target scene in excess of 10,000 frames per second with its visible sensor. What makes the CNN processor so unique is that each processing element includes memory, local data storage, local and global communication devices and a visible sensor supported by a programmable analog or digital computer program.

  6. Massively Parallel Simulations of Diffusion in Dense Polymeric Structures

    SciTech Connect

    Faulon, Jean-Loup, Wilcox, R.T. , Hobbs, J.D. , Ford, D.M.

    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 the 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.

  7. A conventional, massively parallel eigensolver for electronic structure theory

    NASA Astrophysics Data System (ADS)

    Blum, V.; Scheffler, M.; Johanni, R.; Lederer, H.; Auckenthaler, Th.; Huckle, Th.; Bungartz, H.-J.; Krämer, L.; Willems, P.; Lang, B.; Havu, V.

    2011-03-01

    We demonstrate a robust large-scale, massively parallel conventional eigensolver for first-principles theory of molecules and materials. Despite much research into O (N) methods, standard approaches (Kohn-Sham or Hartree-Fock theory and excited-state formalisms) must still rely on conventional but robust O (N3) solvers for many system classes, most notably metals. Our eigensolver overcomes especially parallel scalability limitations, where standard implementations of certain steps (reduction to tridiagonal form, solution of reduced tridiagonal eigenproblem) can be a serious bottleneck already for a few hundred CPUs. We demonstrate scalable implementations of these and all other steps of the full generalized eigenvalue problem. Our largest example is a production run with 1046 Pt (heavy-metal) atoms with converged all-electron accuracy in the numeric atom-centered orbital code FHI-aims, but the implementation is generic and should easily be portable to other codes. ELPA research consortium, funded by German Ministry of Research and Education (BMBF). http://elpa.rzg.mpg.de.

  8. Efficiently modeling neural networks on massively parallel computers

    SciTech Connect

    Farber, R.M.

    1992-01-01

    Neural networks are a very useful tool for analyzing and modeling complex real world systems. Applying neural network simulations to real world problems generally involves large amounts of data and massive amounts of computation. To efficiently handle the computational requirements of large problems, we have implemented at Los Alamos a highly efficient neural network compiler for serial computers, vector computers, vector parallel computers, and fine grain SIMD computers such as the CM-2 connection machine. This paper will describe the mapping used by the compiler to implement feed-forward backpropagation neural networks for a SIMD architecture parallel computer. Thinking Machines Corporation has benchmarked our code at 1.3 billion interconnects per second (approximately 3 gigaflops) on a 64,000 processor CM-2 connection machine (Singer 1990). This mapping is applicable to other SMM computers and can be implemented on computers such as the CM-5 connection machine. Our mapping has virtually no communications overhead with the exception of the communications required for a global summation across the processors. We can efficiently model very large neural networks which have many neurons and interconnects and our mapping can be extend to arbitrarily large networks by merging the memory space of separate processors with fast adjacent processor inter-processor communications. This paper will consider the simulation of only feed forward neural network although this method is extendible to recurrent networks.

  9. Efficiently modeling neural networks on massively parallel computers

    SciTech Connect

    Farber, R.M.

    1992-12-01

    Neural networks are a very useful tool for analyzing and modeling complex real world systems. Applying neural network simulations to real world problems generally involves large amounts of data and massive amounts of computation. To efficiently handle the computational requirements of large problems, we have implemented at Los Alamos a highly efficient neural network compiler for serial computers, vector computers, vector parallel computers, and fine grain SIMD computers such as the CM-2 connection machine. This paper will describe the mapping used by the compiler to implement feed-forward backpropagation neural networks for a SIMD architecture parallel computer. Thinking Machines Corporation has benchmarked our code at 1.3 billion interconnects per second (approximately 3 gigaflops) on a 64,000 processor CM-2 connection machine (Singer 1990). This mapping is applicable to other SMM computers and can be implemented on computers such as the CM-5 connection machine. Our mapping has virtually no communications overhead with the exception of the communications required for a global summation across the processors. We can efficiently model very large neural networks which have many neurons and interconnects and our mapping can be extend to arbitrarily large networks by merging the memory space of separate processors with fast adjacent processor inter-processor communications. This paper will consider the simulation of only feed forward neural network although this method is extendible to recurrent networks.

  10. 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.

  11. Efficiently modeling neural networks on massively parallel computers

    NASA Technical Reports Server (NTRS)

    Farber, Robert M.

    1993-01-01

    Neural networks are a very useful tool for analyzing and modeling complex real world systems. Applying neural network simulations to real world problems generally involves large amounts of data and massive amounts of computation. To efficiently handle the computational requirements of large problems, we have implemented at Los Alamos a highly efficient neural network compiler for serial computers, vector computers, vector parallel computers, and fine grain SIMD computers such as the CM-2 connection machine. This paper describes the mapping used by the compiler to implement feed-forward backpropagation neural networks for a SIMD (Single Instruction Multiple Data) architecture parallel computer. Thinking Machines Corporation has benchmarked our code at 1.3 billion interconnects per second (approximately 3 gigaflops) on a 64,000 processor CM-2 connection machine (Singer 1990). This mapping is applicable to other SIMD computers and can be implemented on MIMD computers such as the CM-5 connection machine. Our mapping has virtually no communications overhead with the exception of the communications required for a global summation across the processors (which has a sub-linear runtime growth on the order of O(log(number of processors)). We can efficiently model very large neural networks which have many neurons and interconnects and our mapping can extend to arbitrarily large networks (within memory limitations) by merging the memory space of separate processors with fast adjacent processor interprocessor communications. This paper will consider the simulation of only feed forward neural network although this method is extendable to recurrent networks.

  12. Massively Parallel Atomic Force Microscope with Digital Holographic Readout

    NASA Astrophysics Data System (ADS)

    Sache, L.; Kawakatsu, H.; Emery, Y.; Bleuler, H.

    2007-03-01

    Massively Parallel Scanning Probe Microscopy is an obvious path for data storage (E Grochowski, R F Hoyt, Future Trends in Hard disc Drives, IEEE Trans. Magn. 1996, 32, 1850- 1854; J L Griffin, S W Schlosser, G R Ganger and D F Nagle, Modeling and Performance of MEMS-Based Storage Devices, Proc. ACM SIGMETRICS, 2000). Current experimental systems still lay far behind Hard Disc Drive (HDD) or Digital Video Disk (DVD), be it in access speed, data throughput, storage density or cost per bit. This paper presents an entirely new approach with the promise to break several of these barriers. The key idea is readout of a Scanning Probes Microscope (SPM) array by Digital Holographic Microscopy (DHM). This technology directly gives phase information at each pixel of a CCD array. This means that no contact line to each individual SPM probes is needed. The data is directly available in parallel form. Moreover, the optical setup needs in principle no expensive components, optical (or, to a large extent, mechanical) imperfections being compensated in the signal processing, i.e. in electronics. This gives the system the potential for a low cost device with fast Terabit readout capability.

  13. CHOLLA: A NEW MASSIVELY PARALLEL HYDRODYNAMICS CODE FOR ASTROPHYSICAL SIMULATION

    SciTech Connect

    Schneider, Evan E.; Robertson, Brant E.

    2015-04-15

    We present Computational Hydrodynamics On ParaLLel Architectures (Cholla ), a new three-dimensional hydrodynamics code that harnesses the power of graphics processing units (GPUs) to accelerate astrophysical simulations. Cholla models the Euler equations on a static mesh using state-of-the-art techniques, including the unsplit Corner Transport Upwind algorithm, a variety of exact and approximate Riemann solvers, and multiple spatial reconstruction techniques including the piecewise parabolic method (PPM). Using GPUs, Cholla evolves the fluid properties of thousands of cells simultaneously and can update over 10 million cells per GPU-second while using an exact Riemann solver and PPM reconstruction. Owing to the massively parallel architecture of GPUs and the design of the Cholla code, astrophysical simulations with physically interesting grid resolutions (≳256{sup 3}) can easily be computed on a single device. We use the Message Passing Interface library to extend calculations onto multiple devices and demonstrate nearly ideal scaling beyond 64 GPUs. A suite of test problems highlights the physical accuracy of our modeling and provides a useful comparison to other codes. We then use Cholla to simulate the interaction of a shock wave with a gas cloud in the interstellar medium, showing that the evolution of the cloud is highly dependent on its density structure. We reconcile the computed mixing time of a turbulent cloud with a realistic density distribution destroyed by a strong shock with the existing analytic theory for spherical cloud destruction by describing the system in terms of its median gas density.

  14. Simulation of hypervelocity impact on massively parallel supercomputer

    SciTech Connect

    Fang, H.E.

    1994-12-31

    Hypervelocity impact studies are important for debris shield and armor/anti-armor research and development. Numerical simulations are frequently performed to complement experimental studies, and to evaluate code accuracy. Parametric computational studies involving material properties, geometry and impact velocity can be used to understand hypervelocity impact processes. These impact simulations normally need to address shock wave physics phenomena, material deformation and failure, and motion of debris particles. Detailed, three-dimensional calculations of such events have large memory and processing time requirements. At Sandia National Laboratories, many impact problems of interest require tens of millions of computational cells. Furthermore, even the inadequately resolved problems often require tens or hundred of Cray CPU hours to complete. Recent numerical studies done by Grady and Kipp at Sandia using the Eulerian shock wave physics code CTH demonstrated very good agreement with many features of a copper sphere-on-steel plate oblique impact experiment, fully utilizing the compute power and memory of Sandia`s Cray supercomputer. To satisfy requirements for more finely resolved simulations in order to obtain a better understanding of the crater formation process and impact ejecta motion, the numerical work has been moved from the shared-memory Cray to a large, distributed-memory, massively parallel supercomputing system using PCTH, a parallel version of CTH. The current work is a continuation of the studies, but done on Sandia`s Intel 1840-processor Paragon X/PS parallel computer. With the great compute power and large memory provided by the Paragon, a highly detailed PCTH calculation has been completed for the copper sphere impacting steel plate experiment. Although the PCTH calculation used a mesh which is 4.5 times bigger than the original Cray setup, it finished in much less CPU time.

  15. Massively Parallel Interrogation of Aptamer Sequence, Structure and Function

    SciTech Connect

    Fischer, N O; Tok, J B; Tarasow, T M

    2008-02-08

    Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

  16. Analysis of composite ablators using massively parallel computation

    NASA Technical Reports Server (NTRS)

    Shia, David

    1995-01-01

    In this work, the feasibility of using massively parallel computation to study the response of ablative materials is investigated. Explicit and implicit finite difference methods are used on a massively parallel computer, the Thinking Machines CM-5. The governing equations are a set of nonlinear partial differential equations. The governing equations are developed for three sample problems: (1) transpiration cooling, (2) ablative composite plate, and (3) restrained thermal growth testing. The transpiration cooling problem is solved using a solution scheme based solely on the explicit finite difference method. The results are compared with available analytical steady-state through-thickness temperature and pressure distributions and good agreement between the numerical and analytical solutions is found. It is also found that a solution scheme based on the explicit finite difference method has the following advantages: incorporates complex physics easily, results in a simple algorithm, and is easily parallelizable. However, a solution scheme of this kind needs very small time steps to maintain stability. A solution scheme based on the implicit finite difference method has the advantage that it does not require very small times steps to maintain stability. However, this kind of solution scheme has the disadvantages that complex physics cannot be easily incorporated into the algorithm and that the solution scheme is difficult to parallelize. A hybrid solution scheme is then developed to combine the strengths of the explicit and implicit finite difference methods and minimize their weaknesses. This is achieved by identifying the critical time scale associated with the governing equations and applying the appropriate finite difference method according to this critical time scale. The hybrid solution scheme is then applied to the ablative composite plate and restrained thermal growth problems. The gas storage term is included in the explicit pressure calculation of both

  17. Massively Parallel Processing for Fast and Accurate Stamping Simulations

    NASA Astrophysics Data System (ADS)

    Gress, Jeffrey J.; Xu, Siguang; Joshi, Ramesh; Wang, Chuan-tao; Paul, Sabu

    2005-08-01

    The competitive automotive market drives automotive manufacturers to speed up the vehicle development cycles and reduce the lead-time. Fast tooling development is one of the key areas to support fast and short vehicle development programs (VDP). In the past ten years, the stamping simulation has become the most effective validation tool in predicting and resolving all potential formability and quality problems before the dies are physically made. The stamping simulation and formability analysis has become an critical business segment in GM math-based die engineering process. As the simulation becomes as one of the major production tools in engineering factory, the simulation speed and accuracy are the two of the most important measures for stamping simulation technology. The speed and time-in-system of forming analysis becomes an even more critical to support the fast VDP and tooling readiness. Since 1997, General Motors Die Center has been working jointly with our software vendor to develop and implement a parallel version of simulation software for mass production analysis applications. By 2001, this technology was matured in the form of distributed memory processing (DMP) of draw die simulations in a networked distributed memory computing environment. In 2004, this technology was refined to massively parallel processing (MPP) and extended to line die forming analysis (draw, trim, flange, and associated spring-back) running on a dedicated computing environment. The evolution of this technology and the insight gained through the implementation of DM0P/MPP technology as well as performance benchmarks are discussed in this publication.

  18. Cloud identification using genetic algorithms and massively parallel computation

    NASA Technical Reports Server (NTRS)

    Buckles, Bill P.; Petry, Frederick E.

    1996-01-01

    As a Guest Computational Investigator under the NASA administered component of the High Performance Computing and Communication Program, we implemented a massively parallel genetic algorithm on the MasPar SIMD computer. Experiments were conducted using Earth Science data in the domains of meteorology and oceanography. Results obtained in these domains are competitive with, and in most cases better than, similar problems solved using other methods. In the meteorological domain, we chose to identify clouds using AVHRR spectral data. Four cloud speciations were used although most researchers settle for three. Results were remarkedly consistent across all tests (91% accuracy). Refinements of this method may lead to more timely and complete information for Global Circulation Models (GCMS) that are prevalent in weather forecasting and global environment studies. In the oceanographic domain, we chose to identify ocean currents from a spectrometer having similar characteristics to AVHRR. Here the results were mixed (60% to 80% accuracy). Given that one is willing to run the experiment several times (say 10), then it is acceptable to claim the higher accuracy rating. This problem has never been successfully automated. Therefore, these results are encouraging even though less impressive than the cloud experiment. Successful conclusion of an automated ocean current detection system would impact coastal fishing, naval tactics, and the study of micro-climates. Finally we contributed to the basic knowledge of GA (genetic algorithm) behavior in parallel environments. We developed better knowledge of the use of subpopulations in the context of shared breeding pools and the migration of individuals. Rigorous experiments were conducted based on quantifiable performance criteria. While much of the work confirmed current wisdom, for the first time we were able to submit conclusive evidence. The software developed under this grant was placed in the public domain. An extensive user

  19. Optimization of virus detection in cells using massively parallel sequencing.

    PubMed

    McClenahan, Shasta D; Uhlenhaut, Christine; Krause, Philip R

    2014-01-01

    Massively parallel sequencing (MPS)-based virus detection has potential regulatory applications. We studied the ability of one of these approaches, based on degenerate oligonucleotide primer (DOP)-polymerase chain reaction (PCR), to detect viral sequences in cell lines known to express viral genes or particles. DOP-PCR was highly sensitive for the detection of small quantities of isolated viral sequences. Detected viral sequences included nodavirus, bracovirus, and endogenous retroviruses in High Five cells, porcine circovirus type 1 and porcine endogenous retrovirus in PK15 cells, human T-cell leukemia virus 1 in MJ cells, human papillomavirus 18 in HeLa cells, human herpesvirus 8 in BCBL-1 cells, and Epstein-Barr Virus in Raji cells. Illumina sequencing (for which primers were most efficiently added using PCR) provided greater sensitivity for virus detection than Roche 454 sequencing. Analyzing nucleic acids extracted both directly from samples and from capsid-enriched preparations provided useful information. Although there are limitations of these methods, these results indicate significant promise for the combination of nonspecific PCR and MPS in identifying contaminants in clinical and biological samples, including cell lines and reagents used to produce vaccines and therapeutic products. PMID:24309095

  20. Three-dimensional radiative transfer on a massively parallel computer

    NASA Technical Reports Server (NTRS)

    Vath, H. M.

    1994-01-01

    We perform 3D radiative transfer calculations in non-local thermodynamic equilibrium (NLTE) in the simple two-level atom approximation on the Mas-Par MP-1, which contains 8192 processors and is a single instruction multiple data (SIMD) machine, an example of the new generation of massively parallel computers. On such a machine, all processors execute the same command at a given time, but on different data. To make radiative transfer calculations efficient, we must re-consider the numerical methods and storage of data. To solve the transfer equation, we adopt the short characteristic method and examine different acceleration methods to obtain the source function. We use the ALI method and test local and non-local operators. Furthermore, we compare the Ng and the orthomin methods of acceleration. We also investigate the use of multi-grid methods to get fast solutions for the NLTE case. In order to test these numerical methods, we apply them to two problems with and without periodic boundary conditions.

  1. Comparing current cluster, massively parallel, and accelerated systems

    SciTech Connect

    Barker, Kevin J; Davis, Kei; Hoisie, Adolfy; Kerbyson, Darren J; Pakin, Scott; Lang, Mike; Sancho Pitarch, Jose C

    2010-01-01

    Currently there is large architectural diversity in high perfonnance computing systems. They include 'commodity' cluster systems that optimize per-node performance for small jobs, massively parallel processors (MPPs) that optimize aggregate perfonnance for large jobs, and accelerated systems that optimize both per-node and aggregate performance but only for applications custom-designed to take advantage of such systems. Because of these dissimilarities, meaningful comparisons of achievable performance are not straightforward. In this work we utilize a methodology that combines both empirical analysis and performance modeling to compare clusters (represented by a 4,352-core IB cluster), MPPs (represented by a 147,456-core BG/P), and accelerated systems (represented by the 129,600-core Roadrunner) across a workload of four applications. Strengths of our approach include the ability to compare architectures - as opposed to specific implementations of an architecture - attribute each application's performance bottlenecks to characteristics unique to each system, and to explore performance scenarios in advance of their availability for measurement. Our analysis illustrates that application performance is essentially unrelated to relative peak performance but that application performance can be both predicted and explained using modeling.

  2. Massively parallel support for a case-based planning system

    NASA Technical Reports Server (NTRS)

    Kettler, Brian P.; Hendler, James A.; Anderson, William A.

    1993-01-01

    Case-based planning (CBP), a kind of case-based reasoning, is a technique in which previously generated plans (cases) are stored in memory and can be reused to solve similar planning problems in the future. CBP can save considerable time over generative planning, in which a new plan is produced from scratch. CBP thus offers a potential (heuristic) mechanism for handling intractable problems. One drawback of CBP systems has been the need for a highly structured memory to reduce retrieval times. This approach requires significant domain engineering and complex memory indexing schemes to make these planners efficient. In contrast, our CBP system, CaPER, uses a massively parallel frame-based AI language (PARKA) and can do extremely fast retrieval of complex cases from a large, unindexed memory. The ability to do fast, frequent retrievals has many advantages: indexing is unnecessary; very large case bases can be used; memory can be probed in numerous alternate ways; and queries can be made at several levels, allowing more specific retrieval of stored plans that better fit the target problem with less adaptation. In this paper we describe CaPER's case retrieval techniques and some experimental results showing its good performance, even on large case bases.

  3. Massively parallel processor networks with optical express channels

    DOEpatents

    Deri, R.J.; Brooks, E.D. III; Haigh, R.E.; DeGroot, A.J.

    1999-08-24

    An optical method for separating and routing local and express channel data comprises interconnecting the nodes in a network with fiber optic cables. A single fiber optic cable carries both express channel traffic and local channel traffic, e.g., in a massively parallel processor (MPP) network. Express channel traffic is placed on, or filtered from, the fiber optic cable at a light frequency or a color different from that of the local channel traffic. The express channel traffic is thus placed on a light carrier that skips over the local intermediate nodes one-by-one by reflecting off of selective mirrors placed at each local node. The local-channel-traffic light carriers pass through the selective mirrors and are not reflected. A single fiber optic cable can thus be threaded throughout a three-dimensional matrix of nodes with the x,y,z directions of propagation encoded by the color of the respective light carriers for both local and express channel traffic. Thus frequency division multiple access is used to hierarchically separate the local and express channels to eliminate the bucket brigade latencies that would otherwise result if the express traffic had to hop between every local node to reach its ultimate destination. 3 figs.

  4. Massively parallel processor networks with optical express channels

    DOEpatents

    Deri, Robert J.; Brooks, III, Eugene D.; Haigh, Ronald E.; DeGroot, Anthony J.

    1999-01-01

    An optical method for separating and routing local and express channel data comprises interconnecting the nodes in a network with fiber optic cables. A single fiber optic cable carries both express channel traffic and local channel traffic, e.g., in a massively parallel processor (MPP) network. Express channel traffic is placed on, or filtered from, the fiber optic cable at a light frequency or a color different from that of the local channel traffic. The express channel traffic is thus placed on a light carrier that skips over the local intermediate nodes one-by-one by reflecting off of selective mirrors placed at each local node. The local-channel-traffic light carriers pass through the selective mirrors and are not reflected. A single fiber optic cable can thus be threaded throughout a three-dimensional matrix of nodes with the x,y,z directions of propagation encoded by the color of the respective light carriers for both local and express channel traffic. Thus frequency division multiple access is used to hierarchically separate the local and express channels to eliminate the bucket brigade latencies that would otherwise result if the express traffic had to hop between every local node to reach its ultimate destination.

  5. Massive Parallel Sequencing Provides New Perspectives on Bacterial Brain Abscesses

    PubMed Central

    Wilhelmsen, Marianne Thulin; Skrede, Steinar; Meisal, Roger; Jakovljev, Aleksandra; Gaustad, Peter; Hermansen, Nils Olav; Vik-Mo, Einar; Solheim, Ole; Ambur, Ole Herman; Sæbø, Øystein; Høstmælingen, Christina Teisner; Helland, Christian

    2014-01-01

    Rapid development within the field of massive parallel sequencing (MPS) is about to bring this technology within reach for diagnostic microbiology laboratories. We wanted to explore its potential for improving diagnosis and understanding of polymicrobial infections, using bacterial brain abscesses as an example. We conducted a prospective nationwide study on bacterial brain abscesses. Fifty-two surgical samples were included over a 2-year period. The samples were categorized as either spontaneous intracerebral, spontaneous subdural, or postoperative. Bacterial 16S rRNA genes were amplified directly from the specimens and sequenced using Ion Torrent technology, with an average of 500,000 reads per sample. The results were compared to those from culture- and Sanger sequencing-based diagnostics. Compared to culture, MPS allowed for triple the number of bacterial identifications. Aggregatibacter aphrophilus, Fusobacterium nucleatum, and Streptococcus intermedius or combinations of them were found in all spontaneous polymicrobial abscesses. F. nucleatum was systematically detected in samples with anaerobic flora. The increased detection rate for Actinomyces spp. and facultative Gram-negative rods further revealed several species associations. We suggest that A. aphrophilus, F. nucleatum, and S. intermedius are key pathogens for the establishment of spontaneous polymicrobial brain abscesses. In addition, F. nucleatum seems to be important for the development of anaerobic flora. MPS can accurately describe polymicrobial specimens when a sufficient number of reads is used to compensate for unequal species concentrations and principles are defined to discard contaminant bacterial DNA in the subsequent data analysis. This will contribute to our understanding of how different types of polymicrobial infections develop. PMID:24671797

  6. PFLOTRAN: Recent Developments Facilitating Massively-Parallel Reactive Biogeochemical Transport

    NASA Astrophysics Data System (ADS)

    Hammond, G. E.

    2015-12-01

    With the recent shift towards modeling carbon and nitrogen cycling in support of climate-related initiatives, emphasis has been placed on incorporating increasingly mechanistic biogeochemistry within Earth system models to more accurately predict the response of terrestrial processes to natural and anthropogenic climate cycles. PFLOTRAN is an open-source subsurface code that is specialized for simulating multiphase flow and multicomponent biogeochemical transport on supercomputers. The object-oriented code was designed with modularity in mind and has been coupled with several third-party simulators (e.g. CLM to simulate land surface processes and E4D for coupled hydrogeophysical inversion). Central to PFLOTRAN's capabilities is its ability to simulate tightly-coupled reactive transport processes. This presentation focuses on recent enhancements to the code that enable the solution of large parameterized biogeochemical reaction networks with numerous chemical species. PFLOTRAN's "reaction sandbox" is described, which facilitates the implementation of user-defined reaction networks without the need for a comprehensive understanding of PFLOTRAN software infrastructure. The reaction sandbox is written in modern Fortran (2003-2008) and leverages encapsulation, inheritance, and polymorphism to provide the researcher with a flexible workspace for prototyping reactions within a massively parallel flow and transport simulation framework. As these prototypical reactions mature into well-accepted implementations, they can be incorporated into PFLOTRAN as native biogeochemistry capability. Users of the reaction sandbox are encouraged to upload their source code to PFLOTRAN's main source code repository, including the addition of simple regression tests to better ensure the long-term code compatibility and validity of simulation results.

  7. Massively parallel computational fluid dynamics calculations for aerodynamics and aerothermodynamics applications

    SciTech Connect

    Payne, J.L.; Hassan, B.

    1998-09-01

    Massively parallel computers have enabled the analyst to solve complicated flow fields (turbulent, chemically reacting) that were previously intractable. Calculations are presented using a massively parallel CFD code called SACCARA (Sandia Advanced Code for Compressible Aerothermodynamics Research and Analysis) currently under development at Sandia National Laboratories as part of the Department of Energy (DOE) Accelerated Strategic Computing Initiative (ASCI). Computations were made on a generic reentry vehicle in a hypersonic flowfield utilizing three different distributed parallel computers to assess the parallel efficiency of the code with increasing numbers of processors. The parallel efficiencies for the SACCARA code will be presented for cases using 1, 150, 100 and 500 processors. Computations were also made on a subsonic/transonic vehicle using both 236 and 521 processors on a grid containing approximately 14.7 million grid points. Ongoing and future plans to implement a parallel overset grid capability and couple SACCARA with other mechanics codes in a massively parallel environment are discussed.

  8. Fast I/O for Massively Parallel Applications

    NASA Technical Reports Server (NTRS)

    OKeefe, Matthew T.

    1996-01-01

    The two primary goals for this report were the design, contruction and modeling of parallel disk arrays for scientific visualization and animation, and a study of the IO requirements of highly parallel applications. In addition, further work in parallel display systems required to project and animate the very high-resolution frames resulting from our supercomputing simulations in ocean circulation and compressible gas dynamics.

  9. SWAMP+: multiple subsequence alignment using associative massive parallelism

    SciTech Connect

    Steinfadt, Shannon Irene; Baker, Johnnie W

    2010-10-18

    A new parallel algorithm SWAMP+ incorporates the Smith-Waterman sequence alignment on an associative parallel model known as ASC. It is a highly sensitive parallel approach that expands traditional pairwise sequence alignment. This is the first parallel algorithm to provide multiple non-overlapping, non-intersecting subsequence alignments with the accuracy of Smith-Waterman. The efficient algorithm provides multiple alignments similar to BLAST while creating a better workflow for the end users. The parallel portions of the code run in O(m+n) time using m processors. When m = n, the algorithmic analysis becomes O(n) with a coefficient of two, yielding a linear speedup. Implementation of the algorithm on the SIMD ClearSpeed CSX620 confirms this theoretical linear speedup with real timings.

  10. QCD on the Massively Parallel Computer AP1000

    NASA Astrophysics Data System (ADS)

    Akemi, K.; Fujisaki, M.; Okuda, M.; Tago, Y.; Hashimoto, T.; Hioki, S.; Miyamura, O.; Takaishi, T.; Nakamura, A.; de Forcrand, Ph.; Hege, C.; Stamatescu, I. O.

    We present the QCD-TARO program of calculations which uses the parallel computer AP1000 of Fujitsu. We discuss the results on scaling, correlation times and hadronic spectrum, some aspects of the implementation and the future prospects.

  11. A massively parallel memory-based story system for psychotherapy.

    PubMed

    Smith, R N; Chen, C C; Feng, F F; Gomez-Gauchia, H

    1993-10-01

    We describe a memory-based system for psychotherapy, Dr. Bob, built to run on the data parallel processor Thinking Machines, Inc., CM-2a Connection Machine. The system retrieves, in parallel, stories of alcohol addiction and sexual abuse which can be used by psychiatrists in working with their patients as part of their work in recovering from addictive behavior and psychological trauma. The program is written in *LISP (pronounced Star LISP), a version of LISP used in programming Connection Machines. PMID:8243067

  12. 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.

  13. A development plan for a massively parallel version of the hydrocode CTH

    SciTech Connect

    Robinson, A.C.; Fang, E.; Holdridge, D.; McGlaun, J.M.

    1990-07-01

    Massively parallel computers and computer networks are beginning to appear as an integral part of the scientific computing workplace. This report documents the goals and the corresponding development plan of the massively parallel project of Departments 1530 and 1420. The main goal of the project is to provide a clear understanding of the issues and difficulties involved in bringing the current production hydrocode CTH to the state of being portable to a number of currently available parallel computing architectures. In the process of this research, various working versions of the code will be produced. 6 refs., 6 figs.

  14. A Massively Parallel Adaptive Fast Multipole Method on Heterogeneous Architectures

    SciTech Connect

    Lashuk, Ilya; Chandramowlishwaran, Aparna; Langston, Harper; Nguyen, Tuan-Anh; Sampath, Rahul S; Shringarpure, Aashay; Vuduc, Richard; Ying, Lexing; Zorin, Denis; Biros, George

    2012-01-01

    We describe a parallel fast multipole method (FMM) for highly nonuniform distributions of particles. We employ both distributed memory parallelism (via MPI) and shared memory parallelism (via OpenMP and GPU acceleration) to rapidly evaluate two-body nonoscillatory potentials in three dimensions on heterogeneous high performance computing architectures. We have performed scalability tests with up to 30 billion particles on 196,608 cores on the AMD/CRAY-based Jaguar system at ORNL. On a GPU-enabled system (NSF's Keeneland at Georgia Tech/ORNL), we observed 30x speedup over a single core CPU and 7x speedup over a multicore CPU implementation. By combining GPUs with MPI, we achieve less than 10 ns/particle and six digits of accuracy for a run with 48 million nonuniformly distributed particles on 192 GPUs.

  15. High density packaging and interconnect of massively parallel image processors

    NASA Technical Reports Server (NTRS)

    Carson, John C.; Indin, Ronald J.

    1991-01-01

    This paper presents conceptual designs for high density packaging of parallel processing systems. The systems fall into two categories: global memory systems where many processors are packaged into a stack, and distributed memory systems where a single processor and many memory chips are packaged into a stack. Thermal behavior and performance are discussed.

  16. Generic, hierarchical framework for massively parallel Wang-Landau sampling.

    PubMed

    Vogel, Thomas; Li, Ying Wai; Wüst, Thomas; Landau, David P

    2013-05-24

    We introduce a parallel Wang-Landau method based on the replica-exchange framework for Monte Carlo simulations. To demonstrate its advantages and general applicability for simulations of complex systems, we apply it to different spin models including spin glasses, the Ising model, and the Potts model, lattice protein adsorption, and the self-assembly process in amphiphilic solutions. Without loss of accuracy, the method gives significant speed-up and potentially scales up to petaflop machines.

  17. A generic, hierarchical framework for massively parallel Wang Landau sampling

    SciTech Connect

    Vogel, Thomas; Li, Ying Wai; Wuest, Thomas; Landau, David P

    2013-01-01

    We introduce a parallel Wang Landau method based on the replica-exchange framework for Monte Carlo simulations. To demonstrate its advantages and general applicability for simulations of com- plex systems, we apply it to the self-assembly process in amphiphilic solutions and to lattice protein adsorption. Without loss of accuracy, the method gives significant speed-up on small architectures like multi-core processors, and should be beneficial for petaflop machines.

  18. Performance Evaluation Methodologies and Tools for Massively Parallel Programs

    NASA Technical Reports Server (NTRS)

    Yan, Jerry C.; Sarukkai, Sekhar; Tucker, Deanne (Technical Monitor)

    1994-01-01

    The need for computing power has forced a migration from serial computation on a single processor to parallel processing on multiprocessors. However, without effective means to monitor (and analyze) program execution, tuning the performance of parallel programs becomes exponentially difficult as program complexity and machine size increase. The recent introduction of performance tuning tools from various supercomputer vendors (Intel's ParAide, TMC's PRISM, CSI'S Apprentice, and Convex's CXtrace) seems to indicate the maturity of performance tool technologies and vendors'/customers' recognition of their importance. However, a few important questions remain: What kind of performance bottlenecks can these tools detect (or correct)? How time consuming is the performance tuning process? What are some important technical issues that remain to be tackled in this area? This workshop reviews the fundamental concepts involved in analyzing and improving the performance of parallel and heterogeneous message-passing programs. Several alternative strategies will be contrasted, and for each we will describe how currently available tuning tools (e.g., AIMS, ParAide, PRISM, Apprentice, CXtrace, ATExpert, Pablo, IPS-2)) can be used to facilitate the process. We will characterize the effectiveness of the tools and methodologies based on actual user experiences at NASA Ames Research Center. Finally, we will discuss their limitations and outline recent approaches taken by vendors and the research community to address them.

  19. Smoldyn on graphics processing units: massively parallel Brownian dynamics simulations.

    PubMed

    Dematté, Lorenzo

    2012-01-01

    Space is a very important aspect in the simulation of biochemical systems; recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and detailed models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localized fluctuations, transportation phenomena, and diffusion. A common drawback of spatial models lies in their complexity: models can become very large, and their simulation could be time consuming, especially if we want to capture the systems behavior in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to scale up the size of models we are able to simulate, moving from sequential to parallel simulation algorithms. In this paper, we analyze Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of Graphics Processing Units (GPUs). The implementation executes the most computational demanding steps (computation of diffusion, unimolecular, and bimolecular reaction, as well as the most common cases of molecule-surface interaction) on the GPU, computing them in parallel on each molecule of the system. The implementation offers good speed-ups and real time, high quality graphics output

  20. Casting pearls ballistically: Efficient massively parallel simulation of particle deposition

    SciTech Connect

    Lubachevsky, B.D.; Privman, V.; Roy, S.C.

    1996-06-01

    We simulate ballistic particle deposition wherein a large number of spherical particles are {open_quotes}cast{close_quotes} vertically over a planar horizontal surface. Upon first contact (with the surface or with a previously deposited particle) each particle stops. This model helps material scientists to study the adsorption and sediment formation. The model is sequential, with particles deposited one by one. We have found an equivalent formulation using a continuous time random process and we simulate the latter in parallel using a method similar to the one previously employed for simulating Ising spins. We augment the parallel algorithm for simulating Ising spins with several techniques aimed at the increase of efficiency of producing the particle configuration and statistics collection. Some of these techniques are similar to earlier ones. We implement the resulting algorithm on a 16K PE MasPar MP-1 and a 4K PE MasPar MP-2. The parallel code runs on MasPar computers nearly two orders of magnitude faster than an optimized sequential code runs on a fast workstation. 17 refs., 9 figs.

  1. Fast parallel Markov clustering in bioinformatics using massively parallel computing on GPU with CUDA and ELLPACK-R sparse format.

    PubMed

    Bustamam, Alhadi; Burrage, Kevin; Hamilton, Nicholas A

    2012-01-01

    Markov clustering (MCL) is becoming a key algorithm within bioinformatics for determining clusters in networks. However,with increasing vast amount of data on biological networks, performance and scalability issues are becoming a critical limiting factor in applications. Meanwhile, GPU computing, which uses CUDA tool for implementing a massively parallel computing environment in the GPU card, is becoming a very powerful, efficient, and low-cost option to achieve substantial performance gains over CPU approaches. The use of on-chip memory on the GPU is efficiently lowering the latency time, thus, circumventing a major issue in other parallel computing environments, such as MPI. We introduce a very fast Markov clustering algorithm using CUDA (CUDA-MCL) to perform parallel sparse matrix-matrix computations and parallel sparse Markov matrix normalizations, which are at the heart of MCL. We utilized ELLPACK-R sparse format to allow the effective and fine-grain massively parallel processing to cope with the sparse nature of interaction networks data sets in bioinformatics applications. As the results show, CUDA-MCL is significantly faster than the original MCL running on CPU. Thus, large-scale parallel computation on off-the-shelf desktop-machines, that were previously only possible on supercomputing architectures, can significantly change the way bioinformaticians and biologists deal with their data.

  2. 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.

  3. Performance of the Wavelet Decomposition on Massively Parallel Architectures

    NASA Technical Reports Server (NTRS)

    El-Ghazawi, Tarek A.; LeMoigne, Jacqueline; Zukor, Dorothy (Technical Monitor)

    2001-01-01

    Traditionally, Fourier Transforms have been utilized for performing signal analysis and representation. But although it is straightforward to reconstruct a signal from its Fourier transform, no local description of the signal is included in its Fourier representation. To alleviate this problem, Windowed Fourier transforms and then wavelet transforms have been introduced, and it has been proven that wavelets give a better localization than traditional Fourier transforms, as well as a better division of the time- or space-frequency plane than Windowed Fourier transforms. Because of these properties and after the development of several fast algorithms for computing the wavelet representation of any signal, in particular the Multi-Resolution Analysis (MRA) developed by Mallat, wavelet transforms have increasingly been applied to signal analysis problems, especially real-life problems, in which speed is critical. In this paper we present and compare efficient wavelet decomposition algorithms on different parallel architectures. We report and analyze experimental measurements, using NASA remotely sensed images. Results show that our algorithms achieve significant performance gains on current high performance parallel systems, and meet scientific applications and multimedia requirements. The extensive performance measurements collected over a number of high-performance computer systems have revealed important architectural characteristics of these systems, in relation to the processing demands of the wavelet decomposition of digital images.

  4. Scientific development of a massively parallel ocean climate model. Final report

    SciTech Connect

    Semtner, A.J.; Chervin, R.M.

    1996-09-01

    Over the last three years, very significant advances have been made in refining the grid resolution of ocean models and in improving the physical and numerical treatments of ocean hydrodynamics. Some of these advances have occurred as a result of the successful transition of ocean models onto massively parallel computers, which has been led by Los Alamos investigators. Major progress has been made in simulating global ocean circulation and in understanding various ocean climatic aspects such as the effect of wind driving on heat and freshwater transports. These steps have demonstrated the capability to conduct realistic decadal to century ocean integrations at high resolution on massively parallel computers.

  5. Factorization of large integers on a massively parallel computer

    SciTech Connect

    Davis, J.A.; Holdridge, D.B.

    1988-01-01

    Our interest in integer factorization at Sandia National Laboratories is motivated by cryptographic applications and in particular the security of the RSA encryption-decryption algorithm. We have implemented our version of the quadratic sieve procedure on the NCUBE computer with 1024 processors (nodes). The new code is significantly different in all important aspects from the program used to factor number of order 10/sup 70/ on a single processor CRAY computer. Capabilities of parallel processing and limitation of small local memory necessitated this entirely new implementation. This effort involved several restarts as realizations of program structures that seemed appealing bogged down due to inter-processor communications. We are presently working with integers of magnitude about 10/sup 70/ in tuning this code to the novel hardware. 6 refs., 3 figs.

  6. 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.

  7. Repartitioning Strategies for Massively Parallel Simulation of Reacting Flow

    NASA Astrophysics Data System (ADS)

    Pisciuneri, Patrick; Zheng, Angen; Givi, Peyman; Labrinidis, Alexandros; Chrysanthis, Panos

    2015-11-01

    The majority of parallel CFD simulators partition the domain into equal regions and assign the calculations for a particular region to a unique processor. This type of domain decomposition is vital to the efficiency of the solver. However, as the simulation develops, the workload among the partitions often become uneven (e.g. by adaptive mesh refinement, or chemically reacting regions) and a new partition should be considered. The process of repartitioning adjusts the current partition to evenly distribute the load again. We compare two repartitioning tools: Zoltan, an architecture-agnostic graph repartitioner developed at the Sandia National Laboratories; and Paragon, an architecture-aware graph repartitioner developed at the University of Pittsburgh. The comparative assessment is conducted via simulation of the Taylor-Green vortex flow with chemical reaction.

  8. Massively parallel computing on an organic molecular layer

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, Anirban; Pati, Ranjit; Sahu, Satyajit; Peper, Ferdinand; Fujita, Daisuke

    2010-05-01

    Modern computers operate at enormous speeds-capable of executing in excess of 1013 instructions per second-but their sequential approach to processing, by which logical operations are performed one after another, has remained unchanged since the 1950s. In contrast, although individual neurons of the human brain fire at around just 103 times per second, the simultaneous collective action of millions of neurons enables them to complete certain tasks more efficiently than even the fastest supercomputer. Here we demonstrate an assembly of molecular switches that simultaneously interact to perform a variety of computational tasks including conventional digital logic, calculating Voronoi diagrams, and simulating natural phenomena such as heat diffusion and cancer growth. As well as representing a conceptual shift from serial-processing with static architectures, our parallel, dynamically reconfigurable approach could provide a means to solve otherwise intractable computational problems.

  9. Microfluidic trap array for massively parallel imaging of Drosophila embryos.

    PubMed

    Levario, Thomas J; Zhan, Mei; Lim, Bomyi; Shvartsman, Stanislav Y; Lu, Hang

    2013-04-01

    Here we describe a protocol for the fabrication and use of a microfluidic device to rapidly orient >700 Drosophila embryos in parallel for end-on imaging. The protocol describes master microfabrication (∼1 d), polydimethylsiloxane molding (few hours), system setup and device operation (few minutes) and imaging (depending on application). Our microfluidics-based approach described here is one of the first to facilitate rapid orientation for end-on imaging, and it is a major breakthrough for quantitative studies on Drosophila embryogenesis. The operating principle of the embryo trap is based on passive hydrodynamics, and it does not require direct manipulation of embryos by the user; biologists following the protocol should be able to repeat these procedures. The compact design and fabrication materials used allow the device to be used with traditional microscopy setups and do not require specialized fixtures. Furthermore, with slight modification, this array can be applied to the handling of other model organisms and oblong objects. PMID:23493069

  10. MASSIVELY PARALLEL LATENT SEMANTIC ANALYSES USING A GRAPHICS PROCESSING UNIT

    SciTech Connect

    Cavanagh, J.; Cui, S.

    2009-01-01

    Latent Semantic Analysis (LSA) aims to reduce the dimensions of large term-document datasets using Singular Value Decomposition. However, with the ever-expanding size of datasets, current implementations are not fast enough to quickly and easily compute the results on a standard PC. A graphics processing unit (GPU) can solve some highly parallel problems much faster than a traditional sequential processor or central processing unit (CPU). Thus, a deployable system using a GPU to speed up large-scale LSA processes would be a much more effective choice (in terms of cost/performance ratio) than using a PC cluster. Due to the GPU’s application-specifi c architecture, harnessing the GPU’s computational prowess for LSA is a great challenge. We presented a parallel LSA implementation on the GPU, using NVIDIA® Compute Unifi ed Device Architecture and Compute Unifi ed Basic Linear Algebra Subprograms software. The performance of this implementation is compared to traditional LSA implementation on a CPU using an optimized Basic Linear Algebra Subprograms library. After implementation, we discovered that the GPU version of the algorithm was twice as fast for large matrices (1 000x1 000 and above) that had dimensions not divisible by 16. For large matrices that did have dimensions divisible by 16, the GPU algorithm ran fi ve to six times faster than the CPU version. The large variation is due to architectural benefi ts of the GPU for matrices divisible by 16. It should be noted that the overall speeds for the CPU version did not vary from relative normal when the matrix dimensions were divisible by 16. Further research is needed in order to produce a fully implementable version of LSA. With that in mind, the research we presented shows that the GPU is a viable option for increasing the speed of LSA, in terms of cost/performance ratio.

  11. Massively Parallel Latent Semantic Analyzes using a Graphics Processing Unit

    SciTech Connect

    Cavanagh, Joseph M; Cui, Xiaohui

    2009-01-01

    Latent Semantic Indexing (LSA) aims to reduce the dimensions of large Term-Document datasets using Singular Value Decomposition. However, with the ever expanding size of data sets, current implementations are not fast enough to quickly and easily compute the results on a standard PC. The Graphics Processing Unit (GPU) can solve some highly parallel problems much faster than the traditional sequential processor (CPU). Thus, a deployable system using a GPU to speedup large-scale LSA processes would be a much more effective choice (in terms of cost/performance ratio) than using a computer cluster. Due to the GPU s application-specific architecture, harnessing the GPU s computational prowess for LSA is a great challenge. We present a parallel LSA implementation on the GPU, using NVIDIA Compute Unified Device Architecture and Compute Unified Basic Linear Algebra Subprograms. The performance of this implementation is compared to traditional LSA implementation on CPU using an optimized Basic Linear Algebra Subprograms library. After implementation, we discovered that the GPU version of the algorithm was twice as fast for large matrices (1000x1000 and above) that had dimensions not divisible by 16. For large matrices that did have dimensions divisible by 16, the GPU algorithm ran five to six times faster than the CPU version. The large variation is due to architectural benefits the GPU has for matrices divisible by 16. It should be noted that the overall speeds for the CPU version did not vary from relative normal when the matrix dimensions were divisible by 16. Further research is needed in order to produce a fully implementable version of LSA. With that in mind, the research we presented shows that the GPU is a viable option for increasing the speed of LSA, in terms of cost/performance ratio.

  12. Massively parallel computation of RCS with finite elements

    NASA Technical Reports Server (NTRS)

    Parker, Jay

    1993-01-01

    One of the promising combinations of finite element approaches for scattering problems uses Whitney edge elements, spherical vector wave-absorbing boundary conditions, and bi-conjugate gradient solution for the frequency-domain near field. Each of these approaches may be criticized. Low-order elements require high mesh density, but also result in fast, reliable iterative convergence. Spherical wave-absorbing boundary conditions require additional space to be meshed beyond the most minimal near-space region, but result in fully sparse, symmetric matrices which keep storage and solution times low. Iterative solution is somewhat unpredictable and unfriendly to multiple right-hand sides, yet we find it to be uniformly fast on large problems to date, given the other two approaches. Implementation of these approaches on a distributed memory, message passing machine yields huge dividends, as full scalability to the largest machines appears assured and iterative solution times are well-behaved for large problems. We present times and solutions for computed RCS for a conducting cube and composite permeability/conducting sphere on the Intel ipsc860 with up to 16 processors solving over 200,000 unknowns. We estimate problems of approximately 10 million unknowns, encompassing 1000 cubic wavelengths, may be attempted on a currently available 512 processor machine, but would be exceedingly tedious to prepare. The most severe bottlenecks are due to the slow rate of mesh generation on non-parallel machines and the large transfer time from such a machine to the parallel processor. One solution, in progress, is to create and then distribute a coarse mesh among the processors, followed by systematic refinement within each processor. Elimination of redundant node definitions at the mesh-partition surfaces, snap-to-surface post processing of the resulting mesh for good modelling of curved surfaces, and load-balancing redistribution of new elements after the refinement are auxiliary

  13. Massively parallel algorithms for trace-driven cache simulations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Greenberg, Albert G.; Lubachevsky, Boris D.

    1991-01-01

    Trace driven cache simulation is central to computer design. A trace is a very long sequence of reference lines from main memory. At the t(exp th) instant, reference x sub t is hashed into a set of cache locations, the contents of which are then compared with x sub t. If at the t sup th instant x sub t is not present in the cache, then it is said to be a miss, and is loaded into the cache set, possibly forcing the replacement of some other memory line, and making x sub t present for the (t+1) sup st instant. The problem of parallel simulation of a subtrace of N references directed to a C line cache set is considered, with the aim of determining which references are misses and related statistics. A simulation method is presented for the Least Recently Used (LRU) policy, which regradless of the set size C runs in time O(log N) using N processors on the exclusive read, exclusive write (EREW) parallel model. A simpler LRU simulation algorithm is given that runs in O(C log N) time using N/log N processors. Timings are presented of the second algorithm's implementation on the MasPar MP-1, a machine with 16384 processors. A broad class of reference based line replacement policies are considered, which includes LRU as well as the Least Frequently Used and Random replacement policies. A simulation method is presented for any such policy that on any trace of length N directed to a C line set runs in the O(C log N) time with high probability using N processors on the EREW model. The algorithms are simple, have very little space overhead, and are well suited for SIMD implementation.

  14. 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.

  15. Solution of large linear systems of equations on the massively parallel processor

    NASA Technical Reports Server (NTRS)

    Ida, Nathan; Udawatta, Kapila

    1987-01-01

    The Massively Parallel Processor (MPP) was designed as a special machine for specific applications in image processing. As a parallel machine, with a large number of processors that can be reconfigured in different combinations it is also applicable to other problems that require a large number of processors. The solution of linear systems of equations on the MPP is investigated. The solution times achieved are compared to those obtained with a serial machine and the performance of the MPP is discussed.

  16. The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing

    PubMed Central

    Chung, Jongsuk; Son, Dae-Soon; Jeon, Hyo-Jeong; Kim, Kyoung-Mee; Park, Gahee; Ryu, Gyu Ha; Park, Woong-Yang; Park, Donghyun

    2016-01-01

    Targeted capture massively parallel sequencing is increasingly being used in clinical settings, and as costs continue to decline, use of this technology may become routine in health care. However, a limited amount of tissue has often been a challenge in meeting quality requirements. To offer a practical guideline for the minimum amount of input DNA for targeted sequencing, we optimized and evaluated the performance of targeted sequencing depending on the input DNA amount. First, using various amounts of input DNA, we compared commercially available library construction kits and selected Agilent’s SureSelect-XT and KAPA Biosystems’ Hyper Prep kits as the kits most compatible with targeted deep sequencing using Agilent’s SureSelect custom capture. Then, we optimized the adapter ligation conditions of the Hyper Prep kit to improve library construction efficiency and adapted multiplexed hybrid selection to reduce the cost of sequencing. In this study, we systematically evaluated the performance of the optimized protocol depending on the amount of input DNA, ranging from 6.25 to 200 ng, suggesting the minimal input DNA amounts based on coverage depths required for specific applications. PMID:27220682

  17. Tubal ligation

    MedlinePlus

    ... tying; Tying the tubes; Hysteroscopic tubal occlusion procedure; Contraception - tubal ligation; Family planning - tubal ligation ... Tubal ligation is considered a permanent form of birth control. It is NOT recommended as a short-term ...

  18. Large-eddy simulation of the Rayleigh-Taylor instability on a massively parallel computer

    SciTech Connect

    Amala, P.A.K.

    1995-03-01

    A computational model for the solution of the three-dimensional Navier-Stokes equations is developed. This model includes a turbulence model: a modified Smagorinsky eddy-viscosity with a stochastic backscatter extension. The resultant equations are solved using finite difference techniques: the second-order explicit Lax-Wendroff schemes. This computational model is implemented on a massively parallel computer. Programming models on massively parallel computers are next studied. It is desired to determine the best programming model for the developed computational model. To this end, three different codes are tested on a current massively parallel computer: the CM-5 at Los Alamos. Each code uses a different programming model: one is a data parallel code; the other two are message passing codes. Timing studies are done to determine which method is the fastest. The data parallel approach turns out to be the fastest method on the CM-5 by at least an order of magnitude. The resultant code is then used to study a current problem of interest to the computational fluid dynamics community. This is the Rayleigh-Taylor instability. The Lax-Wendroff methods handle shocks and sharp interfaces poorly. To this end, the Rayleigh-Taylor linear analysis is modified to include a smoothed interface. The linear growth rate problem is then investigated. Finally, the problem of the randomly perturbed interface is examined. Stochastic backscatter breaks the symmetry of the stationary unstable interface and generates a mixing layer growing at the experimentally observed rate. 115 refs., 51 figs., 19 tabs.

  19. Parallel optimization of pixel purity index algorithm for massive hyperspectral images in cloud computing environment

    NASA Astrophysics Data System (ADS)

    Chen, Yufeng; Wu, Zebin; Sun, Le; Wei, Zhihui; Li, Yonglong

    2016-04-01

    With the gradual increase in the spatial and spectral resolution of hyperspectral images, the size of image data becomes larger and larger, and the complexity of processing algorithms is growing, which poses a big challenge to efficient massive hyperspectral image processing. Cloud computing technologies distribute computing tasks to a large number of computing resources for handling large data sets without the limitation of memory and computing resource of a single machine. This paper proposes a parallel pixel purity index (PPI) algorithm for unmixing massive hyperspectral images based on a MapReduce programming model for the first time in the literature. According to the characteristics of hyperspectral images, we describe the design principle of the algorithm, illustrate the main cloud unmixing processes of PPI, and analyze the time complexity of serial and parallel algorithms. Experimental results demonstrate that the parallel implementation of the PPI algorithm on the cloud can effectively process big hyperspectral data and accelerate the algorithm.

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

    PubMed

    Keçeli, Murat; Zhang, Hong; Zapol, Peter; Dixon, David A; Wagner, Albert F

    2016-02-01

    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 SIPs 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. A parallel implementation of assembling the density matrix from the distributed eigenvectors is demonstrated.

  1. Massively parallel implementation of the Penn State/NCAR Mesoscale Model

    SciTech Connect

    Foster, I.; Michalakes, J.

    1992-12-01

    Parallel computing promises significant improvements in both the raw speed and cost performance of mesoscale atmospheric models. On distributed-memory massively parallel computers available today, the performance of a mesoscale model will exceed that of conventional supercomputers; on the teraflops machines expected within the next five years, performance will increase by several orders of magnitude. As a result, scientists will be able to consider larger problems, more complex model processes, and finer resolutions. In this paper. we report on a project at Argonne National Laboratory that will allow scientists to take advantage of parallel computing technology. This Massively Parallel Mesoscale Model (MPMM) will be functionally equivalent to the Penn State/NCAR Mesoscale Model (MM). In a prototype study, we produced a parallel version of MM4 using a static (compile-time) coarse-grained ``patch`` decomposition. This code achieves one-third the performance of a one-processor CRAY Y-MP on twelve Intel 1860 microprocessors. The current version of MPMM is based on all MM5 and uses a more fine-grained approach, decomposing the grid as finely as the mesh itself allows so that each horizontal grid cell is a parallel process. This will allow the code to utilize many hundreds of processors. A high-level language for expressing parallel programs is used to implement communication strearns between the processes in a way that permits dynamic remapping to the physical processors of a particular parallel computer. This facilitates load balancing, grid nesting, and coupling with graphical systems and other models.

  2. Massively parallel implementation of the Penn State/NCAR Mesoscale Model

    SciTech Connect

    Foster, I.; Michalakes, J.

    1992-01-01

    Parallel computing promises significant improvements in both the raw speed and cost performance of mesoscale atmospheric models. On distributed-memory massively parallel computers available today, the performance of a mesoscale model will exceed that of conventional supercomputers; on the teraflops machines expected within the next five years, performance will increase by several orders of magnitude. As a result, scientists will be able to consider larger problems, more complex model processes, and finer resolutions. In this paper. we report on a project at Argonne National Laboratory that will allow scientists to take advantage of parallel computing technology. This Massively Parallel Mesoscale Model (MPMM) will be functionally equivalent to the Penn State/NCAR Mesoscale Model (MM). In a prototype study, we produced a parallel version of MM4 using a static (compile-time) coarse-grained patch'' decomposition. This code achieves one-third the performance of a one-processor CRAY Y-MP on twelve Intel 1860 microprocessors. The current version of MPMM is based on all MM5 and uses a more fine-grained approach, decomposing the grid as finely as the mesh itself allows so that each horizontal grid cell is a parallel process. This will allow the code to utilize many hundreds of processors. A high-level language for expressing parallel programs is used to implement communication strearns between the processes in a way that permits dynamic remapping to the physical processors of a particular parallel computer. This facilitates load balancing, grid nesting, and coupling with graphical systems and other models.

  3. Salinas - An implicit finite element structural dynamics code developed for massively parallel platforms

    SciTech Connect

    BHARDWAJ, MANLJ K.; REESE,GARTH M.; DRIESSEN,BRIAN; ALVIN,KENNETH F.; DAY,DAVID M.

    2000-04-06

    As computational needs for structural finite element analysis increase, a robust implicit structural dynamics code is needed which can handle millions of degrees of freedom in the model and produce results with quick turn around time. A parallel code is needed to avoid limitations of serial platforms. Salinas is an implicit structural dynamics code specifically designed for massively parallel platforms. It computes the structural response of very large complex structures and provides solutions faster than any existing serial machine. This paper gives a current status of Salinas and uses demonstration problems to show Salinas' performance.

  4. Massively parallel per-pixel-based zerotree processing architecture for real-time video compression

    NASA Astrophysics Data System (ADS)

    Alagoda, Geoffrey; Rassau, Alexander M.; Eshraghian, Kamran

    2001-11-01

    In the span of a few years, mobile multimedia communication has rapidly become a significant area of research and development constantly challenging boundaries on a variety of technological fronts. Video compression, a fundamental component for most mobile multimedia applications, generally places heavy demands in terms of the required processing capacity. Hardware implementations of typical modern hybrid codecs require realisation of components such as motion compensation, wavelet transform, quantisation, zerotree coding and arithmetic coding in real-time. While the implementation of such codecs using a fast generic processor is possible, undesirable trade-offs in terms of power consumption and speed must generally be made. The improvement in power consumption that is achievable through the use of a slow-clocked massively parallel processing environment, while maintaining real-time processing speeds, should thus not be overlooked. An architecture to realise such a massively parallel solution for a zerotree entropy coder is, therefore, presented in this paper.

  5. Numerical and physical instabilities in massively parallel LES of reacting flows

    NASA Astrophysics Data System (ADS)

    Poinsot, Thierry

    LES of reacting flows is rapidly becoming mature and providing levels of precision which can not be reached with any RANS (Reynolds Averaged) technique. In addition to the multiple subgrid scale models required for such LES and to the questions raised by the required numerical accurcay of LES solvers, various issues related the reliability, mesh independence and repetitivity of LES must still be addressed, especially when LES is used on massively parallel machines. This talk discusses some of these issues: (1) the existence of non physical waves (known as `wiggles' by most LES practitioners) in LES, (2) the effects of mesh size on LES of reacting flows, (3) the growth of rounding errors in LES on massively parallel machines and more generally (4) the ability to qualify a LES code as `bug free' and `accurate'. Examples range from academic cases (minimum non-reacting turbulent channel) to applied configurations (a sector of an helicopter combustion chamber).

  6. A domain decomposition study of massively parallel computing in compressible gas dynamics

    SciTech Connect

    Wong, C.C.; Blottner, F.G.; Payne, J.L.; Soetrisno, M.

    1995-01-01

    The appropriate utilization of massively parallel computers for solving the Navier-Stokes equations is investigated and determined from an engineering perspective. The issues investigated are: (1) Should strip or patch domain decomposition of the spatial mesh be used to reduce computer time? (2) How many computer nodes should be used for a problem with a given sized mesh to reduce computer time? (3) Is the convergence of the Navier-Stokes solution procedure (LU-SGS) adversely influenced by the domain decomposition approach? The results of the paper show that the present Navier-Stokes solution technique has good performance on a massively parallel computer for transient flow problems. For steady-state problems with a large number of mesh cells, the solution procedure will require significant computer time due to an increased number of iterations to achieve a converged solution. There is an optimum number of computer nodes to use for a problem with a given global mesh size.

  7. Development of Microreactor Array Chip-Based Measurement System for Massively Parallel Analysis of Enzymatic Activity

    NASA Astrophysics Data System (ADS)

    Hosoi, Yosuke; Akagi, Takanori; Ichiki, Takanori

    Microarray chip technology such as DNA chips, peptide chips and protein chips is one of the promising approaches for achieving high-throughput screening (HTS) of biomolecule function since it has great advantages in feasibility of automated information processing due to one-to-one indexing between array position and molecular function as well as massively parallel sample analysis as a benefit of down-sizing and large-scale integration. Mostly, however, the function that can be evaluated by such microarray chips is limited to affinity of target molecules. In this paper, we propose a new HTS system of enzymatic activity based on microreactor array chip technology. A prototype of the automated and massively parallel measurement system for fluorometric assay of enzymatic reactions was developed by the combination of microreactor array chips and a highly-sensitive fluorescence microscope. Design strategy of microreactor array chips and an optical measurement platform for the high-throughput enzyme assay are discussed.

  8. Parallel contributing area calculation with granularity control on massive grid terrain datasets

    NASA Astrophysics Data System (ADS)

    Jiang, Ling; Tang, Guoan; Liu, Xuejun; Song, Xiaodong; Yang, Jianyi; Liu, Kai

    2013-10-01

    The calculation of contributing areas from digital elevation models (DEMs) is one of the important tasks in digital terrain analysis (DTA). The computational process usually involves two steps in a real application: (1) calculating flow directions via a flow model, and (2) computing the contributing area for each grid cell in the DEM. The traditional algorithm for calculating contributing areas is coded as a sequential program executed on a single processor. With the increase of scope and resolution of DEMs, the serial algorithm has become increasingly difficult to perform and is often very time-consuming, especially for DEMs of large areas and fine scales. In recent years, parallel computing is able to meet this challenge with the development of computer technology. However, the parallel implementation with granularity control, an efficient strategy to reap the best parallel performance and to break the limitation of computing resources in processing massive grid terrain datasets, has not been found in DTA research field. This paper develops a message-passing-interface (MPI) parallel approach with granularity control to calculate contributing areas. According to the proposed parallelization strategy, the parallel D8 algorithm with granularity control is designed as well as the parallel AreaD8 algorithm. Based on the domain decomposition of DEM data, it is possible for each process to process multiple partitions decomposed under a grain size. According to an iterative procedure of reading source data, executing the operator and writing resulting data, the partitions achieve the calculation results one by one in each process. The experimental results on a multi-node cluster show that the proposed parallel algorithms with granularity control are the powerful tools to process the big dataset and the parallel D8 algorithm is insensitive to granularity, while the parallel AreaD8 algorithm has an optimal grain size to reap the best parallel performance.

  9. Chemical network problems solved on NASA/Goddard's massively parallel processor computer

    NASA Technical Reports Server (NTRS)

    Cho, Seog Y.; Carmichael, Gregory R.

    1987-01-01

    The single instruction stream, multiple data stream Massively Parallel Processor (MPP) unit consists of 16,384 bit serial arithmetic processors configured as a 128 x 128 array whose speed can exceed that of current supercomputers (Cyber 205). The applicability of the MPP for solving reaction network problems is presented and discussed, including the mapping of the calculation to the architecture, and CPU timing comparisons.

  10. 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.

  11. 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.

  12. ASCI Red -- Experiences and lessons learned with a massively parallel teraFLOP supercomputer

    SciTech Connect

    Christon, M.A.; Crawford, D.A.; Hertel, E.S.; Peery, J.S.; Robinson, A.C.

    1997-06-01

    The Accelerated Strategic Computing Initiative (ASCI) program involves Sandia, Los Alamos and Lawrence Livermore National Laboratories. At Sandia National Laboratories, ASCI applications include large deformation transient dynamics, shock propagation, electromechanics, and abnormal thermal environments. In order to resolve important physical phenomena in these problems, it is estimated that meshes ranging from 10{sup 6} to 10{sup 9} grid points will be required. The ASCI program is relying on the use of massively parallel supercomputers initially capable of delivering over 1 TFLOPs to perform such demanding computations. The ASCI Red machine at Sandia National Laboratories consists of over 4,500 computational nodes with a peak computational rate of 1.8 TFLOPs, 567 GBytes of memory, and 2 TBytes of disk storage. Regardless of the peak FLOP rate, there are many issues surrounding the use of massively parallel supercomputers in a production environment. These issues include parallel I/O, mesh generation, visualization, archival storage, high-bandwidth networking and the development of parallel algorithms. In order to illustrate these issues and their solution with respect to ASCI Red, demonstration calculations of time-dependent buoyancy-dominated plumes, electromechanics, and shock propagation will be presented.

  13. Massively parallel Monte Carlo for many-particle simulations on GPUs

    SciTech Connect

    Anderson, Joshua A.; Jankowski, Eric; Grubb, Thomas L.; Engel, Michael; Glotzer, Sharon C.

    2013-12-01

    Current trends in parallel processors call for the design of efficient massively parallel algorithms for scientific computing. Parallel algorithms for Monte Carlo simulations of thermodynamic ensembles of particles have received little attention because of the inherent serial nature of the statistical sampling. In this paper, we present a massively parallel method that obeys detailed balance and implement it for a system of hard disks on the GPU. We reproduce results of serial high-precision Monte Carlo runs to verify the method. This is a good test case because the hard disk equation of state over the range where the liquid transforms into the solid is particularly sensitive to small deviations away from the balance conditions. On a Tesla K20, our GPU implementation executes over one billion trial moves per second, which is 148 times faster than on a single Intel Xeon E5540 CPU core, enables 27 times better performance per dollar, and cuts energy usage by a factor of 13. With this improved performance we are able to calculate the equation of state for systems of up to one million hard disks. These large system sizes are required in order to probe the nature of the melting transition, which has been debated for the last forty years. In this paper we present the details of our computational method, and discuss the thermodynamics of hard disks separately in a companion paper.

  14. SIMD massively parallel processing system for real-time image processing

    NASA Astrophysics Data System (ADS)

    Chen, Xiaochu; Zhang, Ming; Yao, Qingdong; Liu, Jilin; Ye, Hong; Wu, Song; Li, Dongxiao; Zhang, Yong; Ding, Lei; Yao, Zhongyang; Yang, Weijian; Pan, Qiaohai

    1998-09-01

    This paper will describe the embedded SIMD massively parallel processor that we have developed for real-time image processing applications, such as real-time small target detection and tracking and video processing. The processor array is based on SIMD chip BAP-128 designed by our own, and uses high performance DSP TMS320C31, which can effectively perform serial and floating point calculations, as the host of the SIMD processor array. As a result, the system is able to perform a variety of image processing tasks in real-time. Furthermore, the processor will be connected with a MIMD parallel processor to construct a heterogeneously parallel processor for more complex real- time ATR (Automatic Target Recognition) and computer vision applications.

  15. Molecular Dynamics Simulations from SNL's Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)

    DOE Data Explorer

    Plimpton, Steve; Thompson, Aidan; Crozier, Paul

    LAMMPS (http://lammps.sandia.gov/index.html) stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a code that can be used to model atoms or, as the LAMMPS website says, as a parallel particle simulator at the atomic, meso, or continuum scale. This Sandia-based website provides a long list of animations from large simulations. These were created using different visualization packages to read LAMMPS output, and each one provides the name of the PI and a brief description of the work done or visualization package used. See also the static images produced from simulations at http://lammps.sandia.gov/pictures.html The foundation paper for LAMMPS is: S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995), but the website also lists other papers describing contributions to LAMMPS over the years.

  16. Tubal Ligation

    MedlinePlus

    Tubal ligation (getting your "tubes tied") is a type of surgery. It prevents a woman from getting pregnant. ... to most normal activities within a few days. Tubal ligation can sometimes be reversed, but not always.

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

    SciTech Connect

    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 runs 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

  18. Massively parallel conjugate heat transfer methods relying on large eddy simulation applied to an aeronautical combustor

    NASA Astrophysics Data System (ADS)

    Jaure, S.; Duchaine, F.; Staffelbach, G.; Gicquel, L. Y. M.

    2013-01-01

    Optimizing gas turbines is a complex multi-physical and multi-component problem that has long been based on expensive experiments. Today, computer simulation can reduce design process costs and is acknowledged as a promising path for optimization. However, performing such computations using high-fidelity methods such as a large eddy simulation (LES) on gas turbines is challenging. Nevertheless, such simulations become accessible for specific components of gas turbines. These stand-alone simulations face a new challenge: to improve the quality of the results, new physics must be introduced. Therefore, an efficient massively parallel coupling methodology is investigated. The flow solver modeling relies on the LES code AVBP which has already been ported on massively parallel architectures. The conduction solver is based on the same data structure and thus shares its scalability. Accurately coupling these solvers while maintaining their scalability is challenging and is the actual objective of this work. To obtain such goals, a methodology is proposed and different key issues to code the coupling are addressed: convergence, stability, parallel geometry mapping, transfers and interpolation. This methodology is then applied to a real burner configuration, hence demonstrating the possibilities and limitations of the solution.

  19. Visualizing Network Traffic to Understand the Performance of Massively Parallel Simulations.

    PubMed

    Landge, A G; Levine, J A; Bhatele, A; Isaacs, K E; Gamblin, T; Schulz, M; Langer, S H; Bremer, Peer-Timo; Pascucci, V

    2012-12-01

    The performance of massively parallel applications is often heavily impacted by the cost of communication among compute nodes. However, determining how to best use the network is a formidable task, made challenging by the ever increasing size and complexity of modern supercomputers. This paper applies visualization techniques to aid parallel application developers in understanding the network activity by enabling a detailed exploration of the flow of packets through the hardware interconnect. In order to visualize this large and complex data, we employ two linked views of the hardware network. The first is a 2D view, that represents the network structure as one of several simplified planar projections. This view is designed to allow a user to easily identify trends and patterns in the network traffic. The second is a 3D view that augments the 2D view by preserving the physical network topology and providing a context that is familiar to the application developers. Using the massively parallel multi-physics code pF3D as a case study, we demonstrate that our tool provides valuable insight that we use to explain and optimize pF3D's performance on an IBM Blue Gene/P system. PMID:26357155

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

    PubMed

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

    2010-12-01

    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

  1. 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

  2. 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.

  3. A cost-effective methodology for the design of massively-parallel VLSI functional units

    NASA Technical Reports Server (NTRS)

    Venkateswaran, N.; Sriram, G.; Desouza, J.

    1993-01-01

    In this paper we propose a generalized methodology for the design of cost-effective massively-parallel VLSI Functional Units. This methodology is based on a technique of generating and reducing a massive bit-array on the mask-programmable PAcube VLSI array. This methodology unifies (maintains identical data flow and control) the execution of complex arithmetic functions on PAcube arrays. It is highly regular, expandable and uniform with respect to problem-size and wordlength, thereby reducing the communication complexity. The memory-functional unit interface is regular and expandable. Using this technique functional units of dedicated processors can be mask-programmed on the naked PAcube arrays, reducing the turn-around time. The production cost of such dedicated processors can be drastically reduced since the naked PAcube arrays can be mass-produced. Analysis of the the performance of functional units designed by our method yields promising results.

  4. 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.

  5. 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. PMID:22562950

  6. 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.

  7. 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.

  8. Scalable load balancing for massively parallel distributed Monte Carlo particle transport

    SciTech Connect

    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 Lawrence Livermore National Laboratory. (authors)

  9. Inventory estimation on the massively parallel processor. [from satellite based images

    NASA Technical Reports Server (NTRS)

    Argentiero, P. D.; Strong, J. P.; Koch, D. W.

    1980-01-01

    This paper describes algorithms for efficiently computing inventory estimates from satellite based images. The algorithms incorporate a one dimensional feature extraction which optimizes the pairwise sum of Fisher distances. Biases are eliminated with a premultiplication by the inverse of the analytically derived error matrix. The technique is demonstrated with a numerical example using statistics obtained from an actual Landsat scene. Attention was given to implementation of the Massively Parallel processor (MPP). A timing analysis demonstrates that the inventory estimation can be performed an order of magnitude faster on the MPP than on a conventional serial machine.

  10. 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.

  11. 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.

  12. 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.; Davidson, Gregory G.; Hamilton, Steven P.; Godfrey, Andrew T.

    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

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

    SciTech Connect

    Pandya, Tara M.; Johnson, Seth R.; Evans, Thomas M.; Davidson, Gregory G.; Hamilton, Steven P.; Godfrey, Andrew T.

    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. Some 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.

  14. Massively Parallel Computation of Soil Surface Roughness Parameters on A Fermi GPU

    NASA Astrophysics Data System (ADS)

    Li, Xiaojie; Song, Changhe

    2016-06-01

    Surface roughness is description of the surface micro topography of randomness or irregular. The standard deviation of surface height and the surface correlation length describe the statistical variation for the random component of a surface height relative to a reference surface. When the number of data points is large, calculation of surface roughness parameters is time-consuming. With the advent of Graphics Processing Unit (GPU) architectures, inherently parallel problem can be effectively solved using GPUs. In this paper we propose a GPU-based massively parallel computing method for 2D bare soil surface roughness estimation. This method was applied to the data collected by the surface roughness tester based on the laser triangulation principle during the field experiment in April 2012. The total number of data points was 52,040. It took 47 seconds on a Fermi GTX 590 GPU whereas its serial CPU version took 5422 seconds, leading to a significant 115x speedup.

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

    NASA Astrophysics Data System (ADS)

    Pandya, Tara M.; Johnson, Seth R.; Evans, Thomas M.; Davidson, Gregory G.; Hamilton, Steven P.; Godfrey, Andrew T.

    2016-03-01

    This work discusses the implementation, capabilities, and validation of Shift, a massively parallel Monte Carlo radiation transport package authored at Oak Ridge National Laboratory. Shift has been developed to scale well from laptops to small computing clusters to advanced supercomputers and includes features such as support for multiple geometry and physics engines, hybrid capabilities for variance reduction methods such as the Consistent Adjoint-Driven Importance Sampling methodology, advanced parallel decompositions, and tally methods optimized for scalability on supercomputing architectures. The scaling studies presented in this paper demonstrate good weak and strong scaling behavior for the implemented algorithms. Shift has also been validated and verified against various reactor physics benchmarks, including the Consortium for Advanced Simulation of Light Water Reactors' Virtual Environment for Reactor Analysis criticality test suite and several Westinghouse AP1000® problems presented in this paper. These benchmark results compare well to those from other contemporary Monte Carlo codes such as MCNP5 and KENO.

  16. 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.

  17. A Massively Parallel Solver for the Mechanical Harmonic Analysis of Accelerator Cavities

    SciTech Connect

    O. Kononenko

    2015-02-17

    ACE3P is a 3D massively parallel simulation suite that developed at SLAC National Accelerator Laboratory that can perform coupled electromagnetic, thermal and mechanical study. Effectively utilizing supercomputer resources, ACE3P has become a key simulation tool for particle accelerator R and D. A new frequency domain solver to perform mechanical harmonic response analysis of accelerator components is developed within the existing parallel framework. This solver is designed to determine the frequency response of the mechanical system to external harmonic excitations for time-efficient accurate analysis of the large-scale problems. Coupled with the ACE3P electromagnetic modules, this capability complements a set of multi-physics tools for a comprehensive study of microphonics in superconducting accelerating cavities in order to understand the RF response and feedback requirements for the operational reliability of a particle accelerator. (auth)

  18. Execution of OPS5 production systems on a massively parallel machine

    SciTech Connect

    Hillyer, B.K.; Shaw, D.E.

    1986-06-01

    In this paper, the authors describe an algorithm for executing production systems expressed in the OPS5 language on a massively parallel multiple-SIMD machine called NON-VON, portions of which are currently under construction at Columbia University. The algorithm, a parallel adaptation of Forgy's Rete Match, has been implemented and tested on an instruction-level simulator. They present a detailed performance analysis, based on the implemented code, for the averaged characteristics of six production systems having an average of 910 inference rules each. The analysis predicts an execution rate of more than 850 production firings per second using hardware comparable in cost to a VAX 11/780. By way of comparison, a LISP-based OPS5 interpreter running on a VAX 11/780 typically fires 1 to 5 rules per second, while a Bliss-based interpreter executes 5 to 12 rules per second.

  19. Massively parallel simulation of flow and transport in variably saturated porous and fractured media

    SciTech Connect

    Wu, Yu-Shu; Zhang, Keni; Pruess, Karsten

    2002-01-15

    This paper describes a massively parallel simulation method and its application for modeling multiphase flow and multicomponent transport in porous and fractured reservoirs. The parallel-computing method has been implemented into the TOUGH2 code and its numerical performance is tested on a Cray T3E-900 and IBM SP. The efficiency and robustness of the parallel-computing algorithm are demonstrated by completing two simulations with more than one million gridblocks, using site-specific data obtained from a site-characterization study. The first application involves the development of a three-dimensional numerical model for flow in the unsaturated zone of Yucca Mountain, Nevada. The second application is the study of tracer/radionuclide transport through fracture-matrix rocks for the same site. The parallel-computing technique enhances modeling capabilities by achieving several-orders-of-magnitude speedup for large-scale and high resolution modeling studies. The resulting modeling results provide many new insights into flow and transport processes that could not be obtained from simulations using the single-CPU simulator.

  20. DGDFT: A massively parallel method for large scale density functional theory calculations

    SciTech Connect

    Hu, Wei Yang, Chao; Lin, Lin

    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{sup −4} Hartree/atom in terms of the error of energy and 6.2 × 10{sup −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.

  1. Seismic waves modeling with the Fourier pseudo-spectral method on massively parallel machines.

    NASA Astrophysics Data System (ADS)

    Klin, Peter

    2015-04-01

    The Fourier pseudo-spectral method (FPSM) is an approach for the 3D numerical modeling of the wave propagation, which is based on the discretization of the spatial domain in a structured grid and relies on global spatial differential operators for the solution of the wave equation. This last peculiarity is advantageous from the accuracy point of view but poses difficulties for an efficient implementation of the method to be run on parallel computers with distributed memory architecture. The 1D spatial domain decomposition approach has been so far commonly adopted in the parallel implementations of the FPSM, but it implies an intensive data exchange among all the processors involved in the computation, which can degrade the performance because of communication latencies. Moreover, the scalability of the 1D domain decomposition is limited, since the number of processors can not exceed the number of grid points along the directions in which the domain is partitioned. This limitation inhibits an efficient exploitation of the computational environments with a very large number of processors. In order to overcome the limitations of the 1D domain decomposition we implemented a parallel version of the FPSM based on a 2D domain decomposition, which allows to achieve a higher degree of parallelism and scalability on massively parallel machines with several thousands of processing elements. The parallel programming is essentially achieved using the MPI protocol but OpenMP parts are also included in order to exploit the single processor multi - threading capabilities, when available. The developed tool is aimed at the numerical simulation of the seismic waves propagation and in particular is intended for earthquake ground motion research. We show the scalability tests performed up to 16k processing elements on the IBM Blue Gene/Q computer at CINECA (Italy), as well as the application to the simulation of the earthquake ground motion in the alluvial plain of the Po river (Italy).

  2. On distributed memory MPI-based parallelization of SPH codes in massive HPC context

    NASA Astrophysics Data System (ADS)

    Oger, G.; Le Touzé, D.; Guibert, D.; de Leffe, M.; Biddiscombe, J.; Soumagne, J.; Piccinali, J.-G.

    2016-03-01

    Most of particle methods share the problem of high computational cost and in order to satisfy the demands of solvers, currently available hardware technologies must be fully exploited. Two complementary technologies are now accessible. On the one hand, CPUs which can be structured into a multi-node framework, allowing massive data exchanges through a high speed network. In this case, each node is usually comprised of several cores available to perform multithreaded computations. On the other hand, GPUs which are derived from the graphics computing technologies, able to perform highly multi-threaded calculations with hundreds of independent threads connected together through a common shared memory. This paper is primarily dedicated to the distributed memory parallelization of particle methods, targeting several thousands of CPU cores. The experience gained clearly shows that parallelizing a particle-based code on moderate numbers of cores can easily lead to an acceptable scalability, whilst a scalable speedup on thousands of cores is much more difficult to obtain. The discussion revolves around speeding up particle methods as a whole, in a massive HPC context by making use of the MPI library. We focus on one particular particle method which is Smoothed Particle Hydrodynamics (SPH), one of the most widespread today in the literature as well as in engineering.

  3. Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing.

    PubMed

    Ruiz, Anna; Llort, Gemma; Yagüe, Carmen; Baena, Neus; Viñas, Marina; Torra, Montse; Brunet, Anna; Seguí, Miquel A; Saigí, Eugeni; Guitart, Miriam

    2014-01-01

    High throughput methods such as next generation sequencing are increasingly used in molecular diagnosis. The aim of this study was to develop a workflow for the detection of BRCA1 and BRCA2 mutations using massive parallel sequencing in a 454 GS Junior bench top sequencer. Our approach was first validated in a panel of 23 patients containing 62 unique variants that had been previously Sanger sequenced. Subsequently, 101 patients with familial breast and ovarian cancer were studied. BRCA1 and BRCA2 exon enrichment has been performed by PCR amplification using the BRCA MASTR kit (Multiplicom). Bioinformatic analysis of reads is performed with the AVA software v2.7 (Roche). In total, all 62 variants were detected resulting in a sensitivity of 100%. 71 false positives were called resulting in a specificity of 97.35%. All of them correspond to deletions located in homopolymeric stretches. The analysis of the homopolymers stretches of 6 bp or longer using the BRCA HP kit (Multiplicom) increased the specificity of the detection of BRCA1 and BRCA2 mutations to 99.99%. We show here that massive parallel pyrosequencing can be used as a diagnostic strategy to test for BRCA1 and BRCA2 mutations meeting very stringent sensitivity and specificity parameters replacing traditional Sanger sequencing with a lower cost.

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

    SciTech Connect

    Madduri, Kamesh; Ediger, David; Jiang, Karl; Bader, David A.; Chavarría-Miranda, Daniel

    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. 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.

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

    SciTech Connect

    Madduri, Kamesh; Ediger, David; Jiang, Karl; Bader, David A.; Chavarria-Miranda, Daniel

    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 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.

  6. Transcriptional analysis of endocrine disruption using zebrafish and massively parallel sequencing.

    PubMed

    Baker, Michael E; Hardiman, Gary

    2014-06-01

    Endocrine-disrupting chemicals (EDCs), including plasticizers, pesticides, detergents, and pharmaceuticals, affect a variety of hormone-regulated physiological pathways in humans and wildlife. Many EDCs are lipophilic molecules and bind to hydrophobic pockets in steroid receptors, such as the estrogen receptor and androgen receptor, which are important in vertebrate reproduction and development. Indeed, health effects attributed to EDCs include reproductive dysfunction (e.g. reduced fertility, reproductive tract abnormalities, and skewed male:female sex ratios in fish), early puberty, various cancers, and obesity. A major concern is the effects of exposure to low concentrations of endocrine disruptors in utero and post partum, which may increase the incidence of cancer and diabetes in adults. EDCs affect transcription of hundreds and even thousands of genes, which has created the need for new tools to monitor the global effects of EDCs. The emergence of massive parallel sequencing for investigating gene transcription provides a sensitive tool for monitoring the effects of EDCs on humans and other vertebrates, as well as elucidating the mechanism of action of EDCs. Zebrafish conserve many developmental pathways found in humans, which makes zebrafish a valuable model system for studying EDCs, especially on early organ development because their embryos are translucent. In this article, we review recent advances in massive parallel sequencing approaches with a focus on zebrafish. We make the case that zebrafish exposed to EDCs at different stages of development can provide important insights on EDC effects on human health. PMID:24850832

  7. Transcriptional analysis of endocrine disruption using zebrafish and massively parallel sequencing

    PubMed Central

    Baker, Michael E.; Hardiman, Gary

    2014-01-01

    Endocrine disrupting chemicals (EDCs) including plasticizers, pesticides, detergents and pharmaceuticals, affect a variety of hormone-regulated physiological pathways in humans and wildlife. Many EDCs are lipophilic molecules and bind to hydrophobic pockets in steroid receptors, such as the estrogen receptor and androgen receptor, which are important in vertebrate reproduction and development. Indeed, health effects attributed to EDCs include reproductive dysfunction (e.g., reduced fertility, reproductive tract abnormalities and skewed male/female sex ratios in fish), early puberty, various cancers and obesity. A major concern is the effects of exposure to low concentrations of endocrine disruptors in utero and post partum, which may increase the incidence of cancer and diabetes in adults. EDCs affect transcription of hundreds and even thousands of genes, which has created the need for new tools to monitor the global effects of EDCs. The emergence of massive parallel sequencing for investigating gene transcription provides a sensitive tool for monitoring the effects of EDCs on humans and other vertebrates as well as elucidating the mechanism of action of EDCs. Zebrafish conserve many developmental pathways found in humans, which makes zebrafish a valuable model system for studying EDCs especially on early organ development because their embryos are translucent. In this article we review recent advances in massive parallel sequencing approaches with a focus on zebrafish. We make the case that zebrafish exposed to EDCs at different stages of development, can provide important insights on EDC effects on human health. PMID:24850832

  8. 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.

  9. Massively Parallel Sequencing-Based Clonality Analysis of Synchronous Endometrioid Endometrial and Ovarian Carcinomas.

    PubMed

    Schultheis, Anne M; Ng, Charlotte K Y; De Filippo, Maria R; Piscuoglio, Salvatore; Macedo, Gabriel S; Gatius, Sonia; Perez Mies, Belen; Soslow, Robert A; Lim, Raymond S; Viale, Agnes; Huberman, Kety H; Palacios, Jose C; Reis-Filho, Jorge S; Matias-Guiu, Xavier; Weigelt, Britta

    2016-06-01

    Synchronous early-stage endometrioid endometrial carcinomas (EECs) and endometrioid ovarian carcinomas (EOCs) are associated with a favorable prognosis and have been suggested to represent independent primary tumors rather than metastatic disease. We subjected sporadic synchronous EECs/EOCs from five patients to whole-exome massively parallel sequencing, which revealed that the EEC and EOC of each case displayed strikingly similar repertoires of somatic mutations and gene copy number alterations. Despite the presence of mutations restricted to the EEC or EOC in each case, we observed that the mutational processes that shaped their respective genomes were consistent. High-depth targeted massively parallel sequencing of sporadic synchronous EECs/EOCs from 17 additional patients confirmed that these lesions are clonally related. In an additional Lynch Syndrome case, however, the EEC and EOC were found to constitute independent cancers lacking somatic mutations in common. Taken together, sporadic synchronous EECs/EOCs are clonally related and likely constitute dissemination from one site to the other. PMID:26832770

  10. 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.

  11. Assessment of Whole Genome Amplification for Sequence Capture and Massively Parallel Sequencing

    PubMed Central

    Hasmats, Johanna; Gréen, Henrik; Orear, Cedric; Validire, Pierre; Huss, Mikael; Käller, Max; Lundeberg, Joakim

    2014-01-01

    Exome sequence capture and massively parallel sequencing can be combined to achieve inexpensive and rapid global analyses of the functional sections of the genome. The difficulties of working with relatively small quantities of genetic material, as may be necessary when sharing tumor biopsies between collaborators for instance, can be overcome using whole genome amplification. However, the potential drawbacks of using a whole genome amplification technology based on random primers in combination with sequence capture followed by massively parallel sequencing have not yet been examined in detail, especially in the context of mutation discovery in tumor material. In this work, we compare mutations detected in sequence data for unamplified DNA, whole genome amplified DNA, and RNA originating from the same tumor tissue samples from 16 patients diagnosed with non-small cell lung cancer. The results obtained provide a comprehensive overview of the merits of these techniques for mutation analysis. We evaluated the identified genetic variants, and found that most (74%) of them were observed in both the amplified and the unamplified sequence data. Eighty-nine percent of the variations found by WGA were shared with unamplified DNA. We demonstrate a strategy for avoiding allelic bias by including RNA-sequencing information. PMID:24409309

  12. Assessment of whole genome amplification for sequence capture and massively parallel sequencing.

    PubMed

    Hasmats, Johanna; Gréen, Henrik; Orear, Cedric; Validire, Pierre; Huss, Mikael; Käller, Max; Lundeberg, Joakim

    2014-01-01

    Exome sequence capture and massively parallel sequencing can be combined to achieve inexpensive and rapid global analyses of the functional sections of the genome. The difficulties of working with relatively small quantities of genetic material, as may be necessary when sharing tumor biopsies between collaborators for instance, can be overcome using whole genome amplification. However, the potential drawbacks of using a whole genome amplification technology based on random primers in combination with sequence capture followed by massively parallel sequencing have not yet been examined in detail, especially in the context of mutation discovery in tumor material. In this work, we compare mutations detected in sequence data for unamplified DNA, whole genome amplified DNA, and RNA originating from the same tumor tissue samples from 16 patients diagnosed with non-small cell lung cancer. The results obtained provide a comprehensive overview of the merits of these techniques for mutation analysis. We evaluated the identified genetic variants, and found that most (74%) of them were observed in both the amplified and the unamplified sequence data. Eighty-nine percent of the variations found by WGA were shared with unamplified DNA. We demonstrate a strategy for avoiding allelic bias by including RNA-sequencing information.

  13. 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; Anderson, Steve; Woodward, Paul; Dietz, Hank

    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

  14. MADmap: A Massively Parallel Maximum-Likelihood Cosmic Microwave Background Map-Maker

    SciTech Connect

    Cantalupo, Christopher; Borrill, Julian; Jaffe, Andrew; Kisner, Theodore; Stompor, Radoslaw

    2009-06-09

    MADmap is a software application used to produce maximum-likelihood images of the sky from time-ordered data which include correlated noise, such as those gathered by Cosmic Microwave Background (CMB) experiments. It works efficiently on platforms ranging from small workstations to the most massively parallel supercomputers. Map-making is a critical step in the analysis of all CMB data sets, and the maximum-likelihood approach is the most accurate and widely applicable algorithm; however, it is a computationally challenging task. This challenge will only increase with the next generation of ground-based, balloon-borne and satellite CMB polarization experiments. The faintness of the B-mode signal that these experiments seek to measure requires them to gather enormous data sets. MADmap is already being run on up to O(1011) time samples, O(108) pixels and O(104) cores, with ongoing work to scale to the next generation of data sets and supercomputers. We describe MADmap's algorithm based around a preconditioned conjugate gradient solver, fast Fourier transforms and sparse matrix operations. We highlight MADmap's ability to address problems typically encountered in the analysis of realistic CMB data sets and describe its application to simulations of the Planck and EBEX experiments. The massively parallel and distributed implementation is detailed and scaling complexities are given for the resources required. MADmap is capable of analysing the largest data sets now being collected on computing resources currently available, and we argue that, given Moore's Law, MADmap will be capable of reducing the most massive projected data sets.

  15. MADmap: A MASSIVELY PARALLEL MAXIMUM LIKELIHOOD COSMIC MICROWAVE BACKGROUND MAP-MAKER

    SciTech Connect

    Cantalupo, C. M.; Borrill, J. D.; Kisner, T. S.; Jaffe, A. H.; Stompor, R. E-mail: jdborrill@lbl.gov E-mail: a.jaffe@imperial.ac.uk

    2010-03-01

    MADmap is a software application used to produce maximum likelihood images of the sky from time-ordered data which include correlated noise, such as those gathered by cosmic microwave background (CMB) experiments. It works efficiently on platforms ranging from small workstations to the most massively parallel supercomputers. Map-making is a critical step in the analysis of all CMB data sets, and the maximum likelihood approach is the most accurate and widely applicable algorithm; however, it is a computationally challenging task. This challenge will only increase with the next generation of ground-based, balloon-borne, and satellite CMB polarization experiments. The faintness of the B-mode signal that these experiments seek to measure requires them to gather enormous data sets. MADmap is already being run on up to O(10{sup 11}) time samples, O(10{sup 8}) pixels, and O(10{sup 4}) cores, with ongoing work to scale to the next generation of data sets and supercomputers. We describe MADmap's algorithm based around a preconditioned conjugate gradient solver, fast Fourier transforms, and sparse matrix operations. We highlight MADmap's ability to address problems typically encountered in the analysis of realistic CMB data sets and describe its application to simulations of the Planck and EBEX experiments. The massively parallel and distributed implementation is detailed and scaling complexities are given for the resources required. MADmap is capable of analyzing the largest data sets now being collected on computing resources currently available, and we argue that, given Moore's Law, MADmap will be capable of reducing the most massive projected data sets.

  16. 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

  17. ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains.

    PubMed

    Torre, Emiliano; Canova, Carlos; Denker, Michael; Gerstein, George; Helias, Moritz; Grün, Sonja

    2016-07-01

    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

  18. MPI/OpenMP Hybrid Parallel Algorithm of Resolution of Identity Second-Order Møller-Plesset Perturbation Calculation for Massively Parallel Multicore Supercomputers.

    PubMed

    Katouda, Michio; Nakajima, Takahito

    2013-12-10

    A new algorithm for massively parallel calculations of electron correlation energy of large molecules based on the resolution of identity second-order Møller-Plesset perturbation (RI-MP2) technique is developed and implemented into the quantum chemistry software NTChem. In this algorithm, a Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) hybrid parallel programming model is applied to attain efficient parallel performance on massively parallel supercomputers. An in-core storage scheme of intermediate data of three-center electron repulsion integrals utilizing the distributed memory is developed to eliminate input/output (I/O) overhead. The parallel performance of the algorithm is tested on massively parallel supercomputers such as the K computer (using up to 45 992 central processing unit (CPU) cores) and a commodity Intel Xeon cluster (using up to 8192 CPU cores). The parallel RI-MP2/cc-pVTZ calculation of two-layer nanographene sheets (C150H30)2 (number of atomic orbitals is 9640) is performed using 8991 node and 71 288 CPU cores of the K computer. PMID:26592275

  19. MPI/OpenMP Hybrid Parallel Algorithm of Resolution of Identity Second-Order Møller-Plesset Perturbation Calculation for Massively Parallel Multicore Supercomputers.

    PubMed

    Katouda, Michio; Nakajima, Takahito

    2013-12-10

    A new algorithm for massively parallel calculations of electron correlation energy of large molecules based on the resolution of identity second-order Møller-Plesset perturbation (RI-MP2) technique is developed and implemented into the quantum chemistry software NTChem. In this algorithm, a Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) hybrid parallel programming model is applied to attain efficient parallel performance on massively parallel supercomputers. An in-core storage scheme of intermediate data of three-center electron repulsion integrals utilizing the distributed memory is developed to eliminate input/output (I/O) overhead. The parallel performance of the algorithm is tested on massively parallel supercomputers such as the K computer (using up to 45 992 central processing unit (CPU) cores) and a commodity Intel Xeon cluster (using up to 8192 CPU cores). The parallel RI-MP2/cc-pVTZ calculation of two-layer nanographene sheets (C150H30)2 (number of atomic orbitals is 9640) is performed using 8991 node and 71 288 CPU cores of the K computer.

  20. User's Guide for TOUGH2-MP - A Massively Parallel Version of the TOUGH2 Code

    SciTech Connect

    Earth Sciences Division; Zhang, Keni; Zhang, Keni; Wu, Yu-Shu; Pruess, Karsten

    2008-05-27

    TOUGH2-MP is a massively parallel (MP) version of the TOUGH2 code, designed for computationally efficient parallel simulation of isothermal and nonisothermal flows of multicomponent, multiphase fluids in one, two, and three-dimensional porous and fractured media. In recent years, computational requirements have become increasingly intensive in large or highly nonlinear problems for applications in areas such as radioactive waste disposal, CO2 geological sequestration, environmental assessment and remediation, reservoir engineering, and groundwater hydrology. The primary objective of developing the parallel-simulation capability is to significantly improve the computational performance of the TOUGH2 family of codes. The particular goal for the parallel simulator is to achieve orders-of-magnitude improvement in computational time for models with ever-increasing complexity. TOUGH2-MP is designed to perform parallel simulation on multi-CPU computational platforms. An earlier version of TOUGH2-MP (V1.0) was based on the TOUGH2 Version 1.4 with EOS3, EOS9, and T2R3D modules, a software previously qualified for applications in the Yucca Mountain project, and was designed for execution on CRAY T3E and IBM SP supercomputers. The current version of TOUGH2-MP (V2.0) includes all fluid property modules of the standard version TOUGH2 V2.0. It provides computationally efficient capabilities using supercomputers, Linux clusters, or multi-core PCs, and also offers many user-friendly features. The parallel simulator inherits all process capabilities from V2.0 together with additional capabilities for handling fractured media from V1.4. This report provides a quick starting guide on how to set up and run the TOUGH2-MP program for users with a basic knowledge of running the (standard) version TOUGH2 code, The report also gives a brief technical description of the code, including a discussion of parallel methodology, code structure, as well as mathematical and numerical methods used

  1. 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.

  2. Compact Graph Representations and Parallel Connectivity Algorithms for Massive Dynamic Network Analysis

    SciTech Connect

    Madduri, Kamesh; Bader, David A.

    2009-02-15

    Graph-theoretic abstractions are extensively used to analyze massive data sets. Temporal data streams from socioeconomic interactions, social networking web sites, communication traffic, and scientific computing can be intuitively modeled as graphs. We present the first study of novel high-performance combinatorial techniques for analyzing large-scale information networks, encapsulating dynamic interaction data in the order of billions of entities. We present new data structures to represent dynamic interaction networks, and discuss algorithms for processing parallel insertions and deletions of edges in small-world networks. With these new approaches, we achieve an average performance rate of 25 million structural updates per second and a parallel speedup of nearly28 on a 64-way Sun UltraSPARC T2 multicore processor, for insertions and deletions to a small-world network of 33.5 million vertices and 268 million edges. We also design parallel implementations of fundamental dynamic graph kernels related to connectivity and centrality queries. Our implementations are freely distributed as part of the open-source SNAP (Small-world Network Analysis and Partitioning) complex network analysis framework.

  3. Real-time massively parallel processing of spectral optical coherence tomography data on graphics processing units

    NASA Astrophysics Data System (ADS)

    Sylwestrzak, Marcin; Szlag, Daniel; Szkulmowski, Maciej; Targowski, Piotr

    2011-06-01

    In this contribution we describe a specialised data processing system for Spectral Optical Coherence Tomography (SOCT) biomedical imaging which utilises massively parallel data processing on a low-cost, Graphics Processing Unit (GPU). One of the most significant limitations of SOCT is the data processing time on the main processor of the computer (CPU), which is generally longer than the data acquisition. Therefore, real-time imaging with acceptable quality is limited to a small number of tomogram lines (A-scans). Recent progress in graphics cards technology gives a promising solution of this problem. The newest graphics processing units allow not only for a very high speed three dimensional (3D) rendering, but also for a general purpose parallel numerical calculations with efficiency higher than provided by the CPU. The presented system utilizes CUDATM graphic card and allows for a very effective real time SOCT imaging. The total imaging speed for 2D data consisting of 1200 A-scans is higher than refresh rate of a 120 Hz monitor. 3D rendering of the volume data build of 10 000 A-scans is performed with frame rate of about 9 frames per second. These frame rates include data transfer from a frame grabber to GPU, data processing and 3D rendering to the screen. The software description includes data flow, parallel processing and organization of threads. For illustration we show real time high resolution SOCT imaging of human skin and eye.

  4. Climate system modeling on massively parallel systems: LDRD Project 95-ERP-47 final report

    SciTech Connect

    Mirin, A.A.; Dannevik, W.P.; Chan, B.; Duffy, P.B.; Eltgroth, P.G.; Wehner, M.F.

    1996-12-01

    Global warming, acid rain, ozone depletion, and biodiversity loss are some of the major climate-related issues presently being addressed by climate and environmental scientists. Because unexpected changes in the climate could have significant effect on our economy, it is vitally important to improve the scientific basis for understanding and predicting the earth`s climate. The impracticality of modeling the earth experimentally in the laboratory together with the fact that the model equations are highly nonlinear has created a unique and vital role for computer-based climate experiments. However, today`s computer models, when run at desired spatial and temporal resolution and physical complexity, severely overtax the capabilities of our most powerful computers. Parallel processing offers significant potential for attaining increased performance and making tractable simulations that cannot be performed today. The principal goals of this project have been to develop and demonstrate the capability to perform large-scale climate simulations on high-performance computing systems (using methodology that scales to the systems of tomorrow), and to carry out leading-edge scientific calculations using parallelized models. The demonstration platform for these studies has been the 256-processor Cray-T3D located at Lawrence Livermore National Laboratory. Our plan was to undertake an ambitious program in optimization, proof-of-principle and scientific study. These goals have been met. We are now regularly using massively parallel processors for scientific study of the ocean and atmosphere, and preliminary parallel coupled ocean/atmosphere calculations are being carried out as well. Furthermore, our work suggests that it should be possible to develop an advanced comprehensive climate system model with performance scalable to the teraflops range. 9 refs., 3 figs.

  5. A Massively Parallel Sparse Eigensolver for Structural Dynamics Finite Element Analysis

    SciTech Connect

    Day, David M.; Reese, G.M.

    1999-05-01

    Eigenanalysis is a critical component of structural dynamics which is essential for determinating the vibrational response of systems. This effort addresses the development of numerical algorithms associated with scalable eigensolver techniques suitable for use on massively parallel, distributed memory computers that are capable of solving large scale structural dynamics problems. An iterative Lanczos method was determined to be the best choice for the application. Scalability of the eigenproblem depends on scalability of the underlying linear solver. A multi-level solver (FETI) was selected as most promising for this component. Issues relating to heterogeneous materials, mechanisms and multipoint constraints have been examined, and the linear solver algorithm has been developed to incorporate features that result in a scalable, robust algorithm for practical structural dynamics applications. The resulting tools have been demonstrated on large problems representative of a weapon's system.

  6. Massively parallel low-cost pick-and-place of optoelectronic devices by electrochemical fluidic processing.

    PubMed

    Ozkan, M; Kibar, O; Ozkan, C S; Esener, S C

    2000-09-01

    We describe a novel electrochemical technique for the nonlithographic, fluidic pick-and-place assembly of optoelectronic devices by electrical and optical addressing. An electrochemical cell was developed that consists of indium tin oxide (ITO) and n -type silicon substrates as the two electrode materials and deionized water (R = 18 MOmega) as the electrolytic medium between the two electrodes. 0.8-20-microm-diameter negatively charged polystyrene beads, 50-100-microm-diameter SiO(2) pucks, and 50-microm LED's were successfully integrated upon a patterned silicon substrate by electrical addressing. In addition, 0.8-microm-diameter beads were integrated upon a homogeneous silicon substrate by optical addressing. This method can be applied to massively parallel assembly (>1000 x 1000 arrays) of multiple types of devices (of a wide size range) with very fast (a few seconds) and accurate positioning.

  7. Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness.

    PubMed

    Keren, Leeat; Hausser, Jean; Lotan-Pompan, Maya; Vainberg Slutskin, Ilya; Alisar, Hadas; Kaminski, Sivan; Weinberger, Adina; Alon, Uri; Milo, Ron; Segal, Eran

    2016-08-25

    Data of gene expression levels across individuals, cell types, and disease states is expanding, yet our understanding of how expression levels impact phenotype is limited. Here, we present a massively parallel system for assaying the effect of gene expression levels on fitness in Saccharomyces cerevisiae by systematically altering the expression level of ∼100 genes at ∼100 distinct levels spanning a 500-fold range at high resolution. We show that the relationship between expression levels and growth is gene and environment specific and provides information on the function, stoichiometry, and interactions of genes. Wild-type expression levels in some conditions are not optimal for growth, and genes whose fitness is greatly affected by small changes in expression level tend to exhibit lower cell-to-cell variability in expression. Our study addresses a fundamental gap in understanding the functional significance of gene expression regulation and offers a framework for evaluating the phenotypic effects of expression variation. PMID:27545349

  8. Large-Scale Eigenvalue Calculations for Stability Analysis of Steady Flows on Massively Parallel Computers

    SciTech Connect

    Lehoucq, Richard B.; Salinger, Andrew G.

    1999-08-01

    We present an approach for determining the linear stability of steady states of PDEs on massively parallel computers. Linearizing the transient behavior around a steady state leads to a generalized eigenvalue problem. The eigenvalues with largest real part are calculated using Arnoldi's iteration driven by a novel implementation of the Cayley transformation to recast the problem as an ordinary eigenvalue problem. The Cayley transformation requires the solution of a linear system at each Arnoldi iteration, which must be done iteratively for the algorithm to scale with problem size. A representative model problem of 3D incompressible flow and heat transfer in a rotating disk reactor is used to analyze the effect of algorithmic parameters on the performance of the eigenvalue algorithm. Successful calculations of leading eigenvalues for matrix systems of order up to 4 million were performed, identifying the critical Grashof number for a Hopf bifurcation.

  9. 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.

  10. 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.

  11. Inside the intraterrestrials: The deep biosphere seen through massively parallel sequencing

    NASA Astrophysics Data System (ADS)

    Biddle, J.

    2009-12-01

    Deeply buried marine sediments may house a large amount of the Earth’s microbial population. Initial studies based on 16S rRNA clone libraries suggest that these sediments contain unique phylotypes of microorganisms, particularly from the archaeal domain. Since this environment is so difficult to study, microbiologists are challenged to find ways to examine these populations remotely. A major approach taken to study this environment uses massively parallel sequencing to examine the inner genetic workings of these microorganisms after the sediment has been drilled. Both metagenomics and tagged amplicon sequencing have been employed on deep sediments, and initial results show that different geographic regions can be differentiated through genomics and also minor populations may cause major geochemical changes.

  12. Detection of arboviruses and other micro-organisms in experimentally infected mosquitoes using massively parallel sequencing.

    PubMed

    Hall-Mendelin, Sonja; Allcock, Richard; Kresoje, Nina; van den Hurk, Andrew F; Warrilow, David

    2013-01-01

    Human disease incidence attributed to arbovirus infection is increasing throughout the world, with effective control interventions limited by issues of sustainability, insecticide resistance and the lack of effective vaccines. Several promising control strategies are currently under development, such as the release of mosquitoes trans-infected with virus-blocking Wolbachia bacteria. Implementation of any control program is dependent on effective virus surveillance and a thorough understanding of virus-vector interactions. Massively parallel sequencing has enormous potential for providing comprehensive genomic information that can be used to assess many aspects of arbovirus ecology, as well as to evaluate novel control strategies. To demonstrate proof-of-principle, we analyzed Aedes aegypti or Aedes albopictus experimentally infected with dengue, yellow fever or chikungunya viruses. Random amplification was used to prepare sufficient template for sequencing on the Personal Genome Machine. Viral sequences were present in all infected mosquitoes. In addition, in most cases, we were also able to identify the mosquito species and mosquito micro-organisms, including the bacterial endosymbiont Wolbachia. Importantly, naturally occurring Wolbachia strains could be differentiated from strains that had been trans-infected into the mosquito. The method allowed us to assemble near full-length viral genomes and detect other micro-organisms without prior sequence knowledge, in a single reaction. This is a step toward the application of massively parallel sequencing as an arbovirus surveillance tool. It has the potential to provide insight into virus transmission dynamics, and has applicability to the post-release monitoring of Wolbachia in mosquito populations.

  13. 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

  14. Massively parallel cis-regulatory analysis in the mammalian central nervous system.

    PubMed

    Shen, Susan Q; Myers, Connie A; Hughes, Andrew E O; Byrne, Leah C; Flannery, John G; Corbo, Joseph C

    2016-02-01

    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.

  15. Massive parallel analysis of DNA - Hoechst 33258 binding specificity with a generic oligonucleotide microchip.

    SciTech Connect

    Drobyshev, A. L.; Zasedatelev, A. S.; Yershov, G. M.; Mirzabekov, A. D.; Biochip Technology Center

    1999-10-15

    A generic oligodeoxyribonucleotide microchip was used to determine the sequence specificity of Hoechst 33258 binding to double-stranded DNA. The generic microchip contained 4096 oxctadeoxynucleo-tides in which all possible 4(6)= 4096 hexadeoxy-nucleotide sequences are flanked on both the 3'- and 5'-ends with equimolar mixtures of four bases. The microchip was manufactured by chemical immobilization of presynthesized 8mers within polyacrylamide gel pads. A selected set of immobilized 8mers was converted to double-stranded form by hybridization with a mixture of fluorescently labeled complementary 8mers. Massive parallel measurements of melting curves were carried out for the majority of 2080 6mer duplexes, in both the absence and presence of the Hoechst dye. The sequence-specific affinity for Hoechst 33258 was calculated as the increase in melting temperature caused by ligand binding. The dye exhibited specificity for A:T but not G:C base pairs. The affinity is low for two A:T base pairs, increases significantly for three, and reaches a plateau for four A:T base pairs. The relative ligand affinity for all trinucleotide and tetranucleotide sequences (A/T)(3)and (A/T)(4)was estimated. The free energy of dye binding to several duplexes was calculated from the equilibrium melting curves of the duplexes formed on the oligonucleotide microchips. This method can be used as a general approach for massive screening of the sequence specificity of DNA-binding compounds.

  16. Massively parallel simulation with DOE's ASCI supercomputers : an overview of the Los Alamos Crestone project

    SciTech Connect

    Weaver, R. P.; Gittings, M. L.

    2004-01-01

    The Los Alamos Crestone Project is part of the Department of Energy's (DOE) Accelerated Strategic Computing Initiative, or ASCI Program. The main goal of this software development project is to investigate the use of continuous adaptive mesh refinement (CAMR) techniques for application to problems of interest to the Laboratory. There are many code development efforts in the Crestone Project, both unclassified and classified codes. In this overview I will discuss the unclassified SAGE and the RAGE codes. The SAGE (SAIC adaptive grid Eulerian) code is a one-, two-, and three-dimensional multimaterial Eulerian massively parallel hydrodynamics code for use in solving a variety of high-deformation flow problems. The RAGE CAMR code is built from the SAGE code by adding various radiation packages, improved setup utilities and graphics packages and is used for problems in which radiation transport of energy is important. The goal of these massively-parallel versions of the codes is to run extremely large problems in a reasonable amount of calendar time. Our target is scalable performance to {approx}10,000 processors on a 1 billion CAMR computational cell problem that requires hundreds of variables per cell, multiple physics packages (e.g. radiation and hydrodynamics), and implicit matrix solves for each cycle. A general description of the RAGE code has been published in [l],[ 2], [3] and [4]. Currently, the largest simulations we do are three-dimensional, using around 500 million computation cells and running for literally months of calendar time using {approx}2000 processors. Current ASCI platforms range from several 3-teraOPS supercomputers to one 12-teraOPS machine at Lawrence Livermore National Laboratory, the White machine, and one 20-teraOPS machine installed at Los Alamos, the Q machine. Each machine is a system comprised of many component parts that must perform in unity for the successful run of these simulations. Key features of any massively parallel system

  17. Adaptation and optimization of basic operations for an unstructured mesh CFD algorithm for computation on massively parallel accelerators

    NASA Astrophysics Data System (ADS)

    Bogdanov, P. B.; Gorobets, A. V.; Sukov, S. A.

    2013-08-01

    The design of efficient algorithms for large-scale gas dynamics computations with hybrid (heterogeneous) computing systems whose high performance relies on massively parallel accelerators is addressed. A high-order accurate finite volume algorithm with polynomial reconstruction on unstructured hybrid meshes is used to compute compressible gas flows in domains of complex geometry. The basic operations of the algorithm are implemented in detail for massively parallel accelerators, including AMD and NVIDIA graphics processing units (GPUs). Major optimization approaches and a computation transfer technique are covered. The underlying programming tool is the Open Computing Language (OpenCL) standard, which performs on accelerators of various architectures, both existing and emerging.

  18. Massive parallel IGHV gene sequencing reveals a germinal center pathway in origins of human multiple myeloma.

    PubMed

    Cowan, Graeme; Weston-Bell, Nicola J; Bryant, Dean; Seckinger, Anja; Hose, Dirk; Zojer, Niklas; Sahota, Surinder S

    2015-05-30

    Human multiple myeloma (MM) is characterized by accumulation of malignant terminally differentiated plasma cells (PCs) in the bone marrow (BM), raising the question when during maturation neoplastic transformation begins. Immunoglobulin IGHV genes carry imprints of clonal tumor history, delineating somatic hypermutation (SHM) events that generally occur in the germinal center (GC). Here, we examine MM-derived IGHV genes using massive parallel deep sequencing, comparing them with profiles in normal BM PCs. In 4/4 presentation IgG MM, monoclonal tumor-derived IGHV sequences revealed significant evidence for intraclonal variation (ICV) in mutation patterns. IGHV sequences of 2/2 normal PC IgG populations revealed dominant oligoclonal expansions, each expansion also displaying mutational ICV. Clonal expansions in MM and in normal BM PCs reveal common IGHV features. In such MM, the data fit a model of tumor origins in which neoplastic transformation is initiated in a GC B-cell committed to terminal differentiation but still targeted by on-going SHM. Strikingly, the data parallel IGHV clonal sequences in some monoclonal gammopathy of undetermined significance (MGUS) known to display on-going SHM imprints. Since MGUS generally precedes MM, these data suggest origins of MGUS and MM with IGHV gene mutational ICV from the same GC B-cell, arising via a distinctive pathway.

  19. Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization.

    PubMed

    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.

  20. A two-phase thermal model for subsurface transport on massively parallel computers

    SciTech Connect

    Martinez, M.J.; Hopkins, P.L.

    1997-12-01

    Many research activities in subsurface transport require the numerical simulation of multiphase flow in porous media. This capability is critical to research in environmental remediation (e.g. contaminations with dense, non-aqueous-phase liquids), nuclear waste management, reservoir engineering, and to the assessment of the future availability of groundwater in many parts of the world. This paper presents an unstructured grid numerical algorithm for subsurface transport in heterogeneous porous media implemented for use on massively parallel (MP) computers. The mathematical model considers nonisothermal two-phase (liquid/gas) flow, including capillary pressure effects, binary diffusion in the gas phase, conductive, latent, and sensible heat transport. The Galerkin finite element method is used for spatial discretization, and temporal integration is accomplished via a predictor/corrector scheme. Message-passing and domain decomposition techniques are used for implementing a scalable algorithm for distributed memory parallel computers. Illustrative applications are shown to demonstrate capabilities and performance, one of which is modeling hydrothermal transport at the Yucca Mountain site for a radioactive waste facility.

  1. The divide-expand-consolidate MP2 scheme goes massively parallel

    NASA Astrophysics Data System (ADS)

    Kristensen, Kasper; Kjærgaard, Thomas; Høyvik, Ida-Marie; Ettenhuber, Patrick; Jørgensen, Poul; Jansik, Branislav; Reine, Simen; Jakowski, Jacek

    2013-07-01

    For large molecular systems conventional implementations of second order Møller-Plesset (MP2) theory encounter a scaling wall, both memory- and time-wise. We describe how this scaling wall can be removed. We present a massively parallel algorithm for calculating MP2 energies and densities using the divide-expand-consolidate scheme where a calculation on a large system is divided into many small fragment calculations employing local orbital spaces. The resulting algorithm is linear-scaling with system size, exhibits near perfect parallel scalability, removes memory bottlenecks and does not involve any I/O. The algorithm employs three levels of parallelisation combined via a dynamic job distribution scheme. Results on two molecular systems containing 528 and 1056 atoms (4278 and 8556 basis functions) using 47,120 and 94,240 cores are presented. The results demonstrate the scalability of the algorithm both with respect to the number of cores and with respect to system size. The presented algorithm is thus highly suited for large super computer architectures and allows MP2 calculations on large molecular systems to be carried out within a few hours - for example, the correlated calculation on the molecular system containing 1056 atoms took 2.37 hours using 94240 cores.

  2. Genetic algorithm based task reordering to improve the performance of batch scheduled massively parallel scientific applications

    SciTech Connect

    Sankaran, Ramanan; Angel, Jordan; Brown, W. Michael

    2015-04-08

    The growth in size of networked high performance computers along with novel accelerator-based node architectures has further emphasized the importance of communication efficiency in high performance computing. The world's largest high performance computers are usually operated as shared user facilities due to the costs of acquisition and operation. Applications are scheduled for execution in a shared environment and are placed on nodes that are not necessarily contiguous on the interconnect. Furthermore, the placement of tasks on the nodes allocated by the scheduler is sub-optimal, leading to performance loss and variability. Here, we investigate the impact of task placement on the performance of two massively parallel application codes on the Titan supercomputer, a turbulent combustion flow solver (S3D) and a molecular dynamics code (LAMMPS). Benchmark studies show a significant deviation from ideal weak scaling and variability in performance. The inter-task communication distance was determined to be one of the significant contributors to the performance degradation and variability. A genetic algorithm-based parallel optimization technique was used to optimize the task ordering. This technique provides an improved placement of the tasks on the nodes, taking into account the application's communication topology and the system interconnect topology. As a result, application benchmarks after task reordering through genetic algorithm show a significant improvement in performance and reduction in variability, therefore enabling the applications to achieve better time to solution and scalability on Titan during production.

  3. Genetic algorithm based task reordering to improve the performance of batch scheduled massively parallel scientific applications

    DOE PAGES

    Sankaran, Ramanan; Angel, Jordan; Brown, W. Michael

    2015-04-08

    The growth in size of networked high performance computers along with novel accelerator-based node architectures has further emphasized the importance of communication efficiency in high performance computing. The world's largest high performance computers are usually operated as shared user facilities due to the costs of acquisition and operation. Applications are scheduled for execution in a shared environment and are placed on nodes that are not necessarily contiguous on the interconnect. Furthermore, the placement of tasks on the nodes allocated by the scheduler is sub-optimal, leading to performance loss and variability. Here, we investigate the impact of task placement on themore » performance of two massively parallel application codes on the Titan supercomputer, a turbulent combustion flow solver (S3D) and a molecular dynamics code (LAMMPS). Benchmark studies show a significant deviation from ideal weak scaling and variability in performance. The inter-task communication distance was determined to be one of the significant contributors to the performance degradation and variability. A genetic algorithm-based parallel optimization technique was used to optimize the task ordering. This technique provides an improved placement of the tasks on the nodes, taking into account the application's communication topology and the system interconnect topology. As a result, application benchmarks after task reordering through genetic algorithm show a significant improvement in performance and reduction in variability, therefore enabling the applications to achieve better time to solution and scalability on Titan during production.« less

  4. Measures of effectiveness for BMD mid-course tracking on MIMD massively parallel computers

    SciTech Connect

    VanDyke, J.P.; Tomkins, J.L.; Furnish, M.D.

    1995-05-01

    The TRC code, a mid-course tracking code for ballistic missiles, has previously been implemented on a 1024-processor MIMD (Multiple Instruction -- Multiple Data) massively parallel computer. Measures of Effectiveness (MOE) for this algorithm have been developed for this computing environment. The MOE code is run in parallel with the TRC code. Particularly useful MOEs include the number of missed objects (real objects for which the TRC algorithm did not construct a track); of ghost tracks (tracks not corresponding to a real object); of redundant tracks (multiple tracks corresponding to a single real object); and of unresolved objects (multiple objects corresponding to a single track). All of these are expressed as a function of time, and tend to maximize during the time in which real objects are spawned (multiple reentry vehicles per post-boost vehicle). As well, it is possible to measure the track-truth separation as a function of time. A set of calculations is presented illustrating these MOEs as a function of time for a case with 99 post-boost vehicles, each of which spawns 9 reentry vehicles.

  5. Massively parallel electrical conductivity imaging of the subsurface: Applications to hydrocarbon exploration

    SciTech Connect

    Newman, G.A.; Commer, M.

    2009-06-01

    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.

  6. Practical Realization of Massively Parallel Fiber -Free-Space Optical Interconnects

    NASA Astrophysics Data System (ADS)

    Gruber, Matthias; Jahns, Jürgen; El Joudi, El Mehdi; Sinzinger, Stefan

    2001-06-01

    We propose a novel approach to realizing massively parallel optical interconnects based on commercially available multifiber ribbons with MT-type connectors and custom-designed planar-integrated free-space components. It combines the advantages of fiber optics, that is, a long range and convenient and flexible installation, with those of (planar-integrated) free-space optics, that is, a wide range of implementable functions and a high potential for integration and parallelization. For the interface between fibers and free-space optical systems a low-cost practical solution is presented. It consists of using a metal connector plate that was manufactured on a computer-controlled milling machine. Channel densities are of the order of 100 /mm2 between optoelectronic VLSI chips and the free-space optical systems and 1 /mm2 between the free-space optical systems and MT-type fiber connectors. Experiments in combination with specially designed planar-integrated test systems prove that multiple one-to-one and one-to-many interconnects can be established with not more than 10% uniformity error.

  7. GPAW - massively parallel electronic structure calculations with Python-based software.

    SciTech Connect

    Enkovaara, J.; Romero, N.; Shende, S.; Mortensen, J.

    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 this 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.

  8. A Lightweight Remote Parallel Visualization Platform for Interactive Massive Time-varying Climate Data Analysis

    NASA Astrophysics Data System (ADS)

    Li, J.; Zhang, T.; Huang, Q.; Liu, Q.

    2014-12-01

    Today's climate datasets are featured with large volume, high degree of spatiotemporal complexity and evolving fast overtime. As visualizing large volume distributed climate datasets is computationally intensive, traditional desktop based visualization applications fail to handle the computational intensity. Recently, scientists have developed remote visualization techniques to address the computational issue. Remote visualization techniques usually leverage server-side parallel computing capabilities to perform visualization tasks and deliver visualization results to clients through network. In this research, we aim to build a remote parallel visualization platform for visualizing and analyzing massive climate data. Our visualization platform was built based on Paraview, which is one of the most popular open source remote visualization and analysis applications. To further enhance the scalability and stability of the platform, we have employed cloud computing techniques to support the deployment of the platform. In this platform, all climate datasets are regular grid data which are stored in NetCDF format. Three types of data access methods are supported in the platform: accessing remote datasets provided by OpenDAP servers, accessing datasets hosted on the web visualization server and accessing local datasets. Despite different data access methods, all visualization tasks are completed at the server side to reduce the workload of clients. As a proof of concept, we have implemented a set of scientific visualization methods to show the feasibility of the platform. Preliminary results indicate that the framework can address the computation limitation of desktop based visualization applications.

  9. 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

  10. Parametric Study of CO2 Sequestration in Geologic Media Using the Massively Parallel Computer Code PFLOTRAN

    NASA Astrophysics Data System (ADS)

    Lu, C.; Lichtner, P. C.; Tsimpanogiannis, I. N.

    2005-12-01

    Uncontrolled release of CO2 to the atmosphere has been identified as a major contributing source to the global warming problem. Significant research efforts from the international scientific community are targeted towards stabilization/reduction of CO2 concentrations in the atmosphere while attempting to satisfy our continuously increasing needs for energy. CO2 sequestration (capture, separation, and long term storage) in various media (e.g. geologic such as depleted oil reservoirs, saline aquifers, etc.; oceanic at different depths) has been considered as a possible solution to reduce green house gas emissions. In this study we utilize the PFLOTRAN simulator to investigate geologic sequestration of CO2. PFLOTRAN is a massively parallel 3-D reservoir simulator for modeling supercritical CO2 sequestration in geologic formations based on continuum scale mass and energy conservations. The mass and energy equations are sequentially coupled to reactive transport equations describing multi-component chemical reactions within the formation including aqueous speciation, and precipitation and dissolution of minerals to describe aqueous and mineral CO2 sequestration. The effect of the injected CO2 on pH, CO2 concentration within the aqueous phase, mineral stability, and other factors can be evaluated with this model. Parallelization is carried out using the PETSc parallel library package based on MPI providing a high parallel efficiency and allowing simulations with several tens of millions of degrees of freedom to be carried out-ideal for large-scale field applications involving multi-component chemistry. In this work, our main focus is a parametrical examination on the effects of reservoir and fluid properties on the sequestration process, such as permeability and capillary pressure functions (e.g. linear, van Genuchten, etc.), diffusion coefficients in a multiphase system, the sensitivity of component solubility on pressure, temperature and mole fractions etc. Several

  11. Applicability of the particle filter for high-dimensional problems using a massively parallel computer

    NASA Astrophysics Data System (ADS)

    Nakano, S.; Higuchi, T.

    2012-04-01

    The particle filter (PF) is one of ensemble-based algorithms for data assimilation. The PF obtains an approximation of a posterior PDF of a state by resampling with replacement from a prior ensemble. The procedure of the PF does not assume linearity or Gaussianity. Thus, it can be applied to general nonlinear problems. However, in order to obtain appropriate results for high-dimensional problems, the PF requires an enormous number of ensemble members. Since the PF must calculate the time integral for each particle at each time step, the large ensemble size results in prohibitive computational cost. There exists various methods for reducing the number of particle. In contrast, we employ a straightforward approach to overcome this problem; that is, we use a massively parallel computer to achieve sufficiently large ensemble size. Since the time integral in the PF can be readily be parallelized, we can notably improve the computational efficiency using a parallel computer. However, if we naively implement the PF on a distributed computing system, we encounter another difficulty; that is, many data transfers occur randomly between different nodes of the distributed computing system. Such data transfers can be reduced by dividing the ensemble into small subsets (groups). If we limit the resampling within each of the subsets, the data transfers can be done efficiently in parallel. If the ensemble are divided into small subsets, the risk of local sample impoverishment within each of the subsets is enhanced. However, if we change the grouping at each time step, the information held by a node can be propagated to all of the nodes after a finite number of time steps and the local sample impoverishment can be avoided. In the present study, we compare between the above method based on the local resampling of each group and the naive implementation of the PF based on the global resampling of the whole ensemble. The global resampling enables us to achive a slightly better

  12. Hierarchical Image Segmentation of Remotely Sensed Data using Massively Parallel GNU-LINUX Software

    NASA Technical Reports Server (NTRS)

    Tilton, James C.

    2003-01-01

    A hierarchical set of image segmentations is a set of several image segmentations of the same image at different levels of detail in which the segmentations at coarser levels of detail can be produced from simple merges of regions at finer levels of detail. In [1], Tilton, et a1 describes an approach for producing hierarchical segmentations (called HSEG) and gave a progress report on exploiting these hierarchical segmentations for image information mining. The HSEG algorithm is a hybrid of region growing and constrained spectral clustering that produces a hierarchical set of image segmentations based on detected convergence points. In the main, HSEG employs the hierarchical stepwise optimization (HSWO) approach to region growing, which was described as early as 1989 by Beaulieu and Goldberg. The HSWO approach seeks to produce segmentations that are more optimized than those produced by more classic approaches to region growing (e.g. Horowitz and T. Pavlidis, [3]). In addition, HSEG optionally interjects between HSWO region growing iterations, merges between spatially non-adjacent regions (i.e., spectrally based merging or clustering) constrained by a threshold derived from the previous HSWO region growing iteration. While the addition of constrained spectral clustering improves the utility of the segmentation results, especially for larger images, it also significantly increases HSEG s computational requirements. To counteract this, a computationally efficient recursive, divide-and-conquer, implementation of HSEG (RHSEG) was devised, which includes special code to avoid processing artifacts caused by RHSEG s recursive subdivision of the image data. The recursive nature of RHSEG makes for a straightforward parallel implementation. This paper describes the HSEG algorithm, its recursive formulation (referred to as RHSEG), and the implementation of RHSEG using massively parallel GNU-LINUX software. Results with Landsat TM data are included comparing RHSEG with classic

  13. Genome Analysis of the Domestic Dog (Korean Jindo) by Massively Parallel Sequencing

    PubMed Central

    Kim, Ryong Nam; Kim, Dae-Soo; Choi, Sang-Haeng; Yoon, Byoung-Ha; Kang, Aram; Nam, Seong-Hyeuk; Kim, Dong-Wook; Kim, Jong-Joo; Ha, Ji-Hong; Toyoda, Atsushi; Fujiyama, Asao; Kim, Aeri; Kim, Min-Young; Park, Kun-Hyang; Lee, Kang Seon; Park, Hong-Seog

    2012-01-01

    Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics. PMID:22474061

  14. Medical ultrasound digital beamforming on a massively parallel processing array platform

    NASA Astrophysics Data System (ADS)

    Chen, Paul; Butts, Mike; Budlong, Brad

    2008-03-01

    Digital beamforming has been widely used in modern medical ultrasound instruments. Flexibility is the key advantage of a digital beamformer over the traditional analog approach. Unlike analog delay lines, digital delay can be programmed to implement new ways of beam shaping and beam steering without hardware modification. Digital beamformers can also be focused dynamically by tracking the depth and focusing the receive beam as the depth increases. By constantly updating an element weight table, a digital beamformer can dynamically increase aperture size with depth to maintain constant lateral resolution and reduce sidelobe noise. Because ultrasound digital beamformers have high I/O bandwidth and processing requirements, traditionally they have been implemented using ASICs or FPGAs that are costly both in time and in money. This paper introduces a sample implementation of a digital beamformer that is programmed in software on a Massively Parallel Processor Array (MPPA). The system consists of a host PC and a PCI Express-based beamformer accelerator with an Ambric Am2045 MPPA chip and 512 Mbytes of external memory. The Am2045 has 336 asynchronous RISCDSP processors that communicate through a configurable structure of channels, using a self-synchronizing communication protocol.

  15. Massive Parallel Sequencing for Diagnostic Genetic Testing of BRCA Genes--a Single Center Experience.

    PubMed

    Ermolenko, Natalya A; Boyarskikh, Uljana A; Kechin, Andrey A; Mazitova, Alexandra M; Khrapov, Evgeny A; Petrova, Valentina D; Lazarev, Alexandr F; Kushlinskii, Nikolay E; Filipenko, Maxim L

    2015-01-01

    The aim of this study was to implement massive parallel sequencing (MPS) technology in clinical genetics testing. We developed and tested an amplicon-based method for resequencing the BRCA1 and BRCA2 genes on an Illumina MiSeq to identify disease-causing mutations in patients with hereditary breast or ovarian cancer (HBOC). The coding regions of BRCA1 and BRCA2 were resequenced in 96 HBOC patient DNA samples obtained from different sample types: peripheral blood leukocytes, whole blood drops dried on paper, and buccal wash epithelia. A total of 16 random DNA samples were characterized using standard Sanger sequencing and applied to optimize the variant calling process and evaluate the accuracy of the MPS-method. The best bioinformatics workflow included the filtration of variants using GATK with the following cut-offs: variant frequency >14%, coverage (>25x) and presence in both the forward and reverse reads. The MPS method had 100% sensitivity and 94.4% specificity. Similar accuracy levels were achieved for DNA obtained from the different sample types. The workflow presented herein requires low amounts of DNA samples (170 ng) and is cost-effective due to the elimination of DNA and PCR product normalization steps. PMID:26625824

  16. Ensuring the safety of vaccine cell substrates by massively parallel sequencing of the transcriptome.

    PubMed

    Onions, D; Côté, C; Love, B; Toms, B; Koduri, S; Armstrong, A; Chang, A; Kolman, J

    2011-09-22

    Massively parallel, deep, sequencing of the transcriptome coupled with algorithmic analysis to identify adventitious agents (MP-Seq™) is an important adjunct in ensuring the safety of cells used in vaccine production. Such cells may harbour novel viruses whose sequences are unknown or latent viruses that are only expressed following stress to the cells. MP-Seq is an unbiased and comprehensive method to identify such viruses and other adventitious agents without prior knowledge of the nature of those agents. Here we demonstrate its utility as part of an integrated approach to identify and characterise potential contaminants within commonly used virus and vaccine production cell lines. Through this analysis, in combination with more traditional approaches, we have excluded the presence of porcine circoviruses in the ATCC Vero cell bank (CCL-81), however, we found that a full length betaretrovirus related to SRV can be expressed in these cells, a factor that may be of importance in the production of certain vaccines. Similarly, insect cells are proving to be valuable for the production of virus like particles and sub-unit vaccines, but they can harbour a range of latent viruses. We show that following MP-Seq of the Trichoplusia ni (High Five cell line) transcriptome we were able to detect a contaminating, latent nodavirus and identify an expressed errantivirus genome. Collectively, these studies have reinforced the role of MP-Seq as an integral tool for the identification of contaminating agents in vaccine cell substrates. PMID:21651935

  17. Massively parallel energy space exploration for uncluttered visualization of vascular structures.

    PubMed

    Jeon, Yongkweon; Won, Joong-Ho; Yoon, Sungroh

    2013-01-01

    Images captured using computed tomography and magnetic resonance angiography are used in the examination of the abdominal aorta and its branches. The examination of all clinically relevant branches simultaneously in a single 2-D image without any misleading overlaps facilitates the diagnosis of vascular abnormalities. This problem is called uncluttered single-image visualization (USIV). We can solve the USIV problem by assigning energy-based scores to visualization candidates and then finding the candidate that optimizes the score; this approach is similar to the manner in which the protein side-chain placement problem has been solved. To obtain near-optimum images, we need to explore the energy space extensively, which is often time consuming. This paper describes a method for exploring the energy space in a massively parallel fashion using graphics processing units. According to our experiments, in which we used 30 images obtained from five patients, the proposed method can reduce the total visualization time substantially. We believe that the proposed method can make a significant contribution to the effective visualization of abdominal vascular structures and precise diagnosis of related abnormalities.

  18. Radiation hydrodynamics using characteristics on adaptive decomposed domains for massively parallel star formation simulations

    NASA Astrophysics Data System (ADS)

    Buntemeyer, Lars; Banerjee, Robi; Peters, Thomas; Klassen, Mikhail; Pudritz, Ralph E.

    2016-02-01

    We present an algorithm for solving the radiative transfer problem on massively parallel computers using adaptive mesh refinement and domain decomposition. The solver is based on the method of characteristics which requires an adaptive raytracer that integrates the equation of radiative transfer. The radiation field is split into local and global components which are handled separately to overcome the non-locality problem. The solver is implemented in the framework of the magneto-hydrodynamics code FLASH and is coupled by an operator splitting step. The goal is the study of radiation in the context of star formation simulations with a focus on early disc formation and evolution. This requires a proper treatment of radiation physics that covers both the optically thin as well as the optically thick regimes and the transition region in particular. We successfully show the accuracy and feasibility of our method in a series of standard radiative transfer problems and two 3D collapse simulations resembling the early stages of protostar and disc formation.

  19. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

    PubMed Central

    Kristiansson, Erik; Asker, Noomi; Förlin, Lars; Larsson, DG Joakim

    2009-01-01

    Background The teleost Zoarces viviparus (eelpout) lives along the coasts of Northern Europe and has long been an established model organism for marine ecology and environmental monitoring. The scarce information about this species genome has however restrained the use of efficient molecular-level assays, such as gene expression microarrays. Results In the present study we present the first comprehensive characterization of the Zoarces viviparus liver transcriptome. From 400,000 reads generated by massively parallel pyrosequencing, more than 50,000 pieces of putative transcripts were assembled, annotated and functionally classified. The data was estimated to cover roughly 40% of the total transcriptome and homologues for about half of the genes of Gasterosteus aculeatus (stickleback) were identified. The sequence data was consequently used to design an oligonucleotide microarray for large-scale gene expression analysis. Conclusion Our results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates enough genomic information for adequate de novo assembly of a large number of genes in a higher vertebrate. The generated sequence data, including the validated microarray probes, are publicly available to promote genome-wide research in Zoarces viviparus. PMID:19646242

  20. Adaptive Flow Simulation of Turbulence in Subject-Specific Abdominal Aortic Aneurysm on Massively Parallel Computers

    NASA Astrophysics Data System (ADS)

    Sahni, Onkar; Jansen, Kenneth; Shephard, Mark; Taylor, Charles

    2007-11-01

    Flow within the healthy human vascular system is typically laminar but diseased conditions can alter the geometry sufficiently to produce transitional/turbulent flows in regions focal (and immediately downstream) of the diseased section. The mean unsteadiness (pulsatile or respiratory cycle) further complicates the situation making traditional turbulence simulation techniques (e.g., Reynolds-averaged Navier-Stokes simulations (RANSS)) suspect. At the other extreme, direct numerical simulation (DNS) while fully appropriate can lead to large computational expense, particularly when the simulations must be done quickly since they are intended to affect the outcome of a medical treatment (e.g., virtual surgical planning). To produce simulations in a clinically relevant time frame requires; 1) adaptive meshing technique that closely matches the desired local mesh resolution in all three directions to the highly anisotropic physical length scales in the flow, 2) efficient solution algorithms, and 3) excellent scaling on massively parallel computers. In this presentation we will demonstrate results for a subject-specific simulation of an abdominal aortic aneurysm using stabilized finite element method on anisotropically adapted meshes consisting of O(10^8) elements over O(10^4) processors.

  1. Novel myosin mutations for hereditary hearing loss revealed by targeted genomic capture and massively parallel sequencing.

    PubMed

    Brownstein, Zippora; Abu-Rayyan, Amal; Karfunkel-Doron, Daphne; Sirigu, Serena; Davidov, Bella; Shohat, Mordechai; Frydman, Moshe; Houdusse, Anne; Kanaan, Moien; Avraham, Karen B

    2014-06-01

    Hereditary hearing loss is genetically heterogeneous, with a large number of genes and mutations contributing to this sensory, often monogenic, disease. This number, as well as large size, precludes comprehensive genetic diagnosis of all known deafness genes. A combination of targeted genomic capture and massively parallel sequencing (MPS), also referred to as next-generation sequencing, was applied to determine the deafness-causing genes in hearing-impaired individuals from Israeli Jewish and Palestinian Arab families. Among the mutations detected, we identified nine novel mutations in the genes encoding myosin VI, myosin VIIA and myosin XVA, doubling the number of myosin mutations in the Middle East. Myosin VI mutations were identified in this population for the first time. Modeling of the mutations provided predicted mechanisms for the damage they inflict in the molecular motors, leading to impaired function and thus deafness. The myosin mutations span all regions of these molecular motors, leading to a wide range of hearing phenotypes, reinforcing the key role of this family of proteins in auditory function. This study demonstrates that multiple mutations responsible for hearing loss can be identified in a relatively straightforward manner by targeted-gene MPS technology and concludes that this is the optimal genetic diagnostic approach for identification of mutations responsible for hearing loss.

  2. Asymmetric pores in a silicon membrane acting as massively parallel brownian ratchets.

    PubMed

    Matthias, Sven; Müller, Frank

    2003-07-01

    The brownian motion of mesoscopic particles is ubiquitous and usually random. But in systems with periodic asymmetric barriers to movement, directed or 'rectified' motion can arise and may even modulate some biological processes. In man-made devices, brownian ratchets and variants based on optical or quantum effects have been exploited to induce directed motion, and the dependence of the amplitude of motion on particle size has led to the size-dependent separation of biomolecules. Here we demonstrate that the one-dimensional pores of a macroporous silicon membrane, etched to exhibit a periodic asymmetric variation in pore diameter, can act as massively parallel and multiply stacked brownian ratchets that are potentially suitable for large-scale particle separations. We show that applying a periodic pressure profile with a mean value of zero to a basin separated by such a membrane induces a periodic flow of water and suspended particles through the pores, resulting in a net motion of the particles from one side of the membrane to the other without moving the liquid itself. We find that the experimentally observed pressure dependence of the particle transport, including an inversion of the transport direction, agrees with calculations of the transport properties in the type of ratchet devices used here.

  3. A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations.

    PubMed

    Wei, Xiaomu; Das, Jishnu; Fragoza, Robert; Liang, Jin; Bastos de Oliveira, Francisco M; Lee, Hao Ran; Wang, Xiujuan; Mort, Matthew; Stenson, Peter D; Cooper, David N; Lipkin, Steven M; Smolka, Marcus B; Yu, Haiyuan

    2014-12-01

    Understanding the functional relevance of DNA variants is essential for all exome and genome sequencing projects. However, current mutagenesis cloning protocols require Sanger sequencing, and thus are prohibitively costly and labor-intensive. We describe a massively-parallel site-directed mutagenesis approach, "Clone-seq", leveraging next-generation sequencing to rapidly and cost-effectively generate a large number of mutant alleles. Using Clone-seq, we further develop a comparative interactome-scanning pipeline integrating high-throughput GFP, yeast two-hybrid (Y2H), and mass spectrometry assays to systematically evaluate the functional impact of mutations on protein stability and interactions. We use this pipeline to show that disease mutations on protein-protein interaction interfaces are significantly more likely than those away from interfaces to disrupt corresponding interactions. We also find that mutation pairs with similar molecular phenotypes in terms of both protein stability and interactions are significantly more likely to cause the same disease than those with different molecular phenotypes, validating the in vivo biological relevance of our high-throughput GFP and Y2H assays, and indicating that both assays can be used to determine candidate disease mutations in the future. The general scheme of our experimental pipeline can be readily expanded to other types of interactome-mapping methods to comprehensively evaluate the functional relevance of all DNA variants, including those in non-coding regions.

  4. Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing.

    PubMed

    Kim, Ryong Nam; Kim, Dae-Soo; Choi, Sang-Haeng; Yoon, Byoung-Ha; Kang, Aram; Nam, Seong-Hyeuk; Kim, Dong-Wook; Kim, Jong-Joo; Ha, Ji-Hong; Toyoda, Atsushi; Fujiyama, Asao; Kim, Aeri; Kim, Min-Young; Park, Kun-Hyang; Lee, Kang Seon; Park, Hong-Seog

    2012-06-01

    Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.

  5. The use of targeted genomic capture and massively parallel sequencing in diagnosis of Chinese Leukoencephalopathies

    PubMed Central

    Wang, Xiaole; He, Fang; Yin, Fei; Chen, Chao; Wu, Liwen; Yang, Lifen; Peng, Jing

    2016-01-01

    Leukoencephalopathies are diseases with high clinical heterogeneity. In clinical work, it’s difficult for doctors to make a definite etiological diagnosis. Here, we designed a custom probe library which contains the known pathogenic genes reported to be associated with Leukoencephalopathies, and performed targeted gene capture and massively parallel sequencing (MPS) among 49 Chinese patients who has white matter damage as the main imaging changes, and made the validation by Sanger sequencing for the probands’ parents. As result, a total of 40.8% (20/49) of the patients identified pathogenic mutations, including four associated with metachromatic leukodystrophy, three associated with vanishing white matter leukoencephalopathy, three associated with mitochondrial complex I deficiency, one associated with Globoid cell leukodystrophy (or Krabbe diseases), three associated with megalencephalic leukoencephalopathy with subcortical cysts, two associated with Pelizaeus-Merzbacher disease, two associated with X-linked adrenoleukodystrophy, one associated with Zellweger syndrome and one associated with Alexander disease. Targeted capture and MPS enables to identify mutations of all classes causing leukoencephalopathy. Our study combines targeted capture and MPS technology with clinical and genetic diagnosis and highlights its usefulness for rapid and comprehensive genetic testing in the clinical setting. This method will also expand our knowledge of the genetic and clinical spectra of leukoencephalopathy. PMID:27779215

  6. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.

    PubMed

    Smith, Robin P; Taher, Leila; Patwardhan, Rupali P; Kim, Mee J; Inoue, Fumitaka; Shendure, Jay; Ovcharenko, Ivan; Ahituv, Nadav

    2013-09-01

    Despite continual progress in the cataloging of vertebrate regulatory elements, little is known about their organization and regulatory architecture. Here we describe a massively parallel experiment to systematically test the impact of copy number, spacing, combination and order of transcription factor binding sites on gene expression. A complex library of ∼5,000 synthetic regulatory elements containing patterns from 12 liver-specific transcription factor binding sites was assayed in mice and in HepG2 cells. We find that certain transcription factors act as direct drivers of gene expression in homotypic clusters of binding sites, independent of spacing between sites, whereas others function only synergistically. Heterotypic enhancers are stronger than their homotypic analogs and favor specific transcription factor binding site combinations, mimicking putative native enhancers. Exhaustive testing of binding site permutations suggests that there is flexibility in binding site order. Our findings provide quantitative support for a flexible model of regulatory element activity and suggest a framework for the design of synthetic tissue-specific enhancers. PMID:23892608

  7. Massively parallel network architectures for automatic recognition of visual speech signals. Final technical report

    SciTech Connect

    Sejnowski, T.J.; Goldstein, M.

    1990-01-01

    This research sought to produce a massively-parallel network architecture that could interpret speech signals from video recordings of human talkers. This report summarizes the project's results: (1) A corpus of video recordings from two human speakers was analyzed with image processing techniques and used as the data for this study; (2) We demonstrated that a feed forward network could be trained to categorize vowels from these talkers. The performance was comparable to that of the nearest neighbors techniques and to trained humans on the same data; (3) We developed a novel approach to sensory fusion by training a network to transform from facial images to short-time spectral amplitude envelopes. This information can be used to increase the signal-to-noise ratio and hence the performance of acoustic speech recognition systems in noisy environments; (4) We explored the use of recurrent networks to perform the same mapping for continuous speech. Results of this project demonstrate the feasibility of adding a visual speech recognition component to enhance existing speech recognition systems. Such a combined system could be used in noisy environments, such as cockpits, where improved communication is needed. This demonstration of presymbolic fusion of visual and acoustic speech signals is consistent with our current understanding of human speech perception.

  8. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing

    PubMed Central

    Warshauer, David H.; Churchill, Jennifer D.; Novroski, Nicole; King, Jonathan L.; Budowle, Bruce

    2015-01-01

    Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles. PMID:26391384

  9. New massive parallel sequencing approach improves the genetic characterization of congenital myopathies.

    PubMed

    Oliveira, Jorge; Gonçalves, Ana; Taipa, Ricardo; Melo-Pires, Manuel; Oliveira, Márcia E; Costa, José Luís; Machado, José Carlos; Medeiros, Elmira; Coelho, Teresa; Santos, Manuela; Santos, Rosário; Sousa, Mário

    2016-06-01

    Congenital myopathies (CMs) are a heterogeneous group of muscle diseases characterized by hypotonia, delayed motor skills and muscle weakness with onset during the first years of life. The diagnostic workup of CM is highly dependent on the interpretation of the muscle histology, where typical pathognomonic findings are suggestive of a CM but are not necessarily gene specific. Over 20 loci have been linked to these myopathies, including three exceptionally large genes (TTN, NEB and RYR1), which are a challenge for molecular diagnosis. We developed a new approach using massive parallel sequencing (MPS) technology to simultaneously analyze 20 genes linked to CMs. Assay design was based on the Ion AmpliSeq strategy and sequencing runs were performed on an Ion PGM system. A total of 12 patients were analyzed in this study. Among the 2534 variants detected, 14 pathogenic mutations were successfully identified in the DNM2, NEB, RYR1, SEPN1 and TTN genes. Most of these had not been documented and/or fully characterized, hereby contributing to expand the CM mutational spectrum. The utility of this approach was demonstrated by the identification of mutations in 70% of the patients included in this study, which is relevant for CMs especially considering its wide phenotypic and genetic heterogeneity. PMID:26841830

  10. GRay: A Massively Parallel GPU-based Code for Ray Tracing in Relativistic Spacetimes

    NASA Astrophysics Data System (ADS)

    Chan, Chi-kwan; Psaltis, Dimitrios; Özel, Feryal

    2013-11-01

    We introduce GRay, a massively parallel integrator designed to trace the trajectories of billions of photons in a curved spacetime. This graphics-processing-unit (GPU)-based integrator employs the stream processing paradigm, is implemented in CUDA C/C++, and runs on nVidia graphics cards. The peak performance of GRay using single-precision floating-point arithmetic on a single GPU exceeds 300 GFLOP (or 1 ns per photon per time step). For a realistic problem, where the peak performance cannot be reached, GRay is two orders of magnitude faster than existing central-processing-unit-based ray-tracing codes. This performance enhancement allows more effective searches of large parameter spaces when comparing theoretical predictions of images, spectra, and light curves from the vicinities of compact objects to observations. GRay can also perform on-the-fly ray tracing within general relativistic magnetohydrodynamic algorithms that simulate accretion flows around compact objects. Making use of this algorithm, we calculate the properties of the shadows of Kerr black holes and the photon rings that surround them. We also provide accurate fitting formulae of their dependencies on black hole spin and observer inclination, which can be used to interpret upcoming observations of the black holes at the center of the Milky Way, as well as M87, with the Event Horizon Telescope.

  11. Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics.

    PubMed

    Cheng, Allen A; Ding, Huiming; Lu, Timothy K

    2014-08-26

    New therapeutic strategies are needed to treat infections caused by drug-resistant bacteria, which constitute a major growing threat to human health. Here, we use a high-throughput technology to identify combinatorial genetic perturbations that can enhance the killing of drug-resistant bacteria with antibiotic treatment. This strategy, Combinatorial Genetics En Masse (CombiGEM), enables the rapid generation of high-order barcoded combinations of genetic elements for high-throughput multiplexed characterization based on next-generation sequencing. We created ∼ 34,000 pairwise combinations of Escherichia coli transcription factor (TF) overexpression constructs. Using Illumina sequencing, we identified diverse perturbations in antibiotic-resistance phenotypes against carbapenem-resistant Enterobacteriaceae. Specifically, we found multiple TF combinations that potentiated antibiotic killing by up to 10(6)-fold and delivered these combinations via phagemids to increase the killing of highly drug-resistant E. coli harboring New Delhi metallo-beta-lactamase-1. Moreover, we constructed libraries of three-wise combinations of transcription factors with >4 million unique members and demonstrated that these could be tracked via next-generation sequencing. We envision that CombiGEM could be extended to other model organisms, disease models, and phenotypes, where it could accelerate massively parallel combinatorial genetics studies for a broad range of biomedical and biotechnology applications, including the treatment of antibiotic-resistant infections.

  12. GRay: A MASSIVELY PARALLEL GPU-BASED CODE FOR RAY TRACING IN RELATIVISTIC SPACETIMES

    SciTech Connect

    Chan, Chi-kwan; Psaltis, Dimitrios; Özel, Feryal

    2013-11-01

    We introduce GRay, a massively parallel integrator designed to trace the trajectories of billions of photons in a curved spacetime. This graphics-processing-unit (GPU)-based integrator employs the stream processing paradigm, is implemented in CUDA C/C++, and runs on nVidia graphics cards. The peak performance of GRay using single-precision floating-point arithmetic on a single GPU exceeds 300 GFLOP (or 1 ns per photon per time step). For a realistic problem, where the peak performance cannot be reached, GRay is two orders of magnitude faster than existing central-processing-unit-based ray-tracing codes. This performance enhancement allows more effective searches of large parameter spaces when comparing theoretical predictions of images, spectra, and light curves from the vicinities of compact objects to observations. GRay can also perform on-the-fly ray tracing within general relativistic magnetohydrodynamic algorithms that simulate accretion flows around compact objects. Making use of this algorithm, we calculate the properties of the shadows of Kerr black holes and the photon rings that surround them. We also provide accurate fitting formulae of their dependencies on black hole spin and observer inclination, which can be used to interpret upcoming observations of the black holes at the center of the Milky Way, as well as M87, with the Event Horizon Telescope.

  13. Frequency of Usher syndrome type 1 in deaf children by massively parallel DNA sequencing

    PubMed Central

    Yoshimura, Hidekane; Miyagawa, Maiko; Kumakawa, Kozo; Nishio, Shin-ya; Usami, Shin-ichi

    2016-01-01

    Usher syndrome type 1 (USH1) is the most severe of the three USH subtypes due to its profound hearing loss, absent vestibular response and retinitis pigmentosa appearing at a prepubescent age. Six causative genes have been identified for USH1, making early diagnosis and therapy possible through DNA testing. Targeted exon sequencing of selected genes using massively parallel DNA sequencing (MPS) technology enables clinicians to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using MPS along with direct sequence analysis, we screened 227 unrelated non-syndromic deaf children and detected recessive mutations in USH1 causative genes in five patients (2.2%): three patients harbored MYO7A mutations and one each carried CDH23 or PCDH15 mutations. As indicated by an earlier genotype–phenotype correlation study of the CDH23 and PCDH15 genes, we considered the latter two patients to have USH1. Based on clinical findings, it was also highly likely that one patient with MYO7A mutations possessed USH1 due to a late onset age of walking. This first report describing the frequency (1.3–2.2%) of USH1 among non-syndromic deaf children highlights the importance of comprehensive genetic testing for early disease diagnosis. PMID:26791358

  14. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing.

    PubMed

    Le Crom, Stéphane; Schackwitz, Wendy; Pennacchio, Len; Magnuson, Jon K; Culley, David E; Collett, James R; Martin, Joel; Druzhinina, Irina S; Mathis, Hugues; Monot, Frédéric; Seiboth, Bernhard; Cherry, Barbara; Rey, Michael; Berka, Randy; Kubicek, Christian P; Baker, Scott E; Margeot, Antoine

    2009-09-22

    Trichoderma reesei (teleomorph Hypocrea jecorina) is the main industrial source of cellulases and hemicellulases harnessed for the hydrolysis of biomass to simple sugars, which can then be converted to biofuels such as ethanol and other chemicals. The highly productive strains in use today were generated by classical mutagenesis. To learn how cellulase production was improved by these techniques, we performed massively parallel sequencing to identify mutations in the genomes of two hyperproducing strains (NG14, and its direct improved descendant, RUT C30). We detected a surprisingly high number of mutagenic events: 223 single nucleotides variants, 15 small deletions or insertions, and 18 larger deletions, leading to the loss of more than 100 kb of genomic DNA. From these events, we report previously undocumented non-synonymous mutations in 43 genes that are mainly involved in nuclear transport, mRNA stability, transcription, secretion/vacuolar targeting, and metabolism. This homogeneity of functional categories suggests that multiple changes are necessary to improve cellulase production and not simply a few clear-cut mutagenic events. Phenotype microarrays show that some of these mutations result in strong changes in the carbon assimilation pattern of the two mutants with respect to the wild-type strain QM6a. Our analysis provides genome-wide insights into the changes induced by classical mutagenesis in a filamentous fungus and suggests areas for the generation of enhanced T. reesei strains for industrial applications such as biofuel production.

  15. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing

    SciTech Connect

    Le Crom, Stphane; Schackwitz, Wendy; Pennacchiod, Len; Magnuson, Jon K.; Culley, David E.; Collett, James R.; Martin, Joel X.; Druzhinina, Irina S.; Mathis, Hugues; Monot, Frdric; Seiboth, Bernhard; Cherry, Barbara; Rey, Michael; Berka, Randy; Kubicek, Christian P.; Baker, Scott E.; Margeot, Antoine

    2009-09-22

    Trichoderma reesei (teleomorph Hypocrea jecorina) is the main industrial source of cellulases and hemicellulases harnessed for the hydrolysis of biomass to simple sugars, which can then be converted to biofuels, such as ethanol, and other chemicals. The highly productive strains in use today were generated by classical mutagenesis. To learn how cellulase production was improved by these techniques, we performed massively parallel sequencing to identify mutations in the genomes of two hyperproducing strains (NG14, and its direct improved descendant, RUT C30). We detected a surprisingly high number of mutagenic events: 223 single nucleotides variants, 15 small deletions or insertions and 18 larger deletions leading to the loss of more than 100 kb of genomic DNA. From these events we report previously undocumented non-synonymous mutations in 43 genes that are mainly involved in nuclear transport, mRNA stability, transcription, secretion/vacuolar targeting, and metabolism. This homogeneity of functional categories suggests that multiple changes are necessary to improve cellulase production and not simply a few clear-cut mutagenic events. Phenotype microarrays show that some of these mutations result in strong changes in the carbon assimilation pattern of the two mutants with respect to the wild type strain QM6a. Our analysis provides the first genome-wide insights into the changes induced by classical mutagenesis in a filamentous fungus, and suggests new areas for the generation of enhanced T. reesei strains for industrial applications such as biofuel production.

  16. Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing.

    PubMed

    Just, Rebecca S; Irwin, Jodi A; Parson, Walther

    2015-09-01

    Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Well vetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10-20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method. PMID:26009256

  17. Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples.

    PubMed

    Parson, Walther; Huber, Gabriela; Moreno, Lilliana; Madel, Maria-Bernadette; Brandhagen, Michael D; Nagl, Simone; Xavier, Catarina; Eduardoff, Mayra; Callaghan, Thomas C; Irwin, Jodi A

    2015-03-01

    Though shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, DNA testing has historically focused on the recovery of just about 600 base pairs of the mitochondrial DNA control region. Here, we describe our success in recovering complete mitochondrial genome (mtGenome) data (∼16,569bp) from single shed hairs. By employing massively parallel sequencing (MPS), we demonstrate that particular hair samples yield DNA sufficient in quantity and quality to produce 2-3kb mtGenome amplicons and that entire mtGenome data can be recovered from hair extracts even without PCR enrichment. Most importantly, we describe a small amplicon multiplex assay comprised of sixty-two primer sets that can be routinely applied to the compromised hair samples typically encountered in forensic casework. In all samples tested here, the MPS data recovered using any one of the three methods were consistent with the control Sanger sequence data developed from high quality known specimens. Given the recently demonstrated value of complete mtGenome data in terms of discrimination power among randomly sampled individuals, the possibility of recovering mtGenome data from the most compromised and limited evidentiary material is likely to vastly increase the utility of mtDNA testing for hair evidence. PMID:25438934

  18. ALEGRA -- A massively parallel h-adaptive code for solid dynamics

    SciTech Connect

    Summers, R.M.; Wong, M.K.; Boucheron, E.A.; Weatherby, J.R.

    1997-12-31

    ALEGRA is a multi-material, arbitrary-Lagrangian-Eulerian (ALE) code for solid dynamics designed to run on massively parallel (MP) computers. It combines the features of modern Eulerian shock codes, such as CTH, with modern Lagrangian structural analysis codes using an unstructured grid. ALEGRA is being developed for use on the teraflop supercomputers to conduct advanced three-dimensional (3D) simulations of shock phenomena important to a variety of systems. ALEGRA was designed with the Single Program Multiple Data (SPMD) paradigm, in which the mesh is decomposed into sub-meshes so that each processor gets a single sub-mesh with approximately the same number of elements. Using this approach the authors have been able to produce a single code that can scale from one processor to thousands of processors. A current major effort is to develop efficient, high precision simulation capabilities for ALEGRA, without the computational cost of using a global highly resolved mesh, through flexible, robust h-adaptivity of finite elements. H-adaptivity is the dynamic refinement of the mesh by subdividing elements, thus changing the characteristic element size and reducing numerical error. The authors are working on several major technical challenges that must be met to make effective use of HAMMER on MP computers.

  19. Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing

    PubMed Central

    Just, Rebecca S.; Irwin, Jodi A.; Parson, Walther

    2015-01-01

    Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Well vetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10–20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method. PMID:26009256

  20. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13

    PubMed Central

    Kretz, Colin A.; Dai, Manhong; Soylemez, Onuralp; Yee, Andrew; Desch, Karl C.; Siemieniak, David; Tomberg, Kärt; Kondrashov, Fyodor A.; Meng, Fan; Ginsburg, David

    2015-01-01

    Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1′ substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF. PMID:26170332

  1. Clinical and ethical considerations of massively parallel sequencing in transplantation science.

    PubMed

    Scherer, Andreas

    2013-12-24

    Massively parallel sequencing (MPS), alias next-generation sequencing, is making its way from research laboratories into applied sciences and clinics. MPS is a framework of experimental procedures which offer possibilities for genome research and genetics which could only be dreamed of until around 2005 when these technologies became available. Sequencing of a transcriptome, exome, even entire genomes is now possible within a time frame and precision that we could only hope for 10 years ago. Linking other experimental procedures with MPS enables researchers to study secondary DNA modifications across the entire genome, and protein binding sites, to name a few applications. How the advancements of sequencing technologies can contribute to transplantation science is subject of this discussion: immediate applications are in graft matching via human leukocyte antigen sequencing, as part of systems biology approaches which shed light on gene expression processes during immune response, as biomarkers of graft rejection, and to explore changes of microbiomes as a result of transplantation. Of considerable importance is the socio-ethical aspect of data ownership, privacy, informed consent, and result report to the study participant. While the technology is advancing rapidly, legislation is lagging behind due to the globalisation of data requisition, banking and sharing.

  2. Clinical and ethical considerations of massively parallel sequencing in transplantation science

    PubMed Central

    Scherer, Andreas

    2013-01-01

    Massively parallel sequencing (MPS), alias next-generation sequencing, is making its way from research laboratories into applied sciences and clinics. MPS is a framework of experimental procedures which offer possibilities for genome research and genetics which could only be dreamed of until around 2005 when these technologies became available. Sequencing of a transcriptome, exome, even entire genomes is now possible within a time frame and precision that we could only hope for 10 years ago. Linking other experimental procedures with MPS enables researchers to study secondary DNA modifications across the entire genome, and protein binding sites, to name a few applications. How the advancements of sequencing technologies can contribute to transplantation science is subject of this discussion: immediate applications are in graft matching via human leukocyte antigen sequencing, as part of systems biology approaches which shed light on gene expression processes during immune response, as biomarkers of graft rejection, and to explore changes of microbiomes as a result of transplantation. Of considerable importance is the socio-ethical aspect of data ownership, privacy, informed consent, and result report to the study participant. While the technology is advancing rapidly, legislation is lagging behind due to the globalisation of data requisition, banking and sharing. PMID:24392310

  3. A Massive Parallel Variational Multiscale FEM Scheme Applied to Nonhydrostatic Atmospheric Dynamics

    NASA Astrophysics Data System (ADS)

    Vazquez, Mariano; Marras, Simone; Moragues, Margarida; Jorba, Oriol; Houzeaux, Guillaume; Aubry, Romain

    2010-05-01

    The solution of the fully compressible Euler equations of stratified flows is approached from the point of view of Computational Fluid Dynamics techniques. Specifically, the main aim of this contribution is the introduction of a Variational Multiscale Finite Element (CVMS-FE) approach to solve dry atmospheric dynamics effectively on massive parallel architectures with more than 1000 processors. The conservation form of the equations of motion is discretized in all directions with a Galerkin scheme with stabilization given by the compressible counterpart of the variational multiscale technique of Hughes [1] and Houzeaux et al. [2]. The justification of this effort is twofold: the search of optimal parallelization characteristics and linear scalability trends on petascale machines is one. The development of a numerical algorithm whose local nature helps maintaining minimal the communication among the processors implies, in fact, a large leap towards efficient parallel computing. Second, the rising trend to global models and models of higher spatial resolution naturally suggests the use of adaptive grids to only resolve zones of larger gradients while keeping the computational mesh properly coarse elsewhere (thus keeping the computational cost low). With these two hypotheses in mind, the finite element scheme presented here is an open option to the development of the next generation Numerical Weather Prediction (NWP) codes. This methodology is as new in Computational Fluid Dynamics for compressible flows at low Mach number as it is in Numerical Weather Prediction (NWP). We however mean to show its ability to maintain stability in the solution of thermal, gravity-driven flows in a stratified environment in the specific context of dry atmospheric dynamics. Standard two dimensional benchmarks are implemented and compared against the reference literature. In the context of thermal and gravity-driven flows in a neutral atmosphere, we present: (1) the density current

  4. Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

    PubMed Central

    Hahn, Daniel A; Ragland, Gregory J; Shoemaker, D DeWayne; Denlinger, David L

    2009-01-01

    Background Flesh flies in the genus Sarcophaga are important models for investigating endocrinology, diapause, cold hardiness, reproduction, and immunity. Despite the prominence of Sarcophaga flesh flies as models for insect physiology and biochemistry, and in forensic studies, little genomic or transcriptomic data are available for members of this genus. We used massively parallel pyrosequencing on the Roche 454-FLX platform to produce a substantial EST dataset for the flesh fly Sarcophaga crassipalpis. To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription. Results We obtained 207,110 ESTs with an average read length of 241 bp. These reads assembled into 20,995 contigs and 31,056 singletons. Using BLAST searches of the NR and NT databases we were able to identify 11,757 unique gene elements (E<0.0001) representing approximately 9,000 independent transcripts. Comparison of the distribution of S. crassipalpis unigenes among GO Biological Process functional groups with that of the Drosophila melanogaster transcriptome suggests that our ESTs are broadly representative of the flesh fly transcriptome. Insertion and deletion errors in 454 sequencing present a serious hurdle to comparative transcriptome analysis. Aided by a new approach to correcting for these errors, we performed a comparative analysis of genetic divergence across GO categories among S. crassipalpis, D. melanogaster, and Anopheles gambiae. The results suggest that non-synonymous substitutions occur at similar rates across categories, although genes related to response to stimuli may evolve slightly faster. In addition, we identified over 500 potential microsatellite loci and more than 12,000 SNPs among our ESTs. Conclusion Our data provides the first large-scale EST-project for flesh flies, a much-needed resource for exploring this model species. In addition, we identified a large number of potential

  5. Implementation of a Message Passing Interface into a Cloud-Resolving Model for Massively Parallel Computing

    NASA Technical Reports Server (NTRS)

    Juang, Hann-Ming Henry; Tao, Wei-Kuo; Zeng, Xi-Ping; Shie, Chung-Lin; Simpson, Joanne; Lang, Steve

    2004-01-01

    The capability for massively parallel programming (MPP) using a message passing interface (MPI) has been implemented into a three-dimensional version of the Goddard Cumulus Ensemble (GCE) model. The design for the MPP with MPI uses the concept of maintaining similar code structure between the whole domain as well as the portions after decomposition. Hence the model follows the same integration for single and multiple tasks (CPUs). Also, it provides for minimal changes to the original code, so it is easily modified and/or managed by the model developers and users who have little knowledge of MPP. The entire model domain could be sliced into one- or two-dimensional decomposition with a halo regime, which is overlaid on partial domains. The halo regime requires that no data be fetched across tasks during the computational stage, but it must be updated before the next computational stage through data exchange via MPI. For reproducible purposes, transposing data among tasks is required for spectral transform (Fast Fourier Transform, FFT), which is used in the anelastic version of the model for solving the pressure equation. The performance of the MPI-implemented codes (i.e., the compressible and anelastic versions) was tested on three different computing platforms. The major results are: 1) both versions have speedups of about 99% up to 256 tasks but not for 512 tasks; 2) the anelastic version has better speedup and efficiency because it requires more computations than that of the compressible version; 3) equal or approximately-equal numbers of slices between the x- and y- directions provide the fastest integration due to fewer data exchanges; and 4) one-dimensional slices in the x-direction result in the slowest integration due to the need for more memory relocation for computation.

  6. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing

    PubMed Central

    Walsh, Tom; Lee, Ming K.; Casadei, Silvia; Thornton, Anne M.; Stray, Sunday M.; Pennil, Christopher; Nord, Alex S.; Mandell, Jessica B.; Swisher, Elizabeth M.; King, Mary-Claire

    2010-01-01

    Inherited loss-of-function mutations in the tumor suppressor genes BRCA1, BRCA2, and multiple other genes predispose to high risks of breast and/or ovarian cancer. Cancer-associated inherited mutations in these genes are collectively quite common, but individually rare or even private. Genetic testing for BRCA1 and BRCA2 mutations has become an integral part of clinical practice, but testing is generally limited to these two genes and to women with severe family histories of breast or ovarian cancer. To determine whether massively parallel, “next-generation” sequencing would enable accurate, thorough, and cost-effective identification of inherited mutations for breast and ovarian cancer, we developed a genomic assay to capture, sequence, and detect all mutations in 21 genes, including BRCA1 and BRCA2, with inherited mutations that predispose to breast or ovarian cancer. Constitutional genomic DNA from subjects with known inherited mutations, ranging in size from 1 to >100,000 bp, was hybridized to custom oligonucleotides and then sequenced using a genome analyzer. Analysis was carried out blind to the mutation in each sample. Average coverage was >1200 reads per base pair. After filtering sequences for quality and number of reads, all single-nucleotide substitutions, small insertion and deletion mutations, and large genomic duplications and deletions were detected. There were zero false-positive calls of nonsense mutations, frameshift mutations, or genomic rearrangements for any gene in any of the test samples. This approach enables widespread genetic testing and personalized risk assessment for breast and ovarian cancer. PMID:20616022

  7. Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing

    PubMed Central

    2012-01-01

    Background MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression and play a critical role in development, homeostasis, and disease. Despite their demonstrated roles in age-associated pathologies, little is known about the role of miRNAs in human aging and longevity. Results We employed massively parallel sequencing technology to identify miRNAs expressed in B-cells from Ashkenazi Jewish centenarians, i.e., those living to a hundred and a human model of exceptional longevity, and younger controls without a family history of longevity. With data from 26.7 million reads comprising 9.4 × 108 bp from 3 centenarian and 3 control individuals, we discovered a total of 276 known miRNAs and 8 unknown miRNAs ranging several orders of magnitude in expression levels, a typical characteristics of saturated miRNA-sequencing. A total of 22 miRNAs were found to be significantly upregulated, with only 2 miRNAs downregulated, in centenarians as compared to controls. Gene Ontology analysis of the predicted and validated targets of the 24 differentially expressed miRNAs indicated enrichment of functional pathways involved in cell metabolism, cell cycle, cell signaling, and cell differentiation. A cross sectional expression analysis of the differentially expressed miRNAs in B-cells from Ashkenazi Jewish individuals between the 50th and 100th years of age indicated that expression levels of miR-363* declined significantly with age. Centenarians, however, maintained the youthful expression level. This result suggests that miR-363* may be a candidate longevity-associated miRNA. Conclusion Our comprehensive miRNA data provide a resource for further studies to identify genetic pathways associated with aging and longevity in humans. PMID:22846614

  8. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses.

    PubMed

    Goto, Hiroki; Ryder, Oliver A; Fisher, Allison R; Schultz, Bryant; Kosakovsky Pond, Sergei L; Nekrutenko, Anton; Makova, Kateryna D

    2011-01-01

    The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered-two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117-0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow.

  9. Massively parallel computation of lattice associative memory classifiers on multicore processors

    NASA Astrophysics Data System (ADS)

    Ritter, Gerhard X.; Schmalz, Mark S.; Hayden, Eric T.

    2011-09-01

    Over the past quarter century, concepts and theory derived from neural networks (NNs) have featured prominently in the literature of pattern recognition. Implementationally, classical NNs based on the linear inner product can present performance challenges due to the use of multiplication operations. In contrast, NNs having nonlinear kernels based on Lattice Associative Memories (LAM) theory tend to concentrate primarily on addition and maximum/minimum operations. More generally, the emergence of LAM-based NNs, with their superior information storage capacity, fast convergence and training due to relatively lower computational cost, as well as noise-tolerant classification has extended the capabilities of neural networks far beyond the limited applications potential of classical NNs. This paper explores theory and algorithmic approaches for the efficient computation of LAM-based neural networks, in particular lattice neural nets and dendritic lattice associative memories. Of particular interest are massively parallel architectures such as multicore CPUs and graphics processing units (GPUs). Originally developed for video gaming applications, GPUs hold the promise of high computational throughput without compromising numerical accuracy. Unfortunately, currently-available GPU architectures tend to have idiosyncratic memory hierarchies that can produce unacceptably high data movement latencies for relatively simple operations, unless careful design of theory and algorithms is employed. Advantageously, some GPUs (e.g., the Nvidia Fermi GPU) are optimized for efficient streaming computation (e.g., concurrent multiply and add operations). As a result, the linear or nonlinear inner product structures of NNs are inherently suited to multicore GPU computational capabilities. In this paper, the authors' recent research in lattice associative memories and their implementation on multicores is overviewed, with results that show utility for a wide variety of pattern

  10. Three-dimensional electromagnetic modeling and inversion on massively parallel computers

    SciTech Connect

    Newman, G.A.; Alumbaugh, D.L.

    1996-03-01

    This report has demonstrated techniques that can be used to construct solutions to the 3-D electromagnetic inverse problem using full wave equation modeling. To this point great progress has been made in developing an inverse solution using the method of conjugate gradients which employs a 3-D finite difference solver to construct model sensitivities and predicted data. The forward modeling code has been developed to incorporate absorbing boundary conditions for high frequency solutions (radar), as well as complex electrical properties, including electrical conductivity, dielectric permittivity and magnetic permeability. In addition both forward and inverse codes have been ported to a massively parallel computer architecture which allows for more realistic solutions that can be achieved with serial machines. While the inversion code has been demonstrated on field data collected at the Richmond field site, techniques for appraising the quality of the reconstructions still need to be developed. Here it is suggested that rather than employing direct matrix inversion to construct the model covariance matrix which would be impossible because of the size of the problem, one can linearize about the 3-D model achieved in the inverse and use Monte-Carlo simulations to construct it. Using these appraisal and construction tools, it is now necessary to demonstrate 3-D inversion for a variety of EM data sets that span the frequency range from induction sounding to radar: below 100 kHz to 100 MHz. Appraised 3-D images of the earth`s electrical properties can provide researchers opportunities to infer the flow paths, flow rates and perhaps the chemistry of fluids in geologic mediums. It also offers a means to study the frequency dependence behavior of the properties in situ. This is of significant relevance to the Department of Energy, paramount to characterizing and monitoring of environmental waste sites and oil and gas exploration.

  11. The complete genome of an individual by massively parallel DNA sequencing.

    PubMed

    Wheeler, David A; Srinivasan, Maithreyan; Egholm, Michael; Shen, Yufeng; Chen, Lei; McGuire, Amy; He, Wen; Chen, Yi-Ju; Makhijani, Vinod; Roth, G Thomas; Gomes, Xavier; Tartaro, Karrie; Niazi, Faheem; Turcotte, Cynthia L; Irzyk, Gerard P; Lupski, James R; Chinault, Craig; Song, Xing-zhi; Liu, Yue; Yuan, Ye; Nazareth, Lynne; Qin, Xiang; Muzny, Donna M; Margulies, Marcel; Weinstock, George M; Gibbs, Richard A; Rothberg, Jonathan M

    2008-04-17

    The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'. PMID:18421352

  12. Massively parallel sampling of lattice proteins reveals foundations of thermal adaptation

    NASA Astrophysics Data System (ADS)

    Venev, Sergey V.; Zeldovich, Konstantin B.

    2015-08-01

    Evolution of proteins in bacteria and archaea living in different conditions leads to significant correlations between amino acid usage and environmental temperature. The origins of these correlations are poorly understood, and an important question of protein theory, physics-based prediction of types of amino acids overrepresented in highly thermostable proteins, remains largely unsolved. Here, we extend the random energy model of protein folding by weighting the interaction energies of amino acids by their frequencies in protein sequences and predict the energy gap of proteins designed to fold well at elevated temperatures. To test the model, we present a novel scalable algorithm for simultaneous energy calculation for many sequences in many structures, targeting massively parallel computing architectures such as graphics processing unit. The energy calculation is performed by multiplying two matrices, one representing the complete set of sequences, and the other describing the contact maps of all structural templates. An implementation of the algorithm for the CUDA platform is available at http://www.github.com/kzeldovich/galeprot and calculates protein folding energies over 250 times faster than a single central processing unit. Analysis of amino acid usage in 64-mer cubic lattice proteins designed to fold well at different temperatures demonstrates an excellent agreement between theoretical and simulated values of energy gap. The theoretical predictions of temperature trends of amino acid frequencies are significantly correlated with bioinformatics data on 191 bacteria and archaea, and highlight protein folding constraints as a fundamental selection pressure during thermal adaptation in biological evolution.

  13. The complete genome of an individual by massively parallel DNA sequencing.

    PubMed

    Wheeler, David A; Srinivasan, Maithreyan; Egholm, Michael; Shen, Yufeng; Chen, Lei; McGuire, Amy; He, Wen; Chen, Yi-Ju; Makhijani, Vinod; Roth, G Thomas; Gomes, Xavier; Tartaro, Karrie; Niazi, Faheem; Turcotte, Cynthia L; Irzyk, Gerard P; Lupski, James R; Chinault, Craig; Song, Xing-zhi; Liu, Yue; Yuan, Ye; Nazareth, Lynne; Qin, Xiang; Muzny, Donna M; Margulies, Marcel; Weinstock, George M; Gibbs, Richard A; Rothberg, Jonathan M

    2008-04-17

    The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.

  14. Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing.

    PubMed

    Sánchez-León, Nidia; Arteaga-Vázquez, Mario; Alvarez-Mejía, César; Mendiola-Soto, Javier; Durán-Figueroa, Noé; Rodríguez-Leal, Daniel; Rodríguez-Arévalo, Isaac; García-Campayo, Vicenta; García-Aguilar, Marcelina; Olmedo-Monfil, Vianey; Arteaga-Sánchez, Mario; de la Vega, Octavio Martínez; Nobuta, Kan; Vemaraju, Kalyan; Meyers, Blake C; Vielle-Calzada, Jean-Philippe

    2012-06-01

    The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies.

  15. Massively parallel neural circuits for stereoscopic color vision: encoding, decoding and identification.

    PubMed

    Lazar, Aurel A; Slutskiy, Yevgeniy B; Zhou, Yiyin

    2015-03-01

    Past work demonstrated how monochromatic visual stimuli could be faithfully encoded and decoded under Nyquist-type rate conditions. Color visual stimuli were then traditionally encoded and decoded in multiple separate monochromatic channels. The brain, however, appears to mix information about color channels at the earliest stages of the visual system, including the retina itself. If information about color is mixed and encoded by a common pool of neurons, how can colors be demixed and perceived? We present Color Video Time Encoding Machines (Color Video TEMs) for encoding color visual stimuli that take into account a variety of color representations within a single neural circuit. We then derive a Color Video Time Decoding Machine (Color Video TDM) algorithm for color demixing and reconstruction of color visual scenes from spikes produced by a population of visual neurons. In addition, we formulate Color Video Channel Identification Machines (Color Video CIMs) for functionally identifying color visual processing performed by a spiking neural circuit. Furthermore, we derive a duality between TDMs and CIMs that unifies the two and leads to a general theory of neural information representation for stereoscopic color vision. We provide examples demonstrating that a massively parallel color visual neural circuit can be first identified with arbitrary precision and its spike trains can be subsequently used to reconstruct the encoded stimuli. We argue that evaluation of the functional identification methodology can be effectively and intuitively performed in the stimulus space. In this space, a signal reconstructed from spike trains generated by the identified neural circuit can be compared to the original stimulus.

  16. Investigations on the usefulness of the Massively Parallel Processor for study of electronic properties of atomic and condensed matter systems

    NASA Technical Reports Server (NTRS)

    Das, T. P.

    1988-01-01

    The usefulness of the Massively Parallel Processor (MPP) for investigation of electronic structures and hyperfine properties of atomic and condensed matter systems was explored. The major effort was directed towards the preparation of algorithms for parallelization of the computational procedure being used on serial computers for electronic structure calculations in condensed matter systems. Detailed descriptions of investigations and results are reported, including MPP adaptation of self-consistent charge extended Hueckel (SCCEH) procedure, MPP adaptation of the first-principles Hartree-Fock cluster procedure for electronic structures of large molecules and solid state systems, and MPP adaptation of the many-body procedure for atomic systems.

  17. Recessive RYR1 mutations in a patient with severe congenital nemaline myopathy with ophthalomoplegia identified through massively parallel sequencing.

    PubMed

    Kondo, Eri; Nishimura, Takafumi; Kosho, Tomoki; Inaba, Yuji; Mitsuhashi, Satomi; Ishida, Takefumi; Baba, Atsushi; Koike, Kenichi; Nishino, Ichizo; Nonaka, Ikuya; Furukawa, Toru; Saito, Kayoko

    2012-04-01

    Nemaline myopathy (NM) is a group of congenital myopathies, characterized by the presence of distinct rod-like inclusions "nemaline bodies" in the sarcoplasm of skeletal muscle fibers. To date, ACTA1, NEB, TPM3, TPM2, TNNT1, and CFL2 have been found to cause NM. We have identified recessive RYR1 mutations in a patient with severe congenital NM, through high-throughput screening of congenital myopathy/muscular dystrophy-related genes using massively parallel sequencing with target gene capture. The patient manifested fetal akinesia, neonatal severe hypotonia with muscle weakness, respiratory insufficiency, swallowing disturbance, and ophthalomoplegia. Skeletal muscle histology demonstrated nemaline bodies and small type 1 fibers, but without central cores or minicores. Congenital myopathies, a molecularly, histopathologically, and clinically heterogeneous group of disorders are considered to be a good candidate for massively parallel sequencing. PMID:22407809

  18. Underlying Data for Sequencing the Mitochondrial Genome with the Massively Parallel Sequencing Platform Ion Torrent™ PGM™

    PubMed Central

    2015-01-01

    Background Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simultaneously. Compared with Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis and indeed on a per sample basis. In this study, whole genomes of human mitochondria (mtGenome) were sequenced on the Personal Genome Machine (PGMTM) (Life Technologies, San Francisco, CA), the out data were assessed, and the results were compared with data previously generated on the MiSeqTM (Illumina, San Diego, CA). The objectives of this paper were to determine the feasibility, accuracy, and reliability of sequence data obtained from the PGM. Results 24 samples were multiplexed (in groups of six) and sequenced on the at least 10 megabase throughput 314 chip. The depth of coverage pattern was similar among all 24 samples; however the coverage across the genome varied. For strand bias, the average ratio of coverage between the forward and reverse strands at each nucleotide position indicated that two-thirds of the positions of the genome had ratios that were greater than 0.5. A few sites had more extreme strand bias. Another observation was that 156 positions had a false deletion rate greater than 0.15 in one or more individuals. There were 31-98 (SNP) mtGenome variants observed per sample for the 24 samples analyzed. The total 1237 (SNP) variants were concordant between the results from the PGM and MiSeq. The quality scores for haplogroup assignment for all 24 samples ranged between 88.8%-100%. Conclusions In this study, mtDNA sequence data generated from the PGM were analyzed and the output evaluated. Depth of coverage variation and strand bias were identified but generally were infrequent and did not impact reliability of variant calls. Multiplexing of samples was demonstrated which can improve throughput and reduce cost per sample analyzed

  19. A massively parallel adaptive scheme for melt migration in geodynamics computations

    NASA Astrophysics Data System (ADS)

    Dannberg, Juliane; Heister, Timo; Grove, Ryan

    2016-04-01

    Melt generation and migration are important processes for the evolution of the Earth's interior and impact the global convection of the mantle. While they have been the subject of numerous investigations, the typical time and length-scales of melt transport are vastly different from global mantle convection, which determines where melt is generated. This makes it difficult to study mantle convection and melt migration in a unified framework. In addition, modelling magma dynamics poses the challenge of highly non-linear and spatially variable material properties, in particular the viscosity. We describe our extension of the community mantle convection code ASPECT that adds equations describing the behaviour of silicate melt percolating through and interacting with a viscously deforming host rock. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. This approach includes both melt migration and melt generation with the accompanying latent heat effects, and it incorporates the individual compressibilities of the solid and the fluid phase. For this, we derive an accurate and stable Finite Element scheme that can be combined with adaptive mesh refinement. This is particularly advantageous for this type of problem, as the resolution can be increased in mesh cells where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. Together with a high-performance, massively parallel implementation, this allows for high resolution, 3d, compressible, global mantle convection simulations coupled with melt migration. Furthermore, scalable iterative linear solvers are required to solve the large linear systems arising from the discretized system. Finally, we present benchmarks and scaling tests of our solver up to tens of thousands of cores, show the effectiveness of adaptive mesh refinement when applied to melt migration and compare the

  20. 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.

  1. A massively parallel algorithm for the collision probability calculations in the Apollo-II code using the PVM library

    SciTech Connect

    Stankovski, Z.

    1995-12-31

    The collision probability method in neutron transport, as applied to 2D geometries, consume a great amount of computer time, for a typical 2D assembly calculation about 90% of the computing time is consumed in the collision probability evaluations. Consequently RZ or 3D calculations became prohibitive. In this paper the author presents a simple but efficient parallel algorithm based on the message passing host/node programmation model. Parallelization was applied to the energy group treatment. Such approach permits parallelization of the existing code, requiring only limited modifications. Sequential/parallel computer portability is preserved, which is a necessary condition for a industrial code. Sequential performances are also preserved. The algorithm is implemented on a CRAY 90 coupled to a 128 processor T3D computer, a 16 processor IBM SPI and a network of workstations, using the Public Domain PVM library. The tests were executed for a 2D geometry with the standard 99-group library. All results were very satisfactory, the best ones with IBM SPI. Because of heterogeneity of the workstation network, the author did not ask high performances for this architecture. The same source code was used for all computers. A more impressive advantage of this algorithm will appear in the calculations of the SAPHYR project (with the future fine multigroup library of about 8000 groups) with a massively parallel computer, using several hundreds of processors.

  2. System and method for representing and manipulating three-dimensional objects on massively parallel architectures

    DOEpatents

    Karasick, M.S.; Strip, D.R.

    1996-01-30

    A parallel computing system is described that comprises a plurality of uniquely labeled, parallel processors, each processor capable of modeling a three-dimensional object that includes a plurality of vertices, faces and edges. The system comprises a front-end processor for issuing a modeling 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 modeling 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. 8 figs.

  3. 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.

  4. A Precision Dose Control Circuit for Maskless E-Beam Lithography With Massively Parallel Vertically Aligned Carbon Nanofibers

    SciTech Connect

    Eliza, Sazia A.; Islam, Syed K; Rahman, Touhidur; Bull, Nora D; Blalock, Benjamin; Baylor, Larry R; Ericson, Milton Nance; Gardner, Walter L

    2011-01-01

    This paper describes a highly accurate dose control circuit (DCC) for the emission of a desired number of electrons from vertically aligned carbon nanofibers (VACNFs) in a massively parallel maskless e-beam lithography system. The parasitic components within the VACNF device cause a premature termination of the electron emission, resulting in underexposure of the photoresist. In this paper, we compensate for the effects of the parasitic components and noise while reducing the area of the chip and achieving a precise count of emitted electrons from the VACNFs to obtain the optimum dose for the e-beam lithography.

  5. 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.

  6. Massively Parallel Linear Stability Analysis with P_ARPACK for 3D Fluid Flow Modeled with MPSalsa

    SciTech Connect

    Lehoucq, R.B.; Salinger, A.G.

    1998-10-13

    We are interested in the stability of three-dimensional fluid flows to small dkturbances. One computational approach is to solve a sequence of large sparse generalized eigenvalue problems for the leading modes that arise from discretizating the differential equations modeling the flow. The modes of interest are the eigenvalues of largest real part and their associated eigenvectors. We discuss our work to develop an effi- cient and reliable eigensolver for use by the massively parallel simulation code MPSalsa. MPSalsa allows simulation of complex 3D fluid flow, heat transfer, and mass transfer with detailed bulk fluid and surface chemical reaction kinetics.

  7. A massively parallel algorithm for grand canonical Monte Carlo computer simulation with the short-ranged Lennard-Jones potential

    SciTech Connect

    Heffelfinger, G.S.; Lewitt, M.E.

    1994-05-01

    We present a new massively parallel decomposition for grand canonical Monte Carlo computer simulation (GCMC) suitable for short ranged fluids. Our spatial algorithm relies on the fact that for short-ranged fluids, molecules separated by a greater distance than the reach of the potential act independently, thus different processors can work concurrently in regions of the same system which are sufficiently far apart. Several parallelization issues unique to GCMC are addressed such as the handling of the three different types of Monte Carlo move used in GCMC: the displacement of a molecule, the creation of a molecule, and the destruction of a molecule. The decomposition is shown to scale with system size, making it especially useful for systems where the physical problem dictates the system size, for example, fluid behavior in mesopores.

  8. 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.

  9. Efficient Extraction of Regional Subsets from Massive Climate Datasets using Parallel IO

    SciTech Connect

    Daily, Jeffrey A.; Schuchardt, Karen L.; Palmer, Bruce J.

    2010-09-16

    The size of datasets produced by current climate models is increasing rapidly to the scale of petabytes. To handle data at this scale parallel analysis tools are required, however the majority of climate analysis software remains at the scale of workstations. Further, many climate analysis tools adequately process regularly gridded data but lack sufficient features when handling unstructured grids. This paper presents a data-parallel subsetter capable of correctly handling unstructured grids while scaling to over 2000 cores. The approach is based on the partitioned global address space (PGAS) parallel programming model and one-sided communication. The paper demonstrates that IO remains the single greatest bottleneck for this domain of applications and that parallel analysis of climate data succeeds in practice.

  10. Massively parallel implementation of the multi-reference Brillouin-Wigner CCSD method

    SciTech Connect

    Brabec, Jiri; Krishnamoorthy, Sriram; van Dam, Hubertus JJ; Kowalski, Karol; Pittner, Jiri

    2011-10-06

    This paper reports the parallel implementation of the Brillouin Wigner MultiReference Coupled Cluster method with Single and Double excitations (BW-MRCCSD). Preliminary tests for systems composed of 304 and 440 correlated obritals demonstrate the performance of our implementation across 1000 cores and clearly indicate the advantages of using improved task scheduling. Possible ways for further improvements of the parallel performance are also delineated.

  11. Chemoselective ligation

    DOEpatents

    Saxon, Eliana; Bertozzi, Carolyn R.

    2011-04-12

    The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

  12. Chemoselective ligation

    DOEpatents

    Saxon, Eliana; Bertozzi, Carolyn Ruth

    2011-12-13

    The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

  13. Chemoselective ligation

    DOEpatents

    Saxon, Eliana; Bertozzi, Carolyn Ruth

    2010-11-23

    The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

  14. Chemoselective ligation

    DOEpatents

    Saxon, Eliana; Bertozzi, Carolyn

    2003-05-27

    The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

  15. Chemoselective ligation

    DOEpatents

    Saxon, Eliana; Bertozzi, Carolyn R.

    2011-05-10

    The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

  16. Chemoselective ligation

    DOEpatents

    Saxon, Eliana; Bertozzi, Carolyn R.

    2010-02-23

    The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g. on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

  17. Chemoselective ligation

    DOEpatents

    Saxon, Eliana; Bertozzi, Carolyn

    2006-10-17

    The present invention features a chemoselective ligation reaction that can be carried out under physiological conditions. In general, the invention involves condensation of a specifically engineered phosphine, which can provide for formation of an amide bond between the two reactive partners resulting in a final product comprising a phosphine moiety, or which can be engineered to comprise a cleavable linker so that a substituent of the phosphine is transferred to the azide, releasing an oxidized phosphine byproduct and producing a native amide bond in the final product. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

  18. Satisfiability Test with Synchronous Simulated Annealing on the Fujitsu AP1000 Massively-Parallel Multiprocessor

    NASA Technical Reports Server (NTRS)

    Sohn, Andrew; Biswas, Rupak

    1996-01-01

    Solving the hard Satisfiability Problem is time consuming even for modest-sized problem instances. Solving the Random L-SAT Problem is especially difficult due to the ratio of clauses to variables. This report presents a parallel synchronous simulated annealing method for solving the Random L-SAT Problem on a large-scale distributed-memory multiprocessor. In particular, we use a parallel synchronous simulated annealing procedure, called Generalized Speculative Computation, which guarantees the same decision sequence as sequential simulated annealing. To demonstrate the performance of the parallel method, we have selected problem instances varying in size from 100-variables/425-clauses to 5000-variables/21,250-clauses. Experimental results on the AP1000 multiprocessor indicate that our approach can satisfy 99.9 percent of the clauses while giving almost a 70-fold speedup on 500 processors.

  19. Massively parallel computing simulation of fluid flow in the unsaturated zone of Yucca Mountain, Nevada

    SciTech Connect

    Zhang, Keni; Wu, Yu-Shu; Bodvarsson, G.S.

    2001-08-31

    This paper presents the application of parallel computing techniques to large-scale modeling of fluid flow in the unsaturated zone (UZ) at Yucca Mountain, Nevada. In this study, parallel computing techniques, as implemented into the TOUGH2 code, are applied in large-scale numerical simulations on a distributed-memory parallel computer. The modeling study has been conducted using an over-one-million-cell three-dimensional numerical model, which incorporates a wide variety of field data for the highly heterogeneous fractured formation at Yucca Mountain. The objective of this study is to analyze the impact of various surface infiltration scenarios (under current and possible future climates) on flow through the UZ system, using various hydrogeological conceptual models with refined grids. The results indicate that the one-million-cell models produce better resolution results and reveal some flow patterns that cannot be obtained using coarse-grid modeling models.

  20. Solution of the within-group multidimensional discrete ordinates transport equations on massively parallel architectures

    NASA Astrophysics Data System (ADS)

    Zerr, Robert Joseph

    2011-12-01

    The integral transport matrix method (ITMM) has been used as the kernel of new parallel solution methods for the discrete ordinates approximation of the within-group neutron transport equation. The ITMM abandons the repetitive mesh sweeps of the traditional source iterations (SI) scheme in favor of constructing stored operators that account for the direct coupling factors among all the cells and between the cells and boundary surfaces. The main goals of this work were to develop the algorithms that construct these operators and employ them in the solution process, determine the most suitable way to parallelize the entire procedure, and evaluate the behavior and performance of the developed methods for increasing number of processes. This project compares the effectiveness of the ITMM with the SI scheme parallelized with the Koch-Baker-Alcouffe (KBA) method. The primary parallel solution method involves a decomposition of the domain into smaller spatial sub-domains, each with their own transport matrices, and coupled together via interface boundary angular fluxes. Each sub-domain has its own set of ITMM operators and represents an independent transport problem. Multiple iterative parallel solution methods have investigated, including parallel block Jacobi (PBJ), parallel red/black Gauss-Seidel (PGS), and parallel GMRES (PGMRES). The fastest observed parallel solution method, PGS, was used in a weak scaling comparison with the PARTISN code. Compared to the state-of-the-art SI-KBA with diffusion synthetic acceleration (DSA), this new method without acceleration/preconditioning is not competitive for any problem parameters considered. The best comparisons occur for problems that are difficult for SI DSA, namely highly scattering and optically thick. SI DSA execution time curves are generally steeper than the PGS ones. However, until further testing is performed it cannot be concluded that SI DSA does not outperform the ITMM with PGS even on several thousand or tens of

  1. A Novel Algorithm for Solving the Multidimensional Neutron Transport Equation on Massively Parallel Architectures

    SciTech Connect

    Azmy, Yousry

    2014-06-10

    We employ the Integral Transport Matrix Method (ITMM) as the kernel of new parallel solution methods for the discrete ordinates approximation of the within-group neutron transport equation. The ITMM abandons the repetitive mesh sweeps of the traditional source iterations (SI) scheme in favor of constructing stored operators that account for the direct coupling factors among all the cells' fluxes and between the cells' and boundary surfaces' fluxes. The main goals of this work are to develop the algorithms that construct these operators and employ them in the solution process, determine the most suitable way to parallelize the entire procedure, and evaluate the behavior and parallel performance of the developed methods with increasing number of processes, P. The fastest observed parallel solution method, Parallel Gauss-Seidel (PGS), was used in a weak scaling comparison with the PARTISN transport code, which uses the source iteration (SI) scheme parallelized with the Koch-baker-Alcouffe (KBA) method. Compared to the state-of-the-art SI-KBA with diffusion synthetic acceleration (DSA), this new method- even without acceleration/preconditioning-is completitive for optically thick problems as P is increased to the tens of thousands range. For the most optically thick cells tested, PGS reduced execution time by an approximate factor of three for problems with more than 130 million computational cells on P = 32,768. Moreover, the SI-DSA execution times's trend rises generally more steeply with increasing P than the PGS trend. Furthermore, the PGS method outperforms SI for the periodic heterogeneous layers (PHL) configuration problems. The PGS method outperforms SI and SI-DSA on as few as P = 16 for PHL problems and reduces execution time by a factor of ten or more for all problems considered with more than 2 million computational cells on P = 4.096.

  2. Massively parallel read mapping on GPUs with the q-group index and PEANUT

    PubMed Central

    Rahmann, Sven

    2014-01-01

    We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based read mapper. PEANUT provides the possibility to output both the best hits or all hits of a read. Our benchmarks show that PEANUT outperforms other state-of-the-art read mappers in terms of speed while maintaining or slightly increasing precision, recall and sensitivity. PMID:25289191

  3. Design of electrostatic microcolumn for nanoscale photoemission source in massively parallel electron-beam lithography

    NASA Astrophysics Data System (ADS)

    Wen, Ye; Du, Zhidong; Pan, Liang

    2015-10-01

    Microcolumns are widely used for parallel electron-beam lithography because of their compactness and the ability to achieve high spatial resolution. A design of an electrostatic microcolumn for our recent nanoscale photoemission sources is presented. We proposed a compact column structure (as short as several microns in length) for the ease of microcolumn fabrication and lithography operation. We numerically studied the influence of several design parameters on the optical performance such as microcolumn diameter, electrode thickness, beam current, working voltages, and working distance. We also examined the effect of fringing field between adjacent microcolumns during parallel lithography operations.

  4. Massively Parallel, Three-Dimensional Transport Solutions for the k-Eigenvalue Problem

    SciTech Connect

    Davidson, Gregory G; Evans, Thomas M; Jarrell, Joshua J; Pandya, Tara M; Slaybaugh, R

    2014-01-01

    We have implemented a new multilevel parallel decomposition in the Denovo dis- crete ordinates radiation transport code. In concert with Krylov subspace iterative solvers, the multilevel decomposition allows concurrency over energy in addition to space-angle, enabling scalability beyond the limits imposed by the traditional KBA space-angle partitioning. Furthermore, a new Arnoldi-based k-eigenvalue solver has been implemented. The added phase-space concurrency combined with the high- performance Krylov and Arnoldi solvers has enabled weak scaling to O(100K) cores on the Jaguar XK6 supercomputer. The multilevel decomposition provides sucient parallelism to scale to exascale computing and beyond.

  5. Spatiotemporal Domain Decomposition for Massive Parallel Computation of Space-Time Kernel Density

    NASA Astrophysics Data System (ADS)

    Hohl, A.; Delmelle, E. M.; Tang, W.

    2015-07-01

    Accelerated processing capabilities are deemed critical when conducting analysis on spatiotemporal datasets of increasing size, diversity and availability. High-performance parallel computing offers the capacity to solve computationally demanding problems in a limited timeframe, but likewise poses the challenge of preventing processing inefficiency due to workload imbalance between computing resources. Therefore, when designing new algorithms capable of implementing parallel strategies, careful spatiotemporal domain decomposition is necessary to account for heterogeneity in the data. In this study, we perform octtree-based adaptive decomposition of the spatiotemporal domain for parallel computation of space-time kernel density. In order to avoid edge effects near subdomain boundaries, we establish spatiotemporal buffers to include adjacent data-points that are within the spatial and temporal kernel bandwidths. Then, we quantify computational intensity of each subdomain to balance workloads among processors. We illustrate the benefits of our methodology using a space-time epidemiological dataset of Dengue fever, an infectious vector-borne disease that poses a severe threat to communities in tropical climates. Our parallel implementation of kernel density reaches substantial speedup compared to sequential processing, and achieves high levels of workload balance among processors due to great accuracy in quantifying computational intensity. Our approach is portable of other space-time analytical tests.

  6. Massively parallel solution of the inverse scattering problem for integrated circuit quality control

    SciTech Connect

    Leland, R.W.; Draper, B.L.; Naqvi, S.; Minhas, B.

    1997-09-01

    The authors developed and implemented a highly parallel computational algorithm for solution of the inverse scattering problem generated when an integrated circuit is illuminated by laser. The method was used as part of a system to measure diffraction grating line widths on specially fabricated test wafers and the results of the computational analysis were compared with more traditional line-width measurement techniques. The authors found they were able to measure the line width of singly periodic and doubly periodic diffraction gratings (i.e. 2D and 3D gratings respectively) with accuracy comparable to the best available experimental techniques. They demonstrated that their parallel code is highly scalable, achieving a scaled parallel efficiency of 90% or more on typical problems running on 1024 processors. They also made substantial improvements to the algorithmics and their original implementation of Rigorous Coupled Waveform Analysis, the underlying computational technique. These resulted in computational speed-ups of two orders of magnitude in some test problems. By combining these algorithmic improvements with parallelism the authors achieve speedups of between a few thousand and hundreds of thousands over the original engineering code. This made the laser diffraction measurement technique practical.

  7. Optical binary de Bruijn networks for massively parallel computing: design methodology and feasibility study

    NASA Astrophysics Data System (ADS)

    Louri, Ahmed; Sung, Hongki

    1995-10-01

    The interconnection network structure can be the deciding and limiting factor in the cost and the performance of parallel computers. One of the most popular point-to-point interconnection networks for parallel computers today is the hypercube. The regularity, logarithmic diameter, symmetry, high connectivity, fault tolerance, simple routing, and reconfigurability (easy embedding of other network topologies) of the hypercube make it a very attractive choice for parallel computers. Unfortunately the hypercube possesses a major drawback, which is the links per node increases as the network grows in size. As an alternative to the hypercube, the binary de Bruijn (BdB) network has recently received much attention. The BdB not only provides a logarithmic diameter, fault tolerance, and simple routing but also requires fewer links than the hypercube for the same network size. Additionally, a major advantage of the BdB edges per node is independent of the network size. This makes it very desirable for large-scale parallel systems. However, because of its asymmetrical nature and global connectivity, it poses a major challenge for VLSI technology. Optics, owing to its three-dimensional and global-connectivity nature, seems to be very suitable for implementing BdB networks. We present an implementation methodology for optical BdB networks. The distinctive feature of the proposed implementation methodology is partitionability of the network into a few primitive operations that can be implemented efficiently. We further show feasibility of the

  8. An open source massively parallel solver for Richards equation: Mechanistic modelling of water fluxes at the watershed scale

    NASA Astrophysics Data System (ADS)

    Orgogozo, L.; Renon, N.; Soulaine, C.; Hénon, F.; Tomer, S. K.; Labat, D.; Pokrovsky, O. S.; Sekhar, M.; Ababou, R.; Quintard, M.

    2014-12-01

    In this paper we present a massively parallel open source solver for Richards equation, named the RichardsFOAM solver. This solver has been developed in the framework of the open source generalist computational fluid dynamics tool box OpenFOAM® and is capable to deal with large scale problems in both space and time. The source code for RichardsFOAM may be downloaded from the CPC program library website. It exhibits good parallel performances (up to ˜90% parallel efficiency with 1024 processors both in strong and weak scaling), and the conditions required for obtaining such performances are analysed and discussed. These performances enable the mechanistic modelling of water fluxes at the scale of experimental watersheds (up to few square kilometres of surface area), and on time scales of decades to a century. Such a solver can be useful in various applications, such as environmental engineering for long term transport of pollutants in soils, water engineering for assessing the impact of land settlement on water resources, or in the study of weathering processes on the watersheds.

  9. Analysis and selection of optimal function implementations in massively parallel computer

    DOEpatents

    Archer, Charles Jens; Peters, Amanda; Ratterman, Joseph D.

    2011-05-31

    An apparatus, program product and method optimize the operation of a parallel computer system by, in part, collecting performance data for a set of implementations of a function capable of being executed on the parallel computer system based upon the execution of the set of implementations under varying input parameters in a plurality of input dimensions. The collected performance data may be used to generate selection program code that is configured to call selected implementations of the function in response to a call to the function under varying input parameters. The collected performance data may be used to perform more detailed analysis to ascertain the comparative performance of the set of implementations of the function under the varying input parameters.

  10. PARALLEL HOP: A SCALABLE HALO FINDER FOR MASSIVE COSMOLOGICAL DATA SETS

    SciTech Connect

    Skory, Stephen; Turk, Matthew J.; Norman, Michael L.; Coil, Alison L. E-mail: mjturk@ucsd.ed E-mail: acoil@ucsd.ed

    2010-11-15

    Modern N-body cosmological simulations contain billions (10{sup 9}) of dark matter particles. These simulations require hundreds to thousands of gigabytes of memory and employ hundreds to tens of thousands of processing cores on many compute nodes. In order to study the distribution of dark matter in a cosmological simulation, the dark matter halos must be identified using a halo finder, which establishes the halo membership of every particle in the simulation. The resources required for halo finding are similar to the requirements for the simulation itself. In particular, simulations have become too extensive to use commonly employed halo finders, such that the computational requirements to identify halos must now be spread across multiple nodes and cores. Here, we present a scalable-parallel halo finding method called Parallel HOP for large-scale cosmological simulation data. Based on the halo finder HOP, it utilizes message passing interface and domain decomposition to distribute the halo finding workload across multiple compute nodes, enabling analysis of much larger data sets than is possible with the strictly serial or previous parallel implementations of HOP. We provide a reference implementation of this method as a part of the toolkit {sup yt}, an analysis toolkit for adaptive mesh refinement data that include complementary analysis modules. Additionally, we discuss a suite of benchmarks that demonstrate that this method scales well up to several hundred tasks and data sets in excess of 2000{sup 3} particles. The Parallel HOP method and our implementation can be readily applied to any kind of N-body simulation data and is therefore widely applicable.

  11. Stability Analysis of Large-Scale Incompressible Flow Calculations on Massively Parallel Computers

    SciTech Connect

    LEHOUCQ,RICHARD B.; ROMERO,LOUIS; SALINGER,ANDREW G.

    1999-10-25

    A set of linear and nonlinear stability analysis tools have been developed to analyze steady state incompressible flows in 3D geometries. The algorithms have been implemented to be scalable to hundreds of parallel processors. The linear stability of steady state flows are determined by calculating the rightmost eigenvalues of the associated generalize eigenvalue problem. Nonlinear stability is studied by bifurcation analysis techniques. The boundaries between desirable and undesirable operating conditions are determined for buoyant flow in the rotating disk CVD reactor.

  12. Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing

    PubMed Central

    Lundin, Sverker; Gruselius, Joel; Nystedt, Björn; Lexow, Preben; Käller, Max; Lundeberg, Joakim

    2013-01-01

    Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin, and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system, and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines, and targeting a variable canine mitochondrial region. PMID:23470464

  13. Massive and parallel expression profiling using microarrayed single-cell sequencing

    PubMed Central

    Vickovic, Sanja; Ståhl, Patrik L.; Salmén, Fredrik; Giatrellis, Sarantis; Westholm, Jakub Orzechowski; Mollbrink, Annelie; Navarro, José Fernández; Custodio, Joaquin; Bienko, Magda; Sutton, Lesley-Ann; Rosenquist, Richard; Frisén, Jonas; Lundeberg, Joakim

    2016-01-01

    Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0.13 USD/cell), which is two orders of magnitude less than commercially available systems. Our novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes. PMID:27739429

  14. Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms.

    PubMed

    Ganesan, Narayan; Li, Jie; Sharma, Vishakha; Jiang, Hanyu; Compagnoni, Adriana

    2016-01-01

    Biological systems encompass complexity that far surpasses many artificial systems. Modeling and simulation of large and complex biochemical pathways is a computationally intensive challenge. Traditional tools, such as ordinary differential equations, partial differential equations, stochastic master equations, and Gillespie type methods, are all limited either by their modeling fidelity or computational efficiency or both. In this work, we present a scalable computational framework based on modeling biochemical reactions in explicit 3D space, that is suitable for studying the behavior of large and complex biological pathways. The framework is designed to exploit parallelism and scalability offered by commodity massively parallel processors such as the graphics processing units (GPUs) and other parallel computing platforms. The reaction modeling in 3D space is aimed at enhancing the realism of the model compared to traditional modeling tools and framework. We introduce the Parallel Select algorithm that is key to breaking the sequential bottleneck limiting the performance of most other tools designed to study biochemical interactions. The algorithm is designed to be computationally tractable, handle hundreds of interacting chemical species and millions of independent agents by considering all-particle interactions within the system. We also present an implementation of the framework on the popular graphics processing units and apply it to the simulation study of JAK-STAT Signal Transduction Pathway. The computational framework will offer a deeper insight into various biological processes within the cell and help us observe key events as they unfold in space and time. This will advance the current state-of-the-art in simulation study of large scale biological systems and also enable the realistic simulation study of macro-biological cultures, where inter-cellular interactions are prevalent.

  15. Advances in time-domain electromagnetic simulation capabilities through the use of overset grids and massively parallel computing

    NASA Astrophysics Data System (ADS)

    Blake, Douglas Clifton

    A new methodology is presented for conducting numerical simulations of electromagnetic scattering and wave-propagation phenomena on massively parallel computing platforms. A process is constructed which is rooted in the Finite-Volume Time-Domain (FVTD) technique to create a simulation capability that is both versatile and practical. In terms of versatility, the method is platform independent, is easily modifiable, and is capable of solving a large number of problems with no alterations. In terms of practicality, the method is sophisticated enough to solve problems of engineering significance and is not limited to mere academic exercises. In order to achieve this capability, techniques are integrated from several scientific disciplines including computational fluid dynamics, computational electromagnetics, and parallel computing. The end result is the first FVTD solver capable of utilizing the highly flexible overset-gridding process in a distributed-memory computing environment. In the process of creating this capability, work is accomplished to conduct the first study designed to quantify the effects of domain-decomposition dimensionality on the parallel performance of hyperbolic partial differential equations solvers; to develop a new method of partitioning a computational domain comprised of overset grids; and to provide the first detailed assessment of the applicability of overset grids to the field of computational electromagnetics. Using these new methods and capabilities, results from a large number of wave propagation and scattering simulations are presented. The overset-grid FVTD algorithm is demonstrated to produce results of comparable accuracy to single-grid simulations while simultaneously shortening the grid-generation process and increasing the flexibility and utility of the FVTD technique. Furthermore, the new domain-decomposition approaches developed for overset grids are shown to be capable of producing partitions that are better load balanced and

  16. 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

  17. Massively parallel single cell RNA-Seq for marker-free decomposition of tissues into cell types

    PubMed Central

    Jaitin, Diego Adhemar; Kenigsberg, Ephraim; Keren-Shaul, Hadas; Elefant, Naama; Paul, Franziska; Zaretsky, Irina; Mildner, Alexander; Cohen, Nadav; Jung, Steffen; Tanay, Amos; Amit, Ido

    2015-01-01

    In multi-cellular organisms, biological function emerges when heterogeneous cell types form complex organs. Nevertheless dissection of tissues into mixtures of cellular subpopulations is currently challenging. We introduce an automated massively parallel single-cell RNA sequencing approach for analyzing in vivo transcriptional states in thousands of single cells. Combined with unsupervised classification algorithms, this facilitates ab initio cell type characterization of splenic tissues. Modeling single-cell transcriptional states in dendritic cells and additional hematopoietic cell types uncovers rich cell-type heterogeneity and gene-modules activity in steady-state and after pathogen activation. Cellular diversity is thereby approached through inference of variable and dynamic pathway activity rather than a fixed pre-programmed cell-type hierarchy. These data demonstrate single-cell RNA-Seq as an effective tool for comprehensive cellular decomposition of complex tissues. PMID:24531970

  18. Characterization of MazF-Mediated Sequence-Specific RNA Cleavage in Pseudomonas putida Using Massive Parallel Sequencing.

    PubMed

    Miyamoto, Tatsuki; Kato, Yuka; Sekiguchi, Yuji; Tsuneda, Satoshi; Noda, Naohiro

    2016-01-01

    Under environmental stress, microbes are known to alter their translation patterns using sequence-specific endoribonucleases that we call RNA interferases. However, there has been limited insight regarding which RNAs are specifically cleaved by these RNA interferases, hence their physiological functions remain unknown. In the current study, we developed a novel method to effectively identify cleavage specificities with massive parallel sequencing. This approach uses artificially designed RNAs composed of diverse sequences, which do not form extensive secondary structures, and it correctly identified the cleavage sequence of a well-characterized Escherichia coli RNA interferase, MazF, as ACA. In addition, we also determined that an uncharacterized MazF homologue isolated from Pseudomonas putida specifically recognizes the unique triplet, UAC. Using a real-time fluorescence resonance energy transfer assay, the UAC triplet was further proved to be essential for cleavage in P. putida MazF. These results highlight an effective method to determine cleavage specificity of RNA interferases.

  19. Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

    PubMed Central

    Voelz, Vincent A.; Luttmann, Edgar; Bowman, Gregory R.; Pande, Vijay S.

    2009-01-01

    Recently a temperature-jump FTIR study of a designed three-stranded sheet showing a fast relaxation time of ~140 ± 20 ns was published. We performed massively parallel molecular dynamics simulations in explicit solvent to probe the structural events involved in this relaxation. While our simulations produce similar relaxation rates, the structural ensemble is broad. We observe the formation of turn structure, but only very weak interaction in the strand regions, which is consistent with the lack of strong backbone-backbone NOEs in previous structural NMR studies. These results suggest that either DPDP-II folds at time scales longer than 240 ns, or that DPDP-II is not a well-defined three-stranded β-sheet. This work also provides an opportunity to compare the performance of several popular forcefield models against one another. PMID:19399235

  20. USH2 caused by GPR98 mutation diagnosed by massively parallel sequencing in advance of the occurrence of visual symptoms

    PubMed Central

    Moteki, Hideaki; Yoshimura, Hidekane; Azaiez, Hela; Booth, Kevin T.; Shearer, A Eliot; Sloan, Christina M.; Kolbe, Diana L.; Murata, Toshinori; Smith, Richard J. H.; Usami, Shin-ichi

    2015-01-01

    Objective We present two patients who were identified with mutations in the GPR98 gene that causes Usher syndrome type 2 (USH2). Methods One hundred ninety-four (194) Japanese subjects from unrelated and families were enrolled in the study. Targeted genomic enrichment and massively parallel sequencing of all known non-syndromic hearing loss genes were used to identify the genetic causes of hearing loss. Results We identified causative mutations in the GPR98 gene in one family (two siblings). The patients had moderate sloping hearing loss, and no progression was observed over a period of 10 years. Fundus examinations were normal. However, electroretinogram revealed impaired responses in both patients. Conclusion Early diagnosis of Usher syndrome has many advantages for patients and their families. This study supports the use of comprehensive genetic diagnosis for Usher syndrome, especially prior to the onset of visual symptoms, to provide the highest chance of diagnostic success in early life stages. PMID:25743181

  1. Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™.

    PubMed

    Eduardoff, M; Santos, C; de la Puente, M; Gross, T E; Fondevila, M; Strobl, C; Sobrino, B; Ballard, D; Schneider, P M; Carracedo, Á; Lareu, M V; Parson, W; Phillips, C

    2015-07-01

    Next generation sequencing (NGS) offers the opportunity to analyse forensic DNA samples and obtain massively parallel coverage of targeted short sequences with the variants they carry. We evaluated the levels of sequence coverage, genotyping precision, sensitivity and mixed DNA patterns of a prototype version of the first commercial forensic NGS kit: the HID-Ion AmpliSeq™ Identity Panel with 169-markers designed for the Ion PGM™ system. Evaluations were made between three laboratories following closely matched Ion PGM™ protocols and a simple validation framework of shared DNA controls. The sequence coverage obtained was extensive for the bulk of SNPs targeted by the HID-Ion AmpliSeq™ Identity Panel. Sensitivity studies showed 90-95% of SNP genotypes could be obtained from 25 to 100pg of input DNA. Genotyping concordance tests included Coriell cell-line control DNA analyses checked against whole-genome sequencing data from 1000 Genomes and Complete Genomics, indicating a very high concordance rate of 99.8%. Discordant genotypes detected in rs1979255, rs1004357, rs938283, rs2032597 and rs2399332 indicate these loci should be excluded from the panel. Therefore, the HID-Ion AmpliSeq™ Identity Panel and Ion PGM™ system provide a sensitive and accurate forensic SNP genotyping assay. However, low-level DNA produced much more varied sequence coverage and in forensic use the Ion PGM™ system will require careful calibration of the total samples loaded per chip to preserve the genotyping reliability seen in routine forensic DNA. Furthermore, assessments of mixed DNA indicate the user's control of sequence analysis parameter settings is necessary to ensure mixtures are detected robustly. Given the sensitivity of Ion PGM™, this aspect of forensic genotyping requires further optimisation before massively parallel sequencing is applied to routine casework.

  2. Extended computational kernels in a massively parallel implementation of the Trotter-Suzuki approximation

    NASA Astrophysics Data System (ADS)

    Wittek, Peter; Calderaro, Luca

    2015-12-01

    We extended a parallel and distributed implementation of the Trotter-Suzuki algorithm for simulating quantum systems to study a wider range of physical problems and to make the library easier to use. The new release allows periodic boundary conditions, many-body simulations of non-interacting particles, arbitrary stationary potential functions, and imaginary time evolution to approximate the ground state energy. The new release is more resilient to the computational environment: a wider range of compiler chains and more platforms are supported. To ease development, we provide a more extensive command-line interface, an application programming interface, and wrappers from high-level languages.

  3. Massively Parallel DNA Sequencing Successfully Identifies New Causative Mutations in Deafness Genes in Patients with Cochlear Implantation and EAS

    PubMed Central

    Miyagawa, Maiko; Nishio, Shin-ya; Ikeda, Takuo; Fukushima, Kunihiro; Usami, Shin-ichi

    2013-01-01

    Genetic factors, the most common etiology in severe to profound hearing loss, are one of the key determinants of Cochlear Implantation (CI) and Electric Acoustic Stimulation (EAS) outcomes. Satisfactory auditory performance after receiving a CI/EAS in patients with certain deafness gene mutations indicates that genetic testing would be helpful in predicting CI/EAS outcomes and deciding treatment choices. However, because of the extreme genetic heterogeneity of deafness, clinical application of genetic information still entails difficulties. Target exon sequencing using massively parallel DNA sequencing is a new powerful strategy to discover rare causative genes in Mendelian disorders such as deafness. We used massive sequencing of the exons of 58 target candidate genes to analyze 8 (4 early-onset, 4 late-onset) Japanese CI/EAS patients, who did not have mutations in commonly found genes including GJB2, SLC26A4, or mitochondrial 1555A>G or 3243A>G mutations. We successfully identified four rare causative mutations in the MYO15A, TECTA, TMPRSS3, and ACTG1 genes in four patients who showed relatively good auditory performance with CI including EAS, suggesting that genetic testing may be able to predict the performance after implantation. PMID:24130743

  4. A massively parallel method of characteristic neutral particle transport code for GPUs

    SciTech Connect

    Boyd, W. R.; Smith, K.; Forget, B.

    2013-07-01

    Over the past 20 years, parallel computing has enabled computers to grow ever larger and more powerful while scientific applications have advanced in sophistication and resolution. This trend is being challenged, however, as the power consumption for conventional parallel computing architectures has risen to unsustainable levels and memory limitations have come to dominate compute performance. Heterogeneous computing platforms, such as Graphics Processing Units (GPUs), are an increasingly popular paradigm for solving these issues. This paper explores the applicability of GPUs for deterministic neutron transport. A 2D method of characteristics (MOC) code - OpenMOC - has been developed with solvers for both shared memory multi-core platforms as well as GPUs. The multi-threading and memory locality methodologies for the GPU solver are presented. Performance results for the 2D C5G7 benchmark demonstrate 25-35 x speedup for MOC on the GPU. The lessons learned from this case study will provide the basis for further exploration of MOC on GPUs as well as design decisions for hardware vendors exploring technologies for the next generation of machines for scientific computing. (authors)

  5. Harnessing the killer micros: Applications from LLNL's massively parallel computing initiative

    SciTech Connect

    Belak, J.F.

    1991-07-01

    Recent developments in microprocessor technology have led to performance on scalar applications exceeding traditional supercomputers. This suggests that coupling hundreds or even thousands of these killer-micros'' (all working on a single physical problem) may lead to performance on vector applications in excess of vector supercomputers. Also, future generation killer-micros are expected to have vector floating point units as well. The purpose of this paper is to present an overview of the parallel computing environment at Lawrence Livermore National Laboratory. However, the perspective is necessarily quite narrow and most of the examples are taken from the author's implementation of a large scale molecular dynamics code on the BBN-TC2000 at LLNL. Parallelism is achieved through a geometric domain decomposition -- each processor is assigned a distinct region of space and all atoms contained therein. As the atomic positions evolve, the processors must exchange ownership of specific atoms. This geometric domain decomposition proves to be quite general and we highlight its application to image processing and hydrodynamics simulations as well. 10 refs., 6 figs.

  6. Library Preparation and Multiplex Capture for Massive Parallel Sequencing Applications Made Efficient and Easy

    PubMed Central

    Neiman, Mårten; Sundling, Simon; Grönberg, Henrik; Hall, Per; Czene, Kamila

    2012-01-01

    During the recent years, rapid development of sequencing technologies and a competitive market has enabled researchers to perform massive sequencing projects at a reasonable cost. As the price for the actual sequencing reactions drops, enabling more samples to be sequenced, the relative price for preparing libraries gets larger and the practical laboratory work becomes complex and tedious. We present a cost-effective strategy for simplified library preparation compatible with both whole genome- and targeted sequencing experiments. An optimized enzyme composition and reaction buffer reduces the number of required clean-up steps and allows for usage of bulk enzymes which makes the whole process cheap, efficient and simple. We also present a two-tagging strategy, which allows for multiplex sequencing of targeted regions. To prove our concept, we have prepared libraries for low-pass sequencing from 100 ng DNA, performed 2-, 4- and 8-plex exome capture and a 96-plex capture of a 500 kb region. In all samples we see a high concordance (>99.4%) of SNP calls when comparing to commercially available SNP-chip platforms. PMID:23139805

  7. A new massively parallel version of CRYSTAL for large systems on high performance computing architectures.

    PubMed

    Orlando, Roberto; Delle Piane, Massimo; Bush, Ian J; Ugliengo, Piero; Ferrabone, Matteo; Dovesi, Roberto

    2012-10-30

    Fully ab initio treatment of complex solid systems needs computational software which is able to efficiently take advantage of the growing power of high performance computing (HPC) architectures. Recent improvements in CRYSTAL, a periodic ab initio code that uses a Gaussian basis set, allows treatment of very large unit cells for crystalline systems on HPC architectures with high parallel efficiency in terms of running time and memory requirements. The latter is a crucial point, due to the trend toward architectures relying on a very high number of cores with associated relatively low memory availability. An exhaustive performance analysis shows that density functional calculations, based on a hybrid functional, of low-symmetry systems containing up to 100,000 atomic orbitals and 8000 atoms are feasible on the most advanced HPC architectures available to European researchers today, using thousands of processors.

  8. Massively parallel kinetic Monte Carlo simulations of charge carrier transport in organic semiconductors

    NASA Astrophysics Data System (ADS)

    van der Kaap, N. J.; Koster, L. J. A.

    2016-02-01

    A parallel, lattice based Kinetic Monte Carlo simulation is developed that runs on a GPGPU board and includes Coulomb like particle-particle interactions. The performance of this computationally expensive problem is improved by modifying the interaction potential due to nearby particle moves, instead of fully recalculating it. This modification is achieved by adding dipole correction terms that represent the particle move. Exact evaluation of these terms is guaranteed by representing all interactions as 32-bit floating numbers, where only the integers between -222 and 222 are used. We validate our method by modelling the charge transport in disordered organic semiconductors, including Coulomb interactions between charges. Performance is mainly governed by the particle density in the simulation volume, and improves for increasing densities. Our method allows calculations on large volumes including particle-particle interactions, which is important in the field of organic semiconductors.

  9. Neptune: An astrophysical smooth particle hydrodynamics code for massively parallel computer architectures

    NASA Astrophysics Data System (ADS)

    Sandalski, Stou

    Smooth particle hydrodynamics is an efficient method for modeling the dynamics of fluids. It is commonly used to simulate astrophysical processes such as binary mergers. We present a newly developed GPU accelerated smooth particle hydrodynamics code for astrophysical simulations. The code is named neptune after the Roman god of water. It is written in OpenMP parallelized C++ and OpenCL and includes octree based hydrodynamic and gravitational acceleration. The design relies on object-oriented methodologies in order to provide a flexible and modular framework that can be easily extended and modified by the user. Several pre-built scenarios for simulating collisions of polytropes and black-hole accretion are provided. The code is released under the MIT Open Source license and publicly available at http://code.google.com/p/neptune-sph/.

  10. The transition to massively parallel computing within a production environment at a DOE access center

    SciTech Connect

    McCoy, M.G.

    1993-04-01

    In contemplating the transition from sequential to MP computing, the National Energy Research Supercomputer Center (NERSC) is faced with the frictions inherent in the duality of its mission. There have been two goals, the first has been to provide a stable, serviceable, production environment to the user base, the second to bring the most capable early serial supercomputers to the Center to make possible the leading edge simulations. This seeming conundrum has in reality been a source of strength. The task of meeting both goals was faced before with the CRAY 1 which, as delivered, was all iron; so the problems associated with the advent of parallel computers are not entirely new, but they are serious. Current vector supercomputers, such as the C90, offer mature production environments, including software tools, a large applications base, and generality; these machines can be used to attack the spectrum of scientific applications by a large user base knowledgeable in programming techniques for this architecture. Parallel computers to date have offered less developed, even rudimentary, working environments, a sparse applications base, and forced specialization. They have been specialized in terms of programming models, and specialized in terms of the kinds of applications which would do well on the machines. Given this context, why do many service computer centers feel that now is the time to cease or slow the procurement of traditional vector supercomputers in favor of MP systems? What are some of the issues that NERSC must face to engineer a smooth transition? The answers to these questions are multifaceted and by no means completely clear. However, a route exists as a result of early efforts at the Laboratories combined with research within the HPCC Program. One can begin with an analysis of why the hardware and software appearing shortly should be made available to the mainstream, and then address what would be required in an initial production environment.

  11. 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.

  12. Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs

    PubMed Central

    Rukov, Jakob Lewin; Hagedorn, Peter H.; Høy, Isabel Bro; Feng, Yanping; Lindow, Morten; Vinther, Jeppe

    2015-01-01

    Processing and post-transcriptional regulation of RNA often depend on binding of regulatory molecules to short motifs in RNA. The effects of such interactions are difficult to study, because most regulatory molecules recognize partially degenerate RNA motifs, embedded in a sequence context specific for each RNA. Here, we describe Library Sequencing (LibSeq), an accurate massively parallel reporter method for completely characterizing the regulatory potential of thousands of short RNA sequences in a specific context. By sequencing cDNA derived from a plasmid library expressing identical reporter genes except for a degenerate 7mer subsequence in the 3′UTR, the regulatory effects of each 7mer can be determined. We show that LibSeq identifies regulatory motifs used by RNA-binding proteins and microRNAs. We furthermore apply the method to cells transfected with RNase H recruiting oligonucleotides to obtain quantitative information for >15000 potential target sequences in parallel. These comprehensive datasets provide insights into the specificity requirements of RNase H and allow a specificity measure to be calculated for each tested oligonucleotide. Moreover, we show that inclusion of chemical modifications in the central part of an RNase H recruiting oligonucleotide can increase its sequence-specificity. PMID:26220183

  13. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.

    PubMed

    Adamidi, Catherine; Wang, Yongbo; Gruen, Dominic; Mastrobuoni, Guido; You, Xintian; Tolle, Dominic; Dodt, Matthias; Mackowiak, Sebastian D; Gogol-Doering, Andreas; Oenal, Pinar; Rybak, Agnieszka; Ross, Eric; Sánchez Alvarado, Alejandro; Kempa, Stefan; Dieterich, Christoph; Rajewsky, Nikolaus; Chen, Wei

    2011-07-01

    Freshwater planaria are a very attractive model system for stem cell biology, tissue homeostasis, and regeneration. The genome of the planarian Schmidtea mediterranea has recently been sequenced and is estimated to contain >20,000 protein-encoding genes. However, the characterization of its transcriptome is far from complete. Furthermore, not a single proteome of the entire phylum has been assayed on a genome-wide level. We devised an efficient sequencing strategy that allowed us to de novo assemble a major fraction of the S. mediterranea transcriptome. We then used independent assays and massive shotgun proteomics to validate the authenticity of transcripts. In total, our de novo assembly yielded 18,619 candidate transcripts with a mean length of 1118 nt after filtering. A total of 17,564 candidate transcripts could be mapped to 15,284 distinct loci on the current genome reference sequence. RACE confirmed complete or almost complete 5' and 3' ends for 22/24 transcripts. The frequencies of frame shifts, fusion, and fission events in the assembled transcripts were computationally estimated to be 4.2%-13%, 0%-3.7%, and 2.6%, respectively. Our shotgun proteomics produced 16,135 distinct peptides that validated 4200 transcripts (FDR ≤1%). The catalog of transcripts assembled in this study, together with the identified peptides, dramatically expands and refines planarian gene annotation, demonstrated by validation of several previously unknown transcripts with stem cell-dependent expression patterns. In addition, our robust transcriptome characterization pipeline could be applied to other organisms without genome assembly. All of our data, including homology annotation, are freely available at SmedGD, the S. mediterranea genome database.

  14. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

    PubMed Central

    Adamidi, Catherine; Wang, Yongbo; Gruen, Dominic; Mastrobuoni, Guido; You, Xintian; Tolle, Dominic; Dodt, Matthias; Mackowiak, Sebastian D.; Gogol-Doering, Andreas; Oenal, Pinar; Rybak, Agnieszka; Ross, Eric; Alvarado, Alejandro Sánchez; Kempa, Stefan; Dieterich, Christoph; Rajewsky, Nikolaus; Chen, Wei

    2011-01-01

    Freshwater planaria are a very attractive model system for stem cell biology, tissue homeostasis, and regeneration. The genome of the planarian Schmidtea mediterranea has recently been sequenced and is estimated to contain >20,000 protein-encoding genes. However, the characterization of its transcriptome is far from complete. Furthermore, not a single proteome of the entire phylum has been assayed on a genome-wide level. We devised an efficient sequencing strategy that allowed us to de novo assemble a major fraction of the S. mediterranea transcriptome. We then used independent assays and massive shotgun proteomics to validate the authenticity of transcripts. In total, our de novo assembly yielded 18,619 candidate transcripts with a mean length of 1118 nt after filtering. A total of 17,564 candidate transcripts could be mapped to 15,284 distinct loci on the current genome reference sequence. RACE confirmed complete or almost complete 5′ and 3′ ends for 22/24 transcripts. The frequencies of frame shifts, fusion, and fission events in the assembled transcripts were computationally estimated to be 4.2%–13%, 0%–3.7%, and 2.6%, respectively. Our shotgun proteomics produced 16,135 distinct peptides that validated 4200 transcripts (FDR ≤1%). The catalog of transcripts assembled in this study, together with the identified peptides, dramatically expands and refines planarian gene annotation, demonstrated by validation of several previously unknown transcripts with stem cell-dependent expression patterns. In addition, our robust transcriptome characterization pipeline could be applied to other organisms without genome assembly. All of our data, including homology annotation, are freely available at SmedGD, the S. mediterranea genome database. PMID:21536722

  15. cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems

    PubMed Central

    Besozzi, Daniela; Pescini, Dario; Mauri, Giancarlo

    2014-01-01

    Tau-leaping is a stochastic simulation algorithm that efficiently reconstructs the temporal evolution of biological systems, modeled according to the stochastic formulation of chemical kinetics. The analysis of dynamical properties of these systems in physiological and perturbed conditions usually requires the execution of a large number of simulations, leading to high computational costs. Since each simulation can be executed independently from the others, a massive parallelization of tau-leaping can bring to relevant reductions of the overall running time. The emerging field of General Purpose Graphic Processing Units (GPGPU) provides power-efficient high-performance computing at a relatively low cost. In this work we introduce cuTauLeaping, a stochastic simulator of biological systems that makes use of GPGPU computing to execute multiple parallel tau-leaping simulations, by fully exploiting the Nvidia's Fermi GPU architecture. We show how a considerable computational speedup is achieved on GPU by partitioning the execution of tau-leaping into multiple separated phases, and we describe how to avoid some implementation pitfalls related to the scarcity of memory resources on the GPU streaming multiprocessors. Our results show that cuTauLeaping largely outperforms the CPU-based tau-leaping implementation when the number of parallel simulations increases, with a break-even directly depending on the size of the biological system and on the complexity of its emergent dynamics. In particular, cuTauLeaping is exploited to investigate the probability distribution of bistable states in the Schlögl model, and to carry out a bidimensional parameter sweep analysis to study the oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae. PMID:24663957

  16. Delta: An object-oriented finite element code architecture for massively parallel computers

    SciTech Connect

    Weatherby, J.R.; Schutt, J.A.; Peery, J.S.; Hogan, R.E.

    1996-02-01

    Delta is an object-oriented code architecture based on the finite element method which enables simulation of a wide range of engineering mechanics problems in a parallel processing environment. Written in C{sup ++}, Delta is a natural framework for algorithm development and for research involving coupling of mechanics from different Engineering Science disciplines. To enhance flexibility and encourage code reuse, the architecture provides a clean separation of the major aspects of finite element programming. Spatial discretization, temporal discretization, and the solution of linear and nonlinear systems of equations are each implemented separately, independent from the governing field equations. Other attractive features of the Delta architecture include support for constitutive models with internal variables, reusable ``matrix-free`` equation solvers, and support for region-to-region variations in the governing equations and the active degrees of freedom. A demonstration code built from the Delta architecture has been used in two-dimensional and three-dimensional simulations involving dynamic and quasi-static solid mechanics, transient and steady heat transport, and flow in porous media.

  17. Massively-parallel electrical-conductivity imaging of hydrocarbonsusing the Blue Gene/L supercomputer

    SciTech Connect

    Commer, M.; Newman, G.A.; Carazzone, J.J.; Dickens, T.A.; Green,K.E.; Wahrmund, L.A.; Willen, D.E.; Shiu, J.

    2007-05-16

    Large-scale controlled source electromagnetic (CSEM)three-dimensional (3D) geophysical imaging is now receiving considerableattention for electrical conductivity mapping of potential offshore oiland gas reservoirs. To cope with the typically large computationalrequirements of the 3D CSEM imaging problem, our strategies exploitcomputational parallelism and optimized finite-difference meshing. Wereport on an imaging experiment, utilizing 32,768 tasks/processors on theIBM Watson Research Blue Gene/L (BG/L) supercomputer. Over a 24-hourperiod, we were able to image a large scale marine CSEM field data setthat previously required over four months of computing time ondistributed clusters utilizing 1024 tasks on an Infiniband fabric. Thetotal initial data misfit could be decreased by 67 percent within 72completed inversion iterations, indicating an electrically resistiveregion in the southern survey area below a depth of 1500 m below theseafloor. The major part of the residual misfit stems from transmitterparallel receiver components that have an offset from the transmittersail line (broadside configuration). Modeling confirms that improvedbroadside data fits can be achieved by considering anisotropic electricalconductivities. While delivering a satisfactory gross scale image for thedepths of interest, the experiment provides important evidence for thenecessity of discriminating between horizontal and verticalconductivities for maximally consistent 3D CSEM inversions.

  18. Efficient massively parallel simulation of dynamic channel assignment schemes for wireless cellular communications

    NASA Technical Reports Server (NTRS)

    Greenberg, Albert G.; Lubachevsky, Boris D.; Nicol, David M.; Wright, Paul E.

    1994-01-01

    Fast, efficient parallel algorithms are presented for discrete event simulations of dynamic channel assignment schemes for wireless cellular communication networks. The driving events are call arrivals and departures, in continuous time, to cells geographically distributed across the service area. A dynamic channel assignment scheme decides which call arrivals to accept, and which channels to allocate to the accepted calls, attempting to minimize call blocking while ensuring co-channel interference is tolerably low. Specifically, the scheme ensures that the same channel is used concurrently at different cells only if the pairwise distances between those cells are sufficiently large. Much of the complexity of the system comes from ensuring this separation. The network is modeled as a system of interacting continuous time automata, each corresponding to a cell. To simulate the model, conservative methods are used; i.e., methods in which no errors occur in the course of the simulation and so no rollback or relaxation is needed. Implemented on a 16K processor MasPar MP-1, an elegant and simple technique provides speedups of about 15 times over an optimized serial simulation running on a high speed workstation. A drawback of this technique, typical of conservative methods, is that processor utilization is rather low. To overcome this, new methods were developed that exploit slackness in event dependencies over short intervals of time, thereby raising the utilization to above 50 percent and the speedup over the optimized serial code to about 120 times.

  19. 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. PMID:22558329

  20. Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers

    NASA Astrophysics Data System (ADS)

    Lindner, Benjamin; Smith, Jeremy C.

    2012-07-01

    Massively parallel computers now permit the molecular dynamics (MD) simulation of multi-million atom systems on time scales up to the microsecond. However, the subsequent analysis of the resulting simulation trajectories has now become a high performance computing problem in itself. Here, we present software for calculating X-ray and neutron scattering intensities from MD simulation data that scales well on massively parallel supercomputers. The calculation and data staging schemes used maximize the degree of parallelism and minimize the IO bandwidth requirements. The strong scaling tested on the Jaguar Petaflop Cray XT5 at Oak Ridge National Laboratory exhibits virtually linear scaling up to 7000 cores for most benchmark systems. Since both MPI and thread parallelism is supported, the software is flexible enough to cover scaling demands for different types of scattering calculations. The result is a high performance tool capable of unifying large-scale supercomputing and a wide variety of neutron/synchrotron technology. Catalogue identifier: AELW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 1 003 742 No. of bytes in distributed program, including test data, etc.: 798 Distribution format: tar.gz Programming language: C++, OpenMPI Computer: Distributed Memory, Cluster of Computers with high performance network, Supercomputer Operating system: UNIX, LINUX, OSX Has the code been vectorized or parallelized?: Yes, the code has been parallelized using MPI directives. Tested with up to 7000 processors RAM: Up to 1 Gbytes/core Classification: 6.5, 8 External routines: Boost Library, FFTW3, CMAKE, GNU C++ Compiler, OpenMPI, LibXML, LAPACK Nature of problem: Recent developments in supercomputing allow molecular dynamics simulations to

  1. Modeling cardiovascular hemodynamics using the lattice Boltzmann method on massively parallel supercomputers

    NASA Astrophysics Data System (ADS)

    Randles, Amanda Elizabeth

    the modeling of fluids in vessels with smaller diameters and a method for introducing the deformational forces exerted on the arterial flows from the movement of the heart by borrowing concepts from cosmodynamics are presented. These additional forces have a great impact on the endothelial shear stress. Third, the fluid model is extended to not only recover Navier-Stokes hydrodynamics, but also a wider range of Knudsen numbers, which is especially important in micro- and nano-scale flows. The tradeoffs of many optimizations methods such as the use of deep halo level ghost cells that, alongside hybrid programming models, reduce the impact of such higher-order models and enable efficient modeling of extreme regimes of computational fluid dynamics are discussed. Fourth, the extension of these models to other research questions like clogging in microfluidic devices and determining the severity of co-arctation of the aorta is presented. Through this work, a validation of these methods by taking real patient data and the measured pressure value before the narrowing of the aorta and predicting the pressure drop across the co-arctation is shown. Comparison with the measured pressure drop in vivo highlights the accuracy and potential impact of such patient specific simulations. Finally, a method to enable the simulation of longer trajectories in time by discretizing both spatially and temporally is presented. In this method, a serial coarse iterator is used to initialize data at discrete time steps for a fine model that runs in parallel. This coarse solver is based on a larger time step and typically a coarser discretization in space. Iterative refinement enables the compute-intensive fine iterator to be modeled with temporal parallelization. The algorithm consists of a series of prediction-corrector iterations completing when the results have converged within a certain tolerance. Combined, these developments allow large fluid models to be simulated for longer time durations

  2. Massively Parallel Geostatistical Inversion of Coupled Processes in Heterogeneous Porous Media

    NASA Astrophysics Data System (ADS)

    Ngo, A.; Schwede, R. L.; Li, W.; Bastian, P.; Ippisch, O.; Cirpka, O. A.

    2012-04-01

    another level of parallelization has been added.

  3. Massively-parallel neuromonitoring and neurostimulation rodent headset with nanotextured flexible microelectrodes.

    PubMed

    Bagheri, Arezu; Gabran, S R I; Salam, Muhammad Tariqus; Perez Velazquez, Jose Luis; Mansour, Raafat R; Salama, M M A; Genov, Roman

    2013-10-01

    We present a compact wireless headset for simultaneous multi-site neuromonitoring and neurostimulation in the rodent brain. The system comprises flexible-shaft microelectrodes, neural amplifiers, neurostimulators, a digital time-division multiplexer (TDM), a micro-controller and a ZigBee wireless transceiver. The system is built by parallelizing up to four 0.35 μm CMOS integrated circuits (each having 256 neural amplifiers and 64 neurostimulators) to provide a total maximum of 1024 neural amplifiers and 256 neurostimulators. Each bipolar neural amplifier features 54 dB-72 dB adjustable gain, 1 Hz-5 kHz adjustable bandwidth with an input-referred noise of 7.99 μVrms and dissipates 12.9 μW. Each current-mode bipolar neurostimulator generates programmable arbitrary-waveform biphasic current in the range of 20-250 μA and dissipates 2.6 μW in the stand-by mode. Reconfigurability is provided by stacking a set of dedicated mini-PCBs that share a common signaling bus within as small as 22 × 30 × 15 mm³ volume. The system features flexible polyimide-based microelectrode array design that is not brittle and increases pad packing density. Pad nanotexturing by electrodeposition reduces the electrode-tissue interface impedance from an average of 2 MΩ to 30 kΩ at 100 Hz. The rodent headset and the microelectrode array have been experimentally validated in vivo in freely moving rats for two months. We demonstrate 92.8 percent seizure rate reduction by responsive neurostimulation in an acute epilepsy rat model.

  4. Massively-parallel neuromonitoring and neurostimulation rodent headset with nanotextured flexible microelectrodes.

    PubMed

    Bagheri, Arezu; Gabran, S R I; Salam, Muhammad Tariqus; Perez Velazquez, Jose Luis; Mansour, Raafat R; Salama, M M A; Genov, Roman

    2013-10-01

    We present a compact wireless headset for simultaneous multi-site neuromonitoring and neurostimulation in the rodent brain. The system comprises flexible-shaft microelectrodes, neural amplifiers, neurostimulators, a digital time-division multiplexer (TDM), a micro-controller and a ZigBee wireless transceiver. The system is built by parallelizing up to four 0.35 μm CMOS integrated circuits (each having 256 neural amplifiers and 64 neurostimulators) to provide a total maximum of 1024 neural amplifiers and 256 neurostimulators. Each bipolar neural amplifier features 54 dB-72 dB adjustable gain, 1 Hz-5 kHz adjustable bandwidth with an input-referred noise of 7.99 μVrms and dissipates 12.9 μW. Each current-mode bipolar neurostimulator generates programmable arbitrary-waveform biphasic current in the range of 20-250 μA and dissipates 2.6 μW in the stand-by mode. Reconfigurability is provided by stacking a set of dedicated mini-PCBs that share a common signaling bus within as small as 22 × 30 × 15 mm³ volume. The system features flexible polyimide-based microelectrode array design that is not brittle and increases pad packing density. Pad nanotexturing by electrodeposition reduces the electrode-tissue interface impedance from an average of 2 MΩ to 30 kΩ at 100 Hz. The rodent headset and the microelectrode array have been experimentally validated in vivo in freely moving rats for two months. We demonstrate 92.8 percent seizure rate reduction by responsive neurostimulation in an acute epilepsy rat model. PMID:24144667

  5. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

    PubMed Central

    Stoeck, Thorsten; Behnke, Anke; Christen, Richard; Amaral-Zettler, Linda; Rodriguez-Mora, Maria J; Chistoserdov, Andrei; Orsi, William; Edgcomb, Virginia P

    2009-01-01

    Background Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets. Results The analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries and Sanger sequencing. More than 90% of this diversity was represented by OTUs with less than 10 sequence tags. We detected a substantial number of taxonomic groups like Apusozoa, Chrysomerophytes, Centroheliozoa, Eustigmatophytes, hyphochytriomycetes, Ichthyosporea, Oikomonads, Phaeothamniophytes, and rhodophytes which remained undetected by previous clone library-based diversity surveys of the sampling sites. The most important innovations in our newly developed bioinformatics pipeline employ (i) BLASTN with query parameters adjusted for highly variable domains and a complete database of public ribosomal RNA (rRNA) gene sequences for taxonomic assignments of tags; (ii

  6. LiNbO3: A photovoltaic substrate for massive parallel manipulation and patterning of nano-objects

    NASA Astrophysics Data System (ADS)

    Carrascosa, M.; García-Cabañes, A.; Jubera, M.; Ramiro, J. B.; Agulló-López, F.

    2015-12-01

    The application of evanescent photovoltaic (PV) fields, generated by visible illumination of Fe:LiNbO3 substrates, for parallel massive trapping and manipulation of micro- and nano-objects is critically reviewed. The technique has been often referred to as photovoltaic or photorefractive tweezers. The main advantage of the new method is that the involved electrophoretic and/or dielectrophoretic forces do not require any electrodes and large scale manipulation of nano-objects can be easily achieved using the patterning capabilities of light. The paper describes the experimental techniques for particle trapping and the main reported experimental results obtained with a variety of micro- and nano-particles (dielectric and conductive) and different illumination configurations (single beam, holographic geometry, and spatial light modulator projection). The report also pays attention to the physical basis of the method, namely, the coupling of the evanescent photorefractive fields to the dielectric response of the nano-particles. The role of a number of physical parameters such as the contrast and spatial periodicities of the illumination pattern or the particle deposition method is discussed. Moreover, the main properties of the obtained particle patterns in relation to potential applications are summarized, and first demonstrations reviewed. Finally, the PV method is discussed in comparison to other patterning strategies, such as those based on the pyroelectric response and the electric fields associated to domain poling of ferroelectric materials.

  7. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

    SciTech Connect

    Gihring, Thomas; Green, Stefan; Schadt, Christopher Warren

    2011-01-01

    Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g. Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.

  8. Massively parallel and highly quantitative single-particle analysis on interactions between nanoparticles on supported lipid bilayer.

    PubMed

    Lee, Young Kwang; Kim, Sungi; Oh, Jeong-Wook; Nam, Jwa-Min

    2014-03-12

    Observation of individual single-nanoparticle reactions provides direct information and insight for many complex chemical, physical, and biological processes, but this is utterly challenging with conventional high-resolution imaging techniques on conventional platforms. Here, we developed a photostable plasmonic nanoparticle-modified supported lipid bilayer (PNP-SLB) platform that allows for massively parallel in situ analysis of the interactions between nanoparticles with single-particle resolution on a two-dimensional (2D) fluidic surface. Each particle-by-particle PNP clustering process was monitored in real time and quantified via analysis of individual particle diffusion trajectories and single-particle-level plasmonic coupling. Importantly, the PNP-SLB-based nanoparticle cluster growth kinetics result was fitted well. As an application example, we performed a DNA detection assay, and the result suggests that our approach has very promising sensitivity and dynamic range (high attomolar to high femtomolar) without optimization, as well as remarkable single-base mismatch discrimination capability. The method shown herein can be readily applied for many different types of intermolecular and interparticle interactions and provide convenient tools and new insights for studying dynamic interactions on a highly controllable and analytical platform.

  9. Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy.

    PubMed

    Papadopoulos, Dimitrios K; Krmpot, Aleksandar J; Nikolić, Stanko N; Krautz, Robert; Terenius, Lars; Tomancak, Pavel; Rigler, Rudolf; Gehring, Walter J; Vukojević, Vladana

    2015-11-01

    Hox genes encode transcription factors that control the formation of body structures, segment-specifically along the anterior-posterior axis of metazoans. Hox transcription factors bind nuclear DNA pervasively and regulate a plethora of target genes, deploying various molecular mechanisms that depend on the developmental and cellular context. To analyze quantitatively the dynamics of their DNA-binding behavior we have used confocal laser scanning microscopy (CLSM), single-point fluorescence correlation spectroscopy (FCS), fluorescence cross-correlation spectroscopy (FCCS) and bimolecular fluorescence complementation (BiFC). We show that the Hox transcription factor Sex combs reduced (Scr) forms dimers that strongly associate with its specific fork head binding site (fkh250) in live salivary gland cell nuclei. In contrast, dimers of a constitutively inactive, phospho-mimicking variant of Scr show weak, non-specific DNA-binding. Our studies reveal that nuclear dynamics of Scr is complex, exhibiting a changing landscape of interactions that is difficult to characterize by probing one point at a time. Therefore, we also provide mechanistic evidence using massively parallel FCS (mpFCS). We found that Scr dimers are predominantly formed on the DNA and are equally abundant at the chromosomes and an introduced multimeric fkh250 binding-site, indicating different mobilities, presumably reflecting transient binding with different affinities on the DNA. Our proof-of-principle results emphasize the advantages of mpFCS for quantitative characterization of fast dynamic processes in live cells.

  10. Non-CAR resists and advanced materials for Massively Parallel E-Beam Direct Write process integration

    NASA Astrophysics Data System (ADS)

    Pourteau, Marie-Line; Servin, Isabelle; Lepinay, Kévin; Essomba, Cyrille; Dal'Zotto, Bernard; Pradelles, Jonathan; Lattard, Ludovic; Brandt, Pieter; Wieland, Marco

    2016-03-01

    The emerging Massively Parallel-Electron Beam Direct Write (MP-EBDW) is an attractive high resolution high throughput lithography technology. As previously shown, Chemically Amplified Resists (CARs) meet process/integration specifications in terms of dose-to-size, resolution, contrast, and energy latitude. However, they are still limited by their line width roughness. To overcome this issue, we tested an alternative advanced non-CAR and showed it brings a substantial gain in sensitivity compared to CAR. We also implemented and assessed in-line post-lithographic treatments for roughness mitigation. For outgassing-reduction purpose, a top-coat layer is added to the total process stack. A new generation top-coat was tested and showed improved printing performances compared to the previous product, especially avoiding dark erosion: SEM cross-section showed a straight pattern profile. A spin-coatable charge dissipation layer based on conductive polyaniline has also been tested for conductivity and lithographic performances, and compatibility experiments revealed that the underlying resist type has to be carefully chosen when using this product. Finally, the Process Of Reference (POR) trilayer stack defined for 5 kV multi-e-beam lithography was successfully etched with well opened and straight patterns, and no lithography-etch bias.

  11. Assessing mutant p53 in primary high-grade serous ovarian cancer using immunohistochemistry and massively parallel sequencing

    PubMed Central

    Cole, Alexander J.; Dwight, Trisha; Gill, Anthony J.; Dickson, Kristie-Ann; Zhu, Ying; Clarkson, Adele; Gard, Gregory B.; Maidens, Jayne; Valmadre, Susan; Clifton-Bligh, Roderick; Marsh, Deborah J.

    2016-01-01

    The tumour suppressor p53 is mutated in cancer, including over 96% of high-grade serous ovarian cancer (HGSOC). Mutations cause loss of wild-type p53 function due to either gain of abnormal function of mutant p53 (mutp53), or absent to low mutp53. Massively parallel sequencing (MPS) enables increased accuracy of detection of somatic variants in heterogeneous tumours. We used MPS and immunohistochemistry (IHC) to characterise HGSOCs for TP53 mutation and p53 expression. TP53 mutation was identified in 94% (68/72) of HGSOCs, 62% of which were missense. Missense mutations demonstrated high p53 by IHC, as did 35% (9/26) of non-missense mutations. Low p53 was seen by IHC in 62% of HGSOC associated with non-missense mutations. Most wild-type TP53 tumours (75%, 6/8) displayed intermediate p53 levels. The overall sensitivity of detecting a TP53 mutation based on classification as ‘Low’, ‘Intermediate’ or ‘High’ for p53 IHC was 99%, with a specificity of 75%. We suggest p53 IHC can be used as a surrogate marker of TP53 mutation in HGSOC; however, this will result in misclassification of a proportion of TP53 wild-type and mutant tumours. Therapeutic targeting of mutp53 will require knowledge of both TP53 mutations and mutp53 expression. PMID:27189670

  12. Massively parallel E-beam inspection: enabling next-generation patterned defect inspection for wafer and mask manufacturing

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    SEMATECH aims to identify and enable disruptive technologies to meet the ever-increasing demands of semiconductor high volume manufacturing (HVM). As such, a program was initiated in 2012 focused on high-speed e-beam defect inspection as a complement, and eventual successor, to bright field optical patterned defect inspection [1]. The primary goal is to enable a new technology to overcome the key gaps that are limiting modern day inspection in the fab; primarily, throughput and sensitivity to detect ultra-small critical defects. The program specifically targets revolutionary solutions based on massively parallel e-beam technologies, as opposed to incremental improvements to existing e-beam and optical inspection platforms. Wafer inspection is the primary target, but attention is also being paid to next generation mask inspection. During the first phase of the multi-year program multiple technologies were reviewed, a down-selection was made to the top candidates, and evaluations began on proof of concept systems. A champion technology has been selected and as of late 2014 the program has begun to move into the core technology maturation phase in order to enable eventual commercialization of an HVM system. Performance data from early proof of concept systems will be shown along with roadmaps to achieving HVM performance. SEMATECH's vision for moving from early-stage development to commercialization will be shown, including plans for development with industry leading technology providers.

  13. A bumpy ride on the diagnostic bench of massive parallel sequencing, the case of the mitochondrial genome.

    PubMed

    Vancampenhout, Kim; Caljon, Ben; Spits, Claudia; Stouffs, Katrien; Jonckheere, An; De Meirleir, Linda; Lissens, Willy; Vanlander, Arnaud; Smet, Joél; De Paepe, Boel; Van Coster, Rudy; Seneca, Sara

    2014-01-01

    The advent of massive parallel sequencing (MPS) has revolutionized the field of human molecular genetics, including the diagnostic study of mitochondrial (mt) DNA dysfunction. The analysis of the complete mitochondrial genome using MPS platforms is now common and will soon outrun conventional sequencing. However, the development of a robust and reliable protocol is rather challenging. A previous pilot study for the re-sequencing of human mtDNA revealed an uneven coverage, affecting predominantly part of the plus strand. In an attempt to address this problem, we undertook a comparative study of standard and modified protocols for the Ion Torrent PGM system. We could not improve strand representation by altering the recommended shearing methodology of the standard workflow or omitting the DNA polymerase amplification step from the library construction process. However, we were able to associate coverage bias of the plus strand with a specific sequence motif. Additionally, we compared coverage and variant calling across technologies. The same samples were also sequenced on a MiSeq device which showed that coverage and heteroplasmic variant calling were much improved. PMID:25383547

  14. Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels.

    PubMed

    Choi, Jung-Woo; Liao, Xiaoping; Park, Sairom; Jeon, Heoyn-Jeong; Chung, Won-Hyong; Stothard, Paul; Park, Yeon-Soo; Lee, Jeong-Koo; Lee, Kyung-Tai; Kim, Sang-Hwan; Oh, Jae-Don; Kim, Namshin; Kim, Tae-Hun; Lee, Hak-Kyo; Lee, Sung-Jin

    2013-09-01

    Since the completion of the bovine sequencing projects, a substantial number of genetic variations such as single nucleotide polymorphisms have become available across the cattle genome. Recently, cataloguing such genetic variations has been accelerated using massively parallel sequencing technology. However, most of the recent studies have been concentrated on European Bos taurus cattle breeds, resulting in a severe lack of knowledge for valuable native cattle genetic resources worldwide. Here, we present the first whole-genome sequencing results for an endangered Korean native cattle breed, Chikso, using the Illumina HiSeq 2,000 sequencing platform. The genome of a Chikso bull was sequenced to approximately 25.3-fold coverage with 98.8% of the bovine reference genome sequence (UMD 3.1) covered. In total, 5,874,026 single nucleotide polymorphisms and 551,363 insertion/deletions were identified across all 29 autosomes and the X-chromosome, of which 45% and 75% were previously unknown, respectively. Most of the variations (92.7% of single nucleotide polymorphisms and 92.9% of insertion/deletions) were located in intergenic and intron regions. A total of 16,273 single nucleotide polymorphisms causing missense mutations were detected in 7,111 genes throughout the genome, which could potentially contribute to variation in economically important traits in Chikso. This study provides a valuable resource for further investigations of the genetic mechanisms underlying traits of interest in cattle, and for the development of improved genomics-based breeding tools.

  15. 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

  16. LiNbO{sub 3}: A photovoltaic substrate for massive parallel manipulation and patterning of nano-objects

    SciTech Connect

    Carrascosa, M.; García-Cabañes, A.; Jubera, M.; Ramiro, J. B.; Agulló-López, F.

    2015-12-15

    The application of evanescent photovoltaic (PV) fields, generated by visible illumination of Fe:LiNbO{sub 3} substrates, for parallel massive trapping and manipulation of micro- and nano-objects is critically reviewed. The technique has been often referred to as photovoltaic or photorefractive tweezers. The main advantage of the new method is that the involved electrophoretic and/or dielectrophoretic forces do not require any electrodes and large scale manipulation of nano-objects can be easily achieved using the patterning capabilities of light. The paper describes the experimental techniques for particle trapping and the main reported experimental results obtained with a variety of micro- and nano-particles (dielectric and conductive) and different illumination configurations (single beam, holographic geometry, and spatial light modulator projection). The report also pays attention to the physical basis of the method, namely, the coupling of the evanescent photorefractive fields to the dielectric response of the nano-particles. The role of a number of physical parameters such as the contrast and spatial periodicities of the illumination pattern or the particle deposition method is discussed. Moreover, the main properties of the obtained particle patterns in relation to potential applications are summarized, and first demonstrations reviewed. Finally, the PV method is discussed in comparison to other patterning strategies, such as those based on the pyroelectric response and the electric fields associated to domain poling of ferroelectric materials.

  17. Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system.

    PubMed

    van der Gaag, Kristiaan J; de Leeuw, Rick H; Hoogenboom, Jerry; Patel, Jaynish; Storts, Douglas R; Laros, Jeroen F J; de Knijff, Peter

    2016-09-01

    Current forensic DNA analysis predominantly involves identification of human donors by analysis of short tandem repeats (STRs) using Capillary Electrophoresis (CE). Recent developments in Massively Parallel Sequencing (MPS) technologies offer new possibilities in analysis of STRs since they might overcome some of the limitations of CE analysis. In this study 17 STRs and Amelogenin were sequenced in high coverage using a prototype version of the Promega PowerSeq™ system for 297 population samples from the Netherlands, Nepal, Bhutan and Central African Pygmies. In addition, 45 two-person mixtures with different minor contributions down to 1% were analysed to investigate the performance of this system for mixed samples. Regarding fragment length, complete concordance between the MPS and CE-based data was found, marking the reliability of MPS PowerSeq™ system. As expected, MPS presented a broader allele range and higher power of discrimination and exclusion rate. The high coverage sequencing data were used to determine stutter characteristics for all loci and stutter ratios were compared to CE data. The separation of alleles with the same length but exhibiting different stutter ratios lowers the overall variation in stutter ratio and helps in differentiation of stutters from genuine alleles in mixed samples. All alleles of the minor contributors were detected in the sequence reads even for the 1% contributions, but analysis of mixtures below 5% without prior information of the mixture ratio is complicated by PCR and sequencing artefacts.

  18. 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.

  19. A bumpy ride on the diagnostic bench of massive parallel sequencing, the case of the mitochondrial genome.

    PubMed

    Vancampenhout, Kim; Caljon, Ben; Spits, Claudia; Stouffs, Katrien; Jonckheere, An; De Meirleir, Linda; Lissens, Willy; Vanlander, Arnaud; Smet, Joél; De Paepe, Boel; Van Coster, Rudy; Seneca, Sara

    2014-01-01

    The advent of massive parallel sequencing (MPS) has revolutionized the field of human molecular genetics, including the diagnostic study of mitochondrial (mt) DNA dysfunction. The analysis of the complete mitochondrial genome using MPS platforms is now common and will soon outrun conventional sequencing. However, the development of a robust and reliable protocol is rather challenging. A previous pilot study for the re-sequencing of human mtDNA revealed an uneven coverage, affecting predominantly part of the plus strand. In an attempt to address this problem, we undertook a comparative study of standard and modified protocols for the Ion Torrent PGM system. We could not improve strand representation by altering the recommended shearing methodology of the standard workflow or omitting the DNA polymerase amplification step from the library construction process. However, we were able to associate coverage bias of the plus strand with a specific sequence motif. Additionally, we compared coverage and variant calling across technologies. The same samples were also sequenced on a MiSeq device which showed that coverage and heteroplasmic variant calling were much improved.

  20. Determination of the Allelic Frequency in Smith-Lemli-Opitz Syndrome by Analysis of Massively Parallel Sequencing Data Sets

    PubMed Central

    Cross, Joanna L.; Iben, James; Simpson, Claire; Thurm, Audrey; Swedo, Susan; Tierney, Elaine; Bailey-Wilson, Joan; Biesecker, Leslie G.; Porter, Forbes D.; Wassif, Christopher A.

    2014-01-01

    Data from massively parallel sequencing or “Next Generation Sequencing” of the human exome has reached a critical mass in both public and private databases, in that these collections now allow researchers to critically evaluate population genetics in a manner that was not feasible a decade ago. The ability to determine pathogenic allele frequencies by evaluation of the full coding sequences and not merely a single SNP or series of SNPs will lead to more accurate estimations of incidence. For demonstrative purposes we analyzed the causative gene for the disorder Smith-Lemli-Opitz Syndrome (SLOS), the 7-dehydrocholesterol reductase (DHCR7) gene and determined both the carrier frequency for DHCR7 mutations, and predicted an expected incidence of the disorder. Estimations of the incidence of SLOS have ranged widely from 1:10,000 to 1:70,000 while the carrier frequency has been reported as high as 1 in 30. Using four exome data sets with a total of 17,836 chromosomes, we ascertained a carrier frequency of pathogenic DHRC7 mutations of 1.01%, and predict a SLOS disease incidence of 1/39,215 conceptions. This approach highlights yet another valuable aspect of the exome sequencing databases, to inform clinical and health policy decisions related to genetic counseling, prenatal testing and newborn screening. PMID:24813812

  1. A massively parallel track-finding system for the LEVEL 2 trigger in the CLAS detector at CEBAF

    SciTech Connect

    Doughty, D.C. Jr.; Collins, P.; Lemon, S. ); Bonneau, P. )

    1994-02-01

    The track segment finding subsystem of the LEVEL 2 trigger in the CLAS detector has been designed and prototyped. Track segments will be found in the 35,076 wires of the drift chambers using a massively parallel array of 768 Xilinx XC-4005 FPGA's. These FPGA's are located on daughter cards attached to the front-end boards distributed around the detector. Each chip is responsible for finding tracks passing through a 4 x 6 slice of an axial superlayer, and reports two segment found bits, one for each pair of cells. The algorithm used finds segments even when one or two layers or cells along the track is missing (this number is programmable), while being highly resistant to false segments arising from noise hits. Adjacent chips share data to find tracks crossing cell and board boundaries. For maximum speed, fully combinatorial logic is used inside each chip, with the result that all segments in the detector are found within 150 ns. Segment collection boards gather track segments from each axial superlayer and pass them via a high speed link to the segment linking subsystem in an additional 400 ns for typical events. The Xilinx chips are ram-based and therefore reprogrammable, allowing for future upgrades and algorithm enhancements.

  2. HLA-F coding and regulatory segments variability determined by massively parallel sequencing procedures in a Brazilian population sample.

    PubMed

    Lima, Thálitta Hetamaro Ayala; Buttura, Renato Vidal; Donadi, Eduardo Antônio; Veiga-Castelli, Luciana Caricati; Mendes-Junior, Celso Teixeira; Castelli, Erick C

    2016-10-01

    Human Leucocyte Antigen F (HLA-F) is a non-classical HLA class I gene distinguished from its classical counterparts by low allelic polymorphism and distinctive expression patterns. Its exact function remains unknown. It is believed that HLA-F has tolerogenic and immune modulatory properties. Currently, there is little information regarding the HLA-F allelic variation among human populations and the available studies have evaluated only a fraction of the HLA-F gene segment and/or have searched for known alleles only. Here we present a strategy to evaluate the complete HLA-F variability including its 5' upstream, coding and 3' downstream segments by using massively parallel sequencing procedures. HLA-F variability was surveyed on 196 individuals from the Brazilian Southeast. The results indicate that the HLA-F gene is indeed conserved at the protein level, where thirty coding haplotypes or coding alleles were detected, encoding only four different HLA-F full-length protein molecules. Moreover, a same protein molecule is encoded by 82.45% of all coding alleles detected in this Brazilian population sample. However, the HLA-F nucleotide and haplotype variability is much higher than our current knowledge both in Brazilians and considering the 1000 Genomes Project data. This protein conservation is probably a consequence of the key role of HLA-F in the immune system physiology.

  3. Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system.

    PubMed

    van der Gaag, Kristiaan J; de Leeuw, Rick H; Hoogenboom, Jerry; Patel, Jaynish; Storts, Douglas R; Laros, Jeroen F J; de Knijff, Peter

    2016-09-01

    Current forensic DNA analysis predominantly involves identification of human donors by analysis of short tandem repeats (STRs) using Capillary Electrophoresis (CE). Recent developments in Massively Parallel Sequencing (MPS) technologies offer new possibilities in analysis of STRs since they might overcome some of the limitations of CE analysis. In this study 17 STRs and Amelogenin were sequenced in high coverage using a prototype version of the Promega PowerSeq™ system for 297 population samples from the Netherlands, Nepal, Bhutan and Central African Pygmies. In addition, 45 two-person mixtures with different minor contributions down to 1% were analysed to investigate the performance of this system for mixed samples. Regarding fragment length, complete concordance between the MPS and CE-based data was found, marking the reliability of MPS PowerSeq™ system. As expected, MPS presented a broader allele range and higher power of discrimination and exclusion rate. The high coverage sequencing data were used to determine stutter characteristics for all loci and stutter ratios were compared to CE data. The separation of alleles with the same length but exhibiting different stutter ratios lowers the overall variation in stutter ratio and helps in differentiation of stutters from genuine alleles in mixed samples. All alleles of the minor contributors were detected in the sequence reads even for the 1% contributions, but analysis of mixtures below 5% without prior information of the mixture ratio is complicated by PCR and sequencing artefacts. PMID:27347657

  4. 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

  5. Evaluation of cells and biological reagents for adventitious agents using degenerate primer PCR and massively parallel sequencing.

    PubMed

    McClenahan, Shasta D; Uhlenhaut, Christine; Krause, Philip R

    2014-12-12

    We employed a massively parallel sequencing (MPS)-based approach to test reagents and model cell substrates including Chinese hamster ovary (CHO), Madin-Darby canine kidney (MDCK), African green monkey kidney (Vero), and High Five insect cell lines for adventitious agents. RNA and DNA were extracted either directly from the samples or from viral capsid-enriched preparations, and then subjected to MPS-based non-specific virus detection with degenerate oligonucleotide primer (DOP) PCR. MPS by 454, Illumina MiSeq, and Illumina HiSeq was compared on independent samples. Virus detection using these methods was reproducibly achieved. Unclassified sequences from CHO cells represented cellular sequences not yet submitted to the databases typically used for sequence identification. The sensitivity of MPS-based virus detection was consistent with theoretically expected limits based on dilution of virus in cellular nucleic acids. Capsid preparation increased the number of viral sequences detected. Potential viral sequences were detected in several samples; in each case, these sequences were either artifactual or (based on additional studies) shown not to be associated with replication-competent viruses. Virus-like sequences were more likely to be identified in BLAST searches using virus-specific databases that did not contain cellular sequences. Detected viral sequences included previously described retrovirus and retrovirus-like sequences in CHO, Vero, MDCK and High Five cells, and nodavirus and endogenous bracovirus sequences in High Five insect cells. Bovine viral diarrhea virus, bovine hokovirus, and porcine circovirus sequences were detected in some reagents. A recently described parvo-like virus present in some nucleic acid extraction resins was also identified in cells and extraction controls from some samples. The present study helps to illustrate the potential for MPS-based strategies in evaluating the presence of viral nucleic acids in various sample types

  6. Comprehensive massive parallel DNA sequencing strategy for the genetic diagnosis of the neuro-cardio-facio-cutaneous syndromes.

    PubMed

    Justino, Ana; Dias, Patrícia; João Pina, Maria; Sousa, Sónia; Cirnes, Luís; Berta Sousa, Ana; Carlos Machado, José; Costa, José Luis

    2015-03-01

    Variants in 11 genes of the RAS/MAPK signaling pathway have been causally linked to the neuro-cardio-facio-cutaneous syndromes group (NCFCS). Recently, A2ML1 and RIT1 were also associated with these syndromes. Because of the genetic and clinical heterogeneity of NCFCS, it is challenging to define strategies for their molecular diagnosis. The aim of this study was to develop and validate a massive parallel sequencing (MPS)-based strategy for the molecular diagnosis of NCFCS. A multiplex PCR-based strategy for the enrichment of the 13 genes and a variant prioritization pipeline was established. Two sets of genomic DNA samples were studied using the Ion PGM System: (1) training set (n =15) to optimize the strategy and (2) validation set (n = 20) to validate and evaluate the power of the new methodology. Sanger sequencing was performed to confirm all variants and low covered regions. All variants identified by Sanger sequencing were detected with our MPS approach. The methodology resulted in an experimental approach with a specificity of 99.0% and a maximum analytical sensitivity of ≥ 98.2% with a confidence of 99%. Importantly, two patients (out of 20) harbored described disease-causing variants in genes that are not routinely tested (RIT1 and SHOC2). The addition of less frequently altered genes increased in ≈ 10% the diagnostic yield of the strategy currently used. The presented workflow provides a comprehensive genetic screening strategy for patients with NCFCS in a fast and cost-efficient manner. This approach demonstrates the potential of a combined MPS-Sanger sequencing-based strategy as an effective diagnostic tool for heterogeneous diseases.

  7. Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing.

    PubMed

    Ross, E M; Moate, P J; Marett, L; Cocks, B G; Hayes, B J

    2013-09-01

    Variation in the composition of microorganisms in the rumen (the rumen microbiome) of dairy cattle (Bos taurus) is of great interest because of possible links to methane emission levels. Feed additives are one method being investigated to reduce enteric methane production by dairy cattle. Here we report the effect of 2 methane-mitigating feed additives (grapemarc and a combination of lipids and tannin) on rumen microbiome profiles of Holstein dairy cattle. We used untargeted (shotgun) massively parallel sequencing of microbes present in rumen fluid to generate quantitative rumen microbiome profiles. We observed large effects of the feed additives on the rumen microbiome profiles using multiple approaches, including linear mixed modeling, hierarchical clustering, and metagenomic predictions. The effect on the fecal microbiome profiles was not detectable using hierarchical clustering, but was significant in the linear mixed model and when metagenomic predictions were used, suggesting a more subtle effect of the diets on the lower gastrointestinal microbiome. A differential representation analysis (analogous to differential expression in RNA sequencing) showed significant overlap in the contigs (which are genome fragments representing different microorganism species) that were differentially represented between experiments. These similarities suggest that, despite the different additives used, the 2 diets assessed in this investigation altered the microbiomes of the samples in similar ways. Contigs that were differentially represented in both experiments were tested for associations with methane production in an independent set of animals. These animals were not treated with a methane-mitigating diet, but did show substantial natural variation in methane emission levels. The contigs that were significantly differentially represented in response to both dietary additives showed a significant enrichment for associations with methane production. This suggests that these

  8. My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing.

    PubMed

    Van Neste, Christophe; Vandewoestyne, Mado; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

    2014-03-01

    Forensic scientists are currently investigating how to transition from capillary electrophoresis (CE) to massive parallel sequencing (MPS) for analysis of forensic DNA profiles. MPS offers several advantages over CE such as virtually unlimited multiplexy of loci, combining both short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci, small amplicons without constraints of size separation, more discrimination power, deep mixture resolution and sample multiplexing. We present our bioinformatic framework My-Forensic-Loci-queries (MyFLq) for analysis of MPS forensic data. For allele calling, the framework uses a MySQL reference allele database with automatically determined regions of interest (ROIs) by a generic maximal flanking algorithm which makes it possible to use any STR or SNP forensic locus. Python scripts were designed to automatically make allele calls starting from raw MPS data. We also present a method to assess the usefulness and overall performance of a forensic locus with respect to MPS, as well as methods to estimate whether an unknown allele, which sequence is not present in the MySQL database, is in fact a new allele or a sequencing error. The MyFLq framework was applied to an Illumina MiSeq dataset of a forensic Illumina amplicon library, generated from multilocus STR polymerase chain reaction (PCR) on both single contributor samples and multiple person DNA mixtures. Although the multilocus PCR was not yet optimized for MPS in terms of amplicon length or locus selection, the results show excellent results for most loci. The results show a high signal-to-noise ratio, correct allele calls, and a low limit of detection for minor DNA contributors in mixed DNA samples. Technically, forensic MPS affords great promise for routine implementation in forensic genomics. The method is also applicable to adjacent disciplines such as molecular autopsy in legal medicine and in mitochondrial DNA research.

  9. Evaluation of cells and biological reagents for adventitious agents using degenerate primer PCR and massively parallel sequencing.

    PubMed

    McClenahan, Shasta D; Uhlenhaut, Christine; Krause, Philip R

    2014-12-12

    We employed a massively parallel sequencing (MPS)-based approach to test reagents and model cell substrates including Chinese hamster ovary (CHO), Madin-Darby canine kidney (MDCK), African green monkey kidney (Vero), and High Five insect cell lines for adventitious agents. RNA and DNA were extracted either directly from the samples or from viral capsid-enriched preparations, and then subjected to MPS-based non-specific virus detection with degenerate oligonucleotide primer (DOP) PCR. MPS by 454, Illumina MiSeq, and Illumina HiSeq was compared on independent samples. Virus detection using these methods was reproducibly achieved. Unclassified sequences from CHO cells represented cellular sequences not yet submitted to the databases typically used for sequence identification. The sensitivity of MPS-based virus detection was consistent with theoretically expected limits based on dilution of virus in cellular nucleic acids. Capsid preparation increased the number of viral sequences detected. Potential viral sequences were detected in several samples; in each case, these sequences were either artifactual or (based on additional studies) shown not to be associated with replication-competent viruses. Virus-like sequences were more likely to be identified in BLAST searches using virus-specific databases that did not contain cellular sequences. Detected viral sequences included previously described retrovirus and retrovirus-like sequences in CHO, Vero, MDCK and High Five cells, and nodavirus and endogenous bracovirus sequences in High Five insect cells. Bovine viral diarrhea virus, bovine hokovirus, and porcine circovirus sequences were detected in some reagents. A recently described parvo-like virus present in some nucleic acid extraction resins was also identified in cells and extraction controls from some samples. The present study helps to illustrate the potential for MPS-based strategies in evaluating the presence of viral nucleic acids in various sample types

  10. Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting

    PubMed Central

    2013-01-01

    Background Targeted capture, combined with massively-parallel sequencing, is a powerful technique that allows investigation of specific portions of the genome for less cost than whole genome sequencing. Several methods have been developed, and improvements have resulted in commercial products targeting the human or mouse exonic regions (the exome). In some cases it is desirable to custom-target other regions of the genome, either to reduce the amount of sequence that is targeted or to capture regions that are not targeted by commercial kits. It is important to understand the advantages, limitations, and complexity of a given capture method before embarking on a targeted sequencing experiment. Results We compared two custom targeted capture methods suitable for single chromosome analysis: Solution Hybrid Selection (SHS) and Flow Sorting (FS) of single chromosomes. Both methods can capture targeted material and result in high percentages of genotype identifications across these regions: 59-92% for SHS and 70-79% for FS. FS is amenable to current structural variation detection methods, and variants were detected. Structural variation was also assessed for SHS samples with paired end sequencing, resulting in variant identification. Conclusions While both methods can effectively target genomic regions for genotype determination, several considerations make each method appropriate in different circumstances. SHS is well suited for experiments targeting smaller regions in a larger number of samples. FS is well suited when regions of interest cover large regions of a single chromosome. Although whole genome sequencing is becoming less expensive, the sequencing, data storage, and analysis costs make targeted sequencing using SHS or FS a compelling option. PMID:23586822

  11. Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing.

    PubMed

    Ross, E M; Moate, P J; Marett, L; Cocks, B G; Hayes, B J

    2013-09-01

    Variation in the composition of microorganisms in the rumen (the rumen microbiome) of dairy cattle (Bos taurus) is of great interest because of possible links to methane emission levels. Feed additives are one method being investigated to reduce enteric methane production by dairy cattle. Here we report the effect of 2 methane-mitigating feed additives (grapemarc and a combination of lipids and tannin) on rumen microbiome profiles of Holstein dairy cattle. We used untargeted (shotgun) massively parallel sequencing of microbes present in rumen fluid to generate quantitative rumen microbiome profiles. We observed large effects of the feed additives on the rumen microbiome profiles using multiple approaches, including linear mixed modeling, hierarchical clustering, and metagenomic predictions. The effect on the fecal microbiome profiles was not detectable using hierarchical clustering, but was significant in the linear mixed model and when metagenomic predictions were used, suggesting a more subtle effect of the diets on the lower gastrointestinal microbiome. A differential representation analysis (analogous to differential expression in RNA sequencing) showed significant overlap in the contigs (which are genome fragments representing different microorganism species) that were differentially represented between experiments. These similarities suggest that, despite the different additives used, the 2 diets assessed in this investigation altered the microbiomes of the samples in similar ways. Contigs that were differentially represented in both experiments were tested for associations with methane production in an independent set of animals. These animals were not treated with a methane-mitigating diet, but did show substantial natural variation in methane emission levels. The contigs that were significantly differentially represented in response to both dietary additives showed a significant enrichment for associations with methane production. This suggests that these

  12. Three-dimensional gyrokinetic particle-in-cell simulation of plasmas on a massively parallel computer: Final report on LDRD Core Competency Project, FY 1991--FY 1993

    SciTech Connect

    Byers, J.A.; Williams, T.J.; Cohen, B.I.; Dimits, A.M.

    1994-04-27

    One of the programs of the Magnetic fusion Energy (MFE) Theory and computations Program is studying the anomalous transport of thermal energy across the field lines in the core of a tokamak. We use the method of gyrokinetic particle-in-cell simulation in this study. For this LDRD project we employed massively parallel processing, new algorithms, and new algorithms, and new formal techniques to improve this research. Specifically, we sought to take steps toward: researching experimentally-relevant parameters in our simulations, learning parallel computing to have as a resource for our group, and achieving a 100 {times} speedup over our starting-point Cray2 simulation code`s performance.

  13. Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward 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

    2015-06-01

    In this article, we present a parallel 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 and 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 of a polarizable model that makes 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 nonoptimized, sequential implementations, giving new directions for polarizable molecular dynamics with periodic boundary conditions using massively parallel implementations. PMID:26575557

  14. 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.

  15. Unintended Pulmonary Artery Ligation during PDA Ligation.

    PubMed

    Kim, Dohun; Kim, Si-Wook; Shin, Hong-Ju; Hong, Jong-Myeon; Lee, Ji Hyuk; Han, Heon-Seok

    2016-01-01

    A 10-day-old boy was transferred to our hospital due to tachypnea. Patent ductus arteriosus (PDA), 4.8 mm in diameter, with small ASD was diagnosed on echocardiography. Surgical ligation of the ductus was performed after failure of three cycles of ibuprofen. However, the ductus remained open on routine postoperative echocardiography on the second postoperative day, and chest CT revealed inadvertent ligation of the left pulmonary artery (LPA) rather than the PDA. Emergent operation successfully reopened the clipped LPA and ligated the ductus on the same (second postoperative) day.Mechanical ventilator support was weaned on postoperative day 21, and the baby was discharged on postoperative day 47 with a normal left lung shadow. PMID:27585199

  16. Complete data preparation flow for Massively Parallel E-Beam lithography on 28nm node full-field design

    NASA Astrophysics Data System (ADS)

    Fay, Aurélien; Browning, Clyde; Brandt, Pieter; Chartoire, Jacky; Bérard-Bergery, Sébastien; Hazart, Jérôme; Chagoya, Alexandre; Postnikov, Sergei; Saib, Mohamed; Lattard, Ludovic; Schavione, Patrick

    2016-03-01

    Massively parallel mask-less electron beam lithography (MP-EBL) offers a large intrinsic flexibility at a low cost of ownership in comparison to conventional optical lithography tools. This attractive direct-write technique needs a dedicated data preparation flow to correct both electronic and resist processes. Moreover, Data Prep has to be completed in a short enough time to preserve the flexibility advantage of MP-EBL. While the MP-EBL tools have currently entered an advanced stage of development, this paper will focus on the data preparation side of the work for specifically the MAPPER Lithography FLX-1200 tool [1]-[4], using the ASELTA Nanographics Inscale software. The complete flow as well as the methodology used to achieve a full-field layout data preparation, within an acceptable cycle time, will be presented. Layout used for Data Prep evaluation was one of a 28 nm technology node Metal1 chip with a field size of 26x33mm2, compatible with typical stepper/scanner field sizes and wafer stepping plans. Proximity Effect Correction (PEC) was applied to the entire field, which was then exported as a single file to MAPPER Lithography's machine format, containing fractured shapes and dose assignments. The Soft Edge beam to beam stitching method was employed in the specific overlap regions defined by the machine format as well. In addition to PEC, verification of the correction was included as part of the overall data preparation cycle time. This verification step was executed on the machine file format to ensure pattern fidelity and accuracy as late in the flow as possible. Verification over the full chip, involving billions of evaluation points, is performed both at nominal conditions and at Process Window corners in order to ensure proper exposure and process latitude. The complete MP-EBL data preparation flow was demonstrated for a 28 nm node Metal1 layout in 37 hours. The final verification step shows that the Edge Placement Error (EPE) is kept below 2.25 nm

  17. Massively-parallel electron dynamics calculations in real-time and real-space: Toward applications to nanostructures of more than ten-nanometers in size

    SciTech Connect

    Noda, Masashi; Ishimura, Kazuya; Nobusada, Katsuyuki; Yabana, Kazuhiro; Boku, Taisuke

    2014-05-15

    A highly efficient program of massively parallel calculations for electron dynamics has been developed in an effort to apply the method to optical response of nanostructures of more than ten-nanometers in size. The approach is based on time-dependent density functional theory calculations in real-time and real-space. The computational code is implemented by using simple algorithms with a finite-difference method in space derivative and Taylor expansion in time-propagation. Since the computational program is free from the algorithms of eigenvalue problems and fast-Fourier-transformation, which are usually implemented in conventional quantum chemistry or band structure calculations, it is highly suitable for massively parallel calculations. Benchmark calculations using the K computer at RIKEN demonstrate that the parallel efficiency of the program is very high on more than 60 000 CPU cores. The method is applied to optical response of arrays of C{sub 60} orderly nanostructures of more than 10 nm in size. The computed absorption spectrum is in good agreement with the experimental observation.

  18. 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

  19. 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.

  20. 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; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

    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.

  1. 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.

  2. 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

    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.

  3. 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.

  4. 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.

  5. Tubal ligation (image)

    MedlinePlus

    Surgical sterilization which permanently prevents the transport of the egg to the uterus by means of sealing the fallopian tubes is called tubal ligation, commonly called "having one's tubes tied". This operation ...

  6. Tubal ligation - discharge

    MedlinePlus

    ... Tubal sterilization - discharge; Tube tying - discharge; Tying the tubes - discharge; Contraception - tubal ... You had tubal ligation (or tying the tubes) surgery to close your fallopian tubes. These tubes connect the ovaries to the uterus. After tubal ...

  7. Massively parallel sequencing of patients with intellectual disability, congenital anomalies and/or autism spectrum disorders with a targeted gene panel.

    PubMed

    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

  8. 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. PMID:27208666

  9. 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.

  10. Mapping unstructured grid computations to massively parallel computers. Ph.D. Thesis - Rensselaer Polytechnic Inst., Feb. 1992

    NASA Technical Reports Server (NTRS)

    Hammond, Steven Warren

    1992-01-01

    Investigated here is this mapping problem: assign the tasks of a parallel program to the processors of a parallel computer such that the execution time is minimized. First, a taxonomy of objective functions and heuristics used to solve the mapping problem is presented. Next, we develop a highly parallel heuristic mapping algorithm, called Cyclic Pairwise Exchange (CPE), and discuss its place in the taxonomy. CPE uses local pairwise exchanges of processor assignments to iteratively improve an initial mapping. A variety of initial mapping schemes are tested and recursive spectral bipartitioning (RSB) followed by CPE is shown to result in the best mappings. For the test cases studied here, problems arising in computational fluid dynamics and structural mechanics on unstructured triangular and tetrahedral meshes, RSB and CPE outperform methods based on simulated annealing. Much less time is required to do the mapping and the results obtained are better. Compared with random and naive mappings, RSB and CPE reduce the communication time two fold for the test problems used. Finally, we use CPE in two applications on a CM-2. The first application is a data parallel mesh-vertex upwind finite volume scheme for solving the Euler equations on 2-D triangular unstructured meshes. CPE is used to map grid points to processors. The performance of this code is compared with a similar code on a Cray-YMP and an Intel iPSC/860. The second application is parallel sparse matrix-vector multiplication used in the iterative solution of large sparse linear systems of equations. We map rows of the matrix to processors and use an inner-product based matrix-vector multiplication. We demonstrate that this method is an order of magnitude faster than methods based on scan operations for our test cases.

  11. Rubber band ligation of hemorrhoids: A guide for complications

    PubMed Central

    Albuquerque, Andreia

    2016-01-01

    Rubber band ligation is one of the most important, cost-effective and commonly used treatments for internal hemorrhoids. Different technical approaches were developed mainly to improve efficacy and safety. The technique can be employed using an endoscope with forward-view or retroflexion or without an endoscope, using a suction elastic band ligator or a forceps ligator. Single or multiple ligations can be performed in a single session. Local anaesthetic after ligation can also be used to reduce the post-procedure pain. Mild bleeding, pain, vaso-vagal symptoms, slippage of bands, priapism, difficulty in urination, anal fissure, and chronic longitudinal ulcers are normally considered minor complications, more frequently encountered. Massive bleeding, thrombosed hemorrhoids, severe pain, urinary retention needing catheterization, pelvic sepsis and death are uncommon major complications. Mild pain after rubber band ligation is the most common complication with a high frequency in some studies. Secondary bleeding normally occurs 10 to 14 d after banding and patients taking anti-platelet and/or anti-coagulant medication have a higher risk, with some reports of massive life-threatening haemorrhage. Several infectious complications have also been reported including pelvic sepsis, Fournier’s gangrene, liver abscesses, tetanus and bacterial endocarditis. To date, seven deaths due to these infectious complications were described. Early recognition and immediate treatment of complications are fundamental for a favourable prognosis. PMID:27721924

  12. Performance of a TthPrimPol-based whole genome amplification kit for copy number alteration detection using massively parallel sequencing

    PubMed Central

    Deleye, Lieselot; De Coninck, Dieter; Dheedene, Annelies; De Sutter, Petra; Menten, Björn; Deforce, Dieter; Van Nieuwerburgh, Filip

    2016-01-01

    Starting from only a few cells, current whole genome amplification (WGA) methods provide enough DNA to perform massively parallel sequencing (MPS). Unfortunately, all current WGA methods introduce representation bias which limits detection of copy number aberrations (CNAs) smaller than 3 Mb. A recent WGA method, called TruePrime single cell WGA, uses a recently discovered DNA primase, TthPrimPol, instead of artificial primers to initiate DNA amplification. This method could lead to a lower representation bias, and consequently to a better detection of CNAs. The enzyme requires no complementarity and thus should generate random primers, equally distributed across the genome. The performance of TruePrime WGA was assessed for aneuploidy screening and CNA analysis after MPS, starting from 1, 3 or 5 cells. Although the method looks promising, the single cell TruePrime WGA kit v1 is not suited for high resolution CNA detection after MPS because too much representation bias is introduced. PMID:27546482

  13. Performance of a TthPrimPol-based whole genome amplification kit for copy number alteration detection using massively parallel sequencing.

    PubMed

    Deleye, Lieselot; De Coninck, Dieter; Dheedene, Annelies; De Sutter, Petra; Menten, Björn; Deforce, Dieter; Van Nieuwerburgh, Filip

    2016-01-01

    Starting from only a few cells, current whole genome amplification (WGA) methods provide enough DNA to perform massively parallel sequencing (MPS). Unfortunately, all current WGA methods introduce representation bias which limits detection of copy number aberrations (CNAs) smaller than 3 Mb. A recent WGA method, called TruePrime single cell WGA, uses a recently discovered DNA primase, TthPrimPol, instead of artificial primers to initiate DNA amplification. This method could lead to a lower representation bias, and consequently to a better detection of CNAs. The enzyme requires no complementarity and thus should generate random primers, equally distributed across the genome. The performance of TruePrime WGA was assessed for aneuploidy screening and CNA analysis after MPS, starting from 1, 3 or 5 cells. Although the method looks promising, the single cell TruePrime WGA kit v1 is not suited for high resolution CNA detection after MPS because too much representation bias is introduced. PMID:27546482

  14. Adaptation of a Multi-Block Structured Solver for Effective Use in a Hybrid CPU/GPU Massively Parallel Environment

    NASA Astrophysics Data System (ADS)

    Gutzwiller, David; Gontier, Mathieu; Demeulenaere, Alain

    2014-11-01

    Multi-Block structured solvers hold many advantages over their unstructured counterparts, such as a smaller memory footprint and efficient serial performance. Historically, multi-block structured solvers have not been easily adapted for use in a High Performance Computing (HPC) environment, and the recent trend towards hybrid GPU/CPU architectures has further complicated the situation. This paper will elaborate on developments and innovations applied to the NUMECA FINE/Turbo solver that have allowed near-linear scalability with real-world problems on over 250 hybrid GPU/GPU cluster nodes. Discussion will focus on the implementation of virtual partitioning and load balancing algorithms using a novel meta-block concept. This implementation is transparent to the user, allowing all pre- and post-processing steps to be performed using a simple, unpartitioned grid topology. Additional discussion will elaborate on developments that have improved parallel performance, including fully parallel I/O with the ADIOS API and the GPU porting of the computationally heavy CPUBooster convergence acceleration module. Head of HPC and Release Management, Numeca International.

  15. Massively Parallel Boundary Integral Element Method Modeling of Particles in a Low Reynolds Number Mewtonian Fluid Flow

    SciTech Connect

    INGBER,M.S.; SUBIA,SAMUEL R.; MONDY,LISA ANN

    2000-01-18

    The analysis of many complex multiphase fluid flow systems is based on a scale decoupling procedure. At the macroscale continuum models are used to perform large-scale simulations. At the mesoscale statistical homogenization theory is used to derive continuum models based on representative volume elements (RVEs). At the microscale small-scale features, such as interfacial properties, are analyzed to be incorporated into mesoscale simulations. In this research mesoscopic simulations of hard particles suspended in a Newtonian fluid undergoing nonlinear shear flow are performed using a boundary element method. To obtain an RVE at higher concentrations, several hundred particles are included in the simulations, putting considerable demands on the computational resources both in terms of CPU and memory. Parallel computing provides a viable platform to study these large multiphase systems. The implementation of a portable, parallel computer code based on the boundary element method using a block-block data distribution is discussed in this paper. The code employs updated direct-solver technologies that make use of dual-processor compute nodes.

  16. Covalent ligation studies on the human telomere quadruplex

    PubMed Central

    Qi, Jianying; Shafer, Richard H.

    2005-01-01

    Recent X-ray crystallographic studies on the human telomere sequence d[AGGG(TTAGGG)3] revealed a unimolecular, parallel quadruplex structure in the presence of potassium ions, while earlier NMR results in the presence of sodium ions indicated a unimolecular, antiparallel quadruplex. In an effort to identify and isolate the parallel form in solution, we have successfully ligated into circular products the single-stranded human telomere and several modified human telomere sequences in potassium-containing solutions. Using these sequences with one or two terminal phosphates, we have made chemically ligated products via creation of an additional loop. Circular products have been identified by polyacrylamide gel electrophoresis, enzymatic digestion with exonuclease VII and electrospray mass spectrometry in negative ion mode. Optimum pH for the ligation reaction of the human telomere sequence ranges from 4.5 to 6.0. Several buffers were also examined, with MES yielding the greatest ligation efficiency. Human telomere sequences with two phosphate groups, one each at the 3′ and 5′ ends, were more efficient at ligation, via pyrophosphate bond formation, than the corresponding sequences with only one phosphate group, at the 5′ end. Circular dichroism spectra showed that the ligation product was derived from an antiparallel, single-stranded guanine quadruplex rather than a parallel single-stranded guanine quadruplex structure. PMID:15933211

  17. Anesthetic Management During Emergency Surgical Ligation for Carotid Blowout Syndrome.

    PubMed

    Klein Nulent, Casper G A; de Graaff, Henri J D; Ketelaars, Rein; Sewnaik, Aniel; Maissan, Iscander M

    2016-08-15

    A 44-year-old man presented to our emergency department with a pharyngeal hemorrhage, 6 weeks after a total laryngectomy and extensive neck dissection. Immediate surgical intervention was necessary to stop massive arterial hemorrhage from the pharynx. The head and neck surgeon successfully ligated the common carotid artery during this procedure. We describe the anesthetic strategy and the thromboelastometry (ROTEM®)-guided massive transfusion protocol. PMID:27310900

  18. Partition-of-unity finite-element method for large scale quantum molecular dynamics on massively parallel computational platforms

    SciTech Connect

    Pask, J E; Sukumar, N; Guney, M; Hu, W

    2011-02-28

    Over the course of the past two decades, quantum mechanical calculations have emerged as a key component of modern materials research. However, the solution of the required quantum mechanical equations is a formidable task and this has severely limited the range of materials systems which can be investigated by such accurate, quantum mechanical means. The current state of the art for large-scale quantum simulations is the planewave (PW) method, as implemented in now ubiquitous VASP, ABINIT, and QBox codes, among many others. However, since the PW method uses a global Fourier basis, with strictly uniform resolution at all points in space, and in which every basis function overlaps every other at every point, it suffers from substantial inefficiencies in calculations involving atoms with localized states, such as first-row and transition-metal atoms, and requires substantial nonlocal communications in parallel implementations, placing critical limits on scalability. In recent years, real-space methods such as finite-differences (FD) and finite-elements (FE) have been developed to address these deficiencies by reformulating the required quantum mechanical equations in a strictly local representation. However, while addressing both resolution and parallel-communications problems, such local real-space approaches have been plagued by one key disadvantage relative to planewaves: excessive degrees of freedom (grid points, basis functions) needed to achieve the required accuracies. And so, despite critical limitations, the PW method remains the standard today. In this work, we show for the first time that this key remaining disadvantage of real-space methods can in fact be overcome: by building known atomic physics into the solution process using modern partition-of-unity (PU) techniques in finite element analysis. Indeed, our results show order-of-magnitude reductions in basis size relative to state-of-the-art planewave based methods. The method developed here is

  19. User's guide of TOUGH2-EGS-MP: A Massively Parallel Simulator with Coupled Geomechanics for Fluid and Heat Flow in Enhanced Geothermal Systems VERSION 1.0

    SciTech Connect

    Xiong, Yi; Fakcharoenphol, Perapon; Wang, Shihao; Winterfeld, Philip H.; Zhang, Keni; Wu, Yu-Shu

    2013-12-01

    TOUGH2-EGS-MP is a parallel numerical simulation program coupling geomechanics with fluid and heat flow in fractured and porous media, and is applicable for simulation of enhanced geothermal systems (EGS). TOUGH2-EGS-MP is based on the TOUGH2-MP code, the massively parallel version of TOUGH2. In TOUGH2-EGS-MP, the fully-coupled flow-geomechanics model is developed from linear elastic theory for thermo-poro-elastic systems and is formulated in terms of mean normal stress as well as pore pressure and temperature. Reservoir rock properties such as porosity and permeability depend on rock deformation, and the relationships between these two, obtained from poro-elasticity theories and empirical correlations, are incorporated into the simulation. This report provides the user with detailed information on the TOUGH2-EGS-MP mathematical model and instructions for using it for Thermal-Hydrological-Mechanical (THM) simulations. The mathematical model includes the fluid and heat flow equations, geomechanical equation, and discretization of those equations. In addition, the parallel aspects of the code, such as domain partitioning and communication between processors, are also included. Although TOUGH2-EGS-MP has the capability for simulating fluid and heat flows coupled with geomechanical effects, it is up to the user to select the specific coupling process, such as THM or only TH, in a simulation. There are several example problems illustrating applications of this program. These example problems are described in detail and their input data are presented. Their results demonstrate that this program can be used for field-scale geothermal reservoir simulation in porous and fractured media with fluid and heat flow coupled with geomechanical effects.

  20. Implementation of a flexible and scalable particle-in-cell method for massively parallel computations in the mantle convection code ASPECT

    NASA Astrophysics Data System (ADS)

    Gassmöller, Rene; Bangerth, Wolfgang

    2016-04-01

    Particle-in-cell methods have a long history and many applications in geodynamic modelling of mantle convection, lithospheric deformation and crustal dynamics. They are primarily used to track material information, the strain a material has undergone, the pressure-temperature history a certain material region has experienced, or the amount of volatiles or partial melt present in a region. However, their efficient parallel implementation - in particular combined with adaptive finite-element meshes - is complicated due to the complex communication patterns and frequent reassignment of particles to cells. Consequently, many current scientific software packages accomplish this efficient implementation by specifically designing particle methods for a single purpose, like the advection of scalar material properties that do not evolve over time (e.g., for chemical heterogeneities). Design choices for particle integration, data storage, and parallel communication are then optimized for this single purpose, making the code relatively rigid to changing requirements. Here, we present the implementation of a flexible, scalable and efficient particle-in-cell method for massively parallel finite-element codes with adaptively changing meshes. Using a modular plugin structure, we allow maximum flexibility of the generation of particles, the carried tracer properties, the advection and output algorithms, and the projection of properties to the finite-element mesh. We present scaling tests ranging up to tens of thousands of cores and tens of billions of particles. Additionally, we discuss efficient load-balancing strategies for particles in adaptive meshes with their strengths and weaknesses, local particle-transfer between parallel subdomains utilizing existing communication patterns from the finite element mesh, and the use of established parallel output algorithms like the HDF5 library. Finally, we show some relevant particle application cases, compare our implementation to a

  1. Influence of data volume and EPC on process window in massively parallel e-beam direct write

    NASA Astrophysics Data System (ADS)

    Lin, Shy-Jay; Liu, Pei-Yi; Chen, Cheng-Hung; Wang, Wen-Chuan; Shin, Jaw-Jung; Lin, Burn Jeng; McCord, Mark A.; Shriyan, Sameet K.

    2013-03-01

    Multiple e-beam direct write lithography (MEBDW), using >10,000 e-beams writing in parallel, proposed by MAPPER, KLA-Tencor, and IMS is a potential solution for 20-nm half-pitch and beyond. The raster scan in MEBDW makes bitmap its data format. Data handling becomes indispensable since bitmap needs a huge data volume due to the fine pixel size to keep the CD accuracy after e-beam proximity correction (EPC). In fact, in 10,000-beam MEBDW, for a 10 WPH tool of 1-nm pixel size and 1-bit gray level, the aggregated data transmission rate would be up to 1963 Tera bits per second (bps), requiring 19,630 fibers transmitting 10 Gbps in each fiber. The data rate per beam would be <20 Gbps. Hence data reduction using bigger pixel size, fewer grey levels to achieve sub-nm EPC accuracy, and data truncation have been extensively studied. In this paper, process window assessment through Exposure-Defocus (E-D) Forest to quantitatively characterize the data truncation before and after EPC is reported. REBL electron optics, electron scattering in resist, and resist acid diffusion are considered, to construct the E-D Forest and to analyze the imaging performance of the most representative layers and patterns, such as critical line/space and hole layers with minimum pitch, cutting layers, and implant layers, for the 10-nm, and 7-nm nodes.

  2. Self ligating lingual appliance.

    PubMed

    Juneja, Pankaj; Chopra, S S; Jayan, B K

    2015-12-01

    Adult demand for orthodontics has grown considerably over the past 10 years propelling increased demand for Esthetic Orthodontics. Lingual appliances are a viable option toward providing Esthetic Orthodontics. The lingual surface of the teeth has a unique morphology that makes it difficult to place brackets in ideal positions. Indirect bonding has become the established methods of overcoming these discrepancies, along with the latest designs of self ligating brackets which offer more efficient mechanics and shorter treatment time. PMID:26843757

  3. Massively Parallel Signal Processing using the Graphics Processing Unit for Real-Time Brain-Computer Interface Feature Extraction.

    PubMed

    Wilson, J Adam; Williams, Justin C

    2009-01-01

    The clock speeds of modern computer processors have nearly plateaued in the past 5 years. Consequently, neural prosthetic systems that rely on processing large quantities of data in a short period of time face a bottleneck, in that it may not be possible to process all of the data recorded from an electrode array with high channel counts and bandwidth, such as electrocorticographic grids or other implantable systems. Therefore, in this study a method of using the processing capabilities of a graphics card [graphics processing unit (GPU)] was developed for real-time neural signal processing of a brain-computer interface (BCI). The NVIDIA CUDA system was used to offload processing to the GPU, which is capable of running many operations in parallel, potentially greatly increasing the speed of existing algorithms. The BCI system records many channels of data, which are processed and translated into a control signal, such as the movement of a computer cursor. This signal processing chain involves computing a matrix-matrix multiplication (i.e., a spatial filter), followed by calculating the power spectral density on every channel using an auto-regressive method, and finally classifying appropriate features for control. In this study, the first two computationally intensive steps were implemented on the GPU, and the speed was compared to both the current implementation and a central processing unit-based implementation that uses multi-threading. Significant performance gains were obtained with GPU processing: the current implementation processed 1000 channels of 250 ms in 933 ms, while the new GPU method took only 27 ms, an improvement of nearly 35 times.

  4. Scientific development of a massively parallel ocean climate model. Progress report for 1992--1993 and Continuing request for 1993--1994 to CHAMMP (Computer Hardware, Advanced Mathematics, and Model Physics)

    SciTech Connect

    Semtner, A.J. Jr.; Chervin, R.M.

    1993-05-01

    During the second year of CHAMMP funding to the principal investigators, progress has been made in the proposed areas of research, as follows: investigation of the physics of the thermohaline circulation; examination of resolution effects on ocean general circulation; and development of a massively parallel ocean climate model.

  5. Massively parallel implementations of coupled-cluster methods for electron spin resonance spectra. I. Isotropic hyperfine coupling tensors in large radicals

    SciTech Connect

    Verma, Prakash; Morales, Jorge A.; Perera, Ajith

    2013-11-07

    Coupled cluster (CC) methods provide highly accurate predictions of molecular properties, but their high computational cost has precluded their routine application to large systems. Fortunately, recent computational developments in the ACES III program by the Bartlett group [the OED/ERD atomic integral package, the super instruction processor, and the super instruction architecture language] permit overcoming that limitation by providing a framework for massively parallel CC implementations. In that scheme, we are further extending those parallel CC efforts to systematically predict the three main electron spin resonance (ESR) tensors (A-, g-, and D-tensors) to be reported in a series of papers. In this paper inaugurating that series, we report our new ACES III parallel capabilities that calculate isotropic hyperfine coupling constants in 38 neutral, cationic, and anionic radicals that include the {sup 11}B, {sup 17}O, {sup 9}Be, {sup 19}F, {sup 1}H, {sup 13}C, {sup 35}Cl, {sup 33}S,{sup 14}N, {sup 31}P, and {sup 67}Zn nuclei. Present parallel calculations are conducted at the Hartree-Fock (HF), second-order many-body perturbation theory [MBPT(2)], CC singles and doubles (CCSD), and CCSD with perturbative triples [CCSD(T)] levels using Roos augmented double- and triple-zeta atomic natural orbitals basis sets. HF results consistently overestimate isotropic hyperfine coupling constants. However, inclusion of electron correlation effects in the simplest way via MBPT(2) provides significant improvements in the predictions, but not without occasional failures. In contrast, CCSD results are consistently in very good agreement with experimental results. Inclusion of perturbative triples to CCSD via CCSD(T) leads to small improvements in the predictions, which might not compensate for the extra computational effort at a non-iterative N{sup 7}-scaling in CCSD(T). The importance of these accurate computations of isotropic hyperfine coupling constants to elucidate

  6. Massively parallel implementations of coupled-cluster methods for electron spin resonance spectra. I. Isotropic hyperfine coupling tensors in large radicals.

    PubMed

    Verma, Prakash; Perera, Ajith; Morales, Jorge A

    2013-11-01

    Coupled cluster (CC) methods provide highly accurate predictions of molecular properties, but their high computational cost has precluded their routine application to large systems. Fortunately, recent computational developments in the ACES III program by the Bartlett group [the OED∕ERD atomic integral package, the super instruction processor, and the super instruction architecture language] permit overcoming that limitation by providing a framework for massively parallel CC implementations. In that scheme, we are further extending those parallel CC efforts to systematically predict the three main electron spin resonance (ESR) tensors (A-, g-, and D-tensors) to be reported in a series of papers. In this paper inaugurating that series, we report our new ACES III parallel capabilities that calculate isotropic hyperfine coupling constants in 38 neutral, cationic, and anionic radicals that include the (11)B, (17)O, (9)Be, (19)F, (1)H, (13)C, (35)Cl, (33)S,(14)N, (31)P, and (67)Zn nuclei. Present parallel calculations are conducted at the Hartree-Fock (HF), second-order many-body perturbation theory [MBPT(2)], CC singles and doubles (CCSD), and CCSD with perturbative triples [CCSD(T)] levels using Roos augmented double- and triple-zeta atomic natural orbitals basis sets. HF results consistently overestimate isotropic hyperfine coupling constants. However, inclusion of electron correlation effects in the simplest way via MBPT(2) provides significant improvements in the predictions, but not without occasional failures. In contrast, CCSD results are consistently in very good agreement with experimental results. Inclusion of perturbative triples to CCSD via CCSD(T) leads to small improvements in the predictions, which might not compensate for the extra computational effort at a non-iterative N(7)-scaling in CCSD(T). The importance of these accurate computations of isotropic hyperfine coupling constants to elucidate experimental ESR spectra, to interpret spin

  7. Massively parallel implementations of coupled-cluster methods for electron spin resonance spectra. I. Isotropic hyperfine coupling tensors in large radicals

    NASA Astrophysics Data System (ADS)

    Verma, Prakash; Perera, Ajith; Morales, Jorge A.

    2013-11-01

    Coupled cluster (CC) methods provide highly accurate predictions of molecular properties, but their high computational cost has precluded their routine application to large systems. Fortunately, recent computational developments in the ACES III program by the Bartlett group [the OED/ERD atomic integral package, the super instruction processor, and the super instruction architecture language] permit overcoming that limitation by providing a framework for massively parallel CC implementations. In that scheme, we are further extending those parallel CC efforts to systematically predict the three main electron spin resonance (ESR) tensors (A-, g-, and D-tensors) to be reported in a series of papers. In this paper inaugurating that series, we report our new ACES III parallel capabilities that calculate isotropic hyperfine coupling constants in 38 neutral, cationic, and anionic radicals that include the 11B, 17O, 9Be, 19F, 1H, 13C, 35Cl, 33S,14N, 31P, and 67Zn nuclei. Present parallel calculations are conducted at the Hartree-Fock (HF), second-order many-body perturbation theory [MBPT(2)], CC singles and doubles (CCSD), and CCSD with perturbative triples [CCSD(T)] levels using Roos augmented double- and triple-zeta atomic natural orbitals basis sets. HF results consistently overestimate isotropic hyperfine coupling constants. However, inclusion of electron correlation effects in the simplest way via MBPT(2) provides significant improvements in the predictions, but not without occasional failures. In contrast, CCSD results are consistently in very good agreement with experimental results. Inclusion of perturbative triples to CCSD via CCSD(T) leads to small improvements in the predictions, which might not compensate for the extra computational effort at a non-iterative N7-scaling in CCSD(T). The importance of these accurate computations of isotropic hyperfine coupling constants to elucidate experimental ESR spectra, to interpret spin-density distributions, and to

  8. Sequencing the hypervariable regions of human mitochondrial DNA using massively parallel sequencing: Enhanced data acquisition for DNA samples encountered in forensic testing.

    PubMed

    Davis, Carey; Peters, Dixie; Warshauer, David; King, Jonathan; Budowle, Bruce

    2015-03-01

    Mitochondrial DNA testing is a useful tool in the analysis of forensic biological evidence. In cases where nuclear DNA is damaged or limited in quantity, the higher copy number of mitochondrial genomes available in a sample can provide information about the source of a sample. Currently, Sanger-type sequencing (STS) is the primary method to develop mitochondrial DNA profiles. This method is laborious and time consuming. Massively parallel sequencing (MPS) can increase the amount of information obtained from mitochondrial DNA samples while improving turnaround time by decreasing the numbers of manipulations and more so by exploiting high throughput analyses to obtain interpretable results. In this study 18 buccal swabs, three different tissue samples from five individuals, and four bones samples from casework were sequenced at hypervariable regions I and II using STS and MPS. Sample enrichment for STS and MPS was PCR-based. Library preparation for MPS was performed using Nextera® XT DNA Sample Preparation Kit and sequencing was performed on the MiSeq™ (Illumina, Inc.). MPS yielded full concordance of base calls with STS results, and the newer methodology was able to resolve length heteroplasmy in homopolymeric regions. This study demonstrates short amplicon MPS of mitochondrial DNA is feasible, can provide information not possible with STS, and lays the groundwork for development of a whole genome sequencing strategy for degraded samples.

  9. Non-invasive prenatal testing using massively parallel sequencing of maternal plasma DNA: from molecular karyotyping to fetal whole-genome sequencing.

    PubMed

    Lo, Y M Dennis

    2013-12-01

    The discovery of cell-free fetal DNA in maternal plasma in 1997 has stimulated a rapid development of non-invasive prenatal testing. The recent advent of massively parallel sequencing has allowed the analysis of circulating cell-free fetal DNA to be performed with unprecedented sensitivity and precision. Fetal trisomies 21, 18 and 13 are now robustly detectable in maternal plasma and such analyses have been available clinically since 2011. Fetal genome-wide molecular karyotyping and whole-genome sequencing have now been demonstrated in a number of proof-of-concept studies. Genome-wide and targeted sequencing of maternal plasma has been shown to allow the non-invasive prenatal testing of β-thalassaemia and can potentially be generalized to other monogenic diseases. It is thus expected that plasma DNA-based non-invasive prenatal testing will play an increasingly important role in future obstetric care. It is thus timely and important that the ethical, social and legal issues of non-invasive prenatal testing be discussed actively by all parties involved in prenatal care.

  10. The efficacy of uracil DNA glycosylase pretreatment in amplicon-based massively parallel sequencing with DNA extracted from archived formalin-fixed paraffin-embedded esophageal cancer tissues.

    PubMed

    Serizawa, Masakuni; Yokota, Tomoya; Hosokawa, Ayumu; Kusafuka, Kimihide; Sugiyama, Toshiro; Tsubosa, Yasuhiro; Yasui, Hirofumi; Nakajima, Takashi; Koh, Yasuhiro

    2015-09-01

    Advances in mutation testing for molecular-targeted cancer therapies have led to the increased use of archived formalin-fixed paraffin-embedded (FFPE) tumors. However, DNA extracted from FFPE tumors (FFPE DNA) is problematic for mutation testing, especially for amplicon-based massively parallel sequencing (MPS), owing to DNA fragmentation and artificial C:G > T:A single nucleotide variants (SNVs) caused by deamination of cytosine to uracil. Therefore, to reduce artificial C:G > T:A SNVs in amplicon-based MPS using FFPE DNA, we evaluated the efficacy of uracil DNA glycosylase (UDG) pretreatment, which can eliminate uracil-containing DNA molecules, with 126 archived FFPE esophageal cancer specimens. We also examined the association between the frequency of C:G > T:A SNVs and DNA quality, as assessed by a quantitative PCR (qPCR)-based assay. UDG pretreatment significantly lowered the frequency of C:G > T:A SNVs in highly fragmented DNA (by approximately 60%). This effect was not observed for good- to moderate-quality DNA, suggesting that a predictive assay (i.e., DNA quality assessment) needs to be performed prior to UDG pretreatment. These results suggest that UDG pretreatment is efficacious for mutation testing by amplicon-based MPS with fragmented DNA from FFPE samples.

  11. Using Massive Parallel Sequencing for the Development, Validation, and Application of Population Genetics Markers in the Invasive Bivalve Zebra Mussel (Dreissena polymorpha)

    PubMed Central

    Peñarrubia, Luis; Sanz, Nuria; Pla, Carles; Vidal, Oriol; Viñas, Jordi

    2015-01-01

    The zebra mussel (Dreissena polymorpha, Pallas, 1771) is one of the most invasive species of freshwater bivalves, due to a combination of biological and anthropogenic factors. Once this species has been introduced to a new area, individuals form dense aggregations that are very difficult to remove, leading to many adverse socioeconomic and ecological consequences. In this study, we identified, tested, and validated a new set of polymorphic microsatellite loci (also known as SSRs, Single Sequence Repeats) using a Massive Parallel Sequencing (MPS) platform. After several pruning steps, 93 SSRs could potentially be amplified. Out of these SSRs, 14 were polymorphic, producing a polymorphic yield of 15.05%. These 14 polymorphic microsatellites were fully validated in a first approximation of the genetic population structure of D. polymorpha in the Iberian Peninsula. Based on this polymorphic yield, we propose a criterion for establishing the number of SSRs that require validation in similar species, depending on the final use of the markers. These results could be used to optimize MPS approaches in the development of microsatellites as genetic markers, which would reduce the cost of this process. PMID:25780924

  12. Using Massive Parallel Sequencing for the development, validation, and application of population genetics markers in the invasive bivalve zebra mussel (Dreissena polymorpha).

    PubMed

    Peñarrubia, Luis; Sanz, Nuria; Pla, Carles; Vidal, Oriol; Viñas, Jordi

    2015-01-01

    The zebra mussel (Dreissena polymorpha, Pallas, 1771) is one of the most invasive species of freshwater bivalves, due to a combination of biological and anthropogenic factors. Once this species has been introduced to a new area, individuals form dense aggregations that are very difficult to remove, leading to many adverse socioeconomic and ecological consequences. In this study, we identified, tested, and validated a new set of polymorphic microsatellite loci (also known as SSRs, Single Sequence Repeats) using a Massive Parallel Sequencing (MPS) platform. After several pruning steps, 93 SSRs could potentially be amplified. Out of these SSRs, 14 were polymorphic, producing a polymorphic yield of 15.05%. These 14 polymorphic microsatellites were fully validated in a first approximation of the genetic population structure of D. polymorpha in the Iberian Peninsula. Based on this polymorphic yield, we propose a criterion for establishing the number of SSRs that require validation in similar species, depending on the final use of the markers. These results could be used to optimize MPS approaches in the development of microsatellites as genetic markers, which would reduce the cost of this process. PMID:25780924

  13. Performance of the UCAN2 Gyrokinetic Particle In Cell (PIC) Code on Two Massively Parallel Mainframes with Intel ``Sandy Bridge'' Processors

    NASA Astrophysics Data System (ADS)

    Leboeuf, Jean-Noel; Decyk, Viktor; Newman, David; Sanchez, Raul

    2013-10-01

    The massively parallel, 2D domain-decomposed, nonlinear, 3D, toroidal, electrostatic, gyrokinetic, Particle in Cell (PIC), Cartesian geometry UCAN2 code, with particle ions and adiabatic electrons, has been ported to two emerging mainframes. These two computers, one at NERSC in the US built by Cray named Edison and the other at the Barcelona Supercomputer Center (BSC) in Spain built by IBM named MareNostrum III (MNIII) just happen to share the same Intel ``Sandy Bridge'' processors. The successful port of UCAN2 to MNIII which came online first has enabled us to be up and running efficiently in record time on Edison. Overall, the performance of UCAN2 on Edison is superior to that on MNIII, particularly at large numbers of processors (>1024) for the same Intel IFORT compiler. This appears to be due to different MPI modules (OpenMPI on MNIII and MPICH2 on Edison) and different interconnection networks (Infiniband on MNIII and Cray's Aries on Edison) on the two mainframes. Details of these ports and comparative benchmarks are presented. Work supported by OFES, USDOE, under contract no. DE-FG02-04ER54741 with the University of Alaska at Fairbanks.

  14. Modeling the Backscatter and Transmitted Light of High Power Smoothed Beams with pF3D, a Massively Parallel Laser Plasma Interaction Code

    SciTech Connect

    Berger, R.L.; Divol, L.; Glenzer, S.; Hinkel, D.E.; Kirkwood, R.K.; Langdon, A.B.; Moody, J.D.; Still, C.H.; Suter, L.; Williams, E.A.; Young, P.E.

    2000-06-01

    Using the three-dimensional wave propagation code, F3D[Berger et al., Phys. Fluids B 5,2243 (1993), Berger et al., Phys. Plasmas 5,4337(1998)], and the massively parallel version pF3D, [Still et al. Phys. Plasmas 7 (2000)], we have computed the transmitted and reflected light for laser and plasma conditions in experiments that simulated ignition hohlraum conditions. The frequency spectrum and the wavenumber spectrum of the transmitted light are calculated and used to identify the relative contributions of stimulated forward Brillouin and self-focusing in hydrocarbon-filled balloons, commonly called gasbags. The effect of beam smoothing, smoothing by spectral dispersion (SSD) and polarization smoothing (PS), on the stimulated Brillouin backscatter (SBS) from Scale-1 NOVA hohlraums was simulated with the use nonlinear saturation models that limit the amplitude of the driven acoustic waves. Other experiments on CO{sub 2} gasbags simultaneously measure at a range of intensities the SBS reflectivity and the Thomson scatter from the SBS-driven acoustic waves that provide a more detailed test of the modeling. These calculations also predict that the backscattered light will be very nonuniform in the nearfield (the focusing system optics) which is important for specifying the backscatter intensities be tolerated by the National Ignition Facility laser system.

  15. Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace(®)-application.

    PubMed

    Van Neste, Christophe; Gansemans, Yannick; De Coninck, Dieter; Van Hoofstat, David; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

    2015-03-01

    Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background. We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis. Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data.

  16. Massively parallel multiple interacting continua formulation for modeling flow in fractured porous media using the subsurface reactive flow and transport code PFLOTRAN

    NASA Astrophysics Data System (ADS)

    Kumar, J.; Mills, R. T.; Lichtner, P. C.; Hammond, G. E.

    2010-12-01

    Fracture dominated flows occur in numerous subsurface geochemical processes and at many different scales in rock pore structures, micro-fractures, fracture networks and faults. Fractured porous media can be modeled as multiple interacting continua which are connected to each other through transfer terms that capture the flow of mass and energy in response to pressure, temperature and concentration gradients. However, the analysis of large-scale transient problems using the multiple interacting continuum approach presents an algorithmic and computational challenge for problems with very large numbers of degrees of freedom. A generalized dual porosity model based on the Dual Continuum Disconnected Matrix approach has been implemented within a massively parallel multiphysics-multicomponent-multiphase subsurface reactive flow and transport code PFLOTRAN. Developed as part of the Department of Energy's SciDAC-2 program, PFLOTRAN provides subsurface simulation capabilities that can scale from laptops to ultrascale supercomputers, and utilizes the PETSc framework to solve the large, sparse algebraic systems that arises in complex subsurface reactive flow and transport problems. It has been successfully applied to the solution of problems composed of more than two billions degrees of freedom, utilizing up to 131,072 processor cores on Jaguar, the Cray XT5 system at Oak Ridge National Laboratory that is the world’s fastest supercomputer. Building upon the capabilities and computational efficiency of PFLOTRAN, we will present an implementation of the multiple interacting continua formulation for fractured porous media along with an application case study.

  17. A digital 25 µm pixel-pitch uncooled amorphous silicon TEC-less VGA IRFPA with massive parallel Sigma-Delta-ADC readout

    NASA Astrophysics Data System (ADS)

    Weiler, Dirk; Russ, Marco; Würfel, Daniel; Lerch, Renee; Yang, Pin; Bauer, Jochen; Vogt, Holger

    2010-04-01

    This paper presents an advanced 640 x 480 (VGA) IRFPA based on uncooled microbolometers with a pixel-pitch of 25μm developed by Fraunhofer-IMS. The IRFPA is designed for thermal imaging applications in the LWIR (8 .. 14μm) range with a full-frame frequency of 30 Hz and a high sensitivity with NETD < 100 mK @ f/1. A novel readout architecture which utilizes massively parallel on-chip Sigma-Delta-ADCs located under the microbolometer array results in a high performance digital readout. Sigma-Delta-ADCs are inherently linear. A high resolution of 16 bit for a secondorder Sigma-Delta-modulator followed by a third-order digital sinc-filter can be obtained. In addition to several thousand Sigma-Delta-ADCs the readout circuit consists of a configurable sequencer for controlling the readout clocking signals and a temperature sensor for measuring the temperature of the IRFPA. Since packaging is a significant part of IRFPA's price Fraunhofer-IMS uses a chip-scaled package consisting of an IR-transparent window with antireflection coating and a soldering frame for maintaining the vacuum. The IRFPAs are completely fabricated at Fraunhofer-IMS on 8" CMOS wafers with an additional surface micromachining process. In this paper the architecture of the readout electronics, the packaging, and the electro-optical performance characterization are presented.

  18. A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing

    PubMed Central

    Martí, Eulàlia; Pantano, Lorena; Bañez-Coronel, Mónica; Llorens, Franc; Miñones-Moyano, Elena; Porta, Sílvia; Sumoy, Lauro; Ferrer, Isidre; Estivill, Xavier

    2010-01-01

    Huntington disease (HD) is a neurodegenerative disorder that predominantly affects neurons of the forebrain. We have applied the Illumina massively parallel sequencing to deeply analyze the small RNA populations of two different forebrain areas, the frontal cortex (FC) and the striatum (ST) of healthy individuals and individuals with HD. More than 80% of the small-RNAs were annotated as microRNAs (miRNAs) in all samples. Deep sequencing revealed length and sequence heterogeneity (IsomiRs) for the vast majority of miRNAs. Around 80–90% of the miRNAs presented modifications in the 3′-terminus mainly in the form of trimming and/or as nucleotide addition variants, while the 5′-terminus of the miRNAs was specially protected from changes. Expression profiling showed strong miRNA and isomiR expression deregulation in HD, most being common to both FC and ST. The analysis of the upstream regulatory regions in co-regulated miRNAs suggests a role for RE1-Silencing Transcription Factor (REST) and P53 in miRNAs downregulation in HD. The putative targets of deregulated miRNAs and seed-region IsomiRs strongly suggest that their altered expression contributes to the aberrant gene expression in HD. Our results show that miRNA variability is a ubiquitous phenomenon in the adult human brain, which may influence gene expression in physiological and pathological conditions. PMID:20591823

  19. Second-order Møller-Plesset theory with linear R12 terms (MP2-R12) revisited: auxiliary basis set method and massively parallel implementation.

    PubMed

    Valeev, Edward F; Janssen, Curtis L

    2004-07-15

    matrix elements are necessary in order to make the MP2-R12 method sufficiently accurate when small orbital basis sets are used. The computer code is a part of the latest public release of Sandia's Massively Parallel Quantum Chemistry program available under GNU General Public License.

  20. Development of ballistic hot electron emitter and its applications to parallel processing: active-matrix massive direct-write lithography in vacuum and thin films deposition in solutions

    NASA Astrophysics Data System (ADS)

    Koshida, N.; Kojima, A.; Ikegami, N.; Suda, R.; Yagi, M.; Shirakashi, J.; Yoshida, T.; Miyaguchi, H.; Muroyama, M.; Nishino, H.; Yoshida, S.; Sugata, M.; Totsu, K.; Esashi, M.

    2015-03-01

    Making the best use of the characteristic features in nanocrystalline Si (nc-Si) ballistic hot electron source, the alternative lithographic technology is presented based on the two approaches: physical excitation in vacuum and chemical reduction in solutions. The nc-Si cold cathode is a kind of metal-insulator-semiconductor (MIS) diode, composed of a thin metal film, an nc-Si layer, an n+-Si substrate, and an ohmic back contact. Under a biased condition, energetic electrons are uniformly and directionally emitted through the thin surface electrodes. In vacuum, this emitter is available for active-matrix drive massive parallel lithography. Arrayed 100×100 emitters (each size: 10×10 μm2, pitch: 100 μm) are fabricated on silicon substrate by conventional planar process, and then every emitter is bonded with integrated complementary metal-oxide-semiconductor (CMOS) driver using through-silicon-via (TSV) interconnect technology. Electron multi-beams emitted from selected devices are focused by a micro-electro-mechanical system (MEMS) condenser lens array and introduced into an accelerating system with a demagnification factor of 100. The electron accelerating voltage is 5 kV. The designed size of each beam landing on the target is 10×10 nm2 in square. Here we discuss the fabrication process of the emitter array with TSV holes, implementation of integrated ctive-matrix driver circuit, the bonding of these components, the construction of electron optics, and the overall operation in the exposure system including the correction of possible aberrations. The experimental results of this mask-less parallel pattern transfer are shown in terms of simple 1:1 projection and parallel lithography under an active-matrix drive scheme. Another application is the use of this emitter as an active electrode supplying highly reducing electrons into solutions. A very small amount of metal-salt solutions is dripped onto the nc-Si emitter surface, and the emitter is driven without

  1. Parallel inversion of a massive ERT data set to characterize deep vadose zone contamination beneath former nuclear waste infiltration galleries at the Hanford Site B-Complex (Invited)

    NASA Astrophysics Data System (ADS)

    Johnson, T.; Rucker, D. F.; Wellman, D.

    2013-12-01

    revealed the general footprint of vadose zone contamination beneath infiltration galleries. In 2011, the USDOE commissioned an effort to re-invert the B-Complex ERT data as a whole using a recently developed massively parallel 3D ERT inversion code. The computational mesh included approximately 1.085 million elements and closely honored the 37m of topographic relief as determined by LiDAR imaging. The water table and tank boundaries were also incorporated into the mesh to facilitate regularization disconnects, enabling sharp conductivity contrasts where they occur naturally without penalty. The data were inverted using 1024 processors, requiring 910 Gb of memory and 11.5 hours of computation time. The imaging results revealed previously unrealized detail concerning the distribution and behavior of contaminants migrating through the vadose zone, and are currently being used by site cleanup operators and regulators to understand the origin of a groundwater nitrate plume emerging from one of the infiltration galleries. The results overall demonstrate the utility of high performance computing, unstructured meshing, and custom regularization constraints for optimal processing of massive ERT data sets enabled by modern ERT survey hardware.

  2. Application of high-resolution, massively parallel pyrosequencing for estimation of haplotypes and gene expression levels of swine leukocyte antigen (SLA) class I genes.

    PubMed

    Kita, Yuki F; Ando, Asako; Tanaka, Keiko; Suzuki, Shingo; Ozaki, Yuki; Uenishi, Hirohide; Inoko, Hidetoshi; Kulski, Jerzy K; Shiina, Takashi

    2012-03-01

    The swine is an important animal model for allo- and xeno-transplantation donor studies, which necessitates an extensive characterization of the expression and sequence variations within the highly polygenic and polymorphic swine leukocyte antigen (SLA) region. Massively parallel pyrosequencing is potentially an effective new 2ndGen method for simultaneous high-throughput genotyping and detection of SLA class I gene expression levels. In this study, we compared the 2ndGen method using the Roche Genome Sequencer 454 FLX with the conventional method using sub-cloning and Sanger sequencing to genotype SLA class I genes in five pigs of the Clawn breed and four pigs of the Landrace breed. We obtained an average of 10.4 SLA class I sequences per pig by the 2ndGen method, consistent with the inheritance data, and an average of only 6.0 sequences by the conventional method. We also performed a correlation analysis between the sequence read numbers obtained by the 2ndGen method and the relative expression values obtained by quantitative real-time PCR analysis at the allele level. A significant correlation coefficient (r = 0.899, P < 0.01) was observed between the sequence read numbers and the relative quantitative values for the expressed classical SLA class I genes SLA-1, SLA-2, and SLA-3, suggesting that the sequence read numbers closely reflect the gene expression levels in white blood cells. Overall, five novel class I sequences, different haplotype-specific expression patterns and a splice variant for one of the SLA class I genes were identified by the 2ndGen method at greater efficiency and sensitivity than the conventional method.

  3. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach

    SciTech Connect

    Cardenas, Erick; Leigh, Mary Beth; Marsh, Terence; Tiedje, James M.; Wu, Wei-min; Luo, Jian; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Criddle, Craig; Carley, Jack M; Carroll, Sue L; Gentry, Terry J; Watson, David B; Gu, Baohua; Jardine, Philip M; Zhou, Jizhong

    2010-10-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 M and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

  4. Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique.

    PubMed

    Nagai, Satoshi; Hida, Kohsuke; Urushizaki, Shingo; Onitsuka, Goh; Yasuike, Motoshige; Nakamura, Yoji; Fujiwara, Atushi; Tajimi, Seisuke; Kimoto, Katsunori; Kobayashi, Takanori; Gojobori, Takashi; Ototake, Mitsuru

    2016-02-01

    In this study, we investigated the influence of diurnal sampling bias on the community structure of plankton by comparing the biodiversity among seawater samples (n=9) obtained every 3h for 24h by using massively parallel sequencing (MPS)-based plankton monitoring at a fixed point conducted at Himedo seaport in Yatsushiro Sea, Japan. The number of raw operational taxonomy units (OTUs) and OTUs after re-sampling was 507-658 (558 ± 104, mean ± standard deviation) and 448-544 (467 ± 81), respectively, indicating high plankton biodiversity at the sampling location. The relative abundance of the top 20 OTUs in the samples from Himedo seaport was 48.8-67.7% (58.0 ± 5.8%), and the highest-ranked OTU was Pseudo-nitzschia species (Bacillariophyta) with a relative abundance of 17.3-39.2%, followed by Oithona sp. 1 and Oithona sp. 2 (Arthropoda). During seawater sampling, the semidiurnal tidal current having an amplitude of 0.3ms(-1) was dominant, and the westward residual current driven by the northeasterly wind was continuously observed during the 24-h monitoring. Therefore, the relative abundance of plankton species apparently fluctuated among the samples, but no significant difference was noted according to G-test (p>0.05). Significant differences were observed between the samples obtained from a different locality (Kusuura in Yatsushiro Sea) and at different dates, suggesting that the influence of diurnal sampling bias on plankton diversity, determined using the MPS-based survey, was not significant and acceptable.

  5. Quaternary Morphodynamics of Fluvial Dispersal Systems Revealed: The Fly River, PNG, and the Sunda Shelf, SE Asia, simulated with the Massively Parallel GPU-based Model 'GULLEM'

    NASA Astrophysics Data System (ADS)

    Aalto, R. E.; Lauer, J. W.; Darby, S. E.; Best, J.; Dietrich, W. E.

    2015-12-01

    During glacial-marine transgressions vast volumes of sediment are deposited due to the infilling of lowland fluvial systems and shallow shelves, material that is removed during ensuing regressions. Modelling these processes would illuminate system morphodynamics, fluxes, and 'complexity' in response to base level change, yet such problems are computationally formidable. Environmental systems are characterized by strong interconnectivity, yet traditional supercomputers have slow inter-node communication -- whereas rapidly advancing Graphics Processing Unit (GPU) technology offers vastly higher (>100x) bandwidths. GULLEM (GpU-accelerated Lowland Landscape Evolution Model) employs massively parallel code to simulate coupled fluvial-landscape evolution for complex lowland river systems over large temporal and spatial scales. GULLEM models the accommodation space carved/infilled by representing a range of geomorphic processes, including: river & tributary incision within a multi-directional flow regime, non-linear diffusion, glacial-isostatic flexure, hydraulic geometry, tectonic deformation, sediment production, transport & deposition, and full 3D tracking of all resulting stratigraphy. Model results concur with the Holocene dynamics of the Fly River, PNG -- as documented with dated cores, sonar imaging of floodbasin stratigraphy, and the observations of topographic remnants from LGM conditions. Other supporting research was conducted along the Mekong River, the largest fluvial system of the Sunda Shelf. These and other field data provide tantalizing empirical glimpses into the lowland landscapes of large rivers during glacial-interglacial transitions, observations that can be explored with this powerful numerical model. GULLEM affords estimates for the timing and flux budgets within the Fly and Sunda Systems, illustrating complex internal system responses to the external forcing of sea level and climate. Furthermore, GULLEM can be applied to most ANY fluvial system to

  6. Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

    PubMed

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

    2010-10-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

  7. Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community.

    PubMed

    Tanabe, Akifumi S; Nagai, Satoshi; Hida, Kohsuke; Yasuike, Motoshige; Fujiwara, Atushi; Nakamura, Yoji; Takano, Yoshihito; Katakura, Seiji

    2016-03-01

    The nuclear 18S-rRNA gene has been used as a metabarcoding marker in massively parallel sequencing (MPS)-based environmental surveys for plankton biodiversity research. However, different hypervariable regions have been used in different studies, and their utility has been debated among researchers. In this study, detailed investigations into 18S-rRNA were carried out; we investigated the effective number of sequences deposited in international nucleotide sequence databases (INSDs), the amplification bias, and the amplicon sequence variability among the three variable regions, V1-3, V4-5 and V7-9, using in silico polymerase chain reaction (PCR) amplification based on INSDs. We also examined the primer universality and the taxonomic identification power, using MPS-based environmental surveys in the Sea of Okhotsk, to determine which region is more useful for MPS-based monitoring. The primer universality was not significantly different among the three regions, but the number of sequences deposited in INSDs was markedly larger for the V4-5 region than for the other two regions. The sequence variability was significantly different, with the highest variability in the V1-3 region, followed by the V7-9 region, and the lowest variability in the V4-5 region. The results of the MPS-based environmental surveys showed significantly higher identification power in the V1-3 and V7-9 regions than in the V4-5 region, but no significant difference was detected between the V1-3 and V7-9 regions. We therefore conclude that the V1-3 region will be the most suitable for future MPS-based monitoring of natural eukaryote communities, as the number of sequences deposited in INSDs increases.

  8. A combined massively parallel sequencing indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities

    SciTech Connect

    Cardenas, Erick; Wu, Wei-min; Leigh, Mary Beth; Carley, Jack M; Carroll, Sue L; Gentry, Terry; Luo, Jian; Watson, David B; Gu, Baohua; Ginder-Vogel, Matthew A.; Kitanidis, Peter K.; Jardine, Philip; Kelly, Shelly D; Zhou, Jizhong; Criddle, Craig; Marsh, Terence; Tiedje, James

    2010-08-01

    Massively parallel sequencing has provided a more affordable and high throughput method to study microbial communities, although it has been mostly used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium (VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee, USA. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 {micro}M, and created geochemical gradients in electron donors from the inner loop injection well towards the outer loop and down-gradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical created conditions. Castellaniella, and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity; while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. Abundance of these bacteria as well as the Fe(III)- and U(VI)-reducer Geobacter correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to the electron donor addition and by the groundwater flow path. A false discovery rate approach was implemented to discard false positives by chance given the large amount of data compared.

  9. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

    PubMed Central

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.; Tiedje, James M.

    2010-01-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

  10. Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models.

    PubMed

    Andrews, T D; Whittle, B; Field, M A; Balakishnan, B; Zhang, Y; Shao, Y; Cho, V; Kirk, M; Singh, M; Xia, Y; Hager, J; Winslade, S; Sjollema, G; Beutler, B; Enders, A; Goodnow, C C

    2012-05-01

    Accurate identification of sparse heterozygous single-nucleotide variants (SNVs) is a critical challenge for identifying the causative mutations in mouse genetic screens, human genetic diseases and cancer. When seeking to identify causal DNA variants that occur at such low rates, they are overwhelmed by false-positive calls that arise from a range of technical and biological sources. We describe a strategy using whole-exome capture, massively parallel DNA sequencing and computational analysis, which identifies with a low false-positive rate the majority of heterozygous and homozygous SNVs arising de novo with a frequency of one nucleotide substitution per megabase in progeny of N-ethyl-N-nitrosourea (ENU)-mutated C57BL/6j mice. We found that by applying a strategy of filtering raw SNV calls against known and platform-specific variants we could call true SNVs with a false-positive rate of 19.4 per cent and an estimated false-negative rate of 21.3 per cent. These error rates are small enough to enable calling a causative mutation from both homozygous and heterozygous candidate mutation lists with little or no further experimental validation. The efficacy of this approach is demonstrated by identifying the causative mutation in the Ptprc gene in a lymphocyte-deficient strain and in 11 other strains with immune disorders or obesity, without the need for meiotic mapping. Exome sequencing of first-generation mutant mice revealed hundreds of unphenotyped protein-changing mutations, 52 per cent of which are predicted to be deleterious, which now become available for breeding and experimental analysis. We show that exome sequencing data alone are sufficient to identify induced mutations. This approach transforms genetic screens in mice, establishes a general strategy for analysing rare DNA variants and opens up a large new source for experimental models of human disease.

  11. Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

    PubMed

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

    2010-10-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

  12. Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression.

    PubMed

    Piscuoglio, Salvatore; Ng, Charlotte Ky; Murray, Melissa; Burke, Kathleen A; Edelweiss, Marcia; Geyer, Felipe C; Macedo, Gabriel S; Inagaki, Akiko; Papanastasiou, Anastasios D; Martelotto, Luciano G; Marchio, Caterina; Lim, Raymond S; Ioris, Rafael A; Nahar, Pooja K; Bruijn, Ino De; Smyth, Lillian; Akram, Muzaffar; Ross, Dara; Petrini, John H; Norton, Larry; Solit, David B; Baselga, Jose; Brogi, Edi; Ladanyi, Marc; Weigelt, Britta; Reis-Filho, Jorge S

    2016-03-01

    Phyllodes tumours (PTs) are breast fibroepithelial lesions that are graded based on histological criteria as benign, borderline or malignant. PTs may recur locally. Borderline PTs and malignant PTs may metastasize to distant sites. Breast fibroepithelial lesions, including PTs and fibroadenomas, are characterized by recurrent MED12 exon 2 somatic mutations. We sought to define the repertoire of somatic genetic alterations in PTs and whether these may assist in the differential diagnosis of these lesions. We collected 100 fibroadenomas, 40 benign PTs, 14 borderline PTs and 22 malignant PTs; six, six and 13 benign, borderline and malignant PTs, respectively, and their matched normal tissue, were subjected to targeted massively parallel sequencing (MPS) using the MSK-IMPACT sequencing assay. Recurrent MED12 mutations were found in 56% of PTs; in addition, mutations affecting cancer genes (eg TP53, RB1, SETD2 and EGFR) were exclusively detected in borderline and malignant PTs. We found a novel recurrent clonal hotspot mutation in the TERT promoter (-124 C>T) in 52% and TERT gene amplification in 4% of PTs. Laser capture microdissection revealed that these mutations were restricted to the mesenchymal component of PTs. Sequencing analysis of the entire cohort revealed that the frequency of TERT alterations increased from benign (18%) to borderline (57%) and to malignant PTs (68%; p < 0.01), and TERT alterations were associated with increased levels of TERT mRNA (p < 0.001). No TERT alterations were observed in fibroadenomas. An analysis of TERT promoter sequencing and gene amplification distinguished PTs from fibroadenomas with a sensitivity and a positive predictive value of 100% (CI 95.38-100%) and 100% (CI 85.86-100%), respectively, and a sensitivity and a negative predictive value of 39% (CI 28.65-51.36%) and 68% (CI 60.21-75.78%), respectively. Our results suggest that TERT alterations may drive the progression of PTs, and may assist in the differential diagnosis

  13. The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing

    PubMed Central

    2009-01-01

    Background Recent studies have shown that the fecal microbiota is generally resilient to short-term antibiotic administration, but some bacterial taxa may remain depressed for several months. Limited information is available about the effect of antimicrobials on small intestinal microbiota, an important contributor to gastrointestinal health. The antibiotic tylosin is often successfully used for the treatment of chronic diarrhea in dogs, but its exact mode of action and its effect on the intestinal microbiota remain unknown. The aim of this study was to evaluate the effect of tylosin on canine jejunal microbiota. Tylosin was administered at 20 to 22 mg/kg q 24 hr for 14 days to five healthy dogs, each with a pre-existing jejunal fistula. Jejunal brush samples were collected through the fistula on days 0, 14, and 28 (14 days after withdrawal of tylosin). Bacterial diversity was characterized using massive parallel 16S rRNA gene pyrosequencing. Results Pyrosequencing revealed a previously unrecognized species richness in the canine small intestine. Ten bacterial phyla were identified. Microbial populations were phylogenetically more similar during tylosin treatment. However, a remarkable inter-individual response was observed for specific taxa. Fusobacteria, Bacteroidales, and Moraxella tended to decrease. The proportions of Enterococcus-like organisms, Pasteurella spp., and Dietzia spp. increased significantly during tylosin administration (p < 0.05). The proportion of Escherichia coli-like organisms increased by day 28 (p = 0.04). These changes were not accompanied by any obvious clinical effects. On day 28, the phylogenetic composition of the microbiota was similar to day 0 in only 2 of 5 dogs. Bacterial diversity resembled the pre-treatment state in 3 of 5 dogs. Several bacterial taxa such as Spirochaetes, Streptomycetaceae, and Prevotellaceae failed to recover at day 28 (p < 0.05). Several bacterial groups considered to be sensitive to tylosin increased in their

  14. Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression.

    PubMed

    Piscuoglio, Salvatore; Ng, Charlotte Ky; Murray, Melissa; Burke, Kathleen A; Edelweiss, Marcia; Geyer, Felipe C; Macedo, Gabriel S; Inagaki, Akiko; Papanastasiou, Anastasios D; Martelotto, Luciano G; Marchio, Caterina; Lim, Raymond S; Ioris, Rafael A; Nahar, Pooja K; Bruijn, Ino De; Smyth, Lillian; Akram, Muzaffar; Ross, Dara; Petrini, John H; Norton, Larry; Solit, David B; Baselga, Jose; Brogi, Edi; Ladanyi, Marc; Weigelt, Britta; Reis-Filho, Jorge S

    2016-03-01

    Phyllodes tumours (PTs) are breast fibroepithelial lesions that are graded based on histological criteria as benign, borderline or malignant. PTs may recur locally. Borderline PTs and malignant PTs may metastasize to distant sites. Breast fibroepithelial lesions, including PTs and fibroadenomas, are characterized by recurrent MED12 exon 2 somatic mutations. We sought to define the repertoire of somatic genetic alterations in PTs and whether these may assist in the differential diagnosis of these lesions. We collected 100 fibroadenomas, 40 benign PTs, 14 borderline PTs and 22 malignant PTs; six, six and 13 benign, borderline and malignant PTs, respectively, and their matched normal tissue, were subjected to targeted massively parallel sequencing (MPS) using the MSK-IMPACT sequencing assay. Recurrent MED12 mutations were found in 56% of PTs; in addition, mutations affecting cancer genes (eg TP53, RB1, SETD2 and EGFR) were exclusively detected in borderline and malignant PTs. We found a novel recurrent clonal hotspot mutation in the TERT promoter (-124 C>T) in 52% and TERT gene amplification in 4% of PTs. Laser capture microdissection revealed that these mutations were restricted to the mesenchymal component of PTs. Sequencing analysis of the entire cohort revealed that the frequency of TERT alterations increased from benign (18%) to borderline (57%) and to malignant PTs (68%; p < 0.01), and TERT alterations were associated with increased levels of TERT mRNA (p < 0.001). No TERT alterations were observed in fibroadenomas. An analysis of TERT promoter sequencing and gene amplification distinguished PTs from fibroadenomas with a sensitivity and a positive predictive value of 100% (CI 95.38-100%) and 100% (CI 85.86-100%), respectively, and a sensitivity and a negative predictive value of 39% (CI 28.65-51.36%) and 68% (CI 60.21-75.78%), respectively. Our results suggest that TERT alterations may drive the progression of PTs, and may assist in the differential diagnosis

  15. Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.

    PubMed

    Parson, Walther; Ballard, David; Budowle, Bruce; Butler, John M; Gettings, Katherine B; Gill, Peter; Gusmão, Leonor; Hares, Douglas R; Irwin, Jodi A; King, Jonathan L; Knijff, Peter de; Morling, Niels; Prinz, Mechthild; Schneider, Peter M; Neste, Christophe Van; Willuweit, Sascha; Phillips, Christopher

    2016-05-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established

  16. Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.

    PubMed

    Parson, Walther; Ballard, David; Budowle, Bruce; Butler, John M; Gettings, Katherine B; Gill, Peter; Gusmão, Leonor; Hares, Douglas R; Irwin, Jodi A; King, Jonathan L; Knijff, Peter de; Morling, Niels; Prinz, Mechthild; Schneider, Peter M; Neste, Christophe Van; Willuweit, Sascha; Phillips, Christopher

    2016-05-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established

  17. BerkeleyGW: A massively parallel computer package for the calculation of the quasiparticle and optical properties of materials and nanostructures

    NASA Astrophysics Data System (ADS)

    Deslippe, Jack; Samsonidze, Georgy; Strubbe, David A.; Jain, Manish; Cohen, Marvin L.; Louie, Steven G.

    2012-06-01

    BerkeleyGW is a massively parallel computational package for electron excited-state properties that is based on the many-body perturbation theory employing the ab initio GW and GW plus Bethe-Salpeter equation methodology. It can be used in conjunction with many density-functional theory codes for ground-state properties, including PARATEC, PARSEC, Quantum ESPRESSO, SIESTA, and Octopus. The package can be used to compute the electronic and optical properties of a wide variety of material systems from bulk semiconductors and metals to nanostructured materials and molecules. The package scales to 10 000s of CPUs and can be used to study systems containing up to 100s of atoms. Program summaryProgram title: BerkeleyGW Catalogue identifier: AELG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open source BSD License. See code for licensing details. No. of lines in distributed program, including test data, etc.: 576 540 No. of bytes in distributed program, including test data, etc.: 110 608 809 Distribution format: tar.gz Programming language: Fortran 90, C, C++, Python, Perl, BASH Computer: Linux/UNIX workstations or clusters Operating system: Tested on a variety of Linux distributions in parallel and serial as well as AIX and Mac OSX RAM: (50-2000) MB per CPU (Highly dependent on system size) Classification: 7.2, 7.3, 16.2, 18 External routines: BLAS, LAPACK, FFTW, ScaLAPACK (optional), MPI (optional). All available under open-source licenses. Nature of problem: The excited state properties of materials involve the addition or subtraction of electrons as well as the optical excitations of electron-hole pairs. The excited particles interact strongly with other electrons in a material system. This interaction affects the electronic energies, wavefunctions and lifetimes. It is well known that ground-state theories, such as standard methods

  18. NON-CONFORMING FINITE ELEMENTS; MESH GENERATION, ADAPTIVITY AND RELATED ALGEBRAIC MULTIGRID AND DOMAIN DECOMPOSITION METHODS IN MASSIVELY PARALLEL COMPUTING ENVIRONMENT

    SciTech Connect

    Lazarov, R; Pasciak, J; Jones, J

    2002-02-01

    Construction, analysis and numerical testing of efficient solution techniques for solving elliptic PDEs that allow for parallel implementation have been the focus of the research. A number of discretization and solution methods for solving second order elliptic problems that include mortar and penalty approximations and domain decomposition methods for finite elements and finite volumes have been investigated and analyzed. Techniques for parallel domain decomposition algorithms in the framework of PETC and HYPRE have been studied and tested. Hierarchical parallel grid refinement and adaptive solution methods have been implemented and tested on various model problems. A parallel code implementing the mortar method with algebraically constructed multiplier spaces was developed.

  19. 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

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

    2010-03-01

    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.

  20. [Latex ligation in treatment of chronic hemorrhoids].

    PubMed

    Ektov, V N; Somov, K A

    2015-01-01

    We analyzed the results of treatment of 432 patients with chronic hemorrhoids using different variants of latex ligation. New technique including ligation of mucosa and submucosa of low-ampullar rectum providing ligation of hemorrhoidalvessels, lifting and recto-anal repair is developed and suggested. This method is advisable to use in case of chronic internal hemorrhoids stages I and II. The authors recommend simultaneous combined ligation of mucosa of low-ampullar rectum and internal hemorrhoids for stages III and IV. Different variants of latex ligation with external hemorrhoids excision were used in 103 patients. Pointed variants of latex ligation preserve important advantages including mini-invasiveness, simplicity and wide availability, low cost. Good remote results were obtained after these procedures in 87.3% of observations. Suggested tactics extends use of latex ligation and increases its effectiveness in treatment of different stages and forms of chronic hemorrhoids.

  1. Staudinger ligation as a method for bioconjugation.

    PubMed

    van Berkel, Sander S; van Eldijk, Mark B; van Hest, Jan C M

    2011-09-12

    In 1919 the German chemist Hermann Staudinger was the first to describe the reaction between an azide and a phosphine. It was not until recently, however, that Bertozzi and co-workers recognized the potential of this reaction as a method for bioconjugation and transformed it into the so-called Staudinger ligation. The bio-orthogonal character of both the azide and the phosphine functions has resulted in the Staudinger ligation finding numerous applications in various complex biological systems. For example, the Staudinger ligation has been utilized to label glycans, lipids, DNA, and proteins. Moreover, the Staudinger ligation has been used as a synthetic method to construct glycopeptides, microarrays, and functional biopolymers. In the emerging field of bio-orthogonal ligation strategies, the Staudinger ligation has set a high standard to which most of the new techniques are often compared. This Review summarizes recent developments and new applications of the Staudinger ligation.

  2. MPP parallel forth

    NASA Technical Reports Server (NTRS)

    Dorband, John E.

    1987-01-01

    Massively Parallel Processor (MPP) Parallel FORTH is a derivative of FORTH-83 and Unified Software Systems' Uni-FORTH. The extension of FORTH into the realm of parallel processing on the MPP is described. With few exceptions, Parallel FORTH was made to follow the description of Uni-FORTH as closely as possible. Likewise, the parallel FORTH extensions were designed as philosophically similar to serial FORTH as possible. The MPP hardware characteristics, as viewed by the FORTH programmer, is discussed. Then a description is presented of how parallel FORTH is implemented on the MPP.

  3. 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.

  4. Massively Parallel Combined Monte Carlo and Molecular Dynamics Methods to Study the Long-Time-Scale Evolution of Particulate Matter and Molecular Structures Under Reactive Flow Conditions

    SciTech Connect

    Kubota, A; Mundy, C J; Pitz, W J; Melius, C; Westbrook, C K; Caturla, M

    2003-12-19

    An important challenge in computational modeling is the development of new computational methods and capabilities for studying molecular-scale structures over very large time-scales. In particular, there is great interest in understanding the nucleation and growth of carbon soot particles as well as their fate in the atmosphere. We have recently developed and implemented a new computational tool to time-integrate the detailed structure of atomistically resolved surfaces and nanostructures driven by chemical and physical kinetic rule-based rate expressions. Fundamental chemical and physical processes such as chemical reactions, surface adsorption and surface diffusion are performed using a non-lattice real-space kinetic Monte Carlo scheme and driven by user-defined rule-based kinetic rate expressions, while atomic structure relaxation is approached using molecular dynamics. We demonstrate the sensitivity of particle evolution to chemical and physical kinetic mechanism using a parallel implementation of the combined Monte Carlo and molecular dynamics code.

  5. The Application of a Massively Parallel Computer to the Simulation of Electrical Wave Propagation Phenomena in the Heart Muscle Using Simplified Models

    NASA Technical Reports Server (NTRS)

    Karpoukhin, Mikhii G.; Kogan, Boris Y.; Karplus, Walter J.

    1995-01-01

    The simulation of heart arrhythmia and fibrillation are very important and challenging tasks. The solution of these problems using sophisticated mathematical models is beyond the capabilities of modern super computers. To overcome these difficulties it is proposed to break the whole simulation problem into two tightly coupled stages: generation of the action potential using sophisticated models. and propagation of the action potential using simplified models. The well known simplified models are compared and modified to bring the rate of depolarization and action potential duration restitution closer to reality. The modified method of lines is used to parallelize the computational process. The conditions for the appearance of 2D spiral waves after the application of a premature beat and the subsequent traveling of the spiral wave inside the simulated tissue are studied.

  6. LaMEM: a Massively Parallel Staggered-Grid Finite-Difference Code for Thermo-Mechanical Modeling of Lithospheric Deformation with Visco-Elasto-Plastic Rheologies

    NASA Astrophysics Data System (ADS)

    Kaus, B.; Popov, A.

    2014-12-01

    The complexity of lithospheric rheology and the necessity to resolve the deformation patterns near the free surface (faults and folds) sufficiently well places a great demand on a stable and scalable modeling tool that is capable of efficiently handling nonlinearities. Our code LaMEM (Lithosphere and Mantle Evolution Model) is an attempt to satisfy this demand. The code utilizes a stable and numerically inexpensive finite difference discretization with the spatial staggering of velocity, pressure, and temperature unknowns (a so-called staggered grid). As a time discretization method the forward Euler, or a combination of the predictor-corrector and the fourth-order Runge-Kutta can be chosen. Elastic stresses are rotated on the markers, which are also used to track all relevant material properties and solution history fields. The Newtonian nonlinear iteration, however, is handled at the level of the grid points to avoid spurious averaging between markers and grid. Such an arrangement required us to develop a non-standard discretization of the effective strain-rate second invariant. Important feature of the code is its ability to handle stress-free and open-box boundary conditions, in which empty cells are simply eliminated from the discretization, which also solves the biggest problem of the sticky-air approach - namely large viscosity jumps near the free surface. We currently support an arbitrary combination of linear elastic, nonlinear viscous with multiple creep mechanisms, and plastic rheologies based on either a depth-dependent von Mises or pressure-dependent Drucker-Prager yield criteria.LaMEM is being developed as an inherently parallel code. Structurally all its parts are based on the building blocks provided by PETSc library. These include Jacobian-Free Newton-Krylov nonlinear solvers with convergence globalization techniques (line search), equipped with different linear preconditioners. We have also implemented the coupled velocity-pressure multigrid

  7. Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

    PubMed Central

    2012-01-01

    Background High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). Results We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types

  8. Second-Order Møller-Plesset Perturbation Theory in the Condensed Phase: An Efficient and Massively Parallel Gaussian and Plane Waves Approach.

    PubMed

    Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

    2012-11-13

    A novel algorithm, based on a hybrid Gaussian and plane waves (GPW) approach, is developed for the canonical second-order Møller-Plesset perturbation energy (MP2) of finite and extended systems. The key aspect of the method is that the electron repulsion integrals (ia|λσ) are computed by direct integration between the products of Gaussian basis functions λσ and the electrostatic potential arising from a given occupied-virtual pair density ia. The electrostatic potential is obtained in a plane waves basis set after solving the Poisson equation in Fourier space. In particular, for condensed phase systems, this scheme is highly efficient. Furthermore, our implementation has low memory requirements and displays excellent parallel scalability up to 100 000 processes. In this way, canonical MP2 calculations for condensed phase systems containing hundreds of atoms or more than 5000 basis functions can be performed within minutes, while systems up to 1000 atoms and 10 000 basis functions remain feasible. Solid LiH has been employed as a benchmark to study basis set and system size convergence. Lattice constants and cohesive energies of various molecular crystals have been studied with MP2 and double-hybrid functionals. PMID:26605583

  9. Massive Stars

    NASA Astrophysics Data System (ADS)

    Livio, Mario; Villaver, Eva

    2009-11-01

    Participants; Preface Mario Livio and Eva Villaver; 1. High-mass star formation by gravitational collapse of massive cores M. R. Krumholz; 2. Observations of massive star formation N. A. Patel; 3. Massive star formation in the Galactic center D. F. Figer; 4. An X-ray tour of massive star-forming regions with Chandra L. K. Townsley; 5. Massive stars: feedback effects in the local universe M. S. Oey and C. J. Clarke; 6. The initial mass function in clusters B. G. Elmegreen; 7. Massive stars and star clusters in the Antennae galaxies B. C. Whitmore; 8. On the binarity of Eta Carinae T. R. Gull; 9. Parameters and winds of hot massive stars R. P. Kudritzki and M. A. Urbaneja; 10. Unraveling the Galaxy to find the first stars J. Tumlinson; 11. Optically observable zero-age main-sequence O stars N. R. Walborn; 12. Metallicity-dependent Wolf-Raynet winds P. A. Crowther; 13. Eruptive mass loss in very massive stars and Population III stars N. Smith; 14. From progenitor to afterlife R. A. Chevalier; 15. Pair-production supernovae: theory and observation E. Scannapieco; 16. Cosmic infrared background and Population III: an overview A. Kashlinsky.

  10. Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips.

    SciTech Connect

    Krylov, A. S.; Zasedateleva, O. A.; Prokopenko, D. V.; Rouviere-Yaniv, J.; Mirzabekov, A. D.; Biochip Technology Center; Engelhardt Inst. of Molecular Biology; Inst. de Biologie Physico-Chimique

    2001-06-15

    A generic hexadeoxyribonucleotide microchip has been applied to test the DNA-binding properties of HU histone-like bacterial protein, which is known to have a low sequence specificity. All 4096 hexamers flanked within 8mers by degenerate bases at both the 3'- and 5'-ends were immobilized within the 100 x 100 x 20 mm polyacrylamide gel pads of the microchip. Single-stranded immobilized oligonucleotides were converted in some experiments to the double-stranded form by hybridization with a specified mixture of 8mers. The DNA interaction with HU was characterized by three type of measurements: (i) binding of FITC-labeled HU to microchip oligonucleotides; (ii) melting curves of complexes of labeled HU with single-stranded microchip oligonucleotides; (iii) the effect of HU binding on melting curves of microchip double-stranded DNA labeled with another fluorescent dye, Texas Red. Large numbers of measurements of these parameters were carried out in parallel for all or many generic microchip elements in real time with a multi-wavelength fluorescence microscope. Statistical analysis of these data suggests some preference for HU binding to G/C-rich single-stranded oligonucleotides. HU complexes with double-stranded microchip 8mers can be divided into two groups in which HU binding either increased the melting temperature (T{sub m}) of duplexes or decreased it. The stabilized duplexes showed some preference for presence of the sequence motifs AAG, AGA and AAGA. In the second type of complex, enriched with A/T base pairs, the destabilization effect was higher for longer stretches of A/T duplexes. Binding of HU to labeled duplexes in the second type of complex caused some decrease in fluorescence. This decrease also correlates with the higher A/T content and lower T{sub m}. The results demonstrate that generic microchips could be an efficient approach in analysis of sequence specificity of proteins.

  11. The "Floss-Ligature" Ligation Technique.

    PubMed

    Dugdale, Charlotte Anne; Malik, Ovais Humair; Waring, David Trevor

    2015-01-01

    This clinical pearl describes an alternative technique to aid effective ligation of rotated teeth during the aligning stage of fixed appliance treatment. This technique has the potential to improve patient experience and confidence, by reducing the risk of trauma and discomfort and treatment efficiency, by ensuring complete ligation of even severely rotated teeth.

  12. 21 CFR 876.4400 - Hemorrhoidal ligator.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Hemorrhoidal ligator. 876.4400 Section 876.4400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GASTROENTEROLOGY-UROLOGY DEVICES Surgical Devices § 876.4400 Hemorrhoidal ligator....

  13. 21 CFR 876.4400 - Hemorrhoidal ligator.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Hemorrhoidal ligator. 876.4400 Section 876.4400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GASTROENTEROLOGY-UROLOGY DEVICES Surgical Devices § 876.4400 Hemorrhoidal ligator....

  14. 21 CFR 876.4400 - Hemorrhoidal ligator.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Hemorrhoidal ligator. 876.4400 Section 876.4400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GASTROENTEROLOGY-UROLOGY DEVICES Surgical Devices § 876.4400 Hemorrhoidal ligator....

  15. 21 CFR 876.4400 - Hemorrhoidal ligator.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Hemorrhoidal ligator. 876.4400 Section 876.4400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GASTROENTEROLOGY-UROLOGY DEVICES Surgical Devices § 876.4400 Hemorrhoidal ligator....

  16. 21 CFR 876.4400 - Hemorrhoidal ligator.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Hemorrhoidal ligator. 876.4400 Section 876.4400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GASTROENTEROLOGY-UROLOGY DEVICES Surgical Devices § 876.4400 Hemorrhoidal ligator....

  17. Formation of oligonucleotide-PNA-chimeras by template-directed ligation

    NASA Technical Reports Server (NTRS)

    Koppitz, M.; Nielsen, P. E.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1998-01-01

    DNA sequences have previously been reported to act as templates for the synthesis of PNA, and vice versa. A continuous evolutionary transition from an informational replicating system based on one polymer to a system based on the other would be facilitated if it were possible to form chimeras, that is molecules that contain monomers of both types. Here we show that ligation to form chimeras proceeds efficiently both on PNA and on DNA templates. The efficiency of ligation is primarily determined by the number of backbone bonds at the ligation site and the relative orientation of template and substrate strands. The most efficient reactions result in the formation of chimeras with ligation junctions resembling the structures of the backbones of PNA and DNA and with antiparallel alignment of both components of the chimera with the template, that is, ligations involving formation of 3'-phosphoramidate and 5'-ester bonds. However, double helices involving PNA are stable both with antiparallel and parallel orientation of the two strands. Ligation on PNA but not on DNA templates is, therefore, sometimes possible on templates with reversed orientation. The relevance of these findings to discussions of possible transitions between genetic systems is discussed.

  18. Parallel computing works

    SciTech Connect

    Not Available

    1991-10-23

    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 many 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.

  19. Kinetics of ligation of fibrin oligomers.

    PubMed

    Nelb, G W; Kamykowski, G W; Ferry, J D

    1980-07-10

    Human fibrinogen was treated with thrombin in the presence of fibrinoligase and calcium ion at pH 8.5, ionic strength 0.45, and the ensuring polymerization was interrupted at various time intervals (t) both before and after the clotting time (tc) by solubilization with a solution of sodium dodecyl sulfate and urea. Aliquots of the solubilized protein were subjected to gel electrophoresis on polyacrylamide gels after disulfide reduction by dithiothreitol and on agarose gels without reduction. The degree of gamma-gamma ligation was determined from the former and the size distribution of ligated oligomers, for degree of polymerization x from 1 to 10, from the latter. The degree of gamma-gamma ligation was calculated independently from the size distribution with the assumption that every junction between two fibrin monomers remaining intact after solubilization is ligated, and this agreed well with the direct determination. The size distribution at t/tc = 1.3 to 1.6 differed somewhat from that calculated by the classical theory of linear polycondensation on the assumption that all reactive sites react with equal probability and rate. Analysis of the difference suggests that ligation of a fibrin digomer is not a random process; the probability of ligation of a given junction between two monomers increases with the oligomer length. The number-average degree of polymerization, xn, of ligated oligomers increases approximately linearly with time up to a value of 1.6. PMID:7391026

  20. Cloning of DNA fragments: ligation reactions in agarose gel.

    PubMed

    Furtado, Agnelo

    2014-01-01

    Ligation reactions to ligate a desired DNA fragment into a vector can be challenging to beginners and especially if the amount of the insert is limiting. Although additives known as crowding agents, such as PEG 8000, added to the ligation mixes can increase the success one has with ligation reactions, in practice the amount of insert used in the ligation can determine the success or the failure of the ligation reaction. The method described here, which uses insert DNA in gel slice added directly into the ligation reaction, has two benefits: (a) using agarose as the crowding agent and (b) reducing steps of insert purification. The use of rapid ligation buffer and incubation of the ligation reaction at room temperature greatly increase the efficiency of the ligation reaction even for blunt-ended ligation. PMID:24243199

  1. Reconstruction of the 1997/1998 El Nino from TOPEX/POSEIDON and TOGA/TAO Data Using a Massively Parallel Pacific-Ocean Model and Ensemble Kalman Filter

    NASA Technical Reports Server (NTRS)

    Keppenne, C. L.; Rienecker, M.; Borovikov, A. Y.

    1999-01-01

    Two massively parallel data assimilation systems in which the model forecast-error covariances are estimated from the distribution of an ensemble of model integrations are applied to the assimilation of 97-98 TOPEX/POSEIDON altimetry and TOGA/TAO temperature data into a Pacific basin version the NASA Seasonal to Interannual Prediction Project (NSIPP)ls quasi-isopycnal ocean general circulation model. in the first system, ensemble of model runs forced by an ensemble of atmospheric model simulations is used to calculate asymptotic error statistics. The data assimilation then occurs in the reduced phase space spanned by the corresponding leading empirical orthogonal functions. The second system is an ensemble Kalman filter in which new error statistics are computed during each assimilation cycle from the time-dependent ensemble distribution. The data assimilation experiments are conducted on NSIPP's 512-processor CRAY T3E. The two data assimilation systems are validated by withholding part of the data and quantifying the extent to which the withheld information can be inferred from the assimilation of the remaining data. The pros and cons of each system are discussed.

  2. Massive obstetric haemorrhage with disseminated intravascular coagulopathy.

    PubMed

    Su, Lin Lin; Chong, Yap Seng

    2012-02-01

    Massive obstetric haemorrhage is a major contributor towards maternal morbidity and mortality. The main causes are abruptio placentae, placenta praevia and postpartum haemorrhage. Clinicians managing pregnant women should be equipped with the knowledge and skills for managing massive obstetric haemorrhage to institute timely and appropriate life-saving treatment. Prompt resuscitation and reversal of coagulopathy are critical while definitive measures are carried out to arrest the bleeding. Massive antepartum haemorrhage necessitates deliveries whereas interventions for postpartum haemorrhage range from medical to surgical measures. Algorithms such as haemostasis are useful aids to the systematic and stepwise management of postpartum haemorrhage. Surgical measures used to avoid peripartum haemorrhage include uterine compression sutures, uterine balloon tamponade, uterine artery, and internal iliac artery ligation. Tranexamic acid and recombinant factor VII are more recent medical interventions in massive postpartum haemorrhage. Education, regular drills and adherence to guidelines and protocols are important to reduce haemorrhage-related maternal deaths. PMID:22101177

  3. A comparative study of conventional ligation and self-ligation bracket systems.

    PubMed

    Shivapuja, P K; Berger, J

    1994-11-01

    The increased use of self-ligating bracket systems frequently raises the question of how they compare with conventional ligation systems. An in vitro and clinical investigation was undertaken to evaluate and compare these distinctly different groups, by using five different brackets. The Activa ("A" Company, Johnson & Johnson, San Diego, Calif.), Edgelok (Ormco, Glendora, Calif.), and SPEED (Strite Industries Ltd., Cambridge, Ontario) self-ligating bracket systems displayed a significantly lower level of frictional resistance, dramatically less chairtime for arch wire removal and insertion, and promoted improved infection control, when compared with polyurethane elastomeric and stainless steel tie wire ligation for ceramic and metal twin brackets. PMID:7977187

  4. Modeling groundwater flow on massively parallel computers

    SciTech Connect

    Ashby, S.F.; Falgout, R.D.; Fogwell, T.W.; Tompson, A.F.B.

    1994-12-31

    The authors will explore the numerical simulation of groundwater flow in three-dimensional heterogeneous porous media. An interdisciplinary team of mathematicians, computer scientists, hydrologists, and environmental engineers is developing a sophisticated simulation code for use on workstation clusters and MPPs. To date, they have concentrated on modeling flow in the saturated zone (single phase), which requires the solution of a large linear system. they will discuss their implementation of preconditioned conjugate gradient solvers. The preconditioners under consideration include simple diagonal scaling, s-step Jacobi, adaptive Chebyshev polynomial preconditioning, and multigrid. They will present some preliminary numerical results, including simulations of groundwater flow at the LLNL site. They also will demonstrate the code`s scalability.

  5. High-speed massively parallel scanning

    DOEpatents

    Decker, Derek E.

    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.

  6. Massively parallel X-ray holography

    SciTech Connect

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

    2008-08-01

    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 holography1,2,3 as a promising but, so far, inefficient scheme to do this. We show that a uniformly redundant array4 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

  7. Massively parallel collaboration : a literature review.

    SciTech Connect

    Dornburg, Courtney C.; Stevens, Susan Marie; Davidson, George S.; Forsythe, James Chris

    2007-09-01

    The present paper explores group dynamics and electronic communication, two components of wicked problem solving that are inherent to the national security environment (as well as many other business environments). First, because there can be no ''right'' answer or solution without first having agreement about the definition of the problem and the social meaning of a ''right solution'', these problems (often) fundamentally relate to the social aspects of groups, an area with much empirical research and application still needed. Second, as computer networks have been increasingly used to conduct business with decreased costs, increased information accessibility, and rapid document, database, and message exchange, electronic communication enables a new form of problem solving group that has yet to be well understood, especially as it relates to solving wicked problems.

  8. Robustness of Massively Parallel Sequencing Platforms.

    PubMed

    Kavak, Pınar; Yüksel, Bayram; Aksu, Soner; Kulekci, M Oguzhan; Güngör, Tunga; Hach, Faraz; Şahinalp, S Cenk; Alkan, Can; Sağıroğlu, Mahmut Şamil

    2015-01-01

    The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications.

  9. 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.

  10. Effects of double ligation of Stensen's duct on the rabbit parotid gland.

    PubMed

    Maria, O M; Maria, S M; Redman, R S; Maria, A M; Saad El-Din, T A; Soussa, E F; Tran, S D

    2014-04-01

    Salivary gland duct ligation is an alternative to gland excision for treating sialorrhea or reducing salivary gland size prior to tumor excision. Duct ligation also is used as an approach to study salivary gland aging, regeneration, radiotherapy, sialolithiasis and sialadenitis. Reports conflict about the contribution of each salivary cell population to gland size reduction after ductal ligation. Certain cell populations, especially acini, reportedly undergo atrophy, apoptosis and proliferation during reduction of gland size. Acini also have been reported to de-differentiate into ducts. These contradictory results have been attributed to different animal or salivary gland models, or to methods of ligation. We report here a bilateral double ligature technique for rabbit parotid glands with histologic observations at 1, 7, 14, 30, 60 days after ligation. A large battery of special stains and immunohistochemical procedures was employed to define the cell populations. Four stages with overlapping features were observed that led to progressive shutdown of gland activities: 1) marked atrophy of the acinar cells occurred by 14 days, 2) response to and removal of the secretory material trapped in the acinar and ductal lumens mainly between 30 and 60 days, 3) reduction in the number of parenchymal (mostly acinar) cells by apoptosis that occurred mainly between 14-30 days, and 4) maintenance of steady-state at 60 days with a low rate of fluid, protein, and glycoprotein secretion, which greatly decreased the number of leukocytes engaged in the removal of the luminal contents. The main post- ligation characteristics were dilation of ductal and acinar lumens, massive transient infiltration of mostly heterophils (rabbit polymorphonuclear leukocytes), acinar atrophy, and apoptosis of both acinar and ductal cells. Proliferation was uncommon except in the larger ducts. By 30 days, the distribution of myoepithelial cells had spread from exclusively investing the intercalated ducts

  11. Massive gravity

    NASA Astrophysics Data System (ADS)

    Mukohyama, Shinji

    2013-09-01

    The concept of mass has been central in many areas of physics. Gravitation is not an exception, and it has been one of the long-standing questions whether the graviton, a spin-2 particle that mediates gravity, can have a non-vanishing mass or not. This question is relevant from not only theoretical but also phenomenological viewpoints, since a nonzero graviton mass may lead to late-time acceleration of the universe and thus may be considered as an alternative to dark energy. In 2010, de Rham, Gabadadze and Tolley proposed the first example of a fully nonlinear massive gravity theory and showed that the so called Boulware-Deser ghost, which had been one of the major obstacles against a stable nonlinear theory of massive gravity since 1972, can be removed by construction. Since then, nonlinear massive gravity has been attracting significant interest among physicists and cosmologists. The nonlinear theory of massive gravity provides a theoretical framework in which properties of the remaining five physical degrees of freedom of massive gravity can be studied. As always with any low-energy effective theories, one of the first tasks would be to identify good and bad backgrounds. Depending on the choice of backgrounds, some of the five degrees of freedom may become strongly coupled, may exhibit instantaneous propagation, or may lead to ghost/gradient instabilities. A related subject is to seek interesting solutions such as those relevant for astrophysical objects and those describing self-accelerating cosmology. Those solutions will allow us to study phenomenological and cosmological implications of the theory. Yet another important task would be to seek a possible (partial) UV completion that can be applied beyond the regime of validity of the low-energy effective theory that we currently know of. We invited articles to cover those important subjects in massive gravity. Given the recent rapid developments in the field, however, it must be noted that this focus issue

  12. Parallel Dislocation Simulator

    2006-10-30

    ParaDiS is software capable of simulating the motion, evolution, and interaction of dislocation networks in single crystals using massively parallel computer architectures. The software is capable of outputting the stress-strain response of a single crystal whose plastic deformation is controlled by the dislocation processes.

  13. Massive Bleeding and Massive Transfusion

    PubMed Central

    Meißner, Andreas; Schlenke, Peter

    2012-01-01

    Massive bleeding in trauma patients is a serious challenge for all clinicians, and an interdisciplinary diagnostic and therapeutic approach is warranted within a limited time frame. Massive transfusion usually is defined as the transfusion of more than 10 units of packed red blood cells (RBCs) within 24 h or a corresponding blood loss of more than 1- to 1.5-fold of the body's entire blood volume. Especially male trauma patients experience this life-threatening condition within their productive years of life. An important parameter for clinical outcome is to succeed in stopping the bleeding preferentially within the first 12 h of hospital admission. Additional coagulopathy in the initial phase is induced by trauma itself and aggravated by consumption and dilution of clotting factors. Although different aspects have to be taken into consideration when viewing at bleedings induced by trauma compared to those caused by major surgery, the basic strategy is similar. Here, we will focus on trauma-induced massive hemorrhage. Currently there are no definite, worldwide accepted algorithms for blood transfusion and strategies for optimal coagulation management. There is increasing evidence that a higher ratio of plasma and RBCs (e.g. 1:1) endorsed by platelet transfusion might result in a superior survival of patients at risk for trauma-induced coagulopathy. Several strategies have been evolved in the military environment, although not all strategies should be transferred unproven to civilian practice, e.g. the transfusion of whole blood. Several agents have been proposed to support the restoration of coagulation. Some have been used for years without any doubt on their benefit-to-risk profile, whereas great enthusiasm of other products has been discouraged by inefficacy in terms of blood transfusion requirements and mortality or significant severe side effects. This review surveys current literature on fluid resuscitation, blood transfusion, and hemostatic agents currently

  14. Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry

    PubMed Central

    So, Austin P.; Turner, Robin F. B.; Haynes, Charles A.

    2004-01-01

    The ability of Serial Analysis of Gene Expression (SAGE) to provide a quantitative picture of global gene expression relies not only on the depth and accuracy of sequencing into the SAGE library, but also on the efficiency of each step required to generate the SAGE library from the starting mRNA material. The first critical step is the ligation of adaptors containing a Type IIS recognition sequence to the anchored 3′ end cDNA population that permits the release of short sequence tags (SSTs) from defined sites within the 3′ end of each transcript. Using an in vitro transcript as a template, we observed that only a small fraction of anchored 3′ end cDNA are successfully ligated with added SAGE adaptors under typical reaction conditions currently used in the SAGE protocol. Although the introduction of ∼500-fold molar excess of adaptor or the inclusion of 15% (w/v) PEG-8000 increased the yield of the adaptor-modified product, complete conversion to the desired adaptor:cDNA hetero-ligation product is not achieved. An alternative method of ligation, termed as directed ligation, is described which exploits a favourable mass-action condition created by the presence of NlaIII during ligation in combination with a novel SAGE adaptor containing a methylated base within the ligation site. Using this strategy, we were able to achieve near complete conversion of the anchored 3′ end cDNA into the desired adaptor-modified product. This new protocol therefore greatly increases the probability that a SST will be generated from every transcript, greatly enhancing the fidelity of SAGE. Directed ligation also provides a powerful means to achieve near-complete ligation of any appropriately designed adaptor to its respective target. PMID:15247329

  15. LaMEM: a massively parallel 3D staggered-grid finite-difference code for coupled nonlinear themo-mechanical modeling of lithospheric deformation with visco-elasto-plastic rheology

    NASA Astrophysics Data System (ADS)

    Popov, Anton; Kaus, Boris

    2015-04-01

    This software project aims at bringing the 3D lithospheric deformation modeling to a qualitatively different level. Our code LaMEM (Lithosphere and Mantle Evolution Model) is based on the following building blocks: * Massively-parallel data-distributed implementation model based on PETSc library * Light, stable and accurate staggered-grid finite difference spatial discretization * Marker-in-Cell pedictor-corector time discretization with Runge-Kutta 4-th order * Elastic stress rotation algorithm based on the time integration of the vorticity pseudo-vector * Staircase-type internal free surface boundary condition without artificial viscosity contrast * Geodynamically relevant visco-elasto-plastic rheology * Global velocity-pressure-temperature Newton-Raphson nonlinear solver * Local nonlinear solver based on FZERO algorithm * Coupled velocity-pressure geometric multigrid preconditioner with Galerkin coarsening Staggered grid finite difference, being inherently Eulerian and rather complicated discretization method, provides no natural treatment of free surface boundary condition. The solution based on the quasi-viscous sticky-air phase introduces significant viscosity contrasts and spoils the convergence of the iterative solvers. In LaMEM we are currently implementing an approximate stair-case type of the free surface boundary condition which excludes the empty cells and restores the solver convergence. Because of the mutual dependence of the stress and strain-rate tensor components, and their different spatial locations in the grid, there is no straightforward way of implementing the nonlinear rheology. In LaMEM we have developed and implemented an efficient interpolation scheme for the second invariant of the strain-rate tensor, that solves this problem. Scalable efficient linear solvers are the key components of the successful nonlinear problem solution. In LaMEM we have a range of PETSc-based preconditioning techniques that either employ a block factorization of

  16. Implantation of self-expanding metal stent in the treatment of severe bleeding from esophageal ulcer after endoscopic band ligation.

    PubMed

    Mishin, I; Ghidirim, G; Dolghii, A; Bunic, G; Zastavnitsky, G

    2010-09-01

    Endoscopic variceal ligation is superior to sclerotherapy because of its lower rebleeding and complication rates. However, ligation may be associated with life-threatening bleeding from postbanding esophageal ulcer. We report a case of a 49-year-old male with massive hemorrhage from esophageal ulcer on 8th day after successful band ligation of bleeding esophageal varices caused by postviral liver cirrhosis (Child-Pugh class C). A removable polyurethane membrane-covered self-expanding metal stent (SX-ELLA stent Danis, 135 mm × 25 mm, ELLA-CS, Hradec-Kralove, Czech Republic) was inserted in ICU for preventing fatal hemorrhage. Complete hemostasis was achieved and stent was removed after 8 days without rebleeding or any complications. To the best of our knowledge, this is the first report in English literature regarding life-threatening hemorrhage from postbanding esophageal ulcer successfully treated by self-expanding metal stent in a patient with portal hypertension.

  17. 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.

  18. Bidirectional Glenn with interruption of antegrade pulmonary blood flow: Which is the preferred option: Ligation or division of the pulmonary artery?

    PubMed

    Chowdhury, Ujjwal Kumar; Kapoor, Poonam Malhotra; Rao, Keerthi; Gharde, Parag; Kumawat, Mukesh; Jagia, Priya

    2016-01-01

    We report a rare complication of massive aneurysm of the proximal ligated end of the main pulmonary artery which occurred in the setting of a patient with a functionally univentricular heart and increased pulmonary blood flow undergoing superior cavopulmonary connection. Awareness of this possibility may guide others to electively transect the pulmonary artery in such a clinical setting. PMID:27397472

  19. Differences Between Distributed and Parallel Systems

    SciTech Connect

    Brightwell, R.; Maccabe, A.B.; Rissen, R.

    1998-10-01

    Distributed systems have been studied for twenty years and are now coming into wider use as fast networks and powerful workstations become more readily available. In many respects a massively parallel computer resembles a network of workstations and it is tempting to port a distributed operating system to such a machine. However, there are significant differences between these two environments and a parallel operating system is needed to get the best performance out of a massively parallel system. This report characterizes the differences between distributed systems, networks of workstations, and massively parallel systems and analyzes the impact of these differences on operating system design. In the second part of the report, we introduce Puma, an operating system specifically developed for massively parallel systems. We describe Puma portals, the basic building blocks for message passing paradigms implemented on top of Puma, and show how the differences observed in the first part of the report have influenced the design and implementation of Puma.

  20. 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.

  1. Parallel computers

    SciTech Connect

    Treveaven, P.

    1989-01-01

    This book presents an introduction to object-oriented, functional, and logic parallel computing on which the fifth generation of computer systems will be based. Coverage includes concepts for parallel computing languages, a parallel object-oriented system (DOOM) and its language (POOL), an object-oriented multilevel VLSI simulator using POOL, and implementation of lazy functional languages on parallel architectures.

  2. Atrophy of submandibular gland by the duct ligation and a blockade of SP receptor in rats

    PubMed Central

    Hishida, Sumiyo; Ozaki, Noriyuki; Honda, Takashi; Shigetomi, Toshio; Ueda, Minoru; Hibi, Hideharu; Sugiura, Yasuo

    2016-01-01

    ABSTRACT To clarify the mechanisms underlying the submandibular gland atrophies associated with ptyalolithiasis, morphological changes were examined in the rat submandibular gland following either surgical intervention of the duct or functional blockade at substance P receptors (SPRs). Progressive acinar atrophy was observed after duct ligation or avulsion of periductal tissues. This suggested that damage to periductal tissue involving nerve fibers might contribute to ligation-associated acinar atrophy. Immunohistochemically labeled-substance P positive nerve fibers (SPFs) coursed in parallel with the main duct and were distributed around the interlobular, striated, granular and intercalated duct, and glandular acini. Strong SPR immunoreactivity was observed in the duct. Injection into the submandibular gland of a SPR antagonist induced marked acinar atrophy. The results revealed that disturbance of SPFs and SPRs might be involved in the atrophy of the submandibular gland associated with ptyalolithiasis. PMID:27303108

  3. Potential performance of methods for parallelism across time in ODEs

    SciTech Connect

    Xuhai, Xu; Gear, C.W.

    1990-01-01

    An earlier report described a possible approach to massive parallelism across time. This report describes some numerical experiments on the method and two modifications to the method to increase the parallelism and improve the behavior for nonlinear stiff problems.

  4. Successful Management of Two Cases of Placenta Accreta and a Literature Review: Use of the B-Lynch Suture and Bilateral Uterine Artery Ligation Procedures

    PubMed Central

    Arab, Maliheh; Ghavami, Behnaz; Saraeian, Samaneh; Sheibani, Samaneh; Abbasian Azar, Fatemeh; Hosseini-Zijoud, Seyed-Mostafa

    2016-01-01

    Introduction Placenta accreta is an increasingly common complication of pregnancy that can result in massive hemorrhage. Case Presentation We describe two cases of placenta accreta, with successful conservative management in a referral hospital in Tehran, Iran. In both cases, two procedures were performed: compression suture (B-Lynch) and a perfusion-decreasing procedure (bilateral uterine artery ligation). We also present the results of a narrative literature review. Conclusions The double B-Lynch and uterine arterial ligation procedure in cases of abnormal placentation might be strongly considered in fertility preservation, coagulopathy, coexisting medical disease, blood access shortage, low surgical experience, distant local hospitals, and no help. PMID:27354921

  5. The effects of LAA ligation on LAA electrical activity

    PubMed Central

    Lakkireddy, Dhanunjaya; Rojas, Francia; Bednarek, Jacek; Kapelak, Boguslaw; Bartus, Magdalena; Sadowski, Jerzy; Badhwar, Nitish; Earnest, Mathew; Valderrabano, Miguel; Lee, Randall J.

    2015-01-01

    BACKGROUND The arrhythmic role of the left atrial appendage (LAA) has been implicated in the maintenance of persistent atrial fibrillation. LAA isolation with catheter ablation has been successful but is limited by the risk of tamponade and electromechanical dissociation with the potential for LAA thrombus formation. OBJECTIVE To assess whether LAA ligation results in LAA electrical isolation. METHODS A total of 68 patients with contraindication or intolerance to oral anticoagulation therapy underwent LAA ligation with the LARIAT suture delivery device. Patients had unipolar [n = 30 (44%)] or bipolar [n = 38(56%)] voltage measurements pre- and post-LAA ligation. RESULTS All 68 patients underwent successful LAA ligation. There was a statistically significant reduction in the mean LAA voltage from pre-ligation (unipolar pre-ligation voltage 1.1 ± 0.53 mV; bipolar pre-ligation voltage 4.7 ± 2.83 mV) to post-ligation (unipolar post-ligation voltage 0.3 ± 0.38 mV; bipolar post-ligation voltage 0.6 ± 0.27 mV). Ninety-four percent of the patients had a reduction in the LAA voltage after the closure of the snare, with 10 of 30 (33%) of the patients having complete elimination of LAA voltage with the initial tightening of the suture. Pacing from the LAA after the closure of the snare resulted in lack of capture of the left atrium in 28 of 31 patients. CONCLUSIONS The snare closure of the LAA using the LARIAT device produces an acute reduction in the LAA voltage and inhibits the capture of the left atrium during LAA pacing. Future studies are needed to determine whether LAA ligation affects atrial fibrillation burden. PMID:24444443

  6. Massive transfusion and massive transfusion protocol

    PubMed Central

    Patil, Vijaya; Shetmahajan, Madhavi

    2014-01-01

    Haemorrhage remains a major cause of potentially preventable deaths. Rapid transfusion of large volumes of blood products is required in patients with haemorrhagic shock which may lead to a unique set of complications. Recently, protocol based management of these patients using massive transfusion protocol have shown improved outcomes. This section discusses in detail both management and complications of massive blood transfusion. PMID:25535421

  7. Massive transfusion and massive transfusion protocol.

    PubMed

    Patil, Vijaya; Shetmahajan, Madhavi

    2014-09-01

    Haemorrhage remains a major cause of potentially preventable deaths. Rapid transfusion of large volumes of blood products is required in patients with haemorrhagic shock which may lead to a unique set of complications. Recently, protocol based management of these patients using massive transfusion protocol have shown improved outcomes. This section discusses in detail both management and complications of massive blood transfusion.

  8. Template-directed oligonucleotide ligation on hydroxylapatite

    NASA Technical Reports Server (NTRS)

    Acevedo, O. L.; Orgel, L. E.

    1986-01-01

    It has been suggested that the prebiotic synthesis of the precursors of biopolymers could have occurred on a solid surface such as that provided by clay or some other mineral. One such scheme envisages that growing polymers were localized by adsorption to a mineral surface where an activating agent or activated monomers were supplied continuously or cyclically. Here, it is reported that a sequence of reactions in which initially formed oligo(G)s are reactivated by conversion to phosphorimidazolides in the presence of poly(C) and then allowed to ligate is ideal, in that repeated cycles can be carried out on the surface of hydroxylapatite, whereas in the liquid phase the cycle could be achieved only with considerable difficulty.

  9. Sepsis Induced by Cecal Ligation and Puncture

    PubMed Central

    Wen, Haitao

    2014-01-01

    Summary Despite advances in intensive care unit interventions, including the use of specific antibiotics and anti-inflammation treatment, sepsis with concomitant multiple organ failure is the most common cause of death in many acute care units. In order to understand the mechanisms of clinical sepsis and develop effective therapeutic modalities, there is a need to use effective experimental models that faithfully replicate what occurs in patients with sepsis. Several models are commonly used to study sepsis, including intravenous endotoxin challenge, injection of live organisms into the peritoneal cavity, establishing abscesses in the extremities, and the induction of polymicrobial peritonitis via cecal ligation and puncture (CLP). Here, we describe the surgery procedure of CLP in mice, which has been proposed to closely replicate the nature and course of clinical sepsis in humans. PMID:23824895

  10. Parallel rendering

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas W.

    1995-01-01

    This article provides a broad introduction to the subject of parallel rendering, encompassing both hardware and software systems. The focus is on the underlying concepts and the issues which arise in the design of parallel rendering algorithms and systems. We examine the different types of parallelism and how they can be applied in rendering applications. Concepts from parallel computing, such as data decomposition, task granularity, scalability, and load balancing, are considered in relation to the rendering problem. We also explore concepts from computer graphics, such as coherence and projection, which have a significant impact on the structure of parallel rendering algorithms. Our survey covers a number of practical considerations as well, including the choice of architectural platform, communication and memory requirements, and the problem of image assembly and display. We illustrate the discussion with numerous examples from the parallel rendering literature, representing most of the principal rendering methods currently used in computer graphics.

  11. Enabling N-to-C Ser/Thr Ligation for Convergent Protein Synthesis via Combining Chemical Ligation Approaches.

    PubMed

    Lee, Chi Lung; Liu, Han; Wong, Clarence T T; Chow, Hoi Yee; Li, Xuechen

    2016-08-24

    In this article, Ser/Thr ligation(on/off) has been realized to enable N-to-C successive peptide ligations using a salicylaldehyde semicarbazone (SAL(off)) group by in situ activation with pyruvic acid of the peptide SAL(off) ester into the peptide salicylaldehyde (SAL(on)) ester. In addition, a peptide with a C-terminal thioester and N-terminal Ser or Thr as the middle peptide segment can undergo one-pot Ser/Thr ligation and native chemical ligation in the N-to-C direction. The utility of this combined ligation strategy in the N-to-C direction has been showcased through the convergent assembly of a human cytokine protein sequence, GlcNAcylated interleukin-25. PMID:27479006

  12. Ultrascalable petaflop parallel supercomputer

    DOEpatents

    Blumrich, Matthias A.; Chen, Dong; Chiu, George; Cipolla, Thomas M.; Coteus, Paul W.; Gara, Alan G.; Giampapa, Mark E.; Hall, Shawn; Haring, Rudolf A.; Heidelberger, Philip; Kopcsay, Gerard V.; Ohmacht, Martin; Salapura, Valentina; Sugavanam, Krishnan; Takken, Todd

    2010-07-20

    A massively parallel supercomputer of petaOPS-scale includes node architectures based upon System-On-a-Chip technology, where each processing node comprises a single Application Specific Integrated Circuit (ASIC) having up to four processing elements. The ASIC nodes are interconnected by multiple independent networks that optimally maximize the throughput of packet communications between nodes with minimal latency. The multiple networks may include three high-speed networks for parallel algorithm message passing including a Torus, collective network, and a Global Asynchronous network that provides global barrier and notification functions. These multiple independent networks may be collaboratively or independently utilized according to the needs or phases of an algorithm for optimizing algorithm processing performance. The use of a DMA engine is provided to facilitate message passing among the nodes without the expenditure of processing resources at the node.

  13. Efficient Ligation of the Schistosoma Hammerhead Ribozyme †

    PubMed Central

    Canny, Marella D.; Jucker, Fiona M.; Pardi, Arthur

    2011-01-01

    The hammerhead ribozyme from Schistosoma mansoni is the best characterized of the natural hammerhead ribozymes. Biophysical, biochemical, and structural studies have shown that the formation of the loop-loop tertiary interaction between stems I and II alters the global folding, cleavage kinetics, and conformation of the catalytic core of this hammerhead, leading to a ribozyme that is readily cleaved under physiological conditions. This study investigates the ligation kinetics and the internal equilibrium between cleavage and ligation for the Schistosoma hammerhead. Single turnover kinetic studies on a construct where the ribozyme cleaves and ligates substrate(s) in trans showed up to 23% ligation when starting from fully cleaved products. This was achieved by a ~2,000-fold increase in the rate of ligation compared to a minimal hammerhead without the loop-loop tertiary interaction, yielding an internal equilibrium that ranges from 2–3 at physiological Mg2+ ion concentrations (0.1 –1 mM). Thus, the natural Schistosoma hammerhead ribozyme is almost as efficient at ligation as it is at cleavage. The results here are consistent with a model where formation of the loop-loop tertiary interaction leads to a higher population of catalytically active molecules, and where formation of this tertiary interaction has a much larger effect on the ligation than the cleavage activity of the Schistosoma hammerhead ribozyme. PMID:17319693

  14. Convergent synthesis of proteins by kinetically controlled ligation

    DOEpatents

    Kent, Stephen; Pentelute, Brad; Bang, Duhee; Johnson, Erik; Durek, Thomas

    2010-03-09

    The present invention concerns methods and compositions for synthesizing a polypeptide using kinetically controlled reactions involving fragments of the polypeptide for a fully convergent process. In more specific embodiments, a ligation involves reacting a first peptide having a protected cysteyl group at its N-terminal and a phenylthioester at its C-terminal with a second peptide having a cysteine residue at its N-termini and a thioester at its C-termini to form a ligation product. Subsequent reactions may involve deprotecting the cysteyl group of the resulting ligation product and/or converting the thioester into a thiophenylester.

  15. Parallel fast gauss transform

    SciTech Connect

    Sampath, Rahul S; Sundar, Hari; Veerapaneni, Shravan

    2010-01-01

    We present fast adaptive parallel algorithms to compute the sum of N Gaussians at N points. Direct sequential computation of this sum would take O(N{sup 2}) time. The parallel time complexity estimates for our algorithms are O(N/n{sub p}) for uniform point distributions and O( (N/n{sub p}) log (N/n{sub p}) + n{sub p}log n{sub p}) for non-uniform distributions using n{sub p} CPUs. We incorporate a plane-wave representation of the Gaussian kernel which permits 'diagonal translation'. We use parallel octrees and a new scheme for translating the plane-waves to efficiently handle non-uniform distributions. Computing the transform to six-digit accuracy at 120 billion points took approximately 140 seconds using 4096 cores on the Jaguar supercomputer. Our implementation is 'kernel-independent' and can handle other 'Gaussian-type' kernels even when explicit analytic expression for the kernel is not known. These algorithms form a new class of core computational machinery for solving parabolic PDEs on massively parallel architectures.

  16. Formatting and ligating biopolymers using adjustable nanoconfinement

    NASA Astrophysics Data System (ADS)

    Berard, Daniel J.; Shayegan, Marjan; Michaud, Francois; Henkin, Gil; Scott, Shane; Leslie, Sabrina

    2016-07-01

    Sensitive visualization and conformational control of long, delicate biopolymers present critical challenges to emerging biotechnologies and biophysical studies. Next-generation nanofluidic manipulation platforms strive to maintain the structural integrity of genomic DNA prior to analysis but can face challenges in device clogging, molecular breakage, and single-label detection. We address these challenges by integrating the Convex Lens-induced Confinement (CLiC) technique with a suite of nanotopographies embedded within thin-glass nanofluidic chambers. We gently load DNA polymers into open-face nanogrooves in linear, concentric circular, and ring array formats and perform imaging with single-fluorophore sensitivity. We use ring-shaped nanogrooves to access and visualize confinement-enhanced self-ligation of long DNA polymers. We use concentric circular nanogrooves to enable hour-long observations of polymers at constant confinement in a geometry which eliminates the confinement gradient which causes drift and can alter molecular conformations and interactions. Taken together, this work opens doors to myriad biophysical studies and biotechnologies which operate on the nanoscale.

  17. A Photo-Triggered Traceless Staudinger-Bertozzi Ligation Reaction.

    PubMed

    Hu, Peng; Feng, Tianshi; Yeung, Chi-Chung; Koo, Chi-Kin; Lau, Kai-Chung; Lam, Michael H W

    2016-08-01

    The use of light to control the course of a chemical/biochemical reaction is an attractive idea because of its ease of administration with high precision and fine spatial resolution. Staudinger ligation is one of the commonly adopted conjugation processes that involve a spontaneous reaction between azides and arylphosphines to form iminophosphoranes, which further hydrolyze to give stable amides. We designed an anthracenylmethyl diphenylphosphinothioester (1) that showed promising Staudinger ligation reactivity upon photo-excitation. Broadband photolysis at 360-400 nm in aqueous organic solvents induced heterolytic cleavage of its anthracenylmethyl-phosphorus bond, releasing a diphenylphosphinothioester (2) as an efficient traceless Staudinger-Bertozzi ligation reagent. The quantum yield of such a photo-induced heterolytic bond-cleavage at the optimal wavelength of photolysis (376 nm) at room temperature is ≥0.07. This work demonstrated the feasibility of photocaging arylphosphines to realize the photo-triggering of the Staudinger ligation reaction.

  18. Cross-ligation and exchange reactions catalyzed by hairpin ribozymes.

    PubMed Central

    Komatsu, Y; Koizumi, M; Sekiguchi, A; Ohtsuka, E

    1993-01-01

    The negative strand of the satellite RNA of tobacco ringspot virus (sTobRV(-)) contains a hairpin catalytic domain that shows self-cleavage and self-ligation activities in the presence of magnesium ions. We describe here that the minimal catalytic domain can catalyze a cross-ligation reaction between two kinds of substrates in trans. The cross-ligated product increased when the reaction temperature was decreased during the reaction from 37 degrees C to 4 degrees C. A two-stranded hairpin ribozyme, divided into two fragments between G45 and U46 in a hairpin loop, showed higher ligation activity than the nondivided ribozyme. The two stranded ribozyme also catalyzed an exchange reaction of the 3'-portion of the cleavage site. Images PMID:8441626

  19. Constraining massive star evolution from massive clusters

    NASA Astrophysics Data System (ADS)

    Chene, Andre-Nicolas; Herve, Anthony; Martins, Fabrice; Bouret, Jean-Claude; Borissova, Jordanka; Ramirez, Sebastian; Kurtev, Radostin; Kumar, Nanda; Amigo, Pia; Fierro, Celia

    2013-06-01

    The exact evolution of massive stars is not accurately known at present. The general trend is that stars with masses above 40 - 60 Mo go from O-type stars to H-rich WN stars, and Luminous Blue Variables (?), before turning into H-poor WN stars and finally WC stars. At lower masses, the H-rich WN and LBV phases are replaced by a blue and a red supergiant phases, respectively. However, what are the details of such evolutionary sequences? The study of massive clusters is a golden opportunity to establish this. Indeed, the turn-off mass of massive clusters can be directly translated into the mass, and hence the nature, of the progenitors of their evolved objects contents. So far, only the Arches, Quintuplet, NGC3603, NGC2244 and central clusters have been studied this way. But 6 newly discovered heavily-obscured clusters in the large survey â"VISTA Variables in the Via Lactea" (VVV) have been found to have Wolf-Rayet stars as well as blue and/or red supergiants, together with many main sequence OB stars. This poster presents our efforts to model the massive star components of these clusters using CMFGEN, bringing new blocks to the pavement of massive stellar evolution and more than doubling the number of clusters in which such evolutionary sequence are established.

  20. Protein chemical synthesis by serine and threonine ligation

    PubMed Central

    Zhang, Yinfeng; Lam, Hiu Yung; Lee, Chi Lung; Li, Xuechen

    2013-01-01

    An efficient method has been developed for the salicylaldehyde ester-mediated ligation of unprotected peptides at serine (Ser) or threonine (Thr) residues. The utility of this peptide ligation approach has been demonstrated through the convergent syntheses of two therapeutic peptides––ovine-corticoliberin and Forteo––and the human erythrocyte acylphosphatase protein (∼11 kDa). The requisite peptide salicylaldehyde ester precursor is prepared in an epimerization-free manner via Fmoc–solid-phase peptide synthesis. PMID:23569249

  1. Higher dimensional massive bigravity

    NASA Astrophysics Data System (ADS)

    Do, Tuan Q.

    2016-08-01

    We study higher-dimensional scenarios of massive bigravity, which is a very interesting extension of nonlinear massive gravity since its reference metric is assumed to be fully dynamical. In particular, the Einstein field equations along with the following constraint equations for both physical and reference metrics of a five-dimensional massive bigravity will be addressed. Then, we study some well-known cosmological spacetimes such as the Friedmann-Lemaitre-Robertson-Walker, Bianchi type I, and Schwarzschild-Tangherlini metrics for the five-dimensional massive bigravity. As a result, we find that massive graviton terms will serve as effective cosmological constants in both physical and reference sectors if a special scenario, in which reference metrics are chosen to be proportional to physical ones, is considered for all mentioned metrics. Thanks to the constancy property of massive graviton terms, consistent cosmological solutions will be figured out accordingly.

  2. Rapamycin delays salivary gland atrophy following ductal ligation.

    PubMed

    Bozorgi, S S; Proctor, G B; Carpenter, G H

    2014-03-27

    Salivary gland atrophy is a frequent consequence of head and neck cancer irradiation therapy but can potentially be regulated through the mammalian target of rapamycin (mTOR). Excretory duct ligation of the mouse submandibular gland provokes severe glandular atrophy causing activation of mTOR. This study aims to discover the effects of blocking mTOR signaling in ligation-induced atrophic salivary glands. Following 1 week of unilateral submandibular excretory duct ligation: gland weights were significantly reduced, 4E-BP1 and S6rp were activated, and tissue morphology revealed typical signs of atrophy. However, 3 days following ligation with rapamycin treatment, a selective mTOR inhibitor, gland weights were maintained, 4E-BP1 and S6rp phosphorylation was inhibited, and there were morphological signs of recovery from atrophy. However, following 5 and 7 days of ligation and rapamycin treatment, glands expressed active mTOR and showed signs of considerable atrophy. This evidence suggests that inhibition of mTOR by rapamycin delays ligation-induced atrophy of salivary glands.

  3. Vessel Ligation Training via an Adaptive Simulation Curriculum

    PubMed Central

    Hu, Yinin; Goodrich, Robyn N.; Le, Ivy A.; Brooks, Kendall D.; Sawyer, Robert G.; Smith, Philip W.; Schroen, Anneke T.; Rasmussen, Sara K.

    2015-01-01

    Background A cost-effective model for open vessel ligation is currently lacking. We hypothesized that a novel, inexpensive vessel ligation simulator can efficiently impart transferrable surgical skills to novice trainees. Materials and Methods VesselBox was designed to simulate vessel ligation using surgical gloves as surrogate vessels. Fourth-year medical students performed ligations using VesselBox, and were evaluated by surgical faculty using the Objective Structured Assessments of Technical Skills (OSATS) global rating scale and a task-specific checklist. Subsequently, each student was trained using VesselBox in an adaptive practice session guided by cumulative sum. Post-testing was performed on fresh human cadavers by evaluators blinded to pre-test results. Results Sixteen students completed the study. VesselBox practice sessions averaged 21.8 minutes per participant (IQR 19.5 – 27.7). Blinded post-tests demonstrated increased proficiency, as measured by both OSATS (3.23 vs 2.29, p < 0.001) and checklist metrics (7.33 vs 4.83, p < 0.001). Median speed improved from 128.2 seconds to 97.5 seconds per vessel ligated (p = 0.001). Following this adaptive training protocol, practice volume was not associated with post-test performance. Conclusions VesselBox is a cost-effective, low-fidelity vessel ligation model suitable for graduating medical students and junior residents. Cumulative sum can facilitate an adaptive, individualized curriculum for simulation training. PMID:25796112

  4. Intramyocardial activation in early ventricular arrhythmias following coronary artery ligation.

    PubMed

    Kaplinsky, E; Ogawa, S; Kmetzo, J; Balke, C W; Dreifus, L S

    1980-01-01

    Subendocardial, subepicardial and intramyocardial activation in the ischemic zone was investigated in 20 anesthetized open chest dogs 0-30 minutes after the ligation of the left anterior descending coronary artery. Single and composite electrograms and lead 2 of the ECG were recorded. Coronary artery ligation produced marked delay, fragmentation, and reduction in amplitude in the electrical activity of the subepicardial and intramyocardial muscle layers. The activation remained synchronous in the subendocardial muscle layers. Extension of electrical activity in the ischemic subepicardium and intramyocardium beyond the T wave of the surface ECG preceded the onset of immediate ventricular arrhythmias (IVA) during the initial ten minute period after coronary artery ligation. However, a second surge of delayed ventricular arrhythmias (DVA), 10-30 minutes after ligation, was not associated with the appearance of diastolic electrical activity in any of the subepicardial or myocardial layers. It appears that subepicardial as well as intramyocardial reentry could play an important role in the genesis of the immediate ventricular arrhythmias (1-10 minutes after ligation). In contrast, no obvious reentrant activity as evidenced by delayed and fragmented electrical activity could be observed in the electrogram from any of the myocardial electrical activity could be observed in the electrogram from any of the myocardial layers with the appearance of delayed ventricular ectopic activity 10-30 minutes after ligation.

  5. Ligation with nucleic acid sequence-based amplification.

    PubMed

    Ong, Carmichael; Tai, Warren; Sarma, Aartik; Opal, Steven M; Artenstein, Andrew W; Tripathi, Anubhav

    2012-01-01

    This work presents a novel method for detecting nucleic acid targets using a ligation step along with an isothermal, exponential amplification step. We use an engineered ssDNA with two variable regions on the ends, allowing us to design the probe for optimal reaction kinetics and primer binding. This two-part probe is ligated by T4 DNA Ligase only when both parts bind adjacently to the target. The assay demonstrates that the expected 72-nt RNA product appears only when the synthetic target, T4 ligase, and both probe fragments are present during the ligation step. An extraneous 38-nt RNA product also appears due to linear amplification of unligated probe (P3), but its presence does not cause a false-positive result. In addition, 40 mmol/L KCl in the final amplification mix was found to be optimal. It was also found that increasing P5 in excess of P3 helped with ligation and reduced the extraneous 38-nt RNA product. The assay was also tested with a single nucleotide polymorphism target, changing one base at the ligation site. The assay was able to yield a negative signal despite only a single-base change. Finally, using P3 and P5 with longer binding sites results in increased overall sensitivity of the reaction, showing that increasing ligation efficiency can improve the assay overall. We believe that this method can be used effectively for a number of diagnostic assays. PMID:22449695

  6. Epiregulin is critical for the acinar cell regeneration of the submandibular gland in a mouse duct ligation model.

    PubMed

    Nagai, Koichi; Arai, Hideo; Okudera, Michisato; Yamamura, Takashi; Oki, Hidero; Komiyama, Kazuo

    2014-05-01

    Acinar cell regeneration from tubular structures has been reported to occur in duct-deligated salivary glands. However, the detailed process of acinar cell regeneration has not been clarified. We have developed a mouse duct ligation model to clarify the mechanisms underlying acinar cell regeneration, and we analyzed the epidermal growth factor receptor (EGFR) and epidermal growth factor (EGF) ligands using the model. We studied these ligands expressions in the course of acinar cell regeneration using immunohistochemistry and RT-PCR methods. In the duct-ligated portion of the submandibular gland (SMG) that underwent atrophy, newly formed acinar cells were observed arising from the tubular structures after the release of the duct obstruction. The constitutive expression of EGFR was observed by immunohistochemistry in both the duct-ligated and duct-deligated animals as well as in normal controls. The EGFR phosphorylation detected on the tubular structures after duct ligation paralleled the acinar cell regeneration. RT-PCR showed an increase in the epiregulin and heparin-binding EGF levels from day 0 to day 3 after the release of the duct obstruction. The EGF level was increased only after day 7. In vitro, cultured cells isolated from ligated SMGs proliferated and produced EGF ligands following the addition of epiregulin to the culture medium. These findings suggest that the tubular structures localized in an atrophic gland are the source of acinar cell regeneration of the salivary gland. The induction of EGF ligands, in particular epiregulin, may play an important role in acinar cell regeneration in this model.

  7. Gang scheduling a parallel machine

    SciTech Connect

    Gorda, B.C.; Brooks, E.D. III.

    1991-03-01

    Program development on parallel machines can be a nightmare of scheduling headaches. We have developed a portable time sharing mechanism to handle the problem of scheduling gangs of processors. User program and their gangs of processors are put to sleep and awakened by the gang scheduler to provide a time sharing environment. Time quantums are adjusted according to priority queues and a system of fair share accounting. The initial platform for this software is the 128 processor BBN TC2000 in use in the Massively Parallel Computing Initiative at the Lawrence Livermore National Laboratory. 2 refs., 1 fig.

  8. Parallel pipelining

    SciTech Connect

    Joseph, D.D.; Bai, R.; Liao, T.Y.; Huang, A.; Hu, H.H.

    1995-09-01

    In this paper the authors introduce the idea of parallel pipelining for water lubricated transportation of oil (or other viscous material). A parallel system can have major advantages over a single pipe with respect to the cost of maintenance and continuous operation of the system, to the pressure gradients required to restart a stopped system and to the reduction and even elimination of the fouling of pipe walls in continuous operation. The authors show that the action of capillarity in small pipes is more favorable for restart than in large pipes. In a parallel pipeline system, they estimate the number of small pipes needed to deliver the same oil flux as in one larger pipe as N = (R/r){sup {alpha}}, where r and R are the radii of the small and large pipes, respectively, and {alpha} = 4 or 19/7 when the lubricating water flow is laminar or turbulent.

  9. Octonic Massive Field Equations

    NASA Astrophysics Data System (ADS)

    Demir, Süleyman; Kekeç, Seray

    2016-07-01

    In the present paper we propose the octonic form of massive field equations based on the analogy with electromagnetism and linear gravity. Using the advantages of octon algebra the Maxwell-Dirac-Proca equations have been reformulated in compact and elegant way. The energy-momentum relations for massive field are discussed.

  10. Logistics of massive transfusions.

    PubMed

    DeLoughery, Thomas G

    2010-01-01

    Care of the patient with massive bleeding involves more than aggressive surgery and infusion of large amounts of blood products. The proper management of massive transfusions-whether they are in trauma patients or other bleeding patients-requires coordination of the personnel in the surgical suite or the emergency department, the blood bank, and laboratory.

  11. 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.

  12. Endoscopic banding ligation can effectively remove the submucosal tumor

    PubMed Central

    Xia, Fei-Zhen; Shen, Zhe; Chen, Hong-Tan; Yu, Chao-Hui; Chen, Wei-Xing

    2015-01-01

    Endoscopic band ligation for variceal bleeding in cirrhosis has been proved its safety and efficacy. We tried to treat submucosal tumors the gastrointestinal (GI) tract by endoscopic band ligation. The aim of this study was to evaluate the efficacy and safety of endoscopic band ligation in the treatment of submucosal tumors of the GI tract. There are 29 patients (15 men, 14 women, age range: 25-67 years old) with 30 submucosal lesions of the GI tract, including 15 lesions in the esophagus, 14 lesions in the of stomach and 1 lesion in the duodenal bulb. The average maximum diameter of the lesions was 7.78 mm (range: 2.4-23.6 mm). All submucosal lesions were successfully removed by band ligation. There is no bleeding and perforation in all patients. No recurrence was observed for the one month following-up. Endoscopic band ligation promises could be considered as a safe and effective for the treatment submucosal tumors of the GI tract, especially for the diameter of tumor < 25 mm. PMID:25785162

  13. Collateral Capillary Arterialization following arteriolar ligation in murine skeletal muscle

    PubMed Central

    Mac Gabhann, Feilim; Peirce, Shayn M.

    2010-01-01

    OBJECTIVE Chronic and acute ischemic diseases – peripheral artery disease, coronary artery disease, stroke – result in tissue damage unless blood flow is maintained or restored in a timely manner. Mice of different strains recover from arteriolar ligation (by increasing collateral blood flow) at different speeds. We quantify the spatio-termporal patterns of microvascular network remodeling following arteriolar ligation in different mouse strains to better understand interindividual variability. METHODS Whole-muscle spinotrapezius microvascular networks of mouse strains C57Bl/6, Balb/c and CD1 were imaged using confocal microscopy following ligation of feeding arterioles. RESULTS Baseline arteriolar structures of C57Bl/6 and Balb/c mice feature heavily ramified arcades and unconnected dendritic trees, respectively. This network angioarchitecture identifies ischemia-protected and ischemia-vulnerable tissues: unlike C57Bl/6, downstream capillary perfusion in Balb/c spinotrapezius is lost following ligation. Perfusion recovery requires arterialization (expansion and investment of mural cells) of a subset of capillaries forming a new low-resistance collateral pathway between arteriolar trees. Outbred CD1 exhibit either Balb/c-like or C57Bl/6-like spinotrapezius angioarchitecture, predictive of response to arteriolar ligation. CONCLUSIONS This collateral capillary arterialization process may explain the reported longer time required for blood flow recovery in Balb/c hindlimb ischemia, as low-resistance blood flow pathways along capillary conduits must be formed (‘arterialization’) before reperfusion. PMID:20618691

  14. Massive graph visualization : LDRD final report.

    SciTech Connect

    Wylie, Brian Neil; Moreland, Kenneth D.

    2007-10-01

    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 graphs 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.

  15. Design and Validation of DNA Libraries for Multiplexing Proximity Ligation Assays

    PubMed Central

    Gobet, Nicolas; Ketterer, Simon; Meier, Matthias

    2014-01-01

    Here, we present an in silico, analytical procedure for designing and testing orthogonal DNA templates for multiplexing of the proximity ligation assay (PLA). PLA is a technology for the detection of protein interactions, post-translational modifications, and protein concentrations. To enable multiplexing of the PLA, the target information of antibodies was encoded within the DNA template of a PLA, where each template comprised four single-stranded DNA molecules. Our DNA design procedure followed the principles of minimizing the free energy of DNA cross-hybridization. To validate the functionality, orthogonality, and efficiency of the constructed template libraries, we developed a high-throughput solid-phase rolling-circle amplification assay and solid-phase PLA on a microfluidic platform. Upon integration on a microfluidic chip, 640 miniaturized pull-down assays for oligonucleotides or antibodies could be performed in parallel together with steps of DNA ligation, isothermal amplification, and detection under controlled microenvironments. From a large computed PLA template library, we randomly selected 10 template sets and tested all DNA combinations for cross-reactivity in the presence and absence of antibodies. By using the microfluidic chip application, we determined rapidly the false-positive rate of the design procedure, which was less than 1%. The combined theoretical and experimental procedure is applicable for high-throughput PLA studies on a microfluidic chip. PMID:25386748

  16. Oxidative Deselenization of Selenocysteine: Applications for Programmed Ligation at Serine.

    PubMed

    Malins, Lara R; Mitchell, Nicholas J; McGowan, Sheena; Payne, Richard J

    2015-10-19

    Despite the unique chemical properties of selenocysteine (Sec), ligation at Sec is an under-utilized methodology for protein synthesis. We describe herein an unprecedented protocol for the conversion of Sec to serine (Ser) in a single, high-yielding step. When coupled with ligation at Sec, this transformation provides a new approach to programmed ligations at Ser residues. This new reaction is compatible with a wide range of functionality, including the presence of unprotected amino acid side chains and appended glycans. The utility of the methodology is demonstrated in the rapid synthesis of complex glycopeptide fragments of the epithelial glycoproteins MUC5AC and MUC4 and through the total synthesis of the structured, cysteine (Cys)-free protein eglin C. PMID:26384718

  17. RNA-Catalyzed RNA Ligation on an External RNA Template

    NASA Technical Reports Server (NTRS)

    McGinness, Kathleen E.; Joyce, Gerald F.

    2002-01-01

    Variants of the hc ligase ribozyme, which catalyzes ligation of the 3' end of an RNA substrate to the 5' end of the ribozyme, were utilized to evolve a ribozyme that catalyzes ligation reactions on an external RNA template. The evolved ribozyme catalyzes the joining of an oligonucleotide 3'-hydroxyl to the 5'-triphosphate of an RNA hairpin molecule. The ribozyme can also utilize various substrate sequences, demonstrating a largely sequence-independent mechanism for substrate recognition. The ribozyme also carries out the ligation of two oligonucleotides that are bound at adjacent positions on a complementary template. Finally, it catalyzes addition of mononucleoside '5-triphosphates onto the '3 end of an oligonucleotide primer in a template-dependent manner. The development of ribozymes that catalyze polymerase-type reactions contributes to the notion that an RNA world could have existed during the early history of life on Earth.

  18. The Staudinger ligation-a gift to chemical biology.

    PubMed

    Köhn, Maja; Breinbauer, Rolf

    2004-06-14

    Although the reaction between an azide and a phosphane to form an aza-ylide was discovered by Hermann Staudinger more than 80 years ago and has found widespread application in organic synthesis, its potential as a highly chemoselective ligation method for the preparation of bioconjugates has been recognized only recently. As the two reaction partners are bioorthogonal to almost all functionalities that exist in biological systems and react at room temperature in an aqueous environment, the Staudinger ligation has even found application in the complex environment of living cells. Herein we describe the current state of knowledge on this reaction and its application both for the preparation of bioconjugates and as a ligation method in chemical biology.

  19. Template-Directed Ligation of Peptides to Oligonucleotides

    NASA Technical Reports Server (NTRS)

    Bruick, Richard K.; Dawson, Philip E.; Kent, Stephen BH; Usman, Nassim; Joyce, Gerald F.

    1996-01-01

    Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

  20. A Generic Polymer-Protein Ligation Strategy for Vaccine Delivery.

    PubMed

    Lybaert, Lien; Vanparijs, Nane; Fierens, Kaat; Schuijs, Martijn; Nuhn, Lutz; Lambrecht, Bart N; De Geest, Bruno G

    2016-03-14

    Although the field of cancer immunotherapy is intensively investigated, there is still a need for generic strategies that allow easy, mild and efficient formulation of vaccine antigens. Here we report on a generic polymer-protein ligation strategy to formulate protein antigens into reversible polymeric conjugates for enhanced uptake by dendritic cells and presentation to CD8 T-cells. A N-hydroxypropylmethacrylamide (HPMA)-based copolymer was synthesized via RAFT polymerization followed by introduction of pyridyldisulfide moieties. To enhance ligation efficiency to ovalbumin, which is used as a model protein antigen, protected thiols were introduced onto lysine residues and deprotected in situ in the presence of the polymer. The ligation efficiency was compared for both the thiol-modified versus unmodified ovalbumin, and the reversibility was confirmed. Furthermore, the obtained nanoconjugates were tested in vitro for their interaction and association with dendritic cells, showing enhanced cellular uptake and antigen cross-presentation to CD8 T-cells.