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At least 181 records · Page 10

Distributed Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (DiBELLA) v1.0.0

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, DiBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability.

Ellis, Marquita↗

What Multilevel Parallel Programs do when you are not Watching: A Performance Analysis Case Study Comparing MPI/OpenMP, MLP, and Nested OpenMP

With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors, parallel programming techniques have evolved that support parallelism beyond a single level. When comparing the performance of applications based on different programming paradigms, it is important to differentiate between the influence of the programming model itself and other factors, such as implementation specific behavior of the operating system (OS) or architectural issues. Rewriting-a large scientific application in order to employ a new programming paradigms is usually a time consuming and error prone task. Before embarking on such an endeavor it is important to determine that there is really a gain that would not be possible with the current implementation. A detailed performance analysis is crucial to clarify these issues. The multilevel programming paradigms considered in this study are hybrid MPI/OpenMP, MLP, and nested OpenMP. The hybrid MPI/OpenMP approach is based on using MPI [7] for the coarse grained parallelization and OpenMP [9] for fine grained loop level parallelism. The MPI programming paradigm assumes a private address space for each process. Data is transferred by explicitly exchanging messages via calls to the MPI library. This model was originally designed for distributed memory architectures but is also suitable for shared memory systems. The second paradigm under consideration is MLP which was developed by Taft. The approach is similar to MPi/OpenMP, using a mix of coarse grain process level parallelization and loop level OpenMP parallelization. As it is the case with MPI, a private address space is assumed for each process. The MLP approach was developed for ccNUMA architectures and explicitly takes advantage of the availability of shared memory. A shared memory arena which is accessible by all processes is required. Communication is done by reading from and writing to the shared memory.

Jost, Gabriele↗

Flight Qualified Micro Sun Sensor

A prototype small, lightweight micro Sun sensor (MSS) has been flight qualified as part of the attitude-determination system of a spacecraft or for Mars surface operations. The MSS has previously been reported at a very early stage of development in NASA Tech Briefs, Vol. 28, No. 1 (January 2004). An MSS is essentially a miniature multiple-pinhole electronic camera combined with digital processing electronics that functions analogously to a sundial. A micromachined mask containing a number of microscopic pinholes is mounted in front of an active-pixel sensor (APS). Electronic circuits for controlling the operation of the APS, readout from the pixel photodetectors, and analog-to-digital conversion are all integrated onto the same chip along with the APS. The digital processing includes computation of the centroids of the pinhole Sun images on the APS. The spacecraft computer has the task of converting the Sun centroids into Sun angles utilizing a calibration polynomial. The micromachined mask comprises a 500-micron-thick silicon wafer, onto which is deposited a 57-nm-thick chromium adhesion- promotion layer followed by a 200-nm-thick gold light-absorption layer. The pinholes, 50 microns in diameter, are formed in the gold layer by photolithography. The chromium layer is thin enough to be penetrable by an amount of Sunlight adequate to form measurable pinhole images. A spacer frame between the mask and the APS maintains a gap of .1 mm between the pinhole plane and the photodetector plane of the APS. To minimize data volume, mass, and power consumption, the digital processing of the APS readouts takes place in a single field-programmable gate array (FPGA). The particular FPGA is a radiation- tolerant unit that contains .32,000 gates. No external memory is used so the FPGA calculates the centroids in real time as pixels are read off the APS with minimal internal memory. To enable the MSS to fit into a small package, the APS, the FPGA, and other components are mounted on a single two-sided board following chip-on-board design practices

Liebe, Carl Christian↗

Initial Results from On-Orbit Testing of the Fram Memory Test Experiment on the Fastsat Micro-Satellite

The Memory Test Experiment is a space test of a ferroelectric memory device on a low Earth orbit satellite that launched in November 2010. The memory device being tested is a commercial Ramtron Inc. 512K memory device. The circuit was designed into the satellite avionics and is not used to control the satellite. The test consists of writing and reading data with the ferroelectric based memory device. Any errors are detected and are stored on board the satellite. The data is sent to the ground through telemetry once a day. Analysis of the data can determine the kind of error that was found and will lead to a better understanding of the effects of space radiation on memory systems. The test is one of the first flight demonstrations of ferroelectric memory in a near polar orbit which allows testing in a varied radiation environment. The initial data from the test is presented. This paper details the goals and purpose of this experiment as well as the development process. The process for analyzing the data to gain the maximum understanding of the performance of the ferroelectric memory device is detailed.

MacLeond, Todd C.↗

Register-Like Storage Block Used as Histograms, Cluster Buffers, and Hough Transform Accumulators for HEP Trigger Systems

In high energy physics experiment trigger systems, block memories are utilized for various purposes, especially in binned searching algorithms. In these algorithms, the storages are demanded to perform like a large set of registers. The writing and reading operation must be performed in single clock cycle and once an event is processed, the memory must be globally reset. These demands can be fulfilled with registers but the cost of using registers for large memory is unaffordable. Another common requirement is the boundary coverage feature during reading process. Additionally, when a memory bin is addressed, the stored contents in the addressed bin and its neighboring bin must be output simultaneously. In this paper, a register-like block storage design scheme is described, which allows updating memory locations in single clock cycle, reading two adjacent bins, and effectively refreshing entire memory within a single clock. The implementation and test results are presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Optical Memory, Switching, and Neuromorphic Functionality in Metal Halide Perovskite Materials and Devices

Metal halide perovskite-based materials have emerged over the past few decades as remarkable solution-processable opto-electronic materials with many intriguing properties and potential applications. Notably, these emerging materials have recently been considered for their promise in low-energy memory and information processing applications. In particular, their large optical cross-sections, high photoconductance contrast, large carrier diffusion lengths, and mixed electronic/ionic transport mechanisms are attractive for enabling memory elements and neuromorphic devices that are written and/or read in the optical domain. Here, we review recent progress towards memory and neuromorphic functionality in metal halide perovskite materials and devices where photons are used as a critical degree of freedom for switching, memory, and neuromorphic functionality.

14 SOLAR ENERGY↗

Determining diagnostic coverage for memory using redundant execution

Memory, used by a computer to store data, is generally prone to faults, including permanent faults (i.e. relating to a lifetime of the memory hardware), and also transient faults (i.e. relating to some external cause) which are otherwise known as soft errors. Since soft errors can change the state of the data in the memory and thus cause errors in applications reading and processing the data, there is a desire to characterize the degree of vulnerability of the memory to soft errors. In particular, once the vulnerability for a particular memory to soft errors has been characterized, cost/reliability trade-offs can be determined, or soft error detection mechanisms (e.g. parity) may be selectively employed for the memory. In some cases, memory faults can be diagnosed by redundant execution and a diagnostic coverage may be determined.

Bramley, Richard Gavin↗

Liveness as a factor to evaluate memory vulnerability to soft errors

Memory, used by a computer to store data, is generally prone to faults, including permanent faults (i.e. relating to a lifetime of the memory hardware), and also transient faults (i.e. relating to some external cause) which are otherwise known as soft errors. Since soft errors can change the state of the data in the memory and thus cause errors in applications reading and processing the data, there is a desire to characterize the degree of vulnerability of the memory to soft errors. In particular, once the vulnerability for a particular memory to soft errors has been characterized, cost/reliability trade-offs can be determined, or soft error detection mechanisms (e.g. parity) may be selectively employed for the memory. In some cases, memory faults can be diagnosed by redundant execution and a diagnostic coverage may be determined.

Bramley, Richard Gavin↗

Effects of stress upon psychophysiological responses and performance following sleep deprivation

The usefulness of psychological and physiological variables in predicting performance under stress of 48 hours of sleep deprivation was investigated. Performance tests, with subjects of different ego strength personalities, in concept acquisition, reading comprehension, word association, word memory, and anagrams were conducted, and physiological measurements of (1) the phasic and tonic electrodermal, (2) galvanic skin response, (3) thermal skin resistance, (4) heart rate, (5) respiration, and (6) plethysmographic finger pulse volumn were recorded. It was found that the changes in the pattern of performance were the result of testing subjects at times when they would normally be sleeping, and that sleep deprivation longer than 48 hours must be maintained to produce changes in simple or well learned tasks.

Roessler, R.↗

A PDP-15 to industrial-14 interface at the Lewis Research Center's cyclotron

An interface (hardware and software) was built which permits the loading, monitoring, and control of a digital equipment industrial-14/30 programmable controller by a PDP-15 computer. The interface utilizes the serial mode for data transfer to and from the controller, so that the required hardware is essentially that of a teletype unit except for the speed of transmission. Software described here permits the user to load binary paper tape, read or load individual controller memory locations, and if desired turn controller outputs on and off directly from the computer.

Kebberly, F. R.↗

Calibration For On-Machine Inspections

Permanent calibration setup on numerically-controlled machine tool enables fast and reliable calibration of automated probes for inspection of workpieces while still mounted on machine. Setup includes one or more artifacts, dimensions and locations known precisely and stored in memory of computer controlling machine. Before probes used to inspect newly machined part, used to check artifacts. Probe measurements compared with values in memory to determine whether probe readings need adjustment.

Haymaker, Carlton L., Jr.↗

Vertical bloch line memory

Vertical Bloch Line (VBL) memory is a recently conceived, integrated, solid-state, block-access, VLSI memory which offers the potential of 1Gbit/sq cm real storage density, gigabit per second data rates, and sub-millisecond average access times simultaneously at relatively low mass, volume, and power values when compared to alternative technologies. VBL's are micromagnetic structures within magnetic domain walls which can be manipulated using magnetic fields from integrated conductors. The presence or absence of VBL pairs are used to store binary information. At present, efforts are being directed at developing a single-chip memory using 25Mbit/sq cm technology in magnetic garnet material which integrates, at a single operating point, the writing, storage, reading, and amplification functions needed in a memory. This paper describes the current design architecture, functional elements, and supercomputer simulation results which are used to assist the design process. The current design architecture uses three metal layers, two ion implantation steps for modulating the thickness of the magnetic layer, one ion implantation step for assisting propagation in the major line track, one NiFe soft magnetic layer, one CoPt hard magnetic layer, and one reflective Cr layer for facilitating magneto-optic observation of magnetic structure. Data are stored in a series of elongated magnetic domains, called stripes, which serve as storage sites for arrays of VBL pairs. The ends of these stripes are placed near conductors which serve as VBL read/write gates. A major line track is present to provide a source and propagation path for magnetic bubbles. Writing and reading, respectively, are achieved by converting magnetic bubbles to VBL's and vice versa. The output function is effected by stretching a magnetic bubble and detecting it magnetoresistively. Experimental results from the past design cycle created four design goals for the current design cycle. First, the bias field ranges for the stripes and the major line needed to be matched. Second, the magnetic field barrier between the stripe and the read/write gates needed to be reduced. Third, current conductor routing needed to be improved to reduce occurrences of open-circuiting, short-circuiting, and eddy-current shielding. Fourth, a modified Co-alloy was needed with an increased coercivity and controlled magnetization to allow VBL stabilization to occur without affecting stripe stability.

Katti, R.↗

Memory protection

Accidental overwriting of files or of memory regions belonging to other programs, browsing of personal files by superusers, Trojan horses, and viruses are examples of breakdowns in workstations and personal computers that would be significantly reduced by memory protection. Memory protection is the capability of an operating system and supporting hardware to delimit segments of memory, to control whether segments can be read from or written into, and to confine accesses of a program to its segments alone. The absence of memory protection in many operating systems today is the result of a bias toward a narrow definition of performance as maximum instruction-execution rate. A broader definition, including the time to get the job done, makes clear that cost of recovery from memory interference errors reduces expected performance. The mechanisms of memory protection are well understood, powerful, efficient, and elegant. They add to performance in the broad sense without reducing instruction execution rate.

Denning, Peter J.↗

Integrated Vertical Bloch Line (VBL) memory

Vertical Bloch Line (VBL) Memory is a recently conceived, integrated, solid state, block access, VLSI memory which offers the potential of 1 Gbit/sq cm areal storage density, data rates of hundreds of megabits/sec, and submillisecond average access time simultaneously at relatively low mass, volume, and power values when compared to alternative technologies. VBLs are micromagnetic structures within magnetic domain walls which can be manipulated using magnetic fields from integrated conductors. The presence or absence of BVL pairs are used to store binary information. At present, efforts are being directed at developing a single chip memory using 25 Mbit/sq cm technology in magnetic garnet material which integrates, at a single operating point, the writing, storage, reading, and amplification functions needed in a memory. The current design architecture, functional elements, and supercomputer simulation results are described which are used to assist the design process.

Katti, R. R.↗

Systems and methods for detecting a failure event in a field programmable gate array

An embodiment generally relates to a method of self-detecting an error in a field programmable gate array (FPGA). The method includes writing a signature value into a signature memory in the FPGA and determining a conclusion of a configuration refresh operation in the FPGA. The method also includes reading an outcome value from the signature memory.

Ng, Tak-Kwong↗

Research on variable threshold transistor storage systems

A fully integrated, electrically alterable, nonvolatile, nondestructive readout control memory was developed, using as storage elements metal-nitride-silicon variable threshold transistors. An optimum approach to such a memory was developed in which a three dimensional selection technique was used, both for read and write operations. Electrical isolation of writing and memory circuits was obtained by means of separate memory and write circuit chips. This method provided protection from voltage breakdowns, increased circuit flexibility, and greater ease of testing of interim and final circuit elements.

Wegener, H. A. R.↗

Optical Memory Stores 10 12sup. Bits

Optical Mass Memory has separate recorder (write) and reproducer (read) modules. Data are recorded on fiches and stored in a carrousel. Fische is retrieved from carrousel by transporter in under 10 seconds. Input to optical memory is standard TV camera. TV monitor at memory output displays stored video images when they are retrieved from fisches. Input to the optical memory can also be taken from pseudorandom sequence generator.

Source record↗

Magnetic Analog Random-Access Memory

Proposed integrated, solid-state, analog random-access memory base on principle of magnetic writing and magnetoresistive reading. Current in writing conductor magnetizes storage layer. Remanent magnetization in storage layer penetrates readout layer and detected by magnetoresistive effect or Hall effect. Memory cells are part of integrated circuit including associated reading and writing transistors. Intended to provide high storage density and rapid access, nonvolatile, consumes little power, and relatively invulnerable to ionizing radiation.

Katti, Romney R.↗