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At least 91 records · Page 5

Multibus-based parallel processor for simulation

A Multibus-based parallel processor simulation system is described. The system is intended to serve as a vehicle for gaining hands-on experience, testing system and application software, and evaluating parallel processor performance during development of a larger system based on the horizontal/vertical-bus interprocessor communication mechanism. The prototype system consists of up to seven Intel iSBC 86/12A single-board computers which serve as processing elements, a multiple transmission controller (MTC) designed to support system operation, and an Intel Model 225 Microcomputer Development System which serves as the user interface and input/output processor. All components are interconnected by a Multibus/IEEE 796 bus. An important characteristic of the system is that it provides a mechanism for a processing element to broadcast data to other selected processing elements. This parallel transfer capability is provided through the design of the MTC and a minor modification to the iSBC 86/12A board. The operation of the MTC, the basic hardware-level operation of the system, and pertinent details about the iSBC 86/12A and the Multibus are described.

Ogrady, E. P.↗

Multiphase complete exchange on Paragon, SP2 and CS-2

The overhead of interprocessor communication is a major factor in limiting the performance of parallel computer systems. The complete exchange is the severest communication pattern in that it requires each processor to send a distinct message to every other processor. This pattern is at the heart of many important parallel applications. On hypercubes, multiphase complete exchange has been developed and shown to provide optimal performance over varying message sizes. Most commercial multicomputer systems do not have a hypercube interconnect. However, they use special purpose hardware and dedicated communication processors to achieve very high performance communication and can be made to emulate the hypercube quite well. Multiphase complete exchange has been implemented on three contemporary parallel architectures: the Intel Paragon, IBM SP2 and Meiko CS-2. The essential features of these machines are described and their basic interprocessor communication overheads are discussed. The performance of multiphase complete exchange is evaluated on each machine. It is shown that the theoretical ideas developed for hypercubes are also applicable in practice to these machines and that multiphase complete exchange can lead to major savings in execution time over traditional solutions.

Bokhari, Shahid H.↗

Report for the ASCR Workshop on Visualization for Scientific Discovery, Decision-Making, and Communication

Visualization—the use of visual elements to explore data, form hypotheses, or convey conclusions—is an integral part of the scientific process. Starting from an initial exploration of new data to illustrating outcomes for the general public, visualization is one of the most intuitive and powerful modes of communication. With the explosion of new data sources and types, unprecedented volumes of data, and new technologies, such as virtual reality (VR) and artificial intelligence (AI), visualization has become increasingly essential but also ever more challenging. The Department of Energy’s (DOE) Office of Advanced Scientific Computing Research (ASCR) sponsored a Basic Research Needs workshop in January 2022 to understand the major opportunities and grand challenges in visualization tools and technologies for scientific computing as well as for DOE-relevant applications and goals in general. The workshop identified five priority research directions (PRDs) for visualization to support scientific discovery, decision making, and communication. The first three PRDs describe interconnected research themes addressing the need for new techniques to deal with complex data, uncertainty, and interpretability (PRD 1); the need for scalable and interoperable software stacks (PRD 2); and the challenges and opportunities inherent in new technologies, such as VR, cloud, or exascale computing (PRD 3). The remaining two PRDs describe foundational research themes that recognize the potential of visualizations to provide equitable access to information and to strengthen the scientific discourse (PRD 4); and the need to consider human factors when designing visualizations (PRD 5). Collectively, these PRDs form the pillars for a coherent, long-term research and development strategy in Visualization for Scientific Discovery, Decision-Making, and Communication in the context of the Office of Science’s mission scope.

97 MATHEMATICS AND COMPUTING↗

High performance interconnection between high data rate networks

The bridge/gateway system needed to interconnect a wide range of computer networks to support a wide range of user quality-of-service requirements is discussed. The bridge/gateway must handle a wide range of message types including synchronous and asynchronous traffic, large, bursty messages, short, self-contained messages, time critical messages, etc. It is shown that messages can be classified into three basic classes, synchronous and large and small asynchronous messages. The first two require call setup so that packet identification, buffer handling, etc. can be supported in the bridge/gateway. Identification enables resequences in packet size. The third class is for messages which do not require call setup. Resequencing hardware based to handle two types of resequencing problems is presented. The first is for a virtual parallel circuit which can scramble channel bytes. The second system is effective in handling both synchronous and asynchronous traffic between networks with highly differing packet sizes and data rates. The two other major needs for the bridge/gateway are congestion and error control. A dynamic, lossless congestion control scheme which can easily support effective error correction is presented. Results indicate that the congestion control scheme provides close to optimal capacity under congested conditions. Under conditions where error may develop due to intervening networks which are not lossless, intermediate error recovery and correction takes 1/3 less time than equivalent end-to-end error correction under similar conditions.

Foudriat, E. C.↗

Basic Research Needs for Inverse Methods for Complex Systems under Uncertainty [Brochure]

The four priority research directions outlined in this brochure represent a cohesive vision for advancing the science of inverse problems for complex systems under uncertainty. Together, they address the critical challenges of: discovering, exploiting, and preserving physical and problem structure; overcoming model limitations; integrating disparate, multimodal, and/or dynamic data; and tailoring the solution of inverse problems to downstream tasks. While each PRD focuses on a distinct aspect of inverse-problem research, their interconnected nature highlights the importance of a holistic approach that leverages progress across all areas to achieve transformative solutions. This agenda calls for research across mathematics, statistics, and computer science disciplines, which are guided and complemented by rapid advances in artificial intelligence, high-performance computing, and experimental facilities, to unlock new capabilities, maximize scientific impact, and meet the growing demands of inverse problems that arise across applications that are critical to DOE's mission.

97 MATHEMATICS AND COMPUTING↗

The Sorghum (Sorghum bicolor) Brown Midrib 30 Gene Encodes a Chalcone Isomerase Required for Cell Wall Lignification

In sorghum ( Sorghum bicolor ) and other C 4 grasses, brown midrib ( bmr ) mutants have long been associated with plants impaired in their ability to synthesize lignin. The brown midrib 30 ( Bmr30 ) gene, identified using a bulk segregant analysis and next-generation sequencing, was determined to encode a chalcone isomerase (CHI). Two independent mutations within this gene confirmed that loss of its function was responsible for the brown leaf midrib phenotype and reduced lignin concentration. Loss of the Bmr30 gene function, as shown by histochemical staining of leaf midrib and stalk sections, resulted in altered cell wall composition. In the bmr30 mutants, CHI activity was drastically reduced, and the accumulation of total flavonoids and total anthocyanins was impaired, which is consistent with its function in flavonoid biosynthesis. The level of the flavone lignin monomer tricin was reduced 20-fold in the stem relative to wild type, and to undetectable levels in the leaf tissue of the mutants. The bmr30 mutant, therefore, harbors a mutation in a phenylpropanoid biosynthetic gene that is key to the interconnection between flavonoids and monolignols, both of which are utilized for lignin synthesis in the grasses.

59 BASIC BIOLOGICAL SCIENCES↗

Grand Challenges of Hydrologic Modeling for Food-Energy-Water Nexus Security in High Mountain Asia

Climate-influenced changes in hydrology affect water-food-energy security that may impact up to two billion people downstream of the High Mountain Asia (HMA) region. Changes in water supply affect energy, industry, transportation, and ecosystems (agriculture, fisheries) and as a result, also affect the region's social, environmental, and economic fabrics. Sustaining the highly interconnected food-energy-water nexus (FEWN) will be a fundamental and increasing challenge under a changing climate regime. High variability in topography and distribution of glaciated and snow-covered areas in the HMA region, and scarcity of high resolution (in-situ) data make it difficult to model and project climate change impacts on individual watersheds. We lack basic understanding of the spatial and temporal variations in climate, surface impurities in snow and ice such as black carbon and dust that alter surface albedo, and glacier mass balance and dynamics. These knowledge gaps create challenges in predicting where and when the impact of changes in river flow will be the most significant economically and ecologically. In response to these challenges, the United States National Aeronautics and Space Administration (NASA) established the High Mountain Asia Team (HiMAT) in 2016 to conduct research to address knowledge gaps. This paper summarizes some of the advances HiMAT made over the past 5 years, highlights the scientific challenges in improving our understanding of the hydrology of the HMA region, and introduces an integrated assessment framework to assess the impacts of climate changes on the FEWN for the HMA region. The framework, developed under a NASA HMA project, links climate models, hydrology, hydropower, fish biology, and economic analysis. The framework could be applied to develop scientific understanding of spatio-temporal variability in water availability and the resultant downstream impacts on the FEWN to support water resource management under a changing climate regime.

54 ENVIRONMENTAL SCIENCES↗

A parallel householder tridiagonalization stratagem using scattered row decomposition

Householder's method for tridiagonalizing a real symmetric matrix, a major step in evaluating eigenvalues of the matrix, is modified into a parallel algorithm for a concurrent machine of message passing type. Each processor of the concurrent machine has its own CPU, communications control and local memory. Messages are passed through connections between processors. Although the basic algorithm is inherently serial, the computations can be spread over all processors by scattering different rows of the matrix into processors, hence the term 'Scattered Row Decomposition'. The steps in the serial and the parallel algorithms are identified. Expressions for efficiency and speedup are given in terms of problem and machine parameters. For a concurrent machine of ring type interconnection, a selected representative problem of large order exhibits efficiency approaching 66 per cent.

Chang, H. Y.↗

Constellation Architecture Team-Lunar: Lunar Habitat Concepts

This paper will describe lunar habitat concepts that were defined as part of the Constellation Architecture Team-Lunar (CxAT-Lunar) in support of the Vision for Space Exploration. There are many challenges to designing lunar habitats such as mission objectives, launch packaging, lander capability, and risks. Surface habitats are required in support of sustaining human life to meet the mission objectives of lunar exploration, operations, and sustainability. Lunar surface operations consist of crew operations, mission operations, EVA operations, science operations, and logistics operations. Habitats are crewed pressurized vessels that include surface mission operations, science laboratories, living support capabilities, EVA support, logistics, and maintenance facilities. The challenge is to deliver, unload, and deploy self-contained habitats and laboratories to the lunar surface. The CxAT-Lunar surface campaign analysis focused on three primary trade sets of analysis. Trade set one (TS1) investigated sustaining a crew of four for six months with full outpost capability and the ability to perform long surface mission excursions using large mobility systems. Two basic habitat concepts of a hard metallic horizontal cylinder and a larger inflatable torus concept were investigated as options in response to the surface exploration architecture campaign analysis. Figure 1 and 2 depicts the notional outpost configurations for this trade set. Trade set two (TS2) investigated a mobile architecture approach with the campaign focused on early exploration using two small pressurized rovers and a mobile logistics support capability. This exploration concept will not be described in this paper. Trade set three (TS3) investigated delivery of a "core' habitation capability in support of an early outpost that would mature into the TS1 full outpost capability. Three core habitat concepts were defined for this campaign analysis. One with a four port core habitat, another with a 2 port core habitat, and the third investigated leveraging commonality of the lander ascent module and airlock pressure vessel hard shell. The paper will describe an overview of the various habitat concepts and their functionality. The Crew Operations area includes basic crew accommodations such as sleeping, eating, hygiene and stowage. The EVA Operations area includes additional EVA capability beyond the suit-port airlock function such as redundant airlock(s), suit maintenance, spares stowage, and suit stowage. The Logistics Operations area includes the enhanced accommodations for 180 days such as closed loop life support systems hardware, consumable stowage, spares stowage, interconnection to the other Hab units, and a common interface mechanism for future growth and mating to a pressurized rover. The Mission & Science Operations area includes enhanced outpost autonomy such as an IVA glove box, life support, and medical operations.

Toups, Larry↗

3D superconducting radio-frequency resonators for quantum computing

Superconducting radiofrequency (SRF) technology is being used not only in discovery science programs and basic research but also for several applications that benefit society more directly. The advantage of superconducting resonators over those made of normal-conducting metal is their ability to store electromagnetic energy with much lower dissipation. The high quality factor and longer dissipation time provided by these superconducting resonators can deliver superior performance. Currently, the quantum processing architecture uses resonators and interconnecting circuits operating in the microwave regime with superconducting strip-line technology and low noise electronic devices for switching and communication. The performance of these devices can be enhanced by embedding them in 3D SRF cavity resonators to prolong the coherence time, which improves the utility of the device by reducing error rates and allowing more manipulations (calculations) before the quantum state decays. In this presentation, I will review the current technology and progress towards the three dimensional SRF cavities to enhance the coherence time.

Dhakal, Pashupati↗

Superconducting Radio Frequency Resonators for Quantum Computing: A Short Review

Superconducting radiofrequency (SRF) technology is being used not only in discovery science programs and basic research but also for several applications that benefit society more directly. The advantage of superconducting resonators over those made of normal-conducting metal is their ability to store electromagnetic energy with much lower dissipation. The high-quality factor and longer dissipation time provided by these superconducting resonators can deliver superior performance. Currently, the quantum processing architecture uses resonators and interconnecting circuits operating in the microwave regime with superconducting strip-line technology and low noise electronic devices for switching and communication. The performance of these devices can be enhanced by embedding them in 3D SRF cavity resonators to prolong the coherence time, which improves the utility of the device by reducing error rates and allowing more manipulations (calculations) before the quantum state decays. Here, we present a short review of current microwave technology used in quantum computers and progress towards the 3D resonators to enhance thecoherence time.

Dhakal, Pashupati↗

Visualization and modeling of inhibition of IL-1β and TNF-α mRNA transcription at the single-cell level

Abstract IL-1β and TNF-α are canonical immune response mediators that play key regulatory roles in a wide range of inflammatory responses to both chronic and acute conditions. Here we employ an automated microscopy platform for the analysis of messenger RNA (mRNA) expression of IL-1β and TNF-α at the single-cell level. The amount of IL-1β and TNF-α mRNA expressed in a human monocytic leukemia cell line (THP-1) is visualized and counted using single-molecule fluorescent in-situ hybridization (smFISH) following exposure of the cells to lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria. We show that the small molecule inhibitors MG132 (a 26S proteasome inhibitor used to block NF-κB signaling) and U0126 (a MAPK Kinase inhibitor used to block CCAAT-enhancer-binding proteins C/EBP) successfully block IL-1β and TNF-α mRNA expression. Based upon this single-cell mRNA expression data, we screened 36 different mathematical models of gene expression, and found two similar models that capture the effects by which the drugs U0126 and MG132 affect the rates at which the genes transition into highly activated states. When their parameters were informed by the action of each drug independently, both models were able to predict the effects of the combined drug treatment. From our data and models, we postulate that IL-1β is activated by both NF-κB and C/EBP, while TNF-α is predominantly activated by NF-κB. Our combined single-cell experimental and modeling efforts show the interconnection between these two genes and demonstrates how the single-cell responses, including the distribution shapes, mean expression, and kinetics of gene expression, change with inhibition.

59 BASIC BIOLOGICAL SCIENCES↗

Frequency-bin photonic quantum information

Discrete frequency modes, or bins, present a blend of opportunities and challenges for photonic quantum information processing. Frequency-bin-encoded photons are readily generated by integrated quantum light sources, naturally high-dimensional, stable in optical fiber, and massively parallelizable in a single spatial mode. Yet quantum operations on frequency-bin states require coherent and controllable multifrequency interference, making them significantly more challenging to manipulate than more traditional spatial degrees of freedom. In this mini-review, we describe recent developments that have transformed these challenges and propelled frequency bins forward. Focusing on sources, manipulation schemes, and detection approaches, we introduce the basics of frequency-bin encoding, summarize the state of the art, and speculate on the field’s next phases. Given the combined progress in integrated photonics, high-fidelity quantum gates, and proof-of-principle demonstrations, frequency-bin quantum information is poised to emerge from the lab and leave its mark on practical quantum information processing—particularly in networking where frequency bins offer unique tools for multiplexing, interconnects, and high-dimensional communications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Magma production and migration within the moon

Partial melting is likely to have occurred throughout much of the moon due to heating during accretion and the volumetric heating of radioactive isotopes. Important problems that have received relatively little attention concern the migration of the resulting magmas to form surface or near surface volcanic rock. In the paper the basic mechanism for the migration of the magma through the lunar asthenosphere is considered. A porous flow model is proposed. The magma behaves like a liquid flowing through a porous matrix. The volume fraction of liquid present determines the saturated porosity. The differential buoyancy of the magma drives it upwards. It is shown that the per cent partial melt in the lunar interior will only slightly exceed that required to provide interconnecting porosity. Assuming that the radioactive isotopes are preferentially segregated into the magma, the time dependence of the partial melting of the lunar interior is found. It is shown that the total degree of partial melting of the deep lunar interior is likely to be between five and ten per cent.

Turcotte, D. L.↗

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

59 BASIC BIOLOGICAL SCIENCES↗

A Parallel Multigrid Solver for Viscous Flows on Anisotropic Structured Grids

This paper presents an efficient parallel multigrid solver for speeding up the computation of a 3-D model that treats the flow of a viscous fluid over a flat plate. The main interest of this simulation lies in exhibiting some basic difficulties that prevent optimal multigrid efficiencies from being achieved. As the computing platform, we have used Coral, a Beowulf-class system based on Intel Pentium processors and equipped with GigaNet cLAN and switched Fast Ethernet networks. Our study not only examines the scalability of the solver but also includes a performance evaluation of Coral where the investigated solver has been used to compare several of its design choices, namely, the interconnection network (GigaNet versus switched Fast-Ethernet) and the node configuration (dual nodes versus single nodes). As a reference, the performance results have been compared with those obtained with the NAS-MG benchmark.

Prieto, Manuel↗

Efficient parallel architecture for highly coupled real-time linear system applications

A systematic procedure is developed for exploiting the parallel constructs of computation in a highly coupled, linear system application. An overall top-down design approach is adopted. Differential equations governing the application under consideration are partitioned into subtasks on the basis of a data flow analysis. The interconnected task units constitute a task graph which has to be computed in every update interval. Multiprocessing concepts utilizing parallel integration algorithms are then applied for efficient task graph execution. A simple scheduling routine is developed to handle task allocation while in the multiprocessor mode. Results of simulation and scheduling are compared on the basis of standard performance indices. Processor timing diagrams are developed on the basis of program output accruing to an optimal set of processors. Basic architectural attributes for implementing the system are discussed together with suggestions for processing element design. Emphasis is placed on flexible architectures capable of accommodating widely varying application specifics.

Carroll, Chester C.↗

A Large-Grain Mapping Approach for Multiprocessor Systems Through Data Flow Model Ph.D. Thesis

A large-grain level mapping method is presented of numerical oriented applications onto multiprocessor systems. The method is based on the large-grain data flow representation of the input application and it assumes a general interconnection topology of the multiprocessor system. The large-grain data flow model was used because such representation best exhibits inherited parallelism in many important applications, e.g., CFD models based on partial differential equations can be presented in large-grain data flow format, very effectively. A generalized interconnection topology of the multiprocessor architecture is considered, including such architectural issues as interprocessor communication cost, with the aim to identify the 'best matching' between the application and the multiprocessor structure. The objective is to minimize the total execution time of the input algorithm running on the target system. The mapping strategy consists of the following: (1) large-grain data flow graph generation from the input application using compilation techniques; (2) data flow graph partitioning into basic computation blocks; and (3) physical mapping onto the target multiprocessor using a priority allocation scheme for the computation blocks.

Kim, Hwa-Soo↗