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DOE OSTI2019

A Comparison of Classical and Aggregation-Based Algebraic Multigrid Preconditioners for High-Fidelity Simulation of Wind Turbine Incompressible Flows

This paper presents a comparison of parallel strong scaling performance of classical and aggregation algebraic multigrid (AMG) preconditioners in the context of wind turbine simulations. Fluid motion is governed by the incompressible Navier--Stokes equations, discretized in space with control-volume finite elements and in time with an inexact projection scheme using an implicit integrator. A discontinuous-Galerkin sliding-mesh algorithm captures rotor motion. The momentum equations are solved with iterative Krylov methods, preconditioned by symmetric Gauss--Seidel (SGS) in Trilinos and $\ell_1$ SGS in hypre. The mass-continuity equation is solved with GMRES preconditioned by AMG and can account for the majority of simulation time. Reducing this continuity solve time is crucial. Wind turbine simulations present two unique challenges for AMG preconditioned solvers: the computational meshes include strongly anisotropic elements, and mesh motion requires matrix reinitialization and computation of preconditioners at each time step. Detailed timing profiles are presented and analyzed, and best practices are discussed for both classical and aggregation-based AMG. Results are presented for simulations of two different wind turbines with up to 6 billion grid points on two different computer architectures. For moving mesh problems that require linear-system reinitialization, the well-established strategy of amortizing preconditioner setup costs over a large number of time steps to reduce the solve time is no longer valid. Instead, results show that faster time to solution is achieved by reducing preconditioner setup costs at the expense of linear-system solve costs. Standard smoothed aggregation with Chebyshev relaxation was found to perform poorly when compared with classical AMG in terms of solve time and robustness. However, plain aggregation was comparable to classical AMG.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Weighted relaxation for multigrid reduction in time

Current trends in computer architectures now mean that faster computation speed must come primarily from increased concurrency, not faster clock speeds, which are stagnating. Thus, this situation creates bottlenecks for serial algorithms, including the well-known bottleneck for sequential time-integration, where each individual time-value (i.e., time-step) is computed sequentially. One approach to alleviate this and achieve parallelism in time is with multigrid. Here, in this work, we consider multigrid-reduction-in-time (MGRIT), a multilevel method applied to the time dimension that computes multiple time-steps in parallel. Like all multigrid methods, MGRIT relies on the complementary relationship between relaxation on a fine-grid and a correction from the coarse grid to solve the problem. All current MGRIT implementations are based on unweighted-Jacobi relaxation; here we introduce the concept of weighted relaxation to MGRIT. We derive new convergence bounds for weighted relaxation, and use this analysis to guide the selection of relaxation weights. Numerical results then demonstrate that by choosing appropriate non-unitary relaxation weights, one can achieve faster convergence rates and lower iteration counts for MGRIT when compared with unweighted relaxation. In most cases, weighted relaxation yields a 10%–20% saving in iterations, which is significant when using large high-performance computers. For A-stable integration schemes, results also illustrate that under-relaxation can restore convergence in some cases where unweighted relaxation is not convergent.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles

The successful self-assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally-designed, nanoscale components. This 3D DNA tile owes its “tensegrity” nature to its three rotationally-stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter-junction regions, corresponding to two thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed [Z + 2/3] turn inter-junction segments, yielding right-handed, antiparallel, “J1” junctions. Here, we report here a minimal DNA triangle motif consisting of 3-bp inter-junction segments, or one third of a helical turn. Here, we find that the minimal motif exhibits a reversed morphology with a left-handed tertiary structure mediated by a locally-parallel Holliday junction—the L1 junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. We identify a Rule of Thirds by which supramolecular chirality can be programmed through inter-junction DNA segment length. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under-explored class of self-assembling, chiral nanomaterials for topological processes in biological systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Medium Voltage Solid State Transformer for Extreme Fast Charging Applications

A modular and scalable solid state transformer (SST) with direct medium voltage (MV) AC connectivity is proposed to enable DC extreme fast charging (XFC) of electric vehicles. Single-phase-modules (SPMs), each consisting of an active-front-end (AFE) stage and an isolated DC-DC stage, are connected in input-series-output-parallel (ISOP) configuration. The modular hardware is co-designed with decentralized control of the DC-DC stages where voltage and power balancing are achieved by each SPM using only its local sensor feedback; a centralized controller (CC) regulates the low voltage (LV) DC bus through the AFE stages without any sensor feedback form the SPMs. The controller architecture contrasts sharply with the prior art for MV AC to LV DC SSTs where high-speed bidirectional communication among SPMs and a CC are required for module-level voltage and power balancing, which severely limits the scalability and practical realization of higher voltage and higher power units. Detailed small-signal analysis and controller design guidelines are developed. Furthermore, a soft start-up strategy is presented. The proposed converter and control structure are validated through simulation and experimental results.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Towards a more general understanding of the algorithmic utility of recurrent connections

Lateral and recurrent connections are ubiquitous in biological neural circuits. Yet while the strong computational abilities of feedforward networks have been extensively studied, our understanding of the role and advantages of recurrent computations that might explain their prevalence remains an important open challenge. Foundational studies by Minsky and Roelfsema argued that computations that require propagation of global information for local computation to take place would particularly benefit from the sequential, parallel nature of processing in recurrent networks. Such “tag propagation” algorithms perform repeated, local propagation of information and were originally introduced in the context of detecting connectedness, a task that is challenging for feedforward networks. Here, we advance the understanding of the utility of lateral and recurrent computation by first performing a large-scale empirical study of neural architectures for the computation of connectedness to explore feedforward solutions more fully and establish robustly the importance of recurrent architectures. In addition, we highlight a tradeoff between computation time and performance and construct hybrid feedforward/recurrent models that perform well even in the presence of varying computational time limitations. We then generalize tag propagation architectures to propagating multiple interacting tags and demonstrate that these are efficient computational substrates for more general computations of connectedness by introducing and solving an abstracted biologically inspired decision-making task. Our work thus clarifies and expands the set of computational tasks that can be solved efficiently by recurrent computation, yielding hypotheses for structure in population activity that may be present in such tasks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Compiling Quantum Circuits for Dynamically Field-Programmable Neutral Atoms Array Processors

Dynamically field-programmable qubit arrays (DPQA) have recently emerged as a promising platform for quantum information processing. In DPQA, atomic qubits are selectively loaded into arrays of optical traps that can be reconfigured during the computation itself. Leveraging qubit transport and parallel, entangling quantum operations, different pairs of qubits, even those initially far away, can be entangled at different stages of the quantum program execution. Such reconfigurability and non-local connectivity present new challenges for compilation, especially in the layout synthesis step which places and routes the qubits and schedules the gates. In this paper, we consider a DPQA architecture that contains multiple arrays and supports 2D array movements, representing cutting-edge experimental platforms. Within this architecture, we discretize the state space and formulate layout synthesis as a satisfiability modulo theories problem, which can be solved by existing solvers optimally in terms of circuit depth. For a set of benchmark circuits generated by random graphs with complex connectivities, our compiler OLSQ-DPQA reduces the number of two-qubit entangling gates on small problem instances by 1.7x compared to optimal compilation results on a fixed planar architecture. To further improve scalability and practicality of the method, we introduce a greedy heuristic inspired by the iterative peeling approach in classical integrated circuit routing. Using a hybrid approach that combined the greedy and optimal methods, we demonstrate that our DPQA-based compiled circuits feature reduced scaling overhead compared to a grid fixed architecture, resulting in 5.1X less two-qubit gates for 90 qubit quantum circuits. These methods enable programmable, complex quantum circuits with neutral atom quantum computers, as well as informing both future compilers and future hardware choices.

Physics↗

NASA NTRS1984

Dataflow computing approach in high-speed digital simulation

New computational tools and methodologies for the digital simulation of continuous systems were explored. Programmability, and cost effective performance in multiprocessor organizations for real time simulation was investigated. Approach is based on functional style languages and data flow computing principles, which allow for the natural representation of parallelism in algorithms and provides a suitable basis for the design of cost effective high performance distributed systems. The objectives of this research are to: (1) perform comparative evaluation of several existing data flow languages and develop an experimental data flow language suitable for real time simulation using multiprocessor systems; (2) investigate the main issues that arise in the architecture and organization of data flow multiprocessors for real time simulation; and (3) develop and apply performance evaluation models in typical applications.

Ercegovac, M. D.↗

NASA NTRS1984

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

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.

Bruno, John↗

NASA NTRS2010

Techniques for Assuring NASA Mission Success Using Redundancy and Multi-Functionality Designs

Topics include NASA centers around the country; 2009 highlights of significant successes in space transportation, exploration, and science; significant accomplishments; places to explore include Lagrange points, near-Earth objects, Mars and the Moon, and International Space Station research; Marshall's missions include propulsion and transportation systems, life support systems, and earth and space science spacecraft, systems, and operations; project lifecycle management model; motivation of avionics fault-tolerance, redundancy needs and concerns, redundancy versus reliability; parallel-series configurations; effect of adding redundancy on mission success; example of rules-based approach where reliability and safety interaction impacts design; impact of common cause failure; approach ot bottom-up reliability analysis; three factors that lead to redundant system failure; Apollo 13 multi-functional reliability and example; and mitigating the risk of single string spacecraft architecture;.

Shivers, Herb↗

NASA NTRS2013

V&V of Fault Management: Challenges and Successes

This paper describes the results of a special breakout session of the NASA Independent Verification and Validation (IV&V) Workshop held in the fall of 2012 entitled "V&V of Fault Management: Challenges and Successes." The NASA IV&V Program is in a unique position to interact with projects across all of the NASA development domains. Using this unique opportunity, the IV&V program convened a breakout session to enable IV&V teams to share their challenges and successes with respect to the V&V of Fault Management (FM) architectures and software. The presentations and discussions provided practical examples of pitfalls encountered while performing V&V of FM including the lack of consistent designs for implementing faults monitors and the fact that FM information is not centralized but scattered among many diverse project artifacts. The discussions also solidified the need for an early commitment to developing FM in parallel with the spacecraft systems as well as clearly defining FM terminology within a project.

Verification↗

DOE OSTI2019

Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating

Sensing and responding to environmental water deficiency and osmotic stresses are essential for the growth, development, and survival of plants. Recently, an osmolality-sensing ion channel called OSCA1 was discovered that functions in sensing hyperosmolality in Arabidopsis . In this paper, we report the cryo-electron microscopy (cryo-EM) structure and function of an OSCA1 homolog from rice ( Oryza sativa ; OsOSCA1.2), leading to a model of how it could mediate hyperosmolality sensing and transport pathway gating. The structure reveals a dimer; the molecular architecture of each subunit consists of 11 transmembrane (TM) helices and a cytosolic soluble domain that has homology to RNA recognition proteins. The TM domain is structurally related to the TMEM16 family of calcium-dependent ion channels and lipid scramblases. The cytosolic soluble domain possesses a distinct structural feature in the form of extended intracellular helical arms that are parallel to the plasma membrane. These helical arms are well positioned to potentially sense lateral tension on the inner leaflet of the lipid bilayer caused by changes in turgor pressure. Computational dynamic analysis suggests how this domain couples to the TM portion of the molecule to open a transport pathway. Hydrogen/deuterium exchange mass spectrometry (HDXMS) experimentally confirms the conformational dynamics of these coupled domains. These studies provide a framework to understand the structural basis of proposed hyperosmolality sensing in a staple crop plant, extend our knowledge of the anoctamin superfamily important for plants and fungi, and provide a structural mechanism for potentially translating membrane stress to transport regulation.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1977

High-speed computerized tomography

The development of a high-speed reconstruction processor and a channelized architecture to use with a high-resolution tomographic unit is discussed with attention to the convolution reconstruction algorithm. By means of this algorithm, input data and intermediate result precision required throughout the algorithm execution have been studied with computer simulation using profile data derived from mathematically simulated test objects and experimental animal data. A prototype section for a highly parallel all-digital system executes 60 million arithmetic operations per second, and the full-scale version is expected to reconstruct 500 to 1000 cross sections per second.

Swartzlander, E. E., Jr.↗

NASA NTRS2005

Enhancements to PVM's BEOLIN architecture

.4.3 of PVM had previously been enhanced by the addition of a new architecture, BEOLIN, which allowed a PVM user to abstract a Beowulf class computer with a private network to appear as a single system, visible to the outside world, which could spawn tasks on different internal nodes.

BEOLIN↗

NASA NTRS2017

Cooling the Origins Space Telescope

The NASA Astrophysics Division has commissioned 4 studies for consideration by the 2020 Decadal Survey to be the next flagship mission following WFIRST (Wide Field Infrared Survey Telescope). One of the four studies is the Origins Space Telescope (OST), which will cover wavelengths from 6 microns to 600 microns. To perform at the level of the zodiacal, galactic, and cosmic background, the telescope must be cooled to 4 degrees Kelvin. 4 degrees Kelvin multi-stage mechanical cryocoolers will be employed along with a multilayer sunshield/thermal shield to achieve this temperature with a manageable parasitic heat load. Current state-of-the-art cryocoolers can achieve close to 4 degrees Kelvin, providing about 50 megawatts of cooling at 4 degrees Kelvin with an input power of 500 watts. Multiple coolers at this power level will be used in parallel. These coolers also provide extra cooling power at intermediate temperature stages of 15-20 degrees Kelvin and 50-70 degrees Kelvin . This upper stage cooling will be used to limit the heat conducted to 4 degrees Kelvin . The multi-layer sunshield will limit the radiated thermal energy to the 4 degrees Kelvin volume. This paper will describe the architecture of the cryogenic system for OST along with preliminary thermal models.

cryogenics↗

DOE OSTI2021

Phoenix: A Scalable Streaming Hypergraph Analysis Framework

We present Phoenix, a scalable hypergraph analytics framework for data analytics and knowledge discovery that was implemented on the leadership class computing platforms at Oak Ridge National Laboratory (ORNL). Our software framework comprises a distributed implementation of a streaming server architecture which acts as a gateway for various hypergraph generators/external sources to connect. Phoenix has the capability to utilize diverse hypergraph generators, including HyGen, a very large-scale hypergraph generator developed by ORNL. Phoenix incorporates specific algorithms for efficient data representation by exploiting hidden structures of the hypergraphs. Our experimental results demonstrate Phoenix’s scalable and stable performance on massively parallel computing platforms. Phoenix’s superior performance is due to the merging of high-performance computing with data analytic.

Kurte, Kuldeep↗

NASA NTRS1990

Real-time data system: Incorporating new technology in mission critical environments

If the Space Station Freedom is to remain viable over its 30-year life span, it must be able to incorporate new information systems technologies. These technologies are necessary to enhance mission effectiveness and to enable new NASA missions, such as supporting the Lunar-Mars Initiative. Hi-definition television (HDTV), neural nets, model-based reasoning, advanced languages, CPU designs, and computer networking standards are areas which have been forecasted to make major strides in the next 30 years. A major challenge to NASA is to bring these technologies online without compromising mission safety. In past programs, NASA managers have been understandably reluctant to rely on new technologies for mission critical activities until they are proven in noncritical areas. NASA must develop strategies to allow inflight confidence building and migration of technologies into the trusted tool base. NASA has successfully met this challenge and developed a winning strategy in the Space Shuttle Mission Control Center. This facility, which is clearly among NASA's most critical, is based on 1970's mainframe architecture. Changes to the mainframe are very expensive due to the extensive testing required to prove that changes do not have unanticipated impact on critical processes. Systematic improvement efforts in this facility have been delayed due to this 'risk to change.' In the real-time data system (RTDS) we have introduced a network of engineering computer workstations which run in parallel to the mainframe system. These workstations are located next to flight controller operating positions in mission control and, in some cases, the display units are mounted in the traditional mainframe consoles. This system incorporates several major improvements over the mainframe consoles including automated fault detection by real-time expert systems and color graphic animated schematics of subsystems driven by real-time telemetry. The workstations have the capability of recording telemetry data and providing 'instant replay' for flight controllers. RTDS also provides unique graphics animated by real-time telemetry such as workstation emulation of the shuttle's flight instruments and displays of the remote manipulator system (RMS) position. These systems have been used successfully as prime operational tools since STS-26 and have supported seven shuttle missions.

Muratore, John F.↗

NASA NTRS1987

High-resolution CCD imagers using area-array CCD's for sensing spectral components of an optical line image

CCD imagers with a novel replicated-line-imager architecture are abutted to form an extended line sensor. The sensor is preceded by optics having a slit aperture and having an optical beam splitter or astigmatic lens for projecting multiple line images through an optical color-discriminating stripe filter to the CCD imagers. A very high resolution camera suitable for use in a satellite, for example, is thus provided. The replicated-line architecture of the imager comprises an area-array CCD, successive rows of which are illuminated by replications of the same line segment, as transmitted by respective color filter stripes. The charge packets formed by accumulation of photoresponsive charge in the area-array CCD are read out row by row. Each successive row of charge packets is then converted from parallel to serial format in a CCD line register and its amplitude sensed to generate a line of output signal.

Elabd, Hammam↗

DOE OSTI2020

Enabling Highly Efficient Capsule Networks Processing Through A PIM-Based Architecture Design

In recent years, the CNNs have achieved great successes in the image processing tasks, e.g., image recognition and object detection. Unfortunately, traditional CNN's classication is found to be easily misled by increasingly complex image features due to the usage of pooling operations, hence unable to preserve accurate position and pose information of the objects. To address this challenge, a novel neural network structure called Capsule Network has been proposed, which introduces equivariance through capsules to signicantly enhance the learning ability for image segmentation and object detection. Due to its requirement of performing a high volume of matrix operations, CapsNets have been generally accelerated on modern GPU platforms that provide highly optimized software library for common deep learning tasks. However, based on our performance characterization on modern GPUs, CapsNets exhibit low effciency due to the special program and execution features of their routing procedure, including massive unshareable intermediate variables and intensive syn- chronizations, which are very dicult to optimize at software level. To address these challenges, we propose a hybrid computing architecture design named PIM-CapsNet. It preserves GPU's on-chip computing capability for accelerating CNN types of layers in CapsNet, while pipelining with an off-chip in-memory acceleration solution that effectively tackles routing procedure's ineffciency by leveraging the processing-in-memory capability of today's 3D stacked memory. Using routing procedure's inherent parallellization feature, our design enables hierarchical improvements on CapsNet inference effciency through minimizing data movement and maximizing parallel processing in memory. Evaluation results demonstrate that our proposed design can achieve substantial improvement on both performance and energy savings for CapsNet inference, with almost zero accuracy loss. The results also suggest good performance scalability in optimizing the routing procedure with increasing network size.

Zhang, Xingyao↗