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At least 1,459 records · Page 81

All sources NASA NTRS DOE OSTI

DOE OSTI2017

High-Performance I/O: HDF5 for Lattice QCD

Practitioners of lattice QCD/QFT have been some of the primary pioneer users of the state-of-the-art high-performance-computing systems, and contribute towards the stress tests of such new machines as soon as they become available. As with all aspects of high-performance-computing, I/O is becoming an increasingly specialized component of these systems. In order to take advantage of the latest available high-performance I/O infrastructure, to ensure reliability and backwards compatibility of data files, and to help unify the data structures used in lattice codes, we have incorporated parallel HDF5 I/O into the SciDAC supported USQCD software stack. Here we present the design and implementation of this I/O framework. Our HDF5 implementation outperforms optimized QIO at the 10-20% level and leaves room for further improvement by utilizing appropriate dataset chunking.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Distributed-Memory Breadth-First Search on Massive Graphs. IN: Parallel Graph Algorithms

This chapter studies the problem of traversing large graphs using the breadth-first search order on distributed-memory supercomputers. We consider both the traditional level-synchronous top-down algorithm as well as the recently discovered direction optimizing algorithm. We analyze the performance and scalability trade-offs in using different local data structures such as CSR and DCSC, enabling in-node multithreading, and graph decompositions such as 1D and 2D decomposition.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

System and method for operator control of heterogeneous unmanned system teams

A control architecture and associated control methods are under development to allow a single user to control a team of multiple heterogeneous UMS as they conduct multi-faceted (i.e. multi-objective) missions in real time is disclosed. The control architecture is hierarchical, modular and layered and enables operator interaction at each layer, ensuring the human operator is in close control of the unmanned team at all times. The architecture and key data structures are introduced. Two approaches to distributed collaborative control of heterogeneous unmanned systems are described, including an extension of homogeneous swarm control and a novel application of distributed model predictive control. Initial results are presented, demonstrating heterogeneous UMS teams conducting collaborative missions.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

EnergyPlus Performance Improvements via JSON Input Refactoring

EnergyPlus is the flagship whole-building energy simulation program developed by the U.S. Department of Energy. This paper describes the refactoring efforts around the EnergyPlus input processor to natively support JavaScript Object Notation (JSON), allow validation through use of a JSON schema validator, convert and validate typical EnergyPlus input data file (*.idf) files to JSON files, and improve related metrics such as: read time for schema and input files, parse time for processing input, and time to query/return data from EnergyPlus internal data structure. Performance improvements on sample files result in 14% and 60% reduction in schema and input file reads respectively, 36-62% reduction to process input, and 24-99+% query reduction for functions that take advantage of the new format. For the files tested, overall speedup realized as part of this JSON refactor is 1.6x to 5.4x.

Adams, Mark↗

DOE OSTI2019

Scalable PETSc Implementation of the Three-Phase Unbalanced AC Power Flow Solver

A revolutionary transition of energy infrastructure, spanning across supply and demand sectors, is happening all around the world. Integration of renewable energy sources into our ever-complex power distribution networks is central to the infrastructure planning of the future. One step towards achieving this goal is to solve unbalanced transmission and distribution systems. Traditional approaches and software tools are not suitable because they assume a completely balanced 3-phase system, hence a single-phase equivalent can be solved. Renewable energy such as wind and solar power are intermittent and can pose a challenge when integrating into an already unbalanced power grid. Furthermore, these power grids can be quite large at scale consisting of potentially thousands of buses, which can be computationally demanding. This poster presents preliminary work on designing a robust and scalable 3-phase unbalanced AC power flow solver. The proposed power flow solver will eventually be built on top of the PETSc library and utilizes state-of-the-art parallel data structures like the DMNetwork as well as iterative solvers and preconditioners.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2019

Vectorization of Random Number Generation and Reproducibility of Concurrent Particle Transport Simulation

Efficient random number generation with high quality statistical properties and exact reproducibility of Monte Carlo simulations are important requirements in many areas of computational science. VecRNG is a package providing pseudo-random number generation (pRNG) in the context of a new library VecMath. This library bundles up several general-purpose mathematical utilities, data structures, and algorithms having both SIMD and SIMT (GPUs) support based on VecCore.~Several state-of-the-art RNG algorithms are implemented as kernels supporting parallel generation of random numbers in scalar, vector, and Cuda workflows. In this report, we will present design considerations, implementation details, and computing performance of parallel pRNG engines on both CPU and GPU. Reproducibility of propagating multiple particles in parallel for HEP event simulation is demonstrated, using GeantV-based examples, for both sequential and fine-grain track-level concurrent simulation wor kflows. Strategies for efficient uses of vectorized pRNG and non-overlapping streams of random number sequences in concurrent computing environments is discussed as well.

Jun, S. Y.↗

DOE OSTI2019

Linear optimal power flow system and method

An electric power system or power grid is optimized using a computer-implemented tool the represents in computer memory the optimization function and at least one constraint, which the processor operates upon using a linear programming solver algorithm. The constraints are represented in memory as data structures that include both real and reactive power terms, corresponding to at least one of a power flow model and a transmission line model. The transmission line model is represented using a piecewise linear representation. The power flow model may also include for each node in the power system a real power loss term representing transmission line loss allocated to that node.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2015

Developing Uintah's Runtime System for Forthcoming Architectures

The need to solve ever-more complex science and engineering problems on computer architectures that are rapidly evolving poses considerable challenges for modern simulation frameworks and packages. While the decomposition of software into a programming model that generates a task-graph for execution by a runtime system make portability and performance possible, it also imposes considerable demands on that runtime system. Here, the challenge of meeting those demands for near-term and longer term systems in the context of the Uintah framework is considered in key areas such as support for data structures, tasks on heterogeneous architectures, performance portability, power management and designing for resilience by the use of replication based upon adaptive mesh refinement processes is addressed. Examples of techniques in these areas are used to illustrate performance improvements obtained for present large-scale systems and the needs of proposed systems considered.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Hardware accelerated dynamic work creation on a graphics processing unit

A processor core is configured to execute a parent task that is described by a data structure stored in a memory. A coprocessor is configured to dispatch a child task to the at least one processor core in response to the coprocessor receiving a request from the parent task concurrently with the parent task executing on the at least one processor core. In some cases, the parent task registers the child task in a task pool and the child task is a future task that is configured to monitor a completion object and enqueue another task associated with the future task in response to detecting the completion object. The future task is configured to self-enqueue by adding a continuation future task to a continuation queue for subsequent execution in response to the future task failing to detect the completion object.

Gutierrez, Anthony↗

DOE OSTI2023

Hardware accelerated dynamic work creation on a graphics processing unit

Gutierrez, Anthony T.↗

DOE OSTI2023

Optimized self-designing key-value storage engine

Embodiments of the invention utilize an optimized key-value storage engine to strike the optimal balance between cloud-cost and performance and supports queries, including updates, lookups, range queries, inserts, and read-modify-writes. Cloud cost is manifested in purchasing both storage and processing resources. The improved approach has the ability to self-design and instantiate holistic configurations given a workload, a cloud budget, and optionally performance goals and a set of Service Level Agreement (SLA) specifications. A configuration reflects an optimized storage engine design in terms of, for example, the individual data structures design (in-memory and on-disk) in the engine as well as their algorithms and interactions, a cloud provider, and the exact virtual machines to be used.

Idreos, Stratos↗

DOE OSTI2016

Algorithmic Improvements for Portable Event-Based Monte Carlo Transport Using the Nvidia Thrust Library

High performance computing environments are progressively moving towards many-core computing architectures. The Los Alamos National Laboratory Trinity machine, available in late 2016, will use both Intel Xeon Haswell processors and Intel Xeon Phi Knights Landing many integrated core (MIC) coprocessors. The Lawrence Livermore National Laboratory Sierra machine, available in 2018, will use an IBM PowerPC architecture along with Nvidia graphics processing units (GPUs). Applications that must work in this supercomputing environment must continue to adapt in order to take advantage of the diverse hardware architectures that are coming. A significant consideration is not only the performance of the application on a given platform but also the portability of the application to other platforms. The algorithmic improvements presented in this paper build upon recently-reported work on event-based Monte Carlo transport in the ALPSMC code that models particle transport in one-dimensional binary stochastic media. That paper discussed the lack of available vectorization in the traditional history-based algorithm used for Monte Carlo transport and presented a data parallel event-based algorithm implemented using the Nvidia Thrust library for portability. The performance of the data parallel event-based algorithm implemented using Thrust was compared to a native CUDA implementation. The conclusions from that work were that the Thrust library abstraction technique caused too significant a loss in performance but that the event-based method was a viable option that should be further investigated. In this paper, we describe algorithmic improvements to the data parallel event-based algorithm previously presented. We made further algorithmic optimizations to the event-based CUDA implementation, most notably: data structure changes, a new conditional particle removal scheme in the event-based process, and the use of multiple GPUs. In addition to improvements to the algorithm, we re-implemented the Thrust version from the now further optimized CUDA version, giving a greater chance for success at a performant abstraction. Finally, we revisited our previous assumptions about the inability of the history-based method to achieve performance on vector style architectures such as the MICs and GPUs, with surprising and promising results. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Boron chelate complexes: X-ray and UV photoelectron spectra and electronic structure

Published data on the electronic structure of boron chelates are summarized for the first time. Ultraviolet photoelectron spectra of vapors, X-ray photoelectron spectra of molecular crystals, and results of modeling within the framework of the density functional theory are analyzed. Data on the effect of substituents on the electronic structure of complexes are systematized.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1983

On the determination of airplane model structure form flight data

A procedure based on a modified stepwise regression and several selection criteria is presented for the determination of airplane model structure from flight data. The aerodynamic force and moment coefficients in an airplane model are expresed either as polynomials in output and input variables or as a combination of splines. The procedure is demonstrated in three examples by attempting to determine a local, extended and global model. Some of the resulting models are verified by using the maximum likelihood estimation or by examining model prediction capabilities.

Klein, V.↗

NASA NTRS1983

Use of MAGSAT anomaly data for crustal structure and mineral resources in the US midcontinent

Magnetic field data acquired by NASA's MAGSAT satellite is used to construct a long-wavelength magnetic anomaly map for the U.S. midcontinent. This aids in interpretation of gross crustal geology (structure, lithologic composition, resource potential) of the region. Magnetic properties of minerals and rocks are investigated and assessed, to help in evaluation and modelling of crustal magnetization sources and depth to the Curie-temperature isotherm.

Carmichael, R. S.↗

DOE OSTI2015

In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID

A prototype of a 96-well plate scanner for in situ data collection has been developed at the Structural Biology Center (SBC) beamline 19-ID, located at the Advanced Photon Source, USA. The applicability of this instrument for protein crystal diffraction screening and data collection at ambient temperature has been demonstrated. Several different protein crystals, including selenium-labeled, were used for data collection and successful SAD phasing. Without the common procedure of crystal handling and subsequent cryo-cooling for data collection at T = 100 K, crystals in a crystallization buffer show remarkably low mosaicity (<0.1°) until deterioration by radiation damage occurs. Data presented here show that cryo-cooling can cause some unexpected structural changes. Based on the results of this study, the integration of the plate scanner into the 19-ID end-station with automated controls is being prepared. With improvement of hardware and software, in situ data collection will become available for the SBC user program including remote access.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Symmetry-mode analysis for local structure investigations using pair distribution function data

Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.

36 MATERIALS SCIENCE↗