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At least 1,693 records · Page 94

A survey of software implementations used by application codes in the Exascale Computing Project

The US Department of Energy Office of Science and the National Nuclear Security Administration initiated the Exascale Computing Project (ECP) in 2016 to prepare mission-relevant applications and scientific software for the delivery of the exascale computers starting in 2023. The ECP currently supports 24 efforts directed at specific applications and six supporting co-design projects. These 24 application projects contain 62 application codes that are implemented in three high-level languages—C, C++, and Fortran—and use 22 combinations of graphical processing unit programming models. The most common implementation language is C++, which is used in 53 different application codes. The most common programming models across ECP applications are CUDA and Kokkos, which are employed in 15 and 14 applications, respectively. This article provides a survey of the programming languages and models used in the ECP applications codebase that will be used to achieve performance on the future exascale hardware platforms.

97 MATHEMATICS AND COMPUTING↗

Large-Scale Numerical Simulations of Human Motion

This paper examines the feasibility of using massively-parallel and vector-processing supercomputers to solve large-scale optimal control problems for human movement. Specifically, we compare the computational expense of determining the optimal controls for the single support phase of walking using a conventional serial machine (a Silicon Graphics Personal Iris 4D25 workstation), a MIMD parallel machine (an Intel iPSC/860 comprising 128 processors), and a parallel-vector-processing machine (a Cray Y-MP 8/864). With the human body modeled as a 14 degree-of-freedom linkage actuated by 46 musculotendinous units, computation of the optimal controls for walking could take up to 3 months of CPU time on the Iris. Both the Cray Y-MP and the Intel iPSC/860 are able to reduce this time to practical levels. The optimal control solution for walking can be found with about 77 hours of CPU time on the Cray, and with about 88 hours of CPU time on the Intel. Although the overall speeds of the Cray and the Intel were found to be similar, the unique capabilities of each machine are best suited to different parts of the optimal control algorithm used. The Intel performed best in the calculation of the derivatives of the performance criterion and the constraints. In contrast, the Cray performed best during parameter optimization of the controls. These results suggest that the ideal computer architecture for solving very large-scale optimal control problems is a hybrid system in which a vector-processing machine is integrated into the communication network of a MIMD parallel machine.

Anderson, Frank C.↗

Neutrino Oscillations in Supernovae

A (core-collapse) supernova is the final death call of a massive star during which a gigantic amount of a special kind of elementary particles known as neutrinos are released for a brief period of time. An earlier work by the PI and his collaborators has shown that the dense neutrino gas deep inside the supernova can experience "flavor transformation" or "oscillations" in a collective fashion, a macroscopic quantum phenomenon spanning over distances of 100-1000 kilometers. During this process neutrinos of different energies and propagation directions change their identities simultaneously. This phenomenon may be a key to understanding the mechanism of supernova explosion and the origin of many of the chemical elements found on the earth which were produced in the supernovae exploded in the past. The previous understanding of neutrino oscillations in supernovae was based on a stationary 3-dimensional model with 1 spatial dimension and 2 momentum dimensions. In this "neutrino bulb model" neutrinos are emitted from a spherically symmetric surface and they are decoupled from the motion of matter and the production of chemical elements. In order to accurately model the neutrino oscillations in supernovae and determine its physical consequences, sophisticated 7-dimensional (1 temporal dimension + 3 spatial dimensions + 3 momentum dimensions) modelling of neutrino transport must be performed self-consistently together with the hydrodynamic simulation of the flow of energy and matter inside the supernova and with the calculation of the production and destruction of chemical elements through a large nucleosynthesis network. Although it will be long journey to achieve the lofty goal, our project has made important progress in three different fronts towards this goal. In the first front we explored new computing hardware on which the next generation simulation codes may be run. We ported the neutrino bulb code to the platform of Graphics Processing Unit (GPU) and then later developed a new bulb code that can be run on supercomputers equipped with the Intel Xeon CPUs and/or the Xeon Phi coprocessors. In the second front we developed new algorithms that can be used towards computing neutrino oscillations in multi-dimensional models. We have developed a moment expansion method which is approximately 10 times more efficient than the old algorithm. We have also developed numerical codes to solve neutrino oscillations in toy models with two spatial dimensions. In the last front we used analytic methods to study neutrino oscillations in more sophisticated models, e.g. of multiple spatial dimensions and/or with time dependence. By analyzing the neutrino oscillations in toy models with two spacial dimensions we found that the approximate spacial translation symmetry, which is similar to the spherical symmetry in the neutrino bulb model, can be broken spontaneously as neutrino oscillations begin. By analyzing a time-dependent neutrino bulb model we found that certain modes of neutrino oscillations that are suppressed in the stationary model can become active in the time-dependent model. We have also developed theories which give insights to how ordinary matter may affect neutrino oscillations in supernovae and other astrophysical environments.

Duan, Huaiyu↗

An Architecture for Real-Time Interpretation and Visualization of Structural Sensor Data in a Laboratory Environment

A visualization system is being developed out of the need to monitor, interpret, and make decisions based on the information from several thousand sensors during experimental testing to facilitate development and validation of structural health monitoring algorithms. As an added benefit the system will enable complete real-time sensor assessment of complex test specimens. Complex structural specimens are routinely tested that have hundreds or thousands of sensors. During a test, it is impossible for a single researcher to effectively monitor all the sensors and subsequently interesting phenomena occur that are not recognized until post-test analysis. The ability to detect and alert the researcher to these unexpected phenomena as the test progresses will significantly enhance the understanding and utilization of complex test articles. Utilization is increased by the ability to halt a test when the health monitoring algorithm response is not satisfactory or when an unexpected phenomenon occurs, enabling focused investigation potentially through the installation of additional sensors. Often if the test continues, structural changes make it impossible to reproduce the conditions that exhibited the phenomena. The prohibitive time and costs associated with fabrication, sensoring, and subsequent testing of additional test articles generally makes it impossible to further investigate the phenomena. A scalable architecture is described to address the complex computational demands of structural health monitoring algorithm development and laboratory experimental test monitoring. The researcher monitors the test using a photographic quality 3D graphical model with actual sensor locations identified. In addition, researchers can quickly activate plots displaying time or load versus selected sensor response along with the expected values and predefined limits. The architecture has several key features. First, distributed dissimilar computers may be seamlessly integrated into the information flow. Second, virtual sensors may be defined that are complex functions of existing sensors or other virtual sensors. Virtual sensors represent a calculated value not directly measured by particular physical instrument. They can be used, for example, to represent the maximum difference in a range of sensors or the calculated buckling load based on the current strains. Third, the architecture enables autonomous response to preconceived events, where by the system can be configured to suspend or abort a test if a failure is detected in the load introduction system. Fourth, the architecture is designed to allow cooperative monitoring and control of the test progression from multiple stations both remote and local to the test system. To illustrate the architecture, a preliminary implementation is described monitoring the Stitched Composite Wing recently tested at LaRC.

Doggett, William↗

The Laboratory for Oceans Computing Facility

The first VAX computer in the Laboratory for Oceans Computing Facility (LOCF) was installed and the facility was largely expanded. The growth is not only in hardware and software, but also in the number of users and in supporting research and development projects. The LOCF serves as a general purpose computing facility for: ocean color research projects, sea ice research projects, processing of the Nimbus-7 Coastal Zone Color Scanner data set, real time ingest and analysis of TIROS-N satellite data, study of the Synthetic Aperture Radar data, study of LANDSAT data, and many others. The physical space and the electrical power layout of the computing room were modified to accommodate all the equipment. The LOCF has several image processing stations which include two International Imaging Systems (IIS) model 75 processors and one Adage processor. The facility has the capability of ingesting the TIROS-N HRPT satellite data on a real time basis. More than 30 software packages were installed on the systems. System software packages, network software, FORTRAN and C compilers, database management software, image processing software, graphics, mathematics and statistics packages, TAE, Catalog Manager, GEMPAK, LAS and many other software developed on the LOCF computers such as SEAPAK have greatly advanced the capability of the LOCF.

Kao, R.↗

Fostering Remote Visualization: Experiences in Two Different HPC Sites

Visualization of scientific data is crucial for scientific discovery to gain insight into the results of simulations and experiments. Remote visualization is of crucial importance to access infrastructure, data and computational resources and, to avoid data movement from where data is produced and to where data will be analyzed. Remote visualization enables geographically diverse collaboration and enhances user experience through graphical user interfaces. This paper presents two approaches deployed by two different HPC centers: The SC3 - Supercomputación y Cálculo Científico Center in Colombia and the Oak Ridge Leadership Computing Facility in USA. We overview our remote visualization experiences, adopted technologies, use cases, and challenges encountered. Our contribution is to signal the commonality between approaches in terms of the end goal, showing their fitness for their contexts, while not focusing only on attempting to provide a general picture of remote visualization, given the differences between centers in terms of purposes, needs, resources, and national impact.

Gelvez Cortes, Sergio Augusto↗

Rank-reduced coupled-cluster. III. Tensor hypercontraction of the doubles amplitudes

In this work, we develop a quartic-scaling implementation of coupled-cluster singles and doubles (CCSD) based on low-rank tensor hypercontraction (THC) factorizations of both the electron repulsion integrals (ERIs) and the doubles amplitudes. This extends our rank-reduced (RR) coupled-cluster method to incorporate higher-order tensor factorizations. The THC factorization of the doubles amplitudes accounts for most of the gain in computational efficiency as it is sufficient, in conjunction with a Cholesky decomposition of the ERIs, to reduce the computational complexity of most contributions to the CCSD amplitude equations. Further THC factorization of the ERIs reduces the complexity of certain terms arising from nested commutators between the doubles excitation operator and the two-electron operator. We implement this new algorithm using graphical processing units and demonstrate that it enables CCSD calculations for molecules with 250 atoms and 2500 basis functions using a single computer node. Furthermore, we show that the new method computes correlation energies with comparable accuracy to the underlying RR-CCSD method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of enhanced modern structured analysis techniques to Space Station Freedom electric power system requirements

A team of Space Station Freedom (SSF) system engineers are in the process of extensive analysis of the SSF requirements, particularly those pertaining to the electrical power system (EPS). The objective of this analysis is the development of a comprehensive, computer-based requirements model, using an enhanced modern structured analysis methodology (EMSA). Such a model provides a detailed and consistent representation of the system's requirements. The process outlined in the EMSA methodology is unique in that it allows the graphical modeling of real-time system state transitions, as well as functional requirements and data relationships, to be implemented using modern computer-based tools. These tools permit flexible updating and continuous maintenance of the models. Initial findings resulting from the application of EMSA to the EPS have benefited the space station program by linking requirements to design, providing traceability of requirements, identifying discrepancies, and fostering an understanding of the EPS.

Biernacki, John↗

Deep Space Network (DSN), Network Operations Control Center (NOCC) computer-human interfaces

The Network Operations Control Center (NOCC) of the DSN is responsible for scheduling the resources of DSN, and monitoring all multi-mission spacecraft tracking activities in real-time. Operations performs this job with computer systems at JPL connected to over 100 computers at Goldstone, Australia and Spain. The old computer system became obsolete, and the first version of the new system was installed in 1991. Significant improvements for the computer-human interfaces became the dominant theme for the replacement project. Major issues required innovating problem solving. Among these issues were: How to present several thousand data elements on displays without overloading the operator? What is the best graphical representation of DSN end-to-end data flow? How to operate the system without memorizing mnemonics of hundreds of operator directives? Which computing environment will meet the competing performance requirements? This paper presents the technical challenges, engineering solutions, and results of the NOCC computer-human interface design.

Ellman, Alvin↗

BioRT‐HBV 1.0: A Biogeochemical Reactive Transport Model at the Watershed Scale

Abstract Reactive Transport Models (RTMs) are essential tools for understanding and predicting intertwined ecohydrological and biogeochemical processes on land and in rivers. While traditional RTMs have focused primarily on subsurface processes, recent watershed‐scale RTMs have integrated ecohydrological and biogeochemical interactions between surface and subsurface. These emergent, watershed‐scale RTMs are often spatially explicit and require extensive data, computational power, and computational expertise. There is however a pressing need to create parsimonious models that require minimal data and are accessible to scientists with limited computational background. To that end, we have developed BioRT‐HBV 1.0, a watershed‐scale, hydro‐biogeochemical RTM that builds upon the widely used, bucket‐type HBV model known for its simplicity and minimal data requirements. BioRT‐HBV uses the conceptual structure and hydrology output of HBV to simulate processes including advective solute transport and biogeochemical reactions that depend on reaction thermodynamics and kinetics. These reactions include, for example, chemical weathering, soil respiration, and nutrient transformation. The model uses time series of weather (air temperature, precipitation, and potential evapotranspiration) and initial biogeochemical conditions of subsurface water, soils, and rocks as input, and output times series of reaction rates and solute concentrations in subsurface waters and rivers. This paper presents the model structure and governing equations and demonstrates its utility with examples simulating carbon and nitrogen processes in a headwater catchment. As shown in the examples, BioRT‐HBV can be used to illuminate the dynamics of biogeochemical reactions in the invisible, arduous‐to‐measure subsurface, and their influence on the observed stream or river chemistry and solute export. With its parsimonious structure and easy‐to‐use graphical user interface, BioRT‐HBV can be a useful research tool for users without in‐depth computational training. It can additionally serve as an educational tool that promotes pollination of ideas across disciplines and foster a diverse, equal, and inclusive user community.

Sadayappan, Kayalvizhi↗

A Hybrid Climate Modeling System Using AI-assisted Process Emulators

This white paper addresses Focus Area II. We advocate developing a hybrid modeling system to improve the understanding of decadal- and longer-scale predictability of high impact water cycle components. This hybrid model combines a partial differential equation (PDE)-based dynamic core with AI/ML based emulators to represent many of the computationally expensive processes in Earth’s climate models. The hybrid modeling system has the potential to exploit emerging graphics processing unit (GPU)-accelerated architectures and allows for the generation of large ensemble (~1000’s) simulations to better characterize the model uncertainty and understand predictability.

58 GEOSCIENCES↗

NASTRAN data generation of helicopter fuselages using interactive graphics

The development and implementation of a preprocessor system for the finite element analysis of helicopter fuselages is described. The system utilizes interactive graphics for the generation, display, and editing of NASTRAN data for fuselage models. It is operated from an IBM 2250 cathode ray tube (CRT) console driven by an IBM 370/145 computer. Real time interaction plus automatic data generation reduces the nominal 6 to 10 week time for manual generation and checking of data to a few days. The interactive graphics system consists of a series of satellite programs operated from a central NASTRAN Systems Monitor. Fuselage structural models including the outer shell and internal structure may be rapidly generated. All numbering systems are automatically assigned. Hard copy plots of the model labeled with GRID or elements ID's are also available. General purpose programs for displaying and editing NASTRAN data are included in the system. Utilization of the NASTRAN interactive graphics system has made possible the multiple finite element analysis of complex helicopter fuselage structures within design schedules.

Sainsbury-Carter, J. B.↗

Interactive Exploration of High-Dimensional Phase Diagrams

High-dimensional thermodynamic phase stability databases are becoming increasingly common due to the convergence of three recent trends: (i) the widespread interest in so-called “high-entropy” alloys, (ii) the availability of high-throughput computational assessments of phase stability in broad composition spaces and (iii) the ongoing development of ever-increasingly broad, multicomponent, multiphase CALPHAD databases. Although automated computational tools can readily process such high-dimensional data, scientists are often unable to visualize the relevant phase relations, an ability that is crucial to gaining an intuitive understanding of the stability constraints governing materials design. The present work addresses this need by providing algorithms that enable the interactive exploration of phase equilibria in high-dimensional spaces. These algorithms concentrate the complex nonlinear nonsmooth optimization needed into a preprocessing step that generates a large number of high-dimensional yet elementary graphical primitives. Furthermore, these primitives can then be cross-sectioned to yield 3-dimensional views in a computationally efficient manner that enables an interactive exploration of high-dimensional spaces. All of these operations are highly parallelizable, thus facilitating scaling of this method to large data sets.

36 MATERIALS SCIENCE↗

A computational model-based validation of Guyton's analysis of cardiac output and venous return curves

Guyton developed a popular approach for understanding the factors responsible for cardiac output (CO) regulation in which 1) the heart-lung unit and systemic circulation are independently characterized via CO and venous return (VR) curves, and 2) average CO and right atrial pressure (RAP) of the intact circulation are predicted by graphically intersecting the curves. However, this approach is virtually impossible to verify experimentally. We theoretically evaluated the approach with respect to a nonlinear, computational model of the pulsatile heart and circulation. We developed two sets of open circulation models to generate CO and VR curves, differing by the manner in which average RAP was varied. One set applied constant RAPs, while the other set applied pulsatile RAPs. Accurate prediction of intact, average CO and RAP was achieved only by intersecting the CO and VR curves generated with pulsatile RAPs because of the pulsatility and nonlinearity (e.g., systemic venous collapse) of the intact model. The CO and VR curves generated with pulsatile RAPs were also practically independent. This theoretical study therefore supports the validity of Guyton's graphical analysis.

NASA Discipline Cardiopulmonary↗

Double-buffered, heterogeneous CPU + GPU integral digestion algorithm for single-excitation calculations involving a large number of excited states

The most widely used quantum-chemical models for excited states are single-excitation theories, a category that includes configuration interaction with single substitutions, time-dependent density functional theory, and also a recently developed ab initio exciton model. When a large number of excited states are desired, these calculations incur a significant bottleneck in the “digestion” step in which two-electron integrals are contracted with density or density-like matrices. We present an implementation that moves this step onto graphical processing units (GPUs), and introduce a double-buffer scheme that minimizes latency by computing integrals on the central processing units (CPUs) concurrently with their digestion on the GPUs. An automatic code generation scheme simplifies the implementation of high-performance GPU kernels. For the exciton model, which requires separate excited-state calculations on each electronically coupled chromophore, the heterogeneous implementation described here results in speedups of 2–6× versus a CPU-only implementation. For traditional time-dependent density functional theory calculations, we obtain speedups of up to 5× when a large number of excited states is computed.

97 MATHEMATICS AND COMPUTING↗

Large Colloids in Cholesteric Liquid Crystals

We describe a coarse-grained Landau-de Gennes model of liquid crystals (LCs) including hydrodynamics based on the Beris–Edwards equations. The model is employed to study the impact of large colloids on the long range LC defect structure in the cholesteric LC blue phases. ‘Large’ here means that the particle size is comparable to the cholesteric pitch, the length scale on which the LC order undergoes a helical twist. We investigate the case of a single particle, with either normal or degenerate planar anchoring, placed initially in an equilibrium blue phase LC. It is found that in some cases, well defined steady disclination structure emerges at the particle surface, while in other cases no clear steady state is reached in the simulations, and disclination reorganisation appears to proliferate through the bulk LC. These systems are of potential interest in the context of using LCs to template self-assembly of colloid structure, e.g., for opto-electronic devices. Computationally, we demonstrate a parallel approach using mixed message-passing and threaded model on graphical processing units allows effective and efficient progress for this problem.

Physics↗

Synthesis, crystal structure, electrical properties, and sodium transport pathways of the new arsenate Na{sub 4}Co{sub 7}(AsO{sub 4}){sub 6}

A new sodium cobalt (II) arsenate Na{sub 4}Co{sub 7}(AsO{sub 4}){sub 6} has been synthesized by a solid-state reaction and its crystal structure determined from single crystal X-ray diffraction data. It crystallizes in the monoclinic system, space group C2/m, with a=10.7098(9) Å, b=14.7837(9) Å, c=6.6845(7) Å, and β=105.545(9)°. The structure is described as a three-dimensional framework built up of corner-edge sharing CoO{sub 6}, CoO{sub 4} and AsO{sub 4} polyhedra, with interconnecting channels along [100] in which the Na{sup +} cations are located. The densest ceramics with relative density of 94% was obtained by ball milling and optimization of sintering temperature, and its microstructure characterized by scanning electron microscopy. The electrical properties of the ceramics were studied over a temperature interval from 280 °C to 560 °C using the complex impedance spectroscopy over the range of 13 MHz–5 Hz. The ionic bulk conductivity value of the sample at 360 °C is 2.51 10{sup −5} S cm{sup −1} and the measured activation energy is Ea=1 eV. The sodium migration pathways in the crystal structure were investigated computationally using the bond valence site energy (BVSE) model and classical molecular dynamics (MD) simulations. - Graphical abstract: Correlation between crystal structure, microstructure and ionic conductivity . Display Omitted - Highlights: • A new arsenate Na{sub 4}Co{sub 7}(AsO{sub 4}){sub 6} was prepared by solid state reaction. • Its crystal structure was determined by powder X-ray diffraction. • Na{sup +} ionic conductivity was probed by complex impedance spectroscopy. • Na{sup +} conduction pathways were modeled by bond-valence method and molecular dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SU-E-T-107: Development of a GPU-Based Dose Delivery System for Adaptive Pencil Beam Scanning

Purpose: A description of a GPU-based dose delivery system (G-DDS) to integrate a fast forward planning implementing in real-time the prescribed sequence of pencil beams. The system, which is under development, is designed to evaluate the dose distribution deviations due to range variations and interplay effects affecting mobile tumors treatments. Methods: The Dose Delivery System (DDS) in use at the Italian Centro Nazionale di Adroterapia Oncologica (CNAO), is the starting point for the presented system. A fast and partial forward planning (FP) tool has been developed to evaluate in few seconds the delivered dose distributions using the DDS data (on-line measurements of spot properties, i.e. number of particles and positions). The computation is performed during the intervals between synchrotron spills and, made available at the end of each spill. In the interval between two spills, the G-DDS will evaluate the delivered dose distributions taking into account the real-time target positions measured by a tracking system. The sequence of prescribed pencil beams for the following spill will be adapted taking into account the variations with respect to the original plan due to the target motion. In order to speed up the computation required to modify pencil beams distribution (up to 400 times has been reached), the Graphics Processing Units (GPUs) and advanced Field Programmable Gate Arrays (FPGAs) are used. Results: An existing offline forward planning is going to be optimized for the CUDA architecture: the gain in time will be presented. The preliminary performances of the developed GPU-based FP algorithms will be shown. Conclusion: A prototype of a GPU-based dose delivery system is under development and will be presented. The system workflow will be illustrated together with the approach adopted to integrate the three main systems, i.e. CNAO dose delivery system, fast forward planning, and tumor tracking system.

60 APPLIED LIFE SCIENCES↗