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At least 865 records · Page 48

pyRMG: A framework for high-throughput, large-cell DFT calculations on supercomputers

Exascale computing delivers the raw power to simulate ever larger and more chemically realistic systems, but realizing this potential requires codes that can efficiently use thousands of processors. Our real-space multigrid (RMG) density functional theory (DFT) code’s grid-decomposition approach scales nearly linearly with the number of graphics processing units (GPUs), even for simulations exceeding thousands of atoms. This scalability makes RMG a compelling tool for high-throughput DFT studies of materials that would otherwise be bottlenecked in other codes (for example, by global fast Fourier transforms in plane-wave DFT). However, the limited workflow infrastructure for RMG has thus far constrained its adoption to a small user community. In this work, we present pyRMG, a Python package designed to streamline the setup and execution of RMG DFT calculations. Built on the pymatgen and ASE (Atomic Simulation Environment) computational materials science Python packages, pyRMG automates input generation and convergence checking, and it integrates with modern job schedulers (e.g., Flux) on leadership-class platforms such as Frontier and Perlmutter. Here, we demonstrate pyRMG for a high-throughput study of strain effects in 2D 2L-Bi 2 Se 3 /2L-NbSe 2 heterostructures, which offers chemical insights into this system and shows that RMG-based workflows can converge with limited user intervention.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

HPC Annual Report 2017

Sandia National Laboratories has a long history of significant contributions to the high performance community and industry. Our innovative computer architectures allowed the United States to become the first to break the teraFLOP barrier—propelling us to the international spotlight. Our advanced simulation and modeling capabilities have been integral in high consequence US operations such as Operation Burnt Frost. Strong partnerships with industry leaders, such as Cray, Inc. and Goodyear, have enabled them to leverage our high performance computing (HPC) capabilities to gain a tremendous competitive edge in the marketplace. As part of our continuing commitment to providing modern computing infrastructure and systems in support of Sandia missions, we made a major investment in expanding Building 725 to serve as the new home of HPC systems at Sandia. Work is expected to be completed in 2018 and will result in a modern facility of approximately 15,000 square feet of computer center space. The facility will be ready to house the newest National Nuclear Security Administration/Advanced Simulation and Computing (NNSA/ASC) Prototype platform being acquired by Sandia, with delivery in late 2019 or early 2020. This new system will enable continuing advances by Sandia science and engineering staff in the areas of operating system R&D, operation cost effectiveness (power and innovative cooling technologies), user environment and application code performance.

97 MATHEMATICS AND COMPUTING↗

Fundamental Mixing and Combustion Experiments for Propelled Hypersonic Flight

Two experiments have been conducted to acquire data for the validation of computational fluid dynamics (CFD) codes used in the design of supersonic combustors. The first experiment is a study of a supersonic coaxial jet into stagnant air in which the center jet is of a light gas, the coflow jet is of air, and the mixing layer between them is compressible. The jet flow field is characterized using schlieren imaging, surveys with Pitot, total temperature and gas sampling probes, and RELIEF velocimetry. VULCAN, a structured grid CFD code, is used to solve for the nozzle and jet flow. The second experiment is a study of a supersonic combustor consisting of a diverging duct with single downstream-angled wall injector. Entrance Mach number is 2 and enthalpy is nominally that of Mach 7 flight. Coherent anti-Stokes Raman spectroscopy (CARS) has been used to obtain nitrogen temperature in planes of the flow, and surface pressures and temperatures have also been acquired. Modern-design-of-experiment techniques have been used to maximize the quality of the data set.

Cutler, A. D.↗

Modification and validation of an analytical source model for external beam radiotherapy Monte Carlo dose calculations

Purpose: A dose calculation tool, which combines the accuracy of the dose planning method (DPM) Monte Carlo code and the versatility of a practical analytical multisource model, which was previously reported has been improved and validated for the Varian 6 and 10 MV linear accelerators (linacs). The calculation tool can be used to calculate doses in advanced clinical application studies. One shortcoming of current clinical trials that report dose from patient plans is the lack of a standardized dose calculation methodology. Because commercial treatment planning systems (TPSs) have their own dose calculation algorithms and the clinical trial participant who uses these systems is responsible for commissioning the beam model, variation exists in the reported calculated dose distributions. Today’s modern linac is manufactured to tight specifications so that variability within a linac model is quite low. The expectation is that a single dose calculation tool for a specific linac model can be used to accurately recalculate dose from patient plans that have been submitted to the clinical trial community from any institution. The calculation tool would provide for a more meaningful outcome analysis. Methods: The analytical source model was described by a primary point source, a secondary extra-focal source, and a contaminant electron source. Off-axis energy softening and fluence effects were also included. The additions of hyperbolic functions have been incorporated into the model to correct for the changes in output and in electron contamination with field size. A multileaf collimator (MLC) model is included to facilitate phantom and patient dose calculations. An offset to the MLC leaf positions was used to correct for the rudimentary assumed primary point source. Results: Dose calculations of the depth dose and profiles for field sizes 4 × 4 to 40 × 40 cm agree with measurement within 2% of the maximum dose or 2 mm distance to agreement (DTA) for 95% of the data points tested. The model was capable of predicting the depth of the maximum dose within 1 mm. Anthropomorphic phantom benchmark testing of modulated and patterned MLCs treatment plans showed agreement to measurement within 3% in target regions using thermoluminescent dosimeters (TLD). Using radiochromic film normalized to TLD, a gamma criteria of 3% of maximum dose and 2 mm DTA was applied with a pass rate of least 85% in the high dose, high gradient, and low dose regions. Finally, recalculations of patient plans using DPM showed good agreement relative to a commercial TPS when comparing dose volume histograms and 2D dose distributions. Conclusions: A unique analytical source model coupled to the dose planning method Monte Carlo dose calculation code has been modified and validated using basic beam data and anthropomorphic phantom measurement. While this tool can be applied in general use for a particular linac model, specifically it was developed to provide a singular methodology to independently assess treatment plan dose distributions from those clinical institutions participating in National Cancer Institute trials.

60 APPLIED LIFE SCIENCES↗

Compiler-Driven FPGA Virtualization with SYNERGY

FPGAs are increasingly common in modern applications, and cloud providers now support on-demand FPGA acceleration in datacenters. Applications in datacenters run on virtual infrastructure, where consolidation, multi-tenancy, and workload migration enable economies of scale that are fundamental to the provider's business. However, a general strategy for virtualizing FPGAs has yet to emerge. While manufacturers struggle with hardware-based approaches, we propose a compiler/runtime-based solution called Synergy. We show a compiler transformation for Verilog programs that produces code able to yield control to software atsub-clock-tickgranularity according to the semantics of the original program. Synergy uses this property to efficiently support core virtualization primitives: suspend and resume, program migration, and spatial/temporal multiplexing, on hardware which is availabletoday.We use Synergy to virtualize FPGA workloads across a cluster of Intel SoCs and Xilinx FPGAs on Amazon F1. The workloads require no modification, run within 3--4x of unvirtualized performance, and incur a modest increase in FPGA fabric usage.

Computer Science↗

Trilinos: Enabling Scientific Computing across Diverse Hardware Architectures at Scale

Trilinos is a community-developed, open-source software framework that facilitates building large-scale, complex, multiscale, multiphysics simulation code bases for scientific and engineering problems. Since the Trilinos framework has undergone substantial changes to support new applications and new hardware architectures, this document is an update to “An Overview of the Trilinos project” by Heroux et al. (ACM Transactions on Mathematical Software, 31(3):397–423, 2005). It describes the design of Trilinos, introduces its new organization in product areas, and highlights established and new features available in Trilinos. Particular focus is put on the modernized software stack based on the Kokkos ecosystem to deliver performance portability across heterogeneous hardware architectures. This article also outlines the organization of the Trilinos community and the contribution model to help onboard interested users and contributors.

Heterogeneous Hardware Architectures↗

Developing the User Experience for a Next Generation Nuclear Fuel Cycle Simulator (NGFCS)

This project made substantial progress on its original aim for providing a modern user experience for nuclear fuel cycle analysis while also creating a robust and functional next- generation fuel cycle simulator. The Cyclus kernel experienced a dramatic clari cation of its interfaces and data model, becoming a full- edged agent-based framework, with strong support for third party developers of novel archetypes. The most important contribution of this project to the the development of Cyclus was the introduction of tools to facilitate archetype development. These include automated code generation of routine archetype components, metadata annotations to provide re ection and rich description of each data member's purpose, and mechanisms for input validation and output of complex data. A comprehensive social science investigation of decision makers' interests in nuclear fuel cycles, and speci cally their interests in nuclear fuel cycle simulators (NFCSs) as tools for understanding nuclear fuel cycle options, was conducted. This included document review and analysis, stakeholder interviews, and a survey of decision makers. This information was used to study the role of visualization formats and features in communicating information about nuclear fuel cycles. A exible and user-friendly tool was developed for building Cyclus analysis models, featuring a drag-and-drop interface and automatic input form generation for novel archetypes. Cycic allows users to design fuel cycles from arbitrary collections of facilities for the rst time, with mechanisms that contribute to consistency within that fuel cycle. Interacting with some of the metadata capabilities introduced in the above-mentioned tools to support archetype development, Cycic also automates the generation of user input forms for novel archetypes with little to no special knowledge required by the archetype developers. Translation of the fundamental metrics of Cyclus into more interesting quantities is accomplished in the Cymetric python package. This package is speci cally designed to support the introduction of new metrics by building upon existing metrics. This concept allows for multiple dependencies and encourages building complex metrics out of incremental transformations to those prior metrics. New archetype developers can contribute their own archetype-speci c metric using the same capability. A simple demonstration of this capability focused on generating time-dependent cash ows for reactor deployment that could then be analyzed in di erent ways. Cyclist, a dedicated application for exploration of Cyclus results, was developed. It's primary capabilities at this stage are best-suited to experienced fuel cycle analysts, but it provides a basic platform for simpler visualizations for other audiences. An important part of its interface is the ability to uidly examine di erent slices of what is fundamentally a ve-dimensional sparse data set. A drag-and-drop interface simpli es the process of selecting which data is displayed in the plot as well as which dimensions are being used for

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

WHONDRS-GUI: a web application for global survey of surface water metabolites

Background The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. Results The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811 , which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server ( https://xmlin.shinyapps.io/whondrs/ ).

59 BASIC BIOLOGICAL SCIENCES↗

Applying Ada to Beech Starship avionics

As Ada solidified in its development, it became evident that it offered advantages for avionics systems because of it support for modern software engineering principles and real time applications. An Ada programming support environment was developed for two major avionics subsystems in the Beech Starship. The two subsystems include electronic flight instrument displays and the flight management computer system. Both of these systems use multiple Intel 80186 microprocessors. The flight management computer provides flight planning, navigation displays, primary flight display of checklists and other pilot advisory information. Together these systems represent nearly 80,000 lines of Ada source code and to date approximately 30 man years of effort. The Beech Starship avionics systems are in flight testing.

Funk, David W.↗

NASA low-speed centrifugal compressor for 3-D viscous code assessment and fundamental flow physics research

A low speed centrifugal compressor facility recently built by the NASA Lewis Research Center is described. The purpose of this facility is to obtain detailed flow field measurements for computational fluid dynamic code assessment and flow physics modeling in support of Army and NASA efforts to advance small gas turbine engine technology. The facility is heavily instrumented with pressure and temperature probes, both in the stationary and rotating frames of reference, and has provisions for flow visualization and laser velocimetry. The facility will accommodate rotational speeds to 2400 rpm and is rated at pressures to 1.25 atm. The initial compressor stage being tested is geometrically and dynamically representative of modern high-performance centrifugal compressor stages with the exception of Mach number levels. Preliminary experimental investigations of inlet and exit flow uniformly and measurement repeatability are presented. These results demonstrate the high quality of the data which may be expected from this facility. The significance of synergism between computational fluid dynamic analysis and experimentation throughout the development of the low speed centrifugal compressor facility is demonstrated.

Hathaway, M. D.↗

NASA low-speed centrifugal compressor for 3-D viscous code assessment and fundamental flow physics research

A low speed centrifugal compressor facility recently built by the NASA Lewis Research Center is described. The purpose of this facility is to obtain detailed flow field measurements for computational fluid dynamic code assessment and flow physics modeling in support of Army and NASA efforts to advance small gas turbine engine technology. The facility is heavily instrumented with pressure and temperature probes, both in the stationary and rotating frames of reference, and has provisions for flow visualization and laser velocimetry. The facility will accommodate rotational speeds to 2400 rpm and is rated at pressures to 1.25 atm. The initial compressor stage being tested is geometrically and dynamically representative of modern high-performance centrifugal compressor stages with the exception of Mach number levels. Preliminary experimental investigations of inlet and exit flow uniformly and measurement repeatability are presented. These results demonstrate the high quality of the data which may be expected from this facility. The significance of synergism between computational fluid dynamic analysis and experimentation throughout the development of the low speed centrifugal compressor facility is demonstrated.

Hathaway, M. D.↗

Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism

Significance Reaction centers (RCs) are critical to photosynthetic energy conversion. RCs in all characterized photosynthetic organisms contain two symmetrically arranged branches of chromophores and enable light-induced electron transfer with high yield. We fine-tune the properties of a key bacterial RC symmetry-breaking tyrosine via its replacement with noncanonical tyrosine analogs and determine kinetic outcomes. Results are interpreted through energetic characterization made possible by resonance Stark spectroscopy. Analysis indicates this tyrosine modulates the mechanism of the initial light-induced electron transfer, affording an alternative functional pathway that maintains the RC’s robust electron transfer. Modern molecular biology, ultrafast spectroscopy, crystallography, and energetic characterization enable the mechanistic model we describe. Our results deepen understanding of RC function and may have implications for other photocatalysts and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

A Plug-and-Play Duct System Evaluation

This report describes an air distribution system composed of a series of uniformly-sized ducts that terminate in rooms throughout the home and return to a central manifold, similar in fashion to a “home-run” cross-linked polyethylene plumbing system. With a well-designed manifold, each duct receives an equal static pressure potential for airflow from the air handling unit, and the number of needed ducts for each room are simply attached to fittings located on the manifold; in this sense, the system is plug-and-play (PnP). As indicated, all ducts in the PnP system are identical in size and small enough to fit in the ceiling and wall cavities of a house (i.e., less than 3.5-in. outer diameter). These ducts are also more appropriately sized for the lower airflow requirements of modern, energy-efficient homes; therefore, the velocity of the air moving through the duct is between that of conventional duct systems (approximately 700 ft/min) and high-velocity systems (more than 1,500 ft/min) on the market today. The PnP duct system uses semi-rigid plastic pipes, which have a smooth inner wall and are straightforward to install correctly, resulting in a system that has minimal air leakage. However, plastic ducts are currently not accepted by code for use in residential buildings; therefore, the project team considered other duct materials for the system that are currently accepted by code, such as small-diameter, wirehelix, flexible ductwork.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Plug-and-Play Duct System Evaluation

This report describes an air distribution system composed of a series of uniformly-sized ducts that terminate in rooms throughout the home and return to a central manifold, similar in fashion to a “home-run” cross-linked polyethylene plumbing system. With a well-designed manifold, each duct receives an equal static pressure potential for airflow from the air handling unit, and the number of needed ducts for each room are simply attached to fittings located on the manifold; in this sense, the system is plug-and-play (PnP). As indicated, all ducts in the PnP system are identical in size and small enough to fit in the ceiling and wall cavities of a house (i.e., less than 3.5-in. outer diameter). These ducts are also more appropriately sized for the lower airflow requirements of modern, energy-efficient homes; therefore, the velocity of the air moving through the duct is between that of conventional duct systems (approximately 700 ft/min) and high-velocity systems (more than 1,500 ft/min) on the market today. The PnP duct system uses semi-rigid plastic pipes, which have a smooth inner wall and are straightforward to install correctly, resulting in a system that has minimal air leakage. However, plastic ducts are currently not accepted by code for use in residential buildings; therefore, the project team considered other duct materials for the system that are currently accepted by code, such as small-diameter, wirehelix, flexible ductwork.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Statistical mechanics of neocortical interactions - Dynamics of synaptic modification

A recent study has demonstrated that several scales of neocortical interactions can be consistently analyzed with the use of methods of modern nonlinear nonequilibrium statistical mechanics. The formation, stability, and interaction of spatial-temporal patterns of columnar firings are explicitly calculated, to test hypothesized mechanisms relating to information processing. In this context, most probable patterns of columnar firings are associated with chemical and electrical synaptic modifications. It is stressed that synaptic modifications and shifts in most-probable firing patterns are highly nonlinear and interactive sets of phenomena. A detailed scenario of information processing is calculated of columnar coding of external stimuli, short-term storage via hysteresis, and long-term storage via synaptic modification.

Ingber, L.↗

UPDATES FROM THE INVOLUTE WORKING GROUP

The HFIR, RHF, and FRM II reactors represent a particular class of Research and Test Reactors that provide some of the most intense and continuous neutron fluxes for science, industry, and medical applications. These high-performance reactors have achieved compact cores by operating with Highly Enriched Uranium fuel (HEU, 235U/U ≥ 20 wt. %) and utilizing fuel plates curved as an involute. Due to the proliferation risks, the international community aims to reduce or eliminate, when possible, the use of HEU fuel in civilian facilities by converting them to a Low-Enriched Uranium fuel (LEU, 235U/U < 20 wt. %). Conversion of these reactors without significantly compromising their performance or safety is a challenging endeavor that can tremendously benefit from advanced computational tools and thus, eliminate unnecessary conservatism to ensure sufficient thermal margins. Therefore, models are being developed using modern Computational Fluid Dynamics (CFD) and Computational Structural Mechanics (CSM) software to evaluate the steady-state safety margins of various LEU designs instead of being reliant on the more traditional, conservative methods. To gain the confidence and acceptance of high-fidelity modeling by the nuclear regulators, Argonne National Laboratory (ANL) and the involute reactors have formed an informal scientific group, the Involute Working Group (IWG). The IWG facilitates inter-organizational collaboration on experimental benchmarking, code-to-code comparisons, and Verification and Validation (V&V). This paper describes some of the recent IWG efforts in validating software against the existing experimental data, as well as code-to-code comparisons of different software used by the IWG members.

Bergeron, Aurelien↗

RAPIDS: Reconciling Availability, Accuracy, and Performance in Managing Geo-Distributed Scientific Data

In modern science, big data plays an increasingly important role. Many scientific applications, such as running simulations on supercomputers or conducting experiments on advanced instruments, produce huge amount of data at unprecedented speed. Analyzing and understanding such big data is the key for scientists to make scientific breakthroughs. However, data might become unavailable for scientists to access when outages or maintenance of the storage system occur, which severely hinders scientific discovery. To improve the data availability, data duplication and erasure coding (EC) are often used. But as the scientific data gets larger, using these two methods can cause considerable storage and network overhead.In this paper, we propose RAPIDS, a hybrid approach that combines the multigrid-based error-bounded lossy compression with erasure coding, to significantly reduce the storage and network overhead required for maintaining high data availability. Our experiments show that RAPIDS reduces the storage overhead by up to 7.5x and network overhead by up to 3x to achieve the same level of availability compared to the regular EC method. We improve RAPIDS by building two models to optimize the fault tolerance configurations and data gathering strategy. We demonstrate that RAPIDS significantly improves performance when running on many CPU cores in parallel or on GPUs.

Wan, Lipeng↗

YAHFC: A Code Framework to Model Nuclear Reactions and Estimate Correlated Uncertainties

Reaction modeling is a key ingredient in designing experiments and interpreting their results, and is an essential component in the process of evaluating nuclear data and assembling nuclear data libraries used in nuclear technology applications. Typically, experimental data are available only for a handful of reaction channels and theory models are used to fill in the gaps. In addition, theory is often called upon as the arbitrator between discrepant data. Most importantly, theory and modeling are required for an accurate determination of uncertainties in the evaluated data and the correlations between the multiple channels. A fast, accurate, and flexible modeling capability has been developed at LLNL with the code system YAHFC (Yet Another Hauser-Feshbach Code). YAHFC is a Monte Carlo, Hauser-Feshbach code framework, making full use of dynamic memory allocation, derived types, and parallel computing. YAHFC can generate events to simulate experiments and is guiding experiments designed to measure inelastic neutron scattering from actinide targets. YAHFC is also being used to analyze decays from surrogate experiments, thereby enabling the inference of reaction cross sections inaccessible by direct measurement. Finally, by modeling nuclear reactions with constraints from experimental data, YAHFC can deliver complete nuclear data libraries, with evaluated uncertainties, using the modernized Generalized Nuclear Data Structure (GNDS).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗