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DOE OSTI2021

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.15 User's Manual

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Two-level overlapping additive Schwarz preconditioner for training scientific machine learning applications

In this work we introduce a novel two-level overlapping additive Schwarz preconditioner for accelerating the training of scientific machine learning applications. The design of the proposed preconditioner is motivated by the nonlinear two-level overlapping additive Schwarz preconditioner. The neural network parameters are decomposed into groups (subdomains) with overlapping regions. In addition, the network’s feed-forward structure is indirectly imposed through a novel subdomain-wise synchronization strategy and a coarse-level training step. Through a series of numerical experiments, which consider physicsinformed neural networks and operator learning approaches, we demonstrate that the proposed two-level preconditioner significantly speeds up the convergence of the standard (LBFGS) optimizer while also yielding more accurate machine learning models. Moreover, the devised preconditioner is designed to take advantage of model-parallel computations, which can further reduce the training time.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Systematic Crosstalk Mitigation for Superconducting Qubits via Frequency-Aware Compilation

One of the key challenges in current Noisy Intermediate-Scale Quantum (NISQ) computers is to control a quantum system with high-fidelity quantum gates. There are many reasons a quantum gate can go wrong - for superconducting transmon qubits in particular, one major source of gate error is the unwanted crosstalk between neighboring qubits due to a phenomenon called frequency crowding. We motivate a systematic approach for understanding and mitigating the crosstalk noise when executing near-term quantum programs on superconducting NISQ computers. Here, we present a general software solution to alleviate frequency crowding by systematically tuning qubit frequencies according to input programs, trading parallelism for higher gate fidelity when necessary. The net result is that our work dramatically improves the crosstalk resilience of tunable-qubit, fixed-coupler hardware, matching or surpassing other more complex architectural designs such as tunable-coupler systems. On NISQ benchmarks, we improve worst-case program success rate by 13.3x on average, compared to existing traditional serialization strategies.

Computer architecture↗

DOE OSTI2013

Combinatorial geometry domain decomposition strategies for Monte Carlo simulations

Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

The Kokkos OpenMPTarget Backend: Implementation and Lessons Learned

As the supercomputing landscape diversifies, solutions such as Kokkos to write vendor agnostic applications and libraries have risen in popularity. Kokkos provides a programming model designed for performance portability, which allows developers to write a single source implementation that can run efficiently on various architectures. At its heart, Kokkos maps parallel algorithms to architecture and vendor specific backends written in lower level programming models such as CUDA and HIP. Another approach to writing vendor agnostic parallel code is using OpenMP’s directives based approach, which lets developers annotate code to express parallelism. It is implemented at the compiler level and is supported by all major high performance computing vendors, as well as the primary Open Source toolchains GNU and LLVM. Since its inception, Kokkos has used OpenMP to parallelize on CPU architectures. In this paper, we explore leveraging OpenMP for a GPU backend and discuss the challenges we encountered when mapping the Kokkos APIs and semantics to OpenMP target constructs. As an exemplar workload we chose a simple conjugate gradient solver for sparse matrices. We find that performance on NVIDIA and AMD GPUs varies widely based on details of the implementation strategy and the chosen compiler. Furthermore, the performance of the OpenMP implementations decreases with increasing complexity of the investigated algorithms.

Gayatri, Rahulkumar↗

DOE OSTI2019

Lynx x-ray microcalorimeter

Lynx is an x-ray telescope, one of four large satellite mission concepts currently being studied by NASA to be a flagship mission. One of Lynx’s three instruments is an imaging spectrometer called the Lynx x-ray microcalorimeter (LXM), an x-ray microcalorimeter behind an x-ray optic with an angular resolution of 0.5 arc sec and ~2 m 2 of area at 1 keV. The LXM will provide unparalleled diagnostics of distant extended structures and, in particular, will allow the detailed study of the role of cosmic feedback in the evolution of the Universe. We discuss the baseline design of LXM and some parallel approaches for some of the key technologies. The baseline sensor technology uses transition-edge sensors, but we also consider an alternative approach using metallic magnetic calorimeters. We discuss the requirements for the instrument, the pixel layout, and the baseline readout design, which uses microwave superconducting quantum interference devices and high-electron mobility transistor amplifiers and the cryogenic cooling requirements and strategy for meeting these requirements. For each of these technologies, we discuss the current technology readiness level and our strategy for advancing them to be ready for flight. We also describe the current system design, including the block diagram, and our estimate for the mass, power, and data rate of the instrument.

47 OTHER INSTRUMENTATION↗

DOE OSTI2015

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

We report that polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum , and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Tandem Microwire Solar Cells for Flexible High Efficiency Low Cost Photovoltaics

This project has developed components of a waferless, flexible, low-cost tandem multijunction III-V/Si microwire array solar cell technology which combines the efficiency of wafered III-V photovoltaic technologies with the process designed to meet the Sunshot object. The project focused on design of lattice-matched GaAsP/SiGe two junction cell design and lattice-mismatched GaInP/Si tandem cell design. Combined electromagnetic simulation/device physics models using realistic microwire tandem structures were developed that predict >22% conversion efficiency for known material parameters, such as tunnel junction structure, window layer structure, absorber lifetimes and optical absorption and these model indicate a clear path to 30% efficiency for high quality III-V heterostructures. SiGe microwire arrays were synthesized via Cu-catalyzed vapor-liquid-solid (VLS) growth with inexpensive chlorosilane and chlorogermance precursors in an atmospheric pressure reactor. SiGe alloy composition in microwires was found to be limited to a maximum of 12% Ge incorporation during chlorogermane growth, due to the melting of the alloy near the solidus composition. Lattice mismatched InGaP double heterostructures were grown by selective epitaxy with a thermal oxide mask on Si microwire substrates using metallorganic vapor phase epitaxy. Transmission electron microscopy (TEM) analysis confirms the growth of individual step graded layers and a high density of defects near the wire/III-V interface. Selective epitaxy was initiated with a low temperature nucleation scheme under “atomic layer epitaxy” or “flow mediated epitaxy” conditions whereby the Ga and P containing precursors are alternately introduced into the reactor to promote layer-bylayer growth. In parallel to our efforts on conformal GaInP heteroepitaxy on selectively masked Si microwires, we explored direct, axial growth of GaAs on Si wire arrays as another route to a tandem junction architecture. We proposed axial, lattice-mismatched growth of a GaAs segment that extrude out of a Si wire via a self-aligned SiO 2 hollow cylindrical mask. With this growth strategy, misfit dislocations that would normally form at the GaAs/Si interface during thin film epitaxy may bend over to and thus terminate at the sidewall of the SiO 2 tube. A reactive-ion etching technique was employed 1) to remove Si to form a hollow, self-aligned SiO 2 cylindrical tube as a growth template for GaAs epitaxy using a vertical, showerhead, low-pressure metal-organic chemical-vapor deposition reactor that was operated at 0.1 atm. Successful epitaxy of axial GaAs wires on non-polar, <111>-oriented Si wire substrates was found at temperatures of ~850C. This and the other III-V/Si heterojunction wire synthesis strategies described here are promising approaches to realize future III-V/Si tandem solar cell designs.

14 SOLAR ENERGY↗

DOE OSTI2025

Computational Modeling of Graphite Degradation due to Molten Salt Infiltration and Wear

Molten-salt reactors (MSRs) represent a promising next-generation reactor design, with graphite serving as a moderator and/or reflector in several designs. However, due to limited experimental data and operational experience, a technical understanding of the structural integrity of graphite in molten salt environments remains incomplete. This report presents a modeling-based evaluation of graphite degradation in MSR environments, focusing on the effects of salt infiltration in fuel salt-based designs and surface wear in pebble bed reactor designs. The objective of this study is to enhance understanding of the structural integrity challenges posed by these degradation mechanisms and to provide a framework for assessing graphite behavior in MSRs. The first part of the report investigates the phenomenon of molten salt infiltration into graphite. This infiltration occurs when molten salt permeates the interconnected pore structure of the graphite moderator, driven by factors such as pressure differentials and the physical properties of both the salt and graphite. The infiltration process is influenced by characteristics of the pore structure, viscosity of the molten salt, and the interfacial energies between the graphite, salt, and the atmosphere within the graphite pore. Utilizing a coupled multiphysics modeling approach with Grizzly software, the study evaluates the stress induced by internal heat sources due to infiltration, which can lead to structural concerns. This evaluation is crucial for understanding how infiltration affects the mechanical integrity of graphite components in MSRs. The study considers the Molten-Salt Reactor Experiment (MSRE) graphite stringer geometry due to the availability of relevant data. Through detailed finite element analysis, the study examines stress distributions at varying infiltration percentages, revealing that stress levels increase with higher amounts of infiltration. Rare-event simulations, using the parallel subset simulation (PSS) framework, further quantify the failure probabilities under input uncertainties, with a user-specified failure metric. The PSS framework also identifies critical input parameters that significantly affect the stress values, including infiltration amount, thermal conductivity, and power density. Additionally, considering realistic reactor scenarios, the analysis was performed to account for the combined effects of radiation and infiltration, and modeling strategies on how to analyze new reactor designs or new graphite grades are discussed. The second part of the report focuses on wear mechanisms in pebble bed-based MSRs. As graphite fuel pebbles interact with the graphite reflector block, wear can result in material loss and the formation of surface defects, which may act as stress concentrators. A similar multiphysics modeling framework is employed to assess the impact of wear on the structural integrity of graphite components. This study considers a generic fluoride-cooled high-temperature reactor (gFHR) design due to the availability of comprehensive data. Worst-case scenario dimensions of the reflector blocks were analyzed under thermal and radiation conditions. Subsequently, wear in the form of idealized pits and grooves is modeled on the inner surface of the graphite block, with the maximum stress from previous simulations. The simulations show that groove-type defects are more detrimental than pits, leading to higher stress concentrations. Considering worst-case simulation scenarios and experimental wear rates, it was determined that the formation of a surface defect critical enough to affect the stress may not be possible in a gFHR design. Overall, the findings of this research contribute to the development of robust modeling tools for predicting graphite behavior under various operational conditions in MSRs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2026

Viskores: Integrating Parallel Scientific Visualization Research into Applications

Viskores is a scientific visualization library that is the primary deployment of such algorithms to the parallel accelerated processors of modern DOE supercomputers. In this paper, we review the capabilities provided by Viskores and how these capabilities are leveraged by other software in the high-performance computing ecosystem. We discuss the Viskores data representation and pay particular attention to array management. Through this array management we describe how data is adapted between Viskores and other software along with strategies for converting dynamic, polymorphic objects to static representations better suited to GPU processing. We conclude with several examples of Viskores integrating with high-performance software that is used in production today.

Moreland, Ken [ORNL] (ORCID:0000000270513288)↗

DOE OSTI2021

Towards multiscale modeling of ocean surface turbulent mixing using coupled MPAS-Ocean v6.3 and PALM v5.0

A multiscale modeling approach for studying the ocean surface turbulent mixing is explored by coupling an ocean general circulation model (GCM) MPAS-Ocean with the Parallelized Large Eddy Simulation Model (PALM). The coupling approach is similar to the superparameterization approach that has been used to represent the effects of deep convection in atmospheric GCMs. However, the focus of this multiscale modeling approach is on the small-scale turbulent mixing and their interactions with the larger-scale processes in the ocean, so that a more flexible coupling strategy is used. To reduce the computational cost, a customized version of PALM is ported on the general-purpose graphics processing unit (GPU) with OpenACC, achieving 10–16 times overall speedup as compared to running on a single CPU. Even with the GPU-acceleration technique, a superparameterization-like approach to represent the ocean surface turbulent mixing in GCMs using embedded high fidelity and three-dimensional large eddy simulations (LESs) over the global ocean is still computationally intensive and infeasible for long simulations. However, running PALM regionally on selected MPAS-Ocean grid cells is shown to be a promising approach moving forward. The flexible coupling between MPAS-Ocean and PALM allows further exploration of the interactions between the ocean surface turbulent mixing and larger-scale processes, as well as future development and improvement of ocean surface turbulent mixing parameterizations for GCMs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Towards a Circular Economy for PET Bottles in the U.S. - 4P Model

The United States generates the most plastic waste of any country. Along with that GHG emissions from the global plastic economy are expected to increase to 15% of the global carbon budget by 2050. It is imperative that plastic recycling is made a reality to reduce both plastic pollution in the environment and GHG emissions. A portfolio of end-of-life strategies must be implemented to minimize environmental impacts and retain valuable plastic material, but it is challenging to compare options that generate products with different utility and lifetime. Plastic use reduction, reuse and recycling are thus increasingly important, but making informed policy and research decisions within this space can be challenging given the diverse range of available solutions. The novel analysis framework, Plastic Parallel Pathways Platform (4P) has been equipped with consequential life cycle assessment, techno-economic analysis, and a plastic circularity indicator to estimate the greenhouse gas (GHG) emissions, circularity, and cost of polyethylene terephthalate (PET) down-cycling to lower-quality resin, closed-loop recycling to food-grade PET bottles, up-cycling to fiber-reinforced plastic (FRP), and conversion to non-plastic products (electricity, oil) on a United States economy-wide basis. Integrating system dynamics into this robust plastics model that already incorporates techno-economics, circularity, and environmental impacts will enable identification of key bottlenecks between manufacturers, waste sorters, and reclaimers that currently prevent rapid decarbonization of the plastics economy. System dynamics (SD) explore the evolution of activities and technologies based on changed macro parameters such as plastic demand and supply, market shifts, and cross-sectoral interactions. This project particularly aims to explore the interplay between, waste collection, plastic waste sorting, recycling, and manufacturing, as well as the effect of plastic bale quality and plastic reuse initiatives on the surrounding process stages. This functionality will facilitate combinatory analysis in which a portfolio of end-of-life pathways are assessed simultaneously, with the exact makeup of that portfolio affected by parameters such as technology scales, resource constraints, and waste mitigation efforts. Integrating SD with the 4P framework enables analyzing the effect of increased revenue and reinvestment into improving process efficiencies, sorting and collection quantities. Through that, market effects of increased recycled resin availability can be studied for the plastics systems model for the US. The results will help identify technical or economic bottlenecks that currently limit efforts to decarbonize the U.S. plastics economy.

carbon↗

DOE OSTI2024

Towards a Circular Economy for PET Bottles in the U.S. - 4P Framework

circular economy↗

DOE OSTI2011

DAKOTA : a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis.

The DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. DAKOTA contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the DAKOTA toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the DAKOTA software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of DAKOTA-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of DAKOTA's iterative analysis capabilities.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2013

Tethys: Developing a Commons for Understanding Environmental Effects of Ocean Renewable Energy

A lack of consistent widespread information on potential environmental effects, monitoring outcomes, and mitigation strategies continues to hinder the development and deployment of marine energy systems around the world. To address this need, member nations of the Ocean Energy Systems (OES) formed Annex IV, a three-year collaborative effort (2010-2013) to increase knowledge sharing, research collaborations, and efficient regulatory decision-making associated with investigating and evaluating the potential impacts of wave and tidal energy. In parallel, the US Department of Energy began development of a publically-available, searchable online database of environmental information (called Tethys), housing scientific literature pertaining to the environmental effects of marine energy and offshore wind systems, as well as metadata on international ocean energy projects and research studies collected under Annex IV. In addition to providing broad access to information on environmental effects of marine energy and offshore wind developments, Tethys can act as a commons for bringing together researchers, device and project developers, regulators, and stakeholders, to explore shared interests and information needs for the emerging marine energy industry. This paper will demonstrate the development, existing functionality, and content of Tethys, as well as discuss the future of Annex IV including information updates, improvements, and additional outreach efforts over the next several years.

marine energy, offhore wind, environmental effects↗

DOE OSTI2020

Optimizing the hypre solver for manycore and GPU architectures

The solution of large-scale combustion problems with codes such as Uintah on modern computer architectures requires the use of multithreading and GPUs to achieve performance. Uintah uses a low-Mach number approximation that requires iteratively solving a large system of linear equations. The Hypre iterative solver has solved such systems in a scalable way for Uintah, but the use of OpenMP with Hypre leads to at least slowdown due to OpenMP overheads. The proposed solution uses the MPI Endpoints within Hypre, where each team of threads acts as a different MPI rank. This approach minimizes OpenMP synchronization overhead and performs as fast or (up to 1.44) faster than Hypre's MPI-only version, and allows the rest of Uintah to be optimized using OpenMP. The profiling of the GPU version of Hypre shows the bottleneck to be the launch overhead of thousands of micro-kernels. The GPU performance was improved by fusing these micro-kernels and was further optimized by using Cuda-aware MPI, resulting in an overall speedup of 1.16—1.44 compared to the baseline GPU implementation. The above optimization strategies were published in the International Conference on Computational Science 2020 [1]. This work extends the previously published research by carrying out the second phase of communication-centered optimizations in Hypre to improve its scalability on large-scale supercomputers. Additionally, this includes an efficient non-blocking inter-thread communication scheme, communication-reducing patch assignment, and expression of logical communication parallelism to a new version of the MPICH library that utilizes the underlying network parallelism [2]. The above optimizations avoid communication bottlenecks previously observed during strong scaling and improve performance by up to 2 on 256 nodes of Intel Knight's Landing processor.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Impacts of floating-point non-associativity on reproducibility for HPC and deep learning applications

Run to run variability in parallel programs caused by floating-point non-associativity has been known to significantly affect reproducibility in iterative algorithms, due to accumulating errors. Non-reproducibility can critically affect the efficiency and effectiveness of correctness testing for stochastic programs. Recently, the sensitivity of deep learning training and inference pipelines to floating-point non-associativity has been found to sometimes be extreme. It can prevent certification for commercial applications, accurate assessment of robustness and sensitivity, and bug detection. New approaches in scientific computing applications have coupled deep learning models with high-performance computing, leading to an aggravation of debugging and testing challenges. Here we perform an investigation of the statistical properties of floating-point non-associativity within modern parallel programming models, and analyze performance and productivity impacts of replacing atomic operations with deterministic alternatives on GPUs. We examine the recently-added deterministic options in PyTorch within the context of GPU deployment for deep learning, uncovering and quantifying the impacts of input parameters triggering run to run variability and reporting on the reliability and completeness of the documentation. Finally, we evaluate the strategy of exploiting automatic determinism that could be provided by deterministic hardware, using the Groq LPUTM accelerator for inference portions of the deep learning pipeline. We demonstrate the benefits that a hardware-based strategy can provide within reproducibility and correctness efforts.

Shanmugavelu, Sanjif↗

DOE OSTI2014

Energy-aware Thread and Data Management in Heterogeneous Multi-core, Multi-memory Systems

By 2004, microprocessor design focused on multicore scaling—increasing the number of cores per die in each generation—as the primary strategy for improving performance. These multicore processors typically equip multiple memory subsystems to improve data throughput. In addition, these systems employ heterogeneous processors such as GPUs and heterogeneous memories like non-volatile memory to improve performance, capacity, and energy efficiency. With the increasing volume of hardware resources and system complexity caused by heterogeneity, future systems will require intelligent ways to manage hardware resources. Early research to improve performance and energy efficiency on heterogeneous, multi-core, multi-memory systems focused on tuning a single primitive or at best a few primitives in the systems. The key limitation of past efforts is their lack of a holistic approach to resource management that balances the tradeoff between performance and energy consumption. In addition, the shift from simple, homogeneous systems to these heterogeneous, multicore, multi-memory systems requires in-depth understanding of efficient resource management for scalable execution, including new models that capture the interchange between performance and energy, smarter resource management strategies, and novel low-level performance/energy tuning primitives and runtime systems. Tuning an application to control available resources efficiently has become a daunting challenge; managing resources in automation is still a dark art since the tradeoffs among programming, energy, and performance remain insufficiently understood. In this dissertation, I have developed theories, models, and resource management techniques to enable energy-efficient execution of parallel applications through thread and data management in these heterogeneous multi-core, multi-memory systems. I study the effect of dynamic concurrent throttling on the performance and energy of multi-core, non-uniform memory access (NUMA) systems. I use critical path analysis to quantify memory contention in the NUMA memory system and determine thread mappings. In addition, I implement a runtime system that combines concurrent throttling and a novel thread mapping algorithm to manage thread resources and improve energy efficient execution in multi-core, NUMA systems.

97 MATHEMATICS AND COMPUTING↗