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At least 613 records · Page 34

Integrated End-to-end Performance Prediction and Diagnosis for Extreme Scientific Workflows (IPPD) (Final Report)

This report details the accomplishments from the ASCR funded project “Integrated End-to-end Performance Prediction and Diagnosis for Extreme Scientific Workflows” under the award numbers FWP-66406 and DE-SC0012630, with a focus on the UC San Diego (Award No. DE-SC0012630) part of the accomplishments. We refer to the project as IPPD. The main activities of IPPD were centered on the development and integration of provenance information to capture empirically workflow information and identify the sources of bottlenecks as well as variability, and modeling and simulation to provide insights and predictively explore multiple scenarios for development of advanced techniques for optimization of resources and workflow execution. After a Phase I of the project, a Phase II effort focused on three major aspects: a) observe how data is generated, distributed, and used; b) analyze how data is (repeatedly) consumed with a focus both on repeated patterns and anomalies; and c) explore how to optimize data motion. The project leveraged and extended our existing tools with new research and demonstrated our work on the Belle II workflow suite as well as on workflows from NSLS-II.

97 MATHEMATICS AND COMPUTING↗

Computationally Guided and Experimentally Validated Design of Custom Chelators for Critical Mineral Recovery

Selective, high throughput separation of target critical metals from complex environments such as fly ash leachates and mining process streams presents a significant challenge for economical production. Custom chelators and sorbents are an attractive technology for selective metal extraction, however it can be difficult to predict their performance, and significant experimental efforts are often required to develop chelating technologies. Here, we present a computational strategy focused on modelling chelator-metal binding interactions and benchmark these results versus experimental data. A computational pipeline combining forcefield, semiempirical, and meta-GGA methods with a thermodynamic framework optimized for error cancellation has been developed to predict binding energies of chelator complexes towards critical mineral recovery applications. This approach, originally validated on [2.2.2] cryptates binding mono- and divalent cations, demonstrated robust predictive capabilities with an R2 of 0.850 against experimental aqueous binding energies. The workflow includes metadynamics for exploring high-dimensional potential energy surfaces and a cluster-continuum model for accurate yet computationally efficient solvation modeling. Error cancellation between solvation energies of free and chelator-coordinated ions enables faster convergence, even with finite cluster sizes. Initial studies on the cryptates revealed consistent metal-ligand coordination patterns, with systematic variations influenced by ion size and charge, highlighting key structural features linked to binding selectivity. Further studies of a proprietary chelator have resulted in identification of previously unreported selectivity towards economically significant metals, which in-house experiments have confirmed, demonstrating the feasibility of this approach. By applying this methodology to new chelators targeting critical minerals such as lithium, cobalt, nickel and other strategic metals, we aim to accelerate the discovery of next-generation chelators for efficient recovery, recycling, and separation processes. This computational framework serves as the backbone of a high-throughput design pipeline tailored for sustainable resource utilization and may be applied to a wide range of systems to meet experimental needs.

computational materials↗

Genome Extraction from Shotgun Metagenome Sequence Data

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).

Chivian, Dylan↗

Moab Desert Crust - Sample 4E

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).

Chivian, Dylan↗

Implementation of Combinatorial Optimization Techniques for Automated Fiber Placement Through Thickness Defect Stack-Up Minimization

The Computer Aided Process Planning (CAPP) module was developed to facilitate and accelerate the process planning workflow for Automated Fiber Placement (AFP). CAPP assists process planners in identifying optimal starting point locations and layup strategies for each ply of a laminate. Ply optimization operates on measurement and scoring of geometry-based defects such as gaps, overlaps, angle deviation, and steering. This paper expands on the established framework for analyzing defect stack-up through thickness of a laminate. Four different combinatorial optimization algorithms are implemented and evaluated: (1) genetic algorithm, (2) differential evolution, (3) particle swarm, and (4) greedy search. The algorithms identify the optimal combination of ply-level layup strategies, by scoring potential laminates on defect stacking, using two different objective functions. A final optimization approach is also presented which trades some performance for a large gain in efficiency. These approaches are compared to a randomized combination using a complex tool surface in a virtual case study. The result is a streamlined methodology for comparing different laminate-level manufacturing strategies and minimizing the through thickness defect stack up.

CAPP↗

Privacy by Design in Distributed Edge Systems: Innovating Secure Workflows for Smart Cities

The proliferation of distributed edge systems, such as those in smart cities, healthcare, and industrial IoT, offers unprecedented opportunities for data processing closer to its source, thereby reducing latency and enhancing efficiency. However, these systems also present significant privacy challenges due to the handling of sensitive data from multiple sources. This article explores the critical need for designing privacy-preserving workflows in distributed edge systems to ensure data security while maximizing the potential of edge computing. By examining the challenges, technological advancements, and potential of privacy-by-design approaches, we highlight the importance of integrating advanced privacy-preserving techniques like federated learning, differential privacy, homomorphic encryption, secure multi-party computation, and zero-knowledge proofs. These innovations are crucial for enhancing data security, regulatory compliance, and public trust in smart city applications, ultimately leading to safer and more efficient urban environments.

Kotevska, Olivera↗

Accelerating discoveries at DIII-D with the Integrated Research Infrastructure

DIII-D research is being accelerated by leveraging high performance computing (HPC) and data resources available through the National Energy Research Scientific Computing Center (NERSC) Superfacility initiative. As part of this initiative, a high-resolution, fully automated, whole discharge kinetic equilibrium reconstruction workflow was developed that runs at the NERSC for most DIII-D shots in under 20 min. This has eliminated a long-standing research barrier and opened the door to more sophisticated analyses, including plasma transport and stability. These capabilities would benefit from being automated and executed within the larger Department of Energy Advanced Scientific Computing Research program’s Integrated Research Infrastructure (IRI) framework. The goal of IRI is to empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation. For transport, we are looking at producing flux matched profiles and also using particle tracing to predict fast ion heat deposition from neutral beam injection before a shot takes place. Our starting point for evaluating plasma stability focuses on the pedestal limits that must be navigated to achieve better confinement. This information is meant to help operators run more effective experiments, so it needs to be available rapidly inside the DIII-D control room. So far this has been achieved by ensuring the data is available with existing tools, but as more novel results are produced new visualization tools must be developed. In addition, all of the high-quality data we have generated has been collected into databases that can unlock even deeper insights. This has already been leveraged for model and code validation studies as well as for developing AI/ML surrogates. The workflows developed for this project are intended to serve as prototypes that can be replicated on other experiments and can be run to provide timely and essential information for ITER, as well as next stage fusion power plants.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Hypersonic Simulations with US3D using Unstructured Grids from Fidelity Pointwise

For hypersonic simulations, unstructured flow solvers typically have problems predicting surface heat fluxes when strong shocks are present. This article outlines a workflow that applies best practices for structured and unstructured grids. In addition, unstructured grid generation can significantly reduce the time required to create quality grids for complex geometries. Several examples are computed using DPLR, a structured grid flow solver, and US3D flow, an unstructured flow solver. Results from the two codes are compared and they show excellent agreement. The unstructured grid workflow offers a viable and attractive alternative for hypersonic simulations.

C. Tang↗

Integrating Models with Real-time Field Data for Extreme Events: From Field Sensors to Models and Back with AI in the Loop

Focal Area(s): This whitepaper is responsive to focal area (1) Data acquisition and assimilation enabled by machine learning, AI, and advanced methods including experimental/network design/optimization, unsupervised learning (including deep learning), and hardware-related efforts involving AI (e.g., edge computing). We discuss Artificial Intelligence and Machine Learning (AI/ML) enabled integration of real-time data into the extreme event modeling workflow to improve the predictive capabilities of these models, and deliver real-time feedback to remote sensors, including software and data engineering challenges.

54 ENVIRONMENTAL SCIENCES↗

Candidate ferroelectrics via ab initio high-throughput screening of polar materials

Ferroelectrics are a class of polar and switchable functional materials with diverse applications, from microelectronics to energy conversion. Computational searches for new ferroelectric materials have been constrained by accurate prediction of the polarization and switchability with electric field, properties that, in principle, require a comparison with a nonpolar phase whose atomic-scale unit cell is continuously deformable from the polar ground state. For most polar materials, such a higher-symmetry nonpolar phase does not exist or is unknown. Here, we introduce a general high-throughput workflow that screens polar materials as potential ferroelectrics. We demonstrate our workflow on 1978 polar structures in the Materials Project database, for which we automatically generate a nonpolar reference structure using pseudosymmetries, and then compute the polarization difference and energy barrier between polar and nonpolar phases, comparing the predicted values to known ferroelectrics. Focusing on a subset of 182 potential ferroelectrics, we implement a systematic ranking strategy that prioritizes candidates with large polarization and small polar-nonpolar energy differences. To assess stability and synthesizability, we combine information including the computed formation energy above the convex hull, the Inorganic Crystal Structure Database id number, a previously reported machine learning-based synthesizability score, and ab initio phonon band structures. To distinguish between previously reported ferroelectrics, materials known for alternative applications, and lesser-known materials, we combine this ranking with a survey of the existing literature on these candidates through Google Scholar and Scopus databases, revealing ~130 promising materials uninvestigated as ferroelectric. Our workflow and large-scale high-throughput screening lays the groundwork for the discovery of novel ferroelectrics, revealing numerous candidates materials for future experimental and theoretical endeavors.

36 MATERIALS SCIENCE↗

Enhanced Simulation Techniques in Predicting Sonic Boom Loudness Using CFD

This paper outlines advancements in predicting sonic boom loudness within the Launch, Ascent, and Vehicle Aerodynamics (LAVA) computational framework. Traditionally, a two step process consisting of a steady state computational fluid dynamics problem for near-field analysis and a far-field propagation solver for calculation of loudness metrics has been used. Improvements to this process made in this work include utilizing a high-order space marching method for mid-field computations, developing a novel output-based mesh adaptation method targeting error in near-field pressure sig-natures, and developing a robust scripting system using curvilinear grids to increase robustness and simplify the process of running large databases of simulation cases. These advancements are detailed and applied to the simulation of the X-59, presenting comparative cost and timing analyses between the prior two step workflow and the current three step procedure. We achieve increased accuracy and robustness for loudness predictions with at least a50%computational cost reduction.

CST↗

Future Trends in Nuclear Physics Computing

In nuclear physics (NP) today the study of quarks, gluons and their strong interactions extends across a broad research program at a varied range of collaborative scales, from a few collaborators up to large experiments at scales comparable to those typical of high energy physics (HEP). Overall, the software and computing efforts vary accordingly, from pragmatic do-it-yourself approaches among a few, to substantial organized software and computing activities within large experiments. With new experiments starting up and on the horizon [1], and rapidly increasing data volumes [2, 3] and processing demands even at small experiments, the NP community has in recent years been thinking about the next generation of data processing and analysis workflows that will maximize the science output. One context for this discussion has been a series of workshops, “Future Trends in Nuclear Physics Computing” [4]. The most recent in this series took place in Fall 2020, organized by the authors together with colleagues. The workshop focused on identifying the unique aspects of software and computing in NP, and discussing how the NP community could strengthen common efforts and chart a path forward for the next decade, sure to be an exciting one with rich ongoing scientific programs at Brookhaven National Laboratory (BNL), Jefferson Lab (JLab), and other NP facilities, and culminating in datataking at the Electron-Ion Collider (EIC) [5,6,7] in the early 2030s. Without claiming to present a collective view from the workshop and discussions since—fortunately this is not expected of us in this opinion editorial—we offer here our reflections on the topic, informed by the workshop and the summary we authored with our colleagues [8], as well as discussions and developments in the eventful time since.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Full Detector Simulation with Unprecedented Background Occupancy at a Muon Collider

In recent years, a Muon collider has attracted a lot of interest in the high-energy physics community, thanks to its ability of achieving clean interaction signatures at multi-TeV collision energies in the most cost-effective way. Estimation of the physics potential of such an experiment must take into account the impact of beam-induced background on the detector performance, which has to be carefully evaluated using full detector simulation. Tracing of all the background particles entering the detector region in a single bunch crossing is out of reach for any realistic computing facility due to the unprecedented number of such particles. To make it feasible a number of optimisations have been applied to the detector simulation workflow. This contribution presents an overview of the main characteristics of the beam-induced background at a Muon collider, the detector technologies considered for the experiment and how they are taken into account to strongly reduce the number of irrelevant computations performed during the detector simulation. Special attention is dedicated to the optimisation of track reconstruction with the conformal tracking algorithm in this high-occupancy environment, which is the most computationally demanding part of event reconstruction.

97 MATHEMATICS AND COMPUTING↗

Pitfalls in parameters: practical process development in chemical vapor processing of SiC

Vapor processing of high-value materials, such as silicon carbide (SiC), is of interest for many industries, including aerospace and energy production. Chemical vapor infiltration (CVI) of additively manufactured components is an especially attractive manufacturing process currently in development. Here, a novel development workflow is demonstrated with the H 2 –CH 3 SiCl 3 gas system for SiC to accelerate the process optimization of CVI SiC. A combination of calculated thermodynamics and high-throughput experimental chemical vapor deposition (CVD) coatings substantially reduced the experiments required with slow CVI processes. The computational results accurately predicted changes in the thermodynamic conditions tested, while CVD coatings – characterized by Raman spectroscopy – addressed changes in kinetic parameters. This workflow is also applicable to other vapor-processing systems, such as pyrolytic carbon, ZrC, or Si 3 N 4 .

Lamm, Benjamin W. [Oak Ridge National Laboratory (↗

S4PST: Sustainability for Programming Systems and Tools: May Workshop Report

The US Department of Energy (DOE) Exascale Computing Project (ECP) has fostered and strengthened the use of modern software engineering practices for developing applications and libraries, and this effort has resulted in the coordinated and interoperable E4S1 and xSDK2 ecosystems. Although this approach is cost-effective, it relies on robust programming systems and tools (PST) as the underlying foundation for our HPC software. At present, our primary PST stack consists of traditional high-performance computing (HPC) languages, namely Fortran, C, C++, and the popular Python language for data analysis and AI workflows. These languages support various programming frameworks and run-time abstractions that enable parallelism and concurrency across multiple node architectures and thousands of nodes through a variety of interconnect systems. However, to accommodate users’ diverse needs, certain aspects of the HPC ecosystem are delegated to vendor-specific or third-party implementations that extend beyond a particular scientific domain. This broader scope results in a multitude of specifications and variations, which leads to a complex orchestration of many-ecosystems. Unfortunately, this complexity in the ecosystem imposes additional overhead costs on consumers during the latter stages of the development cycle. In addition to the software ecosystem challenge, the upcoming conclusion of the ECP by December 2023 has raised significant concerns within the HPC programming systems community, from both the economic and social perspectives. The ECP has implemented a management structure for software development and funding decisions across all ECP participants by following a conventional hierarchical and centralized approach. However, this structure has prompted certain considerations within the community, particularly in anticipation of the Software Sustainability initiative by the DOE’s Advanced Scientific Computing Research Program (ASCR). For the success of this new initiative, it is of utmost importance to secure consistent funding and foster close engagement with researchers and core developers of existing programming-system products. This collaboration is vital to maintaining the critical capabilities of the current software during the transition phase while proactively adapting to future technology and workforce trends. The community recognizes the significance of adapting to emerging trends and is aware of the inherent fragility of the HPC software ecosystem, particularly in relation to programming systems that cater to all users. The ability to adapt and evolve is essential to staying relevant and effectively addressing these technical, economic, and social challenges. The S4PST team, which represents one of the six ASCR Software Sustainability seedling projects, is dedicated to tackling these challenges through community-based approaches that go beyond the scope of the DOE. This involves collaboration between national laboratories with academia, non-DOE institutions, hardware and system vendors, and international partners. By fostering these partnerships, we aim to create a robust and sustainable HPC software ecosystem that can effectively meet the needs of the community. This new community effort, driven by the eight DOE labs, will take on the responsibility of guiding funding decisions for programming-systems development and maintenance with transparency and consistency across all decisions. Additionally, the team will offer common technical services to the programming systems community, irrespective of their funding situations, and facilitate community-wide incubation to proactively nurture the software ecosystem. By actively engaging with stakeholders and employing a collaborative approach, we can collectively shape the future of programming systems and ensure a robust and thriving HPC software landscape. On May 11–12, 2023, the S4PST team conducted its inaugural kick-off workshop at the Innovative Computing Laboratory (ICL) in the University of Tennessee, Knoxville, hosted by Hartwig Anzt. The workshop encompassed various sessions dedicated to presentations and discussions, with the aim of comprehending the team members’ perspectives on the vision of software sustainability. Additionally, the workshop aimed to identify the technical, economic, and social requirements for sustaining the programming-systems community in the field of HPC. This report provides a summary of the S4PST effort by highlighting five major thrust areas discussed during the workshop: (i) community, (ii) technical support, (iii) training and diversity, (iv) verification, validation and correctness, and (v) emerging technologies. It also encompasses an overview of the presentations and discussions held throughout the event, our views and potential synergies with other seedling efforts, along with the outcomes and key takeaways from our initial discussions.

97 MATHEMATICS AND COMPUTING↗

FORCE-DISPATCHES Integration - Initial Demonstration

Integrated energy systems (IES) combine, in mutually beneficial ways, power from variable renewable energy sources and nuclear power plants (NPP) to improve economic viability under uncertain market and weather conditions. The open-source Framework for Optimization of Resources and Economics (FORCE) tool suite, developed at Idaho National Laboratory (INL), has enabled comprehensive modeling and simulation of IES. The capabilities within FORCE include grid portfolio optimization through the Holistic Energy Resource Optimization Network (HERON) and the transient process model analysis library HYBRID, among others. Continuous efforts and investments from the IES programs have been made to expand and improve the versatility of the FORCE toolset in fiscal year 2022. Code-coupling and cross-tool communication have been important methods for improving this versatility. This report focuses on an additional workflow in the HERON tool for capacity and dispatch stochastic optimization through integration with the external tool Design Integration and Synthesis Platform to Advance Tightly Coupled Hybrid Energy Systems (DISPATCHES). DISPATCHES was primarily developed by the National Energy Technology Laboratory, in collaboration with other national laboratories, which included INL, universities, and industry partners. It is coupled to a library of algebraic models for specific plant components, and to a framework for stochastic optimization different from that provided in the current Risk Analysis Virtual Environment (RAVEN)-running-RAVEN algorithm in HERON. HERON currently conducts stochastic optimization via an outer-inner loop: it optimizes over variable capacity on the outer loop, and at each step within the capacity parameter space, conducts an inner optimization over scenarios (of market signals, demand, and/or weather patterns) and hourly dispatch throughout a user-specified number of years. On the other hand, DISPATCHES conducts stochastic optimization via an “all-at-once” strategy in which capacity variables are optimized at the same level as dispatch variables, as all scenarios are considered at once. The latter method works especially well for projects of limited size and project length, as the necessary computational power and memory increases with the number of variables and scenarios. The new capability to use the DISPATCHES workflow in HERON enhances standalone simulations by leveraging FORCE tools—namely, the economic metrics from the Tool for Economic Analysis (TEAL) and reduced-order model (ROM) sampling from RAVEN. The initial demonstration of the DISPATCHES workflow simulates an existing nuclear-case flowsheet within the DISPATCHES repository—this models a NPP with a secondary revenue stream for hydrogen production. Electrical output from the plant is converted to hydrogen via a proton-exchange membrane (PEM) electrolyzer, hydrogen tanks are used for storage, and an additional turbine is added for hydrogen combustion. Continued work regarding this FORCE-DISPATCHES integration will include automatic generation of DISPATCHES models from HERON inputs, offering analysts the option of using either the RAVEN-runsRAVEN or DISPATCHES workflow to solve technoeconomic optimization problems.

24 POWER TRANSMISSION AND DISTRIBUTION↗