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DOE OSTI2018

Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained

Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields. However, software itself has not traditionally received focused attention from research communities; rather, software has evolved organically and inconsistently, with its development largely as by-products of other initiatives. Moreover, challenges in scientific software are expanding due to disruptive changes in computer hardware, increasing scale and complexity of data, and demands for more complex simulations involving multiphysics, multiscale modeling and outer-loop analysis. In recent years, community members have established a range of grass-roots organizations and projects to address these growing technical and social challenges in software productivity, quality, reproducibility, and sustainability. This article provides an overview of such groups and discusses opportunities to leverage their synergistic activities while nurturing work toward emerging software ecosystems.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1994

Virtual Environments in Scientific Visualization

Virtual environment technology is a new way of approaching the interface between computers and humans. Emphasizing display and user control that conforms to the user's natural ways of perceiving and thinking about space, virtual environment technologies enhance the ability to perceive and interact with computer generated graphic information. This enhancement potentially has a major effect on the field of scientific visualization. Current examples of this technology include the Virtual Windtunnel being developed at NASA Ames Research Center. Other major institutions such as the National Center for Supercomputing Applications and SRI International are also exploring this technology. This talk will be describe several implementations of virtual environments for use in scientific visualization. Examples include the visualization of unsteady fluid flows (the virtual windtunnel), the visualization of geodesics in curved spacetime, surface manipulation, and examples developed at various laboratories.

Bryson, Steve↗

NASA NTRS1994

Virtual Environments in Scientific Visualization

Bryson, Steve↗

DOE OSTI2021

10 Years Later: Cloud Computing is Closing the Performance Gap

Can cloud computing infrastructures provide HPC-competitive performance for scientific applications broadly? Despite prolific related literature, this question remains open. Answers are crucial for designing future systems and democratizing high-performance computing. We present a multi-level approach to investigate the performance gap between HPC and cloud computing, isolating different variables that contribute to this gap. Our experiments are divided into (i) hardware and system microbenchmarks and (ii) user application proxies. The results show that today’s high-end cloud computing can deliver HPC-competitive performance not only for computationally intensive applications, but also for memory- and communication-intensive applications – at least at modest scales – thanks to the high-speed memory systems and interconnects and dedicated batch scheduling now available on some cloud platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

A terminology for in situ visualization and analysis systems

The term "in situ processing" has evolved over the last decade to mean both a specific strategy for visualizing and analyzing data and an umbrella term for a processing paradigm. The resulting confusion makes it difficult for visualization and analysis scientists to communicate with each other and with their stakeholders. To address this problem, a group of over 50 experts convened with the goal of standardizing terminology. This paper summarizes their findings and proposes a new terminology for describing in situ systems. An important finding from this group was that in situ systems are best described via multiple, distinct axes: integration type, proximity, access, division of execution, operation controls, and output type. This paper discusses these axes, evaluates existing systems within the axes, and explores how currently used terms relate to the axes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Accelerating Science: A Computing Research Agenda

The emergence of "big data" offers unprecedented opportunities for not only accelerating scientific advances but also enabling new modes of discovery. Scientific progress in many disciplines is increasingly enabled by our ability to examine natural phenomena through the computational lens, i.e., using algorithmic or information processing abstractions of the underlying processes; and our ability to acquire, share, integrate and analyze disparate types of data. However, there is a huge gap between our ability to acquire, store, and process data and our ability to make effective use of the data to advance discovery. Despite successful automation of routine aspects of data management and analytics, most elements of the scientific process currently require considerable human expertise and effort. Accelerating science to keep pace with the rate of data acquisition and data processing calls for the development of algorithmic or information processing abstractions, coupled with formal methods and tools for modeling and simulation of natural processes as well as major innovations in cognitive tools for scientists, i.e., computational tools that leverage and extend the reach of human intellect, and partner with humans on a broad range of tasks in scientific discovery (e.g., identifying, prioritizing formulating questions, designing, prioritizing and executing experiments designed to answer a chosen question, drawing inferences and evaluating the results, and formulating new questions, in a closed-loop fashion). This calls for concerted research agenda aimed at: Development, analysis, integration, sharing, and simulation of algorithmic or information processing abstractions of natural processes, coupled with formal methods and tools for their analyses and simulation; Innovations in cognitive tools that augment and extend human intellect and partner with humans in all aspects of science.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Materials Data Science Ontology(MDS-Onto): Unifying Domain Knowledge in Materials and Applied Data Science

Ontologies have gained popularity in the scientific community as a way to standardize terminologies in organizations’ data. Although certain cohorts have created frameworks with rules and guidelines on creating ontologies, there exist significant variations in how Materials Science ontologies are currently developed. We seek to provide guidance in the form of a unified automated framework for developing interoperable and modular ontologies for Materials Data Science that simplifies the ontology terms matching by establishing a semantic bridge up to the Basic Formal Ontology(BFO). This framework provides key recommendations on how ontologies should be positioned within the semantic web, what knowledge representation language is recommended, and where ontologies should be published online to boost their findability and interoperability. Two fundamental components of the MDS-Onto framework are the bilingual package called FAIRmaterials for ontology creation and FAIRLinked, for FAIR data creation. To showcase the practical capabilities of FAIRmaterials, we present two exemplar domain ontologies of MDS-Onto: Synchrotron X-Ray Diffraction and Photovoltaics.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

Scalable Data-Intensive Geocomputation: A Design for Real-Time Continental Flood Inundation Mapping

The convergence of data-intensive and extreme-scale computing enables an integrated software and data ecosystem for scientific discovery. Developments in this realm will fuel transformative research in data-driven interdisciplinary domains. Geocomputation provides computing paradigms in Geographic Information Systems (GIS) for interactive computing of geographic data, processes, models, and maps. Because GIS is data-driven, the computational scalability of a geocomputation workflow is directly related to the scale of the GIS data layers, their resolution and extent, as well as the velocity of the geo-located data streams to be processed. Unique in high user interactivity and low end-to-end latency requirements, geocomputation applications will dramatically benefit from the convergence of high-end data analytics (HDA) and high-performance computing (HPC). The application level challenge, however, is to identify and eliminate computational bottlenecks that arise along a geocomputation workflow. Indeed, poor scalability at any of the workflow components is detrimental to the entire end-to-end pipeline. Here, we study a large geocomputation use case in flood inundation mapping that handles multiple national-scale geospatial datasets and targets low end-to-end latency. We discuss benefits and challenges for harnessing both HDA and HPC for data-intensive geospatial data processing and intensive numerical modeling of geographic processes. We propose an HDA+HPC geocomputation architecture design that couples HDA (e.g., Spark)-based spatial data handling and HPC-based parallel data modeling. Key techniques for coupling HDA and HPC to bridge the two different software stacks are reviewed and discussed.

Liu, Yan↗

DOE OSTI2021

Evaluating adaptive and predictive power management strategies for optimizing visualization performance on supercomputers

Power is becoming an increasingly scarce resource on the next generation of supercomputers, and should be used wisely to improve overall performance. One strategy for improving power usage is hardware overprovisioning, i.e., systems with more nodes than can be run at full power simultaneously without exceeding the system-wide power limit. With this study, we compare two strategies for allocating power throughout an overprovisioned system – adaptation and prediction – in the context of visualization workloads. While adaptation has been suitable for workloads with more regular execution behaviors, it may not be as suitable on visualization workloads, since they can have variable execution behaviors. This study considers a total of 104 experiments, which vary the rendering workload, power budget, allocation strategy, and node concurrency, including tests processing data sets up to 1 billion cells and using up to 18,432 cores across 512 nodes. Overall, we find that prediction is a superior strategy for this use case, improving performance up to 27% compared to an adaptive strategy.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Mechanisms of Semiconducting 2H to Metallic 1T Phase Transition in Two-dimensional MoS 2 Nanosheets

In the present work, phase transition mechanisms from semiconducting 2H phase to metallic 1T phase in MoS 2 nanosheets were studied using density functional theory (DFT) method. Various 2H→1T phase transition mechanisms that consist of nucleation and propagation steps, which simulated by collective rotational and rotational/translational movements, single atom translational movement, as well as the gliding movement of one row for sulfur (S) atoms, on both the basal plane and Mo- and S-edges with different S coverages were investigated. On the perfect basal plane, the 1T phase nucleation is unlikely due to the extremely high barrier of 2.25 eV/atom. Whereas the presence of defective S vacancies on the basal plane dramatically facilitate the 1T phase nucleation and propagation around the defective sites by the collective rotational movement of three S atoms. On the 2H phase basal plane with two S vacancies, the kinetic barriers for the 1T phase nucleation are as low as of 0.66~0.77 eV/atom. Like the promoting effect of S vacancies on the phase transition over the basal plane, DFT results suggest that the S coverage on the Mo- and S-edges will affect the 1T phase nucleation and propagation. The 1T phase nucleation starting with the translational movement of single S atom on the bare Mo-edge and the gliding movement of an entire row of S atoms on the S-edge with 50%S coverage are kinetically favorable. While the 1T phase formation at the Mo-edge with 50%S coverage and the S-edge with 100% S coverage are unlikely. The present work not only confirms the important role of S vacancies/coverages in the 2H-1T phase transition, but also provides new insight into how and where the 2H-1T phase transition occurs at the atomic level, which also sheds light on the general phase transition mechanism for two-dimensional transition metal dichalcogenide materials. The work was financially supported by the National Natural Science Foundation of China (No. 21476012, 21571012, and 91534201). Q. Jin appreciates the joint Ph.D. scholarship support from the China Scholarship Council. The computing time was granted by a scientific theme user proposal in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington. D. Mei is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences.

Molybdenum disulfide, phase transition, sulfur vac↗

DOE OSTI2015

Electronic and chemical state of aluminum from the single- (K) and double-electron excitation (KL II&III , KL I ) x-ray absorption near-edge spectra of α-alumina, sodium aluminate, aqueous Al³⁺•(H₂O)₆, and aqueous Al(OH)₄⁻

We probe, at high energy resolution, the double electron excitation (KL II&II ) x-ray absorption region that lies approximately 115 eV above the main Al K-edge (1566 eV) of α-alumina and sodium aluminate. The two solid standards, α-alumina (octahedral) and sodium aluminate (tetrahedral) are compared to aqueous species that have the same Al coordination symmetries, Al³⁺•6H₂O (octahedral) and Al(OH)₄⁻ (tetrahedral). For the octahedral species, the edge height of the KL II&III -edge is approximately 10% of the main K-edge however the edge height is much weaker (3% of K-edge height) for Al species with tetrahedral symmetry. For the α-alumina and aqueous Al³⁺•6H₂O the KL II&III spectra contain white line features and extended absorption fine structure (EXAFS) that mimics the K-edge spectra. The KL II&III -edge feature interferes with an important region of the extended-XAFS region of the spectra for the K-edge of the crystalline and aqueous standards. The K-edge spectra and K-edge positions are predicted using time-dependent density functional theory (TDDFT). The TDDFT calculations for the K-edge XANES spectra reproduce the observed transitions in the experimental spectra of the four Al species. The KL II&III and KL I onsets and their corresponding chemical shifts for the four standards are estimated using the delta self-consistent field (ΔSCF) method. Research by JLF, NG, EJB, AV, TDS was supported by U.S. Department of Energy’s (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. NG thanks Amity Andersen for help with the α-Al₂O₃ and tetrahedral sodium aluminate (NaAlO₂) clusters. All the calculations were performed using the Molecular Science Computing Capability at EMSL, a national scientific user facility sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle under Contract # AC05-76RL01830.

aluminum↗

DOE OSTI2022

The United States COVID-19 Forecast Hub dataset

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Latent space mapping: Revolutionizing predictive models for divertor plasma detachment control

The inherent complexity of boundary plasma, characterized by multi-scale and multi-physics challenges, has historically restricted high-fidelity simulations to scientific research due to their intensive computational demands. Consequently, routine applications such as discharge control and scenario development have relied on faster but less accurate empirical methods. This work introduces DivControlNN, a novel machine-learning-based surrogate model designed to address these limitations by enabling quasi-real-time predictions (i.e., ~ 0.2 ms) of boundary and divertor plasma behavior. Trained on over 70,000 2D UEDGE simulations from KSTAR tokamak equilibria, DivControlNN employs latent space mapping to efficiently represent complex divertor plasma states, achieving a computational speed-up of over 10 8 compared to traditional simulations while maintaining a relative error below 20% for key plasma property predictions. During the 2024 KSTAR experimental campaign, a prototype detachment control system powered by DivControlNN successfully demonstrated detachment control on its first attempt, even for a new tungsten divertor configuration and without any fine-tuning. These results highlight the transformative potential of DivControlNN in overcoming diagnostic challenges in future fusion reactors by providing fast, robust, and reliable predictions for advanced integrated control systems.

Artificial neural networks↗

DOE OSTI2020

Veridical data science

Building and expanding on principles of statistics, machine learning, and scientific inquiry, we propose the predictability, computability, and stability (PCS) framework for veridical data science. Our framework, composed of both a workflow and documentation, aims to provide responsible, reliable, reproducible, and transparent results across the data science life cycle. The PCS workflow uses predictability as a reality check and considers the importance of computation in data collection/storage and algorithm design. It augments predictability and computability with an overarching stability principle. Stability expands on statistical uncertainty considerations to assess how human judgment calls impact data results through data and model/algorithm perturbations. As part of the PCS workflow, we develop PCS inference procedures, namely PCS perturbation intervals and PCS hypothesis testing, to investigate the stability of data results relative to problem formulation, data cleaning, modeling decisions, and interpretations. We illustrate PCS inference through neuroscience and genomics projects of our own and others. Moreover, we demonstrate its favorable performance over existing methods in terms of receiver operating characteristic (ROC) curves in high-dimensional, sparse linear model simulations, including a wide range of misspecified models. Finally, we propose PCS documentation based on R Markdown or Jupyter Notebook, with publicly available, reproducible codes and narratives to back up human choices made throughout an analysis. The PCS workflow and documentation are demonstrated in a genomics case study available on Zenodo.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Optimization of tomographic reconstruction workflows on geographically distributed resources

New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modeling of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can provide up to 3.13× speedup (on experimented resources). Furthermore, the error rates of the models range between 2.1 and 23.3% (considering workflow execution times), where the accuracy of the model estimations increases with higher computational demands in reconstruction tasks.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2017

Towards a data-centric research and development roadmap for large-scale science user facilities

© 2017 IEEE. The U.S. Department of Energy (DOE) Office of Science (SC) operates approximately four dozen large-scale science user facilities (SUFs), each of which generates a tremendous amount of scientific data from experiments, observations and computations. To better understand the data needs and challenges, DOE has run many workshops in recent years to identify and articulate data-centric challenges and opportunities at varying resolution, from facility to community scale. Building on those workshop reports, as well as others from elsewhere in the community, this article goes beyond the findings-recommendations typical of workshop reports to consider how one might structure a broad, technology- and data-centric, coordinated research effort that would realize progress towards solutions that address the well documented challenges and opportunities. We focus on identifying practical issues of strategic relevance, along with offering a view about the focal points for a coordinated research and development effort that would target meeting data-centric needs of a broad set of science users and SUFs. These focal points would, by their nature, engage a spectrum of researchers from computer science, computational and experimental sciences, and data science in a coordinated fashion.

Bethel, EW↗

DOE OSTI2017

Comprehensive Measurement and Analysis of the User-Perceived I/O Performance in a Production Leadership-Class Storage System

With the increase of the scale and intensity of the parallel I/O workloads generated by those scientific applications running on high performance computing facilities, understanding the I/O dynamics, especially the root cause of the I/O performance variability and degradation in HPC environment, have become extremely critical to the HPC community. In this paper, we run extensive I/O measuring tests on a production leadership-class storage system to capture the performance variabilities of large-scale parallel I/O. Analyzing these results and its statistic correlation revealed some valuable insights into the characteristics of the storage system and the root cause of I/O performance variability. Further, we leverage these findings and propose an I/O middleware design refactoring which can improve the performance of the parallel I/O by optimizing the data striping and placement. Our preliminary evaluation results demonstrate the proposed approach can reduce the average per-process write latency by at least 80% and the maximum per-process write latency by at least 20%.

Wan, Lipeng↗

DOE OSTI2016

Trigger Detection for Adaptive Scientific Workflows Using Percentile Sampling

The increasing complexity of both scientific simulations and high-performance computing system architectures are driving the need for adaptive workflows, in which the composition and execution of computational and data manipulation steps dynamically depend on the evolutionary state of the simulation itself. Consider, for example, the frequency of data storage. Critical phases of the simulation should be captured with high frequency and with high fidelity for postanalysis; however, we cannot afford to retain the same frequency for the full simulation due to the high cost of data movement. We can instead look for triggers, indicators that the simulation will be entering a critical phase, and adapt the workflow accordingly. In this paper, we present a methodology for detecting triggers and demonstrate its use in the context of direct numerical simulations of turbulent combustion using S3D. We show that chemical explosive mode analysis (CEMA) can be used to devise a noise-tolerant indicator for rapid increase in heat release. However, exhaustive computation of CEMA values dominates the total simulation, and thus is prohibitively expensive. To overcome this computational bottleneck, we propose a quantile sampling approach. Our sampling-based algorithm comes with provable error/confidence bounds, as a function of the number of samples. Most importantly, the number of samples is independent of the problem size, and thus our proposed sampling algorithm offers perfect scalability. Our experiments on homogeneous charge compression ignition and reactivity controlled compression ignition simulations show that the proposed method can detect rapid increases in heat release, and its computational overhead is negligible. Our results will be used to make dynamic workflow decisions regarding data storage and mesh resolution in future combustion simulations.

97 MATHEMATICS AND COMPUTING↗