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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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10 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The fortedata R package: open-science datasets from a manipulative experiment testing forest resilience

The fortedata R package is an open data notebook from the Forest Resilience Threshold Experiment (FoRTE) – a modeling and manipulative field experiment that tests the effects of disturbance severity and disturbance type on carbon cycling dynamics in a temperate forest. Package data consist of measurements of carbon pools and fluxes and ancillary measurements to help analyze and interpret carbon cycling over time. Currently the package includes data and metadata from the first three FoRTE field seasons, serves as a central, updatable resource for the FoRTE project team, and is intended as a resource for external users over the course of the experiment and in perpetuity. Further, it supports all associated FoRTE publications, analyses, and modeling efforts. This increases efficiency, consistency, compatibility, and productivity while minimizing duplicated effort and error propagation that can arise as a function of a large, distributed and collaborative effort. More broadly, fortedata represents an innovative, collaborative way of approaching science that unites and expedites the delivery of complementary datasets to the broader scientific community, increasing transparency and reproducibility of taxpayer-funded science. The fortedata package is available via GitHub: https://github.com/FoRTExperiment/fortedata (last access: 19 February 2021), and detailed documentation on the access, used, and applications of fortedata are available at https://fortexperiment.github.io/fortedata/ (last access: 19 February 2021). The first public release, version 1.0.1 is also archived at https://doi.org/10.5281/zenodo.4399601 (Atkins et al., 2020b). All data products are also available outside of the package as .csv files: https://doi.org/10.6084/m9.figshare.13499148.v1 (Atkins et al., 2020c).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Advances in machine-learning-based sampling motivated by lattice quantum chromodynamics

Sampling from known probability distributions is a ubiquitous task in computational science, underlying calculations in domains from linguistics to biology and physics. Generative machine-learning (ML) models have emerged as a promising tool in this space, building on the success of this approach in applications such as image, text, and audio generation. Often, however, generative tasks in scientific domains have unique structures and features—such as complex symmetries and the requirement of exactness guarantees—that present both challenges and opportunities for ML. This Perspective outlines the advances in ML-based sampling motivated by lattice quantum field theory, in particular for the theory of quantum chromodynamics. Enabling calculations of the structure and interactions of matter from our most fundamental understanding of particle physics, lattice quantum chromodynamics is one of the main consumers of open-science supercomputing worldwide. Here, the design of ML algorithms for this application faces profound challenges, including the necessity of scaling custom ML architectures to the largest supercomputers, but also promises immense benefits, and is spurring a wave of development in ML-based sampling more broadly. In lattice field theory, if this approach can realize its early promise it will be a transformative step towards first-principles physics calculations in particle, nuclear and condensed matter physics that are intractable with traditional approaches.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

A Case For Intra-rack Resource Disaggregation in HPC

The expected halt of traditional technology scaling is motivating increased heterogeneity in high-performance computing (HPC) systems with the emergence of numerous specialized accelerators. As heterogeneity increases, so does the risk of underutilizing expensive hardware resources if we preserve today’s rigid node configuration and reservation strategies. This has sparked interest in resource disaggregation to enable finer-grain allocation of hardware resources to applications. However, there is currently no data-driven study of what range of disaggregation is appropriate in HPC. To that end, we perform a detailed analysis of key metrics sampled in NERSC’s Cori, a production HPC system that executes a diverse open-science HPC workload. In addition, we profile a variety of deep-learning applications to represent an emerging workload. We show that for a rack (cabinet) configuration and applications similar to Cori, a central processing unit with intra-rack disaggregation has a 99.5% probability to find all resources it requires inside its rack. In addition, ideal intra-rack resource disaggregation in Cori could reduce memory and NIC resources by 5.36% to 69.01% and still satisfy the worst-case average rack utilization.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Refining HPCToolkit for application performance analysis at exascale

As part of the US Department of Energy’s Exascale Computing Project (ECP), Rice University has been refining its HPCToolkit performance tools to better support measurement and analysis of applications executing on exascale supercomputers. To efficiently collect performance measurements of GPU-accelerated applications, HPCToolkit employs novel non-blocking data structures to communicate performance measurements between tool threads and application threads. To attribute performance information in detail to source lines, loop nests, and inlined call chains, HPCToolkit performs parallel analysis of large CPU and GPU binaries involved in the execution of an exascale application to rapidly recover mappings between machine instructions and source code. To analyze terabytes of performance measurements gathered during executions at exascale, HPCToolkit employs distributed-memory parallelism, multithreading, sparse data structures, and out-of-core streaming analysis algorithms. To support interactive exploration of profiles up to terabytes in size, HPCToolkit’s hpcviewer graphical user interface uses out-of-core methods to visualize performance data. The result of these efforts is that HPCToolkit now supports collection, analysis, and presentation of profiles and traces of GPU-accelerated applications at exascale. These improvements have enabled HPCToolkit to efficiently measure, analyze and explore terabytes of performance data for executions using as many as 64K MPI ranks and 64K GPU tiles on ORNL’s Frontier supercomputer. HPCToolkit’s support for measurement and analysis of GPU-accelerated applications has been employed to study a collection of open-science applications developed as part of ECP. This paper reports on these experiences, which provided insight into opportunities for tuning applications, strengths and weaknesses of HPCToolkit itself, as well as unexpected behaviors in executions at exascale.

Adhianto, Laksono↗
DOE OSTI2024

Matilda v1.0: An R package for probabilistic climate projections using a reduced complexity climate model

A primary advantage to using reduced complexity climate models (RCMs) has been their ability to quickly conduct probabilistic climate projections, a key component of uncertainty quantification in many impact studies and multisector systems. Providing frameworks for such analyses has been a target of several RCMs used in studies of the future co-evolution of the human and Earth systems. In this paper, we present Matilda, an open-science R software package that facilitates probabilistic climate projection analysis, implemented here using the Hector simple climate model in a seamless and easily applied framework. The primary goal of Matilda is to provide the user with a turn-key method to build parameter sets from literature-based prior distributions, run Hector iteratively to produce perturbed parameter ensembles (PPEs), weight ensembles for realism against observed historical climate data, and compute probabilistic projections for different climate variables. This workflow gives the user the ability to explore viable parameter space and propagate uncertainty to model ensembles with just a few lines of code. The package provides significant freedom to select different scoring criteria and algorithms to weight ensemble members, as well as the flexibility to implement custom criteria. Additionally, the architecture of the package simplifies the process of building and analyzing PPEs without requiring significant programming expertise, to accommodate diverse use cases. We present a case study that provides illustrative results of a probabilistic analysis of mean global surface temperature as an example of the software application.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Indicators of Global Climate Change 2023: annual update of key indicators of the state of the climate system and human influence

Intergovernmental Panel on Climate Change (IPCC) assessments are the trusted source of scientific evidence for climate negotiations taking place under the United Nations Framework Convention on Climate Change (UNFCCC). Evidence-based decision-making needs to be informed by up-to-date and timely information on key indicators of the state of the climate system and of the human influence on the global climate system. However, successive IPCC reports are published at intervals of 5–10 years, creating potential for an information gap between report cycles. We follow methods as close as possible to those used in the IPCC Sixth Assessment Report (AR6) Working Group One (WGI) report. We compile monitoring datasets to produce estimates for key climate indicators related to forcing of the climate system: emissions of greenhouse gases and short-lived climate forcers, greenhouse gas concentrations, radiative forcing, the Earth's energy imbalance, surface temperature changes, warming attributed to human activities, the remaining carbon budget, and estimates of global temperature extremes. The purpose of this effort, grounded in an open-data, open-science approach, is to make annually updated reliable global climate indicators available in the public domain. As they are traceable to IPCC report methods, they can be trusted by all parties involved in UNFCCC negotiations and help convey wider understanding of the latest knowledge of the climate system and its direction of travel. The indicators show that, for the 2014–2023 decade average, observed warming was 1.19 [1.06 to 1.30] °C, of which 1.19 [1.0 to 1.4] °C was human-induced. For the single-year average, human-induced warming reached 1.31 [1.1 to 1.7] °C in 2023 relative to 1850–1900. The best estimate is below the 2023-observed warming record of 1.43 [1.32 to 1.53] °C, indicating a substantial contribution of internal variability in the 2023 record. Human-induced warming has been increasing at a rate that is unprecedented in the instrumental record, reaching 0.26 [0.2–0.4] °C per decade over 2014–2023. This high rate of warming is caused by a combination of net greenhouse gas emissions being at a persistent high of 53±5.4 Gt CO 2 e yr -1 over the last decade, as well as reductions in the strength of aerosol cooling. Despite this, there is evidence that the rate of increase in CO 2 emissions over the last decade has slowed compared to the 2000s, and depending on societal choices, a continued series of these annual updates over the critical 2020s decade could track a change of direction for some of the indicators presented here.

54 ENVIRONMENTAL SCIENCES↗