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At least 1,189 records · Page 66

Performance Analysis of Large Scale HPC Workflows for Earth System Models

Climate assessment reports, such as the Intergovernmental Panel on Climate Change’s 5th assesment report [IPCC AR5; IPCC et al., 2014] or the United States National Climate Assessment [U.S. Global Change Research Program, 2014], increasingly rely on many-ensemble climate projections from fully-coupled Earth system models (ESM) to asses possible future climate states. ESM participate in a large set of Coupled Model Intercomparson Projects (CMIP) to better understand their models and the climate system, so that they may provide credible climate projections. However, fully participating in these intercomparison exercises represents an extremely large computational personnel burden for modeling centers [Eyring et al., 2016, Williams et al., 2016a]. However, there has been little attention within the climate modeling community paid to the in situ performance of ESMs up until now. Recently a computational performance model intercomparison project (CPMIP) for CMIP6 has begun [Balaji et al., 2017], but there has not yet been an effort to gather, process, and analyze the historical performance data that has been saved within archived log files from previous modeling efforts, nor the development of performance analysis system capable of providing detailed statistical analyses or visualizations of this performance data. Therefore, we’ve begun a joint effort to analyze the historical and current performance data on both GFDL and OLCF modeling systems. Here, we have developed a preliminary performance analysis system to captue, analyize, and visualize end-to-end in situ performance data and applied it to NOAA/GFDL’s post-processing system. Through the course of the project a number of performance improvements have been made, with the steps necessary to handle the expected volume of data (Big Data) likely to come out of the CMIP6 exercises (TB to PB) provided. We have also begun developing a statistical workload model that will allow modeling centers to determined their expected scientific throughput in the context of expected resource (computational and personnel) availability and accounting for typical workflow disruptions. This will allow them to develop a CMIP participation strategy and maximize their level of participation in the exercises. We expect this infrastructure, and the data it produces, to ultimately allow us to identify performance issues and workflow errors that exist across Earth system modeling centers, and possibly HPC modeling centers in general. Center-independent solutions to workflow or performance issues would help alleviate the computational burden for CMIP6+ modeling projects and should realize both labor and cost savings benefits throughout the CMIP community.

54 ENVIRONMENTAL SCIENCES↗

The Environment for Application Software Integration and Execution (EASIE) version 1.0. Volume 4: System installation and maintenance guide

The Environment for Application Software Integration and Execution (EASIE) provides both a methodology and a set of software utility programs to ease the task of coordinating engineering design and analysis codes. This document provides necessary information for installing the EASIE software on a host computer system. The target host is a DEX VAX running VMS version 4; host dependencies are noted when appropriate. Relevant directories and individual files are identified, and compile/load/execute sequences are specified. In the case of the data management utilities, database management system (DBMS) specific features are described in an effort to assist the maintenance programmer in converting to a new DBMS. The document also describes a sample EASIE program directory structure to guide the program implementer in establishing his/her application dependent environment.

Randall, Donald P.↗

Lessons Learned From Developing Three Generations of Remote Sensing Science Data Processing Systems

The Biospheric Information Systems Branch at NASA s Goddard Space Flight Center has developed three generations of Science Investigator-led Processing Systems for use with various remote sensing instruments. The first system is used for data from the MODIS instruments flown on NASA s Earth Observing Systems @OS) Terra and Aqua Spacecraft launched in 1999 and 2002 respectively. The second generation is for the Ozone Measuring Instrument flying on the EOS Aura spacecraft launched in 2004. We are now developing a third generation of the system for evaluation science data processing for the Ozone Mapping and Profiler Suite (OMPS) to be flown by the NPOESS Preparatory Project (NPP) in 2006. The initial system was based on large scale proprietary hardware, operating and database systems. The current OMI system and the OMPS system being developed are based on commodity hardware, the LINUX Operating System and on PostgreSQL, an Open Source RDBMS. The new system distributes its data archive across multiple server hosts and processes jobs on multiple processor boxes. We have created several instances of this system, including one for operational processing, one for testing and reprocessing and one for applications development and scientific analysis. Prior to receiving the first data from OMI we applied the system to reprocessing information from the Solar Backscatter Ultraviolet (SBUV) and Total Ozone Mapping Spectrometer (TOMS) instruments flown from 1978 until now. The system was able to process 25 years (108,000 orbits) of data and produce 800,000 files (400 GiB) of level 2 and level 3 products in less than a week. We will describe the lessons we have learned and tradeoffs between system design, hardware, operating systems, operational staffing, user support and operational procedures. During each generational phase, the system has become more generic and reusable. While the system is not currently shrink wrapped we believe it is to the point where it could be readily adopted, with substantial cost savings, for other similar tasks.

Tilmes, Curt↗

Constraints on Future Analysis Metadata Systems in High Energy Physics

In high energy physics (HEP), analysis metadata comes in many forms—from theoretical cross-sections, to calibration corrections, to details about file processing. Correctly applying metadata is a crucial and often time-consuming step in an analysis, but designing analysis metadata systems has historically received little direct attention. Among other considerations, an ideal metadata tool should be easy to use by new analysers, should scale to large data volumes and diverse processing paradigms, and should enable future analysis reinterpretation. This document, which is the product of community discussions organised by the HEP Software Foundation, categorises types of metadata by scope and format and gives examples of current metadata solutions. Important design considerations for metadata systems, including sociological factors, analysis preservation efforts, and technical factors, are discussed. A list of best practices and technical requirements for future analysis metadata systems is presented. These best practices could guide the development of a future cross-experimental effort for analysis metadata tools.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dataset and scripts for manuscript "Using Neural Network Ensembles to Separate Ocean Biogeochemical and Physical Drivers of Phytoplankton Biogeography in Earth System Models"

Please note: The title of this version contains an updated title for the manuscript compared to the previous version of this dataset. This is only due to title updates during the peer review process for the manuscript. The zip file contains the scripts, functions, and source files for the manuscript titled "Using Neural Network Ensembles to Separate Ocean Biogeochemical and Physical Drivers of Phytoplankton Biogeography in Earth System Models." The manuscript has been submitted for peer review. Please consult the README file for information on the specifications of the files. These files may occasionally be updated to add annotations to the scripts to make them more user friendly and to correct any errors.

54 ENVIRONMENTAL SCIENCES↗

Knowledge-based machine indexing from natural language text: Knowledge base design, development, and maintenance

One strategy for machine-aided indexing (MAI) is to provide a concept-level analysis of the textual elements of documents or document abstracts. In such systems, natural-language phrases are analyzed in order to identify and classify concepts related to a particular subject domain. The overall performance of these MAI systems is largely dependent on the quality and comprehensiveness of their knowledge bases. These knowledge bases function to (1) define the relations between a controlled indexing vocabulary and natural language expressions; (2) provide a simple mechanism for disambiguation and the determination of relevancy; and (3) allow the extension of concept-hierarchical structure to all elements of the knowledge file. After a brief description of the NASA Machine-Aided Indexing system, concerns related to the development and maintenance of MAI knowledge bases are discussed. Particular emphasis is given to statistically-based text analysis tools designed to aid the knowledge base developer. One such tool, the Knowledge Base Building (KBB) program, presents the domain expert with a well-filtered list of synonyms and conceptually-related phrases for each thesaurus concept. Another tool, the Knowledge Base Maintenance (KBM) program, functions to identify areas of the knowledge base affected by changes in the conceptual domain (for example, the addition of a new thesaurus term). An alternate use of the KBM as an aid in thesaurus construction is also discussed.

Genuardi, Michael T.↗

Digital Elevation Model, 0.25 m, Barrow Environmental Observatory, Utqiagvik (Barrow), Alaska, 2013

This 0.25m horizontal resolution digital elevation model (DEM) was developed from Airborne Laser Altimetry flown by Aerometric Inc, now known as Quantum Spatial, Inc. on July 12, 2013. One Mission was flown and the data jointly processed with LANL personnel to produce a 0.25m DEM covering a region approximately 2.8km wide and 12.4km long extending from the coast above North Salt Lagoon to south of Gas Well Road. This DEM encompasses a diverse range of hydrologic, geomorphic, geophysical and biological features typical of the Barrow Peninsula. Vertical accuracy at the 95% confidence interval was computed as 0.143m. The coordinate system, datum, and geoid for this DEM are UTM Zone 4N, NAD83 (2011), NAVD88 (GEOID09). This dataset includes a variety of file types.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Crystal structure of lubiprostone Polymorph B, C 20 H 32 F 2 O 5

The crystal structure of lubiprostone has been refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Lubiprostone crystallizes in space group P 1 (#1) with a = 9.02025(2), b = 10.72121(2), c = 12.32817(4) Å, α = 78.5566(2), β = 69.6858(2), γ = 77.3292(2)°, V = 1081.069(3) Å 3 , and Z = 2. The two independent molecules occur in an extended conformation, aligned approximately along the c -axis. The hydrophobic side chains are adjacent to each other, resulting in layers parallel to the ac plane. The two carboxylic acid groups form an eight-membered ring, resulting in dimers of the two independent molecules. Each hydroxyl group acts as a hydrogen bond donor to the ketone of the fused ring system. The powder pattern is included in the Powder Diffraction File™ as entry 00-066-1622.

Kaduk, James A. (ORCID:000000016610541X)↗

COMMON – Communications System Monitor v. 1.5

COMMON is a tool for collecting, storing, and displaying critical information to facilitate analysis on Microsoft Windows based IT systems. COMMON was developed to provide insight into the IT infrastructure for operational radiation detection systems, but is applicable to most Windows-based operating systems and TCP/IP network components. The COMMON tool aggregates a host of important Windows Management Instrumentation (WMI) information and as well as network ping responses to provide valuable insight into the performance of the IT system. A unique feature is the creation of daily output files (JSON) from the data collected for off site evaluation by subject matter experts.

Aragon, MonaL↗

Streaming Analytics and Data Engineering

SADE is a software package for rapidly assembling analytic pipelines to manipulate data. The packages consists of the engine that manages the data and coordinates the movement of data between the tasks performing a function, a set of core libraries consisting of plugins that perform common tasks, and a framework to extend the system supporting the development of new plugins. Currently through configuration files, a pipeline can be defined that maps the routing of data through a series of plugins. Pipelines can be run in a batch mode or can process streaming data; they can be executed from the command line or run through a Windows background service. There currently exists over a hundred plugins, over fifty pipeline configurations, and the software is now being used by about a half-dozen projects.

Source record↗

SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)

A set of 24 protein structures/complexes from the SARS CoV-2 proteome and inputs prepared for simulation using the CHARMM36m forcefield in PDB and gromacs formats. Each system contains a pdb and gromacs top and related input files necessary for running a temperature replica-exchange simulation. In addition, we also include: charmm PSF files (generated from the gromacs topology), a list of temperatures at which replica-exchange simulations were done (tempRamp), example gromacs run input mdp files, and initial minimized structures where available (minimized.pdb).

60 APPLIED LIFE SCIENCES↗

Putting error bars on density functional theory dataset

This dataset contains submission files and raw output files from high-throughput DFT simulations to analyze the systemic errors in lattice constant, bulk moduli and formation energy predictions for a range of binary and ternary oxides using four exchange correlation functionals (LDA, PBE, PBEsol and vdW-DF-C09). This data was then used as the basis for employing materials informatics methods to predict the expected errors in the lattice constants of the studied compounds. Predicted errors were also used to better the DFT-predicted lattice parameters. Our results emphasize the link between the computed errors and the electron density and hybridization errors of a functional. In essence, these results provide “error bars” for choosing a functional for the creation of high-accuracy, high-throughput datasets as well as avenues for the development of XC functionals with enhanced performance, thereby enabling the accelerated discovery and design of new materials.

36 MATERIALS SCIENCE↗

TEAMER: Performance mapping of Re Vision's Persistance PTO

Contains datasets from experimental measurements that were used to validate Re Vision's Persistence PTO's efficiency and performance. These measurements were obtained using a dynamometer test bench setup. The data includes open-circuit voltage and loss measurements to validate machine characteristics, efficiency mapping tests to determine the generator's performance mapping, and efficiency mapping tests to determine the converter's efficiency over the feasible operating range. This data was collected between June 2023 and September 2023. The data was collected at the National Renewable Energy Laboratory's Flatirons Campus, Colorado, United States. The data was collected using NREL's 5-kW dynamometer test bench, equipped with a torque sensor and various voltage and current sensors fed to a dedicated data acquisition system. Units for the data are included in the data file headers for each data series. A text editor or spreadsheet software such as Excel is required to view the *.csv data. The data are also provided in *.mat files. To view data plots, a Matlab script with *.mat files are provided.

16 TIDAL AND WAVE POWER↗

CO2 and CH4 leaf-level fluxes and soil porewater concentrations from common vegetation patches in Louisiana’s coastal wetlands

This dataset contains leaf-level flux and soil porewater concentration measurements of carbon dioxide (CO2) and methane (CH4 ) in plots in the footprint of Ameriflux sites US-LA2 and US-LA3. Leaf fluxes in US-LA2 were measured on patches dominated by Sagittaria lancifolia and co-dominated by Sagittaria lancifolia and Typha latifolia. In US-LA3, fluxes were measured from distinct Juncus roemerianus and Spartina alterniflora patches. The porewater concentrations were collected across a vertical profile (~50 cm depth) at centric locations within 25 m2 plots where we measured the leaf fluxes. US-LA3 included an additional set of measurements in open water spots. We aimed to evaluate differences in leaf fluxes and porewater pools of CO2 and CH4 of representative ecohydrological patches across a salinity gradient. We also used this dataset to help develop ELM-Wet, a more realistic representation of wetland carbon biogeochemical processes within the U.S. Department of Energy’s Energy Exascale Earth System Model (E3SM) Land Model version 1 (ELM v.1). The files can be opened with regular text editors or spreadsheet programs. Version 2.0 (8/26/2025): This is the latest version of this dataset. The update includes additional samples of soil porewater CH4/CO2 concentrations from June-2021 to November-2022, as well as minor adjustments made to V1 samples via changing Henry's solubility to account for porewater salinity. Additionally leaf-level measurments of spectral indices, PSRI, NDVI, and PRI have been added to complement Leaf-level flux measurements. All V1 data sets have been integrated into V2 sheets, ensuring data from the previous version is contained with the additional samples and consistent with V2 metadata.

54 ENVIRONMENTAL SCIENCES↗

ENDF/B-VIII.0 Augmented Covariance Data The first iteration [Slides]

Nuclear data are necessary for reliable modeling and simulation of the next generation of nuclear reactors. However, the variation in the ratio of the computed to experimental values (C/E) for certain types of nuclear systems is much less than predicted by evaluated nuclear data file (ENDF)/B covariances. Figure 1 provides an example of a set of metal-plutonium-fueled, fast-spectrum (PU-MET-FAST) integral experiments from the International Criticality Safety Benchmark Evaluation Project (ICSBEP) in the Oak Ridge National Laboratory (ORNL) VALID database. The variation in the C/E values, shown with one standard deviation error bars, is 100% covered by both the SCALE and ENDB/VIII.0 covariance data. This is due to the comparisons to integral data that are essential during the evaluation process. However, the ENDF evaluations represent uncertainties and correlations in differential data only; they do not reflect the impact of the comparison to integral data in the covariance evaluations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

ENDF/B-VIII.0 Augmented Covariance Data The first iteration [Slides]

Nuclear data are necessary for reliable modeling and simulation of the next generation of nuclear reactors. However, the variation in the ratio of the computed to experimental values (C/E) for certain types of nuclear systems is much less than predicted by evaluated nuclear data file (ENDF)/B covariances. Figure 1 provides an example of a set of metal-plutonium-fueled, fast-spectrum (PU-MET-FAST) integral experiments from the International Criticality Safety Benchmark Evaluation Project (ICSBEP) in the Oak Ridge National Laboratory (ORNL) VALID database. The variation in the C/E values, shown with one standard deviation error bars, is 100% covered by both the SCALE and ENDB/VIII.0 covariance data. This is due to the comparisons to integral data that are essential during the evaluation process. However, the ENDF evaluations represent uncertainties and correlations in differential data only; they do not reflect the impact of the comparison to integral data in the covariance evaluations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Calibrated Radar Wind Profiler Precipitation Observations and Vertical Velocity Retrievals

A radar wind profiler (RWP) data set collected during the 2-year Department of Energy Atmospheric Radiation Measurement (ARM) Observations and Modeling of the Green Ocean Amazon (GoAmazon2014/5) campaign is used to estimate vertical velocity, designate bulk meteorological echo classification (e.g., convective, stratiform), and provide calibrated radar reflectivity factor Z measurements (calibrated against collocated ground disdrometer and raingauge observations from T3). Additional fields include surface precipitation from rain gauge and ARM InterpolatedSonde streams utilized in the echo classification methods. This dataset follows methods established in Giangrande et al. [2013] and Giangrande et al. [2016] for informing on convective vertical velocities, mass flux and area coverage in Amazon convective cells from ARM RWP systems. If RWP datastreams were unavailable on a given date, files still contain raingauge and InterpolatedSonde information.

54 ENVIRONMENTAL SCIENCES↗

Thermal Radiation Analysis System (TRASYS)

A user's manual is presented for TRASYS, which is a digital software system with a generalized capability for solving radiation problems. Subroutines, file, and variable definitions are presented along with subroutine and function descriptions for the preprocessor. Definitions and descriptions of components of the processor are also presented.

Connor, R. J.↗