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At least 217 records · Page 12

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DOE OSTI2017

Accessing Data Federations with CVMFS

Data federations have become an increasingly common tool for large collaborations such as CMS and Atlas to efficiently distribute large data files. Unfortunately, these typically are implemented with weak namespace semantics and a non-POSIX API. On the other hand, CVMFS has provided a POSIX-compliant read-only interface for use cases with a small working set size (such as software distribution). The metadata required for the CVMFS POSIX interface is distributed through a caching hierarchy, allowing it to scale to the level of about a hundred thousand hosts. In this paper, we will describe our contributions to CVMFS that merges the data scalability of XRootD-based data federations (such as AAA) with metadata scalability and POSIX interface of CVMFS. We modified CVMFS so it can serve unmodified files without copying them to the repository server. CVMFS 2.2.0 is also able to redirect requests for data files to servers outside of the CVMFS content distribution network. Finally, we added the ability to manage authorization and authentication using security credentials such as X509 proxy certificates. We combined these modifications with the OSGs StashCache regional XRootD caching infrastructure to create a cached data distribution network. Here, we will show performance metrics accessing the data federation through CVMFS compared to direct data federation access. Additionally, we will discuss the improved user experience of providing access to a data federation through a POSIX filesystem.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2022

KokkACC: Enhancing Kokkos with OpenACC

Template metaprogramming is gaining popularity as a high-level solution for achieving performance portability on heterogeneous computing resources. Kokkos is a representative approach that offers programmers high-level abstractions for generic programming while most of the device-specific code generation and optimizations are delegated to the compiler through template specializations. For this, Kokkos provides a set of device-specific code specializations in multiple back ends, such as CUDA and HIP. Unlike CUDA or HIP, OpenACC is a high-level and directive-based programming model. This descriptive model allows developers to insert hints (pragmas) into their code that help the compiler to parallelize the code. The compiler is responsible for the transformation of the code, which is completely transparent to the programmer. This paper presents an OpenACC back end for Kokkos: KokkACC. As an alternative to Kokkos’s existing device-specific back ends, KokkACC is a multi-architecture back end providing a high-productivity programming environment enabled by OpenACC’s high-level and descriptive programming model. Moreover, we have observed competitive performance; in some cases, KokkACC is faster (up to 9×) than NVIDIA’s CUDA back end and much faster than OpenMP’s GPU offloading back end. This work also includes implementation details and a detailed performance study conducted with a set of mini-benchmarks (AXPY and DOT product) and three mini-apps (LULESH, miniFE and SNAP, a LAMMPS proxy mini-app).

Valero Lara, Pedro↗

DOE OSTI2017

Evaluation of Heliostat Standby Aiming Strategies to Reduce Avian Flux Hazards and Impacts on Operational Performance

This paper presents a study of alternative heliostat standby aiming strategies and their impact on avian flux hazards and operational performance of a concentrating solar power plant. A mathematical model was developed that predicts the bird-feather temperature as a function of solar irradiance, thermal emittance, convection, and thermal properties of the feather. The irradiance distribution in the airspace above the Ivanpah Unit 2 heliostat field was simulated using a ray-trace model for two different times of the day, four days of the year, and nine different standby aiming strategies. The impact of the alternative aiming strategies on operational performance was assessed by comparing the heliostat slew times from standby position to the receiver for the different aiming strategies. Increased slew times increased a proxy start-up time that reduced the simulated annual energy production. Results showed that spreading the radial aim points around the receiver to a distance of ~150 m or greater reduced the hazardous exposure times that the feather temperature exceeded the hazard metric of 160 degrees C. The hazardous exposure times were reduced by ~23% and 90% at a radial spread of aim points extending to 150 m and 250 m, respectively, but the simulated annual energy production decreased as a result of increased slew times. Single point-focus aiming strategies were also evaluated, but these strategies increased the exposure hazard relative to other aiming strategies.

14 SOLAR ENERGY↗

NASA NTRS2018

Power-Law Statistics of Driven Reconnection in the Magnetically Closed Corona

Numerous observations have revealed that power-law distributions are ubiquitous in energetic solar processes. Hard X-rays, soft X-rays, extreme ultraviolet radiation, and radio waves all display power-law frequency distributions. Since magnetic reconnection is the driving mechanism for many energetic solar phenomena, it is likely that reconnection events themselves display such power-law distributions. In this work, we perform numerical simulations of the solar corona driven by simple convective motions at the photospheric level. Using temperature changes, current distributions, and Poynting fluxes as proxies for heating, we demonstrate that energetic events occurring in our simulation display power-law frequency distributions, with slopes in good agreement with observations. We suggest that the braiding-associated reconnection in the corona can be understood in terms of a self-organized criticality model driven by convective rotational motions similar to those observed at the photosphere.

Knizhnik, K. J.↗

DOE OSTI2019

Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production

Abstract Optimizing microbial hosts for the large-scale production of valuable metabolites often requires multiple mutations and modifications to the host’s genome. We describe a three-round screen for increased L-DOPA production in S. cerevisiae using FACS enrichment of an enzyme-coupled biosensor for L-DOPA. Multiple rounds of screening were enabled by a single build of a barcoded in vitro transposon-mediated disruption library. New background strains for screening were built for each iteration using results from previous iterations. The same in vitro transposon-mediated disruption library was integrated by homologous recombination into new background strains in each round of screening. Compared with creating new transposon insertions in each round, this method takes less time and saves the cost of additional sequencing to characterize transposon insertion sites. In the first two rounds of screening, we identified deletions that improved biosensor compartmentalization and, consequently, improved our ability to screen for L-DOPA production. In a final round, we discovered that deletion of heme oxygenase (HMX1) increases total heme concentration and increases L-DOPA production, using dopamine measurement as a proxy. We further demonstrated that deleting HMX1 may represent a general strategy for P450 function improvement by improving activity of a second P450 enzyme, BM3, which performs a distinct reaction.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

CoMD Implementation Suite in Emerging Programming Models

CoMD-Em is a software implementation suite of the CoMD [4] proxy app using different emerging programming models. It is intended to analyze the features and capabilities of novel programming models that could help ensure code and performance portability and scalability across heterogeneous platforms while improving programmer productivity. Another goal is to provide the authors and venders with some meaningful feedback regarding the capabilities and limitations of their models. The actual application is a classical molecular dynamics (MD) simulation using either the Lennard-Jones method (LJ) or the embedded atom method (EAM) for primary particle interaction. The code can be extended to support alternate interaction models. The code is expected ro run on a wide class of heterogeneous hardware configurations like shard/distributed/hybrid memory, GPU's and any other platform supported by the underlying programming model.

Haque, Riyaz↗

DOE OSTI2016

Level-2 Milestone 5588: Deliver Strategic Plan and Initial Scalability Assessment by Advanced Architecture and Portability Specialists Team

This report documents the fact that the work in creating a strategic plan and beginning customer engagements has been completed. The description of milestone is: The newly formed advanced architecture and portability specialists (AAPS) team will develop a strategic plan to meet the goals of 1) sharing knowledge and experience with code teams to ensure that ASC codes run well on new architectures, and 2) supplying skilled computational scientists to put the strategy into practice. The plan will be delivered to ASC management in the first quarter. By the fourth quarter, the team will identify their first customers within PEM and IC, perform an initial assessment and scalability and performance bottleneck for next-generation architectures, and embed AAPS team members with customer code teams to assist with initial portability development within standalone kernels or proxy applications.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2013

Investigating the Use of Deep Convective Clouds (DCCT) to Monitor On-orbit Performance of the Geostationary Lightning Mapper (GLM) using Lightning Imaging Sensor (LIS) Measurements

There is a need to monitor the on-orbit performance of the Geostationary Lightning Mapper (GLM) on the Geostationary Operational Environmental Satellite R (GOES-R) for changes in instrument calibration that will affect GLM's lightning detection efficiency. GLM has no onboard calibration so GLM background radiance observations (available every 2.5 min) of Deep Convective Clouds (DCCs) are investigated as invariant targets to monitor GLM performance. Observations from the Lightning Imaging Sensor (LIS) and the Visible and Infrared Scanner (VIRS) onboard the Tropical Rainfall Measuring Mission (TRMM) satellite are used as proxy datasets for GLM and ABI 11 m measurements.

Buechler, Dennis E.↗

DOE OSTI2014

CoMD Implementation Suite in Emerging Programming Models

Haque, Riyaz↗

DOE OSTI2026

Optical diagnostic design for measuring the radiation front with a mid-leg pumped divertor on DIII-D

The design of an optical diagnostic system to localize the radiation front in a mid-leg pumped divertor configuration on DIII-D is presented. Divertor detachment is a key mechanism for handling power exhaust in tokamaks, and mid-leg pumping offers a promising approach to radiatively dissipate power while maintaining acceptable core performance. To predict the location of the radiation front and design a spectroscopic diagnostic to measure its position, a database of SOLPS-ITER simulations across a range of input powers and gas puffing rates representative of DIII-D operation was employed. These simulations provide self-consistent plasma backgrounds for a Cherab-Raysect synthetic diagnostic framework, which incorporates detailed tokamak geometry and physically accurate ray-tracing. Synthetic simulations of optical sightlines and viewing cone geometry were used to calculate line-integrated emission from the plasma, particularly of the C III 465 nm line, to serve as a proxy for the T e ≈ 7 − 10 eV temperature region associated with the onset and evolution of divertor detachment. Neutral deuterium emission is also evaluated for comparison. The synthetic diagnostic is used to assess the performance of existing DIII-D optical systems, including filterscopes and the Multichord Divertor Spectrometer, and to optimize line-of-sight placement within mechanical and installation constraints. The results provide quantitative guidance for diagnostic implementation on DIII-D and demonstrate the advantage of integrated synthetic diagnostics for divertor design studies and future advanced divertor concepts.

Cherab↗

DOE OSTI2017

The Halo Boundary of Galaxy Clusters in the SDSS

Analytical models and simulations predict a rapid decline in the halo density profile associated with the transition from the “infalling” regime outside the halo to the “collapsed” regime within the halo. Using data from SDSS, we explore evidence for such a feature in the density profiles of galaxy clusters using several different approaches. We first estimate the steepening of the outer galaxy density profile around clusters, finding evidence for truncation of the halo profile. Next, we measure the galaxy density profile around clusters using two sets of galaxies selected on color. We find evidence of an abrupt change in galaxy colors that coincides with the location of the steepening of the density profile. Since galaxies that have completed orbits within the cluster are more likely to be quenched of star formation and thus appear redder, this abrupt change in galaxy color can be associated with the transition from single-stream to multi-stream regimes. We also use a standard model comparison approach to measure evidence for a “splashback”-like feature, but find that this approach is very sensitive to modeling assumptions. Finally, we perform measurements using an independent cluster catalog to test for potential systematic errors associated with cluster selection. We identify several avenues for future work: improved understanding of the small-scale galaxy profile, lensing measurements, identification of proxies for the halo accretion rate, and other tests. With upcoming data from the DES, KiDS, and HSC surveys, we can expect significant improvements in the study of halo boundaries.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

DenKv: Addressing Design Trade-offs of Key-value Stores for Scientific Applications

High-performance computing (HPC) facilities have employed flash-based storage tier near to compute nodes to absorb high I/O demand by HPC applications during periodic system-level checkpoints. To accelerate these checkpoints, proxy-based distributed key-value stores (PD-KVS) gained particular attention for their flexibility to support multiple backends and different network configurations. PD-KVS rely internally on monolithic KVS, such as LevelDB or RocksDB, to exploit the KV interface and query support. However, PD-KVS are unaware of the high redundancy factor in checkpoint data, which can be up to GBs to TBs, and therefore, tend to generate high write and space amplification on these storage layers. In this paper, we propose DenKv which is deduplication-extended node-local LSM-tree-based KVS. DenKv employs asynchronous partially inline dedup (APID) and aims to maintain the performance characteristics of LSM-tree-based KVS while reducing the write and space amplification problems. We implemented DenKv atop BlobDB and showed that our proposed solution maintains performance while reducing write amplification up to 2× and space amplification by 4× on average.

Khan, Awais↗

DOE OSTI2020

Intensity measure adequacy assessment for nonlinear site response using Information Theory

Nonlinear site response modeling is a crucial aspect of Probabilistic Seismic Hazard Analysis. Site amplification models routinely rely on a rock intensity measure to characterize the strength of the bedrock motion. However, the adequacy of such intensity measures towards predicting amplifications across the oscillator period range has not been investigated in the literature. This paper analyzes the adequacy of rock intensity measures using state of the art criterion established in Performance-Based Earthquake Engineering and techniques from Information Theory. The efficiency and the sufficiency of several rock intensity measure are assessed. It was found that spectral accelerations at low periods usually are adequate for predicting amplifications across the period range. This supports the current practice of using Peak Ground Acceleration in Ground Motion Models. However, for extremely soft sites, which demonstrate nonlinear effects well into the period range, it is better practice to ensure that amplification and spectral acceleration share the same oscillator period. Lastly, for predicting the peak shear strain (an important parameter that controls nonlinearity of site response), Peak Ground Velocity is generally adequate, and this conclusion is in line with the definition of proxy shear strain.

42 ENGINEERING↗

DOE OSTI2021

Partitioning Net Ecosystem Exchange (NEE) of CO 2 Using Solar-Induced Chlorophyll Fluorescence (SIF)

Accurate partitioning of net ecosystem exchange (NEE) of CO 2 to gross primary production (GPP) and ecosystem respiration (R eco ) is crucial for understanding carbon cycle dynamics under changing climate. However, it remains as a long-standing problem in global ecology due to lack of independent constraining information for the two offsetting component fluxes. solar-induced chlorophyll fluorescence (SIF), a mechanistic proxy for photosynthesis, holds great promise to improve NEE partitioning by constraining GPP. We developed a parsimonious SIF-based approach for NEE partitioning and examined its performance using synthetic simulations and field measurements. This approach outperforms conventional approaches in reproducing simulated GPP and R eco , especially under high vapor pressure deficit. For field measurements, it results in lower daytime GPP and R eco than conventional approaches. Furthermore, this study made the first attempt to demonstrate SIF's potential for improving NEE partitioning accuracy and sets the stage for future efforts to examine its robustness and scalability under real-world environmental conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Probabilistic Prediction of Geomagnetic Storms and the K p index

Geomagnetic activity is often described using summary indices to summarize the likelihood of space weather impacts, as well as when parameterizing space weather models. The geomagnetic index K p in particular, is widely used for these purposes. Current state-of-the-art forecast models provide deterministic K p predictions using a variety of methods – including empirically-derived functions, physics-based models, and neural networks – but do not provide uncertainty estimates associated with the forecast. This paper provides a sample methodology to generate a 3-hour-ahead K p prediction with uncertainty bounds and from this provide a probabilistic geomagnetic storm forecast. Specifically, we have used a two-layered architecture to separately predict storm (K p ≥ 5 – ) and non-storm cases. As solar wind-driven models are limited in their ability to predict the onset of transient-driven activity we also introduce a model variant using solar X-ray flux to assess whether simple models including proxies for solar activity can improve the predictions of geomagnetic storm activity with lead times longer than the L1-to-Earth propagation time. By comparing the performance of these models we show that including operationally-available information about solar irradiance enhances the ability of predictive models to capture the onset of geomagnetic storms and that this can be achieved while also enabling probabilistic forecasts.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

TH-AB-207A-04: Assessment of Patients’ Cumulative Effective Dose From CT Examinations

Purpose: The Joint Commission requires institutions to consider patient’s age and recent imaging exams when deciding on the most appropriate type of imaging exam. Additionally, knowing patient’s imaging history can help prevent duplicate scans. Radiation dose management software affords new opportunities to identify and utilize patients with high cumulative doses as one proxy for subsequent review of imaging history and opportunities in avoiding redundant exams. Methods: Using dose management software (Radimetrics, Bayer Healthcare) a total of 72073 CT examinations performed from Jan 2015 to Jan 2016 were examined to categorize patients with a cumulative effective dose of 100 mSv and above. This threshold was selected based on epidemiological studies on populations exposed to radiation, which demonstrate a statistical increase of cancer risk at doses above 100 mSv. Histories of patients with highest cumulative dose and highest number of exams were further investigated by a Radiologist for appropriateness of recurrent studies and potential opportunities for reduction. Results: Out of 34762 patients, 927 (2.7%) were identified with a cumulative dose of 100 mSv and above. The highest cumulative dose (842 mSv) belonged to an oncology patient who underwent 2 diagnostic exams and 9 interventional ablative CT guided procedures. The patient with highest number of exams (56 counts) and cumulative dose of 170 mSv was a 17 year old trauma patient. An imaging history review of these two patients did not suggest any superfluous scans. Conclusion: Our limited pilot study suggests that recurrent CT exams for patients with oncologic or severe trauma history may be warranted and appropriate. As a result, for future studies we will be focusing on high dose patient cohorts not associated with oncology or severe trauma. Additionally, the review process itself has suggested areas for potential improvement in patient care, including improved documentation and Radiologist involvement in patient management. Dr. McNitt-Gray’s disclosures: Institutional research agreement, Siemens Healthcare; Past recipient, research grant support, Siemens Healthcare; Consultant, Toshiba America Medical Systems; Consultant, Samsung Electronics.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Simple Statistical Models for Predicting Overpressure Due to CO2 and Low-Salinity Waste-Fluid Injection into Deep Saline Formations

Deep saline aquifers have been used for waste-fluid disposal for decades and are the proposed targets for large-scale CO2 storage to mitigate CO2 concentration in the atmosphere. Due to relatively limited experience with CO2 injection in deep saline formations and given that the injection targets for CO2 sometimes are the same as waste-fluid disposal formations, it could be beneficial to model and compare both practices and learn from the waste-fluid disposal industry. In this paper, we model CO2 injection in the Patterson Field, which has been proposed as a site for storage of 50 Mt of industrial CO2 over 25 years. We propose general models that quickly screen the reservoir properties and calculate pressure changes near and far from the injection wellbore, accounting for variable reservoir properties. The reservoir properties we investigated were rock compressibility, injection rate, vertical-to-horizontal permeability ratio, average reservoir permeability and porosity, reservoir temperature and pressure, and the injectant total dissolved solids (TDS) in cases of waste-fluid injection. We used experimental design to select and perform simulation runs, performed a sensitivity analysis to identify the important variables on pressure build-up, and then fit a regression model to the simulation runs to obtain simple proxy models for changes in average reservoir pressure and bottomhole pressure. The CO2 injection created more pressure compared to saline waste-fluids, when similar mass was injected. However, we found a more significant pressure buildup at the caprock-reservoir interface and lower pressure buildup at the bottom of the reservoir when injecting CO2 compared with waste-fluid injection.

Ansari, Esmail↗

DOE OSTI2025

High Performance, High Fidelity: A GPU‐Accelerated Doubly‐Periodic Configuration of the Simple Cloud‐Resolving E3SM Atmosphere Model Version 1 (DP‐SCREAMv1)

The development of the Simplified Cloud Resolving Energy Exascale Earth System Atmosphere Model (SCREAMv1) enables global storm-resolving simulations on modern GPU-based supercomputers. However, the high computational cost of SCREAMv1 limits its routine use for process-level studies, creating a need for efficient proxy configurations. This study addresses this gap by introducing DP-SCREAMv1, a doubly periodic cloud-resolving model designed to be fully consistent with SCREAMv1 while enabling high-resolution, long-duration simulations at significantly reduced computational expense by simulating a limited doubly periodic domain rather than the entire globe. Built on a C++/Kokkos architecture, DP-SCREAMv1 achieves exceptional performance scalability on GPU systems and includes a rich library of cases for validation and scientific exploration. In this work, we demonstrate short wall-clock times at SCREAMv1's default resolution and show that DP-SCREAMv1 supports routine execution of large-domain, high-resolution experiments that were previously challenging in practice. Furthermore, we show that DP-SCREAMv1 enables routine execution of “Giga-LES” style simulations and facilitates large-domain, high-resolution simulations that were recently considered burdensome to perform. These results document an efficient, fully consistent process-level configuration for SCREAMv1 (DP-SCREAMv1) and illustrate its use for long-duration and large-domain experiments at cloud-resolving to eddy-permitting resolution.

Environmental sciences↗