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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

CI/CD Efforts for Validation, Verification and Benchmarking OpenMP Implementations

Software developers must adapt to keep up with the changing capabilities of platforms so that they can utilize the power of High-Performance Computers (HPC), including exascale systems. OpenMP, a directive-based parallel programming model, allows developers to include directives to existing C, C++, or Fortran code to allow node level parallelism without compromising performance. This paper describes our CI/CD efforts to provide easy evaluation of the support of OpenMP across different compilers using existing testsuites and benchmark suites on HPC platforms. Our main contributions include (1) the set of a Continuous Integration (CI) and Continuous Development (CD) workflow that captures bugs and provides faster feedback to compiler developers, (2) an evaluation of OpenMP (offloading) implementations supported by AMD, HPE, GNU, LLVM, and Intel, and (3) evaluation of the quality of compilers across different heterogeneous HPC platforms. With the comprehensive testing through the CI/CD workflow, we aim to provide a comprehensive understanding of the current state of OpenMP (offloading) support in different compilers and heterogeneous platforms consisting of CPUs and GPUs from NVIDIA, AMD, and Intel.

Jarmusch, Aaron↗
DOE OSTI2025

Characterizing GPU Energy Usage in Exascale-Ready Portable Science Applications

We characterize the GPU energy usage of two widely adopted exascale-ready applications representing two classes of particle and mesh solvers: (i) QMCPACK, a quantum Monte Carlo package, and (ii) AMReX-Castro, an adaptive mesh astrophysical code. We analyze power, temperature, utilization, and energy traces from double-/single (mixed)-precision benchmarks on NVIDIA’s A100 and H100 and AMD’s MI250X GPUs using queries in NVML and rocm_smi_lib, respectively. We explore application-specific metrics to provide insights on energy vs. performance trade-offs. Our results suggest that mixed-precision energy savings range between 6–25% on QMCPACK and 45% on AMReX-Castro. Also, we found gaps in the AMD tooling used on Frontier GPUs that need to be understood, while query resolutions on NVML have little variability between 1 ms-1 s. Overall, application level knowledge is crucial to define energy-cost/science-benefit opportunities for the codesign of future supercomputer architectures in the post-Moore era.

Godoy, William [ORNL] (ORCID:0000000225905178)↗
DOE OSTI2016

Environmental Geochemistry and Acid Mine Drainage Evaluation of an Abandoned Coal Waste Pile at the Alborz-Sharghi Coal Washing Plant, NE Iran

In this paper, an abandoned waste coal pile, which is resulted from Alborz-Sharghi coal washing plant, NE of Iran was mineralogically and geochemically characterized to evaluate pyrite oxidation, acid mine drainage (AMD) generation, and trace element mobility. After digging ten trenches and vertical sampling, a quantitative method including the atomic absorption test, and the quality-based methods including optical study were carried out for determination of pyrite fractions in the waste pile. The geochemical results revealed that the fraction of remaining pyrite increased with depth, indicating that pyrite oxidation is limited to the shallower depths of the pile which were confirmed by variations of sulfate, pH, EC, and carbonate with depth of the pile. To evaluate the trend of trace elements and mineralogical constituents of the waste particles, the samples were analyzed by using XRD, ICP-MS, and ICP-OES methods. The results showed the secondary and neutralizing minerals comprising gypsum have been formed below the oxidation zone. Besides, positive values of net neutralization potential indicated that AMD generation has not taken in the waste pile. In addition, variations of trace elements with depth reveal that Pb and Zn exhibited increasing trends from pile surface toward the bottom sampling trenches while another of them such as Cu and Ni had decreasing trends with increasing depth of the waste pile.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Colloidal metal transport in soils developing on historic coal mine spoil

Chemical weathering of pyrite via oxidative dissolution is well-known for generating Fe(III)-bearing colloids at acid mine drainage (AMD) sites; however, the potential for physical weathering of pyrite-bearing materials and subsequent release and transport of colloidal pyrite and associated trace metals has not been studied. Here, we monitored the colloidal metal transport in soil developing on abandoned coal mine spoil with a history of AMD generation to systematically study the contribution of colloids to base and trace metal transport and determine the elemental and mineralogical composition of colloids. Additionally, we collected soil pore water using lysimeters with a pore size of approximately 1.3 μm and centrifugation was used to separate the colloids from aqueous fractions. Metal concentrations of Na, Ca, Mg, K, Si, Al, Mn, Fe, Cu, and Zn were analyzed. Our results show only 14% of the total Al and Cu were present in colloidal fractions whereas 23%, 43%, and 54% of Fe, Mn, and Zn were transported in the colloidal phase, respectively. In contrast, all base metals were primarily present in the aqueous concentration with a small fraction (<10%) present in the colloidal phase. The colloidal fractions of the base metals were inferred to be associated with the concentration of clay colloids. The release of colloids exhibited possible sensitivity toward weather conditions such as alternating high temperatures and rainfall during summer (May–July) compared to fall (August–November). The morphology, elemental, and mineral composition of colloids were determined by a scanning electron microscopy equipped with energy dispersive spectroscopy (SEM-EDS) and X-ray diffraction (XRD). Colloids were dominated by phyllosilicates (biotite, muscovite, and kaolinite) with minor quartz and feldspars. Other minerals phases identified in colloidal fractions were hematite, goethite, arsenopyrite, and chalcopyrite. Colloids consisting of Fe, S, and O with structures resembling framboidal pyrite were identified, which is consistent with the non-silicates minerals identified by XRD. Our study suggests that the physical weathering of pyrite in the mine spoil can generate colloidal pyrite, which is mobilized and transported by soil pore water. Our results also indicate that these pyritic colloids are associated with toxic trace metals including Cu, Mn, and Zn. Colloid mobilization is also impacted by changes in temperature and precipitation, where clay mobilization afer rain events is favored. Further, sudden spikes in aqueous and/or colloidal concentrations may be the result of local heterogeneity within soils developing on mine spoil, indicating that further field-based work is necessary to better characterize pore-scale processes that control aqueous and colloid transport at similar sites to have a better understanding of potential contaminant transport from mine spoil systems.

58 GEOSCIENCES↗
DOE OSTI2018

Inhibition of TBK1 reduces choroidal neovascularization in vitro and in vivo

Highlights: • The expression of TBK1 and VEGF is up-regulated in CNV model. • Knockdown of TBK1 alleviates CNV formation via inhibiting VEGF expression. • TBK1 plays a critical role in the development of CNV. choroidal neovascularization (CNV), a characteristic of wet age-related macular degeneration (AMD), causes severe vision loss among elderly patients. TANK-binding kinase 1 (TBK1) is a ubiquitously expressed serine–threonine kinase and is found to induce endothelial cells proliferation, represent a novel mediator of tumor angiogenesis and exert pro-inflammatory effect. However, the role of TBK1 in choroidal neovascularization has not been investigated so far. In this study, we found that the expression of TBK1 and VEGF was up-regulated in RF/6 A cells chemical hypoxia model and laser-induced mouse CNV model. Silencing of TBK1 suppressed the proliferation and tube formation activity of RF/6 A cells. Intravitreal injection of anti-TBK1 monoclonal antibody ameliorates CNV formation. Taken together, these findings exhibit a proangiogenic role for TBK1 via upregulating the expression of VEGF, and may suggest that TBK1 inhibition offers a unique and alternative method for prevention and treatment of AMD.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Inhibition of TRAF6 alleviates choroidal neovascularization in vivo

Choroidal neovascularization (CNV) is a type of wet age-related macular degeneration (AMD) which is a major cause of blindness in elder patients. Tumor necrosis factor receptor-associated factor 6 (TRAF6) promotes tumor angiogenesis via upregulating the expression of hypoxia-inducible factor 1α (HIF-1α) and vascular endothelial growth factor (VEGF). Additionally, TRAF6 facilitates the inflammatory response in macrophages and microglia. Here, using mouse laser-induced CNV model and TRAF6 siRNA, the study shows that TRAF6 is a critical player in CNV. The expression of TRAF6, HIF-1α, and VEGF increased in the model. TFAF6 siRNA intravitreal (IVT) injection inhibited CNV formation, as well as expression of HIF-1α and VEGF, activation of macrophages and microglia. Together, our data suggest that TFAF6 inhibition reduces CNV formation via down-regulating expression of HIF-1α and VEGF and activation of macrophages and microglia, demonstrating the unique advantages of TRAF6 inhibition in the alleviation of AMD.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

GPU-enabled extreme-scale turbulence simulations: Fourier pseudo-spectral algorithms at the exascale using OpenMP offloading

Fourier pseudo-spectral methods for nonlinear partial differential equations are of wide interest in many areas of advanced computational science, including direct numerical simulation of three-dimensional (3-D) turbulence governed by the Navier-Stokes equations in fluid dynamics. This paper presents a new capability for simulating turbulence at a new record resolution up to 35 trillion grid points, on the world's first exascale computer, Frontier, comprising AMD MI250x GPUs with HPE's Slingshot interconnect and operated by the US Department of Energy's Oak Ridge Leadership Computing Facility (OLCF). Key programming strategies designed to take maximum advantage of the machine architecture involve performing almost all computations on the GPU which has the same memory capacity as the CPU, performing all-to-all communication among sets of parallel processes directly on the GPU, and targeting GPUs efficiently using OpenMP offloading for intensive number-crunching including 1-D Fast Fourier Transforms (FFT) performed using AMD ROCm library calls. With 99% of computing power on Frontier being on the GPU, leaving the CPU idle leads to a net performance gain via avoiding the overhead of data movement between host and device except when needed for some I/O purposes. Memory footprint including the size of communication buffers for MPI_ALLTOALL is managed carefully to maximize the largest problem size possible for a given node count. Detailed performance data including separate contributions from different categories of operations to the elapsed wall time per step are reported for five grid resolutions, from 2048 3 on a single node to 32768 3 on 4096 or 8192 nodes out of 9408 on the system. Both 1D and 2D domain decompositions which divide a 3D periodic domain into slabs and pencils respectively are implemented. The present code suite (labeled by the acronym GESTS, GPUs for Extreme Scale Turbulence Simulations) achieves a figure of merit (in grid points per second) exceeding goals set in the Center for Accelerated Application Readiness (CAAR) program for Frontier. The performance attained is highly favorable in both weak scaling and strong scaling, with notable departures only for 2048 3 where communication is entirely intra-node, and for 32768 3 , where a challenge due to small message sizes does arise. Communication performance is addressed further using a lightweight test code that performs all-to-all communication in a manner matching the full turbulence simulation code. Performance at large problem sizes is affected by both small message size due to high node counts as well as dragonfly network topology features on the machine, but is consistent with official expectations of sustained performance on Frontier. Overall, although not perfect, the scalability achieved at the extreme problem size of 32768 3 (and up to 8192 nodes — which corresponds to hardware rated at just under 1 exaflop/sec of theoretical peak computational performance) is arguably better than the scalability observed using prior state-of-the-art algorithms on Frontier's predecessor machine (Summit) at OLCF. New science results for the study of intermittency in turbulence enabled by this code and its extensions are to be reported separately in the near future.

3D fast Fourier transform↗
DOE OSTI2021

Effect of the sample work function on alkali metal dosing induced electronic structure change

Alkali metal dosing (AMD) has been widely used as a way to control doping without chemical substitution. This technique, in combination with angle resolved photoemission spectroscopy (ARPES), often provides an opportunity to observe unexpected phenomena. However, the amount of transferred charge and the corresponding change in the electronic structure vary significantly depending on the material. Here, we report study on the correlation between the sample work function and alkali metal induced electronic structure change for three iron-based superconductors: FeSe, Ba(Fe 0.94 Co 0.06 ) 2 As 2 and NaFeAs which share a similar Fermi surface topology. Electronic structure change upon monolayer of alkali metal dosing and the sample work function were measured by ARPES. In this work, our results show that the degree of electronic structure change is proportional to the difference between the work function of the sample and Mulliken's absolute electronegativity of the dosed alkali metal. This finding provides a possible way to estimate the AMD induced electronic structure change.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Curcumin analog 1, 5-bis (2-trifluoromethylphenyl)-1, 4-pentadien-3-one exhibits enhanced ability on Nrf2 activation and protection against acrolein-induced ARPE-19 cell toxicity

Curcumin, a phytochemical agent in the spice turmeric, has received increasing attention for its anticancer, anti-inflammatory and antioxidant properties. However, application of curcumin has been limited due to its insolubility in water and poor bioavailability both clinically and experimentally. In addition, the protective effects and mechanisms of curcumin in eye diseases have been poorly studied. In the present study, we synthesized a curcumin analog, 1, 5-bis (2-trifluoromethylphenyl)-1, 4-pentadien-3-one (C3), which displayed improved protective effect against acrolein-induced toxicity in a human retinal pigment epithelial cell line (ARPE-19). At 5 μM, curcumin completely protected against acrolein-induced cell oxidative damage and preserved GSH levels and mitochondrial function. Surprisingly, C3 displayed a complete protective effect at 0.5 μM, which was much more efficient than curcumin. Both 0.5 μM C3 and 5 μM curcumin induced Nrf2 nuclear translocation and Nrf2 target genes transcription similarly. Experiments using Nrf2 siRNA showed that the protective effects of curcumin and C3 were eliminated by Nrf2 knockdown. Additionally, both curcumin and C3 activated the PI3/Akt pathway, however, Nrf2 activation was independent of this pathway, and therefore, we hypothesized that both curcumin and C3 activated phase II enzymes via directly disrupting the Nrf2/Keap1 complex and promoting Nrf2's nuclear translocation. Since acrolein challenge of ARPE-19 cells has been used as a model of smoking and age-related macular degeneration (AMD), we concluded that the curcumin analog, C3, may be a more promising drug candidate for its potential application for the prevention and treatment of eye diseases, such as AMD. - Highlights: • We examine toxicity effects of cigarette smoking component acrolein in retina cells. • We report a more efficient curcumin analog (C3) protecting cellular function. • Mitochondrial function and phase II enzyme activation are the major targets of C3. • C3 is ten-fold more potent than curcumin on activating Nrf2 nuclear translocation. • Nrf2 translocation and Phase II enzyme induction are independent of PI3K/Akt pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Solar Irradiation Induced Transformation of Ferrihydrite in the Presence of Aqueous Fe 2+

Ferrihydrite commonly occurs in soils and sediments, especially in acid mine drainage (AMD). Solar irradiation may affect Fe(II)-catalyzed transformation of metastable ferrihydrite to more stable iron oxides on AMD surface. We investigated the Fe(II)-catalyzed transformation process and mechanism of ferrihydrite under light irradiation. In nitrogen atmosphere, Fe 2+ aq could be oxidized to goethite and lepidocrocite by hydroxyl radical (OH • ), superoxide radical (O 2 •– ) and hole (h vb + ) generated from ferrihydrite under ultraviolet (UV) irradiation (300–400 nm) at pH 6.0, and O 2 •– and h vb + were mainly responsible for Fe 2+ aq oxidation. In addition, the ligand-to-metal charge-transfer (LMCT) process between Fe(II) and ferrihydrite could be promoted by UV irradiation. Goethite proportion increased with increasing Fe 2+ aq concentration. Both visible (vis) and solar irradiation could also lead to the oxidation of Fe 2+ aq to goethite and lepidocrocite, and the proportion of lepidocrocite increased with increasing light intensity. Fe 2+ aq was photochemically oxidized to schwertmannite at pH 3.0 and 4.5, and the oxidation rate was higher than that under dark conditions in air. The photochemical oxidation rate of Fe 2+ aq decreased in the presence of humic acid. This study facilitates a better understanding of the formation and transformation of iron oxides in natural environments and ancient Earth.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Recovering Rare Earth Elements from Aqueous Solution with Porous Amine–Epoxy Networks

Recovering aqueous rare earth elements (REEs) from domestic water sources is one key strategy to diminish the U.S.’s foreign reliance of these precious commodities. Herein, we synthesized an array of porous, amine–epoxy monolith and particle REE recovery sorbents from different polyamine, namely tetraethylenepentamine, and diepoxide (E2), triepoxide (E3), and tetra-epoxide (E4) monomer combinations via a polymer-induced phase separation (PIPS) method. The polyamines provided -NH 2 (primary amine) plus -NH (secondary amine) REE adsorption sites, which were partially reacted with C–O–C (epoxide) groups at different amine/epoxide ratios to precipitate porous materials that exhibited a wide range of apparent porosities and REE recoveries/affinities. Specifically, polymer particles (ground monoliths) were tested for their recovery of La 3+ , Nd 3+ , Eu 3+ , Dy 3+ , and Yb 3+ (Ln 3+ ) species from ppm-level, model REE solutions (pH ≈ 2.4, 5.5, and 6.4) and a ppb-level, simulated acid mine drainage (AMD) solution (pH ≈ 2.6). Screening the sorbents revealed that E3/TEPA-88 (88% theoretical reaction of -NH 2 plus -NH) recovered, overall, the highest percentage of Ln 3+ species of all particles from model 100 ppm- and 500 ppm-concentrated REE solutions. Water swelling (monoliths) and ex situ, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) (ground monoliths/particles) data revealed the high REE uptake by the optimized particles was facilitated by effective distribution of amine and hydroxyl groups within a porous, phase-separated polymer network. In situ DRIFTS results clarified that phase separation, in part, resulted from polymerization of the TEPA-E3 (N-N-diglycidyl-4-glycidyloxyaniline) species in the porogen via C–N bond formation, especially at higher temperatures. Most importantly, the E3/TEPA-88 material cyclically recovered >93% of ppb-level Ln 3+ species from AMD solution in a recovery–strip–recovery scheme, highlighting the efficacy of these materials for practical applications.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota

Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. For this study, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchae ota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Second-generation hexavalent molybdenum oxo-amidinate precursors for atomic layer deposition

Here, the synthesis of molybdenum oxo-amidinate complexes MoO 2 (R 2 AMD) 2 [AMD = N,N'-di-R-acetamidinate; R = Cy (2; cyclohexyl) and iPr (3)], and their characterization by 1 H, 13 C NMR, X-ray diffraction, and thermogravimetric analysis is reported. Quartz-crystal microbalance and X-ray photoelectron spectroscopic studies confirm that 3 is an improved ALD precursor versus the R = t-butyl derivative for MoO 3 film growth. Complex 3 is accessible in higher yields (80%+), is easier to handle without mass loss, and in conjunction with O 3 as the second ALD reagent, yields nitride-free MoO 3 films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A Safety and Management Framework to Enable Automated Mobility Districts in Urban Areas

Automated mobility technology is beginning to emerge as a viable means to create sustainable and effective public mobility systems within denser urban environments. Automated mobility districts (AMDs) describe major urban districts or activity centers in which deployments of multiple automated vehicle (AV) transit and ride-hailing fleets are supported to meet public mobility needs. The authors put forward a framework to enable AMDs and their governing and management jurisdictional authorities to manage safety of AV operations based on lessons learned from the last century of automated guideway transit and roadway intersection traffic control systems. The essential concept is that of operational management and safety-critical control of multiple AV fleets using a “system-of-systems” approach to system safety analysis. The safety analysis would focus on safe passage of the AV fleet vehicles through complex roadway intersections and junctions, especially in the presence of other non-automated modes such as pedestrians and manually operated vehicles.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

The Convergence of Vehicle Electrification and Automation - Enabling Sustainable Automated Mobility Districts

The transportation industry is entering a new frontier with three major simultaneous transformations: electrification, automation, and on-demand services. All three directly affect the same spaces of vehicle technology, infrastructure, and system operational performance. Further, each area of change adds its own driving forces of complexity to the others' design challenges. This paper explores these transformations, framing the implications for vehicle technology and infrastructure and their impact on operating concepts and strategies, which in turn impact the sustainability of the transportation infrastructure in the built environment. Specifically, this paper examines battery-electric vehicles operating in a fully automated fleet within an "automated mobility district" (AMD) setting with multiple on-demand services. From this examination, the paper assesses the implications for transportation electrification, comparing and contrasting traditional fixed-route services with those of on-demand transit and automated transit networks, including the trade-offs between vehicle range (battery capacity), charging parameters, power availability, and operations predictability with respect to policy and infrastructure configurations. The paper also addresses the configuration and management of boarding and alighting zones (also called pickup and drop-off zones), and the need for complementary infrastructure intelligence at intersections and curbs. Finally, conclusions are drawn with respect to the system integration and analysis needs for AMDs regarding resilience and sustainability of mobility infrastructure.

ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2016

Beam dynamic simulation and optimization of the CLIC positron source and the capture linac

The CLIC Positron Source is based on the hybrid target composed of a crystal and an amorphous target. Simulations have been performed from the exit of the amorphous target to the end of pre-injector linac which captures and accelerates the positrons to an energy of 200 MeV. Simulations are performed by the particle tracking code PARMELA. The magnetic field of the AMD is represented in PARMELA by simple coils. Two modes are applied in this study. The first one is accelerating mode based on acceleration after the AMD. The second one is decelerating mode based on deceleration in the first accelerating structure. It is shown that the decelerating mode gives a higher yield for the e{sup +} beam in the end of the Pre-Injector Linac.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗