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DOE OSTI2021

Virtual Log-Structured Storage for High-Performance Streaming

Over the past decade, given the higher number of data sources (e.g., Cloud applications, Internet of things) and critical business demands, Big Data transitioned from batch-oriented to real-time analytics. Stream storage systems, such as Apache Kafka, are well known for their increasing role in real-time Big Data analytics. For scalable stream data ingestion and processing, they logically split a data stream topic into multiple partitions. Stream storage systems keep multiple data stream copies to protect against data loss while implementing a stream partition as a replicated log. This architectural choice enables simplified development while trading cluster size with performance and the number of streams optimally managed. This paper introduces a shared virtual log-structured storage approach for improving the cluster throughput when multiple producers and consumers write and consume in parallel data streams. Stream partitions are associated with shared replicated virtual logs transparently to the user, effectively separating the implementation of stream partitioning (and data ordering) from data replication (and durability). We implement the virtual log technique in the KerA stream storage system. When comparing with Apache Kafka, KerA improves the cluster ingestion throughput by up to 4x when multiple producers write over hundreds of data streams.

consistent stream ordering↗

DOE OSTI2024

Using Median Point in Keeling Plot to Reduce the Uncertainty of the Isotopic Composition of Evapotranspiration

Abstract The isotopic composition of evapotranspirationδ ET is a crucial parameter in isotope-based evapotranspiration (ET) partitioning and moisture recycling studies. The Keeling plot method is the most prevalent method to calculateδ ET , though it contains large extrapolated uncertainties from the least squares regression. Traditional Keeling regression uses the mean point of individual measurements. Here, a modified Keeling plot framework was proposed using the median point of individual measurements. We tested theδ ET uncertainty using the mean point [σ ET (mean)] and median point [σ ET (median)]. Multiple resolutions of input and output data from six independent sites were used to test the performance of the two methods. Theσ ET (mean) would be greater thanσ ET (median) when the mean value of inverse vapor concentration () is greater than the median value of inverse vapor concentration []. When applying the filter ofr 2 > 0.8, around 70% ofσ ET (mean) was greater thanσ ET (median). This phenomenon might be due to the normality of the vapor concentrationC υ producing the asymmetric distribution of 1/C υ . The median method could perform significantly better than the mean method when inputting high-resolution measurements (e.g., 1 Hz) and when the water vapor concentrationC υ is relatively low. Compared to the mean method, applying the median method could on average reduce 6.88% of ET partitioning uncertainties and could on average reduce 9.00% of moisture recycling uncertainties. This study provided a new insight of the Keeling plot method and emphasized handling model output uncertainty from multiple perspectives instead of only from input parameters.

Meteorology & Atmospheric Sciences↗

DOE OSTI2016

TOGA: A TOUGH code for modeling three-phase, multi-component, and non-isothermal processes involved in CO 2 -based Enhanced Oil Recovery

TOGA is a numerical reservoir simulator for modeling non-isothermal flow and transport of water, CO 2 , multicomponent oil, and related gas components for applications including CO 2 -enhanced oil recovery (CO 2 -EOR) and geologic carbon sequestration in depleted oil and gas reservoirs. TOGA uses an approach based on the Peng-Robinson equation of state (PR-EOS) to calculate the thermophysical properties of the gas and oil phases including the gas/oil components dissolved in the aqueous phase, and uses a mixing model to estimate the thermophysical properties of the aqueous phase. The phase behavior (e.g., occurrence and disappearance of the three phases, gas + oil + aqueous) and the partitioning of non-aqueous components (e.g., CO 2 , CH 4 , and n-oil components) between coexisting phases are modeled using K-values derived from assumptions of equal-fugacity that have been demonstrated to be very accurate as shown by comparison to measured data. Models for saturated (water) vapor pressure and water solubility (in the oil phase) are used to calculate the partitioning of the water (H 2 O) component between the gas and oil phases. All components (e.g., CO 2 , H 2 O, and n hydrocarbon components) are allowed to be present in all phases (aqueous, gaseous, and oil). TOGA uses a multiphase version of Darcy’s Law to model flow and transport through porous media of mixtures with up to three phases over a range of pressures and temperatures appropriate to hydrocarbon recovery and geologic carbon sequestration systems. Transport of the gaseous and dissolved components is by advection and Fickian molecular diffusion. New methods for phase partitioning and thermophysical property modeling in TOGA have been validated against experimental data published in the literature for describing phase partitioning and phase behavior. Flow and transport has been verified by testing against related TOUGH2 EOS modules and CMG. The code has also been validated against a CO 2 -EOR experimental core flood involving flow of three phases and 12 components. Results of simulations of a hypothetical 3D CO 2 -EOR problem involving three phases and multiple components are presented to demonstrate the field-scale capabilities of the new code. This user guide provides instructions for use and sample problems for verification and demonstration.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Final Technical Report - Consolidating Biomass Pretreatment with Saccharification by Resolving the Spatial Control Mechanisms of Fungi

Consolidated bioprocessing (CBP) of lignocellulose combines enzymatic sugar release (saccharification) with fermentation, but pretreatments remain separate and costly. In nature, lignocellulose-degrading brown rot fungi consolidate pretreatment and saccharification, likely using spatial gradients to partition these incompatible reactions. With the field of biocatalysis maturing, reaction partitioning is increasingly reproducible for commercial use. Therefore, my goal was to resolve the reaction partitioning mechanisms of brown rot fungi so that they can be applied to bioconversion of lignocellulosic feedstocks. Brown rot fungi consolidate oxidative pretreatments with saccharification and are a focus for biomass refining because 1) they attain >99% sugar yield without destroying lignin, 2) they use a simplified cellulase suite that lacks exoglucanase, and 3) their non-enzymatic pretreatment is facilitative and may be accelerated. Specifically, I hypothesized that during brown rot, oxidative pretreatments occur ahead of enzymatic saccharification, spatially, and the fungus partitions these reactions using gradients in pH, lignin reactivity, and plant cell wall porosity. In fact, we found three key results during these experiments for this work: 1) Brown rot fungi have an inducible cellulase system, unlike previous descriptions of a constitutive mechanism. 2) The induction of cellulases is delayed until there is repression of oxidatively-linked genes, allowing the brown rot fungi to coordinate two incompatible reactions (oxidative pretreatment with enzymatic saccharification, to release wood sugars) in the same pieces of wood. 3) This transition is mediated by the same wood sugar, cellobiose, released by the oxidative pretreatment step. Collectively, these findings have been published in excellent journal outlets and have been presented at conferences around the United States, and they offer clear targets for gene discovery en route to making biofuels and biochemicals affordable, commercially.

09 BIOMASS FUELS↗

DOE OSTI2020

Iodine Flowsheet Status Report

A simplified flowsheet was developed to evaluate the impact of varied assumptions of I-129 decontamination factors on the overall I-129 material balance in the Direct Feed Low-Activity Waste (DFLAW) facility. The flowsheet allows inputs for I-129 feed and Decontamination Factors (DFs) for multiple DFLAW unit operations and provides information on I-129 partitioning to output streams. A series of 6 DFs were evaluated, including baseline DFs from a prior Waste Treatment and Immobilization Plant (WTP) study and refined values based on a Savannah River National Laboratory (SRNL) review. The Microsoft Excel flowsheet spreadsheet will be provided to WRPS to allow further evaluation of the impact of DF assumptions on output streams. The spreadsheet is not specific to iodine, the partitioning of any species can be estimated by entering the assumed DFs for each unit operation. Flowsheet outputs matched results from the prior WTP study and show that different assumptions for the DFs can greatly impact iodine partitioning to primary and secondary waste streams. Results from SRNL's baseline DF values suggest less than 50% of I-129 would be retained in glass versus the 96% when using the BNI DF values. In addition, the flowsheet demonstrated that more than 5 DFLAW operational cycles are required to achieve a steady-state of I-129 to the primary waste stream. It is not possible with the data available to determine whether the BNI approach or the approach taken in this study will be a better match for the iodine partitioning once the LAW facility begins operation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

Distribution of Infiltration in the 216-U-10 and 216-B-3 Pond Systems 1944-1997

A modeling system to simulate fate and transport of contaminant plumes in groundwater beneath the Central Plateau to support the Cumulative Impact Evaluation (CIE) and Composite Analysis (CA) is being developed. The CIE will evaluate the cumulative effect of multiple Central Plateau radiological and chemical sources on groundwater quality (DOE/RL-2018-69, Cumulative Impact Evaluation Technical Approach Document ). This will enable cleanup decisions to be evaluated in the context of all Central Plateau waste sites and existing groundwater conditions. The CA evaluates the cumulative effect of all sources of radioactive materials on radiological dose to future members of the public (DOE/RL-2018-60, Annual Status Report (FY 2018): Composite Analysis of Low Level Waste Disposal in the Central Plateau of the Hanford Site ). Fate and transport modeling will be used to forecast future groundwater concentrations for both the CIE and CA. The CIE/CA subsurface modeling system is divided into source (inventory), vadose zone, and saturated zone facets. Source inventory is a necessary input to the vadose zone facet, and releases from the vadose zone to groundwater are inputs to the saturated zone facet. The vadose zone facet simulates historical and future releases from the vadose zone to groundwater for both liquid waste and solid waste disposal sites. Effluent release volumes and radionuclide inventory estimates for liquid waste sites are contained in ECFHANFORD- 17-0079, Hanford Soil Inventory Model (SIM-v2) Calculated Radionuclide Inventory of Direct Liquid Discharges to Soil in the Hanford Site’s 200 Areas , herein referred to as SIM-v2. The liquid waste sites in SIM-v2 include the 216-B-3 Pond near 200 East Area and the 216-U-10 Pond in 200 West Area. The 216-B-3 Pond system consisted of a main pond and 3 expansion lobes that were operational during overlapping time periods. It also included influent ditches, but these are not listed as liquid waste sources in SIM-v2 and are not included in the CIE/CA modeling. The total effluent volume released to the pond system was measured, but the partitioning of this volume to the various expansion lobes was not determined and is not accounted for in SIM-v2. Regarding the 216-U-10 Pond, it received water from several influent ditches. The pond and the influent ditches are listed as liquid waste sites in SIM-v2 and are included as sources in the CIE/CA modeling. Because water in the ditches flowed into the pond, only a portion of the effluent volumes and contaminant inventories assigned to the ditches in SIM-v2 infiltrated from the ditches. Thus, partitioning of infiltration and contaminant inventories between the ditches and the pond is not fully accounted for in SIM-v2. Further, some of the water in the 216-U-10 Pond entered overflow ditches and the amount of this overflow was not recorded and is not accounted for in SIM-v2. Thus, the purpose of this Environmental Calculation File (ECF) is to partition the infiltration of wastewater and contaminant inventory between the main pond and each expansion lobe of the 216-B-3 Pond system, and to partition the infiltration of wastewater and contaminant inventory between the ditches and pond of the 216-U-10 Pond system.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2016

FERROMAGNETISM AND PARTICLE COLLISIONS: APPLICATIONS TO PROTOPLANETARY DISKS AND THE METEORITICAL RECORD

The meteoritical record shows both iron partitioning and tungsten isotopic partitioning between the matrix and chondrules. Tungsten is not abundant enough to have driven its own isotopic partitioning, but if tungsten were correlated with iron then ferromagnetic interaction grains could help explain both observations. We derive a practical parameterization for the increase in particle–particle collision rates caused by mutually attracting particle magnetic dipole moments. While the appropriate magnetic parameters remain uncertain, we show that ambient magnetic fields in protoplanetary disks are expected to be strong enough to magnetize iron metal bearing dust grains sufficiently to drive large increases in their collision rates. Such increased collision rates between iron-metal-rich grains could help preserve primordial iron and W isotopic inhomogeneities, and would help explain why the meteoritical record shows their partitioning in the solar nebula. The importance of magnetic interactions for larger grains whose growth is balanced by fragmentation is less clear and will require future laboratory or numerical studies.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Evaluating the Community Land Model in a pine stand with shading manipulations and 13 CO 2 labeling

Carbon partitioning and flow through ecosystems regulates land surface atmosphere CO 2 exchange and thus is a key, albeit uncertain component of mechanistic models. The Partitioning in Trees and Soil (PiTS) experiment-model project tracked C partitioning through a young Pinus taeda stand following pulse-labeling with 13 CO 2 and two levels of shading. The field component of this project provided process-oriented data that was used to evaluate and improve terrestrial biosphere model simulations of rapid shifts in carbon partitioning and hydrological dynamics under varying environmental conditions. Here we tested the performance of the Community Land Model version 4 (CLM4) in capturing short-term carbon and water dynamics in relation to manipulative shading treatments, and the timing and magnitude of carbon fluxes through various compartments of the ecosystem. To constrain CLM4 to closely simulate pretreatment conditions, we calibrated select model parameters with the pretreatment observational data. Compared to CLM4 simulations with default parameters, CLM4 with calibrated model parameters was better able to simulate pretreatment vegetation carbon pools, light response curves, and other initial states and fluxes of carbon and water. Over a 3-week treatment period, the calibrated CLM4 generally reproduced the impacts of shading on average soil moisture at 15-95 cm depth, transpiration, relative change in stem carbon, and soil CO 2 efflux rate, although some discrepancies in the estimation of magnitudes and temporal evolutions existed. CLM4, however, was not able to track the progression of the 13 CO 2 label from the atmosphere through foliage, phloem, roots or surface soil CO 2 efflux, even when optimized model parameters were used. This model bias arises, in part, from the lack of a short-term non-structural carbohydrate storage pool and progressive timing of within-plant transport, thus indicating a need for future work to improve the allocation routines in CLM4. Overall, these types of detailed evaluations of CLM4, paired with intensive field manipulations, can help to identify model strengths and weaknesses, model uncertainties, and additional observations necessary for future model development.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1973

Cooling histories of lunar rocks based on opaque mineral geothermometers

The application of experimentally derived data on (1) the Zr partitioning between coexisting ilmenite and ulvospinel and (2) the Ti partitioning between coexisting troilite and ilmenite has allowed the discernment of differences in subsolidus cooling histories of lunar rocks - e.g., the Apollo 15 Type I Mare basalts. The rocks which show Zr partitionings reequilibrated to lower temperature (i.e., below 950 C), as a result of slow cooling, also show evidence for subsolidus reduction of ulvospinel to ilmenite + native Fe. It is suggested that the presence of ulvospinel reduction is not evidence a priori that these rocks have undergone more reducing conditions than the other Apollo 15 Mare basalts; it may only indicate that the cooling rates were slower in that subsolidus temperature range (i.e., much less than 900 C) where oxygen fugacity values were favorable for ulvospinel reduction. The rocks with higher temperature Zr partitionings and no ulvospinel reduction may have cooled under the same fugacity conditions but at a faster rate.

Taylor, L. A.↗

NASA NTRS1983

Experimental investigations of trace element fractionation in iron meteorites. II - The influence of sulfur

The partitioning of Ir, Ge, Ga, W, Cr, Au, P, and Ni between solid metal and metallic liquid is investigated as a function of temperature and the S-concentration of the metallic liquid. The partition coefficients for siderophile elements, such as Ir, W, Ga, and Ge, are found to increase by factors of 10-100 as the S-concentration of the metallic liquid increases from 0-30 wt percent. Partition coefficients for other siderophile elements, such as Ni, Au, and P, increase by factors of only 2-3. In contrast, a decrease is seen in the partition coefficients for the more chalcophile element Cr. These experimentally determined coefficients are used in conjunction with a fractional crystallization model to reproduce the geochemical behavior of Ni, P, Au, and Ir during the magmatic evolution of groups IIAB, IIIAB, IVA and IVB iron meteorites. The mean S-concentration for each group increases in the order IVB, IVA, IIIAB, IIAB, which is in accordance with cosmochemical prediction. However, the geochemical behavior of Ge, Ga, W, and Cr cannot be reproduced in an internally consistent way. It is concluded that the magmatic histories of these iron meteorite groups are more complex than has been generally assumed.

Jones, J. H.↗

NASA NTRS1982

Countercurrent distribution of biological cells

Detailed physiochemical studies of dextran/poly(ethylene glycol) (PEG) two phase systems were carried out to characterize and provide understanding of the properties of the systems which determine cell partition and the electrophoretic behavior of phase drops responsible for electric field driven phase separation. A detailed study of the electrostatic and electrokinetic potentials developed in these systems was carried out. The salt partition was examined both in phase systems and with pure polymer solutions via equilibrium dialysis and mechanism of sulfate, chloride and phosphate partition shown to be exclusion by PEG rather than binding by dextran. Salt partition was shown to have a strong effect on the polymer compositions of the phases as well, an effect which produces large changes in the interfacial tension between them. These effects were characterized and the interfacial tension shown to obey a power law with respect to its dependence on the length of the tie line describing the system composition on a phase diagram. The electrostatic potential differences measured via salt bridges were shown to obey thermodynamic predictions. The electrophoretic mobilities measured were utilized to provide a partial test of Levine's incomplete theory of phase drop electrophoresis. The data were consistent with Levine's expression over a limited range of the variables tested.

Brooks, D. E.↗

NASA NTRS1984

Buoyant production and consumption of turbulence kinetic energy in cloud-topped mixed layers

It is pointed out that studies of the entraining planetary boundary layer (PBL) have generally emphasized the role of buoyancy fluxes in driving entrainment. The buoyancy flux is proportional to the rate of conversion of the potential energy of the mean flow into the kinetic energy of the turbulence. It is not unusual for conversion to proceed in both directions simultaneously. This occurs, for instance, in both clear and cloudy convective mixed layers which are capped by inversions. A partitioning of the net conversion into positive parts, generating turbulence kinetic energy (TKE), and negative parts (TKE-consuming), would make it possible to include the positive part in the gross production rate, and closure would be achieved. Three different approaches to partitioning have been proposed. The present investigation is concerned with a comparison of the three partitioning theories. Particular attention is given to the cloud-topped mixed layer because in this case the differences between two partitioning approaches are most apparent.

Randall, D. A.↗

NASA NTRS1986

Multiply scaled constrained nonlinear equation solvers

To improve the numerical stability of nonlinear equation solvers, a partitioned multiply scaled constraint scheme is developed. This scheme enables hierarchical levels of control for nonlinear equation solvers. To complement the procedure, partitioned convergence checks are established along with self-adaptive partitioning schemes. Overall, such procedures greatly enhance the numerical stability of the original solvers. To demonstrate and motivate the development of the scheme, the problem of nonlinear heat conduction is considered. In this context the main emphasis is given to successive substitution-type schemes. To verify the improved numerical characteristics associated with partitioned multiply scaled solvers, results are presented for several benchmark examples.

Padovan, Joe↗

NASA NTRS1986

A distributable APSE

A distributed Ada program library is a key element in a distributed Ada Program Support Environment (APSE). To implement this successfully, the program library universe as defined by the Ada Reference Manual must be broken up into independently manageable pieces. This in turn requires the support of a distributed database system, as well as a mechanism for identifying compilation units, linkable subprograms, and Ada types in a decentralized way, to avoid falling victim to the bottlenecks of a global database and/or global unique-identifier manager. It was found that the ability to decentralize Ada program library activity is a major advantage in the management of large Ada programs. Currently, there are 18 resource-catalog revision sets, each in its own Host Interface (HIF) partition, plus 18 partitions for testing each of these, plus 11 partitions for the top-level compiler/linker/program library manager components. Compiling and other development work can proceed in parallel in each of these partitions, without suffering the performance bottlenecks of global locks or global unique-identifier generation.

Taft, Tucker, S.↗

NASA NTRS1989

Run-time scheduling and execution of loops on message passing machines

Sparse system solvers and general purpose codes for solving partial differential equations are examples of the many types of problems whose irregularity can result in poor performance on distributed memory machines. Often, the data structures used in these problems are very flexible. Crucial details concerning loop dependences are encoded in these structures rather than being explicitly represented in the program. Good methods for parallelizing and partitioning these types of problems require assignment of computations in rather arbitrary ways. Naive implementations of programs on distributed memory machines requiring general loop partitions can be extremely inefficient. Instead, the scheduling mechanism needs to capture the data reference patterns of the loops in order to partition the problem. First, the indices assigned to each processor must be locally numbered. Next, it is necessary to precompute what information is needed by each processor at various points in the computation. The precomputed information is then used to generate an execution template designed to carry out the computation, communication, and partitioning of data, in an optimized manner. The design is presented for a general preprocessor and schedule executer, the structures of which do not vary, even though the details of the computation and of the type of information are problem dependent.

Crowley, Kay↗

NASA NTRS1989

Unconditionally stable concurrent procedures for transient finite-element analysis

A family of algorithms was outlined which would appear to be particularly well-suited for implementation in a parallel environment. This is due to the fact that for any partition of the mesh each subdomain in the partition can be processed over a time step simultaneously and independently of the rest. The method eliminates the need for assembling and factorizing large global arrays while retaining the unconditional stability properties of the algorithms used at the local level. To critically appraise the proposed methodology, two limiting cases were considered: element-by-element mesh partitions, and coarse mesh partitions. It was concluded that while the proposed methodology can be useful in sequential machines, it would appear to be promising as it bears on computation. It should also be emphasized that extensions of the method to nonlinear problems are possible.

Ortiz, Michael↗

NASA NTRS1988

Efficiency of shear induced entrainment in convectively mixed layers

Lidar data of mixed layer height are used to compare the model of process partitioning to that of Eulerian partitioning. It is found that the Eulerian partitioning model more closely follows the data and that the process partitioning model underpredicts the mixed layer depth. The results suggest that shear production and consumption of turbulent kinetic energy at the mixed layer top are local processes.

Boers, Reinout↗

NASA NTRS1990

Run-time scheduling and execution of loops on message passing machines

Saltz, Joel↗