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DOE OSTI2022

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Water balance model (WBM) v.1.0.0: a scalable gridded global hydrologic model with water-tracking functionality

Abstract. This paper describes the University of New Hampshire Water Balance Model, WBM, a process-based gridded global hydrologic model that simulates the land surface components of the global water cycle and includes water extraction for use in agriculture and domestic sectors. The WBM was first published in 1989; here, we describe the first fully open-source WBM version (v.1.0.0). Earlier descriptions of WBM methods provide the foundation for the most recent model version that is detailed here. We present an overview of the model functionality, utility, and evaluation of simulated global river discharge and irrigation water use. This new version adds a novel suite of water source tracking modules that enable the analysis of flow-path histories on water supply. A key feature of WBM v.1.0.0 is the ability to identify the partitioning of sources for each stock or flux within the model. Three different categories of tracking are available: (1) primary inputs of water to the surface of the terrestrial hydrologic cycle (liquid precipitation, snowmelt, glacier melt, and unsustainable groundwater); (2) water that has been extracted for human use and returned to the terrestrial hydrologic system; and (3) runoff originating from user-defined spatial land units. Such component tracking provides a more fully transparent model in that users can identify the underlying mechanisms generating the simulated behavior. We find that WBM v.1.0.0 simulates global river discharge and irrigation water withdrawals well, even with default parameter settings, and for the first time, we are able to show how the simulation arrives at these fluxes by using the novel tracking functions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Accurate assessment of land–atmosphere coupling in climate models requires high-frequency data output

Land–atmosphere (L–A) interactions are important for understanding convective processes, climate feedbacks, the development and perpetuation of droughts, heatwaves, pluvials, and other land-centered climate anomalies. Local L–A coupling (LoCo) metrics capture relevant L–A processes, highlighting the impact of soil and vegetation states on surface flux partitioning and the impact of surface fluxes on boundary layer (BL) growth and development and the entrainment of air above the BL. A primary goal of the Climate Process Team in the Coupling Land and Atmospheric Subgrid Parameterizations (CLASP) project is parameterizing and characterizing the impact of subgrid heterogeneity in global and regional Earth system models (ESMs) to improve the connection between land and atmospheric states and processes. A critical step in achieving that aim is the incorporation of L–A metrics, especially LoCo metrics, into climate model diagnostic process streams. However, because land–atmosphere interactions span timescales of minutes (e.g., turbulent fluxes), hours (e.g., BL growth and decay), days (e.g., soil moisture memory), and seasons (e.g., variability in behavioral regimes between soil moisture and latent heat flux), with multiple processes of interest happening in different geographic regions at different times of year, there is not a single metric that captures all the modes, means, and methods of interaction between the land and the atmosphere. And while monthly means of most of the LoCo-relevant variables are routinely saved from ESM simulations, data storage constraints typically preclude routine archival of the hourly data that would enable the calculation of all LoCo metrics. Here, we outline a reasonable data request that would allow for adequate characterization of sub-daily coupling processes between the land and the atmosphere, preserving enough sub-daily output to describe, analyze, and better understand L–A coupling in modern climate models. A secondary request involves embedding calculations within the models to determine mean properties in and above the BL to further improve characterization of model behavior. Higher-frequency model output will (i) allow for more direct comparison with observational field campaigns on process-relevant timescales, (ii) enable demonstration of inter-model spread in L–A coupling processes, and (iii) aid in targeted identification of sources of deficiencies and opportunities for improvement of the models.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2005

Re-187-Os-187, Pt-190-Os-186 Isotopic and Highly Siderophile Element Systematics of Group IVA Irons

We have recently completed Re-187-Os-187 and Pt-190-Os-186 isotopic and elemental studies of the two largest magmatic iron meteorite groups, IIAB and IIIAB [1]. These studies revealed closed-system behavior of both isotopic systems, but complex trace element behavior for Re, Pt and Os in group IIIAB. Here we examine isotopic and trace elemental systematics of group IVA irons. The IVA irons are not as extensively fractionated as IIAB and IIIAB and their apparently less complex crystallization history may make for more robust interpretation of the relative partitioning behavior of Re, Pt and Os, as well as the other highly siderophile elements (HSE) measured here; Pd, Ru and Ir [e.g. 2]. An additional goal of our continuing research plan for iron meteorites is to assess the possibility of relating certain ungrouped irons with major groups via trace element modeling. Here, the isotopic and trace element systematics of the ungrouped irons Nedagolla and EET 83230 are compared with the IVA irons.

Walker, R. J.↗

DOE OSTI2025

Quantifying Message Aggregation Optimisations for Energy Savings in PGAS Models

Upon breaking past the exascale barrier, HPC systems are facing their greatest challenge yet - a power wall that must be addressed through new methods in both hardware and software. While energy costs are becoming a major issue at all levels, of particular concern is that of the network, as the relative cost of moving data is increasing faster than ever. The partitioned global address space (PGAS) model is critical within certain HPC domains, but is known to suffer from the small message problem, where irregular many-to-many access patterns result in congesting the network with excessive numbers of small messages. To address this, the conveyor aggregation library was developed to defer individual messages and group them for subsequent bulk processing. In this paper, we investigate its impact on energy use related to the network, with a focus on the Slingshot 11 interconnect. We will demonstrate that this strategy is not only highly performant, but also crucial to reducing energy footprints to remain within target power envelopes.

Welch, Aaron [ORNL]↗

DOE OSTI2020

Integrative Circuit-Host Modeling of a Genetic Switch in Varying Environments

Synthetic biology is advancing into a new phase where real-world applications are emphasized. There is hence an urgent need for mathematical modeling that can quantitatively describe the behaviors of genetic devices in natural, fluctuating environments. We utilize an integrative circuit-host modeling framework to examine the dynamics of a genetic switch and its host cell in varying environments. For both steady-state and transient cases, we find increasing nutrient reduces the bistability region of the phase space and eventually drives the switch from bistability to monostability. In response, cellular growth and proteome partitioning experience the same transition. Antibiotic perturbations cause the similar circuit and host responses as nutrient variations. However, one difference is the trend of growth rate, which augments with nutrient but declines with antibiotic levels. The framework provides a mechanistic scheme to account for both the dynamic and static characteristics of the circuit-host system upon environmental perturbations, underscoring the intimacy of gene circuits and their hosts and elucidating the complexity of circuit behaviors arising from environmental variations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Progress Toward Simulating Departure from Nucleate Boiling at High-Pressure Applications with Selected Wall Boiling Closures

Recently, a Eulerian-based two-fluid computational fluid dynamics (CFD) framework with a wall heat flux partitioning approach has been intensively investigated for departure from nucleate boiling (DNB) simulation under the U.S. Department of Energy–funded Consortium for Advanced Simulation of Light Water Reactors (CASL) program. Understanding of the DNB characteristics over a range of pressurized water reactor–like operating conditions and accurate prediction of boiling crisis in the nuclear power system have been grand challenges because of the large impact of DNB on reactor safety and operational economics. The ultimate goal of this task in the CASL program is to introduce a robust multiphase CFD–based DNB modeling framework that is capable of characterizing an entire boiling history in which the wall boiling mode experiences the following through multiple stages of heat transfer mode: (1) single-phase convective heat transfer, (2) nucleate boiling heat transfer, and (3) identification of the departure of nucleate boiling. To validate the CASL boiling model, we have benchmarked simulated DNB over three different flow channel configurations (pipe flow, 5 × 5 fuel bundle with mixing vane tests, and 5 × 5 fuel bundle without mixing vane tests) against experimental measurements, and the validation result with open literature is reported. The DNB detection criteria in the simulation are checked by monitoring the peak wall temperature, wall dryout factor, and net energy balance. In addition to the DNB performance test, some preliminary sensitivity results on closure model selection are reported to address the prediction capability of local void profile against measurements. The boiling simulation tested in this study exhibits a maximum deviation of 24% from the measured DNB value in a high-pressure (i.e., 138 bars) subcooled pipe flow test. The ranges of operating conditions are as follows: 1650 to 2650 kg/m 2 ·s for mass flux and 8.5 to 96 K for subcooled inlet temperature. The deviation is even reduced to 7% when the subcooled temperature is less than 40 K. Besides accuracy, base practice guidelines for DNB detection criteria are tested by monitoring three simulation variables: (1) maximum wall temperature, (2) wall dryout factor (i.e., K-value), and (3) energy balance. Numerical robustness of DNB simulation is largely achieved in most of the validation test except for a few high subcooled test cases.

42 ENGINEERING↗

DOE OSTI2025

Characterization of Li in the Salton Sea Geothermal Field

Abstract The behavior of lithium during geothermal brine and host-rock interactions in the Salton Sea geothermal field is underconstrained. The lithium brine reservoir inventory is between 4 and 18 million metric tons of lithium carbonate equivalent, with an even larger amount present within the reservoir rock mineral phases. Here, we present bulk-rock and brine Li concentration and δ7Li, and in situ Li concentrations of minerals from the California State 2-14 scientific drill core and commercial wells in the Salton Sea geothermal field to identify the mineral hosts of Li and constrain Li behavior during brine-rock interactions. Lithium contents are highest in chlorite (270–580 ppm, ~2,358 m), which encases pyrite, indicating that Li is fixed from the brine into the host rocks during hydrothermal alteration. Lithium abundances in chlorite decrease with depth (70–100 ppm, ~2,882 m), as does whole-rock Li content, whereas whole-rock δ7Li increases (δ7Li = 2.0–4.3‰, ~2,485-m depth; δ7Li = 4.3–7.9‰ from ~2,819 to ~2,882 m). This change in behavior of Li at ~2,500 m suggests temperature dependent partitioning of Li in chlorite; Li becomes more incompatible in chlorite at depths >~2,500 m, corresponding to ~325°C in the reservoir. The brines have δ7Li = 3.7 to 4.7‰ and calculated isotopic fractionation factors between the brine and the host rock agree with a change in Li behavior at ~325°C. Simple closed-system batch modeling does not describe the geothermal system, suggesting open-system behavior of Li within the Salton Sea geothermal field.

Humphreys, J↗

NASA NTRS1994

PCLIPS: Parallel CLIPS

A parallel version of CLIPS 5.1 has been developed to run on Intel Hypercubes. The user interface is the same as that for CLIPS with some added commands to allow for parallel calls. A complete version of CLIPS runs on each node of the hypercube. The system has been instrumented to display the time spent in the match, recognize, and act cycles on each node. Only rule-level parallelism is supported. Parallel commands enable the assertion and retraction of facts to/from remote nodes working memory. Parallel CLIPS was used to implement a knowledge-based command, control, communications, and intelligence (C(sup 3)I) system to demonstrate the fusion of high-level, disparate sources. We discuss the nature of the information fusion problem, our approach, and implementation. Parallel CLIPS has also be used to run several benchmark parallel knowledge bases such as one to set up a cafeteria. Results show from running Parallel CLIPS with parallel knowledge base partitions indicate that significant speed increases, including superlinear in some cases, are possible.

Hall, Lawrence O.↗

DOE OSTI2026

Cave-based chronology of valley incision in the glaciated Northern Carpathians

While glaciers leave a mark on mountain landscapes, the importance of glacial erosion in mountains at a global scale remains insufficiently constrained despite over a century of research aimed at quantifying the rates and magnitudes of such erosion. Measuring rates of landscape change across the Quaternary in repeatedly glaciated mountain landscapes requires the ability to accurately partition the relative role of glacial versus fluvial processes in forming relief; however, the modification of landforms by surface erosion hinders quantification of process rates over the last few million years. This study presents 32 paired 26 Al and 10 Be cosmogenic nuclide burial ages from allochthonous, quartz-bearing sediment deposited within a paleophreatic karst system in the northern Carpathians. These data quantify Pliocene-to-present timing of valley incision and karst system reactivation, as well as erosion rates over time. Post-burial, muon production-correction yields 24 fully resolved ages, six minimum ages, and two unresolvable ages. Burial ages are interpreted to document the tempo of valley incision via phreatic passage formation and reveal that ∼80% of current valley relief (∼700 m) had developed by approximately 1.6 Ma. Paleoerosion rates derived from this dataset suggest little change in the processes generating sediment washed into the karst networks since the Pliocene. These results suggest that river incision dominated relief creation in Carpathian valleys that bear the imprint of glaciation. Our findings suggest the importance of investigating other mid-latitude mountainous regions worldwide to determine if they have similar erosion and topographic histories.

Carpathians↗

NASA NTRS1987

Steady and transient least square solvers for thermal problems

This paper develops a hierarchical least square solution algorithm for highly nonlinear heat transfer problems. The methodology's capability is such that both steady and transient implicit formulations can be handled. This includes problems arising from highly nonlinear heat transfer systems modeled by either finite-element or finite-difference schemes. The overall procedure developed enables localized updating, iteration, and convergence checking as well as constraint application. The localized updating can be performed at a variety of hierarchical levels, i.e., degree of freedom, substructural, material-nonlinear groups, and/or boundary groups. The choice of such partitions can be made via energy partitioning or nonlinearity levels as well as by user selection. Overall, this leads to extremely robust computational characteristics. To demonstrate the methodology, problems are drawn from nonlinear heat conduction. These are used to quantify the robust capabilities of the hierarchical least square scheme.

Padovan, Joe↗

NASA NTRS2003

Experimental Determination of Spinel/Melt, Olivine/Melt, and Pyroxene/Melt Partition Coefficients for Re, Ru, Pd, Au, and Pt

Experimental studies have identified spinels as important hosts phases for many of the highly siderophile elements (HSE). Yet experimental studies involving chromite or Cr-rich spinel have been lacking. Experimental studies of partitioning of HSEs between silicate, oxides and silicate melt are plagued by low solubilities and the presence of small metallic nuggets at oxygen fugacities relevant to magmas, which interfere with analysis of the phases of interest. We have circumvented these problems in two ways: 1) performing experiments at oxidized conditions, which are still relevant to natural systems but in which nuggets are not observed, and 2) analysis of run products with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), allowing a combination of high sensitivity and good spatial resolution.

Righter, K.↗

NASA NTRSDate not supplied

Calcium and Magnesium Distribution Between Sulfide and Silicate Melts: Thermodynamic Modeling and Insights into Mercury's Mantle-Crust Differentiation

Mercury stands out as the terrestrial planet with the lowest degree of oxidation among all planets of our solar system. It is characterized by a high abundance of sulfur, which is expected to replace oxygen in silicate melts. This sulfur enrichment could lead to sulfide saturation in its mantle, potentially resulting in the formation of sulfides rich in calcium and magnesium. Utilizing experimental data from the literature, we constructed a thermodynamic model to explore the partitioning of calcium and magnesium between sulfide and silicate melts. This model aims to improve our comprehension of the chemical equilibria driving the process of mantle-crust differentiation on Mercury. Our models indicate that increased temperature, decreased pressure, and low concentrations of iron, oxygen, and carbon within the sulfide phase, along with low sulfur concentrations in the silicate phase, favor calcium’s partitioning into the sulfide. Additionally, magnesium partitioning into the sulfide melt is favored with decreased pressure, decreased temperature, low concentrations of iron and calcium within the sulfide, and low concentrations of sulfur within the silicate. Our results suggest that up 9.4% and 5.6% Ca and Mg, respectively, can be present in sulfides equilibrated with sulfide-saturated silicate melts during mantle-crust differentiation. Further investigation will focus on the distribution of sulfide phases within the mantle and crust to better constrain Mercury’s internal structure.

Taylor McCombs↗

NASA NTRS2003

Biogeochemistry of fluoride in a plant-solution system

Fluoride (F-) pollutants can harm plants and the animals feeding on them. However, it is largely unknown how complexing and chelating agents affect F bioavailability. Two studies were conducted that measured F- bioavailability and uptake by rice (Oryza sativa L.). In the first study, rice was grown in solution culture (pH 5.0) with 0, 2, or 4 mM F- as KF to compare the interaction of F- with humic acid (HA) and with a conventional chelating agent, N-hydroxyethylenthylenediaminetriacetic acid (HEDTA). In the second study, F was supplied at 0, 0.5, 1.0, and 2.0 mM KF with an additional 2 mM F- treatment containing solution Ca at 2x (2 mM Ca) the level used in the first study, to test the effect added Ca had on F- availability and uptake. Total biomass was greatest with HEDTA and F- < 1 mM. Leaf and stem F concentrations increased exponentially as solution F- increased linearly, with nearly no F partitioning into the seed. Results suggest that F was taken up as HF0 while F- uptake was likely restricted. Additionally, F- competed with HA for Ca, thus preventing the formation of Ca-HA flocculents. The addition of soluble Ca resulted in the precipitation of CaF2 solids on the root surface, as determined by tissue analysis and energy dispersive X-ray spectroscopy.

NASA Discipline Life Support Systems↗

DOE OSTI2021

Data-Driven Multi-agent Deep Reinforcement Learning for Distribution System Decentralized Voltage Control with High Penetration of PVs

This paper proposes a novel model-free/data-driven centralized training and decentralized execution multi-agent deep reinforcement learning (MADRL) framework for distribution system voltage control with high penetration of PVs. The proposed MADRL can coordinate both the real and reactive power control of PVs with existing static var compensators and battery storage systems. Unlike the existing DRL-based voltage control methods, our proposed method does not rely on a system model during both the training and execution stages. This is achieved by developing a new interaction scheme between the surrogate modeling of the original system and the multi-agent soft actor critic (MASAC) MADRL algorithm. In particular, the sparse pseudo-Gaussian process with a few-shots of measurements is utilized to construct the surrogate model of the original environment, i.e., power flow model. This is a data-driven process and no model parameters are needed. Furthermore, the MASAC enabled MADRL allows to achieve better scalability by dividing the original system into different voltage control regions with the aid of real and reactive power sensitivities to voltage, where each region is treated as an agent. This also serves as the foundation for the centralized training and decentralized execution, thus significantly reducing the communication requirements as only local measurements are required for control. Comparative results with other alternatives on the IEEE 123-nodes and 342-nodes systems demonstrate the superiority of the proposed method.

14 SOLAR ENERGY↗

NASA NTRS1990

One-dimensional calculations of a large impact on Uranus

One-dimensional, spherically symmetric hydrodynamic calculations of the effect of the impact of a 1-2 earth mass body on the gaseous envelope of Uranus, characterizing the impact as a partition of energy such that a fraction is deposited directly into the envelope, while the rest heats the core. A sharp transition is found between the cases of nearly-complete retention and dispersal, corresponding to energy-deposition values above or below a critical value. Within a realistic parameter range, the angular momentum of the Uranus system may be explained, together with the retention of a gaseous envelope of about 1 earth mass.

Korycansky, D. G.↗

NASA NTRS1995

Confined-Pyrolysis as an Experimental Method for Hydrothermal Organic Synthesis

A closed pyrolysis system has been developed as a tool for studying the reactions of organic compounds under extreme hydrothermal conditions. Small high pressure stainless steel vessels in which the ratio of sediment or sample to water has been adjusted to eliminate the headspace at peak experimental conditions confines the organic components to the bulk solid matrix and eliminates the partitioning of the organic compounds away from the inorganic components during the experiment. Confined pyrolysis experiments were performed to simulate thermally driven catagenetic changes in sedimentary organic matter using a solids to water ratio of 3.4 to 1. The extent of alteration was measured by monitoring the steroid and triterpenoid biomarkers and polycyclic aromatic hydrocarbon distributions. These pyrolysis experiments duplicated the hydrothermal transformations observed in nature. Molecular probe experiments using alkadienes, alkenes and alkanes in H2O and D2O elucidated the isomerization and hydrogenation reactions of aliphatic and the competing oxidative reactions occurring under hydrothermal conditions. This confined pyrolysis technique is being applied to test experiments on organic synthesis of relevance to chemical evolution for the origin of life.

Leif, Roald N.↗

NASA NTRS1987

Analysis of lateral stability of X-29 drop model using system identification methodology

A 22-percent dynamically scaled replica of the X-29 forward-swept-wing aircraft is currently being flown in radio-controlled drop tests at NASA Langley's Plumtree Test Site. Flight data were recorded from early flights in the test program, which consisted mainly of large amplitude maneuvers over wide angle-of-attack ranges with several uncontrolled wing rock episodes. A system identification study of the recorded data was undertaken to examine the stability and control derivatives which influence the lateral behavior of this vehicle with particular emphasis on the wing rock phenomenon. All major lateral stability derivatives and the damping-in-roll derivative were identified for 5-80 deg angle-of-attack by using a data partitioning methodology and a modified stepwise regression algorithm. No control effectiveness derivatives could be identified from the flights conducted so far.

Raney, David L.↗