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At least 559 records · Page 31

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↗

High-fidelity multiphysics load following and accidental transient modeling of microreactors using NEAMS tools: Application of NEAMS codes to perform multiphysics modeling analyses of micro-reactor concepts

The feasibility of modeling microreactors using high-fidelity models with the Nuclear Energy Advanced Modeling and Simulation (NEAMS) tools is investigated in this report. Three overarching questions guided this research: can NEAMS tools readily be applied for high-fidelity multiphysics modeling of different types of transients in microreactor designs; how accurate are the results obtained; and are improvements needed in accuracy or user experience of NEAMS tools, especially considering newly developed capabilities? This work builds upon FY-2022 work, and two microreactor concepts considering heat pipe (HP-MR) and gas-cooled (GC-MR) technologies were further analyzed using high-fidelity multiphysics simulations. The NEAMS tools considered and coupled within the MultiApp environment are Griffin for neutronics, BISON for thermo-mechanics, Sockeye for heat pipe modeling (in HP-MR), SAM for 1D Fluid – 3D solid modeling of coolant channels and system modeling of balance of plant components (in GC-MR), and the SWIFT code for hydrogen redistribution in hydride moderator. The Heat Pipe MicroReactor (HP-MR) concept was further analyzed in FY-2023 to demonstrate the stochastic TRISO failure modeling capability in BISON to check operational limits of the TRISO fuel. A new full-core Gas-Cooled MicroReactor (GC-MR) model was developed based on the initial assembly-model used in Y-2022 and used for steady-state and accidental depressurization transient simulations. Accuracy of the simulations performed was assessed through 1) verification analyses completed on the different physics with code-to-code comparison, and 2) validation of the multiphysics simulations based on modeling of the Kilopower Reactor Using Stirling Technology (KRUSTY) experiment. In FY-2023, the mesh and model of KRUSTY was updated to closely match publicly available data, and the neutronic model was verified and validated against experimental control rod worth measurements. The multiphysics model of KRUSTY was developed and used for steady-state analysis and for modeling reactivity insertion transient. The calculated power increase and stabilization agrees well with experimental data following adjustment in fuel thermal expansion coefficient. As an important component of this project, the ANL team gathered experience with a wide range of NEAMS tools: the MOOSE Mesh System, Griffin, BISON, SWIFT, Sockeye, SAM, Workbench, and the MOOSE MultiApp System, and provided assessment of new capabilities. Noteworthy are the user assessment of the “vapor-only” flow model in Sockeye and development of a multiphysics startup transient in HP-MR unit cell for use as tutorial in Sockeye. The full-core GC-MR model was used for assessment of SAM for balance of plant modeling and for demonstrating the SWIFT code capability for hydrogen redistribution modeling in multiphysics transient analyses. In this process, several bugs/issues were identified and reported to developers. Finally, the assembly GC-MR model developed in FY-2022 coupling Griffin, BISON and SAM through flow blockage and rod ejection transients was published to the National Reactor Innovation Center (NRIC) Virtual Test Bed (VTB). The Heat Pipe MicroReactor (HP-MR) concept high-fidelity multiphysics coupling of Griffin/BISON/Sockeye in load-following and heat pipe failure transients was also published on the VTB. Those submissions are enabling thorough review of these models as well as wide distribution to industry, regulator, and university users. In this analysis, several new research questions were uncovered, and follow-up analyses are recommended to further improve some models, consider additional transients, and continue development of VTB models.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

IDAES-PSE 2.7.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.7.0 Release Highlights New features: AutoScaler and CustomScalerBase classes: Such tools are the core of the new scaling framework being implemented in IDAES. Wider adoption of scaling tools among users will result in quicker and more robust model solutions. Scaler for equilibrium reactor and saponification properties: These scaler models are examples to follow for how to use the new scaling tools. ONNX Surrogate support from Optimization & Machine Learning Toolkit (OMLT): ONNX is an open standard format to save and load ML/AI models that is widely supported by all major frameworks. This capability makes it easier for IDAES users to create surrogate models and use them without having to support each framework individually. 1D Membrane Model for CO2 Capture and Utilization: Supports ongoing efforts for modeling and optimizing polymer membrane processes for CO2 capture and conversion into formic acid. StreamScaler unit model: Unrelated to the CustomScalerBase, this unit model allows a stream’s extensive variables to be scaled by a fixed factor. This allows streams being processed by multiple units in parallel to be scaled down to unit scale and scaled back up to process scale. Bug fixes or improvements: Scaling, EoS, Diagnostics tool, Modular Properties, tests & documentation Deprecations: Old Cubic EoS

AS↗

NASA/DOD earth orbit shuttle traffic models based on side by side loading of payloads

An analysis of the spacecraft configurations and space missions for the Earth Orbit Shuttle traffic model based on side-by-side loading of payloads is presented. The reusable tugs to be employed for the mission are examined. The space missions are described with respect to the following: (1) number of Earth Orbit Shuttle flights by inclination, (2) total payloads to orbit, (3) energy states required, and (4) characteristics of reusable tug.

Kincade, R. E.↗

Sensitivity analysis of numerical modeling input parameters on floating offshore wind turbine loads

Abstract. Floating wind turbines must withstand a unique and challenging set of loads from the wind and ocean environment. To de-risk development, accurate predictions of these loads are necessary. Uncertainty in modeling predictions leads to larger required safety factors, increasing project costs and the levelized cost of energy. Complex aero-hydro-elastic modeling tools use many input parameters to represent the wind, waves, current, aerodynamic loads, hydrodynamic loads, and structural properties. It is helpful to understand which of these parameters ultimately drives a design. In this work, an ultimate and fatigue-proxy load sensitivity analysis was performed with 35 different input parameters, using an elementary effects approach to identify the most influential parameters for a case study involving the National Renewable Energy Laboratory (NREL) 5 MW baseline wind turbine atop the OC4-DeepCwind semisubmersible during normal operation. The importance of each parameter was evaluated using 14 response quantities of interest across three operational wind speed conditions. The study concludes that turbulent wind velocity standard deviation is the parameter with the strongest sensitivity; this value is important not just for turbine loads, but also for the global system response. The system center of mass in the wind direction is found to have the highest impact on the system rotation and tower loads. The current velocity is found to be the most dominating parameter for the system global motion and consequently the mooring loads. All tested wind turbulence parameters in addition to the standard deviation are also found to be influential. Wave characteristics are influential for some fatigue-proxy loading but do not significantly impact the extreme ultimate loads in these operational load cases. The required number of random seeds for stochastic environmental conditions is considered to ensure that the sensitivities are due to the input parameters and not due to the seed. The required number of analysis points in the parameter space is identified so that the conclusions represent a global sensitivity. The results are specific to the platform, turbine, and choice of parameter ranges, but the demonstrated approach can be applied widely to guide focus in parameter uncertainty.

17 WIND ENERGY↗

Modeling Exhaust-Generated Aerodynamic Pressure Loads on Airfield Matting Repair Systems

Airfield matting systems are commonly used for rapid repair of damaged runways to facilitate continuity of critical operations. Under normal service conditions, matting repair systems are subject not only to wheel loads exerted by airfield traffic but also to aerodynamic pressure loads resulting from high-speed, turbulent exhaust plumes produced by jets during taxi and take-off. Matting systems employed by the U.S. Air Force have been tested with respect to wheel loads, but probabilities of failure because of pressure loads produced by jet exhaust have not yet been established. This study presents a numerical approach for preliminary estimation of worst-case matting anchor forces resulting from exhaust-generated pressure loads. Using a two-dimensional computational fluid dynamics model, system behavior is evaluated by means of a parametric study of six system variables, of which the most significant are: (1) distance between engine and matting, (2) depth of cavity openings at matting edges, and (3) engine exhaust velocity. The results demonstrate that matting systems are likely to experience net uplift in typical service scenarios, driven by the combined effects of flow separation and cavity pressurization. Worst-case anchor pull-out forces, computed according to a tributary-area approach, are estimated to fall in the range of 130 lb (581 N) to 979 lb (4,350 N), depending on assumed load-sharing behavior among anchors and the size of the repair site. Field testing of instrumented matting systems during jet taxi and take-off sequences is recommended as the best next step toward understanding system behavior.

Engineering↗

A title-gap flow model for use in aerodynamic loads assessment of space shuttle thermal protection system: Parallel gap faces

The problem of predicting aerodynamic loads on the insulating tiles of the space shuttle thermal protection system (TPS) is discussed and seen to require a method for predicting pressure and mass flux in the gaps between tiles. A mathematical model of the tile-gap flow is developed, based upon a slow viscous (Stokes) flow analysis, and is verified against experimental data. The tile-gap pressure field is derived from a solution of the two-dimensional Laplace equation; the mass-flux vector is then calculated from the pressure gradient. The means for incorporating this model into a lumped-parameter network analogy for porous-media flow is given. The means for incorporating this model into a lumped-parameter network analogy for porous-media flow is given. The flow model shows tile-gap mass flux to be very sensitive to the gap width indicating a need for coupling the TPS flow and tile displacement calculation. Analytical and experimental work to improve TPS flow predictions and a possible shuttle TPS hardware modification are recommended.

Dwoyer, D. L.↗

Predicting ductility of Mg/SiCp nanocomposite under multiaxial loading conditions based on unit cell modeling

This article presents an investigation on the ductility of Mg/SiCp under nine different multiaxial loading conditions based on a unit cell (or called representative volumetric element, RVE) finite element model. The constitutive relationship of magnesium matrix is characterized by a model combined Lode angle dependent plasticity model with the CPB06 plasticity model, which is able to describe the tension-compression asymmetry in magnesium matrix. The debonding of the matrix-particle interface and matrix fracture are considered by the modified Mohr-Coulomb (MMC) fracture model. Simulation results show that the interface debonding and subsequent matrix fracture are responsible for the ductility and fracture of nanocomposite. The computational results with parametric studies are compared and well correlated with experimental data, and it finally gives a stress-based full fracture locus of Mg/SiCp nanocomposite.

42 ENGINEERING↗

Reconfigurable Real-Time Power Grid Emulator for Systems With High Penetration of Renewables

Novel power system control and new utility devices need to be tested before their actual deployment to the power grid. To assist with such a testing need, real-time digital emulators such as RTDS and Opal-RT can be used to connect to the physical world and form a hardware in the loop (HIL) emulation. However, due to the limitations of today's computational resources, the accuracy and fidelity suffer from different levels of model reductions in purely digital simulations. CURENT has developed a reconfigurable electric grid hardware testbed (HTB) to overcome the limitations of digital emulators. The HTB has been used to develop measurement, control, modeling, and actuation techniques for a national grid with a high penetration of renewables. The power electronic-based system includes emulators for synchronous generators; photovoltaics with grid-interfacing inverter; wind turbines; induction motor loads, ZIP loads, power electronic loads; batteries; ac and dc transmission lines; short circuit faults and grid relay protection; and a multiterminal HVDC overlay including power electronics interfaces. The system contains real elements of power flow, measurement, communication, protection, and control that mimic what would be seen in an actual electric grid. This paper presents an overview of the HTB and several scenarios that have been run to determine control and actions needed for the future power grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Structural analysis model validation using modal test data

The design of a structure which can survive a prescribed dynamic environment is generally based on the use of an analytical model of the structure. The modal test is employed to verify the analytical model. This paper is concerned with the involved validation process, taking into account modal test results from realistic complex spacecraft structural systems as examples to demonstrate the proposed validation procedure. Attention is given to a load analysis model definition, a pretest analysis and test/analysis model, and the correlation parameters. Coordinate transformation is considered along with mode identification, frequency orthogonality, effective mass, mode shape, local kinetic energy, modal force, strain energy, and modal forces by acceleration measurements. Two examples are used to illustrate the procedure.

Chen, J.-C.↗

Simulator of Space Communication Networks

Multimission Advanced Communications Hybrid Environment for Test and Evaluation (MACHETE) is a suite of software tools that simulates the behaviors of communication networks to be used in space exploration, and predict the performance of established and emerging space communication protocols and services. MACHETE consists of four general software systems: (1) a system for kinematic modeling of planetary and spacecraft motions; (2) a system for characterizing the engineering impact on the bandwidth and reliability of deep-space and in-situ communication links; (3) a system for generating traffic loads and modeling of protocol behaviors and state machines; and (4) a system of user-interface for performance metric visualizations. The kinematic-modeling system makes it possible to characterize space link connectivity effects, including occultations and signal losses arising from dynamic slant-range changes and antenna radiation patterns. The link-engineering system also accounts for antenna radiation patterns and other phenomena, including modulations, data rates, coding, noise, and multipath fading. The protocol system utilizes information from the kinematic-modeling and link-engineering systems to simulate operational scenarios of space missions and evaluate overall network performance. In addition, a Communications Effect Server (CES) interface for MACHETE has been developed to facilitate hybrid simulation of space communication networks with actual flight/ground software/hardware embedded in the overall system.

Clare, Loren↗

A Study of Failure in Small Pressurized Cylindrical Shells Containing a Crack

The deformation in the vicinity of axial cracks in thin pressurized cylinders is examined using small experimental The deformation in the vicinity of axial cracks in thin pressurized cylinders is examined using small experimental models. The loading applied was either symmetric or unsymmetric about the crack plane, the latter being caused by structural constraints such as stringers. The objective was two fold - one, to provide the experimental results which will allow computer modeling techniques to be evaluated for deformations that are significantly different from that experienced by flat plates, and the other to examine the deformations and conditions associated with the onset of crack kinking which often precedes crack curving. The stresses which control crack growth in a cylindrical geometry depend on conditions introduced by the axial bulging, which is an integral part of this type of failure. For the symmetric geometry, both the hoop and radial strain just ahead off the crack, r = a, were measured and these results compared with those obtained from a variety of structural analysis codes, in particular STAGS [1], ABAQUS and ANSYS. In addition to these measurements, the pressures at the onset of stable and unstable crack growth were obtained and the corresponding crack deformations measured as the pressures were increased to failure. For the unsymmetric cases, measurements were taken of the crack kinking angle, and the displacements in the vicinity of the crack. In general, the strains ahead of the crack showed good agreement between the three computer codes and between the codes and the experiments. In the case of crack behavior, it was determined that modeling stable tearing with a crack-tip opening displacement fracture criterion could be successfully combined with the finite-element analysis techniques as used in structural analysis codes. The analytic results obtained in this study were very compatible with the experimental observations of crack growth. Measured crack kinking angles also showed good agreement with theories based on the maximum principle stress criterion.

Barwell, Craig A.↗

The Sensitivity of Arctic Ozone Loss to Polar Stratospheric Cloud Volume and Chlorine and Bromine Loading in a Chemistry and Transport Model

The sensitivity of Arctic ozone loss to polar stratospheric cloud volume (V(sub PSC)) and chlorine and bromine loading is explored using chemistry and transport models (CTMs). A simulation using multi-decadal output from a general circulation model (GCM) in the Goddard Space Flight Center (GSFC) CTM complements one recycling a single year s GCM output in the Global Modeling Initiative (GMI) CTM. Winter polar ozone loss in the GSFC CTM depends on equivalent effective stratospheric chlorine (EESC) and polar vortex characteristics (temperatures, descent, isolation, polar stratospheric cloud amount). Polar ozone loss in the GMI CTM depends only on changes in EESC as the dynamics repeat annually. The GSFC CTM simulation reproduces a linear relationship between ozone loss and Vpsc derived from observations for 1992 - 2003 which holds for EESC within approx.85% of its maximum (approx.1990 - 2020). The GMI simulation shows that ozone loss varies linearly with EESC for constant, high V(sub PSC).

Douglass, A. R.↗

NASA/DOD earth orbit shuttle traffic models based on end to end loading of payloads

An analysis of the spacecraft configurations and space missions for the Earth Orbit Shuttle traffic model based on an end-to-end loading of payloads is presented. Two possible reusable tugs are considered. The space missions are described with respect to the following: (1) number of earth orbit shuttle flights by inclination, (2) total payloads to orbit, (3) energy stages required, and (4) characteristics of reusable tug.

Kincade, R. E.↗

RSRA sixth scale wind tunnel test

The sixth scale model of the Sikorsky/NASA/Army rotor systems research aircraft was tested in an 18-foot section of a large subsonic wind tunnel for the purpose of obtaining basic data in the areas of performance, stability, and body surface loads. The model was mounted in the tunnel on the struts arranged in tandem. Basic testing was limited to forward flight with angles of yaw from -20 to +20 degrees and angles of attack from -20 to +25 degrees. Tunnel test speeds were varied up to 172 knots (q = 96 psf). Test data were monitored through a high speed static data acquisition system, linked to a PDP-6 computer. This system provided immediate records of angle of attack, angle of yaw, six component force and moment data, and static and total pressure information. The wind tunnel model was constructed of aluminum structural members with aluminum, fiberglass, and wood skins. Tabulated force and moment data, flow visualization photographs, tabulated surface pressure data are presented for the basic helicopter and compound configurations. Limited discussions of the results of the test are included.

Flemming, R.↗

Agro-IBIS/THMB Modeled Yield, Nitrogen Loss, and Profitability Maps for the Raccoon River Basin, Iowa, USA

This data was used to assess the potential for improving water quality in this watershed when integrating miscanthus, a bioenergy perennial grass, on to areas of low profit under current corn-soybean management and areas of high nitrogen leaching under both current and future climate conditions. This dataset includes all observations (yield, streamflow, nitrogen loads) and model simulation data used from Dr. Kelsie Ferin’s (former PhD student with Dr. Andy VanLoocke, ISU Dept. of Agronomy) dissertation and publication in Global Change Biology – Bioenergy (DOI: 10.1111/gcbb.13078). Modeled output included in this dataset includes corn, soybean, and miscanthus yields, nitrogen leaching rates, net mineralization rates, land use cover fractions with and without the inclusion of miscanthus, profitability maps, additional soil property maps, and simulated streamflow and nitrogen loads near the outlet of the Raccoon River Basin (Van Meter, Iowa) for both historical and future climate conditions. This dataset includes a mixture of netCDF, .tiff, .csv, and .xlsx files. See README.pdf for more information.

Ferin, Kelsie↗