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At least 1,423 records · Page 79

Computer Science Research Needs for Parallel Discrete Event Simulation (PDES)

Historically, scientific computing efforts have demonstrated the clear need for, and effective use of, supercomputing with traditional time-stepped simulations. Nevertheless, there are several areas in the mission spaces of the U.S. Department of Energy and other agencies waiting to tap advanced computing research using a different, discrete event style of modeling, simulation, and analysis. These span a wide spectrum of applications including energy grid resilience, urban planning and policy, transportation science, building technologies, emergency response and planning, environmental impact analysis, computational epidemiology, Internet communications, cyber security, and cyber-physical systems, to name only a few. Even within traditional scientific applications, the role of discrete event modes of execution is increasing in the form of new event-based mathematical solvers such as quantized state integration methods and discrete-continuous hybrid system solvers. Co-design of advanced supercomputing hardware systems is another area that exploits discrete event simulation at its core for effective analyses. Complex systems, entity behaviors and interconnections play a significant role in all these applications, which are mapped to large-scale models with discrete event formulations. To make advancements in all the aforementioned scientific areas, many technical aspects need to be more thoroughly studied and deeply understood in parallel discrete event simulation (PDES). The unique dynamics inherent in a discrete event modeling approach, by their very nature, intersect and influence the entire stack of the computing system, including (a) the unique nature of the instruction sets exercised in PDES workloads without a predominance of high-precision floating point operations, (b) virtual time-constrained multi-threaded execution of many logical processes per processor, (c) extremely variable and difficult to predict network traffic characteristics, (d) interfaces and inter-dependencies with machine learning and artificial intelligence codes at higher software layers, and (e) highly challenging load balancing needs, especially in effectively accounting for accelerated/extremely heterogeneous computing in current and future high-performance computing systems. Efficient and accurate parallel execution of PDES workloads is also dominated by challenges in dealing with their asynchronous concurrency fundamentally present at the model level. Conservative synchronization, optimistic/speculative synchronization, and their hybrid schemes open new questions in fundamental computer science with respect to reversibility of computation and prediction (lookahead) of behaviors inherent within model codes. On the implementation front, there are relatively few scalable, general-purpose parallel discrete event simulators in the world, and even fewer have been studied on emerging hardware platforms. To enable scientific advances using PDES, the research needs in computer science must also be pursued and met in the intersection of the algorithmic and hardware-aware aspects of scalable PDES engines. This report is aimed at capturing a computer science-oriented view of this important area of research in PDES, presenting a sample of important applications with their inherent discrete event technology elements. Needs are outlined in core areas of parallel discrete event research as well as cross-cutting directions in computer science research that positively impact scientific advancements across several important application areas. A selection of priority research opportunities in advanced computing for PDES is identified to serve as reference for key research topics and their order of importance for scientific advancements.

97 MATHEMATICS AND COMPUTING↗

Investigations with methanobacteria and with evolution of the genetic code

Mycoplasma capricolum was found by Osawa et al. to use UGA as the code of tryptophan and to contain 75% A + T in its DNA. This change could have been from evolutionary pressure to replace C + G by A + T. Numerous studies have been reported of evolution of proteins as measured by amino acid replacements that are observed when homologus proteins, such as hemoglobins from various vertebrates, are compared. These replacements result from nucleotide substitutions in amino acid codons in the corresponding genes. Simultaneously, silent nucleotide substitutions take place that can be studied when sequences of the genes are compared. These silent evolutionary changes take place mostly in third positions of codons. Two types of nucleotide substitutions are recognized: pyrimidine-pyrimidine and purine-purine interchanges (transitions) and pyriidine-purine interchanges (transversions). Silent transitions are favored when a corresponding transversion would produce an amino acid replacement. Conversely, silent transversions are favored by probability when transitions and transversions will both be silent. Extensive examples of these situations have been found in protein genes, and it is evident that transversions in silent positions predominate in family boxes in most of the examples studied. In associated research a streptomycete from cow manure was found to produce an extracellular enzyme capable of lysing the pseudomurein-contining methanogen Methanobacterium formicicum.

Jukes, T. H.↗

Program for Automated Real-Time Monitoring

Process-control decisions made by applying rules to process data streams. Expert System Executive computer program demonstrates feasibility of automated real-time monitoring. Using Executives knowledge of system formally coded as set of rules specifying actions taken under various conditions. Program makes inferences about observed data based on rules. Written in C language.

Goodrum, Glenn R.↗

Elevated Temperature Slow Crack Growth of Silicon Nitride Under Dynamic, Static and Cyclic Flexural Loading

The slow crack growth parameters of a hot-pressed silicon nitride were determined at 1200 and 1300 C in air by statically, dynamically and cyclicly loading bend specimens. The fatigue parameters were estimated using the recently developed CARES/Life computer code. Good agreement exists between the flexural results. However, fatigue susceptibility under static uniaxial tensile loading, reported elsewhere, was greater than in flexure. Cyclic flexural loading resulted in the lowest apparent flexural fatigue susceptibility.

Choi, Sung R.↗

Parallel Object-Oriented Computation Applied to a Finite Element Problem

The conventional wisdom in the scientific computing community is that the best way to solve large-scale numerically intensive scientific problems on today's parallel MIMD computers is to use Fortran or C programmed in a data-parallel style using low-level message-passing primitives. This approach inevitably leads to nonportable codes, extensive development time, and restricts parallel programming to the domain of the expert programmer. We believe that these problems are not inherent to parallel computing but are the result of the tools used. We will show that comparable performance can be achieved with little effort if better tools that present higher level abstractions are used.

parallel object-oriented computation scientific pr↗

Scaling Observation Error for Optimal Assimilation of CCI SST Data into a Regional HYCOM EnOI System

South Africa currently possesses no operational ocean forecasting system for the purpose of predicting ocean state variables including temperature,salinity and velocity. Substantial initial efforts towards this goal have been made and resulted in a system using a regional Hybrid Coordinate Ocean Model (HYCOM) along with the Ensemble Optimal Interpolation (EnOI)assimilation scheme. Assimilating only sea surface temperature (SST) observations from the Operational Sea Surface Temperature and Sea Ice Analysis (OSTIA) product into the system resulted in a degraded forecast. Aiming to address this, Climate Change Initiative (CCI) SSTs are assimilated into the system in an effort to improve the forecast skill. Observation errors in the assimilated product are used in the EnOI to determine whether more confidence should be placed in the model or observations in producing the analysis, but overconfidence in observations can shock the model and result in failure. To tweak the impact of the assimilation, a scaling factor is applied in the assimilation code. A scaling factor of 25 was found to produce a favourable result with lowest mean root mean square error (RMSE;1.098°C) between the model and observations over time. Postulating the error to be overconfident, a floor value is introduced in order to set a minimum value for the observation error thereby reducing confidence in the observations. These experiments fared less favourably with a floor value of 0.5 and a scaling factor of 15 producing the best mean RMSE (1.118°C).

Luyt, Hermann↗

Results of the Phenix Dissymmetric Test Benchmark Exercise

In the context of the European H2020 project SESAME, a work package was dedicated to the validation of code coupling for the thermal-hydraulics of pool type reactors. To this end, CEA proposed a benchmark exercise of the so-called dissymmetric test performed at the end of life of the PHENIX reactor. The PHENIX reactor was an experimental reactor operated by CEA in France from 1974 until 2009. The knowledge and data acquired over the lifetime of this reactor are of paramount importance for the development of future sodium-cooled generation IV reactors. At the beginning of this test, the reactor is operated at nominal power (350 MWth) with 3 primary pumps and 4 intermediate heat exchangers. During this test, a pump trip occurs at the secondary side of one of the two loops (one loop provides coolant to two intermediate heat exchangers). The chain reaction is then stopped while the pumps remain operating at nominal speed. Dissymmetric flow patterns are then observed in the cold pool as hot sodium leaves the intermediate heat exchangers that are no longer cooled. The failed secondary pump is then restarted while the rotational speed of the other is reduced. Eventually, a stable homogeneous state is reached. This transient is challenging for both modelers and codes since this exercise tackles an industrial scale reactor featuring complex flows and interactions between different scales. The physical phenomena observed include thermal stratification, flow mixing and buoyancy effects. In order to accurately model these phenomena for a reasonable computational costs, the partners used System Thermal Hydraulics codes coupled with Computational Fluid Dynamics codes and one even included a subchannel code. In this paper, the PHENIX reactor and its behavior during the dissymmetric test are described. Then, a comparison of the different modeling options selected by the partners is offered. Finally, the results are compared to the experimental data and discussed and modelling recommendations are proposed.

code coupling↗

Data for "Which plant traits increase soil carbon sequestration? Empirical evidence from a long-term poplar genetic diversity trial"

This archive contains all data and code used by the following publication: Field, J. L., Sloan, B. P., Craig, M. E., Calloway, P., Ottinger, S. L., Mead, T., Abramoff, R. Z., Venegas, M. P., Chhetri, H. B., Haiby, K., Kalluri, U. C., Muchero, W., Schadt, C. W., & Mayes, M. A. (2025). Which plant traits increase soil carbon sequestration? Empirical evidence from a long-term poplar genetic diversity trial (p. 2025.02.17.638464). bioRxiv. https://doi.org/10.1101/2025.02.17.638464 Our analysis combined several soil and root data sets collected by Oak Ridge National Laboratory (ORNL) researchers/collaborators from the Clatskanie Poplar Common Garden in Clatskanie, OR by from 2009-2024. The raw data data files are located */02-data/01-raw/* which we harmonized using the codes in */01-codes/01-harmonize-clatskanie-data-pub.qmd*. The final processed data set used in the paper is found at */02-data/02-processed/clatskanie-c-fit-data.csv* and its columns are described in the table below.

Sloan, Brandon [ORNL] (ORCID:0000000316304271)↗

Development of the Tensoral Computer Language

The research scientist or engineer wishing to perform large scale simulations or to extract useful information from existing databases is required to have expertise in the details of the particular database, the numerical methods and the computer architecture to be used. This poses a significant practical barrier to the use of simulation data. The goal of this research was to develop a high-level computer language called Tensoral, designed to remove this barrier. The Tensoral language provides a framework in which efficient generic data manipulations can be easily coded and implemented. First of all, Tensoral is general. The fundamental objects in Tensoral represent tensor fields and the operators that act on them. The numerical implementation of these tensors and operators is completely and flexibly programmable. New mathematical constructs and operators can be easily added to the Tensoral system. Tensoral is compatible with existing languages. Tensoral tensor operations co-exist in a natural way with a host language, which may be any sufficiently powerful computer language such as Fortran, C, or Vectoral. Tensoral is very-high-level. Tensor operations in Tensoral typically act on entire databases (i.e., arrays) at one time and may, therefore, correspond to many lines of code in a conventional language. Tensoral is efficient. Tensoral is a compiled language. Database manipulations are simplified optimized and scheduled by the compiler eventually resulting in efficient machine code to implement them.

Ferziger, Joel↗

Developments on two lithium vapor-box linear test-stand experiments

The lithium vapor-box divertor is a possible fusion power exhaust solution.It uses condensation pumping to create a gradient of vapor density in a divertor slot; this should allow a stable detachment front without active feedback.As initial explorations of the concept, two test stands which take the form of three connected cylindrical stainless steel boxes are being developed: one without plasma at PPPL, to test models of lithium evaporation and flow; and one for the linear plasma device Magnum-PSI (at DIFFER in Eindhoven, The Netherlands) to test the ability of a lithium vapor cloud to induce volumetric detachment and redistribute the plasma power.The first experiment uses boxes with diameters of 6 cm, joined by apertures with diameters of 2.2 cm. Up to 1 g of Li is placed in one box, which is heated to up to 600 degrees C. The Li evaporates, then flows to and condenses in the two other, cooler boxes over several minutes. The quantity of Li transported is assessed by weighing the boxes before and after the heating cycle, and is compared to the quantity predicted to flow for the box at its measured temperature using a Direct Simulation Monte Carlo code, SPARTA. With good experimental conditions, the two values agree to within 15%.The experiment on Magnum-PSI is in the conceptual design stage.The design is assessed by simulations using the code B2.5-Eunomia.They show that when the hydrogen-ion plasma beam, with n_e = 4e20 per cubic meter, T_e = 1.5 eV, and r = 1 cm, is passed through a 16 cm long, 12 Pa, 625 degree C Li vapor cloud, the plasma heat flux and pressure on the target are significantly reduced compared to the case without Li.With the Li present, the plasma is cooled by excitation of Li neutrals followed by radiation until it volumetrically recombines, lowering the heat flux from 3.7 MW/m^2 to 0.13 MW/m^2, and the pressure is reduced by 93%, largely by collisions of hydrogen ions with neutral Li.

divertor↗

The MOOSE electromagnetics module

The Multiphysics Object-Oriented Simulation Environment (MOOSE) electromagnetics module has been developed to increase MOOSE physics module capabilities, enabling standalone and coupled computational electromagnetics within the MOOSE multiphysics ecosystem. The module is actively being utilized in the areas of plasma physics and advanced manufacturing, and it currently provides initial demonstrated capability in multi-dimensional, complex-valued electromagnetic wave propagation, electrostatic contact, reflection and transmission, and electromagnetic eigenvalue problems. Two-dimensional wave propagation and one-dimensional wave reflection and transmission are showcased as examples in this work. The modularity, parallelism, and plug-in infrastructure for custom future development is inherited from MOOSE itself, and the module can be used with both MOOSE-based and external codes, giving great flexibility.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Observation of subcritical shocks in a collisional laboratory plasma: scale dependence near the resistive length

We present a study of subcritical shocks in a highly collisional laboratory plasma with a dynamically significant magnetic field. Shocks were produced by placing cylindrical obstacles into the supermagnetosonic ( $M_{{\rm MS}} \sim 1.9$ ) outflow from an inverse wire array z-pinch at the MAGPIE pulsed power facility ( $n_{e} \sim 8.5 \times 10^{17}\,{\rm cm}^{-3}$ , $v \sim 45\,{\rm km}\,{\rm s}^{-1}$ ). We demonstrate the existence of subcritical shocks in this regime and find that secondary stagnation shocks form in the downstream which we infer from interferometry and optical Thomson scattering measurements are hydrodynamic in nature. The subcritical shock width is found to be approximately equal to the resistive diffusion length and we demonstrate the absence of a jump in hydrodynamic parameters. Temperature measurements by collective optical Thomson scattering showed little temperature change across the subcritical shock ( ${<}10\,\%$ of the ion kinetic energy) which is consistent with a balance between adiabatic and Ohmic heating and radiative cooling. We demonstrate the absence of subcritical shocks when the obstacle diameter is less than the resistive diffusion length due to decoupling of the magnetic field from the plasma. These findings are supported by magnetohydrodynamic simulations using the Gorgon and AstroBEAR codes and discrepancies between the simulations and experiment are discussed.

Physics↗

ATLAS-MAP: An Automated Test Station for Gated Electronic Transport Measurements

The diversification of electronic materials in devices provides a strong incentive for methods to rapidly correlate device performance with fabrication decisions. In this work, we present a low-cost automated test station for gated electronic transport measurements of field-effect transistors. Utilizing open-source PyMeasure libraries for transparent instrument control, the “ATLAS-MAP” system serves as a customizable interface between sourcemeters and samples under test and is programmed to conduct transfer curve and van der Pauw methods with static and sweeping gate voltages. Zinc oxide transistors of variable thickness (5, 10, and 20 nm) and channel size (50 μm to 3 mm, of equal length and width) were fabricated to validate the design. Standardization of testing procedures and raw data formatting enabled automated data analysis. A detailed list of parts and code files for the system are provided.

36 MATERIALS SCIENCE↗

Application of machine learning and artificial intelligence to extend EFIT equilibrium reconstruction

Recent progress in the application of machine learning (ML)/artificial intelligence (AI) algorithms to improve the Equilibrium Fitting (EFIT) code equilibrium reconstruction for fusion data analysis applications is presented. A device-independent portable core equilibrium solver capable of computing or reconstructing equilibrium for different tokamaks has been created to facilitate adaptation of ML/AI algorithms. A large EFIT database comprising of DIII-D magnetic, motional Stark effect, and kinetic reconstruction data has been generated for developments of EFIT model-order-reduction (MOR) surrogate models to reconstruct approximate equilibrium solutions. Furthermore, a neural-network MOR surrogate model has been successfully trained and tested using the magnetically reconstructed datasets with encouraging results. Other progress includes developments of a Gaussian process Bayesian framework that can adapt its many hyperparameters to improve processing of experimental input data and a 3D perturbed equilibrium database from toroidal full magnetohydrodynamic linear response modeling using the Magnetohydrodynamic Resistive Spectrum - Feedback (MARS-F) code for developments of 3D-MOR surrogate models.

Gaussian process↗

Fission product yields from the 238 U ( n,f ) reaction at E n = 4.6 MeV

Here, we present cumulative fission product yields from the 238 U (n, f) reaction at an incident energy of 4.6 MeV for fission products with half-lives from less than one second to several hours. We employed direct γ-ray spectroscopy to measure unseparated fission products with a conventional neutron activation analysis and a cyclic activation technique using the RApid Belt-driven Irradiated Target Transfer System (RABITTS). Yields were determined for 78 isotopes and isomers, covering the mass range 84 ≤ A ≤ 148 and the charge range from 33(As) ≤ Z ≤ 58(Ce). Our experimental cumulative yields are compared to the literature and evaluated data at E n ≈0.5 MeV from ENDF/B-VIII.0 and JEFF-3.3 libraries and with theoretical models using the GEF and FREYA codes at E n =4.6 MeV.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗