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At least 235 records · Page 13

The role of data management in discipline-independent data visualization

The common data format (CDF) is described in terms of its support applications for the database management of visualization systems. The CDF is a self-describing data abstraction technique for the storage and manipulation of multidimensional data that are based on block structures. The discipline-independent approach is designed to manage, manipulate, archive, display, and analyze data, and can be applied to heterogeneous equipment communicating different data structures over networks. An improved CDF version incorporates a hyperplane access allowing random aggregate access to subdimensional blocks within a multidimensional variable. The visualization pipeline is also discussed, which controls the flow of data and permits the visualization of different classes of data representation techniques. The system is found to accommodate a large variety of scientific data structures and large disk-based data sets.

Treinish, Lloyd A.↗

Towards a Comprehensive Computational Simulation System for Turbomachinery

The objective of this work is to develop algorithms associated with a comprehensive computational simulation system for turbomachinery flow fields. This development is accomplished in a modular fashion. These modules includes grid generation, visualization, network, simulation, toolbox, and flow modules. An interactive grid generation module is customized to facilitate the grid generation process associated with complicated turbomachinery configurations. With its user-friendly graphical user interface, the user may interactively manipulate the default settings to obtain a quality grid within a fraction of time that is usually required for building a grid about the same geometry with a general-purpose grid generation code. Non-Uniform Rational B-Spline formulations are utilized in the algorithm to maintain geometry fidelity while redistributing grid points on the solid surfaces. Bezier curve formulation is used to allow interactive construction of inner boundaries. It is also utilized to allow interactive point distribution. Cascade surfaces are transformed from three-dimensional surfaces of revolution into two-dimensional parametric planes for easy manipulation. Such a transformation allows these manipulated plane grids to be mapped to surfaces of revolution by any generatrix definition. A sophisticated visualization module is developed to al-low visualization for both grid and flow solution, steady or unsteady. A network module is built to allow data transferring in the heterogeneous environment. A flow module is integrated into this system, using an existing turbomachinery flow code. A simulation module is developed to combine the network, flow, and visualization module to achieve near real-time flow simulation about turbomachinery geometries. A toolbox module is developed to support the overall task. A batch version of the grid generation module is developed to allow portability and has been extended to allow dynamic grid generation for pitch changing turbomachinery configurations. Various applications with different characteristics are presented to demonstrate the success of this system.

Shih, Ming-Hsin↗

Visualizing novel connections and genetic similarities across diseases using a network-medicine based approach

Understanding the genetic relationships between human disorders could lead to better treatment and prevention strategies, especially for individuals with multiple comorbidities. A common resource for studying genetic-disease relationships is the GWAS Catalog, a large and well curated repository of SNP-trait associations from various studies and populations. Some of these populations are contained within mega-biobanks such as the Million Veteran Program (MVP), which has enabled the genetic classification of several diseases in a large well-characterized and heterogeneous population. Here we aim to provide a network of the genetic relationships among diseases and to demonstrate the utility of quantifying the extent to which a given resource such as MVP has contributed to the discovery of such relations. We use a network-based approach to evaluate shared variants among thousands of traits in the GWAS Catalog repository. Our results indicate many more novel disease relationships that did not exist in early studies and demonstrate that the network can reveal clusters of diseases mechanistically related. Finally, we show novel disease connections that emerge when MVP data is included, highlighting methodology that can be used to indicate the contributions of a given biobank.

59 BASIC BIOLOGICAL SCIENCES↗

Asynchronous-many-task systems: Challenges and opportunities - Scaling an AMR astrophysics code on exascale machines using Kokkos and HPX

Dynamic and adaptive mesh refinement is pivotal in high-resolution, multi-physics, multi-model simulations, necessitating precise physics resolution in localized areas across expansive domains. Today’s supercomputers’ extreme heterogeneity presents a significant challenge for dynamically adaptive codes, highlighting the importance of achieving performance portability at scale. Our research focuses on astrophysical simulations, particularly stellar mergers, to elucidate early universe dynamics. Here, we present Octo-Tiger, leveraging Kokkos, HPX, and SIMD for portable performance at scale in complex, massively parallel adaptive multi-physics simulations. Octo-Tiger supports diverse processors, accelerators, and network backends. Experiments demonstrate exceptional scalability across several heterogeneous supercomputers including Perlmutter, Frontier, and Fugaku, encompassing major GPU architectures and x86, ARM, and RISC-V CPUs. Parallel efficiency of 47.59% (110,080 cores and 6880 hybrid A100 GPUs) on a full-system run on Perlmutter (26% HPCG peak performance) and 51.37% (using 32,768 cores and 2048 MI250X) on Frontier are achieved.

97 MATHEMATICS AND COMPUTING↗

Adaptive Interface-PINNs (AdaI-PINNs) for transient diffusion: Applications to forward and inverse problems in heterogeneous media

We model transient diffusion in heterogeneous materials using a novel physics-informed neural networks framework (PINNs) termed Adaptive interface physics-informed neural networks or AdaI-PINNs (Roy et al. arXiv preprint arXiv:2406.04626, 2024). AdaI-PINNs utilize different activation functions with trainable slopes tailored to each material region within the computational domain, allowing for a fully automated and adaptive PINNs approach to model interface problems with strongly and weakly discontinuous solutions. To enhance its performance in highly heterogeneous transient diffusion systems, we prescribe a suite of robust practices, including appropriate non-dimensionalization of equations, a biased sampling method, Glorot initialization, and the hard enforcement of boundary and initial conditions. Here we evaluate the efficacy of the proposed method on several benchmark forward and inverse problems. Comparative studies on one-dimensional and two-dimensional benchmark problems reveal that the modified AdaI-PINNs outperform its unmodified counterpart, achieving root-mean-square errors that are at least two orders of magnitude better in forward problems. For inverse problems, the maximum errors in the approximated diffusion coefficients by modified AdaI-PINNs are four orders of magnitude better than those of the unmodified version. Additionally, modified AdaI-PINNs demonstrate improved stability in problems with large material mismatches.

42 ENGINEERING↗

Upsampling Monte Carlo Reactor Simulation Tallies in Depleted Sodium-Cooled Fast Reactor Assemblies Using a Convolutional Neural Network

The computational demand of neutron Monte Carlo transport simulations can increase rapidly with the spatial and energy resolution of tallied physical quantities. Convolutional neural networks have been used to increase the resolution of Monte Carlo simulations of light water reactor assemblies while preserving accuracy with negligible additional computational cost. Here, we show that a convolutional neural network can also be used to upsample tally results from Monte Carlo simulations of sodium-cooled fast reactor assemblies, thereby extending the applicability beyond thermal systems. The convolutional neural network model is trained using neutron flux tallies from 300 procedurally generated nuclear reactor assemblies simulated using OpenMC. Validation and test datasets included 16 simulations of procedurally generated assemblies, and a realistic simulation of a European sodium-cooled fast reactor assembly was included in the test dataset. We show the residuals between the high-resolution flux tallies predicted by the neural network and high-resolution Monte Carlo tallies on relative and absolute bases. The network can upsample tallies from simulations of fast reactor assemblies with diverse and heterogeneous materials and geometries by a factor of two in each spatial and energy dimension. The network’s predictions are within the statistical uncertainty of the Monte Carlo tallies in almost all cases. This includes test assemblies for which burnup values and geometric parameters were well outside the ranges of those in assemblies used to train the network.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Heterogeneous Dynamics in Shear Thickening Colloids Revealed by Intrinsic Heterodyne Correlation Spectroscopy

Shear induced frictional networks have been proposed to be responsible for the emergence of discontinuous shear thickening (DST) in complex fluids. However, little experimental evidence exists to support this model directly. Here, in this study, using x-ray photon correlation spectroscopy (XPCS), we show the existence of an intrinsic heterodyne feature during shear cessation, which originates from the relative motion of mobile particles against an aggregated or jammed network induced by shear thickening. Upon removing the shear, the shear stress dissipates rather quickly in a two-step fashion, whereas the heterogeneous particle dynamics persist much longer with the relative velocity decaying slowly with time as 𝑡 −1 . More importantly, both continuous shear thickening (CST) and DST show similar heterodyne features, indicating the intrinsic mechanisms causing shear thickening are similar in nature

Complex fluid↗

ZENN: A thermodynamics-inspired computational framework for heterogeneous data–driven modeling

Traditional entropy-based methods—such as cross-entropy loss in classification problems—have long been essential tools for representing the information uncertainty and physical disorder in data and for developing artificial intelligence algorithms. However, the rapid growth of data across various domains has introduced new challenges, particularly the integration of heterogeneous datasets with intrinsic disparities. To address this, we introduce a zentropy-enhanced neural network (ZENN), extending zentropy theory into the data science domain via intrinsic entropy, enabling more effective learning from heterogeneous data sources. ZENN simultaneously learns both energy and intrinsic entropy components, capturing the underlying structure of multisource data. To support this, we redesign the neural network architecture to better reflect the intrinsic properties and variability inherent in diverse datasets. We demonstrate the effectiveness of ZENN on classification tasks and energy landscape reconstructions, showing its superior generalization capabilities and robustness-particularly in predicting high-order derivatives. In image and text classification tasks, ZENN demonstrates superior generalization by introducing a learnable temperature variable that models latent multisource heterogeneity, allowing it to surpass state-of-the-art models on CIFAR-10/100, BBC News, and AG News. As a practical application in materials science, we employ ZENN to reconstruct the Helmholtz energy landscape of Fe3Pt using data generated from density functional theory and capture key material behaviors, including negative thermal expansion and the critical point in the temperature–pressure space. Overall, this work presents a zentropy-grounded framework for data-driven machine learning, positioning ZENN as a versatile and robust approach for scientific problems involving complex, heterogeneous datasets.

36 MATERIALS SCIENCE↗

Self-Assembled Solute Networks in Crowded Electrolyte Solutions and Nanoconfinement of Charged Redoxmer Molecules

Redoxmers are electrochemically active organic molecules storing charge and energy in electrolyte fluids circulating through redox flow batteries (RFBs). Such molecules typically have solvent-repelling cores and solvent-attracting pendant groups introduced to increase solubility in liquid electrolytes. These two features can facilitate nanoscale aggregation of the redoxmer molecules in crowded solutions. In some cases, this aggregation leads to the emergence of continuous networks of solute molecules in contact, and the solution becomes microscopically heterogeneous. In this study, we used small-angle X-ray scattering (SAXS) and molecular dynamics modeling to demonstrate formation of such networks and examine structural factors controlling this self-assembly. We also show that salt ions become excluded from these solute aggregates into small pockets of electrolytes, where these ions strongly associate. This confinement by exclusion is also likely to occur to charged redoxmer molecules in a “sea” of neutral precursors coexisting in the same solution. Here, we demonstrate that the decay lifetime of the confined charged molecules in such solutions can increase several fold compared to dilute solutions. We attribute this behavior to a “microreactor effect” on reverse reactions of the confined species during their decomposition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High Speed Networking and Large-scale Simulation in Geodynamics

Large-scale numerical simulation has been one of the most important approaches for understanding global geodynamical processes. In this approach, peta-scale floating point operations (pflops) are often required to carry out a single physically-meaningful numerical experiment. For example, to model convective flow in the Earth's core and generation of the geomagnetic field (geodynamo), simulation for one magnetic free-decay time (approximately 15000 years) with a modest resolution of 150 in three spatial dimensions would require approximately 0.2 pflops. If such a numerical model is used to predict geomagnetic secular variation over decades and longer, with e.g. an ensemble Kalman filter assimilation approach, approximately 30 (and perhaps more) independent simulations of similar scales would be needed for one data assimilation analysis. Obviously, such a simulation would require an enormous computing resource that exceeds the capacity of a single facility currently available at our disposal. One solution is to utilize a very fast network (e.g. 10Gb optical networks) and available middleware (e.g. Globus Toolkit) to allocate available but often heterogeneous resources for such large-scale computing efforts. At NASA GSFC, we are experimenting with such an approach by networking several clusters for geomagnetic data assimilation research. We shall present our initial testing results in the meeting.

Kuang, Weijia↗

Using the cFS Command and Data Dictionary (CCDD) to Automate Software Development on Habulous

Final paper is attached. The NASA developed Core Flight System (cFS) is a reusable software architecture that has been used on multiple spaceflight missions. By using this framework, missions are able to reuse code from other missions, as well as leverage deployment onto similar computer architectures (i.e. not "reinvent the wheel" on each new mission). The success in the cFS concept can be seen in the large number of projects using cFS at FSW-2018. The Habulous project is an Earth-based testbed, used for hardware and software that may one day be used on a future space habitat unit, with many participating groups from various NASA centers and aerospace organizations around the country. The distributed nature of the various teams mean that defining (and following) an interface definition is critical on the project. Additionally, since various groups use various types of computer hardware (32/64-bit, big/little endian, Linux/VxWorks/Windows) many additional complications exist in interfacing all the various components into a final integrated system. cFS is used on the majority the flight software (FSW) in running in Habulous. But some subsystems have elected to not use cFS, and use a software bridge (called SBN_lib) to interact with the other cFS nodes in Habulous. In order to most efficiently develop the FSW, a central database is used to define and store each message sent by cFS. A Command and Data Dictionary (CDD) is something nearly universal on spacecraft, but as a team we worked to develop the CDD before the SW development was complete, and not treat it like "as built" documentation. To manage the CDD, the cFS Command and Data Dictionary (CCDD) tool was chosen (available from NASA as open source software). The CCDD tool has successfully been used to automate/autocode a large amount of software used on Habulous, as we are hoping to use it to define even more items in the future (time-triggered Ethernet (TTE) network maps, CPU scheduling). Additionally, Habulous has been exploring the use of cFS on wildly heterogeneous CPUs, and how to coordinate all those various machines using/extending the software bus – network (SBN) application in cFS, as well as TTE to coordinate message passing between various synchronized machines. The major topics to be covered in the presentation are: (1) Updating to the CCSDS_v2 extended headers (and using CPU# as subsystem ID). (2) Managing all the message identification numbers for each cFS message sent/received on any of the various CPUs. (3) Using the CCDD information to automatically generate the C-header files that define the structure for all software bus (SB) commands/telemetry messages. (4) Using the CCDD to automatically generate XML Telemetry and Command Exchange (XTCE) files, which streams display production/integration/testing in a web based display architecture (5) Extending/customizing SBN to pass messages among computers on multiple networks. (6) Using "Protobetter" inside SBN to manage different endian-ness/architectures. (7) Using SBN_lib to allow non-cFS node to communicate with cFS nodes. (8) Developing TTE network and schedule tables for all the various CPUs to use.

Hirsh, Robert L.↗

Accelerated Charged Particle Tracking with Graph Neural Networks on FPGAs

We develop and study FPGA implementations of algorithms for charged particle tracking based on graph neural networks. The two complementary FPGA designs are based on OpenCL, a framework for writing programs that execute across heterogeneous platforms, and hls4ml, a high-level-synthesis-based compiler for neural network to firmware conversion. We evaluate and compare the resource usage, latency, and tracking performance of our implementations based on a benchmark dataset. We find a considerable speedup over CPU-based execution is possible, potentially enabling such algorithms to be used effectively in future computing workflows and the FPGA-based Level-1 trigger at the CERN Large Hadron Collider.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Neural network–based pore flow field prediction in porous media using super resolution

Direct pore-scale simulations of fluid flow through porous media are computationally expensive to perform for realistic systems. Previous works have demonstrated using the geometry of the microstructure of porous media to predict the velocity fields therein based on neural networks. However, such trained neural networks do not perform well for unseen porous media with a large degree of heterogeneity. In this study we propose that incorporating a coarse velocity field in the input of neural networks is an effective way to improve the prediction performance. The coarse velocity field can be simulated with a low computational cost and provides global information to regularize the ill-posedness of the learning problem, which is usually caused by the use of local geometries due to the computational resource constraints. We show that incorporating the coarse-mesh velocity field significantly improves the prediction accuracy of the fine-mesh velocity field by comparison to the prediction that relies on geometric information alone, especially for the porous medium with a large interior vuggy pore space. We also show the flexibility of training the network in using coarse velocity fields with various resolutions. The results suggest that even using coarse velocity field with a very low resolution, the predictions are still enhanced and close to the ground truths. The feasibility of the method is further demonstrated by testing the trained network on real rocks. This study highlights the merits of incorporating a coarse-mesh velocity field into the input for neural networks, which provides global, physics-based information for the model, thereby improving the model's generalization capability.

42 ENGINEERING↗

Supramolecular Support of Cuprophilic Network Bonding in 2-D Copper n -Alkanethiolates

Here, the development of heterogeneous materials, catalysts, and semiconductors is often reliant on precise control of self-assembly and crystal packing. Many new materials are initially synthesized as microcrystalline powders, making them incompatible with typical methods of structure determination, such as single-crystal X-ray diffraction. This resultant lack of structural information has made thorough investigation into the effect of metal substitution on crystal structure in metal-organic chalcogenolates (MOChas) challenging. Here, we use small molecule serial femtosecond crystallography (smSFX) to present the structures of four copper n-alkanethiolates: CuSC4, CuSC5, CuSC6, and CuSC7. Divergent patterns of alkyl chain packing are identified from microcrystalline powders via smSFX. An odd-even effect in crystal packing has been identified and attributed to different orientations of symmetry elements in the even- and odd-numbered chains. This results in minute changes in the azimuthal organization of the even-numbered chains and the network of cuprophilic interactions. Additionally, we present a synthesis of crystalline gold n-alkanethiolates to provide the first comparison between three d 10 coinage metals (Cu, Ag, and Au) and their resultant n-alkanethiolates.

Willson, Maggie C. [Univ. of Connecticut, Storrs, ↗

Proton switching molecular magnetoelectricity

Abstract The convergence of proton conduction and multiferroics is generating a compelling opportunity to achieve strong magnetoelectric coupling and magneto-ionics, offering a versatile platform to realize molecular magnetoelectrics. Here we describe machine learning coupled with additive manufacturing to accelerate the design strategy for hydrogen-bonded multiferroic macromolecules accompanied by strong proton dependence of magnetic properties. The proton switching magnetoelectricity occurs in three-dimensional molecular heterogeneous solids. It consists of a molecular magnet network as proton reservoir to modulate ferroelectric polarization, while molecular ferroelectrics charging proton transfer to reversibly manipulate magnetism. The magnetoelectric coupling induces a reversible 29% magnetization control at ferroelectric phase transition with a broad thermal hysteresis width of 160 K (192 K to 352 K), while a room-temperature reversible magnetic modulation is realized at a low electric field stimulus of 1 kV cm −1 . The findings of electrostatic proton transfer provide a pathway of proton mediated magnetization control in hierarchical molecular multiferroics.

36 MATERIALS SCIENCE↗

Parallelization of Rocket Engine System Software (Press)

The main goal is to assess parallelization requirements for the Rocket Engine Numeric Simulator (RENS) project which, aside from gathering information on liquid-propelled rocket engines and setting forth requirements, involve a large FORTRAN based package at NASA Lewis Research Center and TDK software developed by SUBR/UWF. The ultimate aim is to develop, test, integrate, and suitably deploy a family of software packages on various aspects and facets of rocket engines using liquid-propellants. At present, all project efforts by the funding agency, NASA Lewis Research Center, and the HBCU participants are disseminated over the internet using world wide web home pages. Considering obviously expensive methods of actual field trails, the benefits of software simulators are potentially enormous. When realized, these benefits will be analogous to those provided by numerous CAD/CAM packages and flight-training simulators. According to the overall task assignments, Hampton University's role is to collect all available software, place them in a common format, assess and evaluate, define interfaces, and provide integration. Most importantly, the HU's mission is to see to it that the real-time performance is assured. This involves source code translations, porting, and distribution. The porting will be done in two phases: First, place all software on Cray XMP platform using FORTRAN. After testing and evaluation on the Cray X-MP, the code will be translated to C + + and ported to the parallel nCUBE platform. At present, we are evaluating another option of distributed processing over local area networks using Sun NFS, Ethernet, TCP/IP. Considering the heterogeneous nature of the present software (e.g., first started as an expert system using LISP machines) which now involve FORTRAN code, the effort is expected to be quite challenging.

Cezzar, Ruknet↗

The Jade File System

File systems have long been the most important and most widely used form of shared permanent storage. File systems in traditional time-sharing systems, such as Unix, support a coherent sharing model for multiple users. Distributed file systems implement this sharing model in local area networks. However, most distributed file systems fail to scale from local area networks to an internet. Four characteristics of scalability were recognized: size, wide area, autonomy, and heterogeneity. Owing to size and wide area, techniques such as broadcasting, central control, and central resources, which are widely adopted by local area network file systems, are not adequate for an internet file system. An internet file system must also support the notion of autonomy because an internet is made up by a collection of independent organizations. Finally, heterogeneity is the nature of an internet file system, not only because of its size, but also because of the autonomy of the organizations in an internet. The Jade File System, which provides a uniform way to name and access files in the internet environment, is presented. Jade is a logical system that integrates a heterogeneous collection of existing file systems, where heterogeneous means that the underlying file systems support different file access protocols. Because of autonomy, Jade is designed under the restriction that the underlying file systems may not be modified. In order to avoid the complexity of maintaining an internet-wide, global name space, Jade permits each user to define a private name space. In Jade's design, we pay careful attention to avoiding unnecessary network messages between clients and file servers in order to achieve acceptable performance. Jade's name space supports two novel features: (1) it allows multiple file systems to be mounted under one direction; and (2) it permits one logical name space to mount other logical name spaces. A prototype of Jade was implemented to examine and validate its design. The prototype consists of interfaces to the Unix File System, the Sun Network File System, and the File Transfer Protocol.

Rao, Herman Chung-Hwa↗

A model to assess the Mars Telecommunications Network relay robustness

The relatively long mission durations and compatible radio protocols of current and projected Mars orbiters have enabled the gradual development of a heterogeneous constellation providing proximity communication services for surface assets. The current and forecasted capability of this evolving network has reached the point that designers of future surface missions consider complete dependence on it. Such designers, along with those architecting network requirements, have a need to understand the robustness of projected communication service. A model has been created to identify the robustness of the Mars Network as a function of surface location and time. Due to the decade-plus time horizon considered, the network will evolve, with emerging productive nodes and nodes that cease or fail to contribute. The model is a flexible framework to holistically process node information into measures of capability robustness that can be visualized for maximum understanding. Outputs from JPL's Telecom Orbit Analysis Simulation Tool (TOAST) provide global telecom performance parameters for current and projected orbiters. Probabilistic estimates of orbiter fuel life are derived from orbit keeping burn rates, forecasted maneuver tasking, and anomaly resolution budgets. Orbiter reliability is estimated probabilistically. A flexible scheduling framework accommodates the projected mission queue as well as potential alterations.

Mars Telecommunications Orbiter (MTO)↗