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At least 685 records · Page 38

Performance analysis of a large-grain dataflow scheduling paradigm

A paradigm for scheduling computations on a network of multiprocessors using large-grain data flow scheduling at run time is described and analyzed. The computations to be scheduled must follow a static flow graph, while the schedule itself will be dynamic (i.e., determined at run time). Many applications characterized by static flow exist, and they include real-time control and digital signal processing. With the advent of computer-aided software engineering (CASE) tools for capturing software designs in dataflow-like structures, macro-dataflow scheduling becomes increasingly attractive, if not necessary. For parallel implementations, using the macro-dataflow method allows the scheduling to be insulated from the application designer and enables the maximum utilization of available resources. Further, by allowing multitasking, processor utilizations can approach 100 percent while they maintain maximum speedup. Extensive simulation studies are performed on 4-, 8-, and 16-processor architectures that reflect the effects of communication delays, scheduling delays, algorithm class, and multitasking on performance and speedup gains.

Young, Steven D.↗

NuGraph2 with explainability: post-hoc explanations for geometric neural network predictions

With the growing popularity of artificial intelligence (AI) used for scientific applications, the ability of attribute a result to a reasoning process from the network is in high demand for robust scientific generalizations to hold. In this work we aim to motivate the need for and demonstrate the use of post-hoc explainability methods when applied to AI methods used in scientific applications. To this end, we introduce explainability add-ons to the existing graph neural network (GNN) for neutrino tagging, NuGraph2. The explanations take the form of a suite of techniques examining the output of the network (node classifications) and the edge connections between them, and probing of the latent space using novel general-purpose tools applied to this network. We show how none of these methods are singularly sufficient to show network ‘understanding’, but together can give insights into the processes used in classification. While these methods are tested on the NuGraph2 application, they can be applied to a broad range of networks, not limited to GNNs. The code for this work is publicly available on GitHub at https://github.com/voetberg/XNuGraph.

Voetberg, Margaret [Fermilab] (ORCID:0009000527154↗

Theory of magnetic field line random walk in noisy reduced magnetohydrodynamic turbulence

When a magnetic field consists of a mean part and fluctuations, the stochastic wandering of its field lines is often treated as a diffusive process. Under suitable conditions, a stable value is found for the mean square transverse displacement per unit parallel displacement relative to the mean field. Here, we compute the associated field line diffusion coefficient for a highly anisotropic 'noisy' reduced magnetohydrodynamic model of the magnetic field, which is useful in describing low frequency turbulence in the presence of a strong applied DC mean magnetic field, as may be found, for example, in the solar corona, or in certain laboratory devices. Our approach is nonperturbative, based on Corrsin's independence hypothesis, and makes use of recent advances in understanding factors that control decorrelation over a range of parameters described by the Kubo number. Both Bohm and quasilinear regimes are identified.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Neural Networks and Graph Algorithms with Next-Generation Processors

The use of graphical processors for distributed computation revolutionized the field of high performance scientific computing. As the Moore's Law era of computing draws to a close, the development of non-Von Neumann systems: neuromorphic processing units, and quantum annealers; again are redefining new territory for computational methods. While these technologies are still in their nascent stages, we discuss their potential to advance computing in two domains: machine learning, and solving constraint satisfaction problems. Each of these processors utilize fundamentally different theoretical models of computation. This raises questions about how to best use them in the design and implementation of applications. While many processors are being developed with a specific domain target, the ubiquity of spin-glass models and neural networks provides an avenue for multi-functional applications. This provides hints at the future infrastructure needed to integrate many next-generation processing units into conventional high-performance computing systems.

Hamilton, Kathleen↗

Do graph neural networks learn traditional jet substructure?

At the CERN LHC, the task of jet tagging, whose goal is to infer the origin of a jet given a set of final-state particles, is dominated by machine learning methods. Graph neural networks have been used to address this task by treating jets as point clouds with underlying, learnable, edge connections between the particles inside. We explore the decision-making process for one such state-of-the-art network, ParticleNet, by looking for relevant edge connections identified using the layerwise-relevance propagation technique. As the model is trained, we observe changes in the distribution of relevant edges connecting different intermediate clusters of particles, known as subjets. The resulting distribution of subjet connections is different for signal jets originating from top quarks, whose subjets typically correspond to its three decay products, and background jets originating from lighter quarks and gluons. This behavior indicates that the model is using traditional jet substructure observables, such as the number of prongs -- energetic particle clusters -- within a jet, when identifying jets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

INL Senior Project

What did my team set out to accomplish:? Can I put a custom Machine Learning Model on FPGA?? Can I analyze network traffic in real time?? Can a QSFP port be used with an FPGA?? Does a visual representation of the latent space enhance our understanding of network traffic?? What is QSFP QSFP (Quad Small Form-Factor Pluggable)? QSFP supports transfer speeds generally up to 100Gb/s? Runs 4 parallel lines running up to 28 Gb/s? Why the latent space is important to our project ?Latent space is the compressed mapping of data points in a non-linear fashion? Create an understanding of the relationship of data collected? Can represent that relationship of a single network packet in 3 points (X, Y, Z) Project Outline FPGA? Custom Xilinx Petalinux Image for the operating system? Python program to collect packets and run them through the DPU (Data Processing Unit)? The program then sends the information over a socket to a computer? Display Program? Python Program that collects the information sent from the FPGA and display it in a graph

99 GENERAL AND MISCELLANEOUS↗

Enhancing ACPF Analysis: Integrating Newton-Raphson Method with Gradient Descent and Computational Graphs

This paper presents a new method for enhancing Alternating Current Power Flow (ACPF) analysis. The method integrates the Newton-Raphson (NR) method with Enhanced-Gradient Descent (GD) and computational graphs. The integration of renewable energy sources in power systems introduces variability and unpredictability, and this method addresses these challenges. It leverages the robustness of NR for accurate approximations and the flexibility of GD for handling variable conditions, all without requiring Jacobian matrix inversion. Furthermore, computational graphs provide a structured and visual framework that simplifies and systematizes the application of these methods. The goal of this fusion is to overcome the limitations of traditional ACPF methods and improve the resilience, adaptability, and efficiency of modern power grid analyses. We validate the effectiveness of our advanced algorithm through comprehensive testing on established IEEE benchmark systems. Furthermore, our findings demonstrate that our approach not only speeds up the convergence process but also ensures consistent performance across diverse system states, representing a significant advancement in power flow computation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Classification of dynamical Lie algebras generated by spin interactions on undirected graphs

Dynamical Lie algebras (DLAs) are a versatile tool for various topics that span from the expressibility-trainability of variational quantum algorithms (VQAs), to simulation of many body Hamiltonians. Quantum gates and most of the Hamiltonians of interest consist of local interactions; therefore, the analysis of all possible DLAs generated by 1- and 2-local operators is crucial for quantum simulation and VQAs on current hardware. Previously in [R. Wiersema et al ., npj Quantum Inf. 10 , 110 (2024)], we analyzed the DLAs on linear, circular and all-to-all topologies, and obtained results about their dimensions and algebraic structure. Here, in this work, we extend our analysis into any possible hardware topology and provide a classification of all DLAs generated by Pauli strings on any undirected interaction graph. Our results indicate that the DLAs depend solely on whether the connectivity or interaction graph is bipartite or not. In addition, we find that the non-trivial polynomially scaling DLAs appear only on 1D line or circle topologies, and all other DLAs have dimensions scaling exponentially with the system size. Together with the current VQA literature, our results imply that either the majority of VQAs are non-trainable, or we are yet to understand the role of DLAs on the trainability of VQAs.

Algebraic structures↗

STOCHASTIC MODEL OF THE SPIN DISTRIBUTION OF DARK MATTER HALOS

We employ a stochastic approach to probing the origin of the log-normal distributions of halo spin in N-body simulations. After analyzing spin evolution in halo merging trees, it was found that a spin change can be characterized by a stochastic random walk of angular momentum. Also, spin distributions generated by random walks are fairly consistent with those directly obtained from N-body simulations. We derived a stochastic differential equation from a widely used spin definition and measured the probability distributions of the derived angular momentum change from a massive set of halo merging trees. The roles of major merging and accretion are also statistically analyzed in evolving spin distributions. Several factors (local environment, halo mass, merging mass ratio, and redshift) are found to influence the angular momentum change. The spin distributions generated in the mean-field or void regions tend to shift slightly to a higher spin value compared with simulated spin distributions, which seems to be caused by the correlated random walks. We verified the assumption of randomness in the angular momentum change observed in the N-body simulation and detected several degrees of correlation between walks, which may provide a clue for the discrepancies between the simulated and generated spin distributions in the voids. However, the generated spin distributions in the group and cluster regions successfully match the simulated spin distribution. We also demonstrated that the log-normality of the spin distribution is a natural consequence of the stochastic differential equation of the halo spin, which is well described by the Geometric Brownian Motion model.

79 ASTRONOMY AND ASTROPHYSICS↗

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores

Background: There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. Results: This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. Conclusions: In this paper, we presented a highly scalable and efficient genome assembly software, SWAPAssembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler

59 BASIC BIOLOGICAL SCIENCES↗

Organic matter in carbonaceous chondrites, planetary satellites, asteroids and comets

A detailed review is given of the organic compounds found in carbonaceous chondrite meteorites, especially the Murchison meteorite, and detected spectroscopically in other solar-system objects. The chemical processes by which the organic compounds could have formed in the early solar system and the conditions required for these processes are discussed, taking into account the possible alteration of the compounds during the lifetime of the meteoroid. Also considered are the implications for prebiotic evolution and the origin of life. Diagrams, graphs, and tables of numerical data are provided.

Cronin, John R.↗

Application of Modular Modeling System to Predict Evaporation, Infiltration, Air Temperature, and Soil Moisture

Models are used for numerous application including hydrology. The Modular Modeling System (MMS) is one of the few that can simulate a hydrology process. MMS was tested and used to compare infiltration, soil moisture, daily temperature, and potential and actual evaporation for the Elinsboro sandy loam soil and the Mattapex silty loam soil in the Microwave Radiometer Experiment of Soil Moisture Sensing at Beltsville Agriculture Research Test Site in Maryland. An input file for each location was created to nut the model. Graphs were plotted, and it was observed that the model gave a good representation for evaporation for both plots. In comparing the two plots, it was noted that infiltration and soil moisture tend to peak around the same time, temperature peaks in July and August and the peak evaporation was observed on September 15 and July 4 for the Elinsboro Mattapex plot respectively. MMS can be used successfully to predict hydrological processes as long as the proper input parameters are available.

Boggs, Johnny↗

Molecular Hypernetworks for Exploration of Multi-Dimensional Metabolomics Data (Chyper)

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and help address the challenge of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used, for example, in the Global Natural Products Social Molecular Networking platform, are an increasingly popular computational strategy for exploring and visualizing molecular relationships and improving annotation. MNs use graph representations to show the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated to a single molecular identity. However, more advanced methods may better represent the complexity present in samples. Our work aims to increase confidence in annotation propagation by extending molecular network methods to include “molecular hypernetworks” (MHNs), able to natively represent multiway relationships among observations supporting both human and analytical processing. In this paper we first introduce MHNs illustrated with simple examples, and demonstrate how to build them from liquid chromatography- and ion mobility spectrometry- separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

59 BASIC BIOLOGICAL SCIENCES↗

CORE-BFS: Communication-Optimized REctangular-partitioned BFS Achieving 160.845 TeraTEPS on Frontier Supercomputer

Distributed Breadth-First Search (BFS) is fundamental to many large-scale graph applications, but its performance on parallel systems is often limited by high communication overhead. This paper presents CORE-BFS, an extremely scalable GPU-based BFS implementation that introduces a unique rectangular 2D partitioning-based design for Frontier supercomputer. To further improve performance, we propose four key optimizations: (1) Rectangular 2D-partition specific data formats that use two compressed row and one compressed column status array bitmaps combined with a Double Compressed Sparse Row (DCSR) format per partition, reducing memory footprint and inter-rank traffic; (2) Adaptive frontier & communication strategy that unifies top-down and bottom-up traversal on the rectangular layout, uses lazy synchronization in top-down levels, and switches variants based on frontier size to minimize communication overhead; (3) Frontier-split degree-aware update that maps frontier vertices to thread-centric, wavefront-centric, and block-centric kernels based on their degree to improve GPU utilization and memory coalescing; (4) Row-reduction pipeline that overlaps bottom-up adjacency list processing with row-wise bitmap reduction to hide inter-rank latency. Together, these techniques increase parallelism while reducing memory and communication overhead. On the Graph500 benchmark, CORE - BFS scales up to 9,248 Frontier nodes with scale-42 graphs and reaches 160.845 TTEPS, delivering a 5.42 × speedup over our previous Frontier implementation.

Yang, Haoshen [Rutgers University]↗

Using LDPC Code Constraints to Aid Recovery of Symbol Timing

A method of utilizing information available in the constraints imposed by a low-density parity-check (LDPC) code has been proposed as a means of aiding the recovery of symbol timing in the reception of a binary-phase-shift-keying (BPSK) signal representing such a code in the presence of noise, timing error, and/or Doppler shift between the transmitter and the receiver. This method and the receiver architecture in which it would be implemented belong to a class of timing-recovery methods and corresponding receiver architectures characterized as pilotless in that they do not require transmission and reception of pilot signals. Acquisition and tracking of a signal of the type described above have traditionally been performed upstream of, and independently of, decoding and have typically involved utilization of a phase-locked loop (PLL). However, the LDPC decoding process, which is iterative, provides information that can be fed back to the timing-recovery receiver circuits to improve performance significantly over that attainable in the absence of such feedback. Prior methods of coupling LDPC decoding with timing recovery had focused on the use of output code words produced as the iterations progress. In contrast, in the present method, one exploits the information available from the metrics computed for the constraint nodes of an LDPC code during the decoding process. In addition, the method involves the use of a waveform model that captures, better than do the waveform models of the prior methods, distortions introduced by receiver timing errors and transmitter/ receiver motions. An LDPC code is commonly represented by use of a bipartite graph containing two sets of nodes. In the graph corresponding to an (n,k) code, the n variable nodes correspond to the code word symbols and the n-k constraint nodes represent the constraints that the code places on the variable nodes in order for them to form a valid code word. The decoding procedure involves iterative computation of values associated with these nodes. A constraint node represents a parity-check equation using a set of variable nodes as inputs. A valid decoded code word is obtained if all parity-check equations are satisfied. After each iteration, the metrics associated with each constraint node can be evaluated to determine the status of the associated parity check. Heretofore, normally, these metrics would be utilized only within the LDPC decoding process to assess whether or not variable nodes had converged to a codeword. In the present method, it is recognized that these metrics can be used to determine accuracy of the timing estimates used in acquiring the sampled data that constitute the input to the LDPC decoder. In fact, the number of constraints that are satisfied exhibits a peak near the optimal timing estimate. Coarse timing estimation (or first-stage estimation as described below) is found via a parametric search for this peak. The present method calls for a two-stage receiver architecture illustrated in the figure. The first stage would correct large time delays and frequency offsets; the second stage would track random walks and correct residual time and frequency offsets. In the first stage, constraint-node feedback from the LDPC decoder would be employed in a search algorithm in which the searches would be performed in successively narrower windows to find the correct time delay and/or frequency offset. The second stage would include a conventional first-order PLL with a decision-aided timing-error detector that would utilize, as its decision aid, decoded symbols from the LDPC decoder. The method has been tested by means of computational simulations in cases involving various timing and frequency errors. The results of the simulations ined in the ideal case of perfect timing in the receiver.

Jones, Christopher↗

Fast and Accurate Predictions of Total Energy for Solid Solution Alloys with Graph Convolutional Neural Networks

We use graph convolutional neural networks (GCNNs) to produce fast and accurate predictions of the total energy of solid solution binary alloys. GCNNs allow us to abstract the lattice structure of a solid material as a graph, whereby atoms are modeled as nodes and metallic bonds as edges. This representation naturally incorporates information about the structure of the material, thereby eliminating the need for computationally expensive data pre-processing which would be required with standard neural network (NN) approaches. We train GCNNs on ab-initio density functional theory (DFT) for copper-gold (CuAu) and iron-platinum (FePt) data that has been generated by running the LSMS-3 code, which implements a locally self-consistent multiple scattering method, on OLCF supercomputers Titan and Summit. GCNN outperforms the ab-initio DFT simulation by orders of magnitude in terms of computational time to produce the estimate of the total energy for a given atomic configuration of the lattice structure. We compare the predictive performance of GCNN models against a standard NN such as dense feedforward multi-layer perceptron (MLP) by using the root-mean-squared errors to quantify the predictive quality of the deep learning (DL) models. We find that the attainable accuracy of GCNNs is at least an order of magnitude better than that of the MLP.

Lupo Pasini, Massimiliano↗

An integrated approach to optimizing concentration shock wave electrodialysis using 2D multicell simulation and response surface models

Shock wave electrodialysis (SWED) is a highly promising technique for energy-efficient ion separation in the context of a circular economy. This paper presents a approach way of modeling and improving SWED using a two-dimensional multicell model combined with the COMSOL program and response surface methodology. The model integrates the Nernst-Planck equation, Darcy's law, and first-order electroosmosis to examine the local concentration, flux of ionic species, distribution of current, and velocity of flow in SWED cells under various operating conditions. We first illustrate the clear depiction of concentration, velocity, and electric potential distribution through contours which aids in identifying optimal operating conditions and designing scalable SWED systems. The results emphasize the significance of surface charge density and voltage in influencing the features of shock waves for obtaining effective ion separation while optimizing energy consumption and improving current efficiency by controlling the retention time of feed flow. Here, this study defines two crucial characteristics of shock waves, namely the length of the flat depletion zone of a fully developed shock wave (shock wave height) and the distance of shock wave propagation (shock wave length). These properties significantly impact separation performance, as determined by the simulation results. Additionally, the response surface methodology is incorporated with the COMSOL models to develop predictive models and graph responses, enabling a more comprehensive understanding of the interactions between parameters and performance indicators, such as removal ratio, energy consumption, and water recovery. Finally, this work suggests design tactics for expanding SWED processes and outlines potential areas for further research. This research provides valuable insights into the prospective applications, design optimization, and scalability of SWED in the field of electrokinetic separation technologies for green chemistry and a circular economy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗