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This award supported research into turbulence and transport in the edge region of tokamak plasmas, focusing on developing new theory and computational capabilities to address important phenomena including the L-H transition.
Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: They do not scale to process large graphs and/or support only a restricted set of search templates or usage scenarios. Moreover, the algorithms at the core of the existing techniques are not suitable for today’s graph processing infrastructures relying on horizontal scalability and shared-nothing clusters, as most of these algorithms are inherently sequential and difficult to parallelize. In this article we present an algorithmic pipeline that bases pattern matching on constraint checking. The key intuition is that each vertex and edge participating in a match has to meet a set of constraints implicitly specified by the search template. These constraints can be verified independently and typically are less expensive to compute than searching the full template. The pipeline we propose generates these constraints and iterates over them to eliminate all the vertices and edges that do not participate in any match, thus reducing the background graph to a subgraph that is the union of all template matches—the complete set of all vertices and edges that participate in at least one match. Additional analysis can be performed on this annotated, reduced graph, such as full match enumeration, match counting, or computing vertex/edge centrality. Furthermore, a vertex-centric formulation for constraint checking algorithms exists, and this makes it possible to harness existing high-performance, vertex-centric graph processing frameworks. This technique (i) enables highly scalable pattern matching in metadata (labeled) graphs; (ii) supports arbitrary patterns with 100% precision; (iii) enables tradeoffs between precision and time-to-solution, while always selects all vertices and edges that participate in matches, thus offering 100% recall; and (iv) supports a set of popular data analytics scenarios. We implement our approach on top of HavoqGT, an open-source asynchronous graph processing framework, and demonstrate its advantages through strong and weak scaling experiments on massive scale real-world (up to 257 billion edges) and synthetic (up to 4.4 trillion edges) labeled graphs, respectively, and at scales (1,024 nodes / 36,864 cores), orders of magnitude larger than used in the past for similar problems. This article serves two purposes: First, it synthesises the knowledge accumulated during a long-term project. Second, it presents new system features, usage scenarios, optimizations, and comparisons with related work that strengthen the confidence that pattern matching based on iterative pruning via constraint checking is an effective and scalable approach in practice. The new contributions include the following: (i) We demonstrate the ability of the constraint checking approach to efficiently support two additional search scenarios that often emerge in practice, interactive incremental search and exploratory search. (ii) We empirically compare our solution with two additional state-of-the-art systems, Arabsque and TriAD. (iii) We show the ability of our solution to accommodate a more diverse range of datasets with varying properties, e.g., scale, skewness, label distribution, and match frequency. (iv) We introduce or extend a number of system features (e.g., work aggregation, load balancing, and the ability to cap the generated traffic) and design optimizations and demonstrate their advantages with respect to improving performance and scalability. (v) We present bottleneck analysis and insights into artifacts that influence performance. (vi) We present a theoretical complexity argument that motivates the performance gains we observe.
Artificial boundary conditions (BCs) play a ubiquitous role in numerical simulations of transport phenomena in several diverse fields, such as fluid dynamics, electromagnetism, acoustics, geophysics, and many more. They are essential for accurately capturing the behavior of physical systems whenever the simulation domain is truncated for computational efficiency purposes. Ideally, an artificial BC would allow relevant information to enter or leave the computational domain without introducing artifacts or unphysical effects. Boundary conditions designed to control spurious wave reflections are referred to as nonreflective boundary conditions (NRBCs). Another approach is given by the perfectly matched layers (PMLs), in which the computational domain is extended with multiple dampening layers, where outgoing waves are absorbed exponentially in time. Here, in this work, the definition of PML is revised in the context of the lattice Boltzmann method. The impact of adopting different types of BCs at the edge of the dampening zone is evaluated and compared, in terms of both accuracy and computational costs. It is shown that for sufficiently large buffer zones, PMLs allow stable and accurate simulations even when using a simple zeroth-order extrapolation BC. Moreover, employing PMLs in combination with NRBCs potentially offers significant gains in accuracy at a modest computational overhead, provided the parameters of the BC are properly tuned to match the properties of the underlying fluid flow.
X-ray absorption spectroscopy (XAS) is an element-specific materials characterization technique that is sensitive to structural and electronic properties. First-principles simulated XAS has been widely used as a powerful tool to interpret experimental spectra and draw physical insights. Recently, there has also been growing interest in building computational XAS databases to enable data analytics and machine learning applications. However, there are non-trivial differences among commonly used XAS simulation codes, both in underlying theoretical formalism and in technical implementation. Reliable and reproducible computational XAS databases require systematic benchmark studies. In this work, we benchmarked Ti K-edge XAS simulations of ten representative Ti-O binary compounds, which we refer to as the Ti-O-10 dataset, using three state-of-the-art codes: XSPECTRA, OCEAN and exciting. We systematically studied the convergence behavior with respect to the input parameters and developed a workflow to automate and standardize the calculations to ensure converged spectra. Our benchmark comparison considers a 35 eV spectral range starting from the K-edge onset, representative of widely used near-edge spectra. Quantitative comparison over this range is based on Spearman’s rank correlation score (r sp ). Our results show: (1) the two Bethe-Salpeter equation (BSE) codes (OCEAN and exciting) have excellent agreement with an average $r$ $sp$ of 0.998; (2) good agreement is obtained between the core-hole potential code (XSPECTRA) and BSE codes (OCEAN and exciting) with an average $r$ $sp$ of 0.990, and this smaller $r$ $sp$ reflects the noticeable differences in the main edge spectral shape that can be primarily attributed to the difference in the strength of the screened core-hole potential; (3) simulations from both methods overall reproduce well the main experimental spectral features of rutile and anatase, and the different treatments of the screened core-hole potential have visible impact on pre-edge intensities and the peak ratio of the main edge; (4) there exist moderate differences in the relative edge alignment of the three codes with a standard deviation of about 0.2 eV, which arise from multiple contributions including the frozen core approximation, final state effects, and different approximations used for the self-energy correction. In conclusion, our benchmark study provides important standards for first-principles XAS simulations with broad impact in data-driven XAS analysis.
Buildings, as major energy consumers, can provide great untapped demand response (DR) resources for grid services. However, their participation remains low in real-life. One major impediment for popularizing DR in buildings is the lack of cost-effective automation systems that can be widely adopted. Existing optimization-based smart building control algorithms suffer from high costs on both building-specific modeling and on-demand computing resources. To tackle these issues, this paper proposes a cost-effective edge-cloud integrated solution using reinforcement learning (RL). Beside RL’s ability to solve sequential optimal decision-making problems, its adaptability to easy-to-obtain building models and the off-line learning feature are likely to reduce the controller’s implementation cost. Using a surrogate building model learned automatically from building operation data, an RL agent learns an optimal control policy on cloud infrastructure, and the policy is then distributed to edge devices for execution. Simulation results demonstrate the control efficacy and the learning efficiency in buildings of different sizes. A preliminary cost analysis on a 4-zone commercial building shows the annual cost for optimal policy training is only 2.25% of the DR incentive received. Results of this study show a possible approach with higher return on investment for buildings to participate in DR programs.
Parallel computing plays a pivotal role in the efficient processing of large-scale graphs. Complex network analysis stands as a capti- vating research frontier, holding promise across diverse scientific domains such as sociology, biology, online media, and recommenda- tion systems. In this era, Machine Learning (ML) and Deep Learning (DL) have emerged as indispensable tools, underpinning remarkable technological achievements. Within this dynamic landscape, my research revolves around advancing parallel algorithms tailored for large-scale graph operations. To achieve this, I harness the power of cutting-edge technologies including OpenMP, MPI, HIP, and CUDA, on the High-Performance Computing (HPC) platforms to unlock optimal performance. I also apply ML/DL techniques to HPC operational data, to streamline the monitoring and maintenance of supercomputers, alleviating the complexities associated with their upkeep and enhancing user support. My research echoes the syn- ergy between parallel computing, large-scale graph analysis, and ML/DL, improving computational efficiency and user experience.
The de novo design of polar protein–protein interactions is challenging because of the thermodynamic cost of stripping water away from the polar groups. Here, we describe a general approach for designing proteins which complement exposed polar backbone groups at the edge of beta sheets with geometrically matched beta strands. We used this approach to computationally design small proteins that bind to an exposed beta sheet on the human transferrin receptor (hTfR), which shuttles interacting proteins across the blood–brain barrier (BBB), opening up avenues for drug delivery into the brain. We describe a design which binds hTfR with a 20 nM K d , is hyperstable, and crosses an in vitro microfluidic organ-on-a-chip model of the human BBB. Our design approach provides a general strategy for creating binders to protein targets with exposed surface beta edge strands.
Neuromorphic computing has many opportunities in future autonomous systems, especially those that will operate at the edge. However, there are relatively few demonstrations of neuromorphic implementations on real-world applications, partly because of the lack of availability of neuromorphic hardware and software, but also because of the lack of availability of an accessible demonstration platform. In this work, we propose utilizing the F1Tenth platform as an evaluation task for neuromorphic computing. F1Tenth is a competition wherein one tenth scale cars compete in an autonomous racing task; there are significant open source resources in both software and hardware for realizing this task. We present a workflow with neuromorphic hardware, software, and training that can be used to develop a spiking neural network for neuromorphic hardware deployment to perform autonomous racing. We present initial results on utilizing this approach for this small-scale, real-world autonomous vehicle task.
The 2-D edge plasma fluid transport code, UEDGE has been used to simulate the edge and scrape-off layer regions of circular limiter plasmas of ADITYA-U. The computational mesh defining the limiter geometry of ADITYA-U has been introduced in the UEDGE code through an in-house developed routine. It has successfully been integrated with the UEDGE code and the measured radial profile of electron density (n e ) in the edge region is modelled using the simulations. The plasma discharge for the present study has plasma current I P ~ 130 kA, duration ~ 150 ms, chord-averaged electron density ~ 1.3 x 10 19 m -3 , and central electron temperature ~ 270 eV has been observed. The maximum toroidal magnetic field is ~ 1.2 T. It has been found that an inward convective velocity, v conv ~ 1.5 m/s is required in addition to the constant perpendicular diffusion coefficient, D ⟂ ~ 0.2 m 2 /s to adequately match the measured n e profile in typical discharges of ADITYA-U. The value of D ⟂ ~ 0.2 m 2 /s is found to lie between the estimated neoclassical diffusivity and Bohm diffusivity.
In the era of big data, materials science workflows need to handle large-scale data distribution, storage, and computation. Any of these areas can become a performance bottleneck. We present a framework for analyzing internal material structures (e.g., cracks) to mitigate these bottlenecks. We demonstrate the effectiveness of our framework for a workflow performing synchrotron X-ray computed tomography reconstruction and segmentation of a silica-based structure. Our framework provides a cloud-based, cutting-edge solution to challenges such as growing intermediate and output data and heavy resource demands during image reconstruction and segmentation. Specifically, our framework efficiently manages data storage, scaling up compute resources on the cloud. The multi-layer software structure of our framework includes three layers. A top layer uses Jupyter notebooks and serves as the user interface. A middle layer uses Ansible for resource deployment and managing the execution environment. A low layer is dedicated to resource management and provides resource management and job scheduling on heterogeneous nodes (i.e., GPU and CPU). At the core of this layer, Kubernetes supports resource management, and Dask enables large-scale job scheduling for heterogeneous resources. The broader impact of our work is four-fold: through our framework, we hide the complexity of the cloud’s software stack to the user who otherwise is required to have expertise in cloud technologies; we manage job scheduling efficiently and in a scalable manner; we enable resource elasticity and workflow orchestration at a large scale; and we facilitate moving the study of nonporous structures, which has wide applications in engineering and scientific fields, to the cloud. While we demonstrate the capability of our framework for a specific materials science application, it can be adapted for other applications and domains because of its modular, multi-layer architecture.
In quiescent H-mode (QH-mode) regime, edge harmonic oscillations (EHOs) are believed to provide necessary radial transport to prevent occurrence of large edge localized modes. A systematic modeling study is performed here on the low- n EHOs in a DIII-D QH-mode plasma (Chen et al 2016 Nucl. Fusion 56 076011), by utilizing the MARS-Q code (Liu et al 2013 Phys. Plasmas 20 042503). Both the n = 1 and n = 2 instabilities are found to be strongly localized near the plasma edge, exhibiting the edge-peeling characteristics. The DIII-D resistive wall is found to have minor effects on these instabilities. The plasma resistivity is found to strongly modify the mode growth rate. Assuming the Spitzer model for the plasma resistivity, the computed mode growth rate scales as S sup>-1/3 with S being the Lundquist number. Toroidal flow of the plasma slightly stabilizes these edge localized kink-peeling modes. Drift kinetic effects all have a destabilization effect on these modes. Non-perturbative magneto-hydrodynamic-kinetic hybrid computations find that the drift kinetic effects associated with thermal particle species push the peak location of the eigenmode radially inward but still in the pedestal region. The modeled plasma temperature and density fluctuations in the plasma edge region, as well as the poloidal magnetic field perturbations along both the low and high field sides of the plasma surface, are in good agreement with experimental measurements. Finally, the quasi-linear initial value simulations find a strong non-linear interplay between the kink-peeling instability and the toroidal flow near the plasma edge. The combined effect of the damping of the flow amplitude and change of the edge flow shear is found to be the stabilizing factor for the kink-peeling mode, leading to the mode saturation and thus EHOs.
Neuro-Spark, which is a new neuromorphic architecture with a field-programmable gate array (FPGA) implementation for ultrafast spiking neural network (SNN) inference at the edge, facilitates smart-pixel in-sensor filtering for high-energy physics experiments at the Large Hadron Collider (LHC). Utilizing the evolutionary optimization for neuromorphic systems (EONS) training method, we generate compact SNN models with 91% signal efficiency, akin to convolutional neural networks but with half the parameters. However, deploying near the detector poses a challenge because the SNN must handle a sustained input data rate exceeding 1013 GB/s. To overcome this, we propose a novel hardware architecture that uses high-level synthesis to construct a tuned architecture for the EONS-trained SNN. In addition to the analysis and validation with an AMD Xilinx Artix-A7 FPGA, our solution consumes only ç24% of FPGA LUT and flipflops. We also introduce an innovative quantization method that reduces FPGA resource utilization by ç15% without compromising accuracy. Our FPGA implementation achieves computing latency of ç10 ns for smart-pixel application inference on an edge FPGA.
Graphs arising in statistical problems, signal processing, large networks, combinatorial optimization, and data analysis are often dense, which causes both computational and storage bottlenecks. One way of sparsifying a weighted graph, while sharing the same vertices as the original graph but reducing the number of edges, is through spectral sparsification. We study this problem through the perspective of RandNLA. Specifically, we utilize randomized matrix multiplication to give a clean and simple analysis of how sampling according to edge weights gives a spectral approximation to graph Laplacians, without requiring spectral information. Through the CR–MM algorithm, we attain a simple and computationally efficient sparsifier whose resulting Laplacian estimate is unbiased and of minimum variance. Here, we define a new notion of additive spectral sparsifiers, which has not been considered in the literature.
This work will enable improved understanding of tokamak edge flows and impurity-species dynamics and their impact on MHD stability as it relates to ELMs, RMPs and QH-mode by leveraging computational developments of the NIMROD code. Experimentally, it is established that the tokamak flows and impurities species can have a substantial effect on MHD stability. This is particularly true for the edge plasma where, for example, large flow shear is correlated with the occurrence of the Quiescent H-mode (QH- mode) state as opposed to operation with edge localized modes (ELMs). Understanding plasma flows is challenging because of the many physical effects that come into play: particle orbits loss, neutrals dynamics, and interaction between multiple ion species with decoupled motion. We will develop a model that incorporates multiple ion species into the MHD framework that includes self-consistent magnetic-field evolution. With this model we will understand how the presence of impurities impacts the tokamak edge-pedestal flows. Finally, we will quantify the impact of the new multiple species modeling on 3D QH-mode simulations. This work will have broader impacts on all MHD studies when multiple species are present (as is the case in modern tokamaks), as well as contributing to the edge and transport communities who also are interested in the studies of multiple-ion-species flows in the edge pedestal region.
Electrosynthesis of hydrogen peroxide (H 2 O 2 ) via the two-electron oxygen reduction reaction (2e – ORR) is promising for various practical applications, such as wastewater treatment. However, few electrocatalysts are active and selective for 2e – ORR yet are also resistant to catalyst leaching under realistic operating conditions. Here, a joint experimental and computational study reveals active and stable 2e – ORR catalysis in neutral media over layered PdSe 2 with a unique pentagonal puckered ring structure type. Computations predict active and selective 2e – ORR on the basal plane and edge of PdSe 2 , but with distinct kinetic behaviors. Further, electrochemical measurements of hydrothermally synthesized PdSe 2 nanoplates show a higher 2e – ORR activity than other Pd–Se compounds (Pd 4 Se and Pd 17 Se 15 ). PdSe 2 on a gas diffusion electrode can rapidly accumulate H 2 O 2 in buffered neutral solution under a high current density. The electrochemical stability of PdSe 2 is further confirmed by long device operational stability, elemental analysis of the catalyst and electrolyte, and synchrotron X-ray absorption spectroscopy. This work establishes a new efficient and stable 2e – ORR catalyst at practical current densities and opens catalyst designs utilizing the unique layered pentagonal structure motif.
This report provides an overview of the Atmospheric Radiation Measurement (ARM) user facility and a sample of achievements for fiscal year 2024 (FY2024). Strong collaborations between nine DOE national laboratories enable ARM to successfully operate in remote locations around the world. This unique partnership supports the DOE mission to provide for the energy security of the nation. Without the support of the following laboratories, ARM would not be the state-of-the-art facility that it is today. ARM is a multi-laboratory, U.S. Department of Energy (DOE) Office of Science user facility and a key contributor to national and international atmospheric and climate research efforts. ARM offers scientists cutting-edge, ground-based observatories, aerial observation capabilities, and high-performance computing. ARM’s capabilities have enabled more than 30 years of continuous measurements of cloud and aerosol properties and their effects on Earth’s energy balance.
This report details the responsibilities, outcomes, and project details of a summer R&D internship at Los Alamos National Laboratory (LANL). LANL is a multidisciplinary laboratory that focuses on current cutting-edge research in many fields such as national security, engineering, materials science, computational modeling, and advanced manufacturing. The goal of the internship project was to work with lab engineers and resources to develop an energy absorbing structure for high-velocity impact applications. The successful development of this technology and methodology would not only positively impact future project funding but also contribute to the laboratory's commitment to solve national security challenges through simultaneous excellence. Such devices would also support efforts surrounding the research and development of energy absorbing structures and would provide new vital information backed by experimentation. Different computational and modeling methods were used to design these structures, in addition to qualitative background information provided by past literature. The resultant designs were successfully tested, and the test results were successfully quantified. From these results, new computational methods were developed through python programming and modeling to predict ideal materialistic properties for these structures given a sufficiently defined application.
Binary neural networks (BNNs) show promising utilization in cost and power-restricted domains such as edge devices and mobile systems. This is due to its significantly less computation and storage demand, but at the cost of degraded performance. To close the accuracy gap, in this paper we propose to add a complementary activation function (AF) ahead of the sign based binarization, and rely on the genetic algorithm (GA) to automatically search for the ideal AFs. These AFs can help extract extra information from the input data in the forward pass, while allowing improved gradient approximation in the backward pass. Fifteen novel AFs are identified through our GA-based search, while most of them show improved performance (up to 2.54% on ImageNet) when testing on different datasets and network models. Interestingly, periodic functions are identified as a key component for most of the discovered AFs, which rarely exist in human designed AFs. Our method offers a novel approach for designing general and application-specific BNN architecture.