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DOE OSTI2023

Julia as a unifying end-to-end workflow language on the Frontier exascale system

We evaluate Julia as a single language and ecosystem paradigm powered by LLVM to develop workflow components for high-performance computing. We run a Gray-Scott, 2-variable diffusion-reaction application using a memory-bound, 7-point stencil kernel on Frontier, the US Department of Energy’s first exascale supercomputer. We evaluate the performance, scaling, and trade-offs of (i) the computational kernel on AMD’s MI250x GPUs, (ii) weak scaling up to 4,096 MPI processes/GPUs or 512 nodes, (iii) parallel I/O writes using the ADIOS2 library bindings, and (iv) Jupyter Notebooks for interactive analysis. Results suggest that although Julia generates a reasonable LLVM-IR, a nearly 50% performance difference exists vs. native AMD HIP stencil codes when running on the GPUs. As expected, we observed near-zero overhead when using MPI and parallel I/O bindings for system-wide installed implementations. Consequently, Julia emerges as a compelling high-performance and high-productivity workflow composition language, as measured on the fastest supercomputer in the world.

Godoy, William↗

DOE OSTI2021

Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation

Abstract Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.

Wong, Gerard C. L. (ORCID:0000000308936383)↗

DOE OSTI2023

Real Space and Time Imaging of Collective Headgroup Dipole Motions in Zwitterionic Lipid Bilayers

Lipid bilayers are supramolecular structures responsible for a range of processes, such as transmembrane transport of ions and solutes, and sorting and replication of genetic materials, to name just a few. Some of these processes are transient and currently, cannot be visualized in real space and time. Here, we developed an approach using 1D, 2D, and 3D Van Hove correlation functions to image collective headgroup dipole motions in zwitterionic phospholipid bilayers. We show that both 2D and 3D spatiotemporal images of headgroup dipoles are consistent with commonly understood dynamic features of fluids. However, analysis of the 1D Van Hove function reveals lateral transient and re-emergent collective dynamics of the headgroup dipoles—occurring at picosecond time scales—that transmit and dissipate heat at longer times, due to relaxation processes. At the same time, the headgroup dipoles also generate membrane surface undulations due a collective tilting of the headgroup dipoles. A continuous intensity band of headgroup dipole spatiotemporal correlations—at nanometer length and nanosecond time scales—indicates that dipoles undergo stretching and squeezing elastic deformations. Importantly, the above mentioned intrinsic headgroup dipole motions can be externally stimulated at GHz-frequency scale, enhancing their flexoelectric and piezoelectric capabilities (i.e., increased conversion efficiency of mechanical energy into electric energy). In conclusion, we discuss how lipid membranes can provide molecular-level insights about biological learning and memory, and as platforms for the development of the next generation of neuromorphic computers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A participant-derived xenograft model of HIV enables long-term evaluation of autologous immunotherapies

HIV-specific CD8+ T cells partially control viral replication and delay disease progression, but they rarely provide lasting protection, largely due to immune escape. Here, we show that engrafting mice with memory CD4+ T cells from HIV+ donors uniquely allows for the in vivo evaluation of autologous T cell responses while avoiding graft-versus-host disease and the need for human fetal tissues that limit other models. Treating HIV-infected mice with clinically relevant HIV-specific T cell products resulted in substantial reductions in viremia. In vivo activity was significantly enhanced when T cells were engineered with surface-conjugated nanogels carrying an IL-15 superagonist, but it was ultimately limited by the pervasive selection of a diverse array of escape mutations, recapitulating patterns seen in humans. By applying mathematical modeling, we show that the kinetics of the CD8+ T cell response have a profound impact on the emergence and persistence of escape mutations. This “participant-derived xenograft” model of HIV provides a powerful tool for studying HIV-specific immunological responses and facilitating the development of effective cell-based therapies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

The Computational Capacity of Mem-LRC Reservoirs

Reservoir computing has a emerged as a powerful tool in data-driven time series analysis. The possibility of utilizing hardware reservoirs as specialized co-processors has generated interest in the properties of electronic reservoirs, especially those based on memristors as the nonlinearity of these devices should translate to an improved nonlinear computational capacity of the reservoir. However, designing these reservoirs requires a detailed understanding of how memristive networks process information which has thus far been lacking. In this work, we derive an equation for general memristor-inductor-resistor-capacitor (MEM-LRC) reservoirs that includes all network and dynamical constraints explicitly. Utilizing this we undertake a study of the computational capacity of these reservoirs. We demonstrate that hardware reservoirs may be constructed with extensive memory capacity and that the presence of memristors enacts a tradeoff between memory capacity and nonlinear computational capacity. Here, using these principles, we design reservoirs to tackle problems in signal processing, paving the way for applying hardware reservoirs to high-dimensional spatiotemporal systems.

Circuits with memory↗

DOE OSTI2021

Improvement of Numerical Methods in Pronghorn

During the fiscal year of 2021, the finite-volume method (FVM) was deployed in Pronghorn to provide improved efficiency, stability, and accuracy for coarse-mesh, thermal-hydraulics problems. While the main goals of fiscal year 2021 were met, several issues emerged from the early deployment of the finite-volume method in Pronghorn. These issues were: The compressible and incompressible formulations that were implemented are inadequate for many nuclear reactor flow problems; Omission of terms accounting for the porosity and Darcy-Forchheimer body force discontinuities in the Rhie-Chow interpolation lead to oscillations in pressure and velocity at these discontinuities; The FVM lacks a correction for non-orthogonal grids for computing accurate pressure gradient leading to loss of accuracy in regions with skewed elements; The FVM currently uses a monolithic solver. Monolithic solvers have issues dealing with the saddle-point nature of the discretized fluid equations. The result are bad convergence if direct factorization is not used and large memory consumption when direct factorization is used. These four issues are addressed in this report. In particular, we report the completion of the following task: Implementation of a weakly compressible formulation in the MOOSE Navier-Stokes module; Implementation of Moukalled’s method for including body forces in the RCI. Additionally, we identified the need to smooth the porosity using Moukalled’s face-cell smoothing operator; Implementation of a non-orthogonal correction for the Green-Gauss gradient computation; Preliminary implementation of a SIMPLE segregated solver.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Interfacial antiferromagnetic phase induced two-step magnetization reversal in PbZr 0.52 Ti 0.48 O3/La 0.67 Sr 0.33 MnO 3 superlattices

Artificial multiferroic heterostructures have recently attracted much interests due to the demonstrated magnetoelectric coupling (MEC) and unique functionalities, promising a tantalizing perspective of novel applications in next-generation electronic, memory, sensor, and energy harvesting technologies. Herein, we report a two-step magnetization reversal in PbZr 0.52 Ti 0.48 O 3 /La 0.67 Sr 0.33 MnO 3 (PZT/LSMO) superlattices, which originates from the strongly entangled strain-, ferroelectric (FE)-polarization-, and exchange-dependent effects. Specifically, the preferential occupancy of the in-plane Mn d x 2 -y 2 orbitals is triggered via the collective effects of the large tensile strain and FE polarization, giving rise to an interfacial antiferromagnetic (AFM) layer with strong AFM anisotropy. The strong spin exchange coupling between the AFM layer and the adjacent ferromagnetic (FM) layer facilitates the magnetic stratification of the FM layer, leading to two coercivities, i.e., two-step magnetization reversal. Meanwhile, a sizeable exchange bias (EB) field is induced. The emerged two-step magnetization reversal concomitant with the pronounced EB phenomenon should be a signature of an enhanced MEC in PZT/LSMO superlattices. Finally, our results will stimulate further interests in multiferroic superlattices in applications of multiferroic-based devices.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Enhanced deep neural networks with transfer learning for distribution LMP considering load and PV uncertainties

As the flexibility of generation and demand increases in distribution systems, the residential loads are emerging as a promising means to participate in demand response and the transactive energy market. Market pricing is an instrumental mechanism for the distribution system operator to exploit the full potential of the flexible resources. The distribution locational marginal price (DLMP) can be used to guide the residential load consumption. This type of market signal helps the distribution system operator to optimize the scheduling of all resources while satisfying related network constraints through a day-ahead market. However, solving the optimization problem for large-scale systems can be computationally expensive. To address the scalability and practicability limitations of the DLMP framework, a learning-based approach is proposed in this paper to complement the day-ahead distribution market framework. Here, the proposed approach combines long short-term memory and transfer learning to develop deep neural network that can capture the spatial–temporal correlation of the input data. The model can determine the optimal DLMP for each node in a distribution system without the system parameters required to formulate the optimization problem. Testing results on IEEE 33-bus and 123-bus systems show that the proposed approach can generate a comparable DLMP against the optimization solutions.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Hybrid classical-quantum communication networks

Over the past several decades, the proliferation of global classical communication networks has transformed various facets of human society. Concurrently, quantum networking has emerged as a dynamic field of research, driven by its potential applications in distributed quantum computing, quantum sensor networks, and secure communications. This prompts a fundamental question: rather than constructing quantum networks from scratch, can we harness the widely available classical fiber-optic infrastructure to establish hybrid quantum–classical networks? This paper aims to provide a comprehensive review of ongoing research endeavors aimed at integrating quantum communication protocols, such as quantum key distribution, into existing lightwave networks. This approach offers the substantial advantage of reducing implementation costs by allowing classical and quantum communication protocols to share optical fibers, communication hardware, and other network control resources—arguably the most pragmatic solution in the near term. In the long run, classical communication will also reap the rewards of innovative quantum communication technologies, such as quantum memories and repeaters. Accordingly, our vision for the future of the Internet is that of heterogeneous communication networks thoughtfully designed for the seamless support of both classical and quantum communications.

Fiber-optic communication↗

DOE OSTI2024

A High-level Design for Bidirectional Data Streaming to High-Performance Computing Systems from External Science Facilities

Cutting-edge science is increasingly data-driven due to the emergence of scientific machine learning models that can guide scientists toward fruitful areas of exploration. Experimental science facilities such as light and neutron sources, particle colliders, and radio astronomy telescopes are also producing raw measurement data at rates that exceed available data storage and computing capacity at those facilities. As a result, scientific workflows are being developed that concurrently couple experiments at science facilities with high-performance computing (HPC) facilities to enable analysis of experimental data while the experiment is ongoing, and where analysis results are potentially fed back to the experiment for use in experimental control and/or steering in a time-sensitive manner. Our goal is to design, prototype, and deploy a new capability for the Oak Ridge Leadership Computing Facility (OLCF) that enables such workflows through support for bidirectional, memory-based streaming of data from external experiments into and out of OLCF HPC systems. This high-level design document describes the related work and motivating use cases that inform our understanding of the technical requirements for this capability, and describes a proposed architectural solution that meets these requirements and our plans for demonstrating the capability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Time scales for nonlinear processes in preheating after multifield inflation with nonminimal couplings

We have conducted extensive lattice simulations to study the postinflation dynamics of multifield models involving nonminimal couplings. In this work, we explore the parameter dependence of preheating in these models and describe the various time scales that control such nonlinear processes as energy transfer, rescattering, and the approach to radiation domination and thermalization. In the limit of large nonminimal couplings ($ξ_I$ ~ 100), we find that efficient transfer of energy from the inflaton condensate to radiative degrees of freedom, emergence of a radiation-dominated equation of state, and the onset of thermalization each consistently occur within $N_{\text{reh}} ≲ 3 e$-folds after the end of inflation, largely independent of the values of the other couplings in the models. The exception is the case of negative ellipticity, in which there is a misalignment between the dominant direction in field space along which the system evolves and the larger of the nonminimal couplings $ξ_I$. In those cases, the field-space-driven parametric resonance is effectively shut off. More generally, the competition between the scalar fields’ potential and the field-space manifold structure can yield interesting phenomena such as two-stage resonances. Across many regions of parameter space, we find efficient re-scattering between the distinct fields, leading to a partial memory loss of the shape of the initial fluctuation spectrum. Despite the explosive particle production, which can lead to a quick depletion of the background energy density, the nonlinear processes do not induce any superhorizon correlations after the end of inflation in these models, which keeps predictions for cosmic microwave background observables unaffected by the late-time amplification of isocurvature fluctuations. Hence the excellent agreement between primordial observables and recent observations is preserved for this class of models, even when we consider postinflation dynamics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Batched sparse direct solver design and evaluation in SuperLU_DIST

Over the course of interactions with various application teams, the need for batched sparse linear algebra functions has emerged in order to make more efficient use of the GPUs for many small and sparse linear algebra problems. In this paper, we present our recent work on a batched sparse direct solver for GPUs. The sparse LU factorization is computed by the levels of the elimination tree, leveraging the batched dense operations at each level and a new batched Scatter GPU kernel. The sparse triangular solve is computed by the level sets of the directed acyclic graph (DAG) of the triangular matrix. Batched operations overcome the large overhead associated with launching many small kernels. For medium sized matrix batches with not-so-small bandwidth, using an NVIDIA A100 GPU, our new batched sparse direct solver is orders of magnitude faster than a batched banded solver and uses less than one-tenth of the memory.

Boukaram, Wajih↗

DOE OSTI2021

Toward exascale whole-device modeling of fusion devices: Porting the GENE gyrokinetic microturbulence code to GPU

GENE solves the five-dimensional gyrokinetic equations to simulate the development and evolution of plasma microturbulence in magnetic fusion devices. The plasma model used is close to first principles and computationally very expensive to solve in the relevant physical regimes. In order to use the emerging computational capabilities to gain new physics insights, several new numerical and computational developments are required. Here, we focus on the fact that it is crucial to efficiently utilize GPUs (graphics processing units) that provide the vast majority of the computational power on such systems. In this paper, we describe the various porting approaches considered and given the constraints of the GENE code and its development model, justify the decisions made, and describe the path taken in porting GENE to GPUs. We introduce a novel library called gtensor that was developed along the way to support the process. Performance results are presented for the ported code, which in a single node of the Summit supercomputer achieves a speed-up of almost 15× compared to running on central processing unit (CPU) only. Typical GPU kernels are memory-bound, achieving about 90% of peak. Our analysis shows that there is still room for improvement if we can refactor/fuse kernels to achieve higher arithmetic intensity. We also performed a weak parallel scalability study, which shows that the code runs well on a massively parallel system, but communication costs start becoming a significant bottleneck.

Germaschewski, K. (ORCID:0000000284956354)↗

DOE OSTI2026

Industrial Adoption of Carbon Nanotubes

Over the past 30 years, carbon nanotubes have emerged as one of the most exciting classes of nanomaterials due to their unique physicochemical properties. While challenges in nanotube synthesis and processing initially hindered their adoption, many of these barriers have since been addressed by research and manufacturing advances, resulting in substantial industrial application of nanotubes across multiple sectors. However, much of this progress is not known in the academic community. This perspective discusses the current landscape and outlook of industrial integration of carbon nanotubes and key factors mediating widespread integration across all major material-related areas of human activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

FunM2C: A Filter for Uncertainty Visualization of Multivariate Data on Multi-Core Devices

Uncertainty visualization is an emerging research topic in data visualization because neglecting uncertainty in visualization can lead to inaccurate assessments. In this paper, we study the propagation of multivariate data uncertainty in visualization. Although there have been a few advancements in probabilistic uncertainty visualization of multivariate data, three critical challenges remain to be addressed. First, the state-of-the-art probabilistic uncertainty visualization framework is limited to bivariate data (two variables). Second, existing uncertainty visualization algorithms use computationally intensive techniques and lack support for cross-platform portability. Third, as a consequence of the computational expense, integration into production visualization tools is impractical. In this work, we address all three issues and make a threefold contribution. First, we take a step to generalize the state-of-the-art probabilistic framework for bivariate data to multivariate data with an arbitrary number of variables. Second, through utilization of VTK-m’s shared-memory parallelism and cross-platform compatibility features, we demonstrate acceleration of multivariate uncertainty visualization on different many-core architectures, including OpenMP and AMD GPUs. Third, we demonstrate the integration of our algorithms with the ParaView software. We demonstrate the utility of our algorithms through experiments on multivariate simulation data with three and four variables.

Hari, Gautam↗

DOE OSTI2022

Characterizing Electron Flow through Catechol‐Graphene Composite Hydrogels

Abstract Electronic materials that allow the controlled flow of electrons in aqueous media are required for emerging applications that require biocompatibility, safety, and/or sustainability. Here, a composite hydrogel film composed of graphene and catechol is electrofabricated, and that this composite offers synergistic properties is reported. Graphene confers metal‐like conductivity and enables charge‐storage through an electrical double layer mechanism. Catechol confers redox‐activity and enables charge‐storage through a redox mechanism. Importantly, there are two functional populations of catechols: conducting‐catechols (presumably in intimate contact with graphene) allow direct electron‐transfer; and non‐conducting‐catechols (presumably physically separated from graphene) require diffusible mediators to enable electron‐transfer. Using a variety of spectroelectrochemical measurements, that the capacity of the composite for charge‐storage increases in proportion to the extent by which the catechol‐groups can undergo redox‐state switching is demonstrated. To illustrate the broad relevance of this work, how the redox‐state switching can be related to both the charge storage of energy materials and the memory of molecular electronic materials is discussed. The authors believe this work is significant because it demonstrates that: conducting and redox‐active components enable distinctly different mechanisms for charge‐storage and electron‐transfer; these components act synergistically; and mediators provide unique opportunities to extend the capabilities of electronic materials.

36 MATERIALS SCIENCE↗

DOE OSTI2022

A New Evaluation Metric for Demand Response-Driven Real-Time Price Prediction Towards Sustainable Manufacturing

Abstract The increasing industry energy demand highlights the urgency of demand response management, while the emerging smart manufacturing technologies pave the way for the implementation of real-time price (RTP)-based demand response management towards sustainable manufacturing. The demand response management requires scheduling of manufacturing systems based on RTP predictions, and thus the prediction quality can directly alter the effectiveness of demand response. However, since the general price prediction algorithms and prediction evaluation metrics are not specifically designed for RTP in demand response problems, a good RTP prediction obtained and evaluated by these algorithms and metrics may not be suitable for demand response scheduling. Therefore, in this study, the relationships between the effectiveness of demand response for manufacturing systems and evaluation results from six commonly used metrics are investigated. Meanwhile, a new metric called k-peak distance (KPD), considering the characteristics of the demand response problem, is proposed and compared with the other six metrics. Furthermore, an encoder-decoder long short-term memory recurrent neural network with KPD is proposed to provide better RTP prediction for manufacturing demand response problems. The case studies indicate that the proposed KPD metric shows a 1.8–3.6 times higher correlation with the demand response effectiveness compared to the other metrics. In addition, the production schedule based on the RTP prediction obtained from the proposed algorithm can improve the effectiveness of demand response by 23.4% on average.

Engineering↗

DOE OSTI2026

Data Summarization and Inference at Scale

This is the final report for the DOE ASCR grant SC-0022260, Data Summarization and Inference at Scale, PI: Alex Pothen, Purdue University. The goal of the project was to solve data-intensive and compute-intensive problems in the physical sciences, engineering, information science, data science, etc. by designing and implementing new algorithms that could work with a subset of the data. The four subgoals were: (a) The solution of problems where the data is too large to be stored in the memory of a computer. In this streaming model of computation, the data arrives as a stream of elements to the computer, each element is processed as it arrives, and a decision is made to discard the data or to store it; only a small subset of the data proportional to the size of the output solution is stored, and when all the data has been streamed, a solution to the problem is computed from the stored subset. (b) The use of machine learning methods to compute solutions to data-intensive problems. The use of GPUs is critical to obtain high performance on machine learning tasks, but their memory sizes are smaller relative to that of CPUs. For large-scale problems, the data is sampled many times, and small samples are used with repetition, for robustness, to compute solutions to inference tasks. This sampling reduces the memory required to solve the problem, but attention is needed to avoid slow convergence to the solutions, and reduced accuracy of inference. We propose submodular optimization, Large Language Models, and physics-informed neural networks to enable GPU computations here. (c) Modeling and visualization of high-dimensional data using interpretable features. Clinical proteomic data sets from immunology for the detection of cancer and other diseases are temporal and high-dimensional, and algorithms for visualizing these data sets using clinically interpretable features are lacking. We propose methods that compute distances based on the optimal transportation problem and graph edit distances to address this problem. We also propose the use of optimal transport-based distances, spatial statistics, and network structure to classify image data sets, We apply these algorithms to electron micrographs of the peripheral nervous system in the digestive tract. (d) The design of data-intensive algorithms on emerging architectures, specifically, noisy, intermediate-scale quantum (NISQ) devices. Quantum computers offer the possibility of exploring large solution spaces due to the principle of superposition, but current quantum computers are limited by few qubits, short coherence times due to noise, poor interconections among the qubits, etc. We propose the use of the divide and conquer paradigm to solve large-scale problems, wherein collections of small subproblems are solved on the quantum devices, and the solutions to the subproblems are integrated into a solution for the original problem on a classical computer.

97 MATHEMATICS AND COMPUTING↗