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At least 469 records · Page 26

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↗

thornado+FLASH-X: A Hybrid Discontinuous Galerkin–Implicit-explicit and Finite-volume Framework for Neutrino-radiation Hydrodynamics in Core-collapse Supernovae

We present neutrino-transport algorithms implemented in the toolkit for high-order neutrino-radiation hydrodynamics (thornado) and their coupling to self-gravitating hydrodynamics within the adaptive mesh refinement–based multiphysics simulation framework FLASH-X. thornado, developed primarily for simulations of core-collapse supernovae (CCSNe), employs a spectral, six-species two-moment formulation with algebraic closure and special-relativistic observer corrections accurate to $\mathcal{O}(v/c)$, and uses discontinuous Galerkin (DG) methods for phase-space discretization combined with implicit-explicit time stepping. A key development is a nonlinear neutrino–matter coupling algorithm based on nested fixed-point iteration with Anderson acceleration, enabling fully implicit treatment of collisional processes, including energy-coupling interactions such as neutrino–electron scattering and pair production. Coupling to finite-volume (FV) hydrodynamics is achieved through a hybrid DG-FV representation of the fluid variables and operator-split evolution within FLASH-X. The implementation is verified using basic transport tests with idealized opacities and relaxation and deleptonization problems with tabulated microphysics. Spherically symmetric CCSN simulations demonstrate accuracy and robustness of the coupled scheme, including close agreement with the CCSN simulation code Chimera. An axisymmetric CCSN simulation further demonstrates the viability of DG-based neutrino transport for multidimensional supernova modeling within FLASH-X. thornado’s neutrino-transport solver is GPU-enabled using OpenMP offloading or OpenACC, and all CCSN applications included in this work use the GPU implementation. Together, these results establish a foundation for future enhancements in physics fidelity, numerical algorithms, and computational performance, for increasingly realistic large-scale CCSN simulations.

Endeve, Eirik [Oak Ridge National Laboratory (ORNL↗

Structure‐Aware Representation Learning for Effective Performance Prediction

ABSTRACT Application performance is a function of several unknowns stemming from the interactions between the application, runtime, OS, and underlying hardware, making it challenging to model performance using deep learning techniques, especially without a large labeled dataset. Collecting such labeled longitudinal datasets can take weeks. Intuitively, developers could save analysis time during code development by taking a comparative approach between multiple applications. However, the unknown dynamic interactions between applications and execution environments make it difficult for deep learning‐based models to predict the performance of new applications. In this paper, we address these problems by presenting a labeled dataset for the community and taking a comparative analysis approach to explore the source code differences between different correct implementations of the same problem. This paper assesses the feasibility of using purely static information, for example, Abstract Syntax Tree (AST), of applications to predict performance change based on code structure. We evaluate several deep learning‐based representation learning techniques for source code and propose an architecture for the tree‐based Long Short‐Term Memory (LSTM) models to discover latent representations for a source code's hierarchical structure. We demonstrate that our proposed architecture enables feed‐forward predictive models to predict change in performance using source code with up to 84% accuracy.

Ramadan, Tarek [Department of Computer Science Tex↗

Optimization of Desalination Systems with Detailed Water Chemistry through Integration of Reaktoro in WaterTAP

Chemistry predictions are critical for an accurate estimation of performance and costs in desalination process models, which allows for the estimation of the value of new technologies and the viability of treating new water sources. Herein, we present how an implicit function formulation can be used to integrate the chemical modeling package, Reaktoro, into the techno-economic assessment and modeling platform, WaterTAP. This approach resolves the critical issues of integrating large-scale thermodynamic models and databases into equation-oriented process models while allowing more flexibility relative to previously presented surrogate-based methods. We describe how this integration into Pyomo and WaterTAP models is implemented and used through the open-source package Reaktoro-PSE . We first validate this integration approach by performing optimization on a previously presented desalination treatment train with softening and acid addition as the pretreatment steps. Then, to demonstrate the value of this approach, we extend the cost-optimization problem to include the simultaneous addition of lime and soda ash for softening, and HCl and H 2 SO 4 in the acidification steps. Finally, we were able to confirm the previously established results that were obtained by using surrogate models and demonstrate that the implicit function approach enables exploration of different feedwater compositions and a larger number of chemicals and their combinations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Forecasting high-dimensional spatio-temporal systems from sparse measurements

This paper introduces a new neural network architecture designed to forecast high-dimensional spatio-temporal data using only sparse measurements. The architecture uses a two-stage end-to-end framework that combines neural ordinary differential equations (NODEs) with vision transformers. Initially, our approach models the underlying dynamics of complex systems within a low-dimensional space; and then it reconstructs the corresponding high-dimensional spatial fields. Many traditional methods involve decoding high-dimensional spatial fields before modeling the dynamics, while some other methods use an encoder to transition from high-dimensional observations to a latent space for dynamic modeling. In contrast, our approach directly uses sparse measurements to model the dynamics, bypassing the need for an encoder. This direct approach simplifies the modeling process, reduces computational complexity, and enhances the efficiency and scalability of the method for large datasets. We demonstrate the effectiveness of our framework through applications to various spatio-temporal systems, including fluid flows and global weather patterns. Although sparse measurements have limitations, our experiments reveal that they are sufficient to forecast system dynamics accurately over long time horizons. Our results also indicate that the performance of our proposed method remains robust across different sensor placement strategies, with further improvements as the number of sensors increases. This robustness underscores the flexibility of our architecture, particularly in real-world scenarios where sensor data is often sparse and unevenly distributed.

97 MATHEMATICS AND COMPUTING↗

Workshop on Addressing Rigor and Reproducibility in Thermal, Heterogeneous Catalysis

Heterogeneous catalysis has long served as the bedrock of the manufacturing of energy carriers, fuels and chemicals, and various technologies for pollution abatement. The significant complexity and variability spanning the entire breadth of catalyst material properties, synthesis methods, characterization techniques, and evaluation procedures, has focused attention on the need to establish community-accepted best practices for ensuring high-quality, benchmarked, and reproducible data. In addition, increased societal urgency to transition to clean energy and reduce greenhouse gas concentrations has incentivized interdisciplinary, convergent, and translational approaches to catalysis research in recent years. Research engineers and scientists with expertise cutting broadly across materials science, chemical synthesis, interfacial science, spectroscopy, and methods of data science and computational simulation, all bring diverse and important perspectives to catalysis research, but often with little awareness of the complexity of catalytic systems, especially in their working environment. As has already occurred in other scientific fields, there has been growing recognition and consensus in the heterogeneous catalysis research community that mechanisms are needed to improve the rigor and reproducibility (R&R) of experimental measurements, to ensure alignment of the broader research community with a common core of best practices specific to the realization of high-quality catalysis research. Similarly, the field is moving rapidly toward computationally informed and data science-driven catalyst design, but the success of implementing such predictive tools hinges on model training and validation rooted in rigorously obtained and reproducible experimental data that are benchmarked to common specifications. As such, this workshop was convened to prepare a report summarizing best practices for reporting data and performing experiments that researchers can use to benchmark, validate, and reproduce data in specific sub-fields of thermal, heterogeneous catalysis. Additionally, we discussed recommendations for future actions that may improve R&R in this field. The workshop organizers and participants include a diverse range of catalysis researchers from various employment sectors (e.g., academia, industry, national laboratory), institutional mission and resources (e.g., PhD-granting research universities, non-PhD-granting teaching universities), career stage (e.g., early, mid and late-career), technical expertise, and demographic background. This diverse group was involved in the discussion of workshop agenda items, writing this report, and discussing possible future action items for the community to consider, which helped ensure that a broad range of perspectives were captured in the description of the problems at hand and the creation of actionable solutions that may be effectively adopted by the diverse practitioners in catalysis research. Importantly, this group of workshop participants also included very early career researchers (e.g., senior PhD students, postdoctoral scholars) who will become the next generation of scientific leaders in various sectors, thus capturing emerging perspectives of newcomers to the field to shape its future while positively impacting the development of its future workforce. We envision that this effort will help advance the field of catalysis science by improving the rigor and reproducibility of experimental data collected by current researchers and future newcomers to the field, which is of broad importance to health and vitality of any scientific discipline. Therefore, best practices identified in this endeavor for thermal heterogeneous catalysis can be translated to such efforts in other areas of catalysis and other scientific fields involving the study of materials, and vice versa. We also envision this to be an ongoing effort, with future workshops that are convened to discuss issues of rigor and reproducibility on technical topics that were unable to be covered in this workshop due to its scope limitations, and as emerging methods and materials become more prevalent in the research community.

36 MATERIALS SCIENCE↗

Covariant Quantum Error-Correcting Codes with Metrological Entanglement Advantage

Here, we show that a subset of the basis for the irreducible representations of a tensor-product SU(2) rotation forms a covariant approximate quantum error-correcting code with transversal U(1) logical gates. Generalizing previous work on “thermodynamic codes” to general local spin and different irreducible representations using only properties of the angular momentum algebra, we obtain bounds on the code inaccuracy under generic noise on any known 𝑑 sites, under independent and identically distributed noise, and under heralded 𝑑-local erasures. We demonstrate that this family of codes protects a probe state with quantum Fisher information surpassing the standard quantum limit when the sensing parameter couples to the generator of the U(1) logical gate.

quantum error correction↗

Defect Generation and Evolution in Irradiated Epitaxial Films and Heterostructures of Fe 3 O 4 and Cr 2 O 3

Abstract The functionality of nuclear structural materials, sensors, and microelectronics in harsh environments such as radiation relies on understanding defect generation and evolution processes in oxide layers. The initial radiation response of epitaxial thin films of Fe 3 O 4 (111), Cr 2 O 3 (0001), and Fe 3 O 4 (111)/Cr 2 O 3 (0001) heterostructures deposited on Al 2 O 3 (0001) by oxygen‐assisted molecular beam epitaxy and irradiated with 200 keV He + is characterized. X‐ray diffraction and X‐ray absorption near edge spectroscopy showed that the Cr 2 O 3 layers underwent significant lattice expansion and disordering under irradiation, whereas the Fe 3 O 4 layers do not exhibit noticeable changes. In contrast, positron annihilation spectroscopy revealed an evolution of cation vacancy point defects in the Fe 3 O 4 layers into larger vacancy clusters with increasing irradiation, while the cation vacancies in Cr 2 O 3 remained primarily as single vacancies and small clusters. The results suggest that the Fe 3 O 4 lattice can utilize the free volume of the larger vacancy clusters to relax but the small vacancies in the Cr 2 O 3 lattice do not facilitate relaxation. Comparing defect concentrations in the single layer films versus the heterostructure suggests that point defects may cross the interface from Fe 3 O 4 into Cr 2 O 3 . Together, these results enhance the understanding of the initial defect evolution mechanisms in oxide layers in harsh irradiation environments.

36 MATERIALS SCIENCE↗

Generalized geometric speed limits for quantum observables

Leveraging quantum information geometry, we derive generalized quantum speed limits on the rate of change of the expectation values of observables. These bounds subsume and, for Hilbert space dimension ≥3, tighten existing bounds—in some cases by an arbitrarily large multiplicative constant. Our theoretical results are supported by illustrative examples and an experimental demonstration using a superconducting qutrit. We also derive two upper bounds on the generalized quantum Fisher information in terms of the condition number of the density matrix. One of these bounds applies only to coherent dynamics and depends also on the variance of the Hamiltonian. The other bound depends also on the so-called Wigner-Yanase skew information. These bounds generalize well-known bounds on the symmetric logarithmic derivative quantum Fisher information and are tighter than the existing bounds for sufficiently mixed states (e.g., for sufficiently high temperature thermal states).

open quantum systems & decoherence↗

Time-Resolved Geometric Feature Tracking Elucidates Laser-Induced Keyhole Dynamics

In this report, during laser melting of metals, localized metal evaporation resulting in the formation of a keyhole shaped cavity can occur if processing conditions are chosen with high power density. An unstable keyhole can have deleterious effects in certain applications (e.g., laser powder bed fusion) as it increases the likelihood of producing defects such as porosity. In this work, we propose a pipeline that enables complete segmentation and extraction of various geometric features in keyholing conditions. In situ synchrotron high-speed X-ray visualization at the Advanced Photon Source provides large datasets of experimental images with a high spatio-temporal resolution across a range of laser parameters for Ti-6Al- 4 V. Computer vision image processing techniques were used to extract time-resolved quantitative geometric features (e.g., depth, width, front wall angle) throughout keyhole evolution which were subsequently analyzed to understand the relationship between the variation of local keyhole geometry and processing conditions. This analysis is the first to employ a data-driven approach to further our understanding of the keyholing process regime.

36 MATERIALS SCIENCE↗

Advances and opportunities in materials science for scalable quantum computing

We report that by harnessing unique quantum mechanical phenomena, such as superposition and entanglement, quantum computers offer the possibility to drastically outperform classical computers for certain classes of problems. The realization of this potential, however, presents a substantial challenge, because noise and imperfections associated with the materials used to fabricate devices can obscure the delicate quantum mechanical effects that enable quantum computing. Hence, progress in synthesis, characterization, and modeling of materials for quantum computing have driven many exciting advances in recent years and will become increasingly important in the years to come. As progressively more complex, multi-qubit systems come online, and as significant government and industrial investment drives research forward, new challenges and opportunities for materials science continue to emerge. The articles in this issue survey the current state of materials science progress and obstacles for some leading quantum computing platforms; opportunities for deeper involvement by materials scientists abound. Ultimate realization of the full potential of quantum computers will require a multidisciplinary effort spanning many traditional areas of expertise.

36 MATERIALS SCIENCE↗

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimal adjustment sets for causal query estimation in partially observed biomolecular networks

Abstract Causal query estimation in biomolecular networks commonly selects a ‘valid adjustment set’, i.e. a subset of network variables that eliminates the bias of the estimator. A same query may have multiple valid adjustment sets, each with a different variance. When networks are partially observed, current methods use graph-based criteria to find an adjustment set that minimizes asymptotic variance. Unfortunately, many models that share the same graph topology, and therefore same functional dependencies, may differ in the processes that generate the observational data. In these cases, the topology-based criteria fail to distinguish the variances of the adjustment sets. This deficiency can lead to sub-optimal adjustment sets, and to miss-characterization of the effect of the intervention. We propose an approach for deriving ‘optimal adjustment sets’ that takes into account the nature of the data, bias and finite-sample variance of the estimator, and cost. It empirically learns the data generating processes from historical experimental data, and characterizes the properties of the estimators by simulation. We demonstrate the utility of the proposed approach in four biomolecular Case studies with different topologies and different data generation processes. The implementation and reproducible Case studies are at https://github.com/srtaheri/OptimalAdjustmentSet.

59 BASIC BIOLOGICAL SCIENCES↗

ASCR@40: Four Decades of Department of Energy Leadership in Advanced Scientific Computing Research

Throughout its long history, the Office of Advanced Scientific Computing Research (ASCR) has built the critical technologies to ensure U.S. leadership in energy science and national security. It has made its parent agency, the Department of Energy (DOE) and its Office of Science, the world’s recognized leader in computational science. ASCR’s stated mission is “to discover, develop, and deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to the DOE.” To accomplish this goal, ASCR oversees a large complex of computing and networking facilities and is responsible for procuring, deploying and operating high-performance computing (HPC), networking and storage resources; conducting basic research in mathematics and computer science; developing and sustaining a large body of software; and collaborating with other Office of Science programs, academia and industry. ASCR’s computational science leadership has a long history, predating even DOE’s inception. Applied mathematics and advanced computing were both elements of the Manhattan Project’s Theoretical Division. In the 1950s, DOE’s predecessor, the Atomic Energy Commission, created a mathematics program to develop and apply digital computing by supporting researchers at universities and AEC laboratories. Several organizational and name changes later, this program would grow and become ASCR.

97 MATHEMATICS AND COMPUTING↗

Design and Analysis of an Integral MPPT Control Law for Wave Energy Conversion Systems

In this paper, we propose an integral-based maximum power point tracking (MPPT) algorithm for point absorber wave energy conversion (WEC) systems. A permanent magnet synchronous generator (PMSG) is coupled to the point absorber and its drive implements the proposed MPPT control. While the rotating frame of reference of the PMSG implements power control, the slower mechanical frequency of the incident waves are processed with an additional transformation that yields another set of dc dynamics. The computed dc power in the new reference frame, which is focused on slow wave dynamics, is input to the MPPT control law that tunes the emulated resistance of the machine drive to extract peak power from the wave absorber device. We derive a stability condition for the proposed controller and validate our control design on a simulated 10kW system.

wave energy, maximum power point tracking (MPPT), ↗