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At least 523 records · Page 29

Towards Exascale Astrophysics of Mergers and Supernovae (TEAMS)

The TEAMS project brought together cutting-edge simulations, theoretical insights, and collaborative efforts to deepen our understanding of some of the universe’s most extreme phenomena—supernovae, neutron star mergers, and the powerful signals they emit. Using one of the largest suites of 3D supernova simulations ever conducted, researchers uncovered new insights into how massive stars explode, how those explosions vary by stellar mass, and what conditions lead to the birth of neutron stars or black holes. They also studied the radiation and gravitational wave signals emitted during these events, revealing how future observations can be used to uncover what happens deep inside collapsing stars. The team developed improved tools for modeling how light and neutrinos behave in such explosive environments, enabling more accurate predictions of what astronomers might observe. Work also explored how the chemical composition and geometry of kilonovae—the visible explosions that follow neutron star mergers—influence their signals and can reveal the origins of heavy elements like gold. These efforts not only advanced scientific knowledge, but also trained a new generation of researchers at the intersection of astrophysics, computational science, and nuclear theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The sub-leading scattering waveform from amplitudes

We compute the next-to-leading order term in the scattering waveform of uncharged black holes in classical general relativity and of half-BPS black holes in $\mathcal{N}$ = 8 supergravity. We propose criteria, generalizing explicit calculations at next-to-leading or der, for determining the terms in amplitudes that contribute to local observables. For general relativity, we construct the relevant classical integrand through generalized unitary in two distinct ways, (1) in a heavy-particle effective theory and (2) in general relativity minimally-coupled to scalar fields. With a suitable prescription for the matter propagator in the former, we find agreement between the two methods, thus demonstrating the absence of interference of quantum and classically-singular contributions. The classical $\mathcal{N}$ = 8 integrand for massive scalar fields is constructed through dimensional reduction of the known five-point one-loop integrand. Our calculation exhibits novel features compared to conservative calculations and inclusive observables, such as the appearance of master integrals with intersecting matter lines and the appearance of a classical infrared divergence whose absence from classical observables requires a suitable definition of the retarded time.

79 ASTRONOMY AND ASTROPHYSICS↗

Regulating loops in de Sitter spacetime

Perturbative quantum field theory (QFT) calculations in de Sitter space are riddled with contributions that diverge over time. These contributions often arise from loop integrals, which are notoriously hard to compute in de Sitter. We discuss an approach to evaluate loop integrals that contribute to equal-time correlators of a scalar field theory in a fixed de Sitter background. Our method is based on the Mellin-Barnes representation of correlation functions, which allows us to regulate loop divergences by adjusting the masses of the fields, or by gently deforming the underlying de Sitter spacetime. The resulting expressions have a similar structure as a standard answer from dimensional regularization in flat space QFT. These features of the regulator are illustrated with two examples, worked out in detail. Along the way, we illuminate the physical origin of these divergences and their interpretation with the machinery of the dynamical renormalization group. Our approach regulates the IR divergences of massless and massive particles in the same way. For massless scalars, the loop corrections can be incorporated as systematic improvements to the stochastic inflation framework, allowing for a more precise description of the IR dynamics of such fields in de Sitter. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

DIMPLES: Distributed Influence Maximization for Pandemic pLanning on Exascale Systems

We study exascale parallel algorithms for the selection of intervention or monitoring strategies in massive realistic socio-technical networks through scalable Influence Maximization (InfMax) algorithms. We employ novel techniques to enable efficient scaling on up to 8k nodes of OLCF Frontier, with 65k AMD GPUs and 458k AMD CPU cores. Current state-of-the-art InfMax tools are limited to networks with only a few million actors (vertices) and a few hundred million interactions (edges). By overcoming these limitations, we show that our approach is capable of processing a realistic social contact network of the United States with 285 million nodes and about 8 billion edges. This two orders-of-magnitude improvement over the previous state-of-the-art is obtained by leveraging algorithmic advancements for the InfMax problem and designing several problem-specific approaches to overlap communication with computation, improve GPU efficiency, and lower the application’s memory requirements. We evaluate strong scaling for computing 10k most influential seeds using up to 8k nodes of an exascale system, and weak scaling from 128 to 8k system nodes for seed sets ranging from 625 to 40k seeds. We achieve the fastest-known runtime of 25 minutes while performing 48 million diffusion simulations totaling 2.31 petabytes to identify 40k influential seeds using 8k nodes, and take 5.75 minutes to identify 10k seeds while using 4k nodes.

Minutoli, Marco [Pacific Northwest National Labora↗

Integrating ytopt and libEnsemble to autotune OpenMC

Ytopt is a Python machine-learning-based autotuning software package developed within the ECP PROTEAS-TUNE project. The ytopt software adopts an asynchronous search framework that consists of sampling a small number of input parameter configurations and progressively fitting a surrogate model over the input-output space until exhausting the user-defined maximum number of evaluations or the wall-clock time. libEnsemble is a Python toolkit for coordinating workflows of asynchronous and dynamic ensembles of calculations across massively parallel resources developed within the ECP PETSc/TAO project. libEnsemble helps users take advantage of massively parallel resources to solve design, decision, and inference problems and expands the class of problems that can benefit from increased parallelism. In this paper we present our methodology and framework to integrate ytopt and libEnsemble to take advantage of massively parallel resources to accelerate the autotuning process. Specifically, we focus on using the proposed framework to autotune the ECP ExaSMR application OpenMC, an open source Monte Carlo particle transport code. OpenMC has seven tunable parameters some of which have large ranges such as the number of particles in-flight, which is in the range of 100,000 to 8 million, with its default setting of 1 million. Setting the proper combination of these parameter values to achieve the best performance is extremely time-consuming. Therefore, we apply the proposed framework to autotune the MPI/OpenMP offload version of OpenMC based on a user-defined metric such as the figure of merit (FoM) (particles/s) or energy efficiency energy-delay product (EDP) on Crusher at Oak Ridge Leadership Computing Facility. In conclusion, the experimental results show that we achieve the improvement up to 29.49% in FoM and up to 30.44% in EDP.

Autotuning↗

Modeling Dust Production, Growth, and Destruction in Reionization-era Galaxies with the CROC Simulations: Methods and Parameter Exploration

We introduce a model for the explicit evolution of interstellar dust in a cosmological galaxy formation simulation. We post-process a simulation from the Cosmic Reionization on Computers project, integrating an ordinary differential equation for the evolution of the dust-to-gas ratio along pathlines in the simulation sampled with a tracer particle technique. This model incorporates the effects of dust grain production in asymptotic giant branch star winds and supernovae, grain growth due to the accretion of heavy elements from the gas phase of the interstellar medium, and grain destruction due to thermal sputtering in the high-temperature gas of supernova remnants due to thermal sputtering. A main conclusion of our analysis is the importance of a carefully chosen dust destruction model, for which different reasonable parameterizations can predict very different values at the ∼100 pc resolution of the interstellar medium (ISM) in our simulations. We run this dust model on the single most massive galaxy in a 10 h$^{−1}$ comoving megaparsec box, which attains a stellar mass of ∼2 × 10$^{9}$ M $_{⊙}$ by z = 5. We find that the model is capable of reproducing dust masses and dust-sensitive observable quantities broadly consistent with existing data from high-redshift galaxies. The total dust mass in the simulated galaxy is somewhat sensitive to parameter choices for the dust model, especially the timescale for grain growth due to accretion in the ISM. Consequently, observable quantity observations that can constrain galaxy dust masses at these epochs are potentially useful for placing constraints on dust physics.

79 ASTRONOMY AND ASTROPHYSICS↗

Low-Power Deep Learning Inference using the SpiNNaker Neuromorphic Platform

n this presentation we will discuss recent results on using the SpiNNaker neuromorphic platform (48-chip model) for deep learning neural network inference. We use the Sandia Labs developed Whet stone spiking deep learning library to train deep multi-layer perceptrons and convolutional neural networks suitable for the spiking substrate on the neural hardware architecture. By using the massively parallel nature of SpiNNaker, we are able to achieve, under certain network topologies, substantial network tiling and consequentially impressive inference throughput. Such high-throughput systems may have eventual application in remote sensing applications where large images need to be chipped, scanned, and processed quickly. Additionally, we explore complex topologies that push the limits of the SpiNNaker routing hardware and investigate how that impacts mapping software-implemented networks to on-hardware instantiations.

97 MATHEMATICS AND COMPUTING↗

ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design

Abstract Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical ‘starters’ and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.

59 BASIC BIOLOGICAL SCIENCES↗

A massively parallel and scalable multi-CPU material point method

Harnessing the power of modern multi-GPU architectures, we present a massively parallel simulation system based on the Material Point Method (MPM) for simulating physical behaviors of materials undergoing complex topological changes, self-collision, and large deformations. Our system makes three critical contributions. First, we introduce a new particle data structure that promotes coalesced memory access patterns on the GPU and eliminates the need for complex atomic operations on the memory hierarchy when writing particle data to the grid. Second, we propose a kernel fusion approach using a new Grid-to-Particles-to-Grid (G2P2G) scheme, which efficiently reduces GPU kernel launches, improves latency, and significantly reduces the amount of global memory needed to store particle data. Finally, we introduce optimized algorithmic designs that allow for efficient sparse grids in a shared memory context, enabling us to best utilize modern multi-GPU computational platforms for hybrid Lagrangian-Eulerian computational patterns. We demonstrate the effectiveness of our method with extensive benchmarks, evaluations, and dynamic simulations with elastoplasticity, granular media, and fluid dynamics. In comparisons against an open-source and heavily optimized CPU-based MPM codebase [Fang et al. 2019] on an elastic sphere colliding scene with particle counts ranging from 5 to 40 million, our GPU MPM achieves over 100x per-time-step speedup on a workstation with an Intel 8086K CPU and a single Quadro P6000 GPU, exposing exciting possibilities for future MPM simulations in computer graphics and computational science. Moreover, compared to the state-of-the-art GPU MPM method [Hu et al. 2019a], we not only achieve 2x acceleration on a single GPU but our kernel fusion strategy and Array-of-Structs-of-Array (AoSoA) data structure design also generalizes to multi-GPU systems. Our multi-GPU MPM exhibits near-perfect weak and strong scaling with 4 GPUs, enabling performant and large-scale simulations on a 10243 grid with close to 100 million particles with less than 4 minutes per frame on a single 4-GPU workstation and 134 million particles with less than 1 minute per frame on an 8-GPU workstation.

Wang, Xinlei↗

Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.

59 BASIC BIOLOGICAL SCIENCES↗

Do not forget the electrons: Extending moderately-sized nuclear networks for multidimensional hydrodynamic codes

Context.Nuclear networks are widely used coupled with hydrodynamical simulations of explosive scenarios to account for the change of nuclear species and energy generation rate due to nuclear reactions. In this way, there is a feedback mechanism between the hydrodynamical state and the nuclear processes. Unfortunately, the timescale of nuclear reactions is orders of magnitude smaller than the dynamical timescale that drives hydrodynamical simulations. Therefore, these nuclear networks are usually very small, reduced in most cases to a dozen elements, especially when simulations are carried out in more than one dimension. Aims.We present here an extended nuclear network, with 90 species, designed for being coupled with hydrodynamic simulations, which includes neutrons, protons, electrons, positrons, and the corresponding neutrino and anti-neutrino emission. This network is also coupled with temperature, making it extremely robust and, together with its size, unique of its kind. The inclusion of electron captures on free protons makes the network very appropriate for multidimensional studies of Type Ia supernova explosions, especially when the exploding object is a massive white dwarf. Methods.We perform several tests that are relevant to simulate explosive scenarios, such as Type Ia supernovae and core-collapse supernovae. We compare the results of the 90 nuclei network with a standardα-chain network with 14 elements to evaluate the differences in the energy generation rate. We also evaluate the relevance of including the electrons in the network in terms of generated yields and how it affects the pressure of a degenerate fluid such as that of white dwarfs. The results obtained with the 90-nuclei network have been verified with a much larger 2000-nuclei network built from REACLIB (WinNet), in terms of nuclear energy generation rate, pressure, and produced yields. Results.The results obtained with the proposed medium-sized network compare fairly well, to a few percent, with those computed withWinNetin scenarios reproducing the gross physical conditions of current Type Ia supernova explosion models. In those cases where the carbon and oxygen fuel ignites at high density, the high-temperature plateau typical of the nuclear statistical equilibrium regime is well defined and stable, allowing large integration time steps. We show that the inclusion of electron captures on free protons substantially improves the estimation of the electron fraction of the mixture. Therefore, the pressure is better determined than in networks where electron captures are excluded, which will ultimately lead to more reliable hydrodynamic models. Explosive combustion of helium at low density, occurring near the surface layer of a white dwarf, is also better described with the proposed network, which gives nuclear energy generation rates much closer toWinNetthan typical reduced alpha networks. Conclusions.A nuclear network withN= 90 species, including electrons, aimed at multidimensional calculations of supernova explosions is described and verified. The proposed network is suitable for the study of Type Ia supernova explosions because it provides better values of pressure and electron abundance than other existing networks with smaller or even a similar size but without including electron capture processes.

Astronomy & Astrophysics↗

Lignin Utilization

Valorization of lignin has massive potential economic and sustainability benefits for the lignocellulosic biorefinery. However, challenges remain to realize lignin conversion to coproducts, especially related to selective, high yield depolymerization to monomers and quantitative analytics on lignin, the latter of which is critical for accurate process modeling. Towards these goals, the Lignin Utilization project focuses on catalytic lignin deconstruction chemistries for C-O and C-C bond cleavage, development of analytical chemistry techniques to quantitatively characterize lignin, and syntheses of requisite model compounds for understanding lignin transformations. This work is done with and supports multiple BETO projects, including the Biological Lignin Valorization (BLV) project, the Separations Consortium, and others. Outcomes of Lignin Utilization for analytics and synthesis include 1) development of new mass spectrometry (MS) methods to characterize lignin dimers/oligomers in process streams, 2) deployment of a computational-experimental tool (with Biochemical Process Modeling and Simulation) to identify lignin-derived compounds with high fidelity from MS, and 3) delivery of >40 unique compounds. From a catalysis perspective, we have developed new oxidative approaches to cleave C-O and C-C bonds and produce >50% bio-available aromatic monomers for biological funneling for the BLV project and have developed recoverable bases for base-catalyzed deconstruction of lignin.

BIOMASS FUELS↗

Numerical analyses of exponential time-differencing schemes for the solution of atmospheric models

In high-resolution numerical weather prediction models, fast-moving acoustic waves must be treated in a stable manner. Among the implicit–explicit (IMEX) schemes used for the solution of these models, horizontally explicit, vertically implicit (HEVI) methods show good stability and scalability on massively parallel machines. In this work, we present two classes of exponential time-differencing (ETD) methods for atmospheric models that use a HEVI splitting strategy, one being a three-stage method with the addition of artificial diffusion, the second based on a Strang splitting approach. Overall, the stability properties of the methods are analyzed and numerical examples are provided, which compare time-step restrictions and cost-to-accuracy ratios of the new methods with those for existing approaches.

54 ENVIRONMENTAL SCIENCES↗

Sierra/SD – User's Manual – 5.18

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high-fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a user’s guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

97 MATHEMATICS AND COMPUTING↗

Center for Gas Separations (CGS)

The total energy consumption in the U.S. has been rising steadily for decades, and it currently amounts to ~98,000 TBtu/yr, with approximately 30% of this total attributable to the industrial sector. Reasonable estimates indicate that 45–55% of total industry energy consumption derives from chemical separations, and for example, over 120 TBtu/yr alone is used in carrying out olefin/paraffin separations via energy-intensive cryogenic distillation. Therefore, the pursuit of new, even radically different approaches to some of the most energy-intensive industrial separations processes is an imperative scientific pursuit for reducing energy consumption toward a more sustainable future. Adsorbent and membrane-based separations can require a fraction of the energy needed for distillation methods, and as such are considered promising solutions for balancing increasing energy demand in the U.S. with the need for a massive reduction in energy consumption. Although considerable research effort has been devoted to the design of materials capable of carrying out various gas separations, usually operating through size-selective, chemisorptive, or physisorptive mechanisms, it remains a great challenge to design materials that function adequately for real-world applications. Indeed, the chemical and physical differences between molecules in gas mixtures of interest are often small, and therefore it is necessary, through the use of nanoscience and synthetic chemistry, to engineer unprecedented molecular-level control in adsorbate–adsorbent interactions. The overarching mission of the Center for Gas Separations (CGS) was to discover fundamental innovations that have the potential to dramatically reduce the energy associated with critical gas separations. In particular, the CGS developed novel synthetic routes, guided by molecular chemistry principles, as well as advanced characterization and computational methods, that have enabled the discovery of new materials and membranes tailor-made to exhibit exceptional performance for a range of gas separations processes, as required in the clean use of fossil fuels and in reducing CO 2 emissions from industry. A challenge of this magnitude required the collaboration and synergy of a large team of researchers with expertise in materials synthesis, characterization, and computations. During the 11-year project period, the CGS created a range of new materials within the family of highly-tunable, porous solids known as metal–organic frameworks (MOFs). These new frameworks demonstrate novel mechanisms for key industrial gas separations, including revolutionary new cooperative adsorption processes that enable low-energy CO 2 and CO capture, and are capable of efficiently separating olefins from paraffins, O 2 from air, and the shape-selective separation of alkane isomers. In addition, the CGS developed new strategies for incorporating these materials into composite membranes toward highly efficient and selective membrane-based separations. As a testament to the success of the CGS, two start-up companies, Mosaic Materials,4 Inc. and Flux Technology, Inc., grew out of these research efforts, and these companies are seeking to commercialize MOF and composite membranes materials for key separations in industry, including large-scale CO 2 capture and hydrocarbon separations, respectively. Another company, framergy, Inc., licensed IP resulting from CGS research toward the commercialization of adsorbents for various energy-relevant applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward a persistent event-streaming system for high-performance computing applications

High-performance computing (HPC) applications have traditionally relied on parallel file systems and file transfer services to manage data movement and storage. Alternative approaches have been proposed that use direct communications between application components, trading persistence and fault tolerance for speed. Event-driven architectures, as popularized in enterprise contexts, present a compelling middle ground, avoiding the performance cost and API constraints of parallel file systems while retaining persistence and offering impedance matching between application components. However, adapting streaming frameworks to HPC workloads requires addressing challenges unique to HPC systems. This paper investigates the potential for a streaming framework designed for HPC infrastructures and use cases. We introduce Mofka, a persistent event-streaming framework designed specifically for HPC environments. Mofka combines the capabilities of a traditional streaming service with optimizations tailored to the HPC context, such as support for massively multicore nodes, efficient scaling for large producer-consumer workflows, RDMA-enabled high-performance network communications, specialized network fabrics with multiple links per node, and efficient handling of large scientific data payloads. Built using the Mochi suite of HPC data service components, Mofka provides a lightweight, modular, and high-performance solution for persistent streaming in HPC systems. We present the architecture of Mofka and evaluate its performance against Kafka and Redpanda using benchmarks on diverse platforms, including Argonne's Polaris and Oak Ridge's Frontier supercomputers, showing up to 8× improvement in throughput in some scenarios. We then demonstrate its utility in several real-world applications: a tomographic reconstruction pipeline, a workflow for the discovery of metal-organic frameworks for carbon capture, and the instrumentation of Dask workflows for provenance tracking and performance analysis.

HPC↗

Sierra/SD--User's Manual - 4.58

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high-fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a user's guide to the input for Sierra/SD . Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

97 MATHEMATICS AND COMPUTING↗

Sierra/SD - User's Manual - 5.10

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high-fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a user’s guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

97 MATHEMATICS AND COMPUTING↗