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Jonah Miller

Publications and source records attributed to Jonah Miller.

16 recordsLinked to original sources

Characterizing Adaptive Mesh Refinement on Heterogeneous Platforms with Parthenon-VIBE

Hero-class HPC simulations rely on Adaptive Mesh Refinement (AMR) to reduce compute and memory demands while maintaining accuracy. This work analyzes the performance of Parthenon, a block-structured AMR benchmark, on CPU-GPU systems. We show that smaller mesh blocks and deeper AMR levels degrade GPU performance due to increased communication, serial overheads, and inefficient GPU utilization. Through detailed profiling, we identify inefficiencies, low occupancy, and memory access bottlenecks. We further analyze rank scalability and memory constraints, and propose optimizations to improve GPU throughput and reduce memory footprint. Our insights can inform future AMR deployments on Department of Energy's upcoming heterogeneous supercomputers.

cs.DC

The Well: a Large-Scale Collection of Diverse Physics Simulations for Machine Learning

Machine learning based surrogate models offer researchers powerful tools for accelerating simulation-based workflows. However, as standard datasets in this space often cover small classes of physical behavior, it can be difficult to evaluate the efficacy of new approaches. To address this gap, we introduce the Well: a large-scale collection of datasets containing numerical simulations of a wide variety of spatiotemporal physical systems. The Well draws from domain experts and numerical software developers to provide 15TB of data across 16 datasets covering diverse domains such as biological systems, fluid dynamics, acoustic scattering, as well as magneto-hydrodynamic simulations of extra-galactic fluids or supernova explosions. These datasets can be used individually or as part of a broader benchmark suite. To facilitate usage of the Well, we provide a unified PyTorch interface for training and evaluating models. We demonstrate the function of this library by introducing example baselines that highlight the new challenges posed by the complex dynamics of the Well. The code and data is available at https://github.com/PolymathicAI/the_well.

cs.LG

What You See is Not What You Get: Neural Partial Differential Equations and The Illusion of Learning

Differentiable Programming for scientific machine learning (SciML) has recently seen considerable interest and success, as it directly embeds neural networks inside PDEs, often called as NeuralPDEs, derived from first principle physics. Therefore, there is a widespread assumption in the community that NeuralPDEs are more trustworthy and generalizable than black box models. However, like any SciML model, differentiable programming relies predominantly on high-quality PDE simulations as "ground truth" for training. However, mathematics dictates that these are only discrete numerical approximations of the true physics. Therefore, we ask: Are NeuralPDEs and differentiable programming models trained on PDE simulations as physically interpretable as we think? In this work, we rigorously attempt to answer these questions, using established ideas from numerical analysis, experiments, and analysis of model Jacobians. Our study shows that NeuralPDEs learn the artifacts in the simulation training data arising from the discretized Taylor Series truncation error of the spatial derivatives. Additionally, NeuralPDE models are systematically biased, and their generalization capability is likely enabled by a fortuitous interplay of numerical dissipation and truncation error in the training dataset and NeuralPDE, which seldom happens in practical applications. This bias manifests aggressively even in relatively accessible 1-D equations, raising concerns about the veracity of differentiable programming on complex, high-dimensional, real-world PDEs, and in dataset integrity of foundation models. Further, we observe that the initial condition constrains the truncation error in initial-value problems in PDEs, thereby exerting limitations to extrapolation. Finally, we demonstrate that an eigenanalysis of model weights can indicate a priori if the model will be inaccurate for out-of-distribution testing.

cs.LG

Phoebus: Performance Portable GRRMHD for Relativistic Astrophysics

We introduce the open source code PHOEBUS (phifty one ergs blows up a star) for astrophysical general relativistic radiation magnetohydrodynamic simulations. PHOEBUS is designed for, but not limited to, high energy astrophysical environments such as core-collapse supernovae, neutron star mergers, black-hole accretion disks, and similar phenomena. General relativistic magnetohydrodynamics are modeled in the Valencia formulation with conservative finite volume methods. Neutrino radiation transport is included with Monte Carlo and moment methods. PHOEBUS is built on the PARTHENON (Grete et al. 2022) performance portable adaptive mesh refinement framework, uses a GPU first development strategy, and is capable of modeling a large dynamic range in space and time. PHOEBUS utilizes KOKKOS for on-node parallelism and supports both CPU and GPU architectures. We describe the physical model employed in PHOEBUS, the numerical methods used, and demonstrate a suite of test problems to showcase its abilities. We demonstrate weak scaling to over 500 H100 GPUs.

astro-ph.HE

The time evolution of fast flavor crossings in post-merger disks around a black hole remnant

We postprocess a three-dimensional general relativistic, full transport neutrino radiation magnetohydrodynamics simulation of the black hole--accretion disk--wind system thought to be a potential outcome of the GW170817 merger to investigate the presence of electron lepton number (ELN-XLN) crossings in the neutrino angular distribution. Neutrinos are evolved with an explicit Monte Carlo method and can interact with matter via emission, absorption, or scattering. Within the postprocessing framework, we find ubiquitous occurrence of ELN-XLN crossings at early times ($\sim$ 11ms) but this does not hold for later times in the simulation. At postmerger times of $ \sim$ 60 ms and beyond, ELN-XLN crossings are only present near the equator. We provide a detailed analysis of the neutrino radiation field to investigate the origin and time evolution of these crossings. Previous reports have suggested ubiquitous flavor crossings persisting throughout the simulation lifetime, albeit for different sets of conditions for the merger remnant, the treatment of hydrodynamics and neutrino transport. Even though we do not perform a direct comparison with other published works, we qualitatively assess the reasons for the difference with our results. The geometric structure and evolution of the ELN-XLN crossings found in our analysis, and by extension, fast flavor instabilities have important implications for heavy element nucleosynthesis in neutron star mergers.

astro-ph.HE

Magnetic Field Strength Effects on Nucleosynthesis from Neutron Star Merger Outflows

Magnetohydrodynamic turbulence drives the central engine of post-merger remnants, potentially powering both a nucleosynthetically active disk wind and the relativistic jet behind a short gamma ray burst. We explore the impact of the magnetic field on this engine by simulating three post-merger black hole accretion disks using general relativistic magnetohydrodynamics with Monte Carlo neutrino transport, in each case varying the initial magnetic field strength. We find increasing ejecta masses associated with increasing magnetic field strength. We find that a fairly robust main r -process pattern is produced in all three cases, scaled by the ejected mass. Changing the initial magnetic field strength has a considerable effect on the geometry of the outflow and hints at complex central engine dynamics influencing lanthanide outflows. We find that actinide production is especially sensitive to magnetic field strength, with overall actinide mass fraction calculated at 1 Gyr post-merger increasing by more than a factor of six with a tenfold increase in magnetic field strength. This hints at a possible connection to the variability in actinide enhancements exhibited by metal poor, r -process-enhanced stars.

astro-ph.HE

Enabling real-time multi-messenger astrophysics discoveries with deep learning

Multi-messenger astrophysics is a fast-growing, interdisciplinary field that combines data, which vary in volume and speed of data processing, from many different instruments that probe the Universe using different cosmic messengers: electromagnetic waves, cosmic rays, gravitational waves and neutrinos. In this Expert Recommendation, we review the key challenges of real-time observations of gravitational wave sources and their electromagnetic and astroparticle counterparts, and make a number of recommendations to maximize their potential for scientific discovery. These recommendations refer to the design of scalable and computationally efficient machine learning algorithms; the cyber-infrastructure to numerically simulate astrophysical sources, and to process and interpret multi-messenger astrophysics data; the management of gravitational wave detections to trigger real-time alerts for electromagnetic and astroparticle follow-ups; a vision to harness future developments of machine learning and cyber-infrastructure resources to cope with the big-data requirements; and the need to build a community of experts to realize the goals of multi-messenger astrophysics.

gr-qc

Composition Effects on Kilonova Spectra and Light Curves: I

The merger of neutron star binaries is believed to eject a wide range of heavy elements into the universe. By observing the emission from this ejecta, scientists can probe the ejecta properties (mass, velocity and composition distributions). The emission (a.k.a. kilonova) is powered by the radioactive decay of the heavy isotopes produced in the merger and this emission is reprocessed by atomic opacities to optical and infra-red wavelengths. Understanding the ejecta properties requires calculating the dependence of this emission on these opacities. The strong lines in the optical and infra-red in lanthanide opacities have been shown to significantly alter the light-curves and spectra in these wavelength bands, arguing that the emission in these wavelengths can probe the composition of this ejecta. Here we study variations in the kilonova emission by varying individual lanthanide (and the actinide uranium) concentrations in the ejecta. The broad forest of lanthanide lines makes it difficult to determine the exact fraction of individual lanthanides. Nd is an exception. Its opacities above 1 micron are higher than other lanthanides and observations of kilonovae can potentially probe increased abundances of Nd. Similarly, at early times when the ejecta is still hot (first day), the U opacity is strong in the 0.2-1 micron wavelength range and kilonova observations may also be able to constrain these abundances.

astro-ph.HE

Understanding the Engines and Progenitors of Gamma-Ray Bursts

Our understanding of the engines and progenitors of gamma-ray bursts has expanded through the ages as a broader set of diagnostics has allowed us to test our understanding of these objects. Here we review the history of the growth in our understanding, focusing on 3 leading engines and 9 potential progenitors. The first gravitational wave detection of a short burst is the latest in a series of breakthrough observations shaping this understanding and we study the importance of multi-diagnostic, multi-messenger observations on these engines and their progenitors. Our understanding based on a detailed study of nearby bursts can be applied to make predictions for the trends expected as we begin to observe high redshift bursts and we discuss these trends.

astro-ph.HE

Constraints on Gamma-ray Burst Inner Engines in a Blandford-Znajek Framework

Under the assumption that a Gamma-ray Burst (GRB) is ultimately produced by a Blandford-Znajek (BZ) jet from a highly spinning black hole BH, we put limits on the magnetic field and BH mass needed to power observed long and short GRBs. For BHs in the range of $2-10 M_{\odot}$ (for long GRBs) and $0.5-4 M_{\odot}$ (for short GRBs), we find magnetic fields in the range of $5x10^{14} \lesssim B \lesssim 10^{17}$ G are needed to power the observed GRBs. Under the simple assumption of flux conservation, we estimate the magnetic fields of the progenitor systems for both long and short GRBs, finding that single massive star progenitors require fields $\sim 10^{6}$ G and NS merger systems require fields $\sim 10^{15}$ G. We also discuss the implications and consequences of high magnetic fields in GRB BH-disk systems, in terms of MRI field growth and magnetically arrested disks. Finally, we examine the conditions under which the progenitor systems can retain enough angular momentum to create BHs spinning rapidly enough to power BZ jets.

astro-ph.HE

Good Usability Practices in Scientific Software Development

Scientific software often presents very particular requirements regarding usability, which is often completely overlooked in this setting. As computational science has emerged as its own discipline, distinct from theoretical and experimental science, it has put new requirements on future scientific software developments. In this paper, we discuss the background of these problems and introduce nine aspects of good usability. We also highlight best practices for each aspect with an emphasis on applications in computational science.

cs.HC

SpECTRE: A Task-based Discontinuous Galerkin Code for Relativistic Astrophysics

We introduce a new relativistic astrophysics code, SpECTRE, that combines a discontinuous Galerkin method with a task-based parallelism model. SpECTRE's goal is to achieve more accurate solutions for challenging relativistic astrophysics problems such as core-collapse supernovae and binary neutron star mergers. The robustness of the discontinuous Galerkin method allows for the use of high-resolution shock capturing methods in regions where (relativistic) shocks are found, while exploiting high-order accuracy in smooth regions. A task-based parallelism model allows efficient use of the largest supercomputers for problems with a heterogeneous workload over disparate spatial and temporal scales. We argue that the locality and algorithmic structure of discontinuous Galerkin methods will exhibit good scalability within a task-based parallelism framework. We demonstrate the code on a wide variety of challenging benchmark problems in (non)-relativistic (magneto)-hydrodynamics. We demonstrate the code's scalability including its strong scaling on the NCSA Blue Waters supercomputer up to the machine's full capacity of 22,380 nodes using 671,400 threads.

astro-ph.HE

Report on the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)

This report records and discusses the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4). The report includes a description of the keynote presentation of the workshop, the mission and vision statements that were drafted at the workshop and finalized shortly after it, a set of idea papers, position papers, experience papers, demos, and lightning talks, and a panel discussion. The main part of the report covers the set of working groups that formed during the meeting, and for each, discusses the participants, the objective and goal, and how the objective can be reached, along with contact information for readers who may want to join the group. Finally, we present results from a survey of the workshop attendees.

cs.SE

Ab initio holography

We apply the quantum renormalization group to construct a holographic dual for the U(N) vector model for complex bosons defined on a lattice. The bulk geometry becomes dynamical as the hopping amplitudes which determine connectivity of space are promoted to quantum variables. In the large N limit, the full bulk equations of motion for the dynamical hopping fields are numerically solved for finite systems. From finite size scaling, we show that different phases exhibit distinct geometric features in the bulk. In the insulating phase, the space gets fragmented into isolated islands deep inside the bulk, exhibiting ultra-locality. In the superfluid phase, the bulk exhibits a horizon beyond which the geometry becomes non-local. Right at the horizon, the hopping fields decay with a universal power-law in coordinate distance between sites, while they decay in slower power-laws with continuously varying exponents inside the horizon. At the critical point, the bulk exhibits a local geometry whose characteristic length scale diverges asymptotically in the IR limit.

hep-th

A first look at transition amplitudes in (2+1)-dimensional causal dynamical triangulations

We study a lattice regularization of the gravitational path integral--causal dynamical triangulations--for (2+1)-dimensional Einstein gravity with positive cosmological constant in the presence of past and future spacelike boundaries of fixed intrinsic geometries. For spatial topology of a 2-sphere, we determine the form of the Einstein-Hilbert action supplemented by the Gibbons-Hawking-York boundary terms within the Regge calculus of causal triangulations. Employing this action we numerically simulate a variety of transition amplitudes from the past boundary to the future boundary. To the extent that we have so far investigated them, these transition amplitudes appear consistent with the gravitational effective action previously found to characterize the ground state of quantum spacetime geometry within the Euclidean de Sitter-like phase. Certain of these transition amplitudes convincingly demonstrate that the so-called stalks present in this phase are numerical artifacts of the lattice regularization, seemingly indicate that the quantization technique of causal dynamical triangulations differs in detail from that of the no-boundary proposal of Hartle and Hawking, and possibly represent the first numerical simulations of portions of temporally unbounded quantum spacetime geometry within the causal dynamical triangulations approach. We also uncover tantalizing evidence suggesting that Lorentzian not Euclidean de Sitter spacetime dominates the ground state on sufficiently large scales.

gr-qc

A Tale of Two Arc Lengths: Metric notions for curves in surfaces in equiaffine space

In Euclidean geometry, all metric notions (arc length for curves, the first fundamental form for surfaces, etc.) are derived from the Euclidean inner product on tangent vectors, and this inner product is preserved by the full symmetry group of Euclidean space (translations, rotations, and reflections). In equiaffine geometry, there is no invariant notion of inner product on tangent vectors that is preserved by the full equiaffine symmetry group. Nevertheless, it is possible to define an invariant notion of arc length for nondegenerate curves, and an invariant first fundamental form for nondegenerate surfaces in equiaffine space. This leads to two possible notions of arc length for a curve contained in a surface, and these two arc length functions do not necessarily agree. In this paper we will derive necessary and sufficient conditions under which the two arc length functions do agree, and illustrate with examples.

math.DG