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Zarija Lukić

Publications and source records attributed to Zarija Lukić.

At least 19 recordsLinked to original sources

DeepCQ: General-Purpose Deep-Surrogate Framework for Lossy Compression Quality Prediction

Error-bounded lossy compression techniques have become vital for scientific data management and analytics, given the ever-increasing volume of data generated by modern scientific simulations and instruments. Nevertheless, assessing data quality post-compression remains computationally expensive due to the intensive nature of metric calculations. In this work, we present a general-purpose deep-surrogate framework for lossy compression quality prediction (DeepCQ), with the following key contributions: 1) We develop a surrogate model for compression quality prediction that is generalizable to different error-bounded lossy compressors, quality metrics, and input datasets; 2) We adopt a novel two-stage design that decouples the computationally expensive feature-extraction stage from the light-weight metrics prediction, enabling efficient training and modular inference; 3) We optimize the model performance on time-evolving data using a mixture-of-experts design. Such a design enhances the robustness when predicting across simulation timesteps, especially when the training and test data exhibit significant variation. We validate the effectiveness of DeepCQ on four real-world scientific applications. Our results highlight the framework's exceptional predictive accuracy, with prediction errors generally under 10\% across most settings, significantly outperforming existing methods. Our framework empowers scientific users to make informed decisions about data compression based on their preferred data quality, thereby significantly reducing I/O and computational overhead in scientific data analysis.

cs.LG↗

diffhydro: Inverse Multiphysics Modeling and Embedded Machine Learning in Astrophysical Flows

We present the extension of the differentiable hydrodynamics code, diffhydro, enabling scalable PDE-constrained inference and integrated hybrid physics-ML models for a wide range of astrophysical applications. New physics additions include radiative heating/cooling, OU-driven turbulence, and self-gravity via multigrid Poisson. We demonstrate good agreement with the Athena++ code on standard validation tests such as Sedov-Taylor, Kelvin-Helmholtz, and driven/decaying turbulence. We further introduce a solver-in-the-loop neural corrector that reduces coarse-grid errors during time integration while preserving stability. The addition of custom adjoints facilitates efficient end-to-end gradients and multi-device scaling. We present simulations up to 1024^3 elements, run on distributed GPU systems, and we show gradient-based reconstructions of complex initial conditions in turbulent, self-gravitating, radiatively cooling flows. The code is written in JAX, and the solver's modular finite-volume components are compiled by XLA into fused accelerator kernels, delivering high-throughput forward runs and tractable differentiation through long integrations.

astro-ph.IM↗

Nyx-RT: Adaptive Ray Tracing in the Nyx Hydrodynamical Code

Numerical methods for radiative transfer play a key role in modern-day astrophysics and cosmology, including study of the inhomogeneous reionization process. In this context, ray tracing methods are well-regarded for accuracy but notorious for high computational cost. In this work, we extend the capabilities of the Nyx N-body / hydrodynamics code, coupling radiation to gravitational and gas dynamics. We formulate adaptive ray tracing as a novel series of filters and transformations that can be used with AMReX particle abstractions, simplifying implementation and enabling portability across Exascale GPU architectures. To address computational cost, we present a new algorithm for merging sources, which significantly accelerates computation once reionization is well underway. Furthermore, we develop a novel prescription for geometric overlap correction with low-density neighbor cells. We perform verification and validation against standard analytic and numerical test problems. Finally, we demonstrate scaling to up to 1024 nodes and 4096 GPUs running multiphysics cosmological simulations, with 4096^3 Eulerian gas cells, 4096^3 dark matter particles, and ray tracing on a 1024^3 coarse grid. For these full cosmological simulations, we demonstrate convergence in terms of reionization history and post-ionization Lyman-alpha forest flux.

astro-ph.IM↗

Analytic Model for Scattered Ly$\boldsymbolα$ Emission in the Post-reionization Intergalactic Medium

Ly$α$ intensity mapping is emerging as a new probe of faint galaxies consisting the cosmic web that elude traditional surveys. However, the resonant nature of Ly$α$ radiative transfer complicates the interpretation of observed data. In this study, we develop a fast and accurate analytic prescription for computing the Ly$α$ intensity field on Mpc scales in the post-reionization Universe. Motivated by insights from Monte Carlo radiative transfer (MCRT) experiments, we exploit the fact that in a highly ionized intergalactic medium (IGM) with negligible damping-wing opacity, cosmological redshifting quickly drives Ly$α$ photons out of resonance, terminating the scattering process and simplifying their large-scale behavior. Photons emitted blueward of the Ly$α$ line center tend to scatter on a thin, nearly spherical surface of last scattering, with a radius determined by the redshifting distance to resonance. Based on this behavior, we derive closed-form expressions for the scattered emissivity and projected surface brightness that depend only on the source spectrum, the HI density, and the peculiar velocity field. When applied to a source in a realistically simulated IGM at $z = 3$, our model shows mild discrepancies with MCRT results within a physical Mpc of the host halo, where strong gravitational infall redistributes the scattered photons, but achieves better than 5% accuracy beyond that distance in angle-averaged radial surface brightness profile. Our prescription offers a computationally efficient alternative to MCRT for forward-modeling Ly$α$ intensity maps from cosmological simulations, enabling the inference of underlying cosmological and astrophysical parameters from future observations

astro-ph.CO↗

A Gigaparsec-Scale Hydrodynamic Volume Reconstructed with Deep Learning

The next generation of cosmological spectroscopic sky surveys will probe the distribution of matter across several Gigaparsecs (Gpc) or many billion light-years. In order to leverage the rich data in these new maps to gain a better understanding of the physics that shapes the large-scale structure of the cosmos, observed matter distributions must be compared to simulated mock skies. Small mock skies can be produced using precise, physics-driven hydrodynamical simulations. However, the need to capture small, kpc-scale density fluctuations in the intergalactic medium (IGM) places tight restrictions on the necessary minimum resolution of these simulations. Even on the most powerful supercomputers, it is impossible to run simulations of such high resolution in volumes comparable to what will be probed by future surveys, due to the vast quantity of data needed to store such a simulation in computer memory. However, it is possible to represent the essential features of these high-resolution simulations using orders of magnitude less memory. We present a hybrid approach that employs a physics-driven hydrodynamical simulation at a much lower-than-necessary resolution, followed by a data-driven, deep-learning Enhancement. This hybrid approach allows us to produce hydrodynamic mock skies that accurately capture small, kpc-scale features in the IGM but which span hundreds of Megaparsecs. We have produced such a volume which is roughly one Gigaparsec in diameter and examine its relevant large-scale statistical features, emphasizing certain properties that could not be captured by previous smaller simulations. We present this hydrodynamic volume as well as a companion n-body dark matter simulation and halo catalog which we are making publically available to the community for use in calibrating data pipelines for upcoming survey analyses.

astro-ph.CO↗

Emulating the Lyman-Alpha forest 1D power spectrum from cosmological simulations: New models and constraints from the eBOSS measurement

We present the Lyssa suite of high-resolution cosmological simulations of the Lyman-$α$ forest designed for cosmological analyses. These 18 simulations have been run using the Nyx code with $4096^3$ hydrodynamical cells in a 120 Mpc ($\sim$ 81Mpc/h) comoving box and individually provide sub-percent level convergence of the Lyman-$α$ forest 1d flux power spectrum. We build a Gaussian process emulator for the Lyssa simulations in the lym1d likelihood framework to interpolate the power spectrum at arbitrary parameter values. We validate this emulator based on leave-one-out tests and based on the parameter constraints for simulations outside of the training set. We also perform comparisons with a previous emulator, showing a percent level accuracy and a good recovery of the expected cosmological parameters. Using this emulator we derive constraints on the linear matter power spectrum amplitude and slope parameters $A_{\mathrm{Ly}α}$ and $n_{\mathrm{Ly}α}$. While the best-fit Planck $Λ$CDM model has $A_{\mathrm{Ly}α}=8.79$ and $n_{\mathrm{Ly}α}=-2.363$, from DR14 eBOSS data we find that $A_{\mathrm{Ly}α}<7.6$ (95\% CI) and $n_{\mathrm{Ly}α}=-2.369 \pm 0.008$. The low value of $A_{\mathrm{Ly}α}$, in tension with Planck, is driven by the correlation of this parameter with the mean transmission of the Lyman-$α$ forest. This tension disappears when imposing a well-motivated external prior on this mean transmission, in which case we find $A_{\mathrm{Ly}α}=9.8\pm1.1$ in accordance with Planck.

astro-ph.CO↗

The ACCEL$^2$ project: simulating Lyman-$α$ forest in large-volume hydrodynamical simulations

Cosmological information is usually extracted from the Lyman-$α$ forest correlations using only either large-scale information interpreted through linear theory or using small-scale information interpreted by means of expensive hydrodynamical simulations. A complete cosmological interpretation of the 3D correlations at all measurable scales is challenged by the need of more realistic models including the complex growth of non-linear small scales that can only be studied within large hydrodynamical simulations. Past work were often limited by the trade off between the simulated cosmological volume and the resolution of the low-density intergalactic medium from which the Lyman-$α$ signal originates. We conduct a suite of hydrodynamical simulations of the intergalactic medium, including one of the largest Lyman-$α$ simulations ever performed in terms of volume (640 $h^{-1}\mathrm{Mpc}$), alongside simulations in smaller volumes with resolutions up to 25 $h^{-1}\mathrm{kpc}$, which will be further improved to show resolution convergence in future studies. We compare the 3D Lyman-$α$ power spectra predicted by those simulations to different non-linear models. The inferred Lyman-$α$ bias and redshift space distortion (RSD) parameters, $b_α$ and $β_α$ are in remarkable agreement with those measured in SDSS and DESI data. We find that, contrary to intuition, the convergence of large-scale modes of the 3D Lyman-$α$ power spectra, which determines $β_α$, is primarily influenced by the resolution of the simulation box through mode coupling, rather than the box size itself. Finally, we study the BAO signal encoded in the 3D Lyman-$α$ power spectra. For the first time with a hydrodynamical simulation, we clearly detect the BAO signal, however we only marginally detect its damping, associated with the non-linear growth of the structures.

astro-ph.CO↗

A High-Quality Workflow for Multi-Resolution Scientific Data Reduction and Visualization

Multi-resolution methods such as Adaptive Mesh Refinement (AMR) can enhance storage efficiency for HPC applications generating vast volumes of data. However, their applicability is limited and cannot be universally deployed across all applications. Furthermore, integrating lossy compression with multi-resolution techniques to further boost storage efficiency encounters significant barriers. To this end, we introduce an innovative workflow that facilitates high-quality multi-resolution data compression for both uniform and AMR simulations. Initially, to extend the usability of multi-resolution techniques, our workflow employs a compression-oriented Region of Interest (ROI) extraction method, transforming uniform data into a multi-resolution format. Subsequently, to bridge the gap between multi-resolution techniques and lossy compressors, we optimize three distinct compressors, ensuring their optimal performance on multi-resolution data. Lastly, we incorporate an advanced uncertainty visualization method into our workflow to understand the potential impacts of lossy compression. Experimental evaluation demonstrates that our workflow achieves significant compression quality improvements.

cs.DC↗

TensorFlow Hydrodynamics Analysis for Ly-$α$ Simulations

We introduce the Python program THALAS (TensorFlow Hydrodynamics Analysis for Lyman-Alpha Simulations), which maps baryon fields (baryon density, temperature, and velocity) to Ly$α$ optical depth fields in both real space and redshift space. Unlike previous Ly$α$ codes, THALAS is fully differentiable, enabling a wide variety of potential applications for general analysis of hydrodynamical simulations and cosmological inference. To demonstrate THALAS's capabilities, we apply it to the Ly$α$ forest inversion problem: given a Ly$α$ optical depth field, we reconstruct the corresponding real-space dark matter density field. Such applications are relevant to both cosmological and three-dimensional tomographic analyses of Lyman Alpha forest data.

astro-ph.CO↗

Impact of Self-shielding Minihalos on the Ly$α$ Forest at High Redshift

Dense gas in minihalos with masses of $10^6-10^8~M_\odot$ can shield themselves from reionization for $\sim100$ Myr after being exposed to the UV background. These self-shielded systems, often unresolved in cosmological simulations, can introduce strong absorption in quasar spectra. This paper is the first systematic study on the impact of these systems on the Ly$α$ forest. We first derive the HI column density profile of photoevaporating minihalos by conducting 1D radiation-hydrodynamics simulations. We utilize these results to estimate the Ly$α$ opacity from minihalos in a large-scale simulation that cannot resolve self-shielding. When the ionization rate of the background radiation is $0.03\times10^{-12}~{\rm s}^{-1}$, as expected near the end of reionization at $z\sim5.5$, we find that the incidence rate of damped Ly$α$ absorbers increases by a factor of $\sim2-4$ compared to at $z=4.5$. The Ly$α$ flux is, on average, suppressed by $\sim 3\%$ of its mean due to minihalos. The absorption features enhance the 1D power spectrum up to $\sim5\%$ at $k\sim0.1~h~{\rm Mpc}^{-1}~({\rm or}~10^{-3}~{\rm km}^{-1}~{\rm s})$, which is comparable to the enhancement caused by inhomogeneous reionization. The flux is particularly suppressed in the vicinity of large halos along the line-of-sight direction at separations of up to $10~h^{-1}~{\rm Mpc}$ at $r_\perp\lesssim2~h^{-1}~{\rm Mpc}$. However, these effects become much smaller for higher ionizing rates ($\gtrsim0.3\times10^{-12}~{\rm s}^{-1}$) expected in the post-reionization Universe. Our findings highlight the need to consider minihalo absorption when interpreting the Ly$α$ forest at $z\gtrsim5.5$. Moreover, the sensitivity of these quantities to the ionizing background intensity can be exploited to constrain the intensity itself.

astro-ph.CO↗

Measurement of the small-scale 3D Lyman-$α$ forest power spectrum

Small-scale correlations measured in the Lyman-$α$ (Ly$α$) forest encode information about the intergalactic medium and the primordial matter power spectrum. In this article, we present and implement a simple method to measure the 3-dimensional power spectrum, $P_{\rm 3D}$, of the Ly$α$ forest at wavenumbers $k$ corresponding to small, $\sim$ Mpc scales. In order to estimate $P_{\rm 3D}$ from sparsely and unevenly distributed data samples, we rely on averaging 1-dimensional Fourier Transforms, as previously carried out to estimate the 1-dimensional power spectrum of the Ly$α$ forest, $P_{\rm 1D}$. This methodology exhibits a very low computational cost. We confirm the validity of this approach through its application to Nyx cosmological hydrodynamical simulations. Subsequently, we apply our method to the eBOSS DR16 Ly$α$ forest sample, providing as a proof of principle, a first $P_{\rm 3D}$ measurement averaged over two redshift bins $z=2.2$ and $z=2.4$. This work highlights the potential for forthcoming $P_{\rm 3D}$ measurements, from upcoming large spectroscopic surveys, to untangle degeneracies in the cosmological interpretation of $P_{\rm 1D}$.

astro-ph.CO↗

The Lyman-$α$ forest catalog from the Dark Energy Spectroscopic Instrument Early Data Release

We present and validate the catalog of Lyman-$α$ forest fluctuations for 3D analyses using the Early Data Release (EDR) from the Dark Energy Spectroscopic Instrument (DESI) survey. We used 88,511 quasars collected from DESI Survey Validation (SV) data and the first two months of the main survey (M2). We present several improvements to the method used to extract the Lyman-$α$ absorption fluctuations performed in previous analyses from the Sloan Digital Sky Survey (SDSS). In particular, we modify the weighting scheme and show that it can improve the precision of the correlation function measurement by more than 20%. This catalog can be downloaded from https://data.desi.lbl.gov/public/edr/vac/edr/lya/fuji/v0.3 and it will be used in the near future for the first DESI measurements of the 3D correlations in the Lyman-$α$ forest.

astro-ph.CO↗

The impact of varying inhomogeneous reionization histories on metrics of Ly$α$ opacity

The epoch of hydrogen reionization is complete by $z=5$, but its progression at higher redshifts is uncertain. Measurements of Ly$α$ forest opacity show large scatter at $z<6$, suggestive of spatial fluctuations in neutral fraction ($x_\mathrm{HI}$), temperature, or ionizing background, either individually or in combination. However, these effects are degenerate, necessitating modeling these physics in tandem in order to properly interpret the observations. We begin this process by developing a framework for modeling the reionization history and associated temperature fluctuations, with the intention of incorporating ionizing background fluctuations at a later time. To do this, we generate several reionization histories using semi-numerical code AMBER, selecting histories with volume-weighted neutral fractions that adhere to the observed CMB optical depth and dark pixel fractions. Implementing these histories in the \texttt{Nyx} cosmological hydrodynamics code, we examine the evolution of gas within the simulation, and the associated metrics of the Ly$α$ forest opacity. We find that the pressure smoothing scale within the IGM is strongly correlated with the adiabatic index of the temperature-density relation. We find that while models with 20,000 K photoheating at reionization are better able to reproduce the shape of the observed $z=5$ 1D flux power spectrum than those with 10,000 K, they fail to match the highest wavenumbers. The simulated autocorrelation function and optical depth distributions are systematically low and narrow, respectively, compared to the observed values, but are in better agreement when the reionization history is longer in duration, more symmetric in its distribution of reionization redshifts, or if there are remaining neutral regions at $z<6$. The systematically low variance likely requires the addition of a fluctuating UVB.

astro-ph.CO↗

The Dark Energy Spectroscopic Instrument: One-dimensional power spectrum from first Lyman-$α$ forest samples with Fast Fourier Transform

We present the one-dimensional Lyman-$α$ forest power spectrum measurement using the first data provided by the Dark Energy Spectroscopic Instrument (DESI). The data sample comprises $26,330$ quasar spectra, at redshift $z > 2.1$, contained in the DESI Early Data Release and the first two months of the main survey. We employ a Fast Fourier Transform (FFT) estimator and compare the resulting power spectrum to an alternative likelihood-based method in a companion paper. We investigate methodological and instrumental contaminants associated to the new DESI instrument, applying techniques similar to previous Sloan Digital Sky Survey (SDSS) measurements. We use synthetic data based on log-normal approximation to validate and correct our measurement. We compare our resulting power spectrum with previous SDSS and high-resolution measurements. With relatively small number statistics, we successfully perform the FFT measurement, which is already competitive in terms of the scale range. At the end of the DESI survey, we expect a five times larger Lyman-$α$ forest sample than SDSS, providing an unprecedented precise one-dimensional power spectrum measurement.

astro-ph.CO↗

Forecasting constraints on the high-z IGM thermal state from the Lyman-$α$ forest flux auto-correlation function

The auto-correlation function of the Lyman-$α$ (Ly$α$) forest flux from high-z quasars can statistically probe all scales of the intergalactic medium (IGM) just after the epoch of reionization. The thermal state of the IGM, which is determined by the physics of reionization, sets the amount of small-scale power seen in the \lya forest. To study the sensitivity of the auto-correlation function to the thermal state of the IGM, we compute the auto-correlation function from cosmological hydrodynamical simulations with semi-numerical models of the thermal state of the IGM. We create mock data sets of 20 quasars to forecast constraints on $T_0$ and $γ$, which characterize a tight temperature-density relation in the IGM, at $5.4 \leq z \leq 6$. At $z = 5.4$ we find that an ideal data set constrains $T_0$ to 29\% and $γ$ to 9\%. In addition, we investigate four realistic reionization scenarios that combine temperature and ultra-violet background (UVB) fluctuations at $z = 5.8$. We find that, when using mock data generated from a model that includes temperature and UVB fluctuations, we can rule out a model with no temperature or UVB fluctuations at $>1σ$ level 50.5\% of the time.

astro-ph.CO↗

Measurements of the $z > 5$ Lyman-$α$ forest flux auto-correlation functions from the extended XQR-30 data set

Recently, the Lyman-$α$ (Ly$α$) forest flux auto-correlation function has been shown to be sensitive to the mean free path of hydrogen-ionizing photons, $λ_{\text{mfp}}$, for simulations at $z \geq 5.4$. Measuring $λ_{\text{mfp}}$ at these redshifts will give vital information on the ending of reionization. Here we present the first observational measurements of the Ly$α$ forest flux auto-correlation functions in ten redshift bins from $5.1 \leq z \leq 6.0$. We use a sample of 35 quasar sightlines at $z > 5.7$ from the extended XQR-30 data set, this data has signal-to-noise ratios of $> 20$ per spectral pixel. We carefully account for systematic errors in continuum reconstruction, instrumentation, and contamination by damped Ly$α$ systems. With these measurements, we introduce software tools to generate auto-correlation function measurements from any simulation. For an initial comparison, we show our auto-correlation measurements with simulation models for recently measured $λ_{\text{mfp}}$ values and find good agreements. Further work in modeling and understanding the covariance matrices of the data is necessary to get robust measurements of $λ_{\text{mfp}}$ from this data.

astro-ph.CO↗

Reconstructing Lyman-$α$ Fields from Low-Resolution Hydrodynamical Simulations with Deep Learning

Hydrodynamical cosmological simulations are a powerful tool for accurately predicting the properties of the intergalactic medium (IGM) and for producing mock skies that can be compared against observational data. However, the need to resolve density fluctuation in the IGM puts a stringent requirement on the resolution of such simulations which in turn limits the volumes which can be modelled, even on most powerful supercomputers. In this work, we present a novel modeling method which combines physics-driven simulations with data-driven generative neural networks to produce outputs that are qualitatively and statistically close to the outputs of hydrodynamical simulations employing 8 times higher resolution. We show that the Ly-$α$ flux field, as well as the underlying hydrodynamic fields, have greatly improved statistical fidelity over a low-resolution simulation. Importantly, the design of our neural network allows for sampling multiple realizations from a given input, enabling us to quantify the model uncertainty. Using test data, we demonstrate that this model uncertainty correlates well with the true error of the Ly-$α$ flux prediction. Ultimately, our approach allows for training on small simulation volumes and applying it to much larger ones, opening the door to producing accurate Ly-$α$ mock skies in volumes of Hubble size, as will be probed with DESI and future spectroscopic sky surveys.

astro-ph.CO↗

AMRIC: A Novel In Situ Lossy Compression Framework for Efficient I/O in Adaptive Mesh Refinement Applications

As supercomputers advance towards exascale capabilities, computational intensity increases significantly, and the volume of data requiring storage and transmission experiences exponential growth. Adaptive Mesh Refinement (AMR) has emerged as an effective solution to address these two challenges. Concurrently, error-bounded lossy compression is recognized as one of the most efficient approaches to tackle the latter issue. Despite their respective advantages, few attempts have been made to investigate how AMR and error-bounded lossy compression can function together. To this end, this study presents a novel in-situ lossy compression framework that employs the HDF5 filter to improve both I/O costs and boost compression quality for AMR applications. We implement our solution into the AMReX framework and evaluate on two real-world AMR applications, Nyx and WarpX, on the Summit supercomputer. Experiments with 4096 CPU cores demonstrate that AMRIC improves the compression ratio by up to 81X and the I/O performance by up to 39X over AMReX's original compression solution.

cs.DC↗