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Lukic, Zarija

Publications and source records attributed to Lukic, Zarija.

8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

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. These optimizations can improve the compression ratio of SOTA approaches by up to 3.3× under the same data quality loss. 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.

Wang, Daoce↗
DOE OSTI2023

The impact of the $\text{WHIM}$ on the $\text{IGM}$ thermal state determined from the low- z Lyman $\alpha$ forest

At z ≲ 1, shock heating caused by large-scale velocity flows and possibly violent feedback from galaxy formation, converts a significant fraction of the cool gas (T ~ 10 4 K) in the intergalactic medium (IGM) into warm–hot phase (WHIM) with T > 10 5 K, resulting in a significant deviation from the previously tight power-law IGM temperature–density relationship, T = T 0 (P/$\bar{p}$) γ-1 ⁠. This study explores the impact of the WHIM on measurements of the low-z IGM thermal state, [T 0 , γ], based on the b–NH 1 distribution of the Ly α forest. Exploiting a machine learning-enabled simulation-based inference method trained on Nyx hydrodynamical simulations, we demonstrate that [T 0 , γ] can still be reliably measured from the b–NH 1 distribution at z = 0.1, notwithstanding the substantial WHIM in the IGM. To investigate the effects of different feedback, we apply this inference methodology to mock spectra derived from the IllustrisTNG and Illustris simulations at z = 0.1. The results suggest that the underlying [T 0 , γ] of both simulations can be recovered with biases as low as |Δlog(T 0 /K)| ≲ 0.05 dex, |Δγ| ≲ 0.1, smaller than the precision of a typical measurement. Given the large differences in the volume-weighted WHIM fractions between the three simulations (Illustris 38 percent, IllustrisTNG 10 percent, and Nyx 4 per cent), we conclude that the b–N H1 distribution is not sensitive to the WHIM under realistic conditions. Finally, we investigate the physical properties of the detectable Ly α absorbers, and discover that although their T and Δ distributions remain mostly unaffected by feedback, they are correlated with the photoionization rate used in the simulation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

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 512 cores demonstrate that AMRIC improves the compression ratio by 81X and the I/O performance by 39X over AMReX's original compression solution.

Wang, Daoce↗
DOE OSTI2022

Measuring the thermal and ionization state of the low- z IGM using likelihood free inference

ABSTRACT We present a new approach to measure the power-law temperature density relationship $T=T_0 (\rho/ \bar{\rho })^{\gamma -1}$ and the UV background photoionization rate $\Gamma _{{{{\rm H\, {\small I}}}}{}}$ of the intergalactic medium (IGM) based on the Voigt profile decomposition of the Ly α forest into a set of discrete absorption lines with Doppler parameter b and the neutral hydrogen column density $N_{\rm H\, {\small I}}$. Previous work demonstrated that the shape of the $b-N_{{{{\rm H\, {\small I}}}}{}}$ distribution is sensitive to the IGM thermal parameters T0 and γ, whereas our new inference algorithm also takes into account the normalization of the distribution, i.e. the line-density dN/dz, and we demonstrate that precise constraints can also be obtained on $\Gamma _{{{{\rm H\, {\small I}}}}{}}$. We use density-estimation likelihood-free inference (DELFI) to emulate the dependence of the $b-N_{{{{\rm H\, {\small I}}}}{}}$ distribution on IGM parameters trained on an ensemble of 624 nyx hydrodynamical simulations at z = 0.1, which we combine with a Gaussian process emulator of the normalization. To demonstrate the efficacy of this approach, we generate hundreds of realizations of realistic mock HST/COS data sets, each comprising 34 quasar sightlines, and forward model the noise and resolution to match the real data. We use this large ensemble of mocks to extensively test our inference and empirically demonstrate that our posterior distributions are robust. Our analysis shows that by applying our new approach to existing Ly α forest spectra at z ≃ 0.1, one can measure the thermal and ionization state of the IGM with very high precision ($\sigma _{\log T_0} \sim 0.08$ dex, σγ ∼ 0.06, and $\sigma _{\log \Gamma _{{{{\rm H\, {\small I}}}}{}}} \sim 0.07$ dex).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Nyx: A Massively Parallel AMR Code for Computational Cosmology

Nyx is a highly parallel, adaptive mesh, finite-volume N-body compressible hydrodynamics solver for cosmological simulations. It has been used to simulate different cosmological scenarios with a recent focus on the intergalactic medium and Lyman alpha forest. Together, Nyx, the compressible astrophysical simulation code, Castro, and the low Mach number code MAESTROeX, make up the AMReX-Astrophysics Suite of open-source, adaptive mesh, performance-portable astrophysical simulation codes. Other examples of cosmological simulation research codes include Enzo, Enzo-P/Cello, RAMSES, ART, FLASH, Cholla, as well as Gadget, Gasoline, Arepo, Gizmo, and SWIFT.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Performance Analysis, Design Considerations, and Applications of Extreme-Scale In Situ Infrastructures

A key trend facing extreme-scale computational science is the widening gap between computational and I/O rates, and the challenge that follows is how to best gain insight from simulation data when it is increasingly impractical to save it to persistent storage for subsequent visual exploration and analysis. One approach to this challenge is centered around the idea of in situ processing, where visualization and analysis processing is performed while data is still resident in memory. This paper examines several key design and performance issues related to the idea of in situ processing at extreme scale on modern platforms: Scalability, overhead, performance measurement and analysis, comparison and contrast with a traditional post hoc approach, and interfacing with simulation codes. We illustrate these principles in practice with studies, conducted on large-scale HPC platforms, that include a miniapplication and multiple science application codes, one of which demonstrates in situ methods in use at greater than 1M-way concurrency.

Ayachit, Utkarsh↗
DOE OSTI2017

Nyx

Nyx is a highly parallel, adaptive mesh, finite-volume N-body compressible hydrodynamics solver for cosmological simulations. Nyx code solves equations of compressible hydrodynamics on an adaptive grid hierarchy coupled with an N-body treatment of dark matter. The gas dynamics in Nyx uses a finite volume methodology on a set of 3-D Eulerian grids; dark matter is represented as discrete particles moving under the influence of gravity. Particles are evolved via a particle-mesh method, using Cloud-in-Cell deposition/interpolation scheme. Both baryonic and dark matter contribute to the gravitational field. In addition, Nyx includes physics needed to accurately model the intergalactic medium: in optically thin limit and assuming ionization equilibrium, the code calculates heating and cooling processes of the primordial-composition gas in an ionizing ultraviolet background radiation field. Additional physics capabilities are under development.

Sexton, Jean [Lawrence Berkeley National Lab. (LBN↗