Nyx: A MASSIVELY PARALLEL AMR CODE FOR COMPUTATIONAL COSMOLOGY

Almgren, Ann S.; Bell, John B.; Lijewski, Mike J.; Lukic, Zarija; Van Andel, Ethan

doi:10.1088/0004-637X/765/1/39

Nyx: A MASSIVELY PARALLEL AMR CODE FOR COMPUTATIONAL COSMOLOGY

Journal Article · Thu Feb 28 23:00:00 EST 2013 · Astrophysical Journal

DOI:https://doi.org/10.1088/0004-637X/765/1/39· OSTI ID:22167656

Almgren, Ann S.; Bell, John B.; Lijewski, Mike J. ^[1]; Lukic, Zarija ^[2]; Van Andel, Ethan ^[3]

Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)
Computational Cosmology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)
Mathematics Department, UC Berkeley, Berkeley, CA 94720 (United States)

We present a new N-body and gas dynamics code, called Nyx, for large-scale cosmological simulations. Nyx follows the temporal evolution of a system of discrete dark matter particles gravitationally coupled to an inviscid ideal fluid in an expanding universe. The gas is advanced in an Eulerian framework with block-structured adaptive mesh refinement; a particle-mesh scheme using the same grid hierarchy is used to solve for self-gravity and advance the particles. Computational results demonstrating the validation of Nyx on standard cosmological test problems, and the scaling behavior of Nyx to 50,000 cores, are presented.

OSTI ID:: 22167656

Journal Information:: Astrophysical Journal, Journal Name: Astrophysical Journal Journal Issue: 1 Vol. 765; ISSN ASJOAB; ISSN 0004-637X

Country of Publication:: United States

Language:: English

Cited By (51)

Self-Consistent Modeling of Reionization in Cosmological Hydrodynamical Simulations Oñorbe, Jose; Hennawi, Joseph F.; Lukić, Zarija arXiv https://doi.org/10.48550/arxiv.1607.04218	text	January 2016
Modeling the He ii Transverse Proximity Effect: Constraints on Quasar Lifetime and Obscuration Schmidt, Tobias M.; Hennawi, Joseph F.; Worseck, Gábor The Astrophysical Journal, Vol. 861, Issue 2 https://doi.org/10.3847/1538-4357/aac8e4	journal	July 2018
Enzo: An Adaptive Mesh Refinement Code for Astrophysics Collaboration, The Enzo; Bryan, Greg L.; Norman, Michael L. arXiv https://doi.org/10.48550/arxiv.1307.2265	text	January 2013
PyUltraLight: A Pseudo-Spectral Solver for Ultralight Dark Matter Dynamics Edwards, Faber; Kendall, Emily; Hotchkiss, Shaun arXiv https://doi.org/10.48550/arxiv.1807.04037	text	January 2018
Anomaly in the Opacity of the Post-reionization Intergalactic Medium in the Ly α and Ly β Forest Eilers, Anna-Christina; Hennawi, Joseph F.; Davies, Frederick B. The Astrophysical Journal, Vol. 881, Issue 1 https://doi.org/10.3847/1538-4357/ab2b3f	journal	August 2019
PyUltraLight: a pseudo-spectral solver for ultralight dark matter dynamics Edwards, Faber; Kendall, Emily; Hotchkiss, Shaun Journal of Cosmology and Astroparticle Physics, Vol. 2018, Issue 10 https://doi.org/10.1088/1475-7516/2018/10/027	journal	October 2018
Large Eddy Simulations in Astrophysics Schmidt, Wolfram arXiv https://doi.org/10.48550/arxiv.1404.2483	preprint	January 2014
Large Eddy Simulations in Astrophysics Schmidt, Wolfram Living Reviews in Computational Astrophysics, Vol. 1, Issue 1 https://doi.org/10.1007/lrca-2015-2	journal	October 2015
Analyzing Performance of Selected NESAP Applications on the Cori HPC System Kurth, Thorsten; Arndt, William; Barnes, Taylor High Performance Computing https://doi.org/10.1007/978-3-319-67630-2_25	book	January 2017
TARDIS. I. A Constrained Reconstruction Approach to Modeling the z ∼ 2.5 Cosmic Web Probed by Ly α Forest Tomography Horowitz, Benjamin; Lee, Khee-Gan; White, Martin The Astrophysical Journal, Vol. 887, Issue 1 https://doi.org/10.3847/1538-4357/ab4d4c	journal	December 2019
An embedded boundary approach for efficient simulations of viscoplastic fluids in three dimensions Sverdrup, Knut; Almgren, Ann; Nikiforakis, Nikolaos Physics of Fluids, Vol. 31, Issue 9 https://doi.org/10.1063/1.5110654	journal	September 2019
The Opacity of the Intergalactic Medium Measured Along Quasar Sightlines at $z\sim 6$ Eilers, Anna-Christina; Davies, Frederick B.; Hennawi, Joseph F. arXiv https://doi.org/10.48550/arxiv.1807.04229	text	January 2018
AMReX: Block-structured adaptive mesh refinement for multiphysics applications Zhang, Weiqun; Myers, Andrew; Gott, Kevin The International Journal of High Performance Computing Applications https://doi.org/10.1177/10943420211022811	journal	June 2021
Detection of z ∼ 2.3 Cosmic Voids from 3D Ly α Forest Tomography in the COSMOS Field Krolewski, Alex; Lee, Khee-Gan; White, Martin The Astrophysical Journal, Vol. 861, Issue 1 https://doi.org/10.3847/1538-4357/aac829	journal	July 2018
In situ data-driven adaptive sampling for large-scale simulation data summarization Biswas, Ayan; Dutta, Soumya; Pulido, Jesus Proceedings of the Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization - ISAV '18 https://doi.org/10.1145/3281464.3281467	conference	January 2018
The Borg Cube Simulation: Cosmological Hydrodynamics with CRK-SPH Emberson, J. D.; Frontiere, Nicholas; Habib, Salman The Astrophysical Journal, Vol. 877, Issue 2 https://doi.org/10.3847/1538-4357/ab1b31	journal	May 2019
Mapping Quasar Light Echoes in 3D with Ly α Forest Tomography Schmidt, Tobias M.; Hennawi, Joseph F.; Lee, Khee-Gan The Astrophysical Journal, Vol. 882, Issue 2 https://doi.org/10.3847/1538-4357/ab2fcb	journal	September 2019
A Novel Statistical Method for Measuring the Temperature–Density Relation in the IGM Using the b – N _{H i} Distribution of Absorbers in the Ly α Forest Hiss, Hector; Walther, Michael; Oñorbe, Jose The Astrophysical Journal, Vol. 876, Issue 1 https://doi.org/10.3847/1538-4357/ab1418	journal	May 2019
Simulations of solitonic core mergers in ultra-light axion dark matter cosmologies Schwabe, Bodo; Niemeyer, Jens C.; Engels, Jan F. arXiv https://doi.org/10.48550/arxiv.1606.05151	text	January 2016
The Borg Cube Simulation: Cosmological Hydrodynamics with CRK-SPH Emberson, J. D.; Frontiere, Nicholas; Habib, Salman arXiv https://doi.org/10.48550/arxiv.1811.03593	text	January 2018
Flexible and Scalable Particle-in-Cell Methods With Adaptive Mesh Refinement for Geodynamic Computations Gassmöller, Rene; Lokavarapu, Harsha; Heien, Eric Geochemistry, Geophysics, Geosystems, Vol. 19, Issue 9 https://doi.org/10.1029/2018gc007508	journal	September 2018
Influence of adaptive mesh refinement and the hydro solver on shear-induced mass stripping in a minor-merger scenario Schmidt, W.; Schulz, J.; Iapichino, L. arXiv https://doi.org/10.48550/arxiv.1411.7275	text	January 2014
A fast algorithm for identifying friends-of-friends halos Feng, Y.; Modi, C. Astronomy and Computing, Vol. 20 https://doi.org/10.1016/j.ascom.2017.05.004	journal	July 2017
A Fundamental Test for Galaxy Formation Models: Matching the Lyman- α Absorption Profiles of Galactic Halos Over Three Decades in Distance Sorini, Daniele; Oñorbe, José; Hennawi, Joseph F. The Astrophysical Journal, Vol. 859, Issue 2 https://doi.org/10.3847/1538-4357/aabb52	journal	May 2018
Inhomogeneous reionization models in cosmological hydrodynamical simulations Oñorbe, Jose; Davies, F. B.; Lukić, Z. Monthly Notices of the Royal Astronomical Society, Vol. 486, Issue 3 https://doi.org/10.1093/mnras/stz984	journal	May 2019
Enzo: an Adaptive mesh Refinement code for Astrophysics Bryan, Greg L.; Norman, Michael L.; O'Shea, Brian W. The Astrophysical Journal Supplement Series, Vol. 211, Issue 2 https://doi.org/10.1088/0067-0049/211/2/19	journal	March 2014
The Evolution of the He ii-ionizing Background at Redshifts 2.3 < z < 3.8 Inferred from a Statistical Sample of 24 HST /COS He ii Ly α Absorption Spectra Worseck, Gábor; Davies, Frederick B.; Hennawi, Joseph F. The Astrophysical Journal, Vol. 875, Issue 2 https://doi.org/10.3847/1538-4357/ab0fa1	journal	April 2019
WENO–WOMBAT: Scalable Fifth-order Constrained-transport Magnetohydrodynamics for Astrophysical Applications Donnert, J. M. F.; Jang, H.; Mendygral, P. The Astrophysical Journal Supplement Series, Vol. 241, Issue 2 https://doi.org/10.3847/1538-4365/ab09fb	journal	March 2019
Highly parallelisable simulations of time-dependent viscoplastic fluid flow with structured adaptive mesh refinement Sverdrup, Knut; Nikiforakis, Nikolaos; Almgren, Ann Physics of Fluids, Vol. 30, Issue 9 https://doi.org/10.1063/1.5049202	journal	September 2018
Highly parallelisable simulations of time-dependent viscoplastic fluid flow simulations with structured adaptive mesh refinement Sverdrup, Knut; Nikiforakis, Nikolaos; Almgren, Ann arXiv https://doi.org/10.48550/arxiv.1803.00417	text	January 2018
An embedded boundary approach for efficient simulations of viscoplastic fluids in three dimensions Sverdrup, Knut; Almgren, Ann; Nikiforakis, Nikolaos arXiv https://doi.org/10.48550/arxiv.1905.07392	text	January 2019
The first supermassive black holes: indications from models for future observations Amarantidis, Stergios; Afonso, José; Messias, Hugo Monthly Notices of the Royal Astronomical Society, Vol. 485, Issue 2 https://doi.org/10.1093/mnras/stz551	journal	February 2019
Modelling turbulent effects of stellar feedback in cosmological simulations Engels, Jan Frederik; Schmidt, Wolfram; Niemeyer, Jens Monthly Notices of the Royal Astronomical Society, Vol. 482, Issue 4 https://doi.org/10.1093/mnras/sty3037	journal	November 2018
Exascale applications: skin in the game Alexander, Francis; Almgren, Ann; Bell, John Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 378, Issue 2166 https://doi.org/10.1098/rsta.2019.0056	journal	January 2020
Massively parallel computation of accurate densities for N-body dark matter simulations using the phase-space-element method Kaehler, R. Astronomy and Computing, Vol. 20 https://doi.org/10.1016/j.ascom.2017.05.005	journal	July 2017
Quantitative Constraints on the Reionization History from the IGM Damping Wing Signature in Two Quasars at z > 7 Davies, Frederick B.; Hennawi, Joseph F.; Bañados, Eduardo The Astrophysical Journal, Vol. 864, Issue 2 https://doi.org/10.3847/1538-4357/aad6dc	journal	September 2018
Modeling the HeII Transverse Proximity Effect: Constraints on Quasar Lifetime and Obscuration Schmidt, Tobias M.; Hennawi, Joseph F.; Worseck, Gábor arXiv https://doi.org/10.48550/arxiv.1710.04527	text	January 2017
The one-dimensional power spectrum from the SDSS DR14 Lyα forests Chabanier, Solène; Palanque-Delabrouille, Nathalie; Yèche, Christophe Journal of Cosmology and Astroparticle Physics, Vol. 2019, Issue 07 https://doi.org/10.1088/1475-7516/2019/07/017	journal	July 2019
Cosmological particle-in-cell simulations with ultralight axion dark matter Veltmaat, Jan; Niemeyer, Jens C. Physical Review D, Vol. 94, Issue 12 https://doi.org/10.1103/physrevd.94.123523	journal	December 2016
The power spectrum of the Lyman-α Forest at z < 0.5 Khaire, Vikram; Walther, Michael; Hennawi, Joseph F. Monthly Notices of the Royal Astronomical Society, Vol. 486, Issue 1 https://doi.org/10.1093/mnras/stz344	journal	February 2019
Simulations of solitonic core mergers in ultralight axion dark matter cosmologies Schwabe, Bodo; Niemeyer, Jens C.; Engels, Jan F. Physical Review D, Vol. 94, Issue 4 https://doi.org/10.1103/physrevd.94.043513	journal	August 2016
New Constraints on IGM Thermal Evolution from the Ly α Forest Power Spectrum Walther, Michael; Oñorbe, Jose; Hennawi, Joseph F. The Astrophysical Journal, Vol. 872, Issue 1 https://doi.org/10.3847/1538-4357/aafad1	journal	February 2019
Measurement of the small-scale structure of the intergalactic medium using close quasar pairs Rorai, Alberto; Hennawi, Joseph F.; Oñorbe, Jose Science, Vol. 356, Issue 6336 https://doi.org/10.1126/science.aaf9346	journal	April 2017
A New Measurement of the Temperature Density Relation of the IGM From Voigt Profile Fitting Hiss, Hector; Walther, Michael; Hennawi, Joseph F. arXiv https://doi.org/10.48550/arxiv.1710.00700	text	January 2017
Highly parallelisable simulations of time-dependent viscoplastic fluid flow simulations with structured adaptive mesh refinement Sverdrup, Knut; Nikiforakis, Nikolaos; Almgren, Ann Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.27305	text	January 2018
A New Measurement of the Temperature–density Relation of the IGM from Voigt Profile Fitting Hiss, Hector; Walther, Michael; Hennawi, Joseph F. The Astrophysical Journal, Vol. 865, Issue 1 https://doi.org/10.3847/1538-4357/aada86	journal	September 2018
BoxLib with Tiling: An AMR Software Framework Zhang, Weiqun; Almgren, Ann; Day, Marcus arXiv https://doi.org/10.48550/arxiv.1604.03570	preprint	January 2016
A New Method to Measure the Post-reionization Ionizing Background from the Joint Distribution of Ly α and Ly β Forest Transmission Davies, Frederick B.; Hennawi, Joseph F.; Eilers, Anna-Christina The Astrophysical Journal, Vol. 855, Issue 2 https://doi.org/10.3847/1538-4357/aaaf70	journal	March 2018
The Opacity of the Intergalactic Medium Measured along Quasar Sightlines at z ∼ 6 Eilers, Anna-Christina; Davies, Frederick B.; Hennawi, Joseph F. The Astrophysical Journal, Vol. 864, Issue 1 https://doi.org/10.3847/1538-4357/aad4fd	journal	August 2018
Self-consistent Modeling of Reionization in Cosmological Hydrodynamical Simulations Oñorbe, Jose; Hennawi, Joseph F.; Lukić, Zarija The Astrophysical Journal, Vol. 837, Issue 2 https://doi.org/10.3847/1538-4357/aa6031	journal	March 2017
Inhomogeneous Reionization Models in Cosmological Hydrodynamical Simulations Oñorbe, Jose; Davies, F. B.; Lukić, Z. arXiv https://doi.org/10.48550/arxiv.1810.11683	text	January 2018

Similar Records

Nyx: A Massively Parallel AMR Code for Computational Cosmology

Journal Article · Tue Feb 12 23:00:00 EST 2013 · The Astrophysical Journal · OSTI ID:1565016

Nyx: A Massively Parallel AMR Code for Computational Cosmology

Journal Article · Sat Jul 10 00:00:00 EDT 2021 · Journal of Open Source Software · OSTI ID:1827343

Nyx

Software · Thu May 04 20:00:00 EDT 2017 · OSTI ID:code-54357

Related Subjects

79 ASTRONOMY AND ASTROPHYSICS
COMPUTERIZED SIMULATION
COSMOLOGICAL MODELS
COSMOLOGY
COUPLING
GRAVITATION
HYDRODYNAMICS
IDEAL FLOW
N CODES
NONLUMINOUS MATTER
TIME DEPENDENCE
UNIVERSE
VALIDATION

Nyx: A MASSIVELY PARALLEL AMR CODE FOR COMPUTATIONAL COSMOLOGY

Citation Formats

Cited By (51)

Similar Records

Related Subjects