An adaptive mesh, massively-parallel, cosmological simulation code
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 an adaptive 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 currently 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.
While Nyx can run on any Linux system in general, we particularly focus on supercomputer systems. Nyx is parallelized with MPI + X, where "X" can be OpenMP, CUDA, or HIP (DPC++ implementation is ongoing). In the OpenMP regime, Nyx and has been successfully run at parallel concurrency of up to 2,097,152 (on NERSC's Cori-KNL). With Cuda implementation, it was ran on up to 13,824 GPUs (on OLCF's Summit).
More information on Nyx can be found at http://amrex-astro.github.io/Nyx/
To compile the code we require C++11 compliant compilers that support MPI-2 or higher implementation. If threads or accelerators are used, we require OpenMP 4.5 or higher, Cuda 9 or higher, or HIP-Clang.
To use Nyx, you also need AMReX: https://github.com/AMReX-codes/amrex
For example, to compile the Lyman alpha (LyA) executable on Summit:
$ module load gcc/6.4.0 cuda/11.0.3
$ git clone https://github.com/AMReX-Codes/amrex.git
$ git clone https://github.com/AMReX-astro/Nyx.git
$ cd Nyx/Exec/LyA
$ make -j 12 USE_CUDA=TRUEThere is a User's Guide in Nyx/UsersGuide/ (type make to build
from LaTeX source) that will guide you through running your first
problem.
The development branch in also the main branch. We use nightly
regression testing to ensure that no answers change (or if they do, that
the changes were expected). Contributions are welcomed and should be done via pull requests.
A pull request should be generated from your fork of Nyx and should target
the development branch.
For the description of the N-body and adiabatic hydro algorithms in Nyx, see Almgren, Bell, Lijewski, Lukic & Van Andel (2013), ApJ, 765, 39: http://adsabs.harvard.edu/abs/2013ApJ...765...39A
For the reaction and thermal rates of the primordial chemical composition gas (and convergence tests in the context of the Lyman-alpha forest), see Lukic, Stark, Nugent, White, Meiksin & Almgren (2015), MNRAS, 446, 3697: http://adsabs.harvard.edu/abs/2015MNRAS.446.3697L
For considerations regarding the spatially uniform synthesis model of the UV background, which provides the photo-ionization and photo-heating rates, see Onorbe, Hennawi & Lukic (2017), ApJ, 837, 106: http://adsabs.harvard.edu/abs/2017ApJ...837..106O
We have also implemented non-radiative transfer methods to model inhomogeneous reionization, the paper is in preparation.
Nyx outputs certain global diagnostics at each timestep and plot files at regular intervals, or at user-specified redshifts. Visualization packages VisIt, Paraview and yt have built-in support for the AMReX file format used by Nyx.
In addition, Nyx interfaces with two post-processing suites, Reeber and Gimlet. Reeber uses topological methods to construct merge trees of scalar fields, which Nyx in turn uses to find halos. Gimlet computes a variety of quantities related to the Lyman-alpha forest science. These suites are fully MPI-parallel and can be run either "in situ" or "in-transit", or with a combination of both.
Nyx is released under the LBL's modified BSD license, see the license.txt file for details.
For questions, comments, suggestions, contact Ann Almgren at [email protected] or Zarija Lukic at [email protected] .