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-GR

Dendro-GR is a highly-scalable framework that targets problems of interest to the numerical relativity and broader astrophysics communities. This framework combines a parallel octree-refined adaptive mesh (i.e., Dendro libarary) with a wavelet adaptive multiresolution and a physics module to solve the Einstein equations of general relativity. The goal of this work is to perform advanced, massively parallel numerical simulations of binary black holes with mass ratios on the order of 100:1. These studies will be used to generate waveforms as used in LIGO data analysis and to calibrate semi-analytical approximate methods. Our framework consists of a distributed memory octree-based adaptive meshing framework in conjunction with a node-local code generator. Dendro-GR framework achieve excellent performance and scalability on modern leadership architectures. Dendro-GR also has tested strong scalability up to 8 A100s and weak scaling up to 229,376 x86 cores on the Texas Advanced Computing Center’s Frontera system. To the best of our knowledge, Dendro-GR work is the first highly scalable, adaptive, multi-GPU numerical relativity code performing binary black hole mergers.

Dendro framework is an open-source scalable octree algorithms suite, designed to solve partial differential equations using Galerkin, finite difference, finite volume discretization methods. If you are interested in using Dendro please let us know how can we help. You can clone the repository using ,

• Get Dendro-5.01 : git clone https://github.com/paralab/Dendro-5.01.git
• Get Dendro-GR : git cline https://github.com/paralab/Dendro-GR.git

pip3 install --user sympy numpy numba git+https://github.com/moble/quaternion git+https://github.com/moble/spherical_functions cogapp quadpy

To build Dendro-5.0, you need following externeral packages,

• C/C++11 or higher, (tested with GNU and Intel compilers)
• MPI implementation (tested with mvapich2, openmpi and intel compilers)
• BLAS/LAPACK (tested with openBLAS and Intel MKL)
• GSL, need to set GSL_ROOT_DIR to cmake to auto detect GSL library.
• Pyhton packages for code generation, pip3 install --user sympy numpy numba git+https://github.com/moble/quaternion git+https://github.com/moble/spherical_functions cogapp quadpy
• PETSc if building with FEM (CG/DG) support.

To build the code please use the following commands.

$cd <path to root source dir >
$ mkdir build
$ cd build
$ cmake ../
$ make bssnSolverCtx bssnSolverCUDA tpid -j4

• Note that that, -DWITH CUDA=ON build code for both CPU and GPU, while -DWITH CUDA=OFF compilation only happens for the CPU code.
• The above will build three targets in /BSSN GR/ folder these corresponds to CPU BSSN Solver, GPU BSSN Solver and two punctures initial condition solver for the binary black hole problem.

The singularity container definition file is provided in the repository under the folder container. The following command can be used to build the Dendro-GR container which installs all the required dependencies and compile the Dendro-GR code.

sudo singularity build --sandbox dgr-cuda dgr.def
singularity run dgr-cuda dgr.def

• The parameters for the applications has to be provided with .json file. Example parameter files for mass ratios 1, 2, and 4 can be found in BSSN GR/pars folder.

  • BSSN GR/pars/q1.par.json : q=1 binary black hole merger
  • BSSN GR/pars/q2.par.json : q=2 binary black hole merger
  • BSSN GR/pars/q4.par.json : q=4 binary black hole merger

• Create the following folders in the relative path to the BSSN executable.

  • vtu - VTU folder where the solution is written with parallel VTU file format, in the frequency specified by the parameter file (i.e., BSSN IO OUTPUT FREQ).
  • cp - checkpoint folder where the checkpoints are stored in the frequency specified by the parameter file (i.e., BSSN CHECKPT FREQ).
  • dat - dat - Data files, diagnostics data on the binary. Requested modes (i.e., "BSSN GW L MODES": [2,3,4]) of the gravitational waves are extracted by the observers specified by "BSSN GW RADAII": [50,60,70,80,90,100]

• tpid: First run the tpid solver with the chosen parameter file. The above will solve for the initial condition for the binary using Two puncture gauge.

• Once the tpid solver is finished, user can launch the BSSN solver bssnSolverCUDA or bssnSolverCtx for GPU and CPU versions respectively.

$ ./BSSN_GR/tpid q1.par.json <number of threads to use>
$ mpirun -np <number of GPUs> ./BSSN_GR/bssnSolverCUDA q1.par.json 1

Additional scripts files for conducted experiments are presented in the <source dir>/BSSN GR/experiment_scripts/ls6 folder.

• q1-ss : GPU/CPU strong scaling experimental scripts.

• q1-ws : GPU weak scaling experimental scripts.

• Weak scaling: make bssnWSTestCUDA and use bssnWTestCUDA for weak scaling on GPUs. Use mpirun -np <number of GPUs> ./BSSN GR/bssnWSTestCUDA q1 ws.par.json 1

• Strong scaling: Use the parameter file in BSSN GR/pars/scaling/q1_r2.2.par.json.

  • CPU : mpirun -np <number of CPUs> ./BSSN GR/bssnSolverCtx q1_r2.2.par.json 1
  • GPU : mpirun -np <number of GPUs> ./BSSN GR/bssnSolverCUDA q1 r2.2.par.json 1

• Experiments on Octant to Patch and Patch to Octant : make run meshgpu tests to build the benchmark for padding zone computation. Note that this will built the executable in <source dir>/build folder. The parameters should be specified in the order and corresponds to,

  • maximum allowed depth of the octree, tolerance value for refinement, partition tolerance (recommend to keep it at 0.1), order of interpola tion for each octant (all the experiments used 6 order interpolations in the paper), flag 0 for CPU padding zone computations, flag 1 for GPU padding zone computations.
  • CPU tests mpirun -np <number of CPUs> ./run meshgpu tests 8 1e-3 0.1 6 0
  • GPU tests mpirun -np <number of CPUs> ./run meshgpu tests 8 1e-3 0.1 6 1

If you built Dendro-GR with Singularity, the following command can be used to launch the main BSSN solver and other benchmarks.

singularity exec dgr-cuda \
sc22-dgr/build_gpu/BSSN_GR/./bssnSolverCtx sc22-dgr/build_gpu/q1.par.json 1

Dendro-GR consists of sympy based code generation framework (SympyGR) that supports efficient code generaton for both CPUs and GPUs. You can find the sympy BSSNOK file here. Numerical relativity application can be quite overwhelmed for a newcomer for Dendro-GR, hence we provide a simpler NLSigma computation here. Note that the overall workflow of the computational is ideantial to the solving the GR equation but with much simpler set of equations.

NlSigma folder consists of simple, non lineat wave equation with adaptive mesh refinement (AMR). You can copy the parameter file from NLSigma/par folder and simply run mpirun -np 8 ./NLSigma/nlsmSolver nlsm.par.json, on your lattop to large supercomputer with higher resolution.

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You can write the equations in symbolic python which generate the C compute kernel. Look at nlsm.py

import dendro
from sympy import *
###############################################################
#  initialize
###############################################################
r = symbols('r')
# declare functions
chi = dendro.scalar("chi","[pp]")
phi = dendro.scalar("phi","[pp]")
d = dendro.set_first_derivative('grad')    # first argument is direction
d2s = dendro.set_second_derivative('grad2')  # first 2 arguments are directions
d2 = dendro.d2

###############################################################
#  evolution equations
###############################################################

phi_rhs = sum( d2(i,i,chi)  for i in dendro.e_i ) - sin(2*chi)/r**2
chi_rhs = phi

###############################################################
#  evolution equations
###############################################################
outs = [phi_rhs, chi_rhs]
vnames = ['phi_rhs', 'chi_rhs']
dendro.generate(outs, vnames, '[pp]')

Which generate the code,

// Dendro: {{{ 
// Dendro: original ops:  10
// Dendro: printing temp variables

// Dendro: printing variables
//--
phi_rhs[pp] = grad2_0_0_chi[pp] + grad2_1_1_chi[pp] + grad2_2_2_chi[pp] - sin(2*chi[pp])/pow(r, 2);
//--
chi_rhs[pp] = phi[pp];
// Dendro: reduced ops:  10
// Dendro: }}}

• Grid parameters

  • NLSM_GRID_MIN_X, NLSM_GRID_MIN_Y, NLSM_GRID_MIN_Z: The minimum coordinate values for the computational domain in the x-, y-, and z- directions.
  • NLSM_GRID_MAX_X, NLSM_GRID_MAX_Y, NLSM_GRID_MAX_Z: The maximum coordinate values for the computational domain in the x-, y-, and z- directions.

• Evolution parameters

  • NLSM_CFL_FACTOR: The Courant factor used for time integration. dt = NLSM_CFL_FACTOR * dx
  • KO_DISS_SIGMA: Coefficient for Kreiss-Oliger dissipation that is added to the solution.
  • NLSM_RK45_TIME_BEGIN: Initial time label for the evolution, usually this is set to 0.
  • NLSM_RK45_TIME_END: The final time for the evolution. The code exits when this time is reached.
  • NLSM_RK45_TIME_STEP_SIZE: Initial time step for the Runge-Kutta 4-5 adaptive time integrator.
  • NLSM_RK45_DESIRED_TOL: Tolerance for the RK4-5 adaptive time integrator.

• Output parameters

  • NLSM_IO_OUTPUT_FREQ: Frequency for output. Output is written as 3D VTK files.
  • NLSM_VTU_FILE_PREFIX: Prefix for naming the output files. Each processor outputs all variables to a single file labeled by the timestep.
  • NLSM_NUM_EVOL_VARS_VTU_OUTPUT: The number of evolution variables to be output.
  • NLSM_VTU_OUTPUT_EVOL_INDICES: A list of variable indices to specify which variables will be written to output. The first NLSM_NUM_EVOL_VARS_VTU_OUTPUT in this list are written to the output file.

• General refinement parameters

  • NLSM_MAXDEPTH: The maximum refinement depth for the octree. The minimum possible grid resolution is proportional to 1/2^k, where k is the maximum depth.
  • NLSM_REMESH_TEST_FREQ: Frequency for updating an adaptive grid.
  • NLSM_LOAD_IMB_TOL: Dendro load imbalance tolerance for flexible partitioning.
  • NLSM_DENDRO_GRAIN_SZ: Grain size N/p , Where N number of total octants, p number of active cores. This is essentially the number of octants per core, and essentially functions as a measure of the computational load per core. (Dendro does not automatically use all cores that are available in a multiprocessor run, but gives each core a minimum amount of work before adding new cores.)

• Wavelet refinement parameters

  • NLSM_WAVELET_TOL: The wavelet error tolerance for the solution. Refinement is added when the estimated error in the solution, measured by the wavelet coefficient, is larger than this tolerance.
  • NLSM_NUM_REFINE_VARS: The number of variables used to evaluate refinement on the grid.
  • NLSM_REFINE_VARIABLE_INDICES: A list of variable indicies to specify which variables are used to determine the grid refinement. Wavelet coefficients will be calculated for the first NLSM_NUM_REFINE_VARS in this list.
  • NLSM_DENDRO_AMR_FAC: A factor to determine the threshold for coarsening the grid. The grid is coarsened when the wavelet coefficients are less than NLSM_DENDRO_AMR_FAC * NLSM_WAVELET_TOL.

• Block refinement parameters

  • NLSM_ENABLE_BLOCK_ADAPTIVITY: Block adaptivity provides simple fixed-mesh refinement. The grid is refined to the maximum depth (or minimum resolution) inside a fixed region set by NLSM_BLK_MIN_X, NLSM_BLK_MAX_X, and related variables. Set this parameter to "1" to enable block adaptivity, or "0" otherwise (default). Block adaptivity is used primarily for testing and debugging. For example, a uniform grid can be created by specifying maximum refinement region to cover the entire domain.
  • NLSM_BLK_MIN_X: The minimum x-coordinate for the block that is refined to the maximum depth. Same for y- and z-coordinates.
  • NLSM_BLK_MAX_X: The maximum x-coordinate for the block that is refined to the maximum depth. Same for y- and z-coordinates.

• Checkpoint parameters

  • NLSM_RESTORE_SOLVER: Set this parameter to "1" to read from checkpoint files, otherwise set it to "0" (default). When checkpointing is used, the code automatically selects the latest checkpoint files for restoring the solver.
  • NLSM_CHECKPT_FREQ: The checkpoint frequency.
  • NLSM_CHKPT_FILE_PREFIX: A string prefix for naming the checkpoint files.

Dendro supports finite element computations, currently Continous Galerkin (CG) Methods, but in future we will support Discontinous Galerkin (DG) Methods. All FEM related code are in FEM folder, you can write, allplications using the feMatrix.h and feVector.h classes, to represent left and right hand sidesof the variational formulations. oda.h contains the interface class which enables easy integration with petsc matrix based and matrix free methods.

Simple Laplace equation using FEM can be found in FEM/examples/src/heatEq.cpp file.

• Fernando, M., Neilsen, D., Zlochower, Y., Hirschmann, E.W. and Sundar, H., 2023. Massively parallel simulations of binary black holes with adaptive wavelet multiresolution. Physical Review D, 107(6), p.064035.
• Fernando, M., Neilsen, D., Hirschmann, E., Zlochower, Y., Sundar, H., Ghattas, O. and Biros, G., 2022, November. A GPU-accelerated AMR solver for gravitational wave propagation. In 2022 SC22: International Conference for High Performance Computing, Networking, Storage and Analysis (SC) (pp. 1078-1092). IEEE Computer Society.
• Milinda Fernando, David Neilsen, Hyun Lim, Eric Hirschmann, Hari Sundar, ”Massively Parallel Simulations of Binary Black Hole Intermediate-Mass-Ratio Inspirals” SIAM Journal on Scientific Computing 2019. 'https://doi.org/10.1137/18M1196972'
• Milinda Fernando, David Neilsen, Eric Hirschmann, Hari Sundar, ”A scalable framework for Adaptive Computational General Relativity on Heterogeneous Clusters”, (ACM International Conference on Supercomputing, ICS’19)
• Fernando, M. and Sundar, H., 2022. Scalable Local Timestepping on Octree Grids. SIAM Journal on Scientific Computing, 44(2), pp.C156-C183.
• Milinda Fernando, Dmitry Duplyakin, and Hari Sundar. 2017. ”Machine and Application Aware Partitioning for Adaptive Mesh Refinement Applications”. In Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing (HPDC ’17). ACM, New York, NY, USA, 231-242. DOI: 'https://doi.org/10.1145/3078597.3078610'
• Masado Ishii, Milinda Fernando, Kumar Saurabh, Biswajit Khara, Baskar Ganapathysubramanian, and Hari Sundar. 2019. Solving PDEs in space-time: 4D tree-based adaptivity, mesh-free and matrix-free approaches. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’19). Association for Computing Machinery, New York, NY, USA, Article 61, 1–61. DOI:https://doi.org/10.1145/3295500.3356198