FLARES-2 Gridder

The FLARES-2 Gridder computes matter overdensities at uniform, random, or file-provided grid points using spherical top-hat kernels. The C++20 code uses an octree for particle searches, OpenMP within a process, and optional MPI domain decomposition.

Build

Requirements are CMake 3.12+, a C++20 compiler, OpenMP, and HDF5. MPI is optional. Serial HDF5 is used in both builds.

# Serial
cmake -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build

# MPI
cmake -B build_mpi -DENABLE_MPI=ON -DCMAKE_BUILD_TYPE=Release
cmake --build build_mpi

Configure

The parameter reader accepts simple indentation-based YAML-style mappings. See example_params.yml and the parameter reference.

Kernels:
  nkernels: 2
  kernel_radius_1: 0.5
  kernel_radius_2: 1.0

Grid:
  type: uniform
  cdim: 50

Cosmology:
  h: 0.681
  Omega_cdm: 0.256011
  Omega_b: 0.048600

Tree:
  max_leaf_count: 200

Input:
  filepath: snapshot_0000.hdf5
  placeholder: "0000"
  part_gap_fill_fraction: 0.01

Output:
  filepath: output/
  basename: grid_0000.hdf5
  write_masses: 0

The cosmology values are required and determine the mean comoving density used to normalize overdensities.

Run

# Eight OpenMP threads, snapshot number defaults to zero
./build/parent_gridder example_params.yml 8

# Snapshot 42
./build/parent_gridder example_params.yml 8 42

# Four MPI ranks, two OpenMP threads per rank
mpirun -n 4 ./build_mpi/parent_gridder example_params.yml 2 42

Use ./build/parent_gridder --help for runtime arguments. The positional thread argument controls OpenMP in both serial and MPI builds.

Input Format

The input HDF5 snapshot must contain:

• Header attributes Redshift, NumPart_Total, and BoxSize
• Cells/Meta-data attributes dimension and size
• Cells/Counts/PartType1
• Cells/OffsetsInFile/PartType1
• PartType1/Coordinates
• PartType1/Masses

Particle IDs, velocities, input units, and an input cosmology group are not read. The conversion guide describes how to create the required cell index from compatible coordinate and mass datasets.

Tests

pytest tests -v
./tests/run_tests.sh --all

The shell runner is focused rather than exhaustive. See tests/README.md for serial, MPI, and comparison-suite commands.

Generate test input manually with:

python3 tests/make_test_snap.py --help

Documentation

Build the MkDocs site with:

./build_docs.sh

Start with the quickstart, then see the grid types, MPI guide, and conversion guide.