peclet-dem 0.3.2

peclet.dem — performance-portable XPBD Discrete Element Method (Kokkos + ArborX)

peclet-dem (peclet.dem)

Performance-portable Discrete Element Method (DEM) particle simulation: an XPBD solver with SDF-based point-shell collision detection. Built on Kokkos + ArborX, so the same source runs on CUDA, HIP (AMD/LUMI), and OpenMP backends (selected at build time by the install prefix). Optional MPI for domain partitioning, with nanobind Python bindings (zero-copy, via scikit-build-core) for scripting and visualization.

The CUDA implementation was retired (2026-06): the Kokkos peclet.dem module was validated against it before the CUDA sources were removed. Restore point: git tag pre-cuda-retirement.

Features

• Hybrid XPBD Solver: Two-pass velocity/position solver for stable high-density packing.
• SDF Collision: Point-shell collision detection using Signed Distance Fields (supports analytic shapes like hollow cylinders).
• Periodicity: Full periodic boundary conditions (Ghost Particles).
• Python Bindings: Control simulation logic, data initialization, and export entirely from Python.
• MPI Support: Optional Multi-GPU/Node support via domain decomposition.

Folder Structure

├── CMakeLists.txt              # Build configuration (find_package Kokkos + ArborX)
├── src                         # Kokkos sources (header-only, namespace peclet::dem)
│   ├── dem_bindings.cpp        # nanobind module entry point (the `peclet.dem` module)
│   ├── sim.hpp                 # Simulation facade + the demStep XPBD substep
│   ├── integration.hpp         # Time integration & prediction
│   ├── broadphase_arborx.hpp   # ArborX BVH broad-phase
│   ├── narrowphase.hpp         # Narrow-phase point-shell-vs-SDF collision
│   ├── solver_velocity.hpp     # Velocity solver kernels
│   ├── solver_position.hpp     # Position solver kernels (XPBD overlap removal)
│   ├── solver_friction.hpp     # Coulomb friction cluster
│   ├── output_sdf.hpp          # SDF/VTI grid generation (Eikonal)
│   ├── shapes_portable.hpp     # Analytic shapes (sphere / hollow cylinder / box)
│   ├── io.hpp                  # LAMMPS-dump + SDF-VTI export
│   └── mpi_halo.hpp            # Distributed particle halo (core), gated PECLET_DEM_MPI
├── tests                       # C++ unit tests: kokkos/ (kernels), arborx/, kokkos_mpi/
├── docs                        # Documentation
└── *.py                        # Python verification/example scripts (verify_*.py)

Prerequisites

• Linux
• CMake >= 3.24
• Kokkos 5.x + ArborX (C++20) — provisioned by ../tools/bootstrap_deps.sh into ../extern/install/<backend> (nvidia-cuda / host-openmp / lumi-hip). A hard build dependency.
• nanobind + scikit-build-core (found via the active Python interpreter; see pyproject.toml)
• a backend compiler: nvcc (CUDA) on PATH, hipcc (ROCm), or just a host C++ compiler (OpenMP)
• Python >= 3.10
• MPI (optional, -DDEM_MPI=ON) — OpenMPI or MPICH

Build Instructions

python -m venv .venv && source .venv/bin/activate && pip install nanobind numpy
export PATH=/usr/local/cuda-13.2/bin:$PATH        # if building the CUDA backend

# Canonical: build + install the module via scikit-build-core
CMAKE_PREFIX_PATH="$PWD/../extern/install/nvidia-cuda" pip install .

# Or a dev cmake build (nanobind is found via the active interpreter, no cmakedir needed):
cmake -B build -S . -DCMAKE_PREFIX_PATH="$PWD/../extern/install/nvidia-cuda"
cmake --build build -j$(nproc)

Swap the prefix to ../extern/install/host-openmp for the OpenMP backend. -DDEM_MPI=ON links MPI and exposes the distributed step (init_mpi / enable_mpi_step / step_mpi), including dynamic load balancing — enable_mpi_step(..., rebalance_every=N) or an explicit rebalance() re-decomposes by particle count (weighted ORB) and migrates ownership so each rank keeps a near-equal share.

The compiled peclet.dem extension is placed in build/peclet/dem/; run scripts with build/ on PYTHONPATH (import peclet.dem).

Running Simulations

Example scripts are provided in the root directory:

# Add build artifact to python path if needed (or symlink it)
export PYTHONPATH=$PYTHONPATH:$(pwd)/build

# Run a verification script
python verify_packing_hollow_cylinders.py

Output & Visualization

The simulation supports two primary output formats:

1. LAMMPS + STL (Ovito)

For particle visualization (especially non-spherical shapes), we use the LAMMPS dump format combined with an STL mesh.

1. Generate Output: The simulation writes dump.custom.* files.
2. Generate Shape: Run python generate_particles.py to create particle_shape.stl.
3. Visualize:
   • Open Ovito.
   • Load the dump.custom.* sequence.
   • Add a Particle Types modifier.
   • Set the shape visualization to Mesh/User-defined and load particle_shape.stl.
   • Ovito will automatically scale the mesh by the particle radius.

See docs/visualization.md for a detailed guide.

2. VTI (ParaView)

For visualizing fields (like the Signed Distance Field or occupancy grids), the simulation exports VTI files (.vti).

1. Generate Output: Use Simulation.export_sdf("filename.vti", resolution=...).
2. Visualize:
   • Open ParaView.
   • Load the .vti file.
   • Use "Volume" representation or "Slice" filter to inspect the field.

Status

The single-GPU engine is complete and validated: it reaches stable high-density (random close) packing, and energy is conserved to ~0.3% (see docs/packing_investigation.md). Friction is stabilized for spheres; body-body tangential friction is a known follow-up (currently weaker than ideal). Active work is at-scale multi-GPU/MPI tuning.

[!NOTE] The distributed (MPI) step is validated against the single-rank result (tests/kokkos_mpi, np=1,2,4 on OpenMP + CUDA) and supports dynamic load rebalancing; remaining MPI work is at-scale multi-GPU tuning.