bhut 0.1.3

Barnes-Hut N-body accelerator that is array-agnostic (NumPy/Dask)

bhut

A high-performance Barnes-Hut N-body accelerator that is array-agnostic, supporting both NumPy and Dask arrays for distributed computation.

Documentation

Full documentation is available at:

https://maroba.github.io/bhut/

Installation

pip install bhut

For acceleration features and optional dependencies:

pip install bhut[accel]
pip install 'dask[array]'  # For distributed computation
pip install numba         # For JIT acceleration (recommended)

Quick Start

Functional API

import numpy as np
import bhut

# Generate random N-body system
N = 10000
positions = np.random.randn(N, 3)
masses = np.ones(N)

# Compute gravitational accelerations using Barnes-Hut algorithm
accelerations = bhut.accelerations(
    positions, masses, 
    theta=0.5,        # Opening angle criterion
    softening=0.01,   # Gravitational softening
    G=1.0            # Gravitational constant
)

print(f"Acceleration shape: {accelerations.shape}")  # (10000, 3)

Object-Oriented API

import numpy as np
from bhut import Tree

# Create and build tree
positions = np.random.randn(1000, 3)
masses = np.ones(1000)

tree = Tree(positions, masses, leaf_size=32)
tree.build()

# Query accelerations for same particles
self_accel = tree.accelerations(theta=0.5, softening=0.01)

# Query accelerations at different target positions
targets = np.random.randn(500, 3)
target_accel = tree.accelerations(targets, theta=0.5, softening=0.01)

# Efficient tree updates for time evolution
new_positions = positions + 0.1 * np.random.randn(1000, 3)

# Refit: fast update when particles move but topology is similar
tree.refit(new_positions)
accel_refit = tree.accelerations(theta=0.5, softening=0.01)

# Rebuild: complete reconstruction when topology changes significantly
tree.rebuild(new_positions, new_masses=masses * 1.1)
accel_rebuild = tree.accelerations(theta=0.5, softening=0.01)

Distributed Computing with Dask

import numpy as np
import dask.array as da
import bhut

# Create large dataset distributed across chunks
N = 1_000_000
positions_np = np.random.randn(N, 3).astype(np.float64)
masses_np = np.ones(N, dtype=np.float64)

# Convert to Dask arrays with chunking
positions_da = da.from_array(positions_np, chunks=(100_000, 3))
masses_da = da.from_array(masses_np, chunks=(100_000,))

# Compute accelerations in parallel (auto-detects Dask backend)
accelerations_da = bhut.accelerations(positions_da, masses_da, theta=0.5)

# Result preserves chunking structure for efficient downstream processing
print(f"Input chunks: {positions_da.chunks}")
print(f"Output chunks: {accelerations_da.chunks}")

# Compute final result when needed
result = accelerations_da.compute()

Numba JIT Acceleration

For maximum performance with NumPy arrays, install Numba for automatic JIT compilation:

import numpy as np
import bhut

# Numba automatically detected and used if available
positions = np.random.randn(10000, 3)
masses = np.ones(10000)

# First call includes compilation overhead (~1s)
accel1 = bhut.accelerations(positions, masses, theta=0.5)

# Subsequent calls use cached compiled code (~27x faster)
accel2 = bhut.accelerations(positions, masses, theta=0.5)

Performance comparison (10,000 particles):

• Without Numba: ~4.5 seconds (pure Python)
• With Numba: ~0.16 seconds after compilation (~27x speedup)
• Memory: No additional memory overhead
• Compatibility: Falls back gracefully when Numba unavailable

When Numba is used:

• Automatically detected when import numba succeeds
• Only accelerates compute-intensive leaf node interactions
• Pure Python fallback always available
• Works with NumPy arrays (Dask arrays use pure Python)

# Check if Numba acceleration is active
from bhut.traverse.bh import HAVE_NUMBA
print(f"Numba acceleration: {'✓ Available' if HAVE_NUMBA else '✗ Not available'}")

Features

• ** High Performance**: O(N log N) tree construction, O(M log N) force evaluation
• ** Numba Acceleration**: Optional JIT compilation for ~27x speedup in particle interactions
• ** Array-Agnostic**: Seamless support for NumPy and Dask arrays
• ** Distributed**: Built-in Dask integration for large-scale computation
• ** Accurate**: Configurable Barnes-Hut approximation with error control
• ** Efficient Updates**: Tree refit/rebuild for time-stepping simulations

Parameter Tuning Guide

Opening Angle (theta)

Controls the accuracy-performance tradeoff:

Parameter Tuning Guide

Opening Angle (theta)

Controls the accuracy-performance tradeoff:

# High accuracy, slow computation
accel_accurate = bhut.accelerations(pos, masses, theta=0.1)

# Balanced (recommended for most applications)
accel_balanced = bhut.accelerations(pos, masses, theta=0.5)

# Fast approximation, lower accuracy
accel_fast = bhut.accelerations(pos, masses, theta=1.0)

# Direct summation (exact but O(N²))
accel_exact = bhut.accelerations(pos, masses, theta=0.0)

Guidelines:

• theta = 0.0: Exact O(N²) calculation (small systems only)
• theta = 0.1-0.3: High accuracy for precision-critical applications
• theta = 0.5: Good balance for most scientific simulations
• theta = 0.7-1.0: Fast approximation for large-scale surveys
• theta > 1.0: Very approximate, mainly for prototyping

Leaf Size (leaf_size)

Controls tree granularity and performance:

# Fine-grained tree (more memory, potentially faster for large queries)
tree_fine = Tree(pos, masses, leaf_size=16)
tree_fine.build()

# Balanced (recommended default)
tree_balanced = Tree(pos, masses, leaf_size=32)
tree_balanced.build()

# Coarse-grained tree (less memory, faster construction)
tree_coarse = Tree(pos, masses, leaf_size=64)
tree_coarse.build()

Guidelines:

• leaf_size = 8-16: Best for systems with many small query sets
• leaf_size = 32: Recommended default for most applications
• leaf_size = 64-128: Better for large query sets or memory-constrained systems
• leaf_size > 128: May degrade performance due to increased direct summation

Performance Optimization

Tree Refit vs Rebuild

For time-stepping simulations:

tree = Tree(positions, masses)
tree.build()

for timestep in range(num_steps):
    # Compute forces
    accel = tree.accelerations(theta=0.5, softening=0.01)
    
    # Update positions
    positions += velocity * dt + 0.5 * accel * dt**2
    velocity += accel * dt
    
    # Decide whether to refit or rebuild
    if should_refit_vs_rebuild(tree, positions):
        tree.refit(positions)  # Fast: O(N), preserves tree structure
    else:
        tree.rebuild(positions)  # Slower: O(N log N), rebuilds from scratch

Chunking Strategy for Dask

# Good chunking: ~100K-1M particles per chunk
positions_da = da.from_array(positions, chunks=(500_000, 3))

# Avoid: too small chunks (overhead dominates)
positions_bad = da.from_array(positions, chunks=(1_000, 3))

# Avoid: too large chunks (memory issues, poor parallelization)
positions_bad = da.from_array(positions, chunks=(10_000_000, 3))

Performance Characteristics

System Size	Construction Time	Memory Usage	Recommended θ	Numba Speedup
N < 10³	< 1ms	< 1MB	0.0 (exact)	~2x
N ~ 10⁴	~ 10ms	~ 10MB	0.3	~10x
N ~ 10⁵	~ 100ms	~ 100MB	0.5	~27x
N ~ 10⁶	~ 1s	~ 1GB	0.5	~27x
N > 10⁶	Use Dask	Distributed	0.7	N/A*

*Dask arrays use pure Python (Numba optimizations planned for future releases)

Contributing

Contributions are welcome! Please see CONTRIBUTING.md for guidelines.

License

MIT License - see LICENSE file for details.

Citation

If you use bhut in your research, please cite:

@software{bhut,
  title={bhut: A Barnes-Hut N-body Accelerator},
  author={Matthias Baer},
  url={https://github.com/your-org/bhut},
  year={2025}
}