Use contiguous memory layout for neighbor lists #10
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## main #10 +/- ##
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- Coverage 86.94% 84.76% -2.19%
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Files 15 15
Lines 659 689 +30
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+ Hits 573 584 +11
- Misses 86 105 +19
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Pull Request Overview
This PR adds support for using Vector{Vector} as a backend for PrecomputedNeighborhoodSearch, making it more flexible and memory-efficient for certain use cases. It also introduces a freeze_neighborhood_search function to strip unnecessary data structures when preparing neighborhood searches for GPU execution.
- Refactored
PrecomputedNeighborhoodSearchto support configurable backends (DynamicVectorOfVectorsorVector{Vector}) - Added
freeze_neighborhood_searchto optimize GPU transfers by removing internal neighborhood searches - Introduced
max_inner_lengthhelper function to handle backend-specific configuration copying
Reviewed Changes
Copilot reviewed 10 out of 10 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| src/nhs_precomputed.jl | Refactored struct to support configurable backends, added freeze_neighborhood_search implementation |
| src/vector_of_vectors.jl | Added max_inner_length helper for extracting backend configuration |
| src/neighborhood_search.jl | Added generic freeze_neighborhood_search interface |
| src/gpu.jl | Updated GPU adaptation to handle PrecomputedNeighborhoodSearch instead of GridNeighborhoodSearch |
| src/cell_lists/spatial_hashing.jl | Fixed trailing whitespace in documentation |
| src/cell_lists/full_grid.jl | Updated documentation and replaced max_points_per_cell with max_inner_length |
| benchmarks/smoothed_particle_hydrodynamics.jl | Added freeze_neighborhood_search call before GPU transfer |
| benchmarks/n_body.jl | Added freeze_neighborhood_search call before GPU transfer |
| benchmarks/run_benchmarks.jl | Added PrecomputedNeighborhoodSearch to GPU benchmark suite |
| test/neighborhood_search.jl | Added test cases for PrecomputedNeighborhoodSearch with Vector{Vector} backend |
Comments suppressed due to low confidence (1)
src/nhs_precomputed.jl:128
- The element type
Int[]should be consistent with the backend type. When usingVector{Vector{Int32}}backend, this createsVector{Int}elements instead ofVector{Int32}, which is inconsistent. Consider using the element type from the backend or making this type-stable.
neighbor_lists[i] = Int[]
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| - `Vector{Vector{Int32}}`: Scattered memory, but very memory-efficient. | ||
| - `DynamicVectorOfVectors{Int32}`: Contiguous memory, optimizing cache-hits. | ||
| - `DynamicVectorOfVectors{Int32}`: Contiguous memory, optimizing cache-hits | ||
| and GPU compatible. |
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Grammatical inconsistency: 'GPU compatible' should be 'GPU-compatible' to match the hyphenation style used in the PrecomputedNeighborhoodSearch documentation.
Suggested change
| and GPU compatible. | |
| and GPU-compatible. |
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Based on #111.