[RAMSES][AMR] Histogram of AMR Levels and New Block Index Map

[Akos299]

This function computes a histogram of AMR (Adaptive Mesh Refinement) levels.
It returns :

• A buffer containing AMR levels ordered according to the histogram.
• A new block index map that is consistent with the ordering of the returned buffer.

The index map can be used to remap existing block-based data to match the new AMR-level ordering.

[github-actions]

Thanks @Akos299 for opening this PR!

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[gemini-code-assist]

Summary of Changes

Hello @Akos299, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly enhances the Adaptive Mesh Refinement (AMR) system by implementing the capability to compute a histogram of AMR levels and generate a consistent block index map for reordering data. It introduces a new computational step to accurately determine the base cell size for level 0, which is critical for the AMR level calculations. These new functionalities are seamlessly integrated into the solver's graph, with their execution dynamically controlled by the AMR mode configuration, ensuring computations are only performed when necessary.

Highlights

• AMR Level Histogram and Block Index Map: Introduced a new function, amr_block_levels_histogram, to compute a histogram of Adaptive Mesh Refinement (AMR) block levels and generate a reordered block index map. This allows for efficient reordering of block-based data according to their AMR levels.
• New Solver Graph Node for Level 0 Cell Size: Added a new solver graph node, ComputeLevel0CellSize, responsible for determining the maximum size of level 0 cells across different patches, a foundational step for subsequent AMR level calculations.
• Conditional AMR Level Computation: Integrated the new AMR level computation nodes (ComputeLevel0CellSize and ComputeAMRLevel, the latter implied by usage) into the solver's initialization sequence. These computations are now conditionally enabled based on a new no_none_cfg flag within the AMRMode configuration.
• Enhanced AMR Configuration: Extended the AMRMode configuration in SolverConfig.hpp with a no_none_cfg boolean flag and corresponding need_level_zero_compute() and need_amr_level_compute() methods, allowing for fine-grained control over when AMR level-related computations are performed.

Changelog

• src/shammodels/ramses/include/shammodels/ramses/SolverConfig.hpp
  • Added a bool no_none_cfg member to the AMRMode struct.
  • Introduced need_level_zero_compute() and need_amr_level_compute() methods to AMRMode to check the no_none_cfg flag.
• src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp
  • Defined TgridUint as an unsigned type for grid components.
  • Declared a private member function amr_block_levels_histogram for computing AMR block level histograms and reordering indices.
• src/shammodels/ramses/include/shammodels/ramses/modules/ComputeLevel0CellSize.hpp
  • Added a new header file defining the ComputeLevel0CellSize solver graph node, which computes the maximum block size for level 0 cells within each patch.
• src/shammodels/ramses/include/shammodels/ramses/modules/SolverStorage.hpp
  • Added TgridUint type alias.
  • Declared level0_size (a ScalarsEdge<TgridVec>) and amr_block_levels (a Field<TgridUint>) as shared pointers for storing computed data.
  • Updated author information.
• src/shammodels/ramses/src/Solver.cpp
  • Included ComputeAMRLevel.hpp and ComputeLevel0CellSize.hpp.
  • Initialized storage.level0_size as a new ScalarsEdge.
  • Conditionally added ComputeLevel0CellSize and ComputeAMRLevel nodes to the solver_sequence based on solver_config.amr_mode flags.
• src/shammodels/ramses/src/modules/AMRGridRefinementHandler.cpp
  • Implemented the amr_block_levels_histogram function, which calculates block counts per AMR level and generates a reordered index map using SYCL kernels and atomic operations.
• src/shammodels/ramses/src/pyRamsesModel.cpp
  • Modified set_amr_mode_none to set self.amr_mode.no_none_cfg to false.
  • Modified set_amr_mode_density_based to set self.amr_mode.no_none_cfg to true.

Activity

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[gemini-code-assist]

Code Review

This pull request introduces functionality to compute a histogram of AMR levels and a corresponding block index map. The changes include adding new compute nodes to the solver graph for AMR level computation and level 0 cell size, and a new histogramming function.

My review focuses on improving code clarity, performance, and removing unused code:

• In SolverConfig.hpp, I've suggested renaming a boolean flag for better readability.
• In ComputeLevel0CellSize.hpp, I found an unused variable and an unnecessary computation that can be removed.
• In AMRGridRefinementHandler.cpp, I've identified a performance bottleneck in the new histogramming function and suggested a more efficient parallel approach using a scan operation, aligning with best practices for scan accumulator types.

Overall, the changes are a good addition, and with these improvements, the code will be more robust and performant.

[Akos299]

I think This one is ready to be merged.

[github-actions]

Workflow report

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Pre-commit check report

Pre-commit check: ✅

trim trailing whitespace.................................................Passed
fix end of files.........................................................Passed
check for merge conflicts................................................Passed
check that executables have shebangs.....................................Passed
check that scripts with shebangs are executable..........................Passed
check for added large files..............................................Passed
check for case conflicts.................................................Passed
check for broken symlinks................................................Passed
check yaml...............................................................Passed
detect private key.......................................................Passed
No-tabs checker..........................................................Passed
Tabs remover.............................................................Passed
Validate GitHub Workflows................................................Passed
clang-format.............................................................Passed
ruff check...............................................................Passed
ruff format..............................................................Passed
Check doxygen headers....................................................Passed
Check license headers....................................................Passed
Check #pragma once.......................................................Passed
Check SYCL #include......................................................Passed
No ssh in git submodules remote..........................................Passed
No UTF-8 in files (except for authors)...................................Passed

Test pipeline can run.

Clang-tidy diff report

391 warnings generated.
Suppressed 392 warnings (391 in non-user code, 1 NOLINT).
Use -header-filter=.* to display errors from all non-system headers. Use -system-headers to display errors from system headers as well.

418 warnings generated.
Suppressed 419 warnings (418 in non-user code, 1 NOLINT).
Use -header-filter=.* to display errors from all non-system headers. Use -system-headers to display errors from system headers as well.

Doxygen diff with main

Removed warnings : 5
New warnings : 6
Warnings count : 8187 → 8188 (0.0%)

Detailed changes :

+ src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:45: warning: Member TgridUint (typedef) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
- src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:46: warning: Member context (variable) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
+ src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:47: warning: Member context (variable) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
- src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:47: warning: Member solver_config (variable) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
+ src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:48: warning: Member solver_config (variable) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
- src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:48: warning: Member storage (variable) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
+ src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:49: warning: Member storage (variable) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
- src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:50: warning: Member AMRGridRefinementHandler(ShamrockCtx &context, Config &solver_config, Storage &storage) (function) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
+ src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:51: warning: Member AMRGridRefinementHandler(ShamrockCtx &context, Config &solver_config, Storage &storage) (function) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
- src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:53: warning: Member update_refinement() (function) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.
+ src/shammodels/ramses/include/shammodels/ramses/modules/AMRGridRefinementHandler.hpp:54: warning: Member update_refinement() (function) of class shammodels::basegodunov::modules::AMRGridRefinementHandler is not documented.