Navigation performance benchmark - implementing #49

.pre-commit-config.yaml

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 ci:
+  skip: []
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autoupdate_schedule: "monthly"
   autofix_commit_msg: "style: pre-commit fixes"

docs/manual/geombench.md

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+(manual-geombench)=
+
+# Geometry benchmarking
+
+The `remage-geombench` command-line tool helps identify performance bottlenecks
+in detector geometries during the design phase. It systematically samples points
+on three grids of starting positions and simulates geantinos through the volume.
+It returns the median simulation time per geantino. Based on these overview
+plots and statistics are generated.
+
+:::{tip}
+
+Use this tool during geometry development to identify components that may slow
+down simulations. Complex nested structures, boolean operations, and highly
+detailed volumes can significantly increase navigation time.
+
+:::
+
+## Overview
+
+The geometry benchmark works by:
+
+1. Loading a GDML geometry file
+2. Creating three 2D grids in XY, XZ, and YZ direction according to grid
+   specifications
+3. Sampling geantinos and estimating the median simulation time per grid point
+4. Generating statistics and visualizations showing where navigation is slow
+
+This information helps you optimize geometries before running full physics
+simulations, potentially saving significant computation time.
+
+## Basic usage
+
+The simplest usage requires only a GDML file:
+
+```console
+$ remage-geombench detector.gdml
+```
+
+This will:
+
+- Benchmark the entire geometry
+- Use default settings (10M events, 1 mm grid spacing, 25% buffer)
+- Save results to `detector.lh5` in the current directory
+- Print summary statistics to the console and generate overview plots in the
+  current directory
+
+## Command-line options
+
+### Geometry selection
+
+**`geometry`** (required) : Path to the GDML geometry file to benchmark.
+
+**`--logical-volume NAME`** (optional) : Extract and benchmark only a specific
+logical volume including daughters from the geometry. Useful for isolating
+performance issues in complex assemblies.
+
+Example:
+
+```console
+$ remage-geombench l1000.gdml --logical-volume V0101
+```
+
+### Grid configuration
+
+**`--grid-increment SPACING`** (default: `1`) : Uniform spacing between grid
+points in millimeters for all dimensions.
+
+Example (coarse grid for quick tests):
+
+```console
+$ remage-geombench l1000.gdml --grid-increment 5
+```
+
+**`--grid-increments DICT`** (optional) : Specify different spacing per
+dimension using a Python dictionary literal. Overrides `--grid-increment` if
+provided.
+
+Example:
+
+```console
+$ remage-geombench l1000.gdml --grid-increments "{'x': 1.0, 'y': 2.0, 'z': 0.5}"
+```
+
+### Buffer region
+
+**`--buffer-fraction FRACTION`** (default: `0.25`) : Fractional buffer space
+around the geometry. A value of 0.25 adds 12.5% extra space on each side,
+creating a world volume large enough to contain the geometry with margin.
+
+Example (tighter bounds):
+
+```console
+$ remage-geombench l1000.gdml --buffer-fraction 0.1
+```
+
+### Simulation control
+
+**`--num-events N`** (default: `10000000`) : Number of navigation events to
+simulate. Higher values give more stable statistics but take longer.
+
+Example (quick test):
+
+```console
+$ remage-geombench l1000.gdml --num-events 1000000
+```
+
+**`--output-dir PATH`** (default: `./`) : Directory to store output files.
+
+Example:
+
+```console
+$ remage-geombench l1000.gdml --output-dir ./benchmark_results/
+```
+
+**`--dry-run`** : Generate and display the macro file without running the
+simulation. Useful for verifying configuration before long runs.
+
+Example:
+
+```console
+$ remage-geombench l1000.gdml --dry-run
+```
+
+## Interpreting results
+
+The tool generates an LH5 output file containing spatial navigation performance
+data and prints summary statistics:
+
+```
+Geometry Benchmark Analysis Results:
+mean_navigation_time: 2.45 ns
+median_navigation_time: 1.89 ns
+std_navigation_time: 1.23 ns
+max_navigation_time: 45.67 ns
+min_navigation_time: 0.34 ns
+```
+
+In addition, the visualization of the data can help identify hotspots.
+
+### Key metrics
+
+**Mean navigation time** : Average time spent navigating to each point. Lower is
+better.
+
+**Max navigation time** : Slowest navigation time encountered. High values
+indicate geometry hotspots.
+
+**Standard deviation** : Variability in navigation time. High values suggest
+non-uniform complexity.
+
+:::{warning}
+
+Navigation times are relative and depend on the hardware. Focus on identifying
+spatial patterns and relative differences between geometric components rather
+than absolute timing values.
+
+In addition, these statistics also depend on the ratio of empty space to actual
+material. If one is not interested in potential slowdowns far away from the
+object, one should choose a small enough buffer to reduce the impact of the
+empty space.
+
+:::
+
+## Workflow examples
+
+### Full detector benchmark
+
+Benchmark an entire detector assembly with default settings:
+
+```console
+$ remage-geombench l1000.gdml --output-dir benchmarks/
+```
+
+### Component isolation
+
+Test a specific problematic component:
+
+```console
+$ remage-geombench l1000.gdml --logical-volume V0101 \
+    --grid-increment 0.5 --output-dir component_tests/
+```
+
+This generates a `part_{logical-volume}.lh5` and
+`part_{logical-volume}_[...].pdf` files in the output directory.
+
+### Anisotropic sampling
+
+For elongated geometries, use different grid spacing per dimension:
+
+```console
+$ remage-geombench l1000.gdml \
+    --grid-increments "{'x': 0.5, 'y': 0.5, 'z': 2.0}"
+```
+
+## Performance optimization tips
+
+Based on benchmark results, consider these optimization strategies:
+
+1. **Simplify boolean operations**: Multiple nested unions/subtractions are
+   expensive. Consider alternative representations.
+
+2. **Reduce tessellated solid complexity**: Decrease facet count where possible
+   without losing essential features.
+
+3. **Material boundaries**: Excessive material changes force more boundary
+   checks. Consolidate materials where physics allows.
+
+4. **Envelope optimization**: Proper envelope volumes can accelerate navigation
+   in complex assemblies.
+
+## Technical details
+
+The benchmark uses the `GeomBench` generator, which systematically steps through
+three 2D grids and measures median simulation time per grid point. The geometry
+is automatically wrapped in a world volume sized to contain it with the
+specified buffer fraction.
+
+When extracting a specific logical volume, the tool:
+
+1. Identifies the volume in the GDML registry
+2. Copies all dependent resources (materials, solids, daughter volumes)
+3. Creates a minimal world volume containing only the extracted component
+4. Applies the buffer and generates a temporary GDML file for benchmarking
+
+This allows testing individual components without the overhead of the full
+geometry.
+
+## See also
+
+- {ref}`manual-geometry` – General geometry setup
+- {ref}`manual-running` – Running simulations
+- {ref}`manual-output` – Output data formats

docs/manual/index.md

@@ -7,6 +7,7 @@ install.md
 containers.md
 running.md
 geometry.md
+geombench.md
 physicslist.md
 confinement.md
 generators.md

include/RMGGeomBench.hh

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+// Copyright (C) 2025 Moritz Neuberger <https://orcid.org/0009-0001-8471-9076>
+#ifndef _RMG_GENERATOR_GEOMBENCH_HH_
+#define _RMG_GENERATOR_GEOMBENCH_HH_
+
+#include <chrono>
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "CLHEP/Units/SystemOfUnits.h"
+#include "G4AnalysisManager.hh"
+#include "G4GenericMessenger.hh"
+#include "G4LogicalVolume.hh"
+#include "G4ParticleGun.hh"
+#include "G4VPhysicalVolume.hh"
+
+#include "RMGGeomBenchOutputScheme.hh"
+#include "RMGVGenerator.hh"
+
+namespace u = CLHEP;
+
+class RMGGeomBench : public RMGVGenerator {
+
+  public:
+
+    RMGGeomBench();
+    ~RMGGeomBench();
+
+    RMGGeomBench(RMGGeomBench const&) = delete;
+    RMGGeomBench& operator=(RMGGeomBench const&) = delete;
+    RMGGeomBench(RMGGeomBench&&) = delete;
+    RMGGeomBench& operator=(RMGGeomBench&&) = delete;
+
+    void GeneratePrimaries(G4Event* event) override;
+    void SetParticlePosition(G4ThreeVector) override{};
+    void RecordBatchTime(size_t pixel_idx, double batch_time);
+    void SaveAllPixels();
+
+    void BeginOfRunAction(const G4Run* r) override;
+    void EndOfRunAction(const G4Run* r) override;
+
+  private:
+
+    // Helper to find the benchmark output scheme if it's active
+    RMGGeomBenchOutputScheme* GetBenchmarkOutputScheme();
+
+    std::unique_ptr<G4ParticleGun> fGun = nullptr;
+
+    std::unique_ptr<G4GenericMessenger> fMessenger = nullptr;
+    void DefineCommands();
+
+    long totalnevents;
+    size_t totalnpixels;
+    int npixelsperrow;
+    int neventsperpixel;
+    double cubesize;
+
+    // Configurable sampling parameters (user-specified increments)
+    G4ThreeVector user_increment;
+    G4ThreeVector sampling_width;
+
+    // Calculated number of pixels based on increments and widths
+    size_t npixels_x;
+    size_t npixels_y;
+    size_t npixels_z;
+    size_t ID;
+
+    double starttime;
+    double currenttime;
+    double bunchstarttime;
+
+    // For tracking batches and calculating median
+    std::vector<std::vector<double>> pixel_batch_times; // One vector of batch times per pixel
+    int events_per_bunch;
+    int total_batch_rounds;
+    int current_batch_event;
+    int current_pixel_index;
+    int current_batch_round;
+
+    G4ThreeVector origin;
+    G4ThreeVector limit;
+    G4ThreeVector increment;
+};
+
+#endif