perf(precomputation): cleaned up allocations

recovered about 5% execution time

.gitignore

@@ -121,3 +121,5 @@ meson-boost-test/
 *_pynucastro_network.py
 
 cross/python_includes
+
+*.whl

build-python/fix_rpaths.py

@@ -78,7 +78,7 @@ def fix_rpaths(binary_path):
 
 def main():
     if len(sys.argv) != 2:
-        print(f"--- Error: Expected one argument (path to .so file), got {sys.argv}", file=sys.stderr)
+        print(f"--- Error: Expected one argument (path to .dylib/.so file), got {sys.argv}", file=sys.stderr)
         sys.exit(1)
 
     # Get the file path directly from the command line argument

src/include/gridfire/engine/engine_abstract.h

@@ -53,7 +53,7 @@ namespace gridfire::engine {
     struct StepDerivatives {
         std::map<fourdst::atomic::Species, T> dydt{}; ///< Derivatives of abundances (dY/dt for each species).
         T nuclearEnergyGenerationRate = T(0.0); ///< Specific energy generation rate (e.g., erg/g/s).
-        std::map<fourdst::atomic::Species, std::unordered_map<std::string, T>> reactionContributions{};
+        std::optional<std::map<fourdst::atomic::Species, std::unordered_map<std::string, T>>> reactionContributions = std::nullopt;
         T neutrinoEnergyLossRate = T(0.0); // (erg/g/s)
         T totalNeutrinoFlux = T(0.0);      // (neutrinos/g/s)
 

src/include/gridfire/engine/engine_graph.h

@@ -753,6 +753,14 @@ namespace gridfire::engine {
         [[nodiscard]]
         SpeciesStatus getSpeciesStatus(const fourdst::atomic::Species &species) const override;
 
+        [[nodiscard]] bool get_store_intermediate_reaction_contributions() const {
+            return m_store_intermediate_reaction_contributions;
+        }
+
+        void set_store_intermediate_reaction_contributions(const bool value) {
+            m_store_intermediate_reaction_contributions = value;
+        }
+
 
     private:
         struct PrecomputedReaction {
@@ -879,6 +887,7 @@ namespace gridfire::engine {
 
         bool m_usePrecomputation = true; ///< Flag to enable or disable using precomputed reactions for efficiency. Mathematically, this should not change the results. Generally end users should not need to change this.
         bool m_useReverseReactions = true; ///< Flag to enable or disable reverse reactions. If false, only forward reactions are considered.
+        bool m_store_intermediate_reaction_contributions = false; ///< Flag to enable or disable storing intermediate reaction contributions for debugging.
 
         BuildDepthType m_depth;
 
@@ -1207,7 +1216,10 @@ namespace gridfire::engine {
                 const T nu_ij = static_cast<T>(reaction.stoichiometry(species));
                 const T dydt_increment = threshold_flag * molarReactionFlow * nu_ij;
                 dydt_vec[speciesIdx] += dydt_increment;
-                result.reactionContributions[species][std::string(reaction.id())] = dydt_increment;
+
+                if (m_store_intermediate_reaction_contributions) {
+                    result.reactionContributions.value()[species][std::string(reaction.id())] = dydt_increment;
+                }
             }
 
         }

src/include/gridfire/solver/strategies/CVODE_solver_strategy.h

@@ -237,7 +237,7 @@ namespace gridfire::solver {
         };
 
         struct CVODERHSOutputData {
-            std::map<fourdst::atomic::Species, std::unordered_map<std::string, double>> reaction_contribution_map;
+            std::optional<std::map<fourdst::atomic::Species, std::unordered_map<std::string, double>>> reaction_contribution_map;
             double neutrino_energy_loss_rate;
             double total_neutrino_flux;
         };

src/lib/engine/engine_graph.cpp

@@ -684,7 +684,7 @@ namespace gridfire::engine {
             // --- Efficient lookup of only the active reactions ---
             uint64_t reactionHash = utils::hash_reaction(*reaction);
             const size_t reactionIndex = m_precomputedReactionIndexMap.at(reactionHash);
-            PrecomputedReaction precomputedReaction = m_precomputedReactions[reactionIndex];
+            const PrecomputedReaction& precomputedReaction = m_precomputedReactions[reactionIndex];
 
             // --- Forward abundance product ---
             double forwardAbundanceProduct = 1.0;
@@ -697,12 +697,12 @@ namespace gridfire::engine {
                     forwardAbundanceProduct = 0.0;
                     break; // No need to continue if one of the reactants has zero abundance
                 }
-                double factor = std::pow(comp.getMolarAbundance(reactant), power);
+                const double factor = std::pow(comp.getMolarAbundance(reactant), power);
                 if (!std::isfinite(factor)) {
                     LOG_CRITICAL(m_logger, "Non-finite factor encountered in forward abundance product for reaction '{}'. Check input abundances for validity.", reaction->id());
                     throw exceptions::BadRHSEngineError("Non-finite factor encountered in forward abundance product.");
                 }
-                forwardAbundanceProduct *= std::pow(comp.getMolarAbundance(reactant), power);
+                forwardAbundanceProduct *= factor;
             }
 
             const double bare_rate = bare_rates.at(reactionCounter);
@@ -764,8 +764,8 @@ namespace gridfire::engine {
                     default: ;
                 }
 
-                double local_neutrino_loss =  molarReactionFlows.back() * q_abs * neutrino_loss_fraction * m_constants.Na * m_constants.MeV_to_erg;
-                double local_neutrino_flux = molarReactionFlows.back() * m_constants.Na;
+                const double local_neutrino_loss =  molarReactionFlows.back() * q_abs * neutrino_loss_fraction * m_constants.Na * m_constants.MeV_to_erg;
+                const double local_neutrino_flux = molarReactionFlows.back() * m_constants.Na;
 
                 result.totalNeutrinoFlux += local_neutrino_flux;
                 result.neutrinoEnergyLossRate += local_neutrino_loss;
@@ -782,7 +782,7 @@ namespace gridfire::engine {
 
         reactionCounter = 0;
         for (const auto& reaction: activeReactions) {
-            size_t j = m_precomputedReactionIndexMap.at(utils::hash_reaction(*reaction));
+            const size_t j = m_precomputedReactionIndexMap.at(utils::hash_reaction(*reaction));
             const auto& precomp = m_precomputedReactions[j];
             const double R_j = molarReactionFlows[reactionCounter];
 
@@ -793,9 +793,12 @@ namespace gridfire::engine {
                 const int stoichiometricCoefficient = precomp.stoichiometric_coefficients[i];
 
                 // Update the derivative for this species
-                double dydt_increment = static_cast<double>(stoichiometricCoefficient) * R_j;
+                const double dydt_increment = static_cast<double>(stoichiometricCoefficient) * R_j;
                 result.dydt.at(species) += dydt_increment;
-                result.reactionContributions[species][std::string(reaction->id())] = dydt_increment;
+
+                if (m_store_intermediate_reaction_contributions) {
+                    result.reactionContributions.value()[species][std::string(reaction->id())] = dydt_increment;
+                }
             }
             reactionCounter++;
         }

utils/wheels/build-wheels-macos_aarch64.sh

@@ -1,6 +1,7 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
+# 1. Validation
 if [[ $(uname -m) != "arm64" ]]; then
   echo "Error: This script is intended to run on an Apple Silicon (arm64) Mac."
   exit 1
@@ -11,11 +12,12 @@ if [[ $# -ne 1 ]]; then
   exit 1
 fi
 
-# --- Initial Setup ---
+# 2. Setup Directories
 REPO_URL="$1"
 WORK_DIR="$(pwd)"
 WHEEL_DIR="${WORK_DIR}/wheels_macos_aarch64_tmp"
 FINAL_WHEEL_DIR="${WORK_DIR}/wheels_macos_aarch64"
+RPATH_SCRIPT="${WORK_DIR}/../../build-python/fix_rpaths.py" # Assumes script is in this location relative to execution
 
 echo "➤ Creating wheel output directories"
 mkdir -p "${WHEEL_DIR}"
@@ -26,10 +28,22 @@ echo "➤ Cloning ${REPO_URL} → ${TMPDIR}/project"
 git clone --depth 1 "${REPO_URL}" "${TMPDIR}/project"
 cd "${TMPDIR}/project"
 
-# --- macOS Build Configuration ---
+# 3. Build Configuration
 export MACOSX_DEPLOYMENT_TARGET=15.0
 
+# Meson options passed to pip via config-settings
+# Note: We use an array to keep the command clean
+MESON_ARGS=(
+    "-Csetup-args=-Dunity=off"
+    "-Csetup-args=-Dbuild-python=true"
+    "-Csetup-args=-Dbuild-fortran=false"
+    "-Csetup-args=-Dbuild-tests=false"
+    "-Csetup-args=-Dpkg-config=false"
+    "-Csetup-args=-Dunity-safe=true"
+)
+
 PYTHON_VERSIONS=("3.8.20" "3.9.23" "3.10.18" "3.11.13" "3.12.11" "3.13.5" "3.13.5t" "3.14.0rc1" "3.14.0rc1t" 'pypy3.10-7.3.19' "pypy3.11-7.3.20")
+PYTHON_VERSIONS=("3.9.23" "3.10.18" "3.11.13" "3.12.11" "3.13.5" "3.13.5t" "3.14.0rc1" "3.14.0rc1t" 'pypy3.10-7.3.19' "pypy3.11-7.3.20")
 
 if ! command -v pyenv &> /dev/null; then
     echo "Error: pyenv not found. Please install it to manage Python versions."
@@ -37,55 +51,48 @@ if ! command -v pyenv &> /dev/null; then
 fi
 eval "$(pyenv init -)"
 
+# 4. Build Loop
 for PY_VERSION in "${PYTHON_VERSIONS[@]}"; do
   (
     set -e
 
-    if ! pyenv versions --bare --filter="${PY_VERSION}." &>/dev/null; then
-        echo "⚠️  Python version matching '${PY_VERSION}.*' not found by pyenv. Skipping."
+    # Check if version exists in pyenv
+    if ! pyenv versions --bare --filter="${PY_VERSION}" &>/dev/null; then
+        echo "⚠️  Python version matching '${PY_VERSION}' not found by pyenv. Skipping."
         continue
     fi
     
     pyenv shell "${PY_VERSION}"
-
     PY="$(pyenv which python)"
-    echo "➤ Building for $($PY --version) on macOS arm64 (target: ${MACOSX_DEPLOYMENT_TARGET})"
     
+    echo "----------------------------------------------------------------"
+    echo "➤ Building for $($PY --version) on macOS arm64"
+    echo "----------------------------------------------------------------"
+
+    # Install build deps explicitly so we can skip build isolation
     "$PY" -m pip install --upgrade pip setuptools wheel meson meson-python delocate
 
-    CC=clang CXX=clang++ "$PY" -m pip wheel . \
+    # PERF: --no-build-isolation prevents creating a fresh venv and reinstalling meson/ninja 
+    # for every single build, saving significant I/O and network time.
+    CC="ccache clang" CXX="ccache clang++" "$PY" -m pip wheel . \
+      --no-build-isolation \
+      "${MESON_ARGS[@]}" \
        -w "${WHEEL_DIR}" -vv
 
-    echo "➤ Sanitizing RPATHs before delocation..."
-    
+    # We expect exactly one new wheel in the tmp dir per iteration
     CURRENT_WHEEL=$(find "${WHEEL_DIR}" -name "*.whl" | head -n 1)
 
-    if [ -f "$CURRENT_WHEEL" ]; then
-        "$PY" -m wheel unpack "$CURRENT_WHEEL" -d "${WHEEL_DIR}/unpacked"
-        
-        UNPACKED_ROOT=$(find "${WHEEL_DIR}/unpacked" -mindepth 1 -maxdepth 1 -type d)
-
-        find "$UNPACKED_ROOT" -name "*.so" | while read -r SO_FILE; do
-            echo "   Processing: $SO_FILE"
-            "$PY" "../../build-python/fix_rpaths.py" "$SO_FILE"
-        done
-
-        "$PY" -m wheel pack "$UNPACKED_ROOT" -d "${WHEEL_DIR}"
-        
-        rm -rf "${WHEEL_DIR}/unpacked"
-    else
-        echo "Error: No wheel found to sanitize!"
-        exit 1
-    fi
-
-    echo "➤ Repairing wheel(s) with delocate"
-    delocate-wheel -w "${FINAL_WHEEL_DIR}" "${WHEEL_DIR}"/*.whl
-
-    rm "${WHEEL_DIR}"/*.whl
+    echo "➤ Repairing wheel with delocate"
+    # Delocate moves the repaired wheel to FINAL_WHEEL_DIR
+    delocate-wheel -w "${FINAL_WHEEL_DIR}" "$CURRENT_WHEEL"
 
+    # Clean up the intermediate wheel from this iteration so it doesn't confuse the next
+    rm "$CURRENT_WHEEL"
   )
 done
 
+# Cleanup
 rm -rf "${TMPDIR}"
 rm -rf "${WHEEL_DIR}"
 
+echo "✅ All builds complete. Artifacts in ${FINAL_WHEEL_DIR}"

utils/wheels/repair_wheel_macos.sh

@@ -0,0 +1,90 @@
+#!/bin/zsh
+
+set -e
+# Color codes for output
+RED='\033[0;31m'
+YELLOW='\033[1;33m'
+GREEN='\033[0;32m'
+NC='\033[0m' # No Color
+
+function fix_file_rpaths() {
+    local file_path="$1"
+    echo -e "${YELLOW}Fixing RPATHs in file: $file_path...${NC}"
+    python3 "$FIX_RPATH_SCRIPT" "$file_path"
+    if [ $? -ne 0 ]; then
+        echo -e "${RED}Error: RPATH fix script failed for file: $file_path${NC}"
+        exit 1
+    fi
+    echo -e "${GREEN}RPATHs fixed for file: $file_path${NC}"
+}
+
+export -f fix_file_rpaths
+
+echo -e "${YELLOW}"
+echo "========================================================================="
+echo "                    TEMPORARY WHEEL REPAIR WORKAROUND"
+echo "========================================================================="
+echo -e "${NC}"
+echo ""
+echo -e "${YELLOW}WARNING:${NC} This script applies a temporary patch to fix"
+echo "a known issue with meson-python that causes duplicate RPATH entries in"
+echo "built Python wheels on macOS, preventing module imports."
+echo ""
+echo "This workaround will:"
+echo "  1. Unzip the wheel file"
+echo "  2. Locate the extension modules"
+echo "  3. Remove duplicate RPATH entries using install_name_tool"
+echo "  4. Resign the wheel if necessary"
+echo "  5. Repackage the wheel file"
+echo ""
+
+FIX_RPATH_SCRIPT="../../build-python/fix_rpaths.py"
+
+# get the wheel directory to scan through
+WHEEL_DIR="$1"
+if [ -z "$WHEEL_DIR" ]; then
+    echo -e "${RED}Error: No wheel directory specified.${NC}"
+    echo "Usage: $0 /path/to/wheel_directory"
+    exit 1
+fi
+
+REPAIRED_WHEELS_DIR="repaired_wheels"
+mkdir -p "$REPAIRED_WHEELS_DIR"
+
+REPAIRED_DELOCATED_WHEELS_DIR="${REPAIRED_WHEELS_DIR}/delocated"
+
+# Scal all files ending in .whl and not starting with a dot
+for WHEEL_PATH in "$WHEEL_DIR"/*.whl; do
+    if [ ! -f "$WHEEL_PATH" ]; then
+        echo -e "${YELLOW}No wheel files found in directory: $WHEEL_DIR${NC}"
+        exit 0
+    fi
+    echo ""
+    echo -e "${GREEN}Processing wheel: $WHEEL_PATH${NC}"
+
+    WHEEL_NAME=$(basename "$WHEEL_PATH")
+    TEMP_DIR=$(mktemp -d)
+
+    echo -e "${GREEN}Step 1: Unzipping wheel...${NC}"
+    python -m wheel unpack "$WHEEL_PATH" -d "$TEMP_DIR"
+
+    echo -e "${GREEN}Step 2: Locating extension modules...${NC}"
+    while IFS= read -r -d '' so_file; do
+        echo "Found library: $so_file"
+        fix_file_rpaths "$so_file"
+    done < <(find "$TEMP_DIR" -name "*.so" -print0)
+
+    echo -e "${GREEN}Step 4: Repackaging wheel...${NC}"
+    python -m wheel pack "$TEMP_DIR/gridfire-0.7.4rc2" -d "$REPAIRED_WHEELS_DIR"
+
+    REPAIRED_WHEEL_PATH="${REPAIRED_WHEELS_DIR}/${WHEEL_NAME}"
+
+    echo -e "${GREEN}Step 5: Delocating wheel...${NC}"
+    # Ensure delocate is installed
+    pip install delocate
+    delocate-wheel -w "$REPAIRED_DELOCATED_WHEELS_DIR" "$REPAIRED_WHEEL_PATH"
+
+    echo -e "${GREEN}Repaired wheel saved to: ${REPAIRED_DELOCATED_WHEELS_DIR}/${WHEEL_NAME}${NC}"
+    # Clean up temporary directory
+    rm -rf "$TEMP_DIR"
+done