build(GridFire): building on gcc and clang

resolved some issues preventing GridFire from building on both gcc and clang. Also resolved all warnings on both compilers.

build-config/eigen/meson.build

@@ -2,4 +2,4 @@ eigen_dep = dependency(
     'eigen3',
     version : '>=3.3',
     fallback : ['eigen', 'eigen_dep']
-)
+).as_system()

meson.build

@@ -22,8 +22,20 @@ project('GridFire', 'cpp', version: '0.0.1a', default_options: ['cpp_std=c++23']
 
 # Add default visibility for all C++ targets
 add_project_arguments('-fvisibility=default', language: 'cpp')
+
+message('Found CXX compiler: ' + meson.get_compiler('cpp').get_id())
+
+if meson.get_compiler('cpp').get_id() == 'clang'
     # We disable these because of CppAD
+    message('disabling bitwise-instead-of-logical warnings for clang')
     add_project_arguments('-Wno-bitwise-instead-of-logical', language: 'cpp')
+endif
+
+if meson.get_compiler('cpp').get_id() == 'gcc'
+    # We disable these because of boost notes about abi changes from C++10 -> C++17 make the build too noisey
+    message('disabling psabi warnings for gcc')
+    add_project_arguments('-Wno-psabi', language: 'cpp')
+endif
 
 # For Eigen
 add_project_arguments('-Wno-deprecated-declarations', language: 'cpp')

src/include/gridfire/reaction/reaclib.h

@@ -4,7 +4,7 @@
 
 namespace gridfire::reaclib {
 
-    static bool s_initialized = false;
+    [[maybe_unused]] static bool s_initialized = false;
 
     /**
      * @brief Provides global access to the fully initialized REACLIB reaction set.

src/include/gridfire/reaction/reaction.h

@@ -536,7 +536,7 @@ namespace gridfire::reaction {
         ///
         friend std::ostream& operator<<(std::ostream& os, const TemplatedReactionSet<ReactionT>& r) {
             os << "(ReactionSet: [";
-            int counter = 0;
+            size_t counter = 0;
             for (const auto& reaction : r.m_reactions) {
                 os << reaction;
                 if (counter < r.m_reactions.size() - 2) {

src/lib/engine/engine_graph.cpp

@@ -860,7 +860,7 @@ namespace gridfire {
             // Dynamic cast to REACLIBReaction to access specific properties
             csvFile << reaction.id() << ";";
             // Reactants
-            int count = 0;
+            size_t count = 0;
             for (const auto& reactant : reaction.reactants()) {
                 csvFile << reactant.name();
                 if (++count < reaction.reactants().size()) {

src/lib/engine/views/engine_adaptive.cpp

@@ -339,7 +339,7 @@ namespace gridfire {
     }
 
     size_t AdaptiveEngineView::mapCulledToFullSpeciesIndex(size_t culledSpeciesIndex) const {
-        if (culledSpeciesIndex < 0 || culledSpeciesIndex >= static_cast<int>(m_speciesIndexMap.size())) {
+        if (culledSpeciesIndex < 0 || culledSpeciesIndex >= m_speciesIndexMap.size()) {
             LOG_ERROR(m_logger, "Culled index {} is out of bounds for species index map of size {}.", culledSpeciesIndex, m_speciesIndexMap.size());
             m_logger->flush_log();
             throw std::out_of_range("Culled index " + std::to_string(culledSpeciesIndex) + " is out of bounds for species index map of size " + std::to_string(m_speciesIndexMap.size()) + ".");
@@ -348,7 +348,7 @@ namespace gridfire {
     }
 
     size_t AdaptiveEngineView::mapCulledToFullReactionIndex(size_t culledReactionIndex) const {
-        if (culledReactionIndex < 0 || culledReactionIndex >= static_cast<int>(m_reactionIndexMap.size())) {
+        if (culledReactionIndex < 0 || culledReactionIndex >= m_reactionIndexMap.size()) {
             LOG_ERROR(m_logger, "Culled index {} is out of bounds for reaction index map of size {}.", culledReactionIndex, m_reactionIndexMap.size());
             m_logger->flush_log();
             throw std::out_of_range("Culled index " + std::to_string(culledReactionIndex) + " is out of bounds for reaction index map of size " + std::to_string(m_reactionIndexMap.size()) + ".");

src/lib/engine/views/engine_defined.cpp

@@ -293,7 +293,7 @@ namespace gridfire {
     }
 
     size_t DefinedEngineView::mapViewToFullSpeciesIndex(size_t culledSpeciesIndex) const {
-        if (culledSpeciesIndex < 0 || culledSpeciesIndex >= static_cast<int>(m_speciesIndexMap.size())) {
+        if (culledSpeciesIndex < 0 || culledSpeciesIndex >= m_speciesIndexMap.size()) {
             LOG_ERROR(m_logger, "Defined index {} is out of bounds for species index map of size {}.", culledSpeciesIndex, m_speciesIndexMap.size());
             m_logger->flush_log();
             throw std::out_of_range("Defined index " + std::to_string(culledSpeciesIndex) + " is out of bounds for species index map of size " + std::to_string(m_speciesIndexMap.size()) + ".");
@@ -302,7 +302,7 @@ namespace gridfire {
     }
 
     size_t DefinedEngineView::mapViewToFullReactionIndex(size_t culledReactionIndex) const {
-        if (culledReactionIndex < 0 || culledReactionIndex >= static_cast<int>(m_reactionIndexMap.size())) {
+        if (culledReactionIndex < 0 || culledReactionIndex >= m_reactionIndexMap.size()) {
             LOG_ERROR(m_logger, "Defined index {} is out of bounds for reaction index map of size {}.", culledReactionIndex, m_reactionIndexMap.size());
             m_logger->flush_log();
             throw std::out_of_range("Defined index " + std::to_string(culledReactionIndex) + " is out of bounds for reaction index map of size " + std::to_string(m_reactionIndexMap.size()) + ".");

src/lib/engine/views/engine_multiscale.cpp

@@ -1,15 +1,13 @@
 #include "gridfire/engine/views/engine_multiscale.h"
 #include "gridfire/exceptions/error_engine.h"
 
-#include <numeric>
-
-#include "fourdst/logging/logging.h"
-
 #include <stdexcept>
 #include <vector>
 #include <unordered_map>
 #include <unordered_set>
 
+#include <queue>
+
 #include <ranges>
 #include <algorithm>
 
@@ -531,7 +529,7 @@ namespace gridfire {
             m_algebraic_species.size(),
             [&]() -> std::string {
                 std::stringstream ss;
-                int count = 0;
+                size_t count = 0;
                 for (const auto& species : m_algebraic_species) {
                     ss << species.name();
                     if (m_algebraic_species.size() > 1 && count < m_algebraic_species.size() - 1) {
@@ -1256,7 +1254,7 @@ namespace gridfire {
                 } else {
                     msg << "nuclei ";
                     // TODO: Refactor nice list printing into utility function somewhere
-                    int counter = 0;
+                    size_t counter = 0;
                     for (const auto& seed_idx : seed_indices) {
                         msg << m_baseEngine.getNetworkSpecies()[seed_idx].name();
                         if (counter < seed_indices.size() - 2) {
@@ -1309,7 +1307,7 @@ namespace gridfire {
 
         size_t slowest_pool_index = 0; // Default to the first pool if no valid pool is found
         double slowest_mean_timescale = std::numeric_limits<double>::min();
-        int count = 0;
+        size_t count = 0;
         for (const auto& pool : pools) {
             double mean_timescale = 0.0;
             for (const auto& species_idx : pool) {
@@ -1321,7 +1319,7 @@ namespace gridfire {
                 LOG_CRITICAL(m_logger, "Encountered infinite mean timescale for pool {} with species: {}",
                     count, [&]() -> std::string {
                         std::stringstream ss;
-                        int iCount = 0;
+                        size_t iCount = 0;
                         for (const auto& idx : pool) {
                             ss << all_species[idx].name() << ": " << all_timescales.at(all_species[idx]);
                             if (iCount < pool.size() - 1) {

src/lib/partition/composite/partition_composite.cpp

@@ -76,7 +76,7 @@ namespace gridfire::partition {
     std::string CompositePartitionFunction::type() const {
         std::stringstream ss;
         ss << "CompositePartitionFunction(";
-        int count = 0;
+        size_t count = 0;
         for (const auto& partitionFunction : m_partitionFunctions) {
             ss << partitionFunction->type();
             if (count < m_partitionFunctions.size() - 1) {

src/lib/solver/solver.cpp

@@ -221,8 +221,8 @@ namespace gridfire::solver {
         size_t numSpecies = m_engine.getNetworkSpecies().size();
         J.resize(numSpecies+1, numSpecies+1);
         J.clear();
-        for (int i = 0; i < numSpecies; ++i) {
+        for (size_t i = 0; i < numSpecies; ++i) {
-            for (int j = 0; j < numSpecies; ++j) {
+            for (size_t j = 0; j < numSpecies; ++j) {
                 J(i, j) = m_engine.getJacobianMatrixEntry(i, j);
             }
         }

subprojects/fourdst.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 url = https://github.com/4D-STAR/fourdst
-revision = v0.5.1
+revision = v0.5.2
 depth = 1