Now it compiles!

BioDynaMo · Sep 16, 2024 · f6d897c · f6d897c
1 parent 3f71ebf
commit f6d897c
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Showing 10 changed files with 65 additions and 6 deletions.
diff --git a/cmake/BioDynaMo.cmake b/cmake/BioDynaMo.cmake
@@ -112,15 +112,24 @@ function(build_shared_library TARGET)
     set(DICT_FILE "${CMAKE_CURRENT_BINARY_DIR}/lib${TARGET}_dict")
     set(BDM_DICT_FILE "${CMAKE_CURRENT_BINARY_DIR}/lib${TARGET}_bdm_dict.cc")
     set(module "${TARGET}")
-    string(REPLACE "${CMAKE_SOURCE_DIR}/src/" "" ROOT_HEADERS "${ARG_HEADERS}")
+
+    if (runtime_cxxmodules)
+      set(MODULEMAP "--moduleMapFile=${CMAKE_SOURCE_DIR}/src/module.modulemap")
+    endif()
+
+    if (NOT ${TARGET} STREQUAL "biodynamo")
+      #set(DEPENDENCY_OPTION "-m ${CMAKE_CURRENT_BINARY_DIR}/lib/biodynamo.pcm")
+      #set(NO_MODULE "NO_CXXMODULE")
+      #set(MODULEMAP)
+    endif()
 
     # Since the location of the CMake files differ in the build and installation
     # directory, we check if BDM_CMAKE_DIR is already set (in build directory
     # case). Otherwise, set it to the installation directory
     if(NOT DEFINED BDM_CMAKE_DIR)
       set(BDM_CMAKE_DIR $ENV{BDMSYS}/share/cmake)
     endif()
-    ROOT_GENERATE_DICTIONARY(${DICT_FILE} ${ROOT_HEADERS} MODULE ${module} LINKDEF ${BDM_CMAKE_DIR}/${ARG_SELECTION} REFLEX OPTIONS -I src --noIncludePaths --inlineInputHeader --moduleMapFile=${CMAKE_SOURCE_DIR}/src/module.modulemap)
+    ROOT_GENERATE_DICTIONARY(${DICT_FILE} ${ARG_HEADERS} MODULE ${module} LINKDEF ${BDM_CMAKE_DIR}/${ARG_SELECTION} REFLEX ${NO_MODULE} OPTIONS ${DEPENDENCY_OPTION} -I src --inlineInputHeader --noIncludePaths ${MODULEMAP})
     if (BDM_OUT_OF_SOURCE)
       set(BDM_DICT_BIN_PATH "$ENV{BDMSYS}/bin")
     else()

diff --git a/cmake/RootMacros.cmake b/cmake/RootMacros.cmake
@@ -743,7 +743,7 @@ function(ROOT_GENERATE_DICTIONARY dictionary)
     # Install the C++ module if we generated one.
     if (cpp_module_file)
       install(FILES ${cpp_module_file}
-                    DESTINATION ${shared_lib_install_dir} COMPONENT libraries)
+        DESTINATION ${CMAKE_BINARY_DIR}/lib COMPONENT libraries)
     endif()
 
     if(ARG_STAGE1)

diff --git a/cmake/selection-libbiodynamo.xml b/cmake/selection-libbiodynamo.xml
@@ -149,6 +149,7 @@
     <class name="bdm::neuroscience::SplitNeuriteElementEvent" />
     <class name="bdm::neuroscience::NeuriteElement::MechanicalForcesFunctor" />
     <class name="bdm::Spinlock" />
+    <class name="bdm::SharedData<std::vector<bdm::AgentUid>>" />
     <class name="bdm::SharedData<uint64_t>" />
     <class name="bdm::SharedData<bdm::MathArray<double,3>>" />
     <class name="bdm::SharedData<bdm::MathArray<double,4>>" />

diff --git a/cmake/selection.xml b/cmake/selection.xml
@@ -6,14 +6,51 @@
     <class pattern="std::vector<bdm::*>" />
   </selection>
   <exclusion>
+    <class pattern="vector<bdm::OptimizationParamType*>" />
+    <class pattern="*bdm::OptimizationParamType*"/>
+    <class pattern="*bdm::OptimizationParam*"/>
     <class pattern="bdm::OpenCLState*"/>
     <class name="bdm::ParallelResizeVector<pair<unsigned int,const bdm::UniformGridEnvironment::Box*> >" />
-    <class name="bdm::OptimizationParam" />
-    <class name="bdm::OptimizationParamType"/>
+    <class name="bdm::FixedSizeVector<pair<unsigned int,const bdm::UniformGridEnvironment::Box*> >" />
+    <class name="bdm::FixedSizeVector<const bdm::UniformGridEnvironment::Box*, 27>" />
+    <class pattern="bdm::UniformGridEnvironment::*" />
+    <class pattern="bdm::AgentFlatIdxMap*" />
+    <class pattern="bdm::AgentVector*"  />
+    <class pattern="bdm::NanoFlannAdapter*"  />
+    <class pattern="bdm::MortonOrder*"  />
+    <class pattern="bdm::AgentContainer*"  />
+    <class pattern="bdm::Exporter*"  />
+    <class pattern="bdm::BasicExporter*"  />
+    <class pattern="bdm::MatlabExporter*" />
+    <class pattern="bdm::NeuroMLExporter*"  />
+    <class pattern="bdm::ParaviewExporter*"  />
+    <class pattern="bdm::GpuHelper*"  />
+    <class pattern="bdm::MechanicalForcesOpCudaKernel*" />
+    <class pattern="bdm::experimental::Algorithm*"  />
+    <class name="bdm::SumReduction<unsigned long>" />
+    <class pattern="bdm::experimental::AlgorithmRegistry*"  />
+    <class pattern="bdm::experimental::Database*" />
+    <class pattern="bdm::experimental::MultiSimulation*"  />
+    <class pattern="bdm::experimental::MultiSimulationManager*" />
+    <class pattern="bdm::experimental::Worker*" />
+    <class name="bdm::VisualizationAdaptor" />
+    <class pattern="bdm::ContinuumOp*"  />
+    <class pattern="bdm::LoadBalancingOp*"  />
+    <class pattern="bdm::MechanicalForcesOpCuda*" />
+    <class pattern="bdm::MechanicalForcesOpOpenCL*" />
+    <class pattern="bdm::VisualizationOp*"  />
+    <class name="bdm::CSVReader"  />
+    <class name="bdm::JitForEachDataMemberFunctor"  />
+    <class name="bdm::JitHeaders" />
+    <class name="bdm::VTuneTask"  />
+    <class name="vector<bdm::experimental::Status>" />
+    <class pattern="*vector<bdm::AgentPointer<bdm::neuroscience::NeuriteElement>>*"  />
+    <class pattern="*bdm::AgentPointer<bdm::neuroscience::NeuriteElement>*"  />
     <class name="bdm::SetParam"/>
     <class name="bdm::ParticleSwarmParam"/>
     <class name="bdm::LogRangeParam"/>
     <class name="bdm::RangeParam"/>
+    <class name="vector<bdm::UniformGridEnvironment::GridNeighborMutexBuilder::MutexWrapper>" />
     <class name="bdm::experimental::MPIObject" />
     <class name="bdm::OperationImpl" />
     <class pattern="cl::*" />
@@ -86,7 +123,7 @@
     <class name="bdm::InlineVector<bdm::Behavior*, 2>" noStreamer="true" />
     <class name="bdm::InlineVector<bdm::Behavior*, 3>" noStreamer="true" />
     <class name="bdm::VectorTypeWrapper<bdm::Behavior*>" />
-    <class name="bdm::experimental::TimeSeries" />
+    <class pattern="*bdm::experimental::TimeSeries*" />
     <class name="bdm::experimental::DataTransformer" />
     <class name="bdm::experimental::LinearTransformer" />
     <class name="bdm::experimental::TimeSeries::Data" />
@@ -184,6 +221,7 @@
     <class name="bdm::neuroscience::SideNeuriteExtensionEvent" />
     <class name="bdm::neuroscience::SplitNeuriteElementEvent" />
     <class name="bdm::neuroscience::NeuriteElement::MechanicalForcesFunctor" />
+    <class name="bdm::SharedData<std::vector<bdm::AgentUid>>" />
     <class name="bdm::SharedData<uint64_t>" />
     <class name="bdm::SharedData<bdm::MathArray<double,3>>" />
     <class name="bdm::SharedData<bdm::MathArray<double,4>>" />

diff --git a/demo/soma_clustering/src/validation_criterion.h b/demo/soma_clustering/src/validation_criterion.h
@@ -18,6 +18,11 @@
 #include <vector>
 #include "biodynamo.h"
 #include "my_cell.h"
+#include "core/real_t.h"
+#include "core/agent/agent.h"
+#include "core/simulation.h"
+#include "core/container/math_array.h"
+#include "core/resource_manager.h"
 
 namespace bdm {
 namespace soma_clustering {

diff --git a/src/core/environment/uniform_grid_environment.h b/src/core/environment/uniform_grid_environment.h
@@ -625,6 +625,7 @@ class UniformGridEnvironment : public Environment {
         uint64_t start, uint64_t end,
         Functor<void, Iterator<AgentHandle>*>& f) const override;
 
+   private:
     UniformGridEnvironment* grid_;
     MortonOrder mo_;
     ParallelResizeVector<Box*> sorted_boxes_;

diff --git a/src/core/gpu/mechanical_forces_op_cuda_kernel.h b/src/core/gpu/mechanical_forces_op_cuda_kernel.h
@@ -17,6 +17,7 @@
 
 #include <math.h>
 #include <stdint.h>
+#include "core/real_t.h"
 #include "stdio.h"
 
 #ifdef USE_CUDA

diff --git a/src/core/operation/load_balancing_op.h b/src/core/operation/load_balancing_op.h
@@ -16,6 +16,7 @@
 #define CORE_OPERATION_LOAD_BALANCING_OP_H_
 
 #include "core/operation/operation.h"
+#include "core/operation/operation_registry.h"
 #include "core/resource_manager.h"
 #include "core/simulation.h"
 

diff --git a/src/core/util/partition.h b/src/core/util/partition.h
@@ -15,6 +15,7 @@
 #ifndef CORE_UTIL_PARTITION_H_
 #define CORE_UTIL_PARTITION_H_
 
+#include <bits/stdint-uintn.h>
 #include <cmath>
 
 namespace bdm {

diff --git a/test/unit/core/count_neighbor_functor.h b/test/unit/core/count_neighbor_functor.h
@@ -16,7 +16,9 @@
 #define COUNT_NEIGHBOR_FUNCTOR_H_
 
 #include "core/agent/agent.h"
+#include "core/agent/cell.h"
 #include "core/functor.h"
+#include "core/resource_manager.h"
 #include "core/simulation.h"
 #include "gtest/gtest.h"