Merge branch 'restructure' into 'v0.x'

Refactor build process

See merge request naaice/poet!20

CMakeLists.txt

@@ -24,7 +24,6 @@ find_package(RRuntime REQUIRED)
 
 add_subdirectory(src)
 add_subdirectory(R_lib)
-add_subdirectory(app)
 add_subdirectory(bench)
 
 # as tug will also pull in doctest as a dependency

app/CMakeLists.txt

@@ -1,7 +0,0 @@
-configure_file(poet.h.in poet.h)
-
-add_executable(poet poet.cpp)
-target_include_directories(poet PUBLIC "${CMAKE_CURRENT_BINARY_DIR}")
-target_link_libraries(poet PUBLIC poet_lib MPI::MPI_CXX)
-
-install(TARGETS poet DESTINATION bin)

app/poet.h.in

@@ -1,11 +0,0 @@
-#ifndef POET_H
-#define POET_H
-
-#include "poet/ChemistryModule.hpp"
-#include <Rcpp.h>
-const char *poet_version = "@POET_VERSION@";
-
-const char *CHEMISTRY_MODULE_NAME = "state_C";
-
-
-#endif // POET_H

src/Base/Grid.cpp

@@ -18,7 +18,9 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
-#include "poet/SimParams.hpp"
+#include "Grid.hpp"
+#include "SimParams.hpp"
+
 #include <RInside.h>
 #include <Rcpp.h>
 #include <algorithm>
@@ -26,7 +28,6 @@
 #include <cstdint>
 #include <new>
 #include <numeric>
-#include <poet/Grid.hpp>
 #include <stdexcept>
 #include <string>
 #include <vector>

src/Base/Grid.hpp

@@ -21,7 +21,8 @@
 #ifndef GRID_H
 #define GRID_H
 
-#include "poet/SimParams.hpp"
+#include "SimParams.hpp"
+
 #include <RInside.h>
 #include <Rcpp.h>
 #include <array>

src/Base/SimParams.cpp

@@ -20,11 +20,13 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
-#include "poet/enums.hpp"
+#include "SimParams.hpp"
+
+#include "../Chemistry/enums.hpp"
+
 #include <algorithm>
 #include <cassert>
 #include <cstdint>
-#include <poet/SimParams.hpp>
 
 #include <RInside.h>
 #include <Rcpp.h>

src/Base/SimParams.hpp

@@ -21,6 +21,12 @@
 #ifndef PARSER_H
 #define PARSER_H
 
+#include "../DataStructures/DataStructures.hpp"
+#include "Macros.hpp"
+#include "RInsidePOET.hpp"
+
+#include "argh.hpp" // Argument handler https://github.com/adishavit/argh
+
 #include <cstdint>
 #include <optional>
 #include <string>
@@ -28,10 +34,6 @@
 #include <unordered_map>
 #include <vector>
 
-#include "DataStructures.hpp"
-#include "Macros.hpp"
-#include "RInsidePOET.hpp"
-#include "argh.hpp" // Argument handler https://github.com/adishavit/argh
 #include <RInside.h>
 #include <Rcpp.h>
 // BSD-licenced

src/CMakeLists.txt

@@ -1,13 +1,27 @@
-file(GLOB_RECURSE poet_lib_SRC
+add_library(poetlib
-  CONFIGURE_DEPENDS
+  Base/Grid.cpp
-  "*.cpp" "*.c")
+  Base/SimParams.cpp
+  Chemistry/ChemistryModule.cpp
+  Chemistry/MasterFunctions.cpp 
+  Chemistry/WorkerFunctions.cpp 
+  Chemistry/SurrogateModels/DHT_Wrapper.cpp 
+  Chemistry/SurrogateModels/DHT.c 
+  Chemistry/SurrogateModels/HashFunctions.cpp 
+  Chemistry/SurrogateModels/InterpolationModule.cpp 
+  Chemistry/SurrogateModels/ProximityHashTable.cpp
+  DataStructures/Field.cpp
+  Transport/DiffusionModule.cpp
+)
 
-add_library(poet_lib ${poet_lib_SRC})
+target_link_libraries(poetlib PUBLIC
-target_include_directories(poet_lib PUBLIC ${PROJECT_SOURCE_DIR}/include)
+  MPI::MPI_C 
-target_link_libraries(poet_lib PUBLIC
+  ${MATH_LIBRARY} 
-  MPI::MPI_CXX ${MATH_LIBRARY} RRuntime PhreeqcRM tug)
+  RRuntime 
+  PhreeqcRM 
+  tug
+)
 
-target_compile_definitions(poet_lib PUBLIC STRICT_R_HEADERS OMPI_SKIP_MPICXX)
+target_compile_definitions(poetlib PUBLIC STRICT_R_HEADERS OMPI_SKIP_MPICXX)
 
 mark_as_advanced(PHREEQCRM_BUILD_MPI PHREEQCRM_DISABLE_OPENMP)
 set(PHREEQCRM_DISABLE_OPENMP ON CACHE BOOL "" FORCE)
@@ -15,11 +29,19 @@ set(PHREEQCRM_DISABLE_OPENMP ON CACHE BOOL "" FORCE)
 option(POET_DHT_DEBUG "Build with DHT debug info" OFF)
 
 if(POET_DHT_DEBUG)
-  target_compile_definitions(poet_lib PRIVATE DHT_STATISTICS)
+  target_compile_definitions(poetlib PRIVATE DHT_STATISTICS)
 endif()
 
 option(POET_PHT_ADDITIONAL_INFO "Enables additional information in the PHT" OFF)
 
 if (POET_PHT_ADDITIONAL_INFO)
-  target_compile_definitions(poet_lib PRIVATE POET_PHT_ADD)
+  target_compile_definitions(poetlib PRIVATE POET_PHT_ADD)
 endif()
+
+configure_file(poet.hpp.in poet.hpp)
+
+add_executable(poet poet.cpp)
+target_link_libraries(poet PRIVATE poetlib MPI::MPI_C RRuntime)
+target_include_directories(poet PRIVATE "${CMAKE_CURRENT_BINARY_DIR}")
+
+install(TARGETS poet DESTINATION bin)

src/Chemistry/ChemistryModule.cpp

@@ -1,7 +1,9 @@
-#include "poet/ChemistryModule.hpp"
+#include "ChemistryModule.hpp"
-#include "PhreeqcRM.h"
+
-#include "poet/DHT_Wrapper.hpp"
+#include "SurrogateModels/DHT_Wrapper.hpp"
-#include "poet/Interpolation.hpp"
+#include "SurrogateModels/Interpolation.hpp"
+
+#include <PhreeqcRM.h>
 
 #include <algorithm>
 #include <cassert>

src/Chemistry/ChemistryModule.hpp

@@ -3,12 +3,13 @@
 #ifndef CHEMISTRYMODULE_H_
 #define CHEMISTRYMODULE_H_
 
-#include "DHT_Wrapper.hpp"
+#include "../Base/SimParams.hpp"
-#include "DataStructures.hpp"
+#include "../DataStructures/DataStructures.hpp"
-#include "Interpolation.hpp"
+#include "SurrogateModels/DHT_Wrapper.hpp"
-#include "IrmResult.h"
+#include "SurrogateModels/Interpolation.hpp"
-#include "PhreeqcRM.h"
+
-#include "SimParams.hpp"
+#include <IrmResult.h>
+#include <PhreeqcRM.h>
 
 #include <array>
 #include <cstddef>

src/Chemistry/MasterFunctions.cpp

@@ -1,5 +1,6 @@
-#include "PhreeqcRM.h"
+#include "ChemistryModule.hpp"
-#include "poet/ChemistryModule.hpp"
+
+#include <PhreeqcRM.h>
 
 #include <algorithm>
 #include <cstddef>

src/Chemistry/SurrogateModels/DHT.c

@@ -16,8 +16,9 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
+#include "DHT.h"
+
 #include <mpi.h>
-#include <poet/DHT.h>
 
 #include <inttypes.h>
 #include <math.h>

src/Chemistry/SurrogateModels/DHT_Wrapper.cpp

@@ -20,14 +20,7 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
-#include "poet/DHT_Wrapper.hpp"
+#include "DHT_Wrapper.hpp"
-#include "poet/HashFunctions.hpp"
-#include "poet/Interpolation.hpp"
-#include "poet/LookupKey.hpp"
-#include "poet/Rounding.hpp"
-#include "poet/enums.hpp"
-
-#include "poet/RInsidePOET.hpp"
 
 #include <algorithm>
 #include <cassert>
@@ -150,8 +143,7 @@ void DHT_Wrapper::fillDHT(const WorkPackage &work_package) {
       uint32_t proc, index;
       auto &key = dht_results.keys[i];
       const auto data =
-          (with_interp
+          (with_interp ? outputToInputAndRates(work_package.input[i],
-               ? outputToInputAndRates(work_package.input[i],
                                                work_package.output[i])
                        : work_package.output[i]);
       // void *data = (void *)&(work_package[i * this->data_count]);

src/Chemistry/SurrogateModels/DHT_Wrapper.hpp

@@ -23,14 +23,14 @@
 #ifndef DHT_WRAPPER_H
 #define DHT_WRAPPER_H
 
-#include "DataStructures.hpp"
+#include "../../Base/RInsidePOET.hpp"
+#include "../../Base/SimParams.hpp"
+#include "../../DataStructures/DataStructures.hpp"
+#include "../enums.hpp"
+#include "HashFunctions.hpp"
 #include "LookupKey.hpp"
-#include "RInsidePOET.hpp"
+#include "Rounding.hpp"
-#include "SimParams.hpp"
+
-#include "enums.hpp"
-#include "poet/HashFunctions.hpp"
-#include "poet/LookupKey.hpp"
-#include "poet/Rounding.hpp"
 #include <array>
 #include <cstdint>
 #include <limits>

src/Chemistry/SurrogateModels/HashFunctions.cpp

@@ -24,7 +24,7 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
-#include "poet/HashFunctions.hpp"
+#include "HashFunctions.hpp"
 
 #if defined(_MSC_VER)
 

src/Chemistry/SurrogateModels/Interpolation.hpp

@@ -3,13 +3,12 @@
 #ifndef INTERPOLATION_H_
 #define INTERPOLATION_H_
 
-#include "DHT.h"
+#include "../../Base/SimParams.hpp"
+#include "../../DataStructures/DataStructures.hpp"
 #include "DHT_Wrapper.hpp"
-#include "DataStructures.hpp"
 #include "LookupKey.hpp"
-#include "poet/DHT_Wrapper.hpp"
+#include "Rounding.hpp"
-#include "poet/Rounding.hpp"
+
-#include "poet/SimParams.hpp"
 #include <cassert>
 #include <iostream>
 #include <list>
@@ -17,11 +16,11 @@
 #include <mpi.h>
 #include <string>
 #include <utility>
+
 extern "C" {
-#include "poet/DHT.h"
+#include "DHT.h"
 }
 
-#include "poet/LookupKey.hpp"
 #include <cstdint>
 #include <functional>
 #include <unordered_map>

src/Chemistry/SurrogateModels/InterpolationModule.cpp

@@ -1,13 +1,15 @@
 //  Time-stamp: "Last modified 2023-08-16 17:02:31 mluebke"
+#include "Interpolation.hpp"
 
-#include "poet/DHT_Wrapper.hpp"
+#include "../../DataStructures/DataStructures.hpp"
-#include "poet/DataStructures.hpp"
+#include "DHT_Wrapper.hpp"
-#include "poet/HashFunctions.hpp"
+#include "HashFunctions.hpp"
-#include "poet/Interpolation.hpp"
+#include "LookupKey.hpp"
-#include "poet/LookupKey.hpp"
+#include "Rounding.hpp"
-#include "poet/Rounding.hpp"
+
-#include <Rcpp/vector/instantiation.h>
+#include <Rcpp.h>
 #include <Rinternals.h>
+
 #include <algorithm>
 #include <array>
 #include <cassert>
@@ -20,8 +22,9 @@
 #include <string>
 #include <utility>
 #include <vector>
+
 extern "C" {
-#include "poet/DHT.h"
+#include "DHT.h"
 }
 
 namespace poet {

src/Chemistry/SurrogateModels/LookupKey.hpp

@@ -3,7 +3,8 @@
 #ifndef LOOKUPKEY_H_
 #define LOOKUPKEY_H_
 
-#include "poet/HashFunctions.hpp"
+#include "HashFunctions.hpp"
+
 #include <cstdint>
 #include <cstring>
 #include <vector>

src/Chemistry/SurrogateModels/ProximityHashTable.cpp

@@ -1,10 +1,11 @@
 //  Time-stamp: "Last modified 2023-08-15 14:50:59 mluebke"
+#include "Interpolation.hpp"
+
+#include "DHT_Wrapper.hpp"
+#include "HashFunctions.hpp"
+#include "LookupKey.hpp"
+#include "Rounding.hpp"
 
-#include "poet/DHT_Wrapper.hpp"
-#include "poet/HashFunctions.hpp"
-#include "poet/Interpolation.hpp"
-#include "poet/LookupKey.hpp"
-#include "poet/Rounding.hpp"
 #include <cassert>
 #include <cstddef>
 #include <cstdint>
@@ -12,8 +13,9 @@
 #include <memory>
 #include <unordered_set>
 #include <vector>
+
 extern "C" {
-#include "poet/DHT.h"
+#include "DHT.h"
 }
 
 namespace poet {

src/Chemistry/WorkerFunctions.cpp

@@ -1,8 +1,8 @@
 //  Time-stamp: "Last modified 2023-08-16 14:50:04 mluebke"
 
-#include "poet/ChemistryModule.hpp"
+#include "ChemistryModule.hpp"
-#include "poet/DHT_Wrapper.hpp"
+#include "SurrogateModels/DHT_Wrapper.hpp"
-#include "poet/Interpolation.hpp"
+#include "SurrogateModels/Interpolation.hpp"
 
 #include <IrmResult.h>
 #include <algorithm>

src/ChemistryModule/SurrogateModels/CMakeLists.txt

@@ -1,21 +0,0 @@
-file(GLOB surrogate_models_SRC
-  CONFIGURE_DEPENDS
-  "*.cpp" "*.c")
-
-find_library(MATH_LIBRARY m)
-
-add_library(surrogate_models ${surrogate_models_SRC})
-target_include_directories(surrogate_models PUBLIC ${PROJECT_SOURCE_DIR}/include)
-target_link_libraries(surrogate_models PUBLIC
-    MPI::MPI_CXX ${MATH_LIBRARY})
-target_compile_definitions(surrogate_models PUBLIC OMPI_SKIP_MPICXX)
-
-option(POET_PHT_ADDITIONAL_INFO "Enables additional information in the PHT" OFF)
-
-if (POET_PHT_ADDITIONAL_INFO)
-  target_compile_definitions(surrogate_models PRIVATE POET_PHT_ADD)
-endif()
-
-if(POET_DHT_DEBUG)
-  target_compile_definitions(surrogate_models PRIVATE DHT_STATISTICS)
-endif()

src/DataStructures/DataStructures.hpp

@@ -1,7 +1,7 @@
 #ifndef DATASTRUCTURES_H_
 #define DATASTRUCTURES_H_
 
-#include "enums.hpp"
+#include "../Chemistry/enums.hpp"
 
 #include <Rcpp.h>
 
@@ -13,6 +13,7 @@
 #include <string>
 #include <utility>
 #include <vector>
+
 namespace poet {
 
 struct WorkPackage {

src/DataStructures/Field.cpp

@@ -1,4 +1,5 @@
-#include "poet/DataStructures.hpp"
+#include "DataStructures.hpp"
+
 #include <Rcpp.h>
 #include <Rinternals.h>
 #include <cstddef>

src/Transport/DiffusionModule.cpp

@@ -18,15 +18,15 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
+#include "DiffusionModule.hpp"
+#include "../Base/Macros.hpp"
+
+#include <tug/BoundaryCondition.hpp>
+#include <tug/Diffusion.hpp>
+
 #include <Rcpp.h>
 #include <algorithm>
 #include <cstdint>
-#include <poet/DiffusionModule.hpp>
-#include <poet/Grid.hpp>
-#include <poet/Macros.hpp>
-#include <poet/SimParams.hpp>
-#include <tug/BoundaryCondition.hpp>
-#include <tug/Diffusion.hpp>
 
 #include <array>
 #include <cassert>
@@ -177,11 +177,11 @@ void DiffusionModule::simulate(double dt) {
 
   t_field = field_2d;
 
-
   sim_a_transport = MPI_Wtime();
 
   transport_t += sim_a_transport - sim_b_transport;
-  std::cout << " done in "<< sim_a_transport - sim_b_transport << "sec" << std::endl;
+  std::cout << " done in " << sim_a_transport - sim_b_transport << "sec"
+            << std::endl;
 }
 
 void DiffusionModule::end() {

src/Transport/DiffusionModule.hpp

@@ -21,16 +21,17 @@
 #ifndef DIFFUSION_MODULE_H
 #define DIFFUSION_MODULE_H
 
-#include "DataStructures.hpp"
+#include "../Base/Grid.hpp"
-#include "SimParams.hpp"
+#include "../Base/SimParams.hpp"
-#include "poet/SimParams.hpp"
+#include "../DataStructures/DataStructures.hpp"
+
+#include <tug/BoundaryCondition.hpp>
+#include <tug/Diffusion.hpp>
+
 #include <array>
 #include <cmath>
 #include <cstdint>
-#include <poet/Grid.hpp>
 #include <string>
-#include <tug/BoundaryCondition.hpp>
-#include <tug/Diffusion.hpp>
 #include <vector>
 
 namespace poet {

src/poet.cpp

@@ -18,15 +18,18 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
+#include "Base/Grid.hpp"
+#include "Base/Macros.hpp"
+#include "Base/RInsidePOET.hpp"
+#include "Base/SimParams.hpp"
+#include "Chemistry/ChemistryModule.hpp"
+#include "Transport/DiffusionModule.hpp"
+
+#include <poet.hpp>
+
 #include <Rcpp.h>
 #include <cstdint>
 #include <cstdlib>
-#include <poet/ChemistryModule.hpp>
-#include <poet/DiffusionModule.hpp>
-#include <poet/Grid.hpp>
-#include <poet/Macros.hpp>
-#include <poet/RInsidePOET.hpp>
-#include <poet/SimParams.hpp>
 
 #include <cstring>
 #include <iostream>
@@ -34,7 +37,6 @@
 #include <vector>
 
 #include <mpi.h>
-#include <poet.h>
 
 using namespace std;
 using namespace poet;

src/poet.hpp.in

@@ -0,0 +1,8 @@
+#ifndef POET_H
+#define POET_H
+
+static const char *poet_version = "@POET_VERSION@";
+
+static const char *CHEMISTRY_MODULE_NAME = "state_C";
+
+#endif // POET_H

test/CMakeLists.txt

@@ -3,7 +3,8 @@ file(GLOB test_SRC
   "*.cpp" "*.c")
 
 add_executable(testPOET ${test_SRC})
-target_link_libraries(testPOET doctest poet_lib)
+target_link_libraries(testPOET doctest poetlib)
+target_include_directories(testPOET PRIVATE "${PROJECT_SOURCE_DIR}/src")
 
 get_filename_component(TEST_RInsideSourceFile "RInsidePOET_funcs.R" REALPATH)
 configure_file(testDataStructures.hpp.in testDataStructures.hpp)

test/testField.cpp

@@ -5,11 +5,12 @@
 #include <cstdint>
 #include <doctest/doctest.h>
 #include <iostream>
-#include <poet/DataStructures.hpp>
-#include <poet/RInsidePOET.hpp>
 #include <string>
 #include <vector>
 
+#include <Base/RInsidePOET.hpp>
+#include <DataStructures/DataStructures.hpp>
+
 #include "testDataStructures.hpp"
 
 using namespace poet;

test/testNamedVector.cpp

@@ -1,11 +1,12 @@
 #include <Rcpp.h>
 #include <cstddef>
 #include <doctest/doctest.h>
-#include <poet/DataStructures.hpp>
-#include <poet/RInsidePOET.hpp>
 #include <utility>
 #include <vector>
 
+#include <Base/RInsidePOET.hpp>
+#include <DataStructures/DataStructures.hpp>
+
 #include "testDataStructures.hpp"
 
 TEST_CASE("NamedVector") {

test/testRounding.cpp

@@ -1,6 +1,6 @@
 #include <doctest/doctest.h>
 
-#include "poet/Rounding.hpp"
+#include <Chemistry/SurrogateModels/Rounding.hpp>
 
 TEST_CASE("Rounding") {
   constexpr int signif = 3;