feat: Implement checkpointing

Co-authored-by: hmars-t <hmars-t@users.noreply.github.com>

src/CMakeLists.txt

@@ -1,8 +1,27 @@
+include(FetchContent)
+FetchContent_Declare(
+  cli11
+  QUIET 
+  GIT_REPOSITORY https://github.com/CLIUtils/CLI11.git
+  GIT_TAG v2.4.2
+)
+
+FetchContent_Declare(
+  highfive
+  QUIET
+  GIT_REPOSITORY https://github.com/highfive-devs/highfive.git
+  GIT_TAG v3.0.0
+)
+
+FetchContent_MakeAvailable(cli11)
+FetchContent_MakeAvailable(highfive)
+
 add_library(POETLib
   Init/InitialList.cpp 
   Init/GridInit.cpp 
   Init/DiffusionInit.cpp
   Init/ChemistryInit.cpp
+  IO/checkpoint.cpp
   DataStructures/Field.cpp
   Transport/DiffusionModule.cpp
   Chemistry/ChemistryModule.cpp
@@ -30,18 +49,10 @@ target_link_libraries(
   PUBLIC RRuntime
   PUBLIC IPhreeqcPOET
   PUBLIC tug
-  PUBLIC MPI::MPI_C
+  PUBLIC MPI::MPI_C 
+  PUBLIC HighFive::HighFive
 )
 
-include(FetchContent)
-FetchContent_Declare(
-  cli11
-  QUIET 
-  GIT_REPOSITORY https://github.com/CLIUtils/CLI11.git
-  GIT_TAG v2.4.2
-)
-
-FetchContent_MakeAvailable(cli11)
 
 # add_library(poetlib
 #   Base/Grid.cpp

src/IO/Datatypes.hpp

@@ -0,0 +1,9 @@
+#pragma once 
+
+#include <cstdint>
+#include <DataStructures/Field.hpp>
+
+struct Checkpoint_s {
+    poet::Field &field;
+    uint32_t iteration;
+};

src/IO/HDF5Functions.hpp

@@ -0,0 +1,8 @@
+#pragma once 
+
+#include <string>
+#include "Datatypes.hpp"
+
+int write_checkpoint(const std::string &file_path, struct Checkpoint_s &&checkpoint);
+
+int read_checkpoint(const std::string &file_path, struct Checkpoint_s &checkpoint);

src/IO/checkpoint.cpp

@@ -0,0 +1,28 @@
+#include "IO/Datatypes.hpp"
+#include <cstdint>
+#include <highfive/H5Easy.hpp>
+
+int write_checkpoint(const std::string &file_path, struct Checkpoint_s &&checkpoint){
+
+    // TODO: errorhandling
+    H5Easy::File file(file_path, H5Easy::File::Overwrite);
+
+
+    H5Easy::dump(file, "/MetaParam/Iterations", checkpoint.iteration);
+    H5Easy::dump(file, "/Grid/Names", checkpoint.field.GetProps());
+    H5Easy::dump(file, "/Grid/Chemistry", checkpoint.field.As2DVector());
+
+    return 0;
+}
+
+int read_checkpoint(const std::string &file_path, struct Checkpoint_s &checkpoint){
+
+     H5Easy::File file(file_path, H5Easy::File::ReadOnly);
+
+     checkpoint.iteration = H5Easy::load<uint32_t>(file, "/MetaParam/Iterations");
+
+     checkpoint.field = H5Easy::load<std::vector<std::vector<double>>>(file, "/Grid/Chemistry");
+
+    return 0;
+}
+

src/poet.cpp

@@ -26,6 +26,8 @@
 #include "CLI/CLI.hpp"
 #include "Chemistry/ChemistryModule.hpp"
 #include "DataStructures/Field.hpp"
+#include "IO/Datatypes.hpp"
+#include "IO/HDF5Functions.hpp"
 #include "Init/InitialList.hpp"
 #include "Transport/DiffusionModule.hpp"
 
@@ -393,6 +395,18 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
     // store_result is TRUE)
     call_master_iter_end(R, diffusion.getField(), chem.getField());
 
+    // TODO: write checkpoint
+    // checkpoint struct --> field and iteration
+
+    if (iter == 1) {
+      write_checkpoint("checkpoint1.hdf5",
+                       {.field = chem.getField(), .iteration = iter});
+    } else if (iter == 2) {
+      Checkpoint_s checkpoint_read{.field = chem.getField()};
+      read_checkpoint("checkpoint1.hdf5", checkpoint_read);
+      iter = checkpoint_read.iteration;
+    }
+
     diffusion.getField().update(chem.getField());
 
     MSG("End of *coupling* iteration " + std::to_string(iter) + "/" +