Merge branch 'BaseLibMPI' into 'master'

Small MPI wrappers for gather and reduce operations See merge request ogs/ogs!5149
ufz · Nov 25, 2024 · a624b9d · a624b9d
2 parents b2817c6 + ff9e84a
commit a624b9d
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Showing 93 changed files with 637 additions and 1,458 deletions.
diff --git a/Applications/ApplicationsLib/LinearSolverLibrarySetup.h b/Applications/ApplicationsLib/LinearSolverLibrarySetup.h
@@ -19,6 +19,7 @@
 /// The default implementation is empty providing polymorphic behaviour when
 /// using this class.
 
+#include "BaseLib/MPI.h"
 #include "NumLib/DOF/GlobalMatrixProviders.h"
 
 #if defined(USE_PETSC)
@@ -28,9 +29,8 @@ namespace ApplicationsLib
 {
 struct LinearSolverLibrarySetup final
 {
-    LinearSolverLibrarySetup(int argc, char* argv[])
+    LinearSolverLibrarySetup(int argc, char* argv[]) : mpi_setup(argc, argv)
     {
-        MPI_Init(&argc, &argv);
         char help[] = "ogs6 with PETSc \n";
         PetscInitialize(&argc, &argv, nullptr, help);
         MPI_Comm_set_errhandler(PETSC_COMM_WORLD, MPI_ERRORS_RETURN);
@@ -40,8 +40,9 @@ struct LinearSolverLibrarySetup final
     {
         NumLib::cleanupGlobalMatrixProviders();
         PetscFinalize();
-        MPI_Finalize();
     }
+
+    BaseLib::MPI::Setup mpi_setup;
 };
 }    // ApplicationsLib
 #elif defined(USE_LIS)

diff --git a/Applications/ApplicationsLib/TestDefinition.cpp b/Applications/ApplicationsLib/TestDefinition.cpp
@@ -20,9 +20,9 @@
 #include "BaseLib/ConfigTree.h"
 #include "BaseLib/Error.h"
 #include "BaseLib/FileTools.h"
-#ifdef USE_PETSC
-#include <petsc.h>
+#include "BaseLib/MPI.h"
 
+#ifdef USE_PETSC
 #include "MeshLib/IO/VtkIO/VtuInterface.h"  // For petsc file name conversion.
 #endif
 
@@ -197,16 +197,13 @@ TestDefinition::TestDefinition(BaseLib::ConfigTree const& config_tree,
                 //! \ogs_file_param{prj__test_definition__vtkdiff__file}
                 vtkdiff_config.getConfigParameter<std::string>("file");
 #ifdef USE_PETSC
-            int mpi_size;
-            MPI_Comm_size(PETSC_COMM_WORLD, &mpi_size);
-            if (mpi_size > 1)
+            BaseLib::MPI::Mpi mpi;
+            if (mpi.size > 1)
             {
-                int rank;
-                MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
                 filename =
                     MeshLib::IO::getVtuFileNameForPetscOutputWithoutExtension(
                         filename) +
-                    "_" + std::to_string(rank) + ".vtu";
+                    "_" + std::to_string(mpi.rank) + ".vtu";
             }
 #endif  // OGS_USE_PETSC
             filenames.push_back(filename);

diff --git a/Applications/Utils/FileConverter/ConvertSHPToGLI.cpp b/Applications/Utils/FileConverter/ConvertSHPToGLI.cpp
@@ -14,17 +14,14 @@
 
 #include <tclap/CmdLine.h>
 
-#ifdef USE_PETSC
-#include <mpi.h>
-#endif
-
 // STL
 #include <fstream>
 #include <vector>
 
 // ShapeLib
 #include <shapefil.h>
 
+#include "BaseLib/MPI.h"
 #include "GeoLib/GEOObjects.h"
 #include "GeoLib/IO/XmlIO/Qt/XmlGmlInterface.h"
 #include "GeoLib/IO/XmlIO/Qt/XmlStnInterface.h"
@@ -185,9 +182,7 @@ int main(int argc, char* argv[])
 
     cmd.parse(argc, argv);
 
-#ifdef USE_PETSC
-    MPI_Init(&argc, &argv);
-#endif
+    BaseLib::MPI::Setup mpi_setup(argc, argv);
 
     std::string fname(shapefile_arg.getValue());
 
@@ -207,9 +202,6 @@ int main(int argc, char* argv[])
             ERR("Shape file contains {:d} polylines.", number_of_elements);
             ERR("This programme only handles only files containing points.");
             SHPClose(hSHP);
-#ifdef USE_PETSC
-            MPI_Finalize();
-#endif
             return EXIT_SUCCESS;
         }
         SHPClose(hSHP);
@@ -304,8 +296,5 @@ int main(int argc, char* argv[])
         ERR("Could not open the database file.");
     }
 
-#ifdef USE_PETSC
-    MPI_Finalize();
-#endif
     return EXIT_SUCCESS;
 }
diff --git a/Applications/Utils/FileConverter/FEFLOW2OGS.cpp b/Applications/Utils/FileConverter/FEFLOW2OGS.cpp
@@ -14,12 +14,8 @@
 // ThirdParty
 #include <tclap/CmdLine.h>
 
-#ifdef USE_PETSC
-#include <mpi.h>
-#endif
-
-// BaseLib
 #include "BaseLib/FileTools.h"
+#include "BaseLib/MPI.h"
 #include "BaseLib/RunTime.h"
 #include "InfoLib/GitInfo.h"
 #ifndef WIN32
@@ -62,9 +58,7 @@ int main(int argc, char* argv[])
 
     cmd.parse(argc, argv);
 
-#ifdef USE_PETSC
-    MPI_Init(&argc, &argv);
-#endif
+    BaseLib::MPI::Setup mpi_setup(argc, argv);
 
     // *** read mesh
     INFO("Reading {:s}.", feflow_mesh_arg.getValue());
@@ -81,9 +75,6 @@ int main(int argc, char* argv[])
     if (mesh == nullptr)
     {
         INFO("Could not read mesh from {:s}.", feflow_mesh_arg.getValue());
-#ifdef USE_PETSC
-        MPI_Finalize();
-#endif
         return EXIT_FAILURE;
     }
 #ifndef WIN32
@@ -99,8 +90,5 @@ int main(int argc, char* argv[])
     INFO("Writing {:s}.", ogs_mesh_fname);
     MeshLib::IO::writeMeshToFile(*mesh, ogs_mesh_fname);
     INFO("\tDone.");
-#ifdef USE_PETSC
-    MPI_Finalize();
-#endif
     return EXIT_SUCCESS;
 }
diff --git a/Applications/Utils/FileConverter/GMSH2OGS.cpp b/Applications/Utils/FileConverter/GMSH2OGS.cpp
@@ -19,12 +19,8 @@
 // ThirdParty
 #include <tclap/CmdLine.h>
 
-#ifdef USE_PETSC
-#include <mpi.h>
-#endif
-
-// BaseLib
 #include "BaseLib/FileTools.h"
+#include "BaseLib/MPI.h"
 #include "BaseLib/RunTime.h"
 #include "InfoLib/GitInfo.h"
 #ifndef WIN32
@@ -176,9 +172,7 @@ int main(int argc, char* argv[])
 
     cmd.parse(argc, argv);
 
-#ifdef USE_PETSC
-    MPI_Init(&argc, &argv);
-#endif
+    BaseLib::MPI::Setup mpi_setup(argc, argv);
 
     // *** read mesh
     INFO("Reading {:s}.", gmsh_mesh_arg.getValue());
@@ -194,9 +188,6 @@ int main(int argc, char* argv[])
     if (mesh == nullptr)
     {
         INFO("Could not read mesh from {:s}.", gmsh_mesh_arg.getValue());
-#ifdef USE_PETSC
-        MPI_Finalize();
-#endif
         return -1;
     }
 #ifndef WIN32
@@ -279,8 +270,5 @@ int main(int argc, char* argv[])
     MeshLib::IO::writeMeshToFile(*mesh, ogs_mesh_arg.getValue());
 
     delete mesh;
-#ifdef USE_PETSC
-    MPI_Finalize();
-#endif
     return EXIT_SUCCESS;
 }
diff --git a/Applications/Utils/FileConverter/GocadSGridReader.cpp b/Applications/Utils/FileConverter/GocadSGridReader.cpp
@@ -12,16 +12,13 @@
 #include <spdlog/spdlog.h>
 #include <tclap/CmdLine.h>
 
-#ifdef USE_PETSC
-#include <mpi.h>
-#endif
-
 #include <fstream>
 #include <sstream>
 #include <string>
 
 #include "Applications/FileIO/GocadIO/GenerateFaceSetMeshes.h"
 #include "BaseLib/FileTools.h"
+#include "BaseLib/MPI.h"
 #include "InfoLib/GitInfo.h"
 #include "MeshLib/Elements/Element.h"
 #include "MeshLib/IO/writeMeshToFile.h"
@@ -61,9 +58,7 @@ int main(int argc, char* argv[])
 
     cmd.parse(argc, argv);
 
-#ifdef USE_PETSC
-    MPI_Init(&argc, &argv);
-#endif
+    BaseLib::MPI::Setup mpi_setup(argc, argv);
 
     // read the Gocad SGrid
     INFO("Start reading Gocad SGrid.");
@@ -82,8 +77,5 @@ int main(int argc, char* argv[])
 
     INFO("Writing mesh to '{:s}'.", mesh_output_arg.getValue());
     MeshLib::IO::writeMeshToFile(*mesh, mesh_output_arg.getValue());
-#ifdef USE_PETSC
-    MPI_Finalize();
-#endif
     return EXIT_SUCCESS;
 }
diff --git a/Applications/Utils/FileConverter/GocadTSurfaceReader.cpp b/Applications/Utils/FileConverter/GocadTSurfaceReader.cpp
@@ -9,11 +9,8 @@
 
 #include <tclap/CmdLine.h>
 
-#ifdef USE_PETSC
-#include <mpi.h>
-#endif
-
 #include "Applications/FileIO/GocadIO/GocadAsciiReader.h"
+#include "BaseLib/MPI.h"
 #include "InfoLib/GitInfo.h"
 #include "MeshLib/IO/VtkIO/VtuInterface.h"
 #include "MeshLib/Mesh.h"
@@ -65,17 +62,12 @@ int main(int argc, char* argv[])
 
     cmd.parse(argc, argv);
 
-#ifdef USE_PETSC
-    MPI_Init(&argc, &argv);
-#endif
+    BaseLib::MPI::Setup mpi_setup(argc, argv);
 
     if (export_lines_arg.isSet() && export_surfaces_arg.isSet())
     {
         ERR("Both the 'lines-only'-flag and 'surfaces-only'-flag are set. Only "
             "one is allowed at a time.");
-#ifdef USE_PETSC
-        MPI_Finalize();
-#endif
         return 2;
     }
 
@@ -94,9 +86,6 @@ int main(int argc, char* argv[])
     if (!FileIO::Gocad::GocadAsciiReader::readFile(file_name, meshes, t))
     {
         ERR("Error reading file.");
-#ifdef USE_PETSC
-        MPI_Finalize();
-#endif
         return 1;
     }
     INFO("{:d} meshes found.", meshes.size());
@@ -115,8 +104,5 @@ int main(int argc, char* argv[])
         MeshLib::IO::VtuInterface vtu(mesh.get(), data_mode, compressed);
         vtu.writeToFile(dir + delim + mesh->getName() + ".vtu");
     }
-#ifdef USE_PETSC
-    MPI_Finalize();
-#endif
     return 0;
 }
diff --git a/Applications/Utils/FileConverter/Mesh2Raster.cpp b/Applications/Utils/FileConverter/Mesh2Raster.cpp
@@ -9,15 +9,12 @@
 
 #include <tclap/CmdLine.h>
 
-#ifdef USE_PETSC
-#include <mpi.h>
-#endif
-
 #include <filesystem>
 #include <fstream>
 #include <memory>
 #include <string>
 
+#include "BaseLib/MPI.h"
 #include "GeoLib/AABB.h"
 #include "InfoLib/GitInfo.h"
 #include "MeshLib/IO/readMeshFromFile.h"
@@ -52,28 +49,20 @@ int main(int argc, char* argv[])
     cmd.add(input_arg);
     cmd.parse(argc, argv);
 
-#ifdef USE_PETSC
-    MPI_Init(&argc, &argv);
-#endif
+    BaseLib::MPI::Setup mpi_setup(argc, argv);
 
     INFO("Rasterising mesh...");
     std::unique_ptr<MeshLib::Mesh> const mesh(
         MeshLib::IO::readMeshFromFile(input_arg.getValue()));
     if (mesh == nullptr)
     {
         ERR("Error reading mesh file.");
-#ifdef USE_PETSC
-        MPI_Finalize();
-#endif
         return 1;
     }
     if (mesh->getDimension() != 2)
     {
         ERR("The programme requires a mesh containing two-dimensional elements "
             "(i.e. triangles or quadrilaterals.");
-#ifdef USE_PETSC
-        MPI_Finalize();
-#endif
         return 2;
     }
 
@@ -178,8 +167,5 @@ int main(int argc, char* argv[])
     }
     out.close();
     INFO("Result written to {:s}", output_name);
-#ifdef USE_PETSC
-    MPI_Finalize();
-#endif
     return 0;
 }
diff --git a/Applications/Utils/FileConverter/Mesh2Shape.cpp b/Applications/Utils/FileConverter/Mesh2Shape.cpp
@@ -9,11 +9,8 @@
 
 #include <tclap/CmdLine.h>
 
-#ifdef USE_PETSC
-#include <mpi.h>
-#endif
-
 #include "Applications/FileIO/SHPInterface.h"
+#include "BaseLib/MPI.h"
 #include "InfoLib/GitInfo.h"
 #include "MeshLib/IO/readMeshFromFile.h"
 #include "MeshLib/Mesh.h"
@@ -43,22 +40,14 @@ int main(int argc, char* argv[])
 
     cmd.parse(argc, argv);
 
-#ifdef USE_PETSC
-    MPI_Init(&argc, &argv);
-#endif
+    BaseLib::MPI::Setup mpi_setup(argc, argv);
 
     std::string const file_name(input_arg.getValue());
     std::unique_ptr<MeshLib::Mesh> const mesh(
         MeshLib::IO::readMeshFromFile(file_name));
     if (FileIO::SHPInterface::write2dMeshToSHP(output_arg.getValue(), *mesh))
     {
-#ifdef USE_PETSC
-        MPI_Finalize();
-#endif
         return EXIT_SUCCESS;
     }
-#ifdef USE_PETSC
-    MPI_Finalize();
-#endif
     return EXIT_FAILURE;
 }