Add inline example

Tutorial/gray-scott/CMakeLists.txt

@@ -32,55 +32,82 @@ add_executable(pdf_calc analysis/pdf_calc.cpp)
 target_link_libraries(pdf_calc adios2::adios2 MPI::MPI_C)
 
 option(VTK "Build VTK apps")
-if (VTK_ROOT)
+if(VTK_ROOT)
   set(VTK ON)
-endif(VTK_ROOT)
+endif()
 
-if (VTK)
+if(VTK)
   message(STATUS "Configuring VTK apps")
 
-  find_package(VTK COMPONENTS
-    vtkFiltersCore
-    vtkIOImage
-    vtkIOXML
-  )
-
+  find_package(VTK COMPONENTS vtkFiltersCore vtkIOImage vtkIOXML)
   if(VTK_FOUND)
+    message(STATUS "Adding isosurface")
     add_executable(isosurface analysis/isosurface.cpp)
-    target_link_libraries(isosurface adios2::adios2 ${VTK_LIBRARIES}
-      MPI::MPI_C)
-  endif(VTK_FOUND)
+    target_include_directories(isosurface PRIVATE ${VTK_INCLUDE_DIRS})
+    target_link_libraries(isosurface
+      adios2::adios2 MPI::MPI_C ${VTK_LIBRARIES}
+    )
+  endif()
 
   find_package(VTK COMPONENTS
-    vtkFiltersCore
-    vtkFiltersGeometry
+    vtkCommonCore vtkCommonDataModel vtkFiltersCore vtkFiltersGeneral
+    vtkIOImage vtkIOXML vtkIOParallelXML vtkParallelMPI
   )
-
+  if(VTK_FOUND)
+    message(STATUS "Adding libisosurface")
+    add_library(libisosurface analysis/lib-isosurface.cpp)
+    target_include_directories(libisosurface
+      INTERFACE ${CMAKE_CURRENT_SOURCE_DIR}/analysis
+      PRIVATE ${VTK_INCLUDE_DIRS}
+    )
+    target_link_libraries(libisosurface
+      PUBLIC adios2::adios2 MPI::MPI_C
+      PRIVATE ${VTK_LIBRARIES}
+    )
+
+    message(STATUS "Adding block-isosurface")
+    add_executable(block-isosurface analysis/block-isosurface.cpp)
+    target_link_libraries(block-isosurface
+      adios2::adios2 MPI::MPI_C libisosurface
+    )
+
+    message(STATUS "Adding gray-scott-iso")
+    add_executable(gray-scott-iso
+      simulation/main.cpp
+      simulation/gray-scott.cpp
+      simulation/settings.cpp
+      simulation/writer.cpp
+    )
+    target_link_libraries(gray-scott-iso
+      adios2::adios2 MPI::MPI_C libisosurface
+    )
+    target_compile_definitions(gray-scott-iso PRIVATE USE_INLINE_ISOSURFACE=1)
+  endif()
+
+  find_package(VTK COMPONENTS vtkFiltersCore vtkFiltersGeometry vtkIOXML)
   if(VTK_FOUND)
     add_executable(find_blobs analysis/find_blobs.cpp)
-    target_link_libraries(find_blobs adios2::adios2 ${VTK_LIBRARIES}
-      MPI::MPI_C)
-  endif(VTK_FOUND)
-
-  find_package(VTK COMPONENTS
-    vtkFiltersGeneral
-  )
+    target_include_directories(find_blobs PRIVATE ${VTK_INCLUDE_DIRS})
+    target_link_libraries(find_blobs
+      adios2::adios2 MPI::MPI_C ${VTK_LIBRARIES}
+    )
+  endif()
 
+  find_package(VTK COMPONENTS vtkFiltersGeneral)
   if(VTK_FOUND)
     add_executable(compute_curvature analysis/curvature.cpp)
-    target_link_libraries(compute_curvature adios2::adios2 ${VTK_LIBRARIES}
-      MPI::MPI_C)
-  endif(VTK_FOUND)
-
-
-  find_package(VTK COMPONENTS
-    vtkRenderingOpenGL2
-    vtkViewsInfovis
-  )
+    target_include_directories(compute_curvature PRIVATE ${VTK_INCLUDE_DIRS})
+    target_link_libraries(compute_curvature
+      adios2::adios2 MPI::MPI_C ${VTK_LIBRARIES}
+    )
+  endif()
 
+  find_package(VTK COMPONENTS vtkRenderingOpenGL2 vtkViewsInfovis)
   if(VTK_FOUND)
     add_executable(render_isosurface plot/render_isosurface.cpp)
-    target_link_libraries(render_isosurface adios2::adios2 ${VTK_LIBRARIES}
-      MPI::MPI_C)
-  endif(VTK_FOUND)
-endif(VTK)
+    target_include_directories(render_isosurface PRIVATE ${VTK_INCLUDE_DIRS})
+    target_link_libraries(render_isosurface
+      adios2::adios2 MPI::MPI_C ${VTK_LIBRARIES}
+    )
+  endif()
+endif()

Tutorial/gray-scott/analysis/block-isosurface.cpp

@@ -0,0 +1,59 @@
+#include <iostream>
+#include <string>
+#include <stdexcept>
+#include <vector>
+
+#include <mpi.h>
+#include <adios2.h>
+
+#ifdef ENABLE_TIMERS
+#include "../common/timer.hpp"
+#endif
+
+#include <lib-isosurface.h>
+
+int main(int argc, char **argv)
+{
+    int mpiRank;
+    MPI_Init(&argc, &argv);
+    MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
+
+    if(argc < 4)
+    {
+        if(mpiRank == 0)
+        {
+            std::cerr << "Error: Too few arguments\n"
+                      << "Usage: " << argv[0] << " input output isovalues...\n";
+        }
+        MPI_Abort(MPI_COMM_WORLD, -1);
+    }
+
+    const std::string inputFName(argv[1]);
+    const std::string outputFName(argv[2]);
+
+    std::vector<double> isoValues;
+    for (int i = 3; i < argc; i++)
+    {
+        isoValues.push_back(std::stod(argv[i]));
+    }
+
+    try
+    {
+        adios2::ADIOS adios("adios2.xml", MPI_COMM_WORLD, adios2::DebugON);
+        adios2::IO io = adios.DeclareIO("SimulationOutput");
+
+        IsoSurface analysis(MPI_COMM_WORLD, io, inputFName, outputFName,
+                            isoValues, false);
+
+        while(analysis.Step());
+    }
+    catch(const std::exception &ex)
+    {
+        std::cerr << "Error: " << ex.what() << "\n";
+        MPI_Abort(MPI_COMM_WORLD, -2);
+    }
+
+    MPI_Finalize();
+
+    return 0;
+}