Issue 398 - Implement dynamic testing

.jenkins/gnu_compiler_checks.gvy

@@ -25,7 +25,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 1 -c 10'
                     }
                 }
                 stages {

.jenkins/intel_compiler_checks.gvy

@@ -21,7 +21,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 1 -c 10'
                     }
                     axis{
                         name 'SIMD'

.jenkins/nvidia_compiler_checks.gvy

@@ -21,7 +21,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON; -n 1 -c 10'
                     }
                     axis{
                         name 'DeviceSpace'

CMakeLists.txt

@@ -197,12 +197,15 @@ add_library(
         src/IO/sources.cpp
         src/IO/receivers.cpp
         src/IO/mesh.cpp
+        # Fortran 2D part
         src/IO/mesh/impl/fortran/dim2/read_boundaries.cpp
         src/IO/mesh/impl/fortran/dim2/read_elements.cpp
         src/IO/mesh/impl/fortran/dim2/read_material_properties.cpp
         src/IO/mesh/impl/fortran/dim2/read_mesh_database.cpp
         src/IO/mesh/impl/fortran/dim2/read_interfaces.cpp
         src/IO/mesh/impl/fortran/dim2/read_parameters.cpp
+        # Fortran 3D part
+        src/IO/mesh/impl/fortran/dim3/read_parameters.cpp
 )
 
 if (NOT HDF5_CXX_BUILD)

CMakePresets.json

@@ -0,0 +1,43 @@
+{
+  "version": 6,
+  "configurePresets": [
+    {
+      "name": "release",
+      "displayName": "Default Release -- SIMD enabled",
+      "binaryDir": "build/release",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Release",
+        "BUILD_TESTS": "ON",
+        "ENABLE_SIMD": "ON",
+        "Kokkos_ARCH_NATIVE": "ON",
+        "Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION": "ON",
+        "Kokkos_ENABLE_ATOMICS_BYPASS": "ON"
+      }
+    },
+    {
+      "name": "debug",
+      "displayName": "Default Debug -- SIMD enabled",
+      "binaryDir": "build/debug",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Debug",
+        "BUILD_TESTS": "ON",
+        "ENABLE_SIMD": "ON",
+        "Kokkos_ARCH_NATIVE": "ON",
+        "Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION": "ON",
+        "Kokkos_ENABLE_ATOMICS_BYPASS": "ON"
+      }
+    }
+  ],
+  "buildPresets": [
+    {
+      "name": "release",
+      "configurePreset": "release",
+      "targets": ["all"]
+    },
+    {
+      "name": "debug",
+      "configurePreset": "debug",
+      "targets": ["all"]
+    }
+  ]
+}

examples/dim3/homogeneous_halfspace/specfem_config.yaml

@@ -45,6 +45,7 @@ parameters:
   ## databases
   databases:
     mesh-database: "OUTPUT_FILES/DATABASES_MPI/proc000000_external_mesh.bin"
+    mesh-parameters: "OUTPUT_FILES/DATABASES_MPI/mesh_parameters.bin"
 
   ## sources
   sources: "/Users/lsawade/SPECFEMPP/examples/homogeneous-medium-flat-topography/source.yaml"

fortran/meshfem3d/generate_databases/save_parameters.f90

@@ -5,7 +5,7 @@ subroutine save_parameters()
   use shared_parameters, only: LOCAL_PATH, MAX_STRING_LEN
 
   use generate_databases_par, only: &
-    IOUT, myrank, &
+    IOUT, myrank, sizeprocs, &
     NDIM, NSPEC_AB, NGLOB_AB, &
     NGLLX, NGLLY, NGLLZ, nfaces_surface, num_neighbors_all, NGLLSQUARE, &
     nspec2D_xmin, nspec2D_xmin, nspec2D_ymin, nspec2D_ymin, &
@@ -58,7 +58,6 @@ subroutine save_parameters()
       WRITE(IOUT) APPROXIMATE_OCEAN_LOAD
       WRITE(IOUT) USE_MESH_COLORING_GPU
 
-
       ! Write test parameter
       itest = 9998
       WRITE(IOUT) itest
@@ -70,34 +69,35 @@ subroutine save_parameters()
       WRITE(IOUT) NGLLY
       WRITE(IOUT) NGLLZ
       WRITE(IOUT) NGLLSQUARE
+      WRITE(IOUT) sizeprocs
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9997
+      WRITE(IOUT) itest
 
       WRITE(IOUT) NSPEC_AB ! nspec
       WRITE(IOUT) NSPEC_PORO ! nspec_poro == nspec, if POROELASTIC_SIMULATION
       WRITE(IOUT) NGLOB_AB ! nglob
       WRITE(IOUT) NGLOB_OCEAN
-      WRITE(IOUT) NSPEC2D_BOTTOM
-      WRITE(IOUT) NSPEC2D_TOP
-      WRITE(IOUT) nspec_irregular
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9996
+      WRITE(IOUT) itest
 
-      WRITE(IOUT) num_neighbors_all
-      WRITE(IOUT) nfaces_surface
-      WRITE(IOUT) nspec2D_xmin
+      WRITE(IOUT) NSPEC2D_BOTTOM
+      WRITE(IOUT) NSPEC2D_TOP
       WRITE(IOUT) nspec2D_xmin
+      WRITE(IOUT) nspec2D_xmax
       WRITE(IOUT) nspec2D_ymin
-      WRITE(IOUT) nspec2D_ymin
+      WRITE(IOUT) nspec2D_ymax
+      WRITE(IOUT) nspec_irregular
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9995
+      WRITE(IOUT) itest
 
+      WRITE(IOUT) num_neighbors_all
+      WRITE(IOUT) nfaces_surface
       WRITE(IOUT) num_abs_boundary_faces
       WRITE(IOUT) num_free_surface_faces
       WRITE(IOUT) num_coupling_ac_el_faces
@@ -108,8 +108,8 @@ subroutine save_parameters()
       WRITE(IOUT) max_nibool_interfaces_ext_mesh
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9994
+      WRITE(IOUT) itest
 
       WRITE(IOUT) nspec_inner_acoustic
       WRITE(IOUT) nspec_outer_acoustic
@@ -119,8 +119,8 @@ subroutine save_parameters()
       WRITE(IOUT) nspec_outer_poroelastic
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9993
+      WRITE(IOUT) itest
 
       WRITE(IOUT) num_phase_ispec_acoustic
       WRITE(IOUT) num_phase_ispec_elastic
@@ -131,8 +131,8 @@ subroutine save_parameters()
       WRITE(IOUT) num_colors_outer_elastic
 
       ! Write test parameter
-      WRITE(IOUT) itest
       itest = 9992
+      WRITE(IOUT) itest
   endif
 
 end subroutine save_parameters

include/IO/interface.hpp

@@ -25,7 +25,9 @@ specfem::mesh::mesh<specfem::dimension::type::dim2>
 read_2d_mesh(const std::string filename, const specfem::MPI::MPI *mpi);
 
 specfem::mesh::mesh<specfem::dimension::type::dim3>
-read_3d_mesh(const std::string filename, const specfem::MPI::MPI *mpi);
+read_3d_mesh(const std::string mesh_parameters_file,
+             const std::string mesh_databases_file,
+             const specfem::MPI::MPI *mpi);
 /**
  * @brief Read station file
  *

include/IO/mesh/impl/fortran/dim3/read_parameters.hpp

@@ -0,0 +1,30 @@
+#pragma once
+
+#include "IO/fortranio/interface.hpp"
+#include "mesh/parameters/parameters.hpp"
+#include "specfem_mpi/interface.hpp"
+
+namespace specfem {
+namespace IO {
+namespace mesh {
+namespace impl {
+namespace fortran {
+namespace dim3 {
+
+/*
+ * @brief Read paramters from 3D mesh database
+ *
+ * @param stream Input stream
+ * @param mpi MPI object
+ * @return specfem::mesh::parameters<specfem::dimension::type::dim2> Mesh
+ * parameters
+ */
+specfem::mesh::parameters<specfem::dimension::type::dim3>
+read_mesh_parameters(std::ifstream &stream, const specfem::MPI::MPI *mpi);
+
+} // namespace dim3
+} // namespace fortran
+} // namespace impl
+} // namespace mesh
+} // namespace IO
+} // namespace specfem

include/mesh/mesh.hpp

@@ -5,6 +5,7 @@
 #include "coupled_interfaces/coupled_interfaces.hpp"
 #include "elements/axial_elements.hpp"
 #include "elements/tangential_elements.hpp"
+#include "enumerations/dimension.hpp"
 #include "enumerations/interface.hpp"
 #include "materials/materials.hpp"
 #include "mesh/tags/tags.hpp"
@@ -104,6 +105,10 @@ template <> struct mesh<specfem::dimension::type::dim3> {
   constexpr static auto dimension =
       specfem::dimension::type::dim3; ///< Dimension
 
+  // Struct to store all the mesh parameter
+  specfem::mesh::parameters<dimension> parameters;
+
+  //
   // int npgeo; ///< Total number of spectral element control nodes
   // int nspec; ///< Total number of spectral elements
   // int nproc; ///< Total number of processors