Reorganise tests (#367)

* move xdmf test in a dedicated directory

* do not use xdmf in sedov test

* move dump checks in a dedicated directory

* add back sedov and IO tests to github actions

* add back the linear wave test, and fix tolerance

* Hard code pybind11 venv path from cmake

Author: glesur

.github/workflows/idefix-ci-jobs.yml

@@ -21,6 +21,7 @@ env:
   PYTHONPATH: ${{ github.workspace }}
   IDEFIX_DIR: ${{ github.workspace }}
 
+
 jobs:
   ShocksHydro:
     runs-on: self-hosted
@@ -35,6 +36,8 @@ jobs:
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/sod-iso -all $TESTME_OPTIONS
       - name: Mach reflection test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD//MachReflection -all $TESTME_OPTIONS
+      - name: Sedov blast wave
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/SedovBlastWave -all $TESTME_OPTIONS
 
   ParabolicHydro:
     runs-on: self-hosted
@@ -63,8 +66,10 @@ jobs:
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sod-iso -all $TESTME_OPTIONS
       - name: Orszag Tang
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/OrszagTang -all $TESTME_OPTIONS
-      - name: Orszag Tang 3D+restart tests
+      - name: Orszag Tang 3D
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/OrszagTang3D -all $TESTME_OPTIONS
+      - name: Linear wave test
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/LinearWaveTest -all $TESTME_OPTIONS
       - name: Axis Flux tube
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/AxisFluxTube -all $TESTME_OPTIONS
 
@@ -207,3 +212,23 @@ jobs:
         run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/dumpImage -all $TESTME_OPTIONS
       - name: Column density
         run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/columnDensity -all $TESTME_OPTIONS
+
+  IOs:
+    needs: [Fargo, Dust, Planet, ShearingBox, SelfGravity]
+    runs-on: self-hosted
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+      - name: Restart dumps
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/IO/dump -all $TESTME_OPTIONS
+      - name: Pydefix
+        run: |
+          python3 -m venv $IDEFIX_DIR/test/IO/pydefix/env
+          source $IDEFIX_DIR/test/IO/pydefix/env/bin/activate
+          python3 -m pip install -r $IDEFIX_DIR/test/IO/pydefix/python_requirements.txt
+          scripts/ci/run-tests $IDEFIX_DIR/test/IO/pydefix -all $TESTME_OPTIONS
+
+      - name: xdmf
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/IO/xdmf -all $TESTME_OPTIONS

CMakeLists.txt

@@ -115,14 +115,30 @@ if(Idefix_HDF5)
   )
   find_package(HDF5 REQUIRED)
   target_link_libraries(idefix "${HDF5_LIBRARIES}")
-  target_include_directories(idefix "${HDF5_INCLUDE_DIRS}")
+  message(STATUS "Found HDF5 include directories: ${HDF5_INCLUDE_DIRS}")
+  target_include_directories(idefix PUBLIC "${HDF5_INCLUDE_DIRS}")
+  if(Idefix_MPI)
+    if(NOT HDF5_IS_PARALLEL)
+      message(FATAL_ERROR "Parallel HDF5 required for Idefix_MPI but the found HDF5 library does not support it")
+    endif()
+  endif()
   message(STATUS "XDMF (hdf5+xmf) dumps enabled")
 else()
   set(Idefix_HDF5 OFF)
 endif()
 
 if(Idefix_PYTHON)
   add_compile_definitions("WITH_PYTHON")
+  find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
+
+  execute_process(
+    COMMAND "${Python3_EXECUTABLE}" -m pybind11 --cmakedir
+    OUTPUT_VARIABLE PYBIND11_CMAKE_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    COMMAND_ERROR_IS_FATAL ANY
+  )
+
+  list(APPEND CMAKE_PREFIX_PATH "${PYBIND11_CMAKE_DIR}")
   if (NOT DEFINED Python_FIND_FRAMEWORK)
     set(Python_FIND_FRAMEWORK "LAST") # Use Apple's python only at last resort on Macos
   endif ()

reference

@@ -286,18 +286,18 @@ int Xdmf::Write() {
   idfx::pushRegion("Xdmf::Write");
   fs::path filename;
   fs::path filename_xmf;
-  hid_t err;
+  [[maybe_unused]] hid_t err;
   idfx::cout << "Xdmf: Write file n " << xdmfFileNumber << "..." << std::flush;
   timer.reset();
 
   // Create a copy of the dataBlock on Host, and sync it.
 
   #if DIMENSIONS == 1
-  int tot_dim = 1;
+  [[maybe_unused]] int tot_dim = 1;
   #elif DIMENSIONS == 2
   int tot_dim = 2;
   #elif DIMENSIONS == 3
-  int tot_dim = 3;
+  [[maybe_unused]] int tot_dim = 3;
   #endif
 
   std::stringstream ssfileName, ssfileNameXmf, ssxdmfFileNum;
@@ -344,7 +344,8 @@ int Xdmf::Write() {
   #endif
 
   // Layout of the field data in memory
-  hsize_t field_data_size[3], field_data_start[3], field_data_subsize[3], stride[3];
+  [[maybe_unused]] hsize_t field_data_size[3], field_data_start[3];
+  [[maybe_unused]] hsize_t field_data_subsize[3], stride[3];
   #ifdef WITH_MPI
   for(int dir = 0; dir < 3 ; dir++) {
     field_data_size[dir] = static_cast<hsize_t>(this->mpi_data_size[dir]);
@@ -454,11 +455,10 @@ void Xdmf::WriteHeader(
   hid_t tspace, tattr;
   hid_t unit_info, unit_attr;
   hid_t group;
-  hid_t file_access = 0;
   #ifdef WITH_MPI
   hid_t plist_id_mpiio = 0; /* for collective MPI I/O */
   #endif
-  hid_t err;
+  [[maybe_unused]] hid_t err;
 
   hsize_t dimstr;
 
@@ -814,7 +814,7 @@ void Xdmf::WriteScalar(
   dataset_name = var_name.c_str();
   std::string dataset_label = dataset_name.c_str();
   std::transform(dataset_label.begin(), dataset_label.end(), dataset_label.begin(), ::tolower);
-  hid_t err, dataset;
+  [[maybe_unused]] hid_t err, dataset;
 
   // We define the dataset that contain the fields.
 

src/output/xdmf.cpp

@@ -68,7 +68,7 @@ py::array_t<real, py::array::c_style> GatherIdefixArray(IdefixHostArray3D<real>
       // np_int: size that should be copied into global
       // beg: offset in the incoming array where copy should begin
       // gbeg: offset in the global array where copy should be begin
-      std::array<int,3> np_int,np_tot, beg, gbeg;
+      [[maybe_unused]] std::array<int,3> np_int,np_tot, beg, gbeg;
       IdefixHostArray3D<real> buf;
 
       if(rank==0) {
@@ -127,7 +127,7 @@ py::array_t<real, py::array::c_style> GatherIdefixArray(IdefixHostArray3D<real>
     }// End loop on target rank for root process
   } else { // MPI prank >0
     std::array<int,3> np_int = dataHost.np_int;
-    std::array<int,3> np_tot = dataHost.np_tot;
+    [[maybe_unused]] std::array<int,3> np_tot = dataHost.np_tot;
     std::array<int,3> gbeg = dataHost.gbeg;
     std::array<int,3> beg = dataHost.beg;
 
@@ -278,6 +278,9 @@ Pydefix::Pydefix(Input &input) {
       idfx::cout << "Pydefix: start Python interpreter." << std::endl;
 
       py::initialize_interpreter();
+      py::exec("import sys; print(f'Pydefix: Python Version: {sys.version}')");
+      py::exec("print(f'Pydefix: Executable Path: {sys.executable}')");
+      py::exec("print(f'Pydefix: Sys Path: {sys.path}')");
     }
     this->scriptFilename = input.Get<std::string>("Python","script",0);
     if(scriptFilename.substr(scriptFilename.length() - 3, 3).compare(".py")==0) {

src/pydefix.cpp

@@ -12,7 +12,9 @@
 // own implementation of the constructor, initflow and destructor
 
 __attribute__((weak)) Setup::Setup(Input &input, Grid &grid, DataBlock &data, Output &output) {
-  IDEFIX_WARNING("Caution, this is the default Setup constructor and it does nothing!");
+  #ifndef WITH_PYTHON
+    IDEFIX_WARNING("Caution, this is the default Setup constructor and it does nothing!");
+  #endif
 }
 
 __attribute__((weak)) void Setup::InitFlow(DataBlock &data) {

src/setup.cpp

@@ -25,6 +25,5 @@ X3-beg    periodic
 X3-end    periodic
 
 [Output]
-vtk     0.1
-xdmf    0.1
-dmp     0.1
+vtk    0.1
+dmp    0.1

test/HD/SedovBlastWave/idefix.ini

@@ -0,0 +1 @@
+enable_idefix_property(Idefix_MHD)

test/IO/dump/CMakeLists.txt

@@ -0,0 +1,5 @@
+#define     COMPONENTS      3
+#define     DIMENSIONS      3
+//#define DEBUG
+
+#define     GEOMETRY        CARTESIAN