Merge topic 'parallel_unstructured_grid_io_crash'

23c83c08 fixed test - index error
874296aa fixed shadowed variable
a547d36d

 fixed a segfault when reading polyhedral cells from pvtp files
Acked-by: Kitware Robot <kwrobot@kitware.com>
Merge-request: !3532

IO/ParallelXML/Testing/Cxx/CMakeLists.txt

+# note, to enable testing the vtkParallelMPI module should be enabled
+
+vtk_add_test_cxx(${vtk-module}CxxTests tests
+  TestParallelUnstructuredGridIO.cxx,No_DATA,NO_VALID
+  )
+
+vtk_test_cxx_executable(${vtk-module}CxxTests tests)

IO/ParallelXML/Testing/Cxx/TestParallelUnstructuredGridIO.cxx

+#include "vtkNew.h"
+#include <string>
+
+#include <vtkCell.h>
+#include <vtkIdList.h>
+#include <vtkMultiProcessController.h>
+#include <vtkPoints.h>
+#include <vtkUnstructuredGrid.h>
+#include <vtkTestUtilities.h>
+#include <vtkXMLUnstructuredGridReader.h>
+#include <vtkXMLPUnstructuredGridWriter.h>
+#include <vtkXMLPUnstructuredGridReader.h>
+
+using namespace std;
+
+bool CompareGrids(vtkUnstructuredGrid *s, vtkUnstructuredGrid *t)
+{
+  if (s->GetNumberOfCells() != t->GetNumberOfCells())
+  {
+    cerr << "The number of cells does not match: " << s->GetNumberOfCells() << " != " << t->GetNumberOfCells() << endl;
+    return false;
+  }
+  for(vtkIdType i = 0; i < s->GetNumberOfCells(); ++i)
+  {
+    if (s->GetCellType(i) != t->GetCellType(i))
+    {
+      cerr << "The cell type does not match: " << s->GetCellType(i) << " != " << t->GetCellType(i) << endl;
+      return false;
+    }
+    vtkNew<vtkIdList> sIds, tIds;
+    if (s->GetCellType(i) == VTK_POLYHEDRON)
+    {
+      s->GetFaceStream(i, sIds.GetPointer());
+      t->GetFaceStream(i, tIds.GetPointer());
+    }
+    else
+    {
+      s->GetCellPoints(i, sIds.GetPointer());
+      t->GetCellPoints(i, tIds.GetPointer());
+    }
+    if (sIds->GetNumberOfIds() != tIds->GetNumberOfIds())
+    {
+      cerr << "Cell type : " << s->GetCellType(i) << endl;
+      cerr << "The number of ids does not match: " << sIds->GetNumberOfIds() << " != " << tIds->GetNumberOfIds() << endl;
+      return false;
+    }
+
+    for(vtkIdType j = 0; j < sIds->GetNumberOfIds(); ++j)
+    {
+      vtkIdType sId = sIds->GetId(j);
+      vtkIdType tId = tIds->GetId(j);
+
+      if(sId != tId)
+      {
+        cerr << "Cell type : " << s->GetCellType(i) << endl;
+        cerr << "The id at position " << j << " does not match: " << sId << " != " << tId << endl;
+        return false;
+      }
+    }
+  }
+
+  return true;
+}
+
+int TestParallelUnstructuredGridIO(int argc, char* argv[])
+{
+ vtkNew<vtkPoints> points;
+
+  points->InsertNextPoint(0, 0, 0);
+  points->InsertNextPoint(1, 0, 0);
+  points->InsertNextPoint(1, 1, 0);
+  points->InsertNextPoint(0, 1, 0);
+
+  points->InsertNextPoint(0, 0, 1);
+  points->InsertNextPoint(1, 0, 1);
+  points->InsertNextPoint(1, 1, 1);
+  points->InsertNextPoint(0, 1, 1);
+
+  points->InsertNextPoint(.5, .5, 2);
+  points->InsertNextPoint(.5, .5, -1);
+
+  vtkNew<vtkUnstructuredGrid> ug;
+  ug->SetPoints(points);
+
+  ug->Allocate(3); // allocate for 3 cells
+
+  vtkNew<vtkIdList> ids;
+
+  // add a hexahedron of the first 8 points (i.e. a cube)
+  ids->InsertNextId(0);
+  ids->InsertNextId(1);
+  ids->InsertNextId(2);
+  ids->InsertNextId(3);
+  ids->InsertNextId(4);
+  ids->InsertNextId(5);
+  ids->InsertNextId(6);
+  ids->InsertNextId(7);
+  ug->InsertNextCell(VTK_HEXAHEDRON, ids.GetPointer());
+  ids->Reset();
+
+  // add a polyhedron comprise of the top hexahedron face
+  // and four triangles to the 9th point
+  ids->InsertNextId(4);
+  ids->InsertNextId(5);
+  ids->InsertNextId(6);
+  ids->InsertNextId(7);
+  ids->InsertNextId(8);
+
+  vtkNew<vtkIdList> faces;
+  // top face of four points
+  faces->InsertNextId(4);
+
+  faces->InsertNextId(4);
+  faces->InsertNextId(5);
+  faces->InsertNextId(6);
+  faces->InsertNextId(7);
+
+  // four triangle side faces, each of three points
+  faces->InsertNextId(3);
+  faces->InsertNextId(4);
+  faces->InsertNextId(5);
+  faces->InsertNextId(8);
+
+  faces->InsertNextId(3);
+  faces->InsertNextId(5);
+  faces->InsertNextId(6);
+  faces->InsertNextId(8);
+
+  faces->InsertNextId(3);
+  faces->InsertNextId(6);
+  faces->InsertNextId(7);
+  faces->InsertNextId(8);
+
+  faces->InsertNextId(3);
+  faces->InsertNextId(7);
+  faces->InsertNextId(4);
+  faces->InsertNextId(8);
+
+  // insert the polyhedron cell
+  ug->InsertNextCell(VTK_POLYHEDRON, 5, ids.GetPointer()->GetPointer(0), 5, faces.GetPointer()->GetPointer(0));
+
+  // put another pyramid on the bottom towards the 10th point
+  faces->Reset();
+  ids->Reset();
+
+  // the list of points that the pyramid references
+  ids->InsertNextId(0);
+  ids->InsertNextId(1);
+  ids->InsertNextId(2);
+  ids->InsertNextId(3);
+  ids->InsertNextId(9);
+
+  // bottom face of four points
+  faces->InsertNextId(4);
+
+  faces->InsertNextId(0);
+  faces->InsertNextId(1);
+  faces->InsertNextId(2);
+  faces->InsertNextId(3);
+
+  // four side faces, each of three points
+  faces->InsertNextId(3);
+  faces->InsertNextId(0);
+  faces->InsertNextId(1);
+  faces->InsertNextId(9);
+
+  faces->InsertNextId(3);
+  faces->InsertNextId(1);
+  faces->InsertNextId(2);
+  faces->InsertNextId(9);
+
+  faces->InsertNextId(3);
+  faces->InsertNextId(2);
+  faces->InsertNextId(3);
+  faces->InsertNextId(9);
+
+  faces->InsertNextId(3);
+  faces->InsertNextId(3);
+  faces->InsertNextId(0);
+  faces->InsertNextId(9);
+
+  // insert the cell. We now have two pyramids with a cube in between
+  ug->InsertNextCell(VTK_POLYHEDRON, 5, ids.GetPointer()->GetPointer(0), 5, faces.GetPointer()->GetPointer(0));
+
+  vtkMultiProcessController* ctrl = vtkMultiProcessController::GetGlobalController();
+  vtkNew<vtkXMLPUnstructuredGridWriter> w;
+  w->SetController(ctrl);
+  w->SetInputData(ug);
+  w->SetUseSubdirectory(true);
+  char* tempDir = vtkTestUtilities::GetArgOrEnvOrDefault("-T", argc, argv,
+                                                         "VTK_TEMP_DIR",
+                                                         "Testing/Temporary");
+  std::string dir(tempDir);
+  std::string fn = dir + "/ug.pvtu";
+  w->SetFileName(fn.c_str());
+  w->SetDataModeToAscii();
+  w->Update();
+
+  ifstream f(fn.c_str());
+  if (!f.good())
+  {
+    std::cerr << "File " << fn << " does not exist." << std::endl;
+    return EXIT_FAILURE;
+  }
+
+  vtkNew<vtkXMLUnstructuredGridReader> r;
+  std::string piece = dir + "/ug/ug_0.vtu";
+  r->SetFileName(piece.c_str());
+  r->Update();
+
+  // first try reading the piece with a non-parallel reader
+  vtkUnstructuredGrid* read = r->GetOutput();
+  cout << "Comparing original with .vtu" << endl;
+  if (!CompareGrids(ug.GetPointer(), read)) return EXIT_FAILURE;
+
+  // now read the .pvtu file with the paralle reader
+  vtkNew<vtkXMLPUnstructuredGridReader> pr;
+  pr->SetFileName(fn.c_str());
+  // this will give a SIGSEGV on vtkXMLPUnstructuredGridReader::ReadPieceData()
+  pr->Update();
+
+  read = pr->GetOutput();
+  cout << "Comparing original with .pvtu" << endl;
+  if (!CompareGrids(ug.GetPointer(), read)) return EXIT_FAILURE;
+
+  return EXIT_SUCCESS;
+
+}

IO/ParallelXML/module.cmake

@@ -2,7 +2,9 @@ vtk_module(vtkIOParallelXML
   GROUPS
     StandAlone
   TEST_DEPENDS
+    vtkIOParallelXML
     vtkParallelMPI
+    vtkTestingCore
   KIT
     vtkParallel
   DEPENDS
@@ -14,4 +16,4 @@ vtk_module(vtkIOParallelXML
     vtkCommonMisc
     vtkParallelCore
     vtksys
-  )
\ No newline at end of file
+  )

IO/XML/vtkXMLPUnstructuredGridReader.cxx

@@ -175,6 +175,11 @@ int vtkXMLPUnstructuredGridReader::ReadPieceData()
     {
       outputFaceLocations->InsertNextValue(outputFaces->GetMaxId() + 1);
       vtkIdType location = inputFaceLocations->GetValue(i);
+      if (location < 0) // the face offsets array contains -1 for regular cells
+      {
+        continue;
+      }
+
       vtkIdType numFaces = inputFaces->GetValue(location);
       location++;
       outputFaces->InsertNextValue(numFaces);