adding sources for a simple simulation code, setting user

docs.it4i/software/viz/insitu/CMakeLists.txt

+cmake_minimum_required(VERSION 3.3)
+project(CatalystCxxFullExample)
+
+include_directories(/apps/all/ParaView/5.6.0-intel-2017a-mpi/include/paraview-5.6/)
+link_directories(/apps/all/ParaView/5.6.0-intel-2017a-mpi/lib/)
+
+set(USE_CATALYST ON CACHE BOOL "Link the simulator with Catalyst")
+if(USE_CATALYST)
+  find_package(ParaView 4.1 REQUIRED COMPONENTS vtkPVPythonCatalyst)
+  include("${PARAVIEW_USE_FILE}")
+  set(Adaptor_SRCS
+    FEAdaptor.cxx
+    )
+  add_library(CxxFullExampleAdaptor ${Adaptor_SRCS})
+  target_link_libraries(CxxFullExampleAdaptor vtkPVPythonCatalyst vtkParallelMPI)
+  add_definitions("-DUSE_CATALYST")
+  if(NOT PARAVIEW_USE_MPI)
+    message(SEND_ERROR "ParaView must be built with MPI enabled")
+  endif()
+else()
+  find_package(MPI REQUIRED)
+  include_directories(${MPI_C_INCLUDE_PATH})
+endif()
+
+add_executable(CxxFullExample FEDriver.cxx FEDataStructures.cxx)
+if(USE_CATALYST)
+  target_link_libraries(CxxFullExample LINK_PRIVATE CxxFullExampleAdaptor)
+  include(vtkModuleMacros)
+  include(vtkMPI)
+  vtk_mpi_link(CxxFullExample)
+else()
+  target_link_libraries(CxxFullExample LINK_PRIVATE ${MPI_LIBRARIES})
+endif()
+
+option(BUILD_TESTING "Build Testing" OFF)
+# Setup testing.
+if (BUILD_TESTING)
+  include(CTest)
+  add_test(NAME CxxFullExampleTest COMMAND CxxFullExample ${CMAKE_CURRENT_SOURCE_DIR}/SampleScripts/feslicescript.py)
+  set_tests_properties(CxxFullExampleTest PROPERTIES LABELS "PARAVIEW;CATALYST")
+endif()

docs.it4i/software/viz/insitu/FEAdaptor.cxx

+#include "FEAdaptor.h"
+#include "FEDataStructures.h"
+#include <iostream>
+
+#include <vtkCPDataDescription.h>
+#include <vtkCPInputDataDescription.h>
+#include <vtkCPProcessor.h>
+#include <vtkCPPythonScriptPipeline.h>
+#include <vtkCellData.h>
+#include <vtkCellType.h>
+#include <vtkDoubleArray.h>
+#include <vtkFloatArray.h>
+#include <vtkNew.h>
+#include <vtkPointData.h>
+#include <vtkPoints.h>
+#include <vtkUnstructuredGrid.h>
+
+namespace
+{
+vtkCPProcessor* Processor = NULL;
+vtkUnstructuredGrid* VTKGrid;
+
+void BuildVTKGrid(Grid& grid)
+{
+  // create the points information
+  vtkNew<vtkDoubleArray> pointArray;
+  pointArray->SetNumberOfComponents(3);
+  pointArray->SetArray(
+    grid.GetPointsArray(), static_cast<vtkIdType>(grid.GetNumberOfPoints() * 3), 1);
+  vtkNew<vtkPoints> points;
+  points->SetData(pointArray.GetPointer());
+  VTKGrid->SetPoints(points.GetPointer());
+
+  // create the cells
+  size_t numCells = grid.GetNumberOfCells();
+  VTKGrid->Allocate(static_cast<vtkIdType>(numCells * 9));
+  for (size_t cell = 0; cell < numCells; cell++)
+  {
+    unsigned int* cellPoints = grid.GetCellPoints(cell);
+    vtkIdType tmp[8] = { cellPoints[0], cellPoints[1], cellPoints[2], cellPoints[3], cellPoints[4],
+      cellPoints[5], cellPoints[6], cellPoints[7] };
+    VTKGrid->InsertNextCell(VTK_HEXAHEDRON, 8, tmp);
+  }
+}
+
+void UpdateVTKAttributes(Grid& grid, Attributes& attributes, vtkCPInputDataDescription* idd)
+{
+  if (idd->IsFieldNeeded("velocity", vtkDataObject::POINT) == true)
+  {
+    if (VTKGrid->GetPointData()->GetNumberOfArrays() == 0)
+    {
+      // velocity array
+      vtkNew<vtkDoubleArray> velocity;
+      velocity->SetName("velocity");
+      velocity->SetNumberOfComponents(3);
+      velocity->SetNumberOfTuples(static_cast<vtkIdType>(grid.GetNumberOfPoints()));
+      VTKGrid->GetPointData()->AddArray(velocity.GetPointer());
+    }
+    vtkDoubleArray* velocity =
+      vtkDoubleArray::SafeDownCast(VTKGrid->GetPointData()->GetArray("velocity"));
+    // The velocity array is ordered as vx0,vx1,vx2,..,vy0,vy1,vy2,..,vz0,vz1,vz2,..
+    // so we need to create a full copy of it with VTK's ordering of
+    // vx0,vy0,vz0,vx1,vy1,vz1,..
+    double* velocityData = attributes.GetVelocityArray();
+    vtkIdType numTuples = velocity->GetNumberOfTuples();
+    for (vtkIdType i = 0; i < numTuples; i++)
+    {
+      double values[3] = { velocityData[i], velocityData[i + numTuples],
+        velocityData[i + 2 * numTuples] };
+      velocity->SetTypedTuple(i, values);
+    }
+  }
+  if (idd->IsFieldNeeded("pressure", vtkDataObject::CELL) == true)
+  {
+    if (VTKGrid->GetCellData()->GetNumberOfArrays() == 0)
+    {
+      // pressure array
+      vtkNew<vtkFloatArray> pressure;
+      pressure->SetName("pressure");
+      pressure->SetNumberOfComponents(1);
+      VTKGrid->GetCellData()->AddArray(pressure.GetPointer());
+    }
+    vtkFloatArray* pressure =
+      vtkFloatArray::SafeDownCast(VTKGrid->GetCellData()->GetArray("pressure"));
+    // The pressure array is a scalar array so we can reuse
+    // memory as long as we ordered the points properly.
+    float* pressureData = attributes.GetPressureArray();
+    pressure->SetArray(pressureData, static_cast<vtkIdType>(grid.GetNumberOfCells()), 1);
+  }
+}
+
+void BuildVTKDataStructures(Grid& grid, Attributes& attributes, vtkCPInputDataDescription* idd)
+{
+  if (VTKGrid == NULL)
+  {
+    // The grid structure isn't changing so we only build it
+    // the first time it's needed. If we needed the memory
+    // we could delete it and rebuild as necessary.
+    VTKGrid = vtkUnstructuredGrid::New();
+    BuildVTKGrid(grid);
+  }
+  UpdateVTKAttributes(grid, attributes, idd);
+}
+}
+
+namespace FEAdaptor
+{
+
+void Initialize(int numScripts, char* scripts[])
+{
+  if (Processor == NULL)
+  {
+    Processor = vtkCPProcessor::New();
+    Processor->Initialize();
+  }
+  else
+  {
+    Processor->RemoveAllPipelines();
+  }
+  for (int i = 0; i < numScripts; i++)
+  {
+    vtkNew<vtkCPPythonScriptPipeline> pipeline;
+    pipeline->Initialize(scripts[i]);
+    Processor->AddPipeline(pipeline.GetPointer());
+  }
+}
+
+void Finalize()
+{
+  if (Processor)
+  {
+    Processor->Delete();
+    Processor = NULL;
+  }
+  if (VTKGrid)
+  {
+    VTKGrid->Delete();
+    VTKGrid = NULL;
+  }
+}
+
+void CoProcess(
+  Grid& grid, Attributes& attributes, double time, unsigned int timeStep, bool lastTimeStep)
+{
+  vtkNew<vtkCPDataDescription> dataDescription;
+  dataDescription->AddInput("input");
+  dataDescription->SetTimeData(time, timeStep);
+  if (lastTimeStep == true)
+  {
+    // assume that we want to all the pipelines to execute if it
+    // is the last time step.
+    dataDescription->ForceOutputOn();
+  }
+  if (Processor->RequestDataDescription(dataDescription.GetPointer()) != 0)
+  {
+    vtkCPInputDataDescription* idd = dataDescription->GetInputDescriptionByName("input");
+    BuildVTKDataStructures(grid, attributes, idd);
+    idd->SetGrid(VTKGrid);
+    Processor->CoProcess(dataDescription.GetPointer());
+  }
+}
+} // end of Catalyst namespace

docs.it4i/software/viz/insitu/FEAdaptor.h

+#ifndef FEADAPTOR_HEADER
+#define FEADAPTOR_HEADER
+
+class Attributes;
+class Grid;
+
+namespace FEAdaptor
+{
+void Initialize(int numScripts, char* scripts[]);
+
+void Finalize();
+
+void CoProcess(
+  Grid& grid, Attributes& attributes, double time, unsigned int timeStep, bool lastTimeStep);
+}
+
+#endif

docs.it4i/software/viz/insitu/FEDataStructures.cxx

+#include "FEDataStructures.h"
+
+#include <iostream>
+#include <mpi.h>
+
+Grid::Grid()
+{
+}
+
+void Grid::Initialize(const unsigned int numPoints[3], const double spacing[3])
+{
+  if (numPoints[0] == 0 || numPoints[1] == 0 || numPoints[2] == 0)
+  {
+    std::cerr << "Must have a non-zero amount of points in each direction.\n";
+  }
+  // in parallel, we do a simple partitioning in the x-direction.
+  int mpiSize = 1;
+  int mpiRank = 0;
+  MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
+  MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
+
+  unsigned int startXPoint = mpiRank * numPoints[0] / mpiSize;
+  unsigned int endXPoint = (mpiRank + 1) * numPoints[0] / mpiSize;
+  if (mpiSize != mpiRank + 1)
+  {
+    endXPoint++;
+  }
+
+  // create the points -- slowest in the x and fastest in the z directions
+  double coord[3] = { 0, 0, 0 };
+  for (unsigned int i = startXPoint; i < endXPoint; i++)
+  {
+    coord[0] = i * spacing[0];
+    for (unsigned int j = 0; j < numPoints[1]; j++)
+    {
+      coord[1] = j * spacing[1];
+      for (unsigned int k = 0; k < numPoints[2]; k++)
+      {
+        coord[2] = k * spacing[2];
+        // add the coordinate to the end of the vector
+        std::copy(coord, coord + 3, std::back_inserter(this->Points));
+      }
+    }
+  }
+  // create the hex cells
+  unsigned int cellPoints[8];
+  unsigned int numXPoints = endXPoint - startXPoint;
+  for (unsigned int i = 0; i < numXPoints - 1; i++)
+  {
+    for (unsigned int j = 0; j < numPoints[1] - 1; j++)
+    {
+      for (unsigned int k = 0; k < numPoints[2] - 1; k++)
+      {
+        cellPoints[0] = i * numPoints[1] * numPoints[2] + j * numPoints[2] + k;
+        cellPoints[1] = (i + 1) * numPoints[1] * numPoints[2] + j * numPoints[2] + k;
+        cellPoints[2] = (i + 1) * numPoints[1] * numPoints[2] + (j + 1) * numPoints[2] + k;
+        cellPoints[3] = i * numPoints[1] * numPoints[2] + (j + 1) * numPoints[2] + k;
+        cellPoints[4] = i * numPoints[1] * numPoints[2] + j * numPoints[2] + k + 1;
+        cellPoints[5] = (i + 1) * numPoints[1] * numPoints[2] + j * numPoints[2] + k + 1;
+        cellPoints[6] = (i + 1) * numPoints[1] * numPoints[2] + (j + 1) * numPoints[2] + k + 1;
+        cellPoints[7] = i * numPoints[1] * numPoints[2] + (j + 1) * numPoints[2] + k + 1;
+        std::copy(cellPoints, cellPoints + 8, std::back_inserter(this->Cells));
+      }
+    }
+  }
+}
+
+size_t Grid::GetNumberOfPoints()
+{
+  return this->Points.size() / 3;
+}
+
+size_t Grid::GetNumberOfCells()
+{
+  return this->Cells.size() / 8;
+}
+
+double* Grid::GetPointsArray()
+{
+  if (this->Points.empty())
+  {
+    return NULL;
+  }
+  return &(this->Points[0]);
+}
+
+double* Grid::GetPoint(size_t pointId)
+{
+  if (pointId >= this->Points.size())
+  {
+    return NULL;
+  }
+  return &(this->Points[pointId * 3]);
+}
+
+unsigned int* Grid::GetCellPoints(size_t cellId)
+{
+  if (cellId >= this->Cells.size())
+  {
+    return NULL;
+  }
+  return &(this->Cells[cellId * 8]);
+}
+
+Attributes::Attributes()
+{
+  this->GridPtr = NULL;
+}
+
+void Attributes::Initialize(Grid* grid)
+{
+  this->GridPtr = grid;
+}
+
+void Attributes::UpdateFields(double time)
+{
+  size_t  numPoints = this->GridPtr->GetNumberOfPoints();
+  this->Velocity.resize(numPoints * 3);
+  
+  // provide different update setting for different parallel process
+  int mpiSize = 1;
+  int mpiRank = 0;
+  MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
+  MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
+  double setting = 1.0 + (double) mpiRank / (double) mpiSize;
+  
+  for (size_t pt = 0; pt < numPoints; pt++)
+  {
+    double* coord = this->GridPtr->GetPoint(pt);
+    this->Velocity[pt] = coord[1] * time * setting;
+  }
+  std::fill(this->Velocity.begin() + numPoints, this->Velocity.end(), 0.0);
+
+  size_t numCells = this->GridPtr->GetNumberOfCells();
+  this->Pressure.resize(numCells);
+  std::fill(this->Pressure.begin(), this->Pressure.end(), setting);
+}
+
+double* Attributes::GetVelocityArray()
+{
+  if (this->Velocity.empty())
+  {
+    return NULL;
+  }
+  return &this->Velocity[0];
+}
+
+float* Attributes::GetPressureArray()
+{
+  if (this->Pressure.empty())
+  {
+    return NULL;
+  }
+  return &this->Pressure[0];
+}

docs.it4i/software/viz/insitu/FEDataStructures.h

+#ifndef FEDATASTRUCTURES_HEADER
+#define FEDATASTRUCTURES_HEADER
+
+#include <cstddef>
+#include <vector>
+
+class Grid
+{
+public:
+  Grid();
+  void Initialize(const unsigned int numPoints[3], const double spacing[3]);
+  size_t GetNumberOfPoints();
+  size_t GetNumberOfCells();
+  double* GetPointsArray();
+  double* GetPoint(size_t pointId);
+  unsigned int* GetCellPoints(size_t cellId);
+
+private:
+  std::vector<double> Points;
+  std::vector<unsigned int> Cells;
+};
+
+class Attributes
+{
+  // A class for generating and storing point and cell fields.
+  // Velocity is stored at the points and pressure is stored
+  // for the cells. The current velocity profile is for a
+  // shearing flow with U(y,t) = y*t, V = 0 and W = 0.
+  // Pressure is constant through the domain.
+public:
+  Attributes();
+  void Initialize(Grid* grid);
+  void UpdateFields(double time);
+  double* GetVelocityArray();
+  float* GetPressureArray();
+
+private:
+  std::vector<double> Velocity;
+  std::vector<float> Pressure;
+  Grid* GridPtr;
+};
+#endif

docs.it4i/software/viz/insitu/FEDriver.cxx

+#include "FEDataStructures.h"
+#include <mpi.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <iostream>
+#include <stdlib.h>
+
+#ifdef USE_CATALYST
+#include "FEAdaptor.h"
+#endif
+
+// Example of a C++ adaptor for a simulation code
+
+int main(int argc, char** argv)
+{
+  // Check the input arguments for area size
+  if (argc < 4) {
+	printf("Not all arguments for grid definition supplied\n");
+	return 0;
+  }
+
+  unsigned int pointsX = abs(std::stoi(argv[1])); 
+  unsigned int pointsY = abs(std::stoi(argv[2]));
+  unsigned int pointsZ = abs(std::stoi(argv[3]));
+  
+  //MPI_Init(&argc, &argv);
+  MPI_Init(NULL, NULL);
+  Grid grid;
+
+  unsigned int numPoints[3] = { pointsX, pointsY, pointsZ };
+  double spacing[3] = { 1, 1.1, 1.3 };
+  grid.Initialize(numPoints, spacing);
+  Attributes attributes;
+  attributes.Initialize(&grid);
+
+#ifdef USE_CATALYST
+  // The first argument is the program name
+  FEAdaptor::Initialize(argc - 4, &argv[4]);
+#endif
+  unsigned int numberOfTimeSteps = 1000;
+  for (unsigned int timeStep = 0; timeStep < numberOfTimeSteps; timeStep++)
+  {
+    // use a time step length of 0.1
+    double time = timeStep * 0.1;
+    attributes.UpdateFields(time);
+#ifdef USE_CATALYST
+    FEAdaptor::CoProcess(grid, attributes, time, timeStep, timeStep == numberOfTimeSteps - 1);
+#endif
+    
+    // Get the name of the processor
+    char processor_name[MPI_MAX_PROCESSOR_NAME];
+    int name_len;
+    MPI_Get_processor_name(processor_name, &name_len);
+
+    printf("This is processor %s, time step: %0.3f\n", processor_name, time);
+    usleep(500000);
+  }
+
+#ifdef USE_CATALYST
+  FEAdaptor::Finalize();
+#endif
+  MPI_Finalize();
+
+  return 0;
+}

docs.it4i/software/viz/insitu/feslicescript.py

+from paraview.simple import *
+from paraview import coprocessing
+
+#--------------------------------------------------------------
+# Code generated from cpstate.py to create the CoProcessor.
+
+
+# ----------------------- CoProcessor definition -----------------------
+
+def CreateCoProcessor():
+  def _CreatePipeline(coprocessor, datadescription):
+    class Pipeline:
+      filename_3_pvtu = coprocessor.CreateProducer( datadescription, "input" )
+
+      Slice1 = Slice( guiName="Slice1", Crinkleslice=0, SliceOffsetValues=[0.0], Triangulatetheslice=1, SliceType="Plane" )
+      Slice1.SliceType.Offset = 0.0
+      Slice1.SliceType.Origin = [34.5, 32.45, 27.95]
+      Slice1.SliceType.Normal = [1.0, 0.0, 0.0]
+
+      # create a new 'Parallel PolyData Writer'
+      parallelPolyDataWriter1 = servermanager.writers.XMLPPolyDataWriter(Input=Slice1)
+
+      # register the writer with coprocessor
+      # and provide it with information such as the filename to use,
+      # how frequently to write the data, etc.
+      coprocessor.RegisterWriter(parallelPolyDataWriter1, filename='slice_%t.pvtp', freq=10)
+
+      # create a new 'Parallel UnstructuredGrid Writer'
+      unstructuredGridWriter1 = servermanager.writers.XMLPUnstructuredGridWriter(Input=filename_3_pvtu)
+
+      # register the writer with coprocessor
+      # and provide it with information such as the filename to use,
+      # how frequently to write the data, etc.
+      coprocessor.RegisterWriter(unstructuredGridWriter1, filename='fullgrid_%t.pvtu', freq=100)
+
+    return Pipeline()
+
+  class CoProcessor(coprocessing.CoProcessor):
+    def CreatePipeline(self, datadescription):
+      self.Pipeline = _CreatePipeline(self, datadescription)
+
+  coprocessor = CoProcessor()
+  freqs = {'input': [10, 100]}
+  coprocessor.SetUpdateFrequencies(freqs)
+  return coprocessor
+
+#--------------------------------------------------------------
+# Global variables that will hold the pipeline for each timestep
+# Creating the CoProcessor object, doesn't actually create the ParaView pipeline.
+# It will be automatically setup when coprocessor.UpdateProducers() is called the
+# first time.
+coprocessor = CreateCoProcessor()
+
+#--------------------------------------------------------------
+# Enable Live-Visualizaton with ParaView
+coprocessor.EnableLiveVisualization(False)
+
+
+# ---------------------- Data Selection method ----------------------
+
+def RequestDataDescription(datadescription):
+    "Callback to populate the request for current timestep"
+    global coprocessor
+    if datadescription.GetForceOutput() == True:
+        # We are just going to request all fields and meshes from the simulation
+        # code/adaptor.
+        for i in range(datadescription.GetNumberOfInputDescriptions()):
+            datadescription.GetInputDescription(i).AllFieldsOn()
+            datadescription.GetInputDescription(i).GenerateMeshOn()
+        return
+
+    # setup requests for all inputs based on the requirements of the
+    # pipeline.
+    coprocessor.LoadRequestedData(datadescription)
+
+# ------------------------ Processing method ------------------------
+
+def DoCoProcessing(datadescription):
+    "Callback to do co-processing for current timestep"
+    global coprocessor
+
+    # Update the coprocessor by providing it the newly generated simulation data.
+    # If the pipeline hasn't been setup yet, this will setup the pipeline.
+    coprocessor.UpdateProducers(datadescription)
+
+    # Write output data, if appropriate.
+    coprocessor.WriteData(datadescription);
+
+    # Write image capture (Last arg: rescale lookup table), if appropriate.
+    coprocessor.WriteImages(datadescription, rescale_lookuptable=False)
+
+    # Live Visualization, if enabled.
+    coprocessor.DoLiveVisualization(datadescription, "localhost", 22222)