从多个MPI输出合成VTK文件
and*_*eee 6 parallel-processing mpi scientific-computing vtk paraview
对于盖驱动腔（CFD）的Lattice Boltzmann模拟，我将立方域分解为（也是立方）8个子域，这些子域由8个等级独立计算。每个MPI等级都会为每个时间步生成一个VTK文件，并且由于我使用的是ParaView，因此我希望将整个内容可视化为一个多维数据集。更具体地说明我要实现的目标：
- 我有一个长度为8（每个方向的元素数）=> 8x8x8 = 512个元素的多维数据集。
- 每个维度分配给2个等级，即每个等级处理4x4x4 = 64个元素。
- 每个等级都会将结果写入
lbm_out_<rank>.<timestep>.vtsVTKStructuredGrid格式的文件中。 - 我想生成一个
.pvts文件，该*.vts文件收集文件并将包含子域的文件合并为一个文件，ParaView可以将其视为整个域。
不幸的是，我遇到了许多问题，因为我觉得ParaView和VTK的文档记录非常差，并且来自ParaView的错误消息完全没有用。
我有以下*.pvts文件，其中包括一个幽灵层和：
<?xml version="1.0"?>
<VTKFile type="PStructuredGrid" version="0.1" byte_order="LittleEndian">
<PStructuredGrid WholeExtent="0 7 0 7 0 7 " GhostLevel="1">
<PPoints>
<PDataArray NumberOfComponents="3" type="Float32" />
</PPoints>
<Piece Extent="0 4 0 4 0 4" Source="lbm_out_0.0.vts"/>
<Piece Extent="3 7 0 4 0 4" Source="lbm_out_1.0.vts"/>
<Piece Extent="0 4 3 7 0 4" Source="lbm_out_2.0.vts"/>
<Piece Extent="3 7 3 7 0 4" Source="lbm_out_3.0.vts"/>
<Piece Extent="0 4 0 4 3 7" Source="lbm_out_4.0.vts"/>
<Piece Extent="3 7 0 4 3 7" Source="lbm_out_5.0.vts"/>
<Piece Extent="0 4 3 7 3 7" Source="lbm_out_6.0.vts"/>
<Piece Extent="3 7 3 7 3 7" Source="lbm_out_7.0.vts"/>
</PStructuredGrid>
</VTKFile>
拥有该文件（我认为它应该可以正常工作）（请注意，还没有参数，只有简单的几何信息），我的域范围被完全弄乱了，尽管每个*.vts文件都可以正常工作。我附带了一个屏幕截图，以使事情更清楚：
可能是什么问题？是否可以将旧版VTK文件用于此任务？我可以做些完全错误的事情吗？我真的不知道如何完成这项任务，而我在Google中找到的资源非常有限。谢谢。
不幸的是，没有vtkXMLPStructuredGridWriter类的示例（示例中未使用 VTK 类）。因此，我决定编写最简单的代码来为结构化网格生成 *.vts 和 .pvts 文件，与您正在寻找的情况非常相似。
以下代码使用 MPI 和 VTK 编写并行结构化网格文件。在此示例中，我们有两个进程创建自己的 .vts 文件，并且 vtkXMLPStructuredGridWriter 类写入 .pvts 文件：
// MPI Library
#include <mpi.h>
//VTK Library
#include <vtkXMLPStructuredGridWriter.h>
#include <vtkStructuredGrid.h>
#include <vtkSmartPointer.h>
#include <vtkFloatArray.h>
#include <vtkCellData.h>
#include <vtkMPIController.h>
#include <vtkProgrammableFilter.h>
#include <vtkInformation.h>
struct Args {
vtkProgrammableFilter* pf;
int local_extent[6];
};
// function to operate on the point attribute data
void execute (void* arg) {
Args* args = reinterpret_cast<Args*>(arg);
auto info = args->pf->GetOutputInformation(0);
auto output_tmp = args->pf->GetOutput();
auto input_tmp = args->pf->GetInput();
vtkStructuredGrid* output = dynamic_cast<vtkStructuredGrid*>(output_tmp);
vtkStructuredGrid* input = dynamic_cast<vtkStructuredGrid*>(input_tmp);
output->ShallowCopy(input);
output->SetExtent(args->local_extent);
}
int main (int argc, char *argv[]) {
MPI_Init (&argc, &argv);
int myrank;
MPI_Comm_rank (MPI_COMM_WORLD, &myrank);
int lx {10}, ly{10}, lz{10}; //local dimensions of the process's grid
int dims[3] = {lx+1, ly+1, lz+1};
int global_extent[6] = {0, 2*lx, 0, ly, 0, lz};
int local_extent[6] = {myrank*lx, (myrank+1)*lx, 0, ly, 0, lz};
// Create and Initialize vtkMPIController
auto contr = vtkSmartPointer<vtkMPIController>::New();
contr->Initialize(&argc, &argv, 1);
int nranks = contr->GetNumberOfProcesses();
int rank = contr->GetLocalProcessId();
// Create grid points, allocate memory and Insert them
auto points = vtkSmartPointer<vtkPoints>::New();
points->Allocate(dims[0]*dims[1]*dims[2]);
for (int k=0; k<dims[2]; ++k)
for (int j=0; j<dims[1]; ++j)
for (int i=0; i<dims[0]; ++i)
points->InsertPoint(i + j*dims[0] + k*dims[0]*dims[1],
i+rank*(dims[0]-1), j, k);
// Create a density field. Note that the number of cells is always less than
// number of grid points by an amount of one so we use dims[i]-1
auto density = vtkSmartPointer<vtkFloatArray>::New();
density->SetNumberOfComponents(1);
density->SetNumberOfTuples((dims[0]-1)*(dims[1]-1)*(dims[2]-1));
density->SetName ("density");
int index;
for (int k=0; k<lz; ++k)
for (int j=0; j<ly; ++j)
for (int i=0; i<lx; ++i) {
index = i + j*(dims[0]-1) + k*(dims[0]-1)*(dims[1]-1);
density->SetValue(index, i+j+k);
}
// Create a vtkProgrammableFilter
auto pf = vtkSmartPointer<vtkProgrammableFilter>::New();
// Initialize an instance of Args
Args args;
args.pf = pf;
for(int i=0; i<6; ++i) args.local_extent[i] = local_extent[i];
pf->SetExecuteMethod(execute, &args);
// Create a structured grid and assign point data and cell data to it
auto structuredGrid = vtkSmartPointer<vtkStructuredGrid>::New();
structuredGrid->SetExtent(global_extent);
pf->SetInputData(structuredGrid);
structuredGrid->SetPoints(points);
structuredGrid->GetCellData()->AddArray(density);
// Create the parallel writer and call some functions
auto parallel_writer = vtkSmartPointer<vtkXMLPStructuredGridWriter>::New();
parallel_writer->SetInputConnection(pf->GetOutputPort());
parallel_writer->SetController(contr);
parallel_writer->SetFileName("test.pvts");
parallel_writer->SetNumberOfPieces(nranks);
parallel_writer->SetStartPiece(rank);
parallel_writer->SetEndPiece(rank);
parallel_writer->SetDataModeToBinary();
parallel_writer->Update();
parallel_writer->Write();
contr->Finalize();
// WARNING: it seems that MPI_Finalize is not necessary since we are using
// Finalize() function from vtkMPIController class. Uncomment the following
// line and see what happens.
// MPI_Finalize ();
return 0;
}
此代码仅将一些数据（在本例中为标量的密度）写入文件中，并且不渲染它。对于可视化，您需要像 Paraview 这样的软件。要运行此代码，您可以使用此 CMake 文件：
cmake_minimum_required(VERSION 2.8)
PROJECT(PXMLStructuredGridWriter)
add_executable(PXMLStructuredGridWriter parallel_vtk.cpp)
find_package(VTK REQUIRED)
include(${VTK_USE_FILE})
target_link_libraries(PXMLStructuredGridWriter ${VTK_LIBRARIES})
find_package(MPI REQUIRED)
include_directories(${MPI_INCLUDE_PATH})
target_link_libraries(PXMLStructuredGridWriter ${MPI_LIBRARIES})
最后，您将在可执行文件所在的同一目录中找到如下所示的 xml 文件：
cmake_minimum_required(VERSION 2.8)
PROJECT(PXMLStructuredGridWriter)
add_executable(PXMLStructuredGridWriter parallel_vtk.cpp)
find_package(VTK REQUIRED)
include(${VTK_USE_FILE})
target_link_libraries(PXMLStructuredGridWriter ${VTK_LIBRARIES})
find_package(MPI REQUIRED)
include_directories(${MPI_INCLUDE_PATH})
target_link_libraries(PXMLStructuredGridWriter ${MPI_LIBRARIES})