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VTK
9.1.0
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VTK
9.1.0
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VTK 10.0 introduces the VTK HDF format for VTK datasets. The goal of this work is to provide simulations with a way to save data in HDF that could be easily loaded in VTK without the need for external data description (such as XDMF). We use the same extension for serial and parallel formats and for all types of datasets. We use HDF standard file extensions such as hdf, hdf5, h5 or he5.
In the following diagrams showing the HDF file structure for VTK datasets, the rounded blue rectangles are HDF groups and the gray rectangles are HDF datasets. Each rectangle shows the name of the group or dataset in bold font and the attributes underneath with regular font.
VTK HDF files start with a group called VTKHDF with one attribute: Version, an array of two integers. Additional attributes can follow depending on the dataset type stored in the file.
The data type for each HDF dataset is part of the dataset and it is determined at write time. The reader matches the type of the dataset with a H5T_NATIVE_ type and creates the VTK array of that type. Consequently, the type at writing might be different than the type at reading even on the same machine because for instance long can be the same type as long long or int can be the same as long on certain platforms. Also, vtkIdType is read as the C++ type it represents (long or long long). Endianness conversions are done automatically.
An ImageData (regular grid) is not split into partitions for parallel processing. We rely on the writer to chunk the data to optimize reading for a certain number of MPI ranks. Attribute data is stored in a PointData or CellData array using hyper slabs. WholeExtent, Origin, Spacing and Direction attributes have the same meaning as the coresponding attributes for vtkImageData. Scalars, Vectors, ... string atributes for the PointData and CellData groups specify the active attributes in the dataset.
The unstructured grid is split into partitions, with a partition for each MPI node. This is reflected in the HDF5 file structure. Each HDF dataset is obtained by concatenating the data for each partition. The offset O(i) where we store the data for partition i is computed using:
O(i) = S(0) + ... + S(i-1), i > 1 with O(0) = 0.
where S(i) is the size of partition i.
An unstructured grid file has a HDF5 structure shown in the next picture. We describe the split into partitions using HDF5 datasets NumberOfConnectivityIds, NumberOfPoints and NumberOfCells. Let n be the number of partitions which usually correspond to the number of the MPI ranks. NumberOfConnectivityIds has size n where NumberOfConnectivityIds[i] represents the size of the Connectivity array for partition i. NumberOfPoints and NumberOfCells are arrays of size n, where NumberOfPoints[i] and NumberOfCells[i] are the number of points and number of cells for partition i. The Points array contains the points of the VTK dataset. Offsets is an array of size ∑ S(i), where S(i) is the size of partition i, indicating the index in the Connectivity array where each cell's points start. Connectivity stores the lists of point ids for each cell, and Types contain the cell information stored as described in vtkCellArray documentation. Data for each partition is appended in a HDF dataset for Points, Connectivity, Offsets, Types, PointData and CellData. We can compute the size of partition i using the following formulas:
| Size of partition i | |
|---|---|
| Points | NumberOfPoints[i] * 3 * sizeof(Points[0][0]) |
| Connectivity | NumberOfConnectivityIds[i] * sizeof(Connectivity[0]) |
| Offsets | (NumberOfCells[i] + 1) * sizeof(Offsets[0]) |
| Types | NumberOfCells[i] * sizeof(Types[i]) |
| PointData | NumberOfPoints[i] * sizeof(point_array_k[0]) |
| CellData | NumberOfCells[i] * sizeof(cell_array_k[0]) |
To read the data for its rank a node reads the information about all partitions, compute the correct offset and then read data from that offset.
This specification and the reader available in VTK currently only supports ImageData and UnstructuredGrid. Other dataset types may be added later dependeing on interest and funding.
We present two examples of VTK HDF files, shown using h5dump -A one image file and one unstructured grid. These files can be examined in the VTK source code, by building VTK and enabling testing (VTK_BUILD_TESTING). The two files are in the build directory ExternalData at Testing/Data/mandelbrot-vti.hdf for the ImageData and at Testing/Data/can-pvtu.hdf for the partitioned UnstructuredGrid.
The image data file is a wavelet source produced in ParaView. Note that we don't partition image data, so the same format is used for serial and parallel processing.
The unstructured grid is the can example (only the can, not the brick) from ParaView, partitioned in three:
1.9.4