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Parallel files

The parallel file formats do not actually store any data in the file. Instead, the data is broken into pieces, each of which is stored in a serial file, and an extra header file is created containing pointers to the corresponding serial files. The header file extension is the serial extension prepended with a p. For instance, for serial vtu files, the corresponding header file extension is pvtu.

Generating a parallel data file

The parallel header file and the corresponding serial files are generated by a single call to pvtk_grid. Its signature is

pvtk_grid(
    filename, args...;
    part, nparts, ismain = (part == 1), ghost_level = 0, kwargs...,
)

which returns a handler representing a parallel VTK file that can be appended with cell and point data and eventually written to disk with vtk_save as usual. In an MPI job, vtk_save will cause each rank to write a serial file and just a single rank (e.g., rank 0) will write the header file.

This signature is valid for unstructured grids. For the case of structured grids, there are small differences detailed further below.

Positional and keyword arguments in args and kwargs are passed to vtk_grid verbatim. Note that serial filenames are automatically generated from filename and from the process id part.

The following keyword arguments only apply to parallel VTK file formats.

Mandatory ones are:

  • part: current (1-based) part id (typically MPI rank + 1),
  • nparts: total number of parts (typically the MPI communicator size).

Optional ones are:

  • ismain: true if the current part id part is the main (the only one that will write the header file),
  • ghost_level: ghost level.

Parallel structured files

For structured grids, one needs to specify the portion of the grid associated to each process. This is done via the extents keyword argument, which must be an array containing the data ranges along each dimension associated to each process. For example, for a dataset of global dimensions $15×12×4$ distributed across 4 processes, this array may look like the following:

extents = [
    ( 1:10,  1:5, 1:4),  # process 1
    (10:15,  1:5, 1:4),  # process 2
    ( 1:10, 5:12, 1:4),  # process 3
    (10:15, 5:12, 1:4),  # process 4
]

In practice, in parallel applications, all processes need to have this information, and the extents argument must be the same for all processes. Also note that the length of the extents array gives the number of processes, and therefore the nparts argument is redundant and not needed for structured grids.

Finally, note that in the example above the extents for different processes overlap (for instance, the ranges 1:10 and 10:15 overlap at the index i = 10). This is a requirement of VTK, and without it the full data cannot be visualised in ParaView. For MPI applications, this typically means that ghost data need to be exchanged before writing VTK files.

Example 1: Unstructured files

This generates two serial files (typically held by two different processes) and a header file combining them:

all_data = [
    # Process 1
    (
        points = rand(3, 5),  # 5 points on process 1
        cells = [             # 2 cells  on process 1
            MeshCell(VTKCellTypes.VTK_TRIANGLE, [1, 4, 2]),
            MeshCell(VTKCellTypes.VTK_QUAD, [2, 4, 3, 5]),
        ],
    ),

    # Process 2
    (
        points = rand(3, 4),  # 4 points on process 2
        cells = [             # 1 cell   on process 2
            MeshCell(VTKCellTypes.VTK_QUAD, [1, 2, 3, 4]),
        ]
    ),
]

saved_files = Vector{Vector{String}}(undef, 2)  # files saved by each "process"

for part = 1:2
    data = all_data[part]
    saved_files[part] = pvtk_grid(
            "simulation", data.points, data.cells;
            part = part, nparts = 2,
        ) do pvtk
        pvtk["Pressure"] = sum(data.points; dims = 1)
    end
end

In this example, saved_files lists the files saved by each "process":

julia> saved_files
2-element Vector{Vector{String}}:
 ["simulation.pvtu", "simulation/simulation_1.vtu"]
 ["simulation/simulation_2.vtu"]

Note that the files containing the actual data (in this case simulation_*.vtu) are stored in a separate simulation directory.

Example 2: Structured files

This generates 4 serial image data files (.vti) and a header file (.pvti) combining them:

# Global grid
xs_global = range(0, 2; length = 15)
ys_global = range(-1, 1; length = 12)
zs_global = range(0, 1; length = 4)

extents = [
    ( 1:10,  1:5, 1:4),  # process 1
    (10:15,  1:5, 1:4),  # process 2
    ( 1:10, 5:12, 1:4),  # process 3
    (10:15, 5:12, 1:4),  # process 4
]

saved_files = Vector{Vector{String}}(undef, 4)  # files saved by each "process"

for part = 1:4
    is, js, ks = extents[part]  # local indices
    xs, ys, zs = xs_global[is], ys_global[js], zs_global[ks]  # local grid
    saved_files[part] = pvtk_grid(
            "fields", xs, ys, zs;
            part = part, extents = extents,
        ) do pvtk
        pvtk["Temperature"] = [x + 2y + 3z for x ∈ xs, y ∈ ys, z ∈ zs]
    end
end

As in the previous example, saved_files lists the files saved by each "process":

julia> saved_files
4-element Vector{Vector{String}}:
 ["fields.pvti", "fields/fields_1.vti"]
 ["fields/fields_2.vti"]
 ["fields/fields_3.vti"]
 ["fields/fields_4.vti"]

Acknowledgements

Thanks to Francesc Verdugo and Alberto F. Martin for the initial parallel file format implementation, and to Corentin Lothode for the initial work on structured grids.