HdfData.cpp

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#include "HdfData.h"
 
#include <hdf5.h>
 
#include <map>
 
#include "BaseLib/Error.h"
#include "BaseLib/Logging.h"
#include "partition.h"
 
namespace MeshLib::IO
{
static hid_t meshPropertyType2HdfType(MeshPropertyDataType const ogs_data_type)
{
    std::map<MeshPropertyDataType const, hid_t> ogs_to_hdf_type = {
        {MeshPropertyDataType::float64, H5T_NATIVE_DOUBLE},
        {MeshPropertyDataType::float32, H5T_NATIVE_FLOAT},
        {MeshPropertyDataType::int32, H5T_NATIVE_INT32},
        {MeshPropertyDataType::int64, H5T_NATIVE_INT64},
        {MeshPropertyDataType::uint32, H5T_NATIVE_UINT32},
        {MeshPropertyDataType::uint64, H5T_NATIVE_UINT64},
        {MeshPropertyDataType::int8, H5T_NATIVE_INT8},
        {MeshPropertyDataType::uint8, H5T_NATIVE_UINT8},
        {MeshPropertyDataType::char_native, H5T_NATIVE_CHAR},
        {MeshPropertyDataType::uchar, H5T_NATIVE_UCHAR}};
    try
    {
        return ogs_to_hdf_type.at(ogs_data_type);
    }
    catch (std::exception const& e)
    {
        OGS_FATAL("No known HDF5 type for OGS type. {:s}", e.what());
    }
}
 
HdfData::HdfData(void const* data_start, std::size_t const size_partitioned_dim,
                 std::size_t const size_tuple, std::string const& name,
                 MeshPropertyDataType const mesh_property_data_type,
                 unsigned int const n_files,
                 unsigned int const chunk_size_bytes)
    : data_start(data_start), name(name)
{
    data_type = meshPropertyType2HdfType(mesh_property_data_type);
 
    auto const& partition_info =
        getPartitionInfo(size_partitioned_dim, n_files);
    auto const& offset_partitioned_dim = partition_info.local_offset;
    offsets = {offset_partitioned_dim, 0};
 
    std::size_t const unified_length = partition_info.local_length;
    int const type_size = H5Tget_size(data_type);
    std::size_t const space =
        (chunk_size_bytes > 0)
            ? std::min(std::size_t(std::lround(float(chunk_size_bytes) /
                                                   (size_tuple * type_size) +
                                               0.5)),
                       partition_info.global_length)
            : partition_info.longest_local_length;
 
    if (chunk_size_bytes > 0 && space == partition_info.global_length)
    {
        INFO("HDF5: Using a single chunk for dataset {:s} .", name);
    }
 
    chunk_space = (size_tuple > 1) ? std::vector<Hdf5DimType>{space, size_tuple}
                                   : std::vector<Hdf5DimType>{space};
 
    data_space = (size_tuple > 1)
                     ? std::vector<Hdf5DimType>{unified_length, size_tuple}
                     : std::vector<Hdf5DimType>{unified_length};
    file_space =
        (size_tuple > 1)
            ? std::vector<Hdf5DimType>{partition_info.global_length, size_tuple}
            : std::vector<Hdf5DimType>{partition_info.global_length};
 
    DBUG(
        "HDF: dataset name: {:s}, offset: {:d}, data_space: {:d}, chunk_space "
        "{:d}, file_space: {:d}, tuples: {:d}",
        name, partition_info.local_offset, data_space[0], chunk_space[0],
        file_space[0], size_tuple);
}
}  // namespace MeshLib::IO