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| 1 | // SPDX-FileCopyrightText: 2022-2023 Dennis Gläser <dennis.glaeser@iws.uni-stuttgart.de> | ||
| 2 | // SPDX-License-Identifier: MIT | ||
| 3 | |||
| 4 | /*! | ||
| 5 | * \file | ||
| 6 | * \ingroup VTK | ||
| 7 | * \brief Common functionality for writing VTK HDF files. | ||
| 8 | */ | ||
| 9 | #ifndef GRIDFORMAT_VTK_HDF_COMMON_HPP_ | ||
| 10 | #define GRIDFORMAT_VTK_HDF_COMMON_HPP_ | ||
| 11 | |||
| 12 | #include <vector> | ||
| 13 | #include <cstddef> | ||
| 14 | #include <numeric> | ||
| 15 | #include <string> | ||
| 16 | |||
| 17 | #include <gridformat/common/hdf5.hpp> | ||
| 18 | #include <gridformat/common/lazy_field.hpp> | ||
| 19 | #include <gridformat/common/string_conversion.hpp> | ||
| 20 | |||
| 21 | namespace GridFormat { | ||
| 22 | |||
| 23 | namespace VTK { | ||
| 24 | |||
| 25 | //! Options for transient vtk-hdf file formats | ||
| 26 | struct HDFTransientOptions { | ||
| 27 | bool static_grid = false; //!< Set to true the grid is the same for all time steps (will only be written once) | ||
| 28 | bool static_meta_data = true; //!< Set to true if the metadata is same for all time steps (will only be written once) | ||
| 29 | }; | ||
| 30 | |||
| 31 | } // namespace VTK | ||
| 32 | |||
| 33 | |||
| 34 | namespace VTKHDF { | ||
| 35 | |||
| 36 | //! Helper class to store processor offsets in parallel writes | ||
| 37 | struct IOContext { | ||
| 38 | const int my_rank; | ||
| 39 | const int num_ranks; | ||
| 40 | const bool is_parallel; | ||
| 41 | const std::vector<std::size_t> rank_cells; | ||
| 42 | const std::vector<std::size_t> rank_points; | ||
| 43 | const std::size_t num_cells_total; | ||
| 44 | const std::size_t num_points_total; | ||
| 45 | const std::size_t my_cell_offset; | ||
| 46 | const std::size_t my_point_offset; | ||
| 47 | |||
| 48 | 189 | IOContext(int _my_rank, | |
| 49 | int _num_ranks, | ||
| 50 | std::vector<std::size_t> _rank_cells, | ||
| 51 | std::vector<std::size_t> _rank_points) | ||
| 52 | 189 | : my_rank{_my_rank} | |
| 53 | 189 | , num_ranks{_num_ranks} | |
| 54 | 189 | , is_parallel{_num_ranks > 1} | |
| 55 | 189 | , rank_cells{std::move(_rank_cells)} | |
| 56 | 189 | , rank_points{std::move(_rank_points)} | |
| 57 |
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189 | , num_cells_total{_accumulate(rank_cells)} |
| 58 |
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189 | , num_points_total{_accumulate(rank_points)} |
| 59 |
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189 | , my_cell_offset{_accumulate_rank_offset(rank_cells)} |
| 60 |
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187 | , my_point_offset{_accumulate_rank_offset(rank_points)} { |
| 61 |
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187 | if (my_rank >= num_ranks) |
| 62 | ✗ | throw ValueError(as_error("Given rank is not within communicator size")); | |
| 63 |
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187 | if (num_ranks != static_cast<int>(rank_cells.size())) |
| 64 |
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2 | throw ValueError(as_error("Cells vector does not match communicator size")); |
| 65 |
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185 | if (num_ranks != static_cast<int>(rank_points.size())) |
| 66 |
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1 | throw ValueError(as_error("Points vector does not match communicator size")); |
| 67 | 194 | } | |
| 68 | |||
| 69 | template<Concepts::Grid Grid, Concepts::Communicator Communicator> | ||
| 70 | 202 | static IOContext from(const Grid& grid, const Communicator& comm, int root_rank = 0) { | |
| 71 |
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202 | const int size = Parallel::size(comm); |
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202 | const int rank = Parallel::rank(comm); |
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202 | const std::size_t num_points = number_of_points(grid); |
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202 | const std::size_t num_cells = number_of_cells(grid); |
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202 | if (size == 1) |
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360 | return IOContext{rank, size, std::vector{num_cells}, std::vector{num_points}}; |
| 77 | |||
| 78 |
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130 | const auto all_num_points = Parallel::gather(comm, num_points, root_rank); |
| 79 |
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130 | const auto all_num_cells = Parallel::gather(comm, num_cells, root_rank); |
| 80 |
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130 | const auto my_all_num_points = Parallel::broadcast(comm, all_num_points, root_rank); |
| 81 |
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130 | const auto my_all_num_cells = Parallel::broadcast(comm, all_num_cells, root_rank); |
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130 | return IOContext{rank, size, my_all_num_cells, my_all_num_points}; |
| 83 | 130 | } | |
| 84 | |||
| 85 | private: | ||
| 86 | 378 | std::size_t _accumulate(const std::vector<std::size_t>& in) const { | |
| 87 | 378 | return std::accumulate(in.begin(), in.end(), std::size_t{0}); | |
| 88 | } | ||
| 89 | |||
| 90 | 376 | std::size_t _accumulate_rank_offset(const std::vector<std::size_t>& in) const { | |
| 91 |
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376 | if (in.size() <= static_cast<std::size_t>(my_rank)) |
| 92 |
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2 | throw ValueError("Rank-vector length must be equal to number of ranks"); |
| 93 | 748 | return std::accumulate(in.begin(), std::next(in.begin(), my_rank), std::size_t{0}); | |
| 94 | } | ||
| 95 | }; | ||
| 96 | |||
| 97 | #if GRIDFORMAT_HAVE_HIGH_FIVE | ||
| 98 | |||
| 99 | /*! | ||
| 100 | * \ingroup VTKHDF | ||
| 101 | * \brief Field implementation that draws values from an open HDF5 file upon request. | ||
| 102 | */ | ||
| 103 | template<typename C> | ||
| 104 | class DataSetField : public LazyField<const HDF5::File<C>&> { | ||
| 105 | using ParentType = LazyField<const HDF5::File<C>&>; | ||
| 106 | |||
| 107 | public: | ||
| 108 | using ParentType::ParentType; | ||
| 109 | |||
| 110 | 30 | explicit DataSetField(const HDF5::File<C>& file, std::string path) | |
| 111 | : ParentType{ | ||
| 112 | file, | ||
| 113 | 30 | MDLayout{file.get_dimensions(path).value()}, | |
| 114 |
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30 | DynamicPrecision{file.get_precision(path).value()}, |
| 115 | 72 | [_p=std::move(path)] (const HDF5::File<C>& file) { | |
| 116 | 60 | return file.visit_dataset(_p, [&] <typename F> (F&& field) { | |
| 117 | 18 | return field.serialized(); | |
| 118 |
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36 | }); |
| 119 | } | ||
| 120 |
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150 | } {} |
| 121 | }; | ||
| 122 | |||
| 123 | template<typename C> | ||
| 124 | DataSetField(const HDF5::File<C>&, std::string) -> DataSetField<C>; | ||
| 125 | |||
| 126 | template<typename C, typename CB> | ||
| 127 | DataSetField(const HDF5::File<C>&, MDLayout, DynamicPrecision, CB&&) -> DataSetField<C>; | ||
| 128 | |||
| 129 | //! Read the vtk-hdf file type from an hdf5 file | ||
| 130 | template<typename C> | ||
| 131 | 184 | std::string get_file_type(const HDF5::File<C>& file) { | |
| 132 |
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368 | if (!file.exists("/VTKHDF")) |
| 133 | ✗ | throw IOError("Given file is not a VTK-HDF file"); | |
| 134 |
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368 | if (!file.has_attribute_at("/VTKHDF/Type")) |
| 135 | ✗ | throw IOError("VTKHDF-Type attribute missing"); | |
| 136 |
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368 | return file.template read_attribute_to<std::string>("/VTKHDF/Type"); |
| 137 | } | ||
| 138 | |||
| 139 | //! Check that the version stated in the file is supported | ||
| 140 | template<typename C> | ||
| 141 | 120 | void check_version_compatibility(const HDF5::File<C>& file, const std::array<std::size_t, 2>& supported) { | |
| 142 |
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240 | if (file.has_attribute_at("/VTKHDF/Version")) |
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462 | file.visit_attribute("/VTKHDF/Version", [&] (auto&& field) { |
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74 | const auto version = field.template export_to<std::vector<std::size_t>>(); |
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222 | if ((version.size() > 0 && version.at(0) > supported[0]) || |
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148 | (version.size() > 1 && version.at(0) == supported[0] && version.at(1) > supported[1])) |
| 147 | ✗ | throw ValueError( | |
| 148 | ✗ | "File version is higher than supported by the reader (" + as_string(supported, ".") + ")" | |
| 149 | ); | ||
| 150 | 74 | }); | |
| 151 | 120 | } | |
| 152 | |||
| 153 | #endif // GRIDFORMAT_HAVE_HIGH_FIVE | ||
| 154 | |||
| 155 | } // namespace VTKHDF | ||
| 156 | } // namespace GridFormat | ||
| 157 | |||
| 158 | #endif // GRIDFORMAT_VTK_HDF_COMMON_HPP_ | ||
| 159 |