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|---|---|---|---|
| 1 | // SPDX-FileCopyrightText: 2022-2023 Dennis Gläser <dennis.glaeser@iws.uni-stuttgart.de> | ||
| 2 | // SPDX-License-Identifier: MIT | ||
| 3 | /*! | ||
| 4 | * \file | ||
| 5 | * \ingroup Common | ||
| 6 | * \brief Helpers for I/O from HDF5 files. | ||
| 7 | */ | ||
| 8 | #ifndef GRIDFORMAT_COMMON_HDF5_HPP_ | ||
| 9 | #define GRIDFORMAT_COMMON_HDF5_HPP_ | ||
| 10 | #if GRIDFORMAT_HAVE_HIGH_FIVE | ||
| 11 | |||
| 12 | #include <type_traits> | ||
| 13 | #include <algorithm> | ||
| 14 | #include <concepts> | ||
| 15 | #include <ranges> | ||
| 16 | #include <cstdint> | ||
| 17 | |||
| 18 | #ifdef GRIDFORMAT_DISABLE_HIGHFIVE_WARNINGS | ||
| 19 | #pragma GCC diagnostic push | ||
| 20 | #pragma GCC diagnostic ignored "-Wold-style-cast" | ||
| 21 | #pragma GCC diagnostic ignored "-Wswitch-enum" | ||
| 22 | #pragma GCC diagnostic ignored "-Wuseless-cast" | ||
| 23 | #pragma GCC diagnostic ignored "-Wcast-qual" | ||
| 24 | #pragma GCC diagnostic ignored "-Wnull-dereference" | ||
| 25 | #pragma GCC diagnostic ignored "-Warray-bounds" | ||
| 26 | #pragma GCC diagnostic ignored "-Wstringop-overflow" | ||
| 27 | #endif // GRIDFORMAT_DISABLE_HIGHFIVE_WARNINGS | ||
| 28 | |||
| 29 | #include <highfive/H5Easy.hpp> | ||
| 30 | #include <highfive/H5File.hpp> | ||
| 31 | |||
| 32 | #ifdef GRIDFORMAT_DISABLE_HIGHFIVE_WARNINGS | ||
| 33 | #pragma GCC diagnostic pop | ||
| 34 | #endif // GRIDFORMAT_DISABLE_HIGHFIVE_WARNINGS | ||
| 35 | |||
| 36 | #include <gridformat/common/field.hpp> | ||
| 37 | #include <gridformat/common/logging.hpp> | ||
| 38 | #include <gridformat/common/concepts.hpp> | ||
| 39 | #include <gridformat/common/md_layout.hpp> | ||
| 40 | #include <gridformat/common/buffer_field.hpp> | ||
| 41 | #include <gridformat/common/precision.hpp> | ||
| 42 | |||
| 43 | #include <gridformat/parallel/communication.hpp> | ||
| 44 | #include <gridformat/grid/grid.hpp> | ||
| 45 | |||
| 46 | |||
| 47 | namespace GridFormat::HDF5 { | ||
| 48 | |||
| 49 | #ifndef DOXYGEN | ||
| 50 | namespace Detail { | ||
| 51 | |||
| 52 | 2644 | HighFive::DataTransferProps parallel_transfer_props() { | |
| 53 | 2644 | HighFive::DataTransferProps xfer_props; | |
| 54 | #if GRIDFORMAT_HAVE_PARALLEL_HIGH_FIVE | ||
| 55 |
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2644 | xfer_props.add(HighFive::UseCollectiveIO{}); |
| 56 | #else | ||
| 57 | throw NotImplemented("Parallel HighFive required for parallel I/O"); | ||
| 58 | #endif | ||
| 59 | 2644 | return xfer_props; | |
| 60 | ✗ | } | |
| 61 | |||
| 62 | template<Concepts::Communicator Communicator> | ||
| 63 | 354 | auto parallel_file_access_props([[maybe_unused]] const Communicator& communicator) { | |
| 64 | 354 | HighFive::FileAccessProps fapl; | |
| 65 | #if GRIDFORMAT_HAVE_PARALLEL_HIGH_FIVE | ||
| 66 | if constexpr (!std::is_same_v<Communicator, NullCommunicator>) { | ||
| 67 |
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354 | fapl.add(HighFive::MPIOFileAccess{communicator, MPI_INFO_NULL}); |
| 68 |
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354 | fapl.add(HighFive::MPIOCollectiveMetadata{}); |
| 69 | } else { | ||
| 70 | ✗ | throw TypeError("Cannot establish parallel I/O with null communicator"); | |
| 71 | } | ||
| 72 | #else | ||
| 73 | throw NotImplemented("Parallel HighFive required for parallel I/O"); | ||
| 74 | #endif | ||
| 75 | 354 | return fapl; | |
| 76 | ✗ | } | |
| 77 | |||
| 78 | 2644 | void check_successful_collective_io([[maybe_unused]] const HighFive::DataTransferProps& xfer_props) { | |
| 79 | #if GRIDFORMAT_HAVE_PARALLEL_HIGH_FIVE | ||
| 80 |
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2644 | auto mnccp = HighFive::MpioNoCollectiveCause(xfer_props); |
| 81 |
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2644 | if (mnccp.getLocalCause() || mnccp.getGlobalCause()) |
| 82 | ✗ | log_warning( | |
| 83 | ✗ | std::string{"The operation was successful, but couldn't use collective MPI-IO. "} | |
| 84 | ✗ | + "Local cause: " + std::to_string(mnccp.getLocalCause()) + " " | |
| 85 | ✗ | + "Global cause:" + std::to_string(mnccp.getGlobalCause()) + "\n" | |
| 86 | ); | ||
| 87 | #else | ||
| 88 | throw NotImplemented("Parallel HighFive required for parallel I/O"); | ||
| 89 | #endif | ||
| 90 | 2644 | } | |
| 91 | |||
| 92 | 42819 | std::pair<std::string, std::string> split_group(const std::string& in) { | |
| 93 |
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42819 | if (in.ends_with('/')) |
| 94 | ✗ | return {in, ""}; | |
| 95 | |||
| 96 | 42819 | const auto split_pos = in.find_last_of("/"); | |
| 97 |
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42819 | if (split_pos == std::string::npos ) |
| 98 | ✗ | throw ValueError("Could not split name from given path: " + in); | |
| 99 | return { | ||
| 100 |
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86742 | split_pos > 0 ? in.substr(0, split_pos) : "/", |
| 101 |
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85638 | in.substr(split_pos + 1) |
| 102 | 42819 | }; | |
| 103 | } | ||
| 104 | |||
| 105 | } // namespace Detail | ||
| 106 | #endif // DOXYGEN | ||
| 107 | |||
| 108 | //! Represents a dataset slice | ||
| 109 | struct Slice { | ||
| 110 | std::vector<std::size_t> offset; | ||
| 111 | std::vector<std::size_t> count; | ||
| 112 | std::optional<std::vector<std::size_t>> total_size = {}; | ||
| 113 | }; | ||
| 114 | |||
| 115 | //! Custom string data type using ascii encoding. | ||
| 116 | //! HighFive uses UTF-8, but VTKHDF, for instance, uses ascii. | ||
| 117 | struct AsciiString : public HighFive::DataType { | ||
| 118 | 337 | explicit AsciiString(std::size_t n) { | |
| 119 |
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337 | _hid = H5Tcopy(H5T_C_S1); |
| 120 |
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337 | if (H5Tset_size(_hid, n) < 0) { |
| 121 | ✗ | HighFive::HDF5ErrMapper::ToException<HighFive::DataTypeException>( | |
| 122 | ✗ | "Unable to define datatype size to " + std::to_string(n) | |
| 123 | ); | ||
| 124 | } | ||
| 125 | // define encoding to ASCII | ||
| 126 |
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337 | H5Tset_cset(_hid, H5T_CSET_ASCII); |
| 127 |
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337 | H5Tset_strpad(_hid, H5T_STR_SPACEPAD); |
| 128 | 337 | } | |
| 129 | |||
| 130 | template<std::size_t N> | ||
| 131 | 502 | static AsciiString from(const char (&input)[N]) { | |
| 132 |
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502 | if (input[N-1] == '\0') |
| 133 | 502 | return AsciiString{N-1}; | |
| 134 | ✗ | return AsciiString{N}; | |
| 135 | } | ||
| 136 | |||
| 137 | static AsciiString from(const std::string& n) { | ||
| 138 | return AsciiString{n.size()}; | ||
| 139 | } | ||
| 140 | }; | ||
| 141 | |||
| 142 | /*! | ||
| 143 | * \ingroup Common | ||
| 144 | * \brief Helper class for I/O from HDF5 files. | ||
| 145 | * \note Currently, strings are ascii encoded, in contrast to the standard utf-8 | ||
| 146 | * that HighFive uses. Once necessary, we'll make the encoding settable. | ||
| 147 | */ | ||
| 148 | template<Concepts::Communicator Communicator = NullCommunicator> | ||
| 149 | class File { | ||
| 150 | public: | ||
| 151 | enum Mode { | ||
| 152 | overwrite, //!< remove all content before writing | ||
| 153 | append, //!< append given data to existing datasets | ||
| 154 | read_only //!< only read data | ||
| 155 | }; | ||
| 156 | |||
| 157 | 2 | File(const std::string& filename, Mode mode = Mode::read_only) | |
| 158 | requires(std::same_as<Communicator, NullCommunicator>) | ||
| 159 |
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2 | : File(filename, NullCommunicator{}, mode) |
| 160 | 2 | {} | |
| 161 | |||
| 162 | 599 | File(const std::string& filename, const Communicator& comm, Mode mode = Mode::read_only) | |
| 163 | 354 | : _comm{comm} | |
| 164 | 599 | , _mode{mode} | |
| 165 | 599 | , _file{_open(filename)} | |
| 166 | 599 | {} | |
| 167 | |||
| 168 | //! Clear the contents of the file with the given name | ||
| 169 | 48 | static void clear(const std::string& filename, const Communicator& comm) { | |
| 170 |
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48 | if (Parallel::rank(comm) == 0) // clear file by open it in overwrite mode |
| 171 |
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34 | HighFive::File{filename, HighFive::File::Overwrite}; |
| 172 | 48 | Parallel::barrier(comm); | |
| 173 | 48 | } | |
| 174 | |||
| 175 | //! Write the given values to the attribute with the given name into the given group | ||
| 176 | template<typename Values> | ||
| 177 | 2308 | void write_attribute(const Values& values, const std::string& path) { | |
| 178 |
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2308 | _check_writable(); |
| 179 |
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2308 | const auto [group, name] = Detail::split_group(path); |
| 180 |
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2308 | _clear_attribute(name, group); |
| 181 |
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2308 | _get_group(group).createAttribute(name, values); |
| 182 | 2308 | } | |
| 183 | |||
| 184 | //! Write the given characters to the attribute with the given name into the given group | ||
| 185 | template<std::size_t N> | ||
| 186 | 502 | void write_attribute(const char (&values)[N], const std::string& path) { | |
| 187 |
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502 | _check_writable(); |
| 188 |
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502 | const auto [group, name] = Detail::split_group(path); |
| 189 |
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502 | _clear_attribute(name, group); |
| 190 |
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1004 | auto type_attr = _get_group(group).createAttribute( |
| 191 | name, | ||
| 192 |
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1004 | HighFive::DataSpace{1}, |
| 193 |
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1004 | AsciiString::from(values) |
| 194 | ); | ||
| 195 |
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502 | type_attr.write(values); |
| 196 | 502 | } | |
| 197 | |||
| 198 | //! Write the given values into the dataset with the given path | ||
| 199 | template<std::ranges::range Values> | ||
| 200 | 7768 | void write(const Values& values, | |
| 201 | const std::string& path, | ||
| 202 | const std::optional<Slice>& slice = {}) { | ||
| 203 |
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7768 | _check_writable(); |
| 204 |
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7768 | const auto [group_name, ds_name] = Detail::split_group(path); |
| 205 |
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7768 | const auto space = slice ? HighFive::DataSpace{slice->total_size.value()} |
| 206 | : HighFive::DataSpace::From(values); | ||
| 207 |
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7768 | auto group = _get_group(group_name); |
| 208 |
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7768 | auto [offset, dataset] = _prepare_dataset<FieldScalar<Values>>(group, ds_name, space); |
| 209 |
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14168 | Slice _slice{ |
| 210 |
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21936 | .offset = slice ? slice->offset : std::vector<std::size_t>(space.getNumberDimensions(), 0), |
| 211 |
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7768 | .count = slice ? slice->count : space.getDimensions() |
| 212 | }; | ||
| 213 |
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7768 | _slice.offset.at(0) += offset; |
| 214 | |||
| 215 |
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7768 | if (Parallel::size(_comm) > 1) { |
| 216 |
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4612 | if (slice) { // collective I/O |
| 217 |
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1368 | const auto props = Detail::parallel_transfer_props(); |
| 218 |
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1368 | _write_to(dataset, values, _slice, props); |
| 219 |
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1368 | Detail::check_successful_collective_io(props); |
| 220 |
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4612 | } else if (Parallel::rank(_comm) == 0) { // write only on rank 0 to avoid clashes |
| 221 |
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1622 | _write_to(dataset, values, _slice); |
| 222 | } | ||
| 223 | } else { | ||
| 224 |
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3156 | _write_to(dataset, values, _slice); |
| 225 | } | ||
| 226 |
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7768 | _file.flush(); |
| 227 | 7768 | } | |
| 228 | |||
| 229 | //! Write a field into the dataset with the given path | ||
| 230 | 3359 | void write(const Field& field, | |
| 231 | const std::string& path, | ||
| 232 | const std::optional<Slice>& slice = {}) { | ||
| 233 |
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3359 | _check_writable(); |
| 234 |
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3359 | const auto layout = field.layout(); |
| 235 |
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3359 | const HighFive::DataSpace space{[&] () { |
| 236 |
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3359 | if (slice) |
| 237 |
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2424 | return slice->total_size.value(); |
| 238 |
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935 | std::vector<std::size_t> dims(layout.dimension()); |
| 239 |
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935 | layout.export_to(dims); |
| 240 | 935 | return dims; | |
| 241 |
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7653 | } ()}; |
| 242 | |||
| 243 |
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3359 | const auto [group_name, ds_name] = Detail::split_group(path); |
| 244 |
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3359 | auto group = _get_group(group_name); |
| 245 |
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10077 | field.precision().visit([&] <typename T> (const Precision<T>&) { |
| 246 |
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3359 | auto [offset, dataset] = _prepare_dataset<T>(group, ds_name, space); |
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4294 | Slice _slice{ |
| 248 |
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7653 | .offset = slice ? slice->offset : std::vector<std::size_t>(space.getNumberDimensions(), 0), |
| 249 |
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3359 | .count = slice ? slice->count : space.getDimensions() |
| 250 | }; | ||
| 251 |
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3359 | _slice.offset.at(0) += offset; |
| 252 | |||
| 253 |
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3359 | const auto serialization = field.serialized(); |
| 254 |
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3359 | const std::span<const T> span = serialization.template as_span_of<T>(); |
| 255 | |||
| 256 |
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3359 | if (Parallel::size(_comm) > 1) { |
| 257 |
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2098 | if (slice) { // collective I/O |
| 258 |
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1960 | const auto props = Detail::parallel_transfer_props(); |
| 259 |
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1960 | _write_to(dataset, span.data(), _slice, props); |
| 260 |
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1960 | Detail::check_successful_collective_io(props); |
| 261 |
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2098 | } else if (Parallel::rank(_comm) == 0) { // write only on rank 0 to avoid clashes |
| 262 |
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63 | _write_to(dataset, span.data(), _slice); |
| 263 | } | ||
| 264 | } else { | ||
| 265 |
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1261 | _write_to(dataset, span.data(), _slice); |
| 266 | } | ||
| 267 |
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3359 | _file.flush(); |
| 268 | 3359 | }); | |
| 269 | 3359 | } | |
| 270 | |||
| 271 | //! Read dataset values into an instance of the given T | ||
| 272 | template<typename T> | ||
| 273 | requires(Concepts::ResizableMDRange<T> or Concepts::Scalar<T>) | ||
| 274 | 13170 | T read_dataset_to(const std::string& path, | |
| 275 | const std::optional<Slice>& slice = {}) const { | ||
| 276 |
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26209 | return visit_dataset(path, [&] <typename F> (BufferField<F>&& field) { |
| 277 | 6601 | return field.template export_to<T>(); | |
| 278 |
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26340 | }, slice); |
| 279 | } | ||
| 280 | |||
| 281 | //! Visit the dataset field | ||
| 282 | template<std::invocable<BufferField<int>&&> Visitor> | ||
| 283 | 17200 | decltype(auto) visit_dataset(const std::string& path, | |
| 284 | Visitor&& visitor, | ||
| 285 | const std::optional<Slice>& slice = {}) const { | ||
| 286 |
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17200 | if (!has_dataset_at(path)) |
| 287 | ✗ | throw ValueError("Given data set '" + path + "' does not exist."); | |
| 288 | |||
| 289 |
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17200 | auto [group, name] = Detail::split_group(path); |
| 290 |
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17200 | if (slice) |
| 291 |
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6406 | return _visit_data( |
| 292 | std::forward<Visitor>(visitor), | ||
| 293 |
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28128 | _file.getGroup(group).getDataSet(name).select(slice->offset, slice->count) |
| 294 |
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14064 | ); |
| 295 |
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3136 | return _visit_data(std::forward<Visitor>(visitor), _file.getGroup(group).getDataSet(name)); |
| 296 | 17200 | } | |
| 297 | |||
| 298 | //! Read attribute values into an instance of the given T | ||
| 299 | template<typename T> | ||
| 300 | requires(Concepts::ResizableMDRange<T> or Concepts::Scalar<T>) | ||
| 301 | 464 | T read_attribute_to(const std::string& path) const { | |
| 302 | 696 | return visit_attribute(path, [&] <typename F> (BufferField<F>&& field) { | |
| 303 | 232 | return field.template export_to<T>(); | |
| 304 |
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928 | }); |
| 305 | } | ||
| 306 | |||
| 307 | //! Visit the attribute field | ||
| 308 | template<std::invocable<BufferField<int>&&> Visitor> | ||
| 309 | 680 | decltype(auto) visit_attribute(const std::string& path, Visitor&& visitor) const { | |
| 310 |
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680 | if (!has_attribute_at(path)) |
| 311 | ✗ | throw ValueError("Given attribute '" + path + "' does not exist."); | |
| 312 | |||
| 313 |
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680 | auto [group, name] = Detail::split_group(path); |
| 314 |
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1360 | return _visit_data(std::forward<Visitor>(visitor), _file.getGroup(group).getAttribute(name)); |
| 315 | 680 | } | |
| 316 | |||
| 317 | //! Get the dimensions of a dataset; returns null optional if it doesn't exist. | ||
| 318 | 8344 | std::optional<std::vector<std::size_t>> get_dimensions(const std::string& path) const { | |
| 319 |
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8344 | if (has_dataset_at(path)) { |
| 320 |
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7556 | const auto [group, name] = Detail::split_group(path); |
| 321 |
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7556 | return _file.getGroup(group).getDataSet(name).getDimensions(); |
| 322 | 7556 | } | |
| 323 | 788 | return {}; | |
| 324 | } | ||
| 325 | |||
| 326 | //! Get the precision of a dataset; returns null optional if it doesn't exist. | ||
| 327 | 4379 | std::optional<DynamicPrecision> get_precision(const std::string& path) const { | |
| 328 |
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4379 | if (has_dataset_at(path)) { |
| 329 |
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4379 | const auto [group, name] = Detail::split_group(path); |
| 330 |
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4379 | return _to_precision(_file.getGroup(group).getDataSet(name).getDataType()); |
| 331 | 4379 | } | |
| 332 | ✗ | return {}; | |
| 333 | } | ||
| 334 | |||
| 335 | //! Return the names of all datasets in the given group | ||
| 336 | 332 | std::ranges::range auto dataset_names_in(const std::string& group) const { | |
| 337 |
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664 | return _file.getGroup(group).listObjectNames() |
| 338 |
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1298 | | std::views::filter([&, group=group] (const auto& name) { |
| 339 |
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990 | return _file.getGroup(group).getObjectType(name) == HighFive::ObjectType::Dataset; |
| 340 |
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664 | }); |
| 341 | } | ||
| 342 | |||
| 343 | //! Return true if the given path exists in the file | ||
| 344 | 3218 | bool exists(const std::string& path) const { | |
| 345 | 3218 | return _file.exist(path); | |
| 346 | } | ||
| 347 | |||
| 348 | //! Return true if a dataset exists at the given path | ||
| 349 | 27768 | bool has_dataset_at(const std::string& path) const { | |
| 350 |
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27768 | if (_file.exist(path)) { |
| 351 |
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26980 | const auto [group, name] = Detail::split_group(path); |
| 352 |
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26980 | if (_file.getGroup(group).exist(name)) |
| 353 |
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26980 | return _file.getGroup(group).getObjectType(name) == HighFive::ObjectType::Dataset; |
| 354 |
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26980 | } |
| 355 | 788 | return false; | |
| 356 | } | ||
| 357 | |||
| 358 | //! Return true if an attribute exists at the given path | ||
| 359 | 939 | bool has_attribute_at(const std::string& path) const { | |
| 360 |
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939 | const auto [parent_path, attr_name] = Detail::split_group(path); |
| 361 |
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939 | if (_file.exist(parent_path)) { |
| 362 |
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939 | if (has_dataset_at(parent_path)) { |
| 363 | ✗ | const auto [group, dataset] = Detail::split_group(parent_path); | |
| 364 | ✗ | return _file.getGroup(group).getDataSet(dataset).hasAttribute(attr_name); | |
| 365 | ✗ | } else { | |
| 366 |
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939 | return _file.getGroup(parent_path).hasAttribute(attr_name); |
| 367 | } | ||
| 368 | } | ||
| 369 | ✗ | return false; | |
| 370 | 939 | } | |
| 371 | |||
| 372 | private: | ||
| 373 | 8741 | void _check_writable() const { | |
| 374 |
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8741 | if (_mode == read_only) |
| 375 | ✗ | throw InvalidState("Cannot modify hdf-file opened in read-only mode"); | |
| 376 | 8741 | } | |
| 377 | |||
| 378 | 599 | HighFive::File _open(const std::string& filename) const { | |
| 379 |
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1012 | auto open_mode = _mode == read_only ? HighFive::File::ReadOnly |
| 380 |
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413 | : (_mode == overwrite ? HighFive::File::Overwrite |
| 381 | : HighFive::File::ReadWrite); | ||
| 382 |
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599 | if (Parallel::size(_comm) > 1) |
| 383 |
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708 | return HighFive::File{filename, open_mode, Detail::parallel_file_access_props(_comm)}; |
| 384 | else | ||
| 385 | 245 | return HighFive::File{filename, open_mode}; | |
| 386 | } | ||
| 387 | |||
| 388 | template<typename T> | ||
| 389 | 14486 | auto _prepare_dataset(HighFive::Group& group, | |
| 390 | const std::string& name, | ||
| 391 | const HighFive::DataSpace& space) { | ||
| 392 |
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14486 | if (_mode == overwrite) |
| 393 |
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2670 | return std::make_pair(std::size_t{0}, group.createDataSet(name, space, HighFive::create_datatype<T>())); |
| 394 |
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11816 | else if (_mode == append) { |
| 395 |
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11816 | if (group.exist(name)) { |
| 396 |
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9056 | auto dataset = group.getDataSet(name); |
| 397 |
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9056 | auto out_dimensions = dataset.getDimensions(); |
| 398 |
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9056 | const auto in_dimensions = space.getDimensions(); |
| 399 | |||
| 400 |
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9056 | if (out_dimensions.size() < 1 || in_dimensions.size() < 1) |
| 401 | ✗ | throw ValueError("Cannot extend scalar datasets"); | |
| 402 | 9056 | if ( | |
| 403 |
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9056 | !std::ranges::equal( |
| 404 | 9056 | std::ranges::subrange(out_dimensions.begin() + 1, out_dimensions.end()), | |
| 405 |
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18112 | std::ranges::subrange(in_dimensions.begin() + 1, in_dimensions.end()) |
| 406 | ) | ||
| 407 | ) | ||
| 408 | ✗ | throw ValueError("Dataset extension requires the sub-dimensions to be equal"); | |
| 409 | |||
| 410 | 9056 | const std::size_t offset = out_dimensions[0]; | |
| 411 | 9056 | out_dimensions[0] += in_dimensions[0]; | |
| 412 |
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9056 | dataset.resize(out_dimensions); |
| 413 | 9056 | return std::make_pair(offset, std::move(dataset)); | |
| 414 | 9056 | } else { | |
| 415 |
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2760 | const auto init_dimensions = space.getDimensions(); |
| 416 |
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2760 | if (init_dimensions.size() < 1) |
| 417 | ✗ | throw ValueError("Scalars cannot be written in appended mode. Wrap them in std::array{scalar}"); | |
| 418 | |||
| 419 |
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5520 | const auto chunk_dimensions = std::vector<hsize_t>{init_dimensions.begin(), init_dimensions.end()}; |
| 420 |
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4140 | const auto max_dimensions = [&] () { |
| 421 | 1380 | auto tmp = init_dimensions; | |
| 422 | 1380 | tmp[0] *= HighFive::DataSpace::UNLIMITED; | |
| 423 | 1380 | return tmp; | |
| 424 | } (); | ||
| 425 | |||
| 426 |
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2760 | HighFive::DataSpace out_space(init_dimensions, max_dimensions); |
| 427 | 2760 | HighFive::DataSetCreateProps props; | |
| 428 |
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2760 | props.add(HighFive::Chunking(chunk_dimensions)); |
| 429 | return std::make_pair( | ||
| 430 | 5520 | std::size_t{0}, | |
| 431 |
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5520 | group.createDataSet(name, out_space, HighFive::create_datatype<T>(), props) |
| 432 | 2760 | ); | |
| 433 | 2760 | } | |
| 434 | } else { | ||
| 435 | ✗ | throw NotImplemented("Unknown file mode"); | |
| 436 | } | ||
| 437 | } | ||
| 438 | |||
| 439 | template<typename Values> | ||
| 440 | 6146 | void _write_to(HighFive::DataSet& dataset, | |
| 441 | const Values& values, | ||
| 442 | const Slice& slice, | ||
| 443 | const std::optional<HighFive::DataTransferProps> props = {}) { | ||
| 444 |
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12292 | props ? dataset.select(slice.offset, slice.count).write(values, *props) |
| 445 |
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6146 | : dataset.select(slice.offset, slice.count).write(values); |
| 446 | 6146 | } | |
| 447 | |||
| 448 | template<Concepts::Scalar T> | ||
| 449 | 6568 | void _write_to(HighFive::DataSet& dataset, | |
| 450 | const T* buffer, | ||
| 451 | const Slice& slice, | ||
| 452 | const std::optional<HighFive::DataTransferProps> props = {}) { | ||
| 453 |
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13136 | props ? dataset.select(slice.offset, slice.count).write_raw(buffer, dataset.getDataType(), *props) |
| 454 |
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6568 | : dataset.select(slice.offset, slice.count).write_raw(buffer, dataset.getDataType()); |
| 455 | 6568 | } | |
| 456 | |||
| 457 | template<typename Visitor, typename Source> | ||
| 458 | 17912 | decltype(auto) _visit_data(Visitor&& visitor, const Source& source) const { | |
| 459 |
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17912 | const auto datatype = source.getDataType(); |
| 460 |
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17912 | if (datatype.isFixedLenStr()) { |
| 461 | static constexpr std::size_t N = 100; | ||
| 462 | 224 | HighFive::FixedLenStringArray<N> pre_out; | |
| 463 |
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224 | source.read(pre_out); |
| 464 |
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224 | if (pre_out.size() > 1) |
| 465 | ✗ | throw SizeError("Unexpected string array size"); | |
| 466 | |||
| 467 | 224 | std::string out; | |
| 468 |
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448 | std::ranges::copy( |
| 469 |
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2030 | pre_out.getString(0) | std::views::take_while([] (const char c) { return c != '\0'; }), |
| 470 | std::back_inserter(out) | ||
| 471 | ); | ||
| 472 |
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224 | MDLayout layout{{out.size()}}; |
| 473 |
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224 | return visitor(BufferField{std::move(out), std::move(layout)}); |
| 474 | 224 | } else { | |
| 475 |
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44004 | return _to_precision(datatype).visit([&] <typename T> (const Precision<T>&) { |
| 476 |
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14361 | return visitor(_read_buffer_field<T>(source)); |
| 477 |
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17688 | }); |
| 478 | } | ||
| 479 | 17912 | } | |
| 480 | |||
| 481 | 18844 | DynamicPrecision _to_precision(const HighFive::DataType& datatype) const { | |
| 482 |
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18844 | if (datatype.getClass() == HighFive::DataTypeClass::Float && datatype.getSize() == 8) |
| 483 | 4287 | return float64; | |
| 484 |
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14557 | else if (datatype.getClass() == HighFive::DataTypeClass::Float && datatype.getSize() == 4) |
| 485 | 3396 | return float32; | |
| 486 |
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11161 | else if (datatype.getClass() == HighFive::DataTypeClass::Integer && datatype.getSize() == 1) |
| 487 | 647 | return int8; | |
| 488 |
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10514 | else if (datatype.getClass() == HighFive::DataTypeClass::Integer && datatype.getSize() == 2) |
| 489 | ✗ | return int16; | |
| 490 |
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10514 | else if (datatype.getClass() == HighFive::DataTypeClass::Integer && datatype.getSize() == 4) |
| 491 | 2853 | return int32; | |
| 492 |
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7661 | else if (datatype.getClass() == HighFive::DataTypeClass::Integer && datatype.getSize() == 8) |
| 493 | 7661 | return int64; | |
| 494 | ✗ | else if (datatype.isVariableStr()) | |
| 495 | ✗ | return Precision<char>{}; | |
| 496 | ✗ | else if (datatype.isFixedLenStr()) | |
| 497 | ✗ | return Precision<char>{}; | |
| 498 | ✗ | throw NotImplemented("Could not determine data set precision"); | |
| 499 | } | ||
| 500 | |||
| 501 | template<typename T, typename Source> | ||
| 502 | 17688 | auto _read_buffer_field(const Source& source) const { | |
| 503 |
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17688 | auto dims = source.getMemSpace().getDimensions(); |
| 504 |
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17688 | MDLayout layout = dims.empty() ? MDLayout{{1}} : MDLayout{std::move(dims)}; |
| 505 |
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17688 | std::vector<T> out(layout.number_of_entries()); |
| 506 |
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17688 | source.read(out.data()); |
| 507 |
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35376 | return BufferField(std::move(out), std::move(layout)); |
| 508 | 17688 | } | |
| 509 | |||
| 510 | 10899 | HighFive::Group _get_group(const std::string& group_name) { | |
| 511 |
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10899 | return _file.exist(group_name) ? _file.getGroup(group_name) : _file.createGroup(group_name); |
| 512 | } | ||
| 513 | |||
| 514 | 1498 | void _clear_attribute(const std::string& name, const std::string& group) { | |
| 515 |
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1498 | if (_get_group(group).hasAttribute(name)) |
| 516 |
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660 | _get_group(group).deleteAttribute(name); |
| 517 | 1498 | } | |
| 518 | |||
| 519 | Communicator _comm; | ||
| 520 | Mode _mode; | ||
| 521 | HighFive::File _file; | ||
| 522 | }; | ||
| 523 | |||
| 524 | } // namespace GridFormat::HDF5 | ||
| 525 | |||
| 526 | #endif // GRIDFORMAT_HAVE_HIGH_FIVE | ||
| 527 | #endif // GRIDFORMAT_COMMON_HDF5_HPP_ | ||
| 528 |