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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 | 42860 | std::pair<std::string, std::string> split_group(const std::string& in) { | |
| 93 |
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42860 | if (in.ends_with('/')) |
| 94 | ✗ | return {in, ""}; | |
| 95 | |||
| 96 | 42860 | const auto split_pos = in.find_last_of("/"); | |
| 97 |
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42860 | if (split_pos == std::string::npos ) |
| 98 | ✗ | throw ValueError("Could not split name from given path: " + in); | |
| 99 | return { | ||
| 100 |
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86832 | split_pos > 0 ? in.substr(0, split_pos) : "/", |
| 101 |
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85720 | in.substr(split_pos + 1) |
| 102 | 42860 | }; | |
| 103 | } | ||
| 104 | |||
| 105 | template<typename T> | ||
| 106 | using HighFiveDataType = std::conditional_t<std::is_same_v<T, bool>, char, T>; | ||
| 107 | |||
| 108 | } // namespace Detail | ||
| 109 | #endif // DOXYGEN | ||
| 110 | |||
| 111 | //! Represents a dataset slice | ||
| 112 | struct Slice { | ||
| 113 | std::vector<std::size_t> offset; | ||
| 114 | std::vector<std::size_t> count; | ||
| 115 | std::optional<std::vector<std::size_t>> total_size = {}; | ||
| 116 | }; | ||
| 117 | |||
| 118 | //! Custom string data type using ascii encoding. | ||
| 119 | //! HighFive uses UTF-8, but VTKHDF, for instance, uses ascii. | ||
| 120 | struct AsciiString : public HighFive::DataType { | ||
| 121 | 338 | explicit AsciiString(std::size_t n) { | |
| 122 |
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338 | _hid = H5Tcopy(H5T_C_S1); |
| 123 |
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338 | if (H5Tset_size(_hid, n) < 0) { |
| 124 | ✗ | HighFive::HDF5ErrMapper::ToException<HighFive::DataTypeException>( | |
| 125 | ✗ | "Unable to define datatype size to " + std::to_string(n) | |
| 126 | ); | ||
| 127 | } | ||
| 128 | // define encoding to ASCII | ||
| 129 |
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338 | H5Tset_cset(_hid, H5T_CSET_ASCII); |
| 130 |
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338 | H5Tset_strpad(_hid, H5T_STR_SPACEPAD); |
| 131 | 338 | } | |
| 132 | |||
| 133 | template<std::size_t N> | ||
| 134 | 503 | static AsciiString from(const char (&input)[N]) { | |
| 135 |
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503 | if (input[N-1] == '\0') |
| 136 | 503 | return AsciiString{N-1}; | |
| 137 | ✗ | return AsciiString{N}; | |
| 138 | } | ||
| 139 | |||
| 140 | static AsciiString from(const std::string& n) { | ||
| 141 | return AsciiString{n.size()}; | ||
| 142 | } | ||
| 143 | }; | ||
| 144 | |||
| 145 | /*! | ||
| 146 | * \ingroup Common | ||
| 147 | * \brief Helper class for I/O from HDF5 files. | ||
| 148 | * \note Currently, strings are ascii encoded, in contrast to the standard utf-8 | ||
| 149 | * that HighFive uses. Once necessary, we'll make the encoding settable. | ||
| 150 | */ | ||
| 151 | template<Concepts::Communicator Communicator = NullCommunicator> | ||
| 152 | class File { | ||
| 153 | public: | ||
| 154 | enum Mode { | ||
| 155 | overwrite, //!< remove all content before writing | ||
| 156 | append, //!< append given data to existing datasets | ||
| 157 | read_only //!< only read data | ||
| 158 | }; | ||
| 159 | |||
| 160 | 2 | File(const std::string& filename, Mode mode = Mode::read_only) | |
| 161 | requires(std::same_as<Communicator, NullCommunicator>) | ||
| 162 |
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2 | : File(filename, NullCommunicator{}, mode) |
| 163 | 2 | {} | |
| 164 | |||
| 165 | 601 | File(const std::string& filename, const Communicator& comm, Mode mode = Mode::read_only) | |
| 166 | 354 | : _comm{comm} | |
| 167 | 601 | , _mode{mode} | |
| 168 | 601 | , _file{_open(filename)} | |
| 169 | 601 | {} | |
| 170 | |||
| 171 | //! Clear the contents of the file with the given name | ||
| 172 | 48 | static void clear(const std::string& filename, const Communicator& comm) { | |
| 173 |
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48 | if (Parallel::rank(comm) == 0) // clear file by open it in overwrite mode |
| 174 |
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34 | HighFive::File{filename, HighFive::File::Overwrite}; |
| 175 | 48 | Parallel::barrier(comm); | |
| 176 | 48 | } | |
| 177 | |||
| 178 | //! Write the given values to the attribute with the given name into the given group | ||
| 179 | template<typename Values> | ||
| 180 | 2310 | void write_attribute(const Values& values, const std::string& path) { | |
| 181 |
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2310 | _check_writable(); |
| 182 |
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2310 | const auto [group, name] = Detail::split_group(path); |
| 183 |
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2310 | _clear_attribute(name, group); |
| 184 |
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2310 | _get_group(group).createAttribute(name, values); |
| 185 | 2310 | } | |
| 186 | |||
| 187 | //! Write the given characters to the attribute with the given name into the given group | ||
| 188 | template<std::size_t N> | ||
| 189 | 503 | void write_attribute(const char (&values)[N], const std::string& path) { | |
| 190 |
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503 | _check_writable(); |
| 191 |
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503 | const auto [group, name] = Detail::split_group(path); |
| 192 |
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503 | _clear_attribute(name, group); |
| 193 |
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1006 | auto type_attr = _get_group(group).createAttribute( |
| 194 | name, | ||
| 195 |
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1006 | HighFive::DataSpace{1}, |
| 196 |
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1006 | AsciiString::from(values) |
| 197 | ); | ||
| 198 |
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503 | type_attr.write(values); |
| 199 | 503 | } | |
| 200 | |||
| 201 | //! Write the given values into the dataset with the given path | ||
| 202 | template<std::ranges::range Values> | ||
| 203 | 7780 | void write(const Values& values, | |
| 204 | const std::string& path, | ||
| 205 | const std::optional<Slice>& slice = {}) { | ||
| 206 |
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7780 | _check_writable(); |
| 207 |
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7780 | const auto [group_name, ds_name] = Detail::split_group(path); |
| 208 |
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7780 | const auto space = slice ? HighFive::DataSpace{slice->total_size.value()} |
| 209 | : HighFive::DataSpace::From(values); | ||
| 210 |
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7780 | auto group = _get_group(group_name); |
| 211 |
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7780 | auto [offset, dataset] = _prepare_dataset<FieldScalar<Values>>(group, ds_name, space); |
| 212 |
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14192 | Slice _slice{ |
| 213 |
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21972 | .offset = slice ? slice->offset : std::vector<std::size_t>(space.getNumberDimensions(), 0), |
| 214 |
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7780 | .count = slice ? slice->count : space.getDimensions() |
| 215 | }; | ||
| 216 |
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7780 | _slice.offset.at(0) += offset; |
| 217 | |||
| 218 |
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7780 | if (Parallel::size(_comm) > 1) { |
| 219 |
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4612 | if (slice) { // collective I/O |
| 220 |
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1368 | const auto props = Detail::parallel_transfer_props(); |
| 221 |
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1368 | _write_to(dataset, values, _slice, props); |
| 222 |
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1368 | Detail::check_successful_collective_io(props); |
| 223 |
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4612 | } else if (Parallel::rank(_comm) == 0) { // write only on rank 0 to avoid clashes |
| 224 |
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1622 | _write_to(dataset, values, _slice); |
| 225 | } | ||
| 226 | } else { | ||
| 227 |
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3168 | _write_to(dataset, values, _slice); |
| 228 | } | ||
| 229 |
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7780 | _file.flush(); |
| 230 | 7780 | } | |
| 231 | |||
| 232 | //! Write a field into the dataset with the given path | ||
| 233 | 3362 | void write(const Field& field, | |
| 234 | const std::string& path, | ||
| 235 | const std::optional<Slice>& slice = {}) { | ||
| 236 |
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3362 | _check_writable(); |
| 237 |
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3362 | const auto layout = field.layout(); |
| 238 |
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3362 | const HighFive::DataSpace space{[&] () { |
| 239 |
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3362 | if (slice) |
| 240 |
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2424 | return slice->total_size.value(); |
| 241 |
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938 | std::vector<std::size_t> dims(layout.dimension()); |
| 242 |
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938 | layout.export_to(dims); |
| 243 | 938 | return dims; | |
| 244 |
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7662 | } ()}; |
| 245 | |||
| 246 |
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3362 | const auto [group_name, ds_name] = Detail::split_group(path); |
| 247 |
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3362 | auto group = _get_group(group_name); |
| 248 |
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10086 | field.precision().visit([&] <typename T> (const Precision<T>&) { |
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3362 | auto [offset, dataset] = _prepare_dataset<T>(group, ds_name, space); |
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4300 | Slice _slice{ |
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7662 | .offset = slice ? slice->offset : std::vector<std::size_t>(space.getNumberDimensions(), 0), |
| 252 |
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3362 | .count = slice ? slice->count : space.getDimensions() |
| 253 | }; | ||
| 254 |
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3362 | _slice.offset.at(0) += offset; |
| 255 | |||
| 256 |
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3362 | const auto serialization = field.serialized(); |
| 257 |
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3362 | const std::span<const T> span = serialization.template as_span_of<T>(); |
| 258 | |||
| 259 |
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3362 | if (Parallel::size(_comm) > 1) { |
| 260 |
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2098 | if (slice) { // collective I/O |
| 261 |
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1960 | const auto props = Detail::parallel_transfer_props(); |
| 262 |
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1960 | _write_to(dataset, span.data(), _slice, props); |
| 263 |
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1960 | Detail::check_successful_collective_io(props); |
| 264 |
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2098 | } else if (Parallel::rank(_comm) == 0) { // write only on rank 0 to avoid clashes |
| 265 |
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63 | _write_to(dataset, span.data(), _slice); |
| 266 | } | ||
| 267 | } else { | ||
| 268 |
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1264 | _write_to(dataset, span.data(), _slice); |
| 269 | } | ||
| 270 |
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3362 | _file.flush(); |
| 271 | 3362 | }); | |
| 272 | 3362 | } | |
| 273 | |||
| 274 | //! Read dataset values into an instance of the given T | ||
| 275 | template<typename T> | ||
| 276 | requires(Concepts::ResizableMDRange<T> or Concepts::Scalar<T>) | ||
| 277 | 13174 | T read_dataset_to(const std::string& path, | |
| 278 | const std::optional<Slice>& slice = {}) const { | ||
| 279 |
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26215 | return visit_dataset(path, [&] <typename F> (BufferField<F>&& field) { |
| 280 | 6603 | return field.template export_to<T>(); | |
| 281 |
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26348 | }, slice); |
| 282 | } | ||
| 283 | |||
| 284 | //! Visit the dataset field | ||
| 285 | template<std::invocable<BufferField<int>&&> Visitor> | ||
| 286 | 17208 | decltype(auto) visit_dataset(const std::string& path, | |
| 287 | Visitor&& visitor, | ||
| 288 | const std::optional<Slice>& slice = {}) const { | ||
| 289 |
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17208 | if (!has_dataset_at(path)) |
| 290 | ✗ | throw ValueError("Given data set '" + path + "' does not exist."); | |
| 291 | |||
| 292 |
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17208 | auto [group, name] = Detail::split_group(path); |
| 293 |
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17208 | if (slice) |
| 294 |
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6406 | return _visit_data( |
| 295 | std::forward<Visitor>(visitor), | ||
| 296 |
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28144 | _file.getGroup(group).getDataSet(name).select(slice->offset, slice->count) |
| 297 |
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14072 | ); |
| 298 |
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3136 | return _visit_data(std::forward<Visitor>(visitor), _file.getGroup(group).getDataSet(name)); |
| 299 | 17208 | } | |
| 300 | |||
| 301 | //! Read attribute values into an instance of the given T | ||
| 302 | template<typename T> | ||
| 303 | requires(Concepts::ResizableMDRange<T> or Concepts::Scalar<T>) | ||
| 304 | 466 | T read_attribute_to(const std::string& path) const { | |
| 305 | 699 | return visit_attribute(path, [&] <typename F> (BufferField<F>&& field) { | |
| 306 | 233 | return field.template export_to<T>(); | |
| 307 |
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932 | }); |
| 308 | } | ||
| 309 | |||
| 310 | //! Visit the attribute field | ||
| 311 | template<std::invocable<BufferField<int>&&> Visitor> | ||
| 312 | 684 | decltype(auto) visit_attribute(const std::string& path, Visitor&& visitor) const { | |
| 313 |
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684 | if (!has_attribute_at(path)) |
| 314 | ✗ | throw ValueError("Given attribute '" + path + "' does not exist."); | |
| 315 | |||
| 316 |
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684 | auto [group, name] = Detail::split_group(path); |
| 317 |
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1368 | return _visit_data(std::forward<Visitor>(visitor), _file.getGroup(group).getAttribute(name)); |
| 318 | 684 | } | |
| 319 | |||
| 320 | //! Get the dimensions of a dataset; returns null optional if it doesn't exist. | ||
| 321 | 8352 | std::optional<std::vector<std::size_t>> get_dimensions(const std::string& path) const { | |
| 322 |
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8352 | if (has_dataset_at(path)) { |
| 323 |
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7560 | const auto [group, name] = Detail::split_group(path); |
| 324 |
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7560 | return _file.getGroup(group).getDataSet(name).getDimensions(); |
| 325 | 7560 | } | |
| 326 | 792 | return {}; | |
| 327 | } | ||
| 328 | |||
| 329 | //! Get the precision of a dataset; returns null optional if it doesn't exist. | ||
| 330 | 4381 | std::optional<DynamicPrecision> get_precision(const std::string& path) const { | |
| 331 |
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4381 | if (has_dataset_at(path)) { |
| 332 |
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4381 | const auto [group, name] = Detail::split_group(path); |
| 333 |
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4381 | return _to_precision(_file.getGroup(group).getDataSet(name).getDataType()); |
| 334 | 4381 | } | |
| 335 | ✗ | return {}; | |
| 336 | } | ||
| 337 | |||
| 338 | //! Return the names of all datasets in the given group | ||
| 339 | 333 | std::ranges::range auto dataset_names_in(const std::string& group) const { | |
| 340 |
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666 | return _file.getGroup(group).listObjectNames() |
| 341 |
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1300 | | std::views::filter([&, group=group] (const auto& name) { |
| 342 |
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992 | return _file.getGroup(group).getObjectType(name) == HighFive::ObjectType::Dataset; |
| 343 |
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666 | }); |
| 344 | } | ||
| 345 | |||
| 346 | //! Return true if the given path exists in the file | ||
| 347 | 3223 | bool exists(const std::string& path) const { | |
| 348 | 3223 | return _file.exist(path); | |
| 349 | } | ||
| 350 | |||
| 351 | //! Return true if a dataset exists at the given path | ||
| 352 | 27786 | bool has_dataset_at(const std::string& path) const { | |
| 353 |
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27786 | if (_file.exist(path)) { |
| 354 |
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26994 | const auto [group, name] = Detail::split_group(path); |
| 355 |
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26994 | if (_file.getGroup(group).exist(name)) |
| 356 |
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26994 | return _file.getGroup(group).getObjectType(name) == HighFive::ObjectType::Dataset; |
| 357 |
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26994 | } |
| 358 | 792 | return false; | |
| 359 | } | ||
| 360 | |||
| 361 | //! Return true if an attribute exists at the given path | ||
| 362 | 943 | bool has_attribute_at(const std::string& path) const { | |
| 363 |
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943 | const auto [parent_path, attr_name] = Detail::split_group(path); |
| 364 |
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943 | if (_file.exist(parent_path)) { |
| 365 |
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943 | if (has_dataset_at(parent_path)) { |
| 366 | ✗ | const auto [group, dataset] = Detail::split_group(parent_path); | |
| 367 | ✗ | return _file.getGroup(group).getDataSet(dataset).hasAttribute(attr_name); | |
| 368 | ✗ | } else { | |
| 369 |
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943 | return _file.getGroup(parent_path).hasAttribute(attr_name); |
| 370 | } | ||
| 371 | } | ||
| 372 | ✗ | return false; | |
| 373 | 943 | } | |
| 374 | |||
| 375 | private: | ||
| 376 | 8752 | void _check_writable() const { | |
| 377 |
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8752 | if (_mode == read_only) |
| 378 | ✗ | throw InvalidState("Cannot modify hdf-file opened in read-only mode"); | |
| 379 | 8752 | } | |
| 380 | |||
| 381 | 601 | HighFive::File _open(const std::string& filename) const { | |
| 382 |
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1015 | auto open_mode = _mode == read_only ? HighFive::File::ReadOnly |
| 383 |
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414 | : (_mode == overwrite ? HighFive::File::Overwrite |
| 384 | : HighFive::File::ReadWrite); | ||
| 385 |
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601 | if (Parallel::size(_comm) > 1) |
| 386 |
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708 | return HighFive::File{filename, open_mode, Detail::parallel_file_access_props(_comm)}; |
| 387 | else | ||
| 388 | 247 | return HighFive::File{filename, open_mode}; | |
| 389 | } | ||
| 390 | |||
| 391 | template<Concepts::Scalar S, typename T = Detail::HighFiveDataType<S>> | ||
| 392 | 14504 | auto _prepare_dataset(HighFive::Group& group, | |
| 393 | const std::string& name, | ||
| 394 | const HighFive::DataSpace& space) { | ||
| 395 |
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14504 | if (_mode == overwrite) |
| 396 |
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2688 | return std::make_pair(std::size_t{0}, group.createDataSet(name, space, HighFive::create_datatype<T>())); |
| 397 |
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11816 | else if (_mode == append) { |
| 398 |
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11816 | if (group.exist(name)) { |
| 399 |
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9056 | auto dataset = group.getDataSet(name); |
| 400 |
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9056 | auto out_dimensions = dataset.getDimensions(); |
| 401 |
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9056 | const auto in_dimensions = space.getDimensions(); |
| 402 | |||
| 403 |
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9056 | if (out_dimensions.size() < 1 || in_dimensions.size() < 1) |
| 404 | ✗ | throw ValueError("Cannot extend scalar datasets"); | |
| 405 | 9056 | if ( | |
| 406 |
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9056 | !std::ranges::equal( |
| 407 | 9056 | std::ranges::subrange(out_dimensions.begin() + 1, out_dimensions.end()), | |
| 408 |
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18112 | std::ranges::subrange(in_dimensions.begin() + 1, in_dimensions.end()) |
| 409 | ) | ||
| 410 | ) | ||
| 411 | ✗ | throw ValueError("Dataset extension requires the sub-dimensions to be equal"); | |
| 412 | |||
| 413 | 9056 | const std::size_t offset = out_dimensions[0]; | |
| 414 | 9056 | out_dimensions[0] += in_dimensions[0]; | |
| 415 |
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9056 | dataset.resize(out_dimensions); |
| 416 | 9056 | return std::make_pair(offset, std::move(dataset)); | |
| 417 | 9056 | } else { | |
| 418 |
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2760 | const auto init_dimensions = space.getDimensions(); |
| 419 |
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2760 | if (init_dimensions.size() < 1) |
| 420 | ✗ | throw ValueError("Scalars cannot be written in appended mode. Wrap them in std::array{scalar}"); | |
| 421 | |||
| 422 |
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5520 | const auto chunk_dimensions = std::vector<hsize_t>{init_dimensions.begin(), init_dimensions.end()}; |
| 423 |
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4140 | const auto max_dimensions = [&] () { |
| 424 | 1380 | auto tmp = init_dimensions; | |
| 425 | 1380 | tmp[0] *= HighFive::DataSpace::UNLIMITED; | |
| 426 | 1380 | return tmp; | |
| 427 | } (); | ||
| 428 | |||
| 429 |
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2760 | HighFive::DataSpace out_space(init_dimensions, max_dimensions); |
| 430 | 2760 | HighFive::DataSetCreateProps props; | |
| 431 |
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2760 | props.add(HighFive::Chunking(chunk_dimensions)); |
| 432 | return std::make_pair( | ||
| 433 | 5520 | std::size_t{0}, | |
| 434 |
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5520 | group.createDataSet(name, out_space, HighFive::create_datatype<T>(), props) |
| 435 | 2760 | ); | |
| 436 | 2760 | } | |
| 437 | } else { | ||
| 438 | ✗ | throw NotImplemented("Unknown file mode"); | |
| 439 | } | ||
| 440 | } | ||
| 441 | |||
| 442 | template<typename Values> | ||
| 443 | 6158 | void _write_to(HighFive::DataSet& dataset, | |
| 444 | const Values& values, | ||
| 445 | const Slice& slice, | ||
| 446 | const std::optional<HighFive::DataTransferProps> props = {}) { | ||
| 447 |
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12316 | props ? dataset.select(slice.offset, slice.count).write(values, *props) |
| 448 |
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6158 | : dataset.select(slice.offset, slice.count).write(values); |
| 449 | 6158 | } | |
| 450 | |||
| 451 | template<Concepts::Scalar T> | ||
| 452 | 6574 | void _write_to(HighFive::DataSet& dataset, | |
| 453 | const T* buffer, | ||
| 454 | const Slice& slice, | ||
| 455 | const std::optional<HighFive::DataTransferProps> props = {}) { | ||
| 456 |
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13148 | props ? dataset.select(slice.offset, slice.count).write_raw(buffer, dataset.getDataType(), *props) |
| 457 |
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6574 | : dataset.select(slice.offset, slice.count).write_raw(buffer, dataset.getDataType()); |
| 458 | 6574 | } | |
| 459 | |||
| 460 | template<typename Visitor, typename Source> | ||
| 461 | 17924 | decltype(auto) _visit_data(Visitor&& visitor, const Source& source) const { | |
| 462 |
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17924 | const auto datatype = source.getDataType(); |
| 463 |
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17924 | if (datatype.isFixedLenStr()) { |
| 464 | 226 | std::vector<std::string> pre_out; | |
| 465 |
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226 | source.read(pre_out); |
| 466 |
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226 | if (pre_out.size() > 1 or pre_out.size() == 0) |
| 467 | ✗ | throw SizeError("Unexpected string array size"); | |
| 468 | |||
| 469 | 226 | std::string out = std::move(std::move(pre_out)[0]); | |
| 470 |
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226 | MDLayout layout{{out.size()}}; |
| 471 |
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226 | return visitor(BufferField{std::move(out), std::move(layout)}); |
| 472 | 226 | } else { | |
| 473 |
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44027 | return _to_precision(datatype).visit([&] <typename T> (const Precision<T>&) { |
| 474 |
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14370 | return visitor(_read_buffer_field<T>(source)); |
| 475 |
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17698 | }); |
| 476 | } | ||
| 477 | 17924 | } | |
| 478 | |||
| 479 | 18851 | DynamicPrecision _to_precision(const HighFive::DataType& datatype) const { | |
| 480 |
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18851 | if (datatype.getClass() == HighFive::DataTypeClass::Float && datatype.getSize() == 8) |
| 481 | 4287 | return float64; | |
| 482 |
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14564 | else if (datatype.getClass() == HighFive::DataTypeClass::Float && datatype.getSize() == 4) |
| 483 | 3396 | return float32; | |
| 484 |
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11168 | else if (datatype.getClass() == HighFive::DataTypeClass::Integer && datatype.getSize() == 1) |
| 485 | 651 | return int8; | |
| 486 |
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10517 | else if (datatype.getClass() == HighFive::DataTypeClass::Integer && datatype.getSize() == 2) |
| 487 | ✗ | return int16; | |
| 488 |
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10517 | else if (datatype.getClass() == HighFive::DataTypeClass::Integer && datatype.getSize() == 4) |
| 489 | 2853 | return int32; | |
| 490 |
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7664 | else if (datatype.getClass() == HighFive::DataTypeClass::Integer && datatype.getSize() == 8) |
| 491 | 7664 | return int64; | |
| 492 | ✗ | else if (datatype.isVariableStr()) | |
| 493 | ✗ | return Precision<char>{}; | |
| 494 | ✗ | else if (datatype.isFixedLenStr()) | |
| 495 | ✗ | return Precision<char>{}; | |
| 496 | ✗ | throw NotImplemented("Could not determine data set precision"); | |
| 497 | } | ||
| 498 | |||
| 499 | template<Concepts::Scalar S, typename Source> | ||
| 500 | 17698 | auto _read_buffer_field(const Source& source) const { | |
| 501 |
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17698 | auto dims = source.getMemSpace().getDimensions(); |
| 502 |
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17698 | MDLayout layout = dims.empty() ? MDLayout{{1}} : MDLayout{std::move(dims)}; |
| 503 |
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17698 | std::vector<Detail::HighFiveDataType<S>> out(layout.number_of_entries()); |
| 504 |
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17698 | source.read_raw(out.data()); |
| 505 |
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35396 | return BufferField<S>(std::move(out), std::move(layout)); |
| 506 | 17698 | } | |
| 507 | |||
| 508 | 10912 | HighFive::Group _get_group(const std::string& group_name) { | |
| 509 |
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10912 | return _file.exist(group_name) ? _file.getGroup(group_name) : _file.createGroup(group_name); |
| 510 | } | ||
| 511 | |||
| 512 | 1500 | void _clear_attribute(const std::string& name, const std::string& group) { | |
| 513 |
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1500 | if (_get_group(group).hasAttribute(name)) |
| 514 |
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660 | _get_group(group).deleteAttribute(name); |
| 515 | 1500 | } | |
| 516 | |||
| 517 | Communicator _comm; | ||
| 518 | Mode _mode; | ||
| 519 | HighFive::File _file; | ||
| 520 | }; | ||
| 521 | |||
| 522 | } // namespace GridFormat::HDF5 | ||
| 523 | |||
| 524 | #endif // GRIDFORMAT_HAVE_HIGH_FIVE | ||
| 525 | #endif // GRIDFORMAT_COMMON_HDF5_HPP_ | ||
| 526 |